U.S. patent application number 16/780117 was filed with the patent office on 2020-07-30 for degron fusion constructs and methods for controlling protein production.
The applicant listed for this patent is THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR UNIVERSITY. Invention is credited to Hokyung CHUNG, Conor JACOBS, Michael Z. LIN.
Application Number | 20200239866 16/780117 |
Document ID | 20200239866 / US20200239866 |
Family ID | 1000004752179 |
Filed Date | 2020-07-30 |
Patent Application | download [pdf] |
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United States Patent
Application |
20200239866 |
Kind Code |
A1 |
LIN; Michael Z. ; et
al. |
July 30, 2020 |
DEGRON FUSION CONSTRUCTS AND METHODS FOR CONTROLLING PROTEIN
PRODUCTION
Abstract
Engineered fusion proteins comprising a self-excising degron for
controlling protein production are disclosed. In particular, the
inventors have constructed fusion proteins comprising a degron
connected to a protein of interest through a cleavable linker
comprising a hepatitis C virus (HCV) protease site. The degron can
be removed from the protein of interest by a cis-encoded HCV
protease such that the protein of interest can be produced with
minimal structural modification. Clinically available HCV protease
inhibitors can be used to block protease cleavage such that the
degron is retained after inhibitor addition on subsequently
synthesized protein copies. The degron when attached causes rapid
degradation of the linked protein. Such fusions of a degron to a
protein of interest will be especially useful when control over
protein production with minimal structural modification is
desired.
Inventors: |
LIN; Michael Z.; (Stanford,
CA) ; CHUNG; Hokyung; (Mountain View, CA) ;
JACOBS; Conor; (Stanford, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
THE BOARD OF TRUSTEES OF THE LELAND STANFORD JUNIOR
UNIVERSITY |
Stanford |
CA |
US |
|
|
Family ID: |
1000004752179 |
Appl. No.: |
16/780117 |
Filed: |
February 3, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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15737712 |
Dec 18, 2017 |
10550379 |
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PCT/US2016/039792 |
Jun 28, 2016 |
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16780117 |
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62186339 |
Jun 29, 2015 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12N 9/506 20130101;
C07K 2319/50 20130101; C12N 2760/18443 20130101; C12Y 304/21098
20130101; C12N 9/48 20130101; C12Q 1/70 20130101; C12N 15/86
20130101; C12N 2760/18432 20130101; G01N 33/68 20130101; C12N
2760/18421 20130101; C07K 2319/95 20130101 |
International
Class: |
C12N 9/50 20060101
C12N009/50; C12N 9/48 20060101 C12N009/48; C12Q 1/70 20060101
C12Q001/70; G01N 33/68 20060101 G01N033/68; C12N 15/86 20060101
C12N015/86 |
Goverment Interests
STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT
[0001] This invention was made with Government support under
contract GM098734 awarded by the National Institutes of Health. The
Government has certain rights in the invention.
Claims
1.70. (canceled)
71. A conditionally replicating viral vector comprising a modified
genome of a virus such that production of a polypeptide required
for efficient replication of the virus is controllable, wherein the
viral vector comprises a nucleic acid encoding a fusion protein
comprising: i) the polypeptide required for efficient replication
of the virus; ii) a degron, wherein the degron is operably linked
to the polypeptide required for efficient replication of the virus
when the fusion protein is in an uncleaved state, such that the
degron promotes degradation of the polypeptide in a cell; iii) a
protease, wherein the protease can be inhibited by contacting said
fusion protein with a protease inhibitor; and iv) a cleavable
linker that is located between the polypeptide required for
efficient replication of the virus and the degron, wherein the
cleavable linker comprises a cleavage site recognized by the
protease, wherein cleavage of the cleavable linker by the protease
releases the polypeptide required for efficient replication of the
virus from the fusion protein, such that when the fusion protein is
in a cleaved state, the degron no longer controls degradation of
the polypeptide required for efficient replication of the
virus.
72. The conditionally replicating viral vector of claim 71, wherein
the virus is an RNA virus.
73. The conditionally replicating viral vector of claim 72, wherein
the virus is a measles virus.
74. The conditionally replicating viral vector of claim 73, wherein
the polypeptide required for efficient replication of the virus is
a measles virus phosphoprotein.
75. The conditionally replicating viral vector of claim 74, wherein
the viral vector comprises a nucleotide sequence having at least
80% identity to the nucleotide sequence of SEQ ID NO:9.
76. The conditionally replicating viral vector of claim 71, wherein
the degron comprises an amino acid sequence having at least 80%
identity to an amino acid sequence of SEQ ID NO:1.
77. The conditionally replicating viral vector of claim 76, wherein
the fusion protein comprises a hepatitis C virus (HCV)
nonstructural protein 3 (NS3) protease.
78. The conditionally replicating viral vector of claim 71, wherein
the vector is a plasmid.
79. The conditionally replicating viral vector of claim 71, further
comprising a multiple cloning site.
80. The conditionally replicating viral vector of claim 71, further
comprising a polynucleotide encoding a tag, a detectable label, a
targeting sequence, a linker, or any combination thereof.
81. The conditionally replicating viral vector of claim 80, wherein
the detectable label is a fluorescent protein or a bioluminescent
protein.
82. The conditionally replicating viral vector of claim 71, further
comprising an exogenous nucleic acid.
83. A recombinant virion comprising the conditionally replicating
viral vector of claim 71.
84. A method of controlling production of a virus, the method
comprising: culturing a host cell comprising the conditionally
replicating viral vector of claim 71 under conditions suitable for
producing the virus; and contacting the host cell with a protease
inhibitor, such that the polypeptide required for efficient
replication of the virus is degraded when production of the virus
is no longer desired.
85. The method of claim 84, further comprising removing the
protease inhibitor from the host cell, when resuming production of
the virus is desired.
86. The method of claim 84, further comprising, prior to the
culturing, introducing the conditionally replicating viral vector
into the host cell.
87. The method of claim 84, wherein the viral vector comprises a
nucleotide sequence having at least 80% identity to the nucleotide
sequence of SEQ ID NO:9, wherein production of the virus can be
inhibited with a protease inhibitor.
88. The method of claim 84, wherein the degron comprises an amino
acid sequence having at least 80% identity to an amino acid
sequence of SEQ ID NO:1.
89. The method of claim 88, wherein the fusion protein comprises a
hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease.
90. The method of claim 84, wherein the protease inhibitor is
selected from the group consisting of simeprevir, danoprevir,
asunaprevir, ciluprevir, boceprevir, sovaprevir, paritaprevir and
telaprevir.
Description
TECHNICAL FIELD
[0002] The present invention pertains generally to the field of
protein engineering and methods of controlling the production of
proteins. In particular, the invention relates to engineered fusion
proteins comprising a degron fused to a polypeptide of interest
through a cleavable linker comprising a protease site whose
cleavage can be inhibited with a protease inhibitor such that
degradation of the polypeptide of interest is controllable.
BACKGROUND
[0003] Technology for rapidly shutting off the production of
specific proteins in eukaryotes would be of widespread utility as a
research tool and for gene or cell therapy applications, but a
simple and effective method has yet to be developed. Controlling
protein production through repression of transcription is slow in
onset, as existing mRNA molecules continue to be translated into
proteins after transcriptional inhibition. RNA interference (RNAi)
directly induces mRNA destruction, but RNAi is often only partially
effective and can exhibit both sequence-independent and
sequence-dependent off-target effects (Sigoillot et al. (2011) ACS
Chem Biol 6:47-60). Furthermore, mRNA and protein abundance are not
always correlated due to regulation of the translation rate of
specific mRNAs (Vogel et al. (2012) Nat Rev Genet 13:227-232; Wu et
al. (2013) Nature 499:79-82; Battle et al. (2015) Science
347:664-667). Lastly, both transcriptional repression and RNAi take
days to reverse (Liu et al. (2008) J Gene Med 10:583-592; Matsukura
et al. (2003) Nucleic Acids Res 31:e77).
[0004] Thus, there remains a need for a simple to use system for
controlling protein production.
SUMMARY
[0005] The invention relates to degron fusion constructs and
methods of using them for controlling protein production. In
particular, the inventors have constructed fusion proteins
containing a degron fused to a polypeptide of interest through a
cleavable linker comprising a protease site whose cleavage can be
inhibited with a protease inhibitor such that degradation of the
polypeptide of interest is controllable.
[0006] In one aspect, the invention includes a degron comprising
the amino acid sequence of SEQ ID NO:1 or a variant thereof
comprising a sequence having at least about 80-100% sequence
identity thereto, including any percent identity within this range,
such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95,
96, 97, 98, or 99% sequence identity thereto, wherein the degron is
capable of promoting degradation of a polypeptide.
[0007] In another aspect, the invention includes a degron fusion
protein comprising: a) a polypeptide of interest; b) a degron,
wherein the degron is operably linked to the polypeptide of
interest when the fusion protein is in an uncleaved state, such
that the degron promotes degradation of the polypeptide of interest
in a cell; c) a protease, wherein the protease can be inhibited by
contacting the fusion protein with a protease inhibitor; and c) a
cleavable linker that is located between the polypeptide of
interest and the degron, wherein the cleavable linker comprises a
cleavage site recognized by the protease, wherein cleavage of the
cleavable linker by the protease releases the polypeptide of
interest from the fusion protein, such that when the fusion protein
is in a cleaved state, the degron no longer controls degradation of
the polypeptide of interest.
[0008] In certain embodiments, the fusion protein comprises a
degron comprising the amino acid sequence of SEQ ID NO:1 or a
variant thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, wherein
the degron is capable of promoting degradation of the polypeptide
of interest when the fusion protein is in an uncleaved state.
[0009] In certain embodiments, the protease contained in the fusion
protein is a hepatitis C virus (HCV) nonstructural protein 3 (NS3)
protease, and the cleavable linker of the fusion protein comprises
an NS3 protease cleavage site. Exemplary NS3 protease cleavage
sites include the HCV polyprotein NS3/NS4A, NS4A/NS4B, NS4B/NS5A,
and NS5A/NS5B junction cleavage sites.
[0010] The degron may be linked to the C-terminus of the
polypeptide of interest in the fusion protein. In certain
embodiments, the fusion protein comprises components arranged from
N-terminus to C-terminus in the uncleaved state as follows: a) the
polypeptide of interest, b) the cleavable linker, c) the protease,
and d) the degron. In one embodiment, the fusion protein comprises
a polypeptide comprising the amino acid sequence of SEQ ID NO:7, or
a variant thereof comprising a sequence having at least about
80-100% sequence identity thereto, including any percent identity
within this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,
91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity thereto,
wherein the polypeptide comprises a biologically active degron
capable of promoting degradation of the polypeptide of interest and
a protease capable of cleaving the fusion protein at the cleavage
site, wherein the polypeptide is linked to the C-terminus of the
polypeptide of interest.
[0011] Alternatively, the degron may be linked to the N-terminus of
the polypeptide of interest in the fusion protein. In certain
embodiments, the fusion protein comprises components arranged from
N-terminus to C-terminus in the uncleaved state as follows: a) the
protease, b) the degron, c) the cleavable linker, and c) the
polypeptide of interest. In one embodiment, the fusion protein
comprises a polypeptide comprising the amino acid sequence of SEQ
ID NO:8, or a variant thereof comprising a sequence having at least
about 80-100% sequence identity thereto, including any percent
identity within this range, such as 81, 82, 83, 84, 85, 86, 87, 88,
89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity
thereto, wherein the polypeptide comprises a biologically active
degron capable of promoting degradation of the polypeptide of
interest and a protease capable of cleaving the fusion protein at
the cleavage site, wherein the polypeptide is linked to the
N-terminus of the polypeptide of interest.
[0012] In certain embodiments, the fusion protein further comprises
a targeting sequence. Exemplary targeting sequences includes a
secretory protein signal sequence, a membrane protein signal
sequence, a nuclear localization sequence, a nucleolar localization
signal sequence, an endoplasmic reticulum localization sequence, a
peroxisome localization sequence, a mitochondrial localization
sequence, and a protein binding motif sequence.
[0013] In certain embodiments, the fusion protein further comprises
a tag. Exemplary tags include a His-tag, a Strep-tag, a TAP-tag, an
S-tag, an SBP-tag, an Arg-tag, a calmodulin-binding peptide tag, a
cellulose-binding domain tag, a DsbA tag, a c-myc tag, a
glutathione S-transferase tag, a FLAG tag, a HAT-tag, a
maltose-binding protein tag, a NusA tag, and a thioredoxin tag.
[0014] In certain embodiments, the fusion protein further comprises
a detectable label. The detectable label may comprise any molecule
capable of detection. For example, the detectable label may be a
fluorescent, bioluminescent, chemiluminescent, colorimetric, or
isotopic label. In certain embodiments, the detectable label is a
fluorescent protein or bioluminescent protein.
[0015] In certain embodiments, the polypeptide of interest in the
degron fusion protein is a membrane protein, a receptor, a hormone,
a transport protein, a transcription factor, a cytoskeletal
protein, an extracellular matrix protein, a signal-transduction
protein, an enzyme, or any other protein of interest. The
polypeptide of interest may comprise an entire protein, or a
biologically active domain (e.g., a catalytic domain, a ligand
binding domain, or a protein-protein interaction domain), or a
polypeptide fragment of a selected protein of interest.
[0016] In another aspect, the invention includes a polynucleotide
encoding a degron fusion protein described herein. In one
embodiment, the polynucleotide is a recombinant polynucleotide
comprising a polynucleotide encoding a degron fusion protein
operably linked to a promoter. The recombinant polynucleotide may
comprise an expression vector, for example, a bacterial plasmid
vector or a viral expression vector. Exemplary viral vectors
include measles virus, vesicular stomatitis virus, adenovirus,
retrovirus (e.g., .gamma.-retrovirus and lentivirus), poxvirus,
adeno-associated virus, baculovirus, or herpes simplex virus
vectors.
[0017] In certain embodiments, the recombinant polynucleotide
comprises a polynucleotide encoding a fusion protein comprising a
sequence selected from the group consisting of SEQ ID NO:7 and SEQ
ID NO:8, or a variant thereof comprising a sequence having at least
about 80-100% sequence identity thereto, including any percent
identity within this range, such as 81, 82, 83, 84, 85, 86, 87, 88,
89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity
thereto, wherein the fusion protein comprises a degron operably
linked to a polypeptide of interest, which is capable of promoting
degradation of the polypeptide of interest, and a protease capable
of cleaving the fusion protein at a cleavage site.
[0018] In another aspect, the invention includes a host cell
comprising a recombinant polynucleotide encoding a degron fusion
protein operably linked to a promoter. In one embodiment, the host
cell is a eukaryotic cell. In another embodiment, the host cell is
a mammalian cell. In certain embodiments, the host cell is a stem
cell (e.g., embryonic stem cell or adult stem cell). Host cells may
be cultured as unicellular or multicellular entities (e.g., tissue,
organs, or organoids comprising the recombinant vector). The
promoter may be an endogenous or exogenous promoter. In certain
embodiments, the recombinant polynucleotide encoding the degron
fusion protein resides on an extrachromosomal plasmid or vector. In
other embodiments, the recombinant polynucleotide encoding the
degron fusion protein is integrated into the cellular genome. For
example, the recombinant polynucleotide may integrate into the
cellular genome at a position where the polynucleotide sequence
encoding the fusion protein is operably linked to an endogenous
promoter of a gene.
[0019] In another embodiment, the invention includes a descendant
of the host cell, wherein the descendant has inherited a
recombinant polynucleotide encoding the degron fusion protein.
[0020] In another embodiment, the invention includes an organoid
comprising a recombinant polynucleotide encoding a degron fusion
protein operably linked to a promoter. The promoter may be an
endogenous or exogenous promoter. In certain embodiments, the
recombinant polynucleotide encoding the degron fusion protein
resides on an extrachromosomal plasmid or vector. In other
embodiments, the recombinant polynucleotide encoding the degron
fusion protein is integrated into the organoid genome. For example,
the recombinant polynucleotide may integrate into the organoid
genome at a position where the polynucleotide sequence encoding the
fusion protein is operably linked to an endogenous promoter of a
gene.
[0021] In another embodiment, the invention includes a recombinant
animal comprising a recombinant polynucleotide encoding a degron
fusion protein operably linked to a promoter. The promoter may be
an endogenous or exogenous promoter. In certain embodiments, the
recombinant polynucleotide encoding the degron fusion protein
resides on an extrachromosomal plasmid or vector. In other
embodiments, the recombinant polynucleotide encoding the degron
fusion protein is integrated into the genome of the recombinant
animal For example, the recombinant polynucleotide may integrate
into the genome at a position where the polynucleotide sequence
encoding the fusion protein is operably linked to an endogenous
promoter of a gene.
[0022] In another embodiment, the invention includes a descendant
of the recombinant animal, wherein the descendant has inherited the
recombinant polynucleotide encoding the degron fusion protein.
[0023] In another aspect, the invention includes a method for
producing a degron fusion protein, the method comprising:
transforming a host cell with a recombinant polynucleotide encoding
the fusion protein operably linked to a promoter; culturing the
transformed host cell under conditions whereby the fusion protein
is expressed; and isolating the fusion protein from the host
cell.
[0024] In another aspect, the invention includes a method for
controlling production of a polypeptide of interest, the method
comprising: a) transforming a host cell with a recombinant
polynucleotide encoding a degron fusion protein described herein;
b) culturing the transformed host cell under conditions whereby the
fusion protein is expressed; and c) contacting the cell with a
protease inhibitor that inhibits the protease of the fusion protein
when production of the polypeptide of interest is no longer
desired. The protease inhibitor can be removed when resuming
production of the polypeptide of interest is desired.
[0025] The recombinant polynucleotide encoding the degron fusion
protein preferably is capable of providing efficient production of
the polypeptide of interest with biological activity comparable to
the wild-type polypeptide. Additionally, production of the
polypeptide of interest from the recombinant polynucleotide
preferably can be rapidly and nearly completely suppressed in the
presence of a protease inhibitor. For example, a protease inhibitor
may reduce production of the polypeptide of interest by at least
80%, 90%, or 100%, or any amount in between as compared to levels
of the polypeptide in the absence of the protease inhibitor. In
certain embodiments, production of the polypeptide of interest by
the recombinant polynucleotide in the host cell in the presence of
the protease inhibitor is at least about 90% to 100% suppressed,
including any percent identity within this range, such as 90, 91,
92, 93, 94, 95, 96, 97, 98, or 99%.
[0026] In certain embodiments, the fusion protein used for
controlling production of a polypeptide of interest comprises an
HCV NS3 protease. NS3 protease inhibitors that can be used in the
practice of the invention include, but are not limited to,
simeprevir, danoprevir, asunaprevir, ciluprevir, boceprevir,
sovaprevir, paritaprevir and telaprevir.
[0027] In another aspect, the invention includes a method for
controlling production of a polypeptide of interest in a subject,
the method comprising: a) administering a recombinant
polynucleotide encoding a degron fusion protein to the subject,
such that the fusion protein is expressed in the subject; and b)
administering a protease inhibitor that inhibits the protease of
the fusion protein to the subject when production of the
polypeptide of interest is not desired. The method may further
comprise ceasing administration of the protease inhibitor when
resuming production of the polypeptide of interest in the subject
is desired. The recombinant polynucleotide may comprise an
expression vector, for example, a viral expression vector, such as,
but not limited to, an adenovirus, retrovirus (e.g.,
.gamma.-retrovirus and lentivirus), poxvirus, adeno-associated
virus, baculovirus, or herpes simplex virus vector. In one
embodiment, the recombinant polynucleotide comprises a
polynucleotide sequence encoding the fusion protein operably linked
to an exogenous promoter. In another embodiment, the recombinant
polynucleotide is integrated into the genome of the subject. For
example, the recombinant polynucleotide may integrate into the
genome at a position where the polynucleotide sequence encoding the
fusion protein is operably linked to an endogenous promoter of a
gene in the subject.
[0028] In another aspect, the invention includes a method for
controlling production of a polypeptide of interest in a
recombinant animal, the method comprising: a) administering a
recombinant polynucleotide encoding a degron fusion protein to the
recombinant animal, such that the fusion protein is expressed in
the recombinant animal and b) administering a protease inhibitor
that inhibits the protease of the fusion protein to the recombinant
animal when production of the polypeptide of interest is not
desired.
[0029] In another aspect, the invention includes a method of
controlling production of a polypeptide of interest in an organoid,
the method comprising: a) introducing a recombinant polynucleotide
encoding the fusion protein of claim 4 into an organoid; b)
culturing the organoid under conditions whereby the fusion protein
is produced in the organoid; and c) contacting the organoid with a
protease inhibitor that inhibits the protease of the fusion protein
when production of the polypeptide of interest is no longer
desired.
[0030] In another aspect, the invention includes a method of
measuring the turnover of a polypeptide of interest, the method
comprising: a) introducing a recombinant polynucleotide encoding a
degron fusion protein described herein into a cell; b) measuring
amounts of the polypeptide of interest in the cell before and after
contacting the cell with a protease inhibitor that inhibits the
protease of the fusion protein; and c) calculating the turnover of
the polypeptide of interest based on the amounts of the polypeptide
of interest in the cell before and after adding the protease
inhibitor. Additionally, the half-life of the polypeptide of
interest in the cell can be calculated. The amount of the
polypeptide of interest in the cell can be measured either
continuously or periodically over a period of time.
[0031] In another aspect, the invention includes a conditionally
replicating viral vector comprising a modified genome of a virus
such that production of a polypeptide required for efficient
replication of the virus is controllable, wherein the viral vector
comprises a nucleic acid encoding a fusion protein comprising: i)
the polypeptide required for efficient replication of the virus;
ii) a degron, wherein the degron is operably linked to the
polypeptide required for efficient replication of the virus when
the fusion protein is in an uncleaved state, such that the degron
promotes degradation of the polypeptide in a cell; iii) a protease,
wherein the protease can be inhibited by contacting said fusion
protein with a protease inhibitor; and iv) a cleavable linker that
is located between the polypeptide required for efficient
replication of the virus and the degron, wherein the cleavable
linker comprises a cleavage site recognized by the protease,
wherein cleavage of the cleavable linker by the protease releases
the polypeptide required for efficient replication of the virus
from the fusion protein, such that when the fusion protein is in a
cleaved state, the degron no longer controls degradation of the
polypeptide required for efficient replication of the virus. In
certain embodiments, the virus is an RNA virus (e.g., measles virus
or a vesicular stomatitis virus). In another embodiment, the
conditionally replicating viral vector is a plasmid. The viral
vector may further comprise a multiple cloning site, transcription
promoter, transcription enhancer element, transcription termination
signal, polyadenylation sequence, or exogenous nucleic acid, or any
combination thereof.
[0032] In certain embodiments the conditionally replicating viral
vector comprises a modified measles virus genome comprising a
nucleic acid encoding a degron fusion protein, wherein the
polypeptide required for efficient replication of the virus is a
measles virus phosphoprotein. In one embodiment, the conditionally
replicating viral vector comprises the nucleotide sequence of SEQ
ID NO:9, or a variant thereof comprising a sequence having at least
about 80-100% sequence identity thereto, including any percent
identity within this range, such as 81, 82, 83, 84, 85, 86, 87, 88,
89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence identity
thereto, wherein replication of the virus can be inhibited with an
HCV NS3 protease inhibitor.
[0033] In another aspect, the invention includes a method of
controlling production of a virus, the method comprising: a)
introducing a conditionally replicating viral vector described
herein into a host cell; b) culturing the host cell under
conditions suitable for producing the virus; and c) contacting the
host cell with a protease inhibitor, such that the polypeptide
required for efficient replication of the virus is degraded when
production of the virus is no longer desired. The protease
inhibitor can be removed when resuming production of the virus is
desired.
[0034] The conditionally replicating viral vector preferably is
capable of providing efficient production of the virus in the host
cell in the absence of a protease inhibitor, comparable to the
level of the virus produced by the wild-type viral genome. In
certain embodiments, the level of the virus produced by the
conditionally replicating viral vector in the absence of the
protease inhibitor is at least about 30%, 35%, 40%, 45%, 50%, 55%,
60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or any amount in
between as compared to levels of the virus produced by the
wild-type viral genome.
[0035] Additionally, production of the virus from the conditionally
replicating viral vector preferably can be nearly completely
suppressed in the presence of a protease inhibitor. For example, a
protease inhibitor may reduce production of the virus by 80%, 90%,
100%, or any amount in between as compared to levels of the virus
in the absence of the protease inhibitor. In certain embodiments,
production of the virus by the conditionally replicating viral
vector in the host cell in the presence of the protease inhibitor
is at least about 90% to 100% suppressed, including any percent
identity within this range, such as 90, 91, 92, 93, 94, 95, 96, 97,
98, or 99%.
[0036] In certain embodiments, the conditionally replicating viral
vector, used in controlling production of a virus, expresses a
degron fusion protein comprising an HCV NS3 protease, wherein
addition of an NS3 protease inhibitor can be used to suppress
production of the virus. NS3 protease inhibitors that can be used
include, but are not limited to, simeprevir, danoprevir,
asunaprevir, ciluprevir, boceprevir, sovaprevir, paritaprevir and
telaprevir.
[0037] In another aspect, the invention includes a recombinant
virion comprising a conditionally replicating viral vector
described herein.
[0038] In another aspect, the invention includes a kit for
preparing or using degron fusion proteins according to the methods
described herein. Such kits may comprise one or more degron fusion
proteins, nucleic acids encoding such fusion proteins, expression
vectors, conditionally replicating viral vectors, cells, or other
reagents for preparing or using degron fusion proteins, as
described herein. The kit may further include a protease inhibitor,
such as an HCV NS3 protease inhibitor, including, for example,
simeprevir, danoprevir, asunaprevir, ciluprevir, boceprevir,
sovaprevir, paritaprevir or telaprevir.
[0039] In certain embodiments, the kit comprises a recombinant
polynucleotide encoding a degron fusion protein described herein.
In one embodiment, the kit comprises a recombinant polynucleotide
encoding a fusion protein comprising a sequence selected from the
group consisting of SEQ ID NO:7 and SEQ ID NO:8, or a variant
thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, wherein
the fusion protein comprises a degron operably linked to a
polypeptide of interest, which is capable of promoting degradation
of the polypeptide of interest, and a protease capable of cleaving
the fusion protein at a cleavage site.
[0040] In other embodiments, the kit comprises a conditionally
replicating viral vector as described herein. In one embodiment,
the kit comprises a conditionally replicating viral vector
comprising the nucleotide sequence of SEQ ID NO:9, or a variant
thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, wherein
production of the virus can be inhibited with a protease
inhibitor.
[0041] These and other embodiments of the subject invention will
readily occur to those of skill in the art in view of the
disclosure herein.
BRIEF DESCRIPTION OF THE FIGURES
[0042] FIGS. 1A-1D show the Small Molecule-Assisted Shutoff (SMASh)
concept and development. FIG. 1A illustrates the SMASh concept.
FIG. 1A (Top) shows a protein of interest fused to the SMASh tag
via a HCV NS3 protease recognition site. After protein folding, the
SMASh tag is removed by its internal NS3 protease activity, and is
degraded due to an internal degron activity. FIG. 1A (Bottom) shows
that addition of a protease inhibitor induces the rapid degradation
of subsequently synthesized copies of the tagged protein,
effectively shutting off further protein production. FIG. 1B shows
the amino acid sequence (SEQ ID NO:7) of the SMASh tag. The NS3
protease sequence (light gray), sequence derived from NS3 helicase
(dark gray), and sequence derived from NS4A (light gray) are shown.
Secondary structures (.alpha.-helices and/.beta.-strands) in the
context of the original HCV polyprotein are underlined. The NS4A/4B
protease cleavage site is in dark gray, with an arrow indicating
the site of cleavage. The degron region is marked with a dotted
line. FIG. 1C (Top) shows the organization of fusions of PSD95 with
NS3 protease (NS3pro) or NS3pro-NS4A, with predicted protein
fragment sizes indicated. FIG. 1C (Bottom) shows that for both
constructs, PSD95 appears in HEK293 cells 24 hours
post-transfection in the absence of the protease inhibitor
asunaprevir (ASV) at the expected cleaved size. The PSD95-NS3pro
fusion was expressed at full-length size with asunaprevir,
indicating efficient drug-inhibition of cleavage. However, the
PSD95-NS3proNS4A fusion failed to exhibit expression with
asunaprevir. Locations of size markers are indicated at left. GAPDH
serves as a loading control. FIG. 1D shows that a specific element
in the NS3proNS4A sequence is responsible for degron activity. HeLa
cells were transfected to express YFP fused to the NS3pro-NS4A
cassette (wt), or to a modified cassette in which the putatively
unstructured and hydrophobic stretch derived from NS3 helicase and
the NS4A .alpha.-helix (dotted line in FIG. 1B) was mutated to a
GGS-repeat linker of the same length (GGS). Constructs were
expressed for 24 hours in either DMSO or 2 .mu.M ASV, and lysates
were analyzed by immunoblotting as indicated. Disruption of the
hydrophobic region significantly reduced degradation of YFP in the
+ASV condition. .beta.-actin served as a loading control.
[0043] FIGS. 2A-2C show that proteins can be regulated by SMASh
tags at either terminus. FIG. 2A shows the amino acid sequence (SEQ
ID NO:8) of the N-terminal SMASh tag. NS3 protease sequence (light
gray), sequence derived from NS3 helicase (dark gray), and sequence
derived from NS4A (medium gray) are shown. NS5A/5B-based protease
substrate site is in dark gray. FIG. 2B shows that SMASh can
regulate YFP when fused to either terminus. SMAShYFP and YFP-SMASh
were expressed in HEK293 cells in the absence or presence of ASV
for 24 hours Immunoblotting revealed shutoff of YFP expression by
ASV for both constructs. DMSO was used as vehicle control.
.beta.-actin served as a loading control. FIG. 2C that fluorescence
microscopy confirmed shutoff of YFP expression by ASV for both
constructs. Scale bar, 50 pm.
[0044] FIGS. 3A-3D show that protein regulation by SMASh-tagging is
dose-dependent and reversible. FIG. 3A shows a test of
dose-dependent regulation of protein expression by SMASh. HEK293
cells transfected with YFP-SMASh were cultured for 24 hours without
or with ASV (15 pM to 15 pM) and YFP was detected by immunoblot.
GAPDH served as a loading control. FIG. 3B shows quantification of
YFP levels by immunoblot. Background-subtracted YFP signal was
normalized to background-subtracted GAPDH signal, and then plotted
as a percent of the signal in the untreated condition (n=3, error
bars represent standard deviations). FIG. 3C shows restoration of
YFP expression following drug washout, assayed by immunoblot. HeLa
cells transfected with YFP-SMASh were grown 12 hours in the
presence of 2 pM ASV, then washed and exchanged into fresh media.
Parallel wells were lysed at indicated times afterwards.
.beta.-actin served as a loading control. FIG. 3D shows restoration
of YFP expression following drug washout, assayed by fluorescence
microscopy. HeLa cells cotransfected with untagged RFP and
YFP-SMASh were grown 12 hours in the presence of 2 .mu.M ASV,
washed, exchanged into fresh media, and imaged at indicated times
afterwards. Similarly transfected HeLa cells grown 12 hours in DMSO
are shown at left for comparison. Representative images are shown.
Scale bar, 20 .mu.m.
[0045] FIGS. 4A-4C show that SMASh functions on a variety of
proteins. FIG. 4A shows that SMASh functions on multimerizing
protein, CaMKII.alpha.. TimeSTAMP2-tagged
CaMKII.alpha.(TS2-CaMKII.alpha.) or SMASh-CaMKII.alpha. were
expressed in HEK293 cells for 24 hours in the absence or presence
of ASV. TimeSTAMP2 (TS2) tags contain cis-cleaving NS3 protease
domains but lack NS4A sequences, verifying that drug inhibition of
protein expression is specific to SMASh Immunoblotting revealed
shutoff of CaMKII.alpha. expression by ASV when it was tagged with
SMASh but not when it was tagged with TimeSTAMP2. GAPDH served as a
loading control. The asterisk indicates a cross-reactive protein
also detected in untransfected cells. FIG. 4B shows GluRIIA-CFP
fused to TimeSTAMP2 with an orange fluorescent protein readout
(GluRIIA-CFP-TS2:OFP) or GluRIIA-CFP-SMASh expressed in HEK293
cells for 24 hours in the absence or presence of ciluprevir (CLV)
Immunoblotting revealed shutoff of GluRIIA expression by CLV. The
non-degron-containing TS2:OFP tag verified that drug inhibition of
protein expression is specific to SMASh. Cross-reactive bands at 80
kDa (asterisk) served as a lysate loading control. FIG. 4C shows
CYP21A2 fused to either TimeSTAMP2 or SMASh tested by the same
method as in FIG. 4A. The CYP21A2 level was detected by
immunoblotting. .beta.-actin served as a loading control.
[0046] FIGS. 5A-5C show that SMASh functions in budding yeast. FIG.
5A shows SMASh-YFP or YFP-SMASh expressed from the strong
constitutive GPD promoter in wild-type or drug efflux
pump-deficient yeast cells. The yeast cells were cultured in SD
media in the absence or presence of ASV for 24 hours Immunoblotting
revealed shutoff of YFP expression by ASV for both constructs. DMSO
was used as vehicle control. GAPDH served as a loading control.
FIG. 5B shows quantification of YFP levels in the yeast extract by
immunoblot. Background-subtracted YFP signal was normalized to
background-subtracted GAPDH signal, then plotted as a percent of
the signal in the untreated condition (n=3, error bars represent
standard deviations). FIG. 5C shows fluorescence images of yeast
cultures in (FIG. 5A) showing that the episomally expressed YFP
signal is controlled in a drug-dependent manner Imaging was done in
SD media. Scale bar, 10 .mu.m.
[0047] FIGS. 6A-6D show that SMASh mediated drug control of
chromosomal protein production. FIG. 6A shows that YFP-SMASh under
strong GPD promoter is integrated into the yeast chromosomal LUE
locus. Recombinant yeast was cultured in SD media in the absence or
presence of ASV for 24 hours Immunoblotting revealed shutoff of YFP
expression by ASV. DMSO was used as vehicle control. GAPDH served
as a loading control. FIG. 6B shows fluorescence images of yeast
cultures in FIG. 6A showing that chromosomally-expressed YFP signal
is controlled in a drug-dependent manner Imaging was done in SD
media. Scale bar, 10 .mu.m. FIG. 6C shows results when the HA tag
and the SMASh tag were inserted at the C-terminus of the endogenous
SEC14 coding sequence. Serial dilutions of cells were plated and
incubated for 48 hours at 30.degree. C. and 23.degree. C. in the
absence or presence of ASV (3 .mu.M). FIG. 6D shows results when a
SMASh tag was inserted at the C-terminus of the endogenous YSH1
coding sequence. Serial dilutions of cells were plated and
incubated for 48 hours at 30.degree. C. and 37.degree. C. in the
absence or presence of ASV (10 .mu.M).
[0048] FIGS. 7A-7E show generation of a drug-controllable
"SMAShable" measles vaccine virus. FIG. 7A shows the concept of
controlling MeV replication with P-SMASh. In the absence of the
drug, essentially unmodified phosphoprotein (P, dark gray) is
released and can successfully form replication complexes with
nucleocapsid (N, light gray) and large (L) proteins. FIG. 7B shows
genome organization of MeV-EGFP-PSMASh. Scale bar is 1 kilobase.
FIG. 7C shows regulation of MeV-EGFP-P-SMASh by a drug. Vero cells
infected with MeV-EGFP or MeV-EGFP-P-SMASh at multiplicity of
infection (MOI) of 1 were grown for 72 hours in the absence or
presence of ASV. Drug inhibited syncytium formation and GFP
expression in MeV-EGFP-P-SMASh-infected but not MeV-EGFP-infected
cells. Scale bar, 50 .mu.m. FIG. 7D shows the quantification of
fluorescence from Vero cells infected with MeV-EGFP-P-SMASh at MOI
1 and 0.1 in the absence or presence of 3 .mu.M ASV (n=3, error
bars are standard deviation). FIG. 7E shows that a drug inhibited P
expression in MeV-EGFP-P-SMASh-infected but not MeVEGFP-infected
cells, as assayed by immunoblotting. GAPDH served as a loading
control.
[0049] FIGS. 8A-8D show characterization of a degron contained in
NS3pro-NS4A. FIG. 8A shows that in the native HCV polyprotein, the
non-consensus NS3/4A site is positioned in the active site of NS3
protease by the NS3 helicase domain and cleaved. The hydrophobic
N-terminal of NS4A then inserts into the membrane (right). Elements
are numbered from N-terminus to C-terminus to clarify order of
linkage. FIG. 8B shows that in NS3pro-NS4A, most of NS3 helicase is
deleted, so that the C-terminus of NS3 protease is connected to a
short C-terminal segment of NS3 helicase followed by NS4A. Removal
of the NS3 helicase domain may expose hydrophobic residues in the
helicase C-terminus and prevent cleavage at the NS3/4A site,
preventing membrane insertion of NS4A. Models were generated using
PDB file 1CU1. FIGS. 8C and 8D shows mechanisms of degradation of
proteins fused to NS3pro-NS4A. HeLa cells expressed YFP (FIG. 8C)
or PSD95 (FIG. 8D) fused to NS3pro-NS4A (wt), or the
degron-disrupted mutant (GGS). From 18 to 24 hours
post-transfection, cells were treated with ASV (1 .mu.M) and
degradation inhibitors (MG, MG132 10 .mu.M; BTZ, bortezomib 66 nM;
CHQ, chloroquine 100 .mu.M; BAF, bafilomycin-A1 200 nM). This short
time window was used to avoid toxicity by degradation inhibitors.
Final DMSO concentration was 0.23% (v/v) for all conditions in
(FIG. 8C) and 0.33% for all conditions in (FIG. 8D). The
combination of MG132 and chloroquine inhibited degradation of
YFP-NS3pro-NS4A or PSD95-NS3pro-NS4A cassette to a degree
approaching that of the GGS mutation. .beta.-actin served as a
loading control.
[0050] FIGS. 9A and 9B show optimization of an N-terminal SMASh
tag. FIG. 9A shows that poly-GSS linkers of 6, 12, or 18 amino
acids (aa) inserted in NS4A to improve accessibility of C-terminal
sites to cis cleavage. Two substrate sequences, NS4A/4B
(slow-cleaving) and NS5A/5B (fast-cleaving) were tested. Constructs
were expressed in HEK293 cells for 24 hours without or with ASV,
and then lysates were immunoblotted for Arc. Increasing linker
length from 0 to 6 amino acids reduced off-target cleavage with the
NS4A/4B substrate, which may be due to improving its accessibility
(lanes 1-8). A 6-aa linker with the NS5A/5B substrate allowed
specific cleavage at the desired site without ASV and complete
protein suppression with ASV, while suppression was incomplete with
an 18-aa linker (lanes 9-12). GAPDH served as a loading control.
FIG. 9B shows that SMASh functions at either end of Arc. SMASh-Arc
and Arc-SMASh were transiently expressed in HEK293 cells for 24
hours with or without ASV, and then lysates were immunoblotted for
Arc. .beta.-actin served as a loading control.
[0051] FIGS. 10A and 10B show that SMASh accelerates degradation of
the long-lived protein PSD95 by 12-fold. FIG. 10A shows
determination of the half-life of PSD95 in HEK293 cells.
PSD95-SMASh was expressed in the absence of ASV so that the SMASh
tag removed itself for 24 hours, then 1 .mu.M ASV was added to
switch production to uncleaved PSD95-SMASh. Levels of cleaved PSD95
over time were then followed by immunoblotting.
Background-subtracted PSD95 signal was normalized to
background-subtracted .beta.-actin signal and then divided by the
mean signal at 0 hour (n=3, error bars represent standard
deviations). Values fit an exponential decay function with a
half-life of 12.4 hours. FIG. 10B shows that the half-life of
PSD95-SMASh can be calculated from the half-life of PSD95 and the
ratio of PSD95-SMASh to PSD95 accumulated within the same amount of
time, if they are produced at equal rates (see Methods). To obtain
this ratio, PSD95-SMASh was first expressed with 1 .mu.M ASV for 24
hours, then ASV was washed out for 4 hours (procedure i).
Additional new PSD95 appearing at the cleaved size of 84 kDa was
apparent at 28 hours (lane 2). In parallel, PSD95-SMASh was
expressed without ASV so that all PSD95-SMASh was cleaved to PSD95
for 24 hours, then new PSD95-SMASh was inhibited from cleavage by
addition of 1 .mu.M ASV for 4 hours (procedure ii). The level of
PSD95-SMASh (lane 4) was quantified relative to that of PSD95
produced from the same plasmid over the same time (lane 2).
Background-subtracted PSD95 and PSD95-SMASh signals were normalized
to background-subtracted .beta.-actin signal. To calculate the
produced amount of PSD95 and PSD95-SMASh in 4 hours, normalized
signals at 24 hours (lanes 1 and 3) were subtracted from those at
28 hours (lanes 2 and 4). With these values inputted into the
mathematical model, the half-life of PSD95-SMASh was calculated to
be 1.1 hour.
[0052] FIGS. 11A and 11B show that SMASh accelerates degradation of
the short-lived protein CYP21A2 by 9-fold. FIG. 11A shows
determination of the half-life of CYP21A2 in HEK293 cells.
CYP21A2-SMASh was expressed in the absence of ASV so that the SMASh
tag removed itself for 24 hours, then 1 .mu.M ASV was added to
switch production to uncleaved CYP21A2-SMASh. Levels of cleaved
CYP21A2 over time were then followed by immunoblotting.
Background-subtracted CYP21A2 signal was normalized to
background-subtracted .beta.-actin signal and then divided by the
mean signal at 0 hour (n=3, error bars represent standard
deviations). Values fit an exponential decay function with a
half-life of 130 minutes. FIG. 11B shows that the half-life of
CYP21A2-SMASh can be calculated from the half-life of CYP21A2 and
the ratio of CYP21A2-SMASh to CYP21A2 accumulated within the same
amount of time, if they are produced at equal rates (see Methods).
To obtain this ratio, CYP21A2-SMASh was first expressed with 1
.mu.M ASV for 24 hours, then ASV was washed out for 4 hours
(procedure i). Additional new CYP21A2 appearing at the cleaved size
of 84 kDa was apparent at 28 hours (lane 2). In parallel,
CYP21A2-SMASh was expressed without ASV so that all CYP21A2-SMASh
was cleaved to CYP21A2 for 24 hours, then new CYP21A2-SMASh was
inhibited from cleavage by addition of 1 .mu.M ASV for 4 hours
(procedure ii). The level of CYP21A2-SMASh (lane 4) was quantified
relative to that of CYP21A2 produced from the same plasmid over the
same time (lane 2). Background-subtracted CYP21A2 and CYP21A2-SMASh
signals were normalized to background-subtracted .beta.-actin
signal. To calculate the produced amount of CYP21A2 and
CYP21A2-SMASh in 4 hours, normalized signals at 24 hours (lanes 1
and 3) were subtracted from those at 28 hours (lanes 2 and 4). With
these values inputted into the mathematical model, the half-life of
CYP21A2-SMASh was calculated to be 15 minutes.
[0053] FIGS. 12A and 12B show that SMASh mediates drug-inducible
YFP shutoff in mammalian neurons. FIG. 12A shows rat embryonic day
15 cortico-hippocampal tissue that was dissected, dissociated, and
nucleofected with plasmids encoding RFP and YFP-SMASh. Neurons were
treated with either DMSO at 7 days in vitro (DIV), 3 .mu.M ASV at 7
DIV, or 3 .mu.M ASV at 1 DIV followed by replacement of 50% of old
media with new media containing 3 .mu.M ASV at 4 and 7 DIV.
Untagged RFP verified that drug inhibition of expression was
specific to the SMASh-tagged protein. Live neurons were imaged at
10 DIV in glass-bottom chambers. Representative images are shown.
Scale bar, 20 .mu.m. FIG. 12B shows mouse embryonic day 18 cortical
tissue that was dissected, dissociated, and nucleofected with
plasmid encoding YFP-SMASh. At 1 DIV, neurons were placed in media
with or without 3 .mu.M ASV. ASV-containing chambers had ASV
replenished at 4 DIV via replacement of 50% of old media with new
media containing 2 .mu.M ASV. Live neurons were imaged at 6 DIV in
glass-bottom chambers. Representative images are shown. Scale bar,
100 .mu.m.
[0054] FIGS. 13A and 13B show kinetics of drug-induced shutoff of
protein synthesis. FIG. 13A shows dynamics of SMASh induction
studied by metabolic incorporation of unnatural amino acids and
labeling by click chemistry. HeLa cells expressed P-SMASh for 20
hours before the addition of combinations of the methionine analog
azidohomoalanine (AHA) and/or ASV. For negative wells, an
equivalent volume of DMSO was used as vehicle control. For
AHA-treated wells, methionine-free media was used. Treatment lasted
for 3 hours, after which cells were lysed. FIG. 13B shows a portion
of lysate analyzed by immunoblot to visualize total protein. ASV
treatment for 3 hours caused a drop in P protein consistent with
shutoff (lane 4). HeLa lysate from an empty vector transfection was
used as a control to reveal nonspecific bands (lane 1). The
remainder of the lysate was reacted with biotin-alkyne to label
AHA-containing proteins via azide-alkyne cycloaddition click
chemistry, and labeled proteins were purified with magnetic
streptavidin beads to visualize protein produced in the 3-hour
labeling window. .beta.-actin serves as a loading control for lanes
6-7, and also verifies selectivity of purification, as only minimal
endogenous .beta.-actin is purified without AHA incubation (lane
5). While cleaved P protein produced in the presence of AHA and
absence of ASV is detected after purification (lane 6), no cleaved
P is produced after ASV addition (lane 7), indicating rapid access
of the drug to the protease. Additionally, no P-SMASh is visible,
indicating efficient SMAShinduced degradation of P.
[0055] FIGS. 14A and 14B show MeV-EGFP-P-SMASh validation. FIG. 14A
(Left) shows the design of RT-PCR reactions to verify
MeV-EGFP-P-SMASh RNA genomic structure. Arrows denote primer
locations. FIG. 14A (Right) shows the expected 1659-bp band was
obtained by RT-PCR from Vero cells infected with MeV-EGFPPSMASh
passages 1 and 2 viruses, and by PCR of MeV-EGFP-P-SMASh plasmid
DNA as a positive control. RT-PCR from Vero cells infected with
MeV-EGFP control virus yielded the expected 747-bp band. FIG. 14B
shows time-lapse imaging of Vero cells infected with
MeV-EGFP-P-SMASh at MOI of 0.1 or 1, grown in the absence or
presence of 3 .mu.M ASV Images are representative of 3 replicates.
Scale bar, 50 .mu.m.
DETAILED DESCRIPTION
[0056] The practice of the present invention will employ, unless
otherwise indicated, conventional methods of molecular biology,
chemistry, biochemistry, virology, and immunology, within the skill
of the art. Such techniques are explained fully in the literature.
See, e.g., Hepatitis C Viruses: Genomes and Molecular Biology (S.
L. Tan ed., Taylor & Francis, 2006); Fundamental Virology,
3.sup.rd Edition, vol. I & II (B. N. Fields and D. M. Knipe,
eds.); Handbook of Experimental Immunology, Vols. I-IV (D. M. Weir
and C. C. Blackwell eds., Blackwell Scientific Publications); A. L.
Lehninger, Biochemistry (Worth Publishers, Inc., current addition);
Sambrook, et al., Molecular Cloning: A Laboratory Manual (3.sup.rd
Edition, 2001); Methods In Enzymology (S. Colowick and N. Kaplan
eds., Academic Press, Inc.).
[0057] All publications, patents and patent applications cited
herein, whether supra or infra, are hereby incorporated by
reference in their entireties.
I. Definitions
[0058] In describing the present invention, the following terms
will be employed, and are intended to be defined as indicated
below.
[0059] It must be noted that, as used in this specification and the
appended claims, the singular forms "a," "an" and "the" include
plural referents unless the content clearly dictates otherwise.
Thus, for example, reference to "a fusion protein" includes a
mixture of two or more fusion proteins, and the like.
[0060] The term "about," particularly in reference to a given
quantity, is meant to encompass deviations of plus or minus five
percent.
[0061] A nonstructural protein 3 (NS3) nucleic acid,
oligonucleotide, protein, polypeptide, or peptide refers to a
molecule derived from hepatitis C virus (HCV), including any
isolate of HCV having any genotype (e.g., seven genotypes 1-7) or
subtype. The molecule need not be physically derived from HCV, but
may be synthetically or recombinantly produced. A number of NS3
nucleic acid and protein sequences are known. A representative NS3
sequence is presented in SEQ ID NO:4. Additional representative
sequences are listed in the National Center for Biotechnology
Information (NCBI) database. See, for example, NCBI entries:
Accession Nos. YP_001491553, YP_001469631, YP_001469632, NP_803144,
NP_671491, YP_001469634, YP_001469630, YP_001469633, ADA68311,
ADA68307, AFP99000, AFP98987, ADA68322, AFP99033, ADA68330,
AFP99056, AFP99041, CBF60982, CBF60817, AHH29575, AIZ00747,
AIZ00744, ABI36969, ABN05226, KF516075, KF516074, KF516056,
AB826684, AB826683, JX171009, JX171008, JX171000, EU847455,
EF154714, GU085487, JX171065, JX171063; all of which sequences (as
entered by the date of filing of this application) are herein
incorporated by reference. Any of these sequences or a variant
thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, can be
used to construct a fusion protein or a recombinant polynucleotide
encoding such a fusion protein, as described herein.
[0062] A nonstructural protein 4A (NS4A) nucleic acid,
oligonucleotide, protein, polypeptide, or peptide refers to a
molecule derived from HCV, including any isolate of HCV having any
genotype (e.g., seven genotypes 1-7) or subtype. The molecule need
not be physically derived from HCV, but may be synthetically or
recombinantly produced. A number of NS4A nucleic acid and protein
sequences are known. A representative NS4A sequence is presented in
SEQ ID NO:6. Additional representative sequences are listed in the
National Center for Biotechnology Information (NCBI) database. See,
for example, NCBI entries: Accession Nos. NP_751925, YP_001491554,
GU945462, HQ822054, FJ932208, FJ932207, FJ932205, and FJ932199; all
of which sequences (as entered by the date of filing of this
application) are herein incorporated by reference. Any of these
sequences or a variant thereof comprising a sequence having at
least about 80-100% sequence identity thereto, including any
percent identity within this range, such as 81, 82, 83, 84, 85, 86,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence
identity thereto, can be used to construct a fusion protein or a
recombinant polynucleotide encoding such a fusion protein, as
described herein.
[0063] A polyprotein nucleic acid, oligonucleotide, protein,
polypeptide, or peptide refers to a molecule derived from HCV,
including any isolate of HCV having any genotype (e.g., seven
genotypes 1-7) or subtype. The molecule need not be physically
derived from HCV, but may be synthetically or recombinantly
produced. A number of polyprotein nucleic acid and protein
sequences are known. Representative HCV polyprotein sequences are
listed in the National Center for Biotechnology Information (NCBI)
database. See, for example, NCBI entries: Accession Nos.
YP_001469631, NP_671491, YP_001469633, YP_001469630, YP_001469634,
YP_001469632, NC_009824, NC_004102, NC_009825, NC_009827,
NC_009823, NC_009826, and EF108306; all of which sequences (as
entered by the date of filing of this application) are herein
incorporated by reference. Any of these sequences or a variant
thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, can be
used to construct a fusion protein or a recombinant polynucleotide
encoding such a fusion protein, as described herein.
[0064] For a discussion of genetic diversity and phylogenetic
analysis of hepatitis C virus, see also Smith et al. (2014)
Hepatology 59(1):318-327, Simmonds et al. (2005) Hepatology
42(4):962-973, Kuiken et al. (2009) Methods Mol. Biol. 510:33-53,
Ho et al. (2015) J. Virol. Methods 219:28-37, Echeverria et al.
(2015) World J. Hepatol. 7(6):831-845, and Jackowiak et al. (2014)
Infect Genet Evol. 21:67-82; herein incorporated by reference in
their entireties.
[0065] The terms "fusion protein," "fusion polypeptide," "degron
fusion protein," or "degron fusion" as used herein refer to a
fusion comprising a degron in combination with a protease and a
selected polypeptide of interest as part of a single continuous
chain of amino acids, which chain does not occur in nature. The
degron is connected to the polypeptide of interest through a
cleavable linker comprising a cleavage site capable of being
recognized by the protease of the fusion to allow self-removal of
the protease and degron from the polypeptide of interest. The
position of the cleavage site in the fusion is preferably chosen to
allow release of the polypeptide of interest from the fusion
essentially unmodified or with little modification (e.g., less than
10 extra amino acids). The fusion polypeptides may be designed for
N-terminal or C-terminal attachment of the degron to the
polypeptide of interest. The fusion polypeptides may also contain
sequences exogenous to the degron, protease, and polypeptide of
interest. For example, the fusion may include targeting or
localization sequences, detectable labels, or tag sequences.
[0066] The term "cleavage site" refers to the bond (e.g. a scissile
bond) cleaved by an agent. A cleavage site for a protease includes
the specific amino acid sequence recognized by the protease during
proteolytic cleavage and typically includes the surrounding one to
six amino acids on either side of the scissile bond, which bind to
the active site of the protease and are needed for recognition as a
substrate.
[0067] The term "cleavable linker" refers to a linker comprising a
cleavage site. The cleavable linker may include a cleavage site
specific for an enzyme, such as a protease or other cleavage agent.
A cleavable linker is typically cleavable under physiological
conditions.
[0068] The terms "polypeptide" and "protein" refer to a polymer of
amino acid residues and are not limited to a minimum length. Thus,
peptides, oligopeptides, dimers, multimers, and the like, are
included within the definition. Both full length proteins and
fragments thereof are encompassed by the definition. The terms also
include postexpression modifications of the polypeptide, for
example, glycosylation, acetylation, phosphorylation,
hydroxylation, and the like. Furthermore, for purposes of the
present invention, a "polypeptide" refers to a protein which
includes modifications, such as deletions, additions and
substitutions to the native sequence, so long as the protein
maintains the desired activity. These modifications may be
deliberate, as through site directed mutagenesis, or may be
accidental, such as through mutations of hosts which produce the
proteins or errors due to PCR amplification.
[0069] By "derivative" is intended any suitable modification of the
native polypeptide of interest, of a fragment of the native
polypeptide, or of their respective analogs, such as glycosylation,
phosphorylation, polymer conjugation (such as with polyethylene
glycol), or other addition of foreign moieties, as long as the
desired biological activity of the native polypeptide is retained.
Methods for making polypeptide fragments, analogs, and derivatives
are generally available in the art.
[0070] By "fragment" is intended a molecule consisting of only a
part of the intact full length sequence and structure. The fragment
can include a C-terminal deletion an N-terminal deletion, and/or an
internal deletion of the polypeptide. Active fragments of a
particular protein or polypeptide will generally include at least
about 5-10 contiguous amino acid residues of the full length
molecule, preferably at least about 15-25 contiguous amino acid
residues of the full length molecule, and most preferably at least
about 20-50 or more contiguous amino acid residues of the full
length molecule, or any integer between 5 amino acids and the full
length sequence, provided that the fragment in question retains
biological activity, such as catalytic activity, ligand binding
activity, regulatory activity, degron protein degradation
signaling, or fluorescence characteristics.
[0071] "Substantially purified" generally refers to isolation of a
substance (compound, polynucleotide, protein, polypeptide,
polypeptide composition) such that the substance comprises the
majority percent of the sample in which it resides. Typically in a
sample, a substantially purified component comprises 50%,
preferably 80%-85%, more preferably 90-95% of the sample.
Techniques for purifying polynucleotides and polypeptides of
interest are well-known in the art and include, for example,
ion-exchange chromatography, affinity chromatography and
sedimentation according to density.
[0072] By "isolated" is meant, when referring to a polypeptide,
that the indicated molecule is separate and discrete from the whole
organism with which the molecule is found in nature or is present
in the substantial absence of other biological macro molecules of
the same type. The term "isolated" with respect to a polynucleotide
is a nucleic acid molecule devoid, in whole or part, of sequences
normally associated with it in nature; or a sequence, as it exists
in nature, but having heterologous sequences in association
therewith; or a molecule disassociated from the chromosome.
[0073] The terms "label" and "detectable label" refer to a molecule
capable of detection, including, but not limited to, radioactive
isotopes, stable (non-radioactive) heavy isotopes, fluorescers,
chemiluminescers, enzymes, enzyme substrates, enzyme cofactors,
enzyme inhibitors, chromophores, dyes, metal ions, metal sols,
ligands (e.g., biotin or haptens) and the like. The term
"fluorescer" refers to a substance or a portion thereof that is
capable of exhibiting fluorescence in the detectable range.
Particular examples of labels that may be used with the invention
include, but are not limited to radiolabels (e.g., .sup.3H,
.sup.125I, .sup.35S, .sup.14C, or .sup.32P), stable
(non-radioactive) heavy isotopes (e.g., .sup.13C or .sup.15N),
phycoerythrin, Alexa dyes, fluorescein,
7-nitrobenzo-2-oxa-1,3-diazole (NBD), YPet, CyPet, Cascade blue,
allophycocyanin, Cy3, Cy5, Cy7, rhodamine, dansyl, umbelliferone,
Texas red, luminol, acradimum esters, biotin or other
streptavidin-binding proteins, magnetic beads, electron dense
reagents, green fluorescent protein (GFP), enhanced green
fluorescent protein (EGFP), yellow fluorescent protein (YFP),
enhanced yellow fluorescent protein (EYFP), blue fluorescent
protein (BFP), red fluorescent protein (RFP), Dronpa, Padron,
mApple, mCherry, rsCherry, rsCherryRev, firefly luciferase, Renilla
luciferase, NADPH, beta-galactosidase, horseradish peroxidase,
glucose oxidase, alkaline phosphatase, chloramphenical acetyl
transferase, and urease. Enzyme tags are used with their cognate
substrate. The terms also include color-coded microspheres of known
fluorescent light intensities (see e.g., microspheres with xMAP
technology produced by Luminex (Austin, Tex.); microspheres
containing quantum dot nanocrystals, for example, containing
different ratios and combinations of quantum dot colors (e.g., Qdot
nanocrystals produced by Life Technologies (Carlsbad, Calif.);
glass coated metal nanoparticles (see e.g., SERS nanotags produced
by Nanoplex Technologies, Inc. (Mountain View, Calif.); barcode
materials (see e.g., sub-micron sized striped metallic rods such as
Nanobarcodes produced by Nanoplex Technologies, Inc.), encoded
microparticles with colored bar codes (see e.g., CellCard produced
by Vitra Bioscience, vitrabio.com), and glass microparticles with
digital holographic code images (see e.g., CyVera microbeads
produced by Illumina (San Diego, Calif.). As with many of the
standard procedures associated with the practice of the invention,
skilled artisans will be aware of additional labels that can be
used.
[0074] "Homology" refers to the percent identity between two
polynucleotide or two polypeptide molecules. Two nucleic acid, or
two polypeptide sequences are "substantially homologous" to each
other when the sequences exhibit at least about 50% sequence
identity, preferably at least about 75% sequence identity, more
preferably at least about 80%-85% sequence identity, more
preferably at least about 90% sequence identity, and most
preferably at least about 95%-98% sequence identity over a defined
length of the molecules. As used herein, substantially homologous
also refers to sequences showing complete identity to the specified
sequence.
[0075] In general, "identity" refers to an exact nucleotide to
nucleotide or amino acid to amino acid correspondence of two
polynucleotides or polypeptide sequences, respectively. Percent
identity can be determined by a direct comparison of the sequence
information between two molecules by aligning the sequences,
counting the exact number of matches between the two aligned
sequences, dividing by the length of the shorter sequence, and
multiplying the result by 100. Readily available computer programs
can be used to aid in the analysis, such as ALIGN, Dayhoff, M.O. in
Atlas of Protein Sequence and Structure M.O. Dayhoff ed., 5 Suppl.
3:353 358, National biomedical Research Foundation, Washington, DC,
which adapts the local homology algorithm of Smith and Waterman
Advances in Appl. Math. 2:482 489, 1981 for peptide analysis.
Programs for determining nucleotide sequence identity are available
in the Wisconsin Sequence Analysis Package, Version 8 (available
from Genetics Computer Group, Madison, Wis.) for example, the
BESTFIT, FASTA and GAP programs, which also rely on the Smith and
Waterman algorithm. These programs are readily utilized with the
default parameters recommended by the manufacturer and described in
the Wisconsin Sequence Analysis Package referred to above. For
example, percent identity of a particular nucleotide sequence to a
reference sequence can be determined using the homology algorithm
of Smith and Waterman with a default scoring table and a gap
penalty of six nucleotide positions.
[0076] Another method of establishing percent identity in the
context of the present invention is to use the MPSRCH package of
programs copyrighted by the University of Edinburgh, developed by
John F. Collins and Shane S. Sturrok, and distributed by
IntelliGenetics, Inc. (Mountain View, Calif.). From this suite of
packages the Smith Waterman algorithm can be employed where default
parameters are used for the scoring table (for example, gap open
penalty of 12, gap extension penalty of one, and a gap of six).
From the data generated the "Match" value reflects "sequence
identity." Other suitable programs for calculating the percent
identity or similarity between sequences are generally known in the
art, for example, another alignment program is BLAST, used with
default parameters. For example, BLASTN and BLASTP can be used
using the following default parameters: genetic code=standard;
filter=none; strand=both; cutoff=60; expect=10; Matrix=BLOSUM62;
Descriptions=50 sequences; sort by=HIGH SCORE; Databases=non
redundant, GenBank+EMBL+DDBJ+PDB+GenBank CDS translations+Swiss
protein+Spupdate+PIR. Details of these programs are readily
available.
[0077] Alternatively, homology can be determined by hybridization
of polynucleotides under conditions which form stable duplexes
between homologous regions, followed by digestion with single
stranded specific nuclease(s), and size determination of the
digested fragments. DNA sequences that are substantially homologous
can be identified in a Southern hybridization experiment under, for
example, stringent conditions, as defined for that particular
system. Defining appropriate hybridization conditions is within the
skill of the art. See, e.g., Sambrook et al., supra; DNA Cloning,
supra; Nucleic Acid Hybridization, supra.
[0078] "Recombinant" as used herein to describe a nucleic acid
molecule means a polynucleotide of genomic, cDNA, viral,
semisynthetic, or synthetic origin which, by virtue of its origin
or manipulation, is not associated with all or a portion of the
polynucleotide with which it is associated in nature. The term
"recombinant" as used with respect to a protein or polypeptide
means a polypeptide produced by expression of a recombinant
polynucleotide. In general, the gene of interest is cloned and then
expressed in transformed organisms, as described further below. The
host organism expresses the foreign gene to produce the protein
under expression conditions.
[0079] The term "transformation" refers to the insertion of an
exogenous polynucleotide into a host cell, irrespective of the
method used for the insertion. For example, direct uptake,
transduction or f-mating are included. The exogenous polynucleotide
may be maintained as a non-integrated vector, for example, a
plasmid, or alternatively, may be integrated into the host
genome.
[0080] "Recombinant host cells," "host cells," "cells," "cell
lines," "cell cultures," and other such terms denoting
microorganisms or higher eukaryotic cell lines, refer to cells
which can be, or have been, used as recipients for a recombinant
vector or other transferred DNA, and include the progeny of the
cell which has been transfected. Host cells may be cultured as
unicellular or multicellular entities (e.g., tissue, organs, or
organoids comprising the recombinant vector).
[0081] A "coding sequence" or a sequence that "encodes" a selected
polypeptide is a nucleic acid molecule that is transcribed (in the
case of DNA) and translated (in the case of mRNA) into a
polypeptide in vivo when placed under the control of appropriate
regulatory sequences (or "control elements"). The boundaries of the
coding sequence can be determined by a start codon at the 5'
(amino) terminus and a translation stop codon at the 3' (carboxy)
terminus. A coding sequence can include, but is not limited to,
cDNA from viral, prokaryotic or eukaryotic mRNA, genomic DNA
sequences from viral or prokaryotic DNA, and even synthetic DNA
sequences. A transcription termination sequence may be located 3'
to the coding sequence.
[0082] Typical "control elements," include, but are not limited to,
transcription promoters, transcription enhancer elements,
transcription termination signals, polyadenylation sequences
(located 3' to the translation stop codon), sequences for
optimization of initiation of translation (located 5' to the coding
sequence), and translation termination sequences.
[0083] "Operably linked" refers to an arrangement of elements
wherein the components so described are configured so as to perform
their usual function. For example, a given promoter operably linked
to a coding sequence is capable of effecting the expression of the
coding sequence when the proper enzymes are present. The promoter
need not be contiguous with the coding sequence, so long as it
functions to direct the expression thereof. Thus, for example,
intervening untranslated yet transcribed sequences can be present
between the promoter sequence and the coding sequence and the
promoter sequence can still be considered "operably linked" to the
coding sequence. In another example, a degron operably linked to a
polypeptide is capable of promoting degradation of the polypeptide
when the proper cellular degradation system (e.g., proteasome or
autophagosome degradation) is present. The degron need not be
contiguous with the polypeptide, so long as it functions to direct
degradation of the polypeptide.
[0084] "Encoded by" refers to a nucleic acid sequence which codes
for a polypeptide sequence, wherein the polypeptide sequence or a
portion thereof contains an amino acid sequence of at least 3 to 5
amino acids, more preferably at least 8 to 10 amino acids, and even
more preferably at least 15 to 20 amino acids from a polypeptide
encoded by the nucleic acid sequence.
[0085] "Expression cassette" or "expression construct" refers to an
assembly which is capable of directing the expression of the
sequence(s) or gene(s) of interest. An expression cassette
generally includes control elements, as described above, such as a
promoter which is operably linked to (so as to direct transcription
of) the sequence(s) or gene(s) of interest, and often includes a
polyadenylation sequence as well. Within certain embodiments of the
invention, the expression cassette described herein may be
contained within a plasmid construct. In addition to the components
of the expression cassette, the plasmid construct may also include,
one or more selectable markers, a signal which allows the plasmid
construct to exist as single stranded DNA (e.g., a M13 origin of
replication), at least one multiple cloning site, and a "mammalian"
origin of replication (e.g., a SV40 or adenovirus origin of
replication).
[0086] "Purified polynucleotide" refers to a polynucleotide of
interest or fragment thereof which is essentially free, e.g.,
contains less than about 50%, preferably less than about 70%, and
more preferably less than about at least 90%, of the protein with
which the polynucleotide is naturally associated. Techniques for
purifying polynucleotides of interest are well-known in the art and
include, for example, disruption of the cell containing the
polynucleotide with a chaotropic agent and separation of the
polynucleotide(s) and proteins by ion-exchange chromatography,
affinity chromatography and sedimentation according to density.
[0087] The term "transfection" is used to refer to the uptake of
foreign DNA by a cell. A cell has been "transfected" when exogenous
DNA has been introduced inside the cell membrane. A number of
transfection techniques are generally known in the art. See, e.g.,
Graham et al. (1973) Virology, 52:456, Sambrook et al. (2001)
Molecular Cloning, a laboratory manual, 3.sup.rd edition, Cold
Spring Harbor Laboratories, New York, Davis et al. (1995) Basic
Methods in Molecular Biology, 2nd edition, McGraw-Hill, and Chu et
al. (1981) Gene 13:197. Such techniques can be used to introduce
one or more exogenous DNA moieties into suitable host cells. The
term refers to both stable and transient uptake of the genetic
material, and includes uptake of peptide- or antibody-linked
DNAs.
[0088] A "vector" is capable of transferring nucleic acid sequences
to target cells (e.g., viral vectors, non-viral vectors,
particulate carriers, and liposomes). Typically, "vector
construct," "expression vector, " and "gene transfer vector," mean
any nucleic acid construct capable of directing the expression of a
nucleic acid of interest and which can transfer nucleic acid
sequences to target cells. Thus, the term includes cloning and
expression vehicles, as well as viral vectors.
[0089] The terms "variant," "analog" and "mutein" refer to
biologically active derivatives of the reference molecule that
retain desired activity, such as fluorescence or oligomerization
characteristics. In general, the terms "variant" and "analog" refer
to compounds having a native polypeptide sequence and structure
with one or more amino acid additions, substitutions (generally
conservative in nature) and/or deletions, relative to the native
molecule, so long as the modifications do not destroy biological
activity and which are "substantially homologous" to the reference
molecule as defined below. In general, the amino acid sequences of
such analogs will have a high degree of sequence homology to the
reference sequence, e g , amino acid sequence homology of more than
50%, generally more than 60%-70%, even more particularly 80%-85% or
more, such as at least 90%-95% or more, when the two sequences are
aligned. Often, the analogs will include the same number of amino
acids but will include substitutions, as explained herein. The term
"mutein" further includes polypeptides having one or more amino
acid-like molecules including but not limited to compounds
comprising only amino and/or imino molecules, polypeptides
containing one or more analogs of an amino acid (including, for
example, unnatural amino acids, etc.), polypeptides with
substituted linkages, as well as other modifications known in the
art, both naturally occurring and non-naturally occurring (e.g.,
synthetic), cyclized, branched molecules and the like. The term
also includes molecules comprising one or more N-substituted
glycine residues (a "peptoid") and other synthetic amino acids or
peptides. (See, e.g., U.S. Pat. Nos. 5,831,005; 5,877,278; and
5,977,301; Nguyen et al., Chem. Biol. (2000) 7:463-473; and Simon
et al., Proc. Natl. Acad. Sci. USA (1992) 89:9367-9371 for
descriptions of peptoids). Methods for making polypeptide analogs
and muteins are known in the art and are described further
below.
[0090] As explained above, analogs generally include substitutions
that are conservative in nature, i.e., those substitutions that
take place within a family of amino acids that are related in their
side chains. Specifically, amino acids are generally divided into
four families: (1) acidic--aspartate and glutamate; (2)
basic--lysine, arginine, histidine; (3) non-polar--alanine, valine,
leucine, isoleucine, proline, phenylalanine, methionine,
tryptophan; and (4) uncharged polar--glycine, asparagine,
glutamine, cysteine, serine threonine, and tyrosine. Phenylalanine,
tryptophan, and tyrosine are sometimes classified as aromatic amino
acids. For example, it is reasonably predictable that an isolated
replacement of leucine with isoleucine or valine, an aspartate with
a glutamate, a threonine with a serine, or a similar conservative
replacement of an amino acid with a structurally related amino
acid, will not have a major effect on the biological activity. For
example, the polypeptide of interest may include up to about 5-10
conservative or non-conservative amino acid substitutions, or even
up to about 15-25 conservative or non-conservative amino acid
substitutions, or any integer between 5-25, so long as the desired
function of the molecule remains intact. One of skill in the art
may readily determine regions of the molecule of interest that can
tolerate change by reference to Hopp/Woods and Kyte-Doolittle
plots, well known in the art.
[0091] "Gene transfer" or "gene delivery" refers to methods or
systems for reliably inserting DNA or RNA of interest into a host
cell. Such methods can result in transient expression of
non-integrated transferred DNA, extrachromosomal replication and
expression of transferred replicons (e.g., episomes), or
integration of transferred genetic material into the genomic DNA of
host cells. Gene delivery expression vectors include, but are not
limited to, vectors derived from bacterial plasmid vectors, viral
vectors, non-viral vectors, alphaviruses, pox viruses and vaccinia
viruses.
[0092] The term "derived from" is used herein to identify the
original source of a molecule but is not meant to limit the method
by which the molecule is made which can be, for example, by
chemical synthesis or recombinant means.
[0093] A polynucleotide "derived from" a designated sequence refers
to a polynucleotide sequence which comprises a contiguous sequence
of approximately at least about 6 nucleotides, preferably at least
about 8 nucleotides, more preferably at least about 10-12
nucleotides, and even more preferably at least about 15-20
nucleotides corresponding, i.e., identical or complementary to, a
region of the designated nucleotide sequence. The derived
polynucleotide will not necessarily be derived physically from the
nucleotide sequence of interest, but may be generated in any
manner, including, but not limited to, chemical synthesis,
replication, reverse transcription or transcription, which is based
on the information provided by the sequence of bases in the
region(s) from which the polynucleotide is derived. As such, it may
represent either a sense or an antisense orientation of the
original polynucleotide.
[0094] The term "heterologous" as it relates to nucleic acid
sequences such as coding sequences and control sequences, denotes
sequences that are not normally joined together, and/or are not
normally associated with a particular cell. Thus, a "heterologous"
region of a nucleic acid construct or a vector is a segment of
nucleic acid within or attached to another nucleic acid molecule
that is not found in association with the other molecule in nature.
For example, a heterologous region of a nucleic acid construct
could include a coding sequence flanked by sequences not found in
association with the coding sequence in nature. Another example of
a heterologous coding sequence is a construct where the coding
sequence itself is not found in nature (e.g., synthetic sequences
having codons different from the native gene). Similarly, a cell
transformed with a construct which is not normally present in the
cell would be considered heterologous for purposes of this
invention.
[0095] By "recombinant virus" is meant a virus that has been
genetically altered, e.g., by the addition or insertion of a
heterologous nucleic acid construct into the particle.
[0096] "Recombinant virion," as used herein, refers to a viral
particle containing a recombinant viral vector (e.g., conditionally
replicating viral vector encoding a degron fusion protein).
Generally, a recombinant virion comprises one or more structural
proteins and the viral vector. The recombinant virion may also
contain a nucleocapsid structure, and in some cases, a lipid
envelope derived from the host cell membrane.
[0097] The terms "subject" refers to any invertebrate or vertebrate
subject, including, without limitation, humans and other primates,
including non-human primates such as chimpanzees and other apes and
monkey species; farm animals such as cattle, sheep, pigs, goats and
horses; domestic mammals such as dogs and cats; laboratory animals
including rodents such as mice, rats and guinea pigs; birds,
including domestic, wild and game birds such as chickens, turkeys
and other gallinaceous birds, ducks, geese, and the like. The term
does not denote a particular age. Thus, both adult and newborn
individuals are intended to be covered.
[0098] "Recombinant animal" refers to a nonhuman subject which has
been a recipient of a recombinant vector or other transferred DNA,
and also includes the progeny of a recombinant animal.
II. Modes of Carrying Out the Invention
[0099] Before describing the present invention in detail, it is to
be understood that this invention is not limited to particular
formulations or process parameters as such may, of course, vary. It
is also to be understood that the terminology used herein is for
the purpose of describing particular embodiments of the invention
only, and is not intended to be limiting.
[0100] Although a number of methods and materials similar or
equivalent to those described herein can be used in the practice of
the present invention, the preferred materials and methods are
described herein.
[0101] The present invention is based on the discovery of a novel
degron comprising sequences derived from NS3 and NS4A components of
HCV. This degron can be used in the Small Molecule-Assisted Shutoff
(SMASh) technique, described in Example 1, in which a protein of
interest is fused to a self-excising degron and thereby expressed
in a minimally modified form. The degron can be removed from the
protein of interest by a cis-encoded HCV protease. Clinically
available HCV protease inhibitors can be used to block protease
cleavage such that the degron is retained after inhibitor addition
on subsequently synthesized protein copies. The degron when
attached causes rapid degradation of the linked protein. The
inventors have shown that SMASh allows reversible and
dose-dependent shutoff of various proteins with high dynamic range
in multiple cell types, including yeast and neurons. SMASh was also
used with this degron to confer drug responsiveness on an RNA virus
for which no licensed drug inhibitors exist. As SMASh does not
require permanent fusion of a large domain, this technique will be
useful when control over protein production with minimal structural
modification is desired.
[0102] In order to further an understanding of the invention, a
more detailed discussion is provided below regarding the identified
degron and its use in the SMASh method for controlling production
of proteins and viral replication.
[0103] A. Degron Fusion Proteins
[0104] Degron fusion proteins comprise a degron in combination with
a protease connected to a selected polypeptide of interest in an
arrangement designed to control production of the polypeptide of
interest. The degron is connected to the polypeptide of interest
through a cleavable linker comprising a cleavage site capable of
being recognized by the protease of the fusion protein in order to
allow self-removal of the protease and degron from the polypeptide
of interest. The position of the cleavage site in the fusion is
preferably chosen to allow release of the polypeptide of interest
from the fusion protein essentially unmodified or with little
modification (e.g., less than 10 extra amino acids). The fusion
polypeptides may be designed with N-terminal or C-terminal
attachment of the degron to the polypeptide of interest. The degron
need not be contiguous with the polypeptide of interest, as long as
it functions to direct degradation of the polypeptide. The fusion
protein may also contain sequences exogenous to the degron,
protease, and polypeptide of interest. For example, the fusion may
include targeting or localization sequences, or tag sequences. In
addition, the fusion protein may comprise a detectable label (e.g.,
fluorescent, bioluminescent, chemiluminescent, colorimetric, or
isotopic label) to facilitate monitoring production and degradation
of the polypeptide of interest.
[0105] The polypeptide of interest selected for inclusion in the
fusion protein may be from a membrane protein, a receptor, a
hormone, a transport protein, a transcription factor, a
cytoskeletal protein, an extracellular matrix protein, a
signal-transduction protein, an enzyme, or any other protein of
interest. The polypeptide of interest may comprise an entire
protein, or a biologically active domain (e.g., a catalytic domain,
a ligand binding domain, or a protein-protein interaction domain),
or a polypeptide fragment of a selected protein.
[0106] The degron comprises a sequence of amino acids, which
provides a degradation signal that directs a polypeptide for
cellular degradation. The degron may promote degradation of an
attached polypeptide through either the proteasome or
autophagy-lysosome pathways. In the fusion protein, the degron must
be operably linked to the polypeptide of interest, but need not be
contiguous with it as long as the degron still functions to direct
degradation of the polypeptide of interest. Preferably, the degron
induces rapid degradation of the polypeptide of interest. For a
discussion of degrons and their function in protein degradation,
see, e.g., Kanemaki et al. (2013) Pflugers Arch. 465(3):419-425,
Erales et al. (2014) Biochim Biophys Acta 1843(1):216-221, Schrader
et al. (2009) Nat. Chem. Biol. 5(11):815-822, Ravid et al. (2008)
Nat. Rev. Mol. Cell. Biol. 9(9):679-690, Tasaki et al. (2007)Trends
Biochem Sci. 32(11):520-528, Meinnel et al. (2006) Biol. Chem.
387(7):839-851, Kim et al. (2013) Autophagy 9(7):1100-1103,
Varshaysky (2012) Methods Mol. Biol. 832:1-11, and Fayadat et al.
(2003) Mol Biol Cell. 14(3):1268-1278; herein incorporated by
reference.
[0107] In certain embodiments, the degron comprises portions of the
HCV nonstructural proteins NS3 and NS4A (as described in Example
1). In one embodiment, the degron comprises the amino acid sequence
of SEQ ID NO:1 or a variant thereof comprising a sequence having at
least about 80-100% sequence identity thereto, including any
percent identity within this range, such as 81, 82, 83, 84, 85, 86,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence
identity thereto, wherein the degron is capable of promoting
degradation of a polypeptide. It is to be understood that degrons
comprising the residues corresponding to the reference sequence of
SEQ ID NO:1 in HCV nonstructural proteins NS3 and NS4A obtained
from other strains of HCV are also intended to be encompassed by
the present invention.
[0108] In the fusion protein, the degron may be linked to the
N-terminus or the C-terminus of the polypeptide of interest. For
example, the fusion protein can be represented by the formula
NH.sub.2-P-D-L-X--COOH or NH.sub.2-X-L-P-D-COOH, wherein: P is an
amino acid sequence of a protease; D is an amino acid sequence of a
degron; L is an amino acid sequence of a linker comprising a
cleavage site for the protease; and X is an amino acid sequence of
a selected polypeptide of interest.
[0109] The cleavable linker between the polypeptide of interest and
the degron is designed for selective cleavage by the particular
protease included in the fusion protein. The cleavage site of the
linker includes the specific amino acid sequence recognized by the
protease during proteolytic cleavage and typically includes the
surrounding one to six amino acids on either side of the scissile
bond, which bind to the active site of the protease and are needed
for recognition as a substrate. The cleavable linker may contain
any protease recognition motif known in the art and is typically
cleavable under physiological conditions.
[0110] Exemplary proteases which can be used in fusion proteins
include hepatitis C virus proteases (e.g., NS3 and NS2-3); signal
peptidase; proprotein convertases of the subtilisin/kexin family
(furin, PC1, PC2, PC4, PACE4, PCS, PC); proprotein convertases
cleaving at hydrophobic residues (e.g., Leu, Phe, Val, or Met);
proprotein convertases cleaving at small amino acid residues such
as Ala or Thr; proopiomelanocortin converting enzyme (PCE);
chromaffin granule aspartic protease (CGAP); prohormone thiol
protease; carboxypeptidases (e.g., carboxypeptidase E/H,
carboxypeptidase D and carboxypeptidase Z); aminopeptidases (e.g.,
arginine aminopeptidase, lysine aminopeptidase, aminopeptidase B);
prolyl endopeptidase; aminopeptidase N; insulin degrading enzyme;
calpain; high molecular weight protease; and, caspases 1, 2, 3, 4,
5, 6, 7, 8, and 9. Other proteases include, but are not limited to,
aminopeptidase N; puromycin sensitive aminopeptidase; angiotensin
converting enzyme; pyroglutamyl peptidase II; dipeptidyl peptidase
IV; N-arginine dibasic convertase; endopeptidase 24.15;
endopeptidase 24.16; amyloid precursor protein secretases alpha,
beta and gamma; angiotensin converting enzyme secretase; TGF alpha
secretase; TNF alpha secretase; FAS ligand secretase; TNF
receptor-I and -II secretases; CD30 secretase; KL1 and KL2
secretases; IL6 receptor secretase; CD43, CD44 secretase; CD16-I
and CD16-II secretases; L-selectin secretase; Folate receptor
secretase; MMP 1, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, and 15;
urokinase plasminogen activator; tissue plasminogen activator;
plasmin; thrombin; BMP-1 (procollagen C-peptidase); ADAM 1, 2, 3,
4, 5, 6, 7, 8, 9, 10, and 11; and, granzymes A, B, C, D, E, F, G,
and H. The protease chosen for use in the fusion protein is
preferably highly selective for the cleavage site in the cleavable
linker. Additionally, protease activity is preferably inhibitable
with inhibitors that are cell-permeable and not toxic to the cell
or subject under study. For a discussion of proteases, see, e.g.,
V. Y. H. Hook, Proteolytic and cellular mechanisms in prohormone
and proprotein processing, RG Landes Company, Austin, Tex., USA
(1998); N. M. Hooper et al., Biochem. J. 321: 265-279 (1997); Z.
Werb, Cell 91: 439-442 (1997); T. G. Wolfsberg et al., J. Cell
Biol. 131: 275-278 (1995); K. Murakami and J. D. Etlinger, Biochem.
Biophys. Res. Comm 146: 1249-1259 (1987); T. Berg et al., Biochem.
J. 307: 313-326 (1995); M. J. Smyth and J. A. Trapani, Immunology
Today 16: 202-206 (1995); R. V. Talanian et al., J. Biol. Chem.
272: 9677-9682 (1997); and N. A. Thornberry et al., J. Biol. Chem.
272: 17907-17911 (1997), the disclosures of which are incorporated
herein.
[0111] In certain embodiments, the protease used in the fusion
protein is a hepatitis C virus (HCV) nonstructural protein 3 (NS3)
protease. NS3 consists of an N-terminal serine protease domain and
a C-terminal helicase domain. The protease domain of NS3 forms a
heterodimer with the HCV nonstructural protein 4A (NS4A), which
activates proteolytic activity. An NS3 protease may comprise the
entire NS3 protein or a proteolytically active fragment thereof and
may further comprise an activating NS4A region. Advantages of using
an NS3 protease include that it is highly selective and can be
well-inhibited by a number of non-toxic, cell-permeable drugs,
which are currently clinically available. NS3 protease inhibitors
that can be used in the practice of the invention include, but are
not limited to, simeprevir, danoprevir, asunaprevir, ciluprevir,
boceprevir, sovaprevir, paritaprevir and telaprevir.
[0112] When an NS3 protease is used in a degron fusion protein, the
cleavable linker of the fusion protein should comprise an NS3
protease cleavage site. Exemplary NS3 protease cleavage sites,
which can be used in the cleavable linker, include the four
junctions between nonstructural (NS) proteins of the HCV
polyprotein normally cleaved by the NS3 protease during HCV
infection, including the NS3/NS4A, NS4A/NS4B, NS4B/NS5A, and
NS5A/NS5B junction cleavage sites. For a description of NS3
protease and representative sequences of its cleavage sites for
various strains of HCV, see, e.g., Hepatitis C Viruses: Genomes and
Molecular Biology (S. L. Tan ed., Taylor & Francis, 2006),
Chapter 6, pp. 163-206; herein incorporated by reference in its
entirety.
[0113] NS3 nucleic acid and protein sequences may be derived from
HCV, including any isolate of HCV having any genotype (e.g., seven
genotypes 1-7) or subtype. A number of NS3 nucleic acid and protein
sequences are known. A representative NS3 sequence is presented in
SEQ ID NO:4. Additional representative sequences are listed in the
National Center for Biotechnology Information (NCBI) database. See,
for example, NCBI entries: Accession Nos. YP_001491553,
YP_001469631, YP_001469632, NP_803144, NP_671491, YP_001469634,
YP_001469630, YP_001469633, ADA68311, ADA68307, AFP99000, AFP98987,
ADA68322, AFP99033, ADA68330, AFP99056, AFP99041, CBF60982,
CBF60817, AHH29575, AIZ00747, AIZ00744, ABI36969, ABN05226,
KF516075, KF516074, KF516056, AB826684, AB826683, JX171009,
JX171008, JX171000, EU847455, EF154714, GU085487, JX171065,
JX171063, all of which sequences (as entered by the date of filing
of this application) are herein incorporated by reference. Any of
these sequences or a variant thereof comprising a sequence having
at least about 80-100% sequence identity thereto, including any
percent identity within this range, such as 81, 82, 83, 84, 85, 86,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence
identity thereto, can be used to construct a fusion protein or a
recombinant polynucleotide encoding such a fusion protein, as
described herein.
[0114] NS4A nucleic acid and protein sequences may be derived from
HCV, including any isolate of HCV having any genotype (e.g., seven
genotypes 1-7) or subtype. A number of NS4A nucleic acid and
protein sequences are known. A representative NS4A sequence is
presented in SEQ ID NO:6. Additional representative sequences are
listed in the National Center for Biotechnology Information (NCBI)
database. See, for example, NCBI entries: Accession Nos. NP_751925,
YP_001491554, GU945462, HQ822054, FJ932208, FJ932207, FJ932205, and
FJ932199; all of which sequences (as entered by the date of filing
of this application) are herein incorporated by reference. Any of
these sequences or a variant thereof comprising a sequence having
at least about 80-100% sequence identity thereto, including any
percent identity within this range, such as 81, 82, 83, 84, 85, 86,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence
identity thereto, can be used to construct a fusion protein or a
recombinant polynucleotide encoding such a fusion protein, as
described herein.
[0115] HCV polyprotein nucleic acid and protein sequences may be
derived from HCV, including any isolate of HCV having any genotype
(e.g., seven genotypes 1-7) or subtype. A number of HCV polyprotein
nucleic acid and protein sequences are known. Representative HCV
polyprotein sequences are listed in the National Center for
Biotechnology Information (NCBI) database. See, for example, NCBI
entries: Accession Nos. YP_001469631, NP_671491, YP_001469633,
YP_001469630, YP_001469634, YP_001469632, NC_009824, NC_004102,
NC_009825, NC_009827, NC_009823, NC_009826, and EF108306; all of
which sequences (as entered by the date of filing of this
application) are herein incorporated by reference. Any of these
sequences or a variant thereof comprising a sequence having at
least about 80-100% sequence identity thereto, including any
percent identity within this range, such as 81, 82, 83, 84, 85, 86,
87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% sequence
identity thereto, can be used to construct a fusion protein or a
recombinant polynucleotide encoding such a fusion protein, as
described herein.
[0116] The polypeptides included in the fusion construct may be
connected directly to each other by peptide bonds or may be
separated by intervening amino acid sequences. The fusion
polypeptides may also contain sequences exogenous to the protease
or the selected protein of interest. For example, the fusion
protein may include targeting or localization sequences, tag
sequences, or sequences of fluorescent or bioluminescent
proteins.
[0117] In certain embodiments, tag sequences are located at the
N-terminus or C-terminus of the fusion protein. Exemplary tags that
can be used in the practice of the invention include a His-tag, a
Strep-tag, a TAP-tag, an S-tag, an SBP-tag, an Arg-tag, a
calmodulin-binding peptide tag, a cellulose-binding domain tag, a
DsbA tag, a c-myc tag, a glutathione S-transferase tag, a FLAG tag,
a HAT-tag, a maltose-binding protein tag, a NusA tag, and a
thioredoxin tag.
[0118] In certain embodiments, the fusion protein comprises a
targeting sequence. Exemplary targeting sequences that can be used
in the practice of the invention include a secretory protein signal
sequence, a membrane protein signal sequence, a nuclear
localization sequence, a nucleolar localization signal sequence, an
endoplasmic reticulum localization sequence, a peroxisome
localization sequence, a mitochondrial localization sequence, and a
protein-protein interaction motif sequence. Examples of targeting
sequences include those targeting the nucleus (e.g., KKKRK, SEQ ID
NO:12), mitochondrion (e.g., MLRTSSLFTRRVQPSLFRNILRLQST, SEQ ID
NO:13), endoplasmic reticulum (e.g., KDEL, SEQ ID NO:14),
peroxisome (e.g., SKL), synapses (e.g., S/TDV or fusion to GAP 43,
kinesin or tau), plasma membrane (e.g., CaaX (SEQ ID NO:15) where
"a" is an aliphatic amino acid, CC, CXC, CCXX (SEQ ID NO:16) at
C-terminus), or protein-protein interaction motifs (e.g., SH2, SH3,
PDZ, WW, RGD, Src homology domain, DNA-binding domain, SLiMs).
[0119] In certain embodiments, the fusion protein comprises a
detectable label. The detectable label may comprise any molecule
capable of detection. Detectable labels that may be used in the
practice of the invention include, but are not limited to,
radioactive isotopes, stable (non-radioactive) heavy isotopes,
fluorescers, chemiluminescers, enzymes, enzyme substrates, enzyme
cofactors, enzyme inhibitors, chromophores, dyes, metal ions, metal
sols, ligands (e.g., biotin or haptens) and the like. Particular
examples of labels that may be used with the invention include, but
are not limited to radiolabels (e.g., .sup.3H, .sup.125I, .sup.35S,
.sup.14C, or .sup.32P), stable (non-radioactive) heavy isotopes
(e.g., .sup.13C or .sup.15N), phycoerythrin, Alexa dyes,
fluorescein, 7-nitrobenzo-2-oxa-1,3-diazole (NBD), YPet, CyPet,
Cascade blue, allophycocyanin, Cy3, Cy5, Cy7, rhodamine, dansyl,
umbelliferone, Texas red, luminol, acradimum esters, biotin or
other streptavidin-binding proteins, magnetic beads, electron dense
reagents, green fluorescent protein (GFP), enhanced green
fluorescent protein (EGFP), yellow fluorescent protein (YFP),
enhanced yellow fluorescent protein (EYFP), blue fluorescent
protein (BFP), red fluorescent protein (RFP), Dronpa, Padron,
mApple, mCherry, rsCherry, rsCherryRev, firefly luciferase, Renilla
luciferase, NADPH, beta-galactosidase, horseradish peroxidase,
glucose oxidase, alkaline phosphatase, chloramphenical acetyl
transferase, and urease. Enzyme tags are used with their cognate
substrate. The terms also include color-coded microspheres of known
fluorescent light intensities (see e.g., microspheres with xMAP
technology produced by Luminex (Austin, Tex.); microspheres
containing quantum dot nanocrystals, for example, containing
different ratios and combinations of quantum dot colors (e.g., Qdot
nanocrystals produced by Life Technologies (Carlsbad, Calif.);
glass coated metal nanoparticles (see e.g., SERS nanotags produced
by Nanoplex Technologies, Inc. (Mountain View, Calif.); barcode
materials (see e.g., sub-micron sized striped metallic rods such as
Nanobarcodes produced by Nanoplex Technologies, Inc.), encoded
microparticles with colored bar codes (see e.g., CellCard produced
by Vitra Bioscience, vitrabio.com), and glass microparticles with
digital holographic code images (see e.g., CyVera microbeads
produced by Illumina (San Diego, Calif.). As with many of the
standard procedures associated with the practice of the invention,
skilled artisans will be aware of additional labels that can be
used.
[0120] B. Production of Degron Fusion Proteins
[0121] Degron fusion proteins can be produced using recombinant
techniques well known in the art. One of skill in the art can
readily determine nucleotide sequences that encode the desired
polypeptides using standard methodology and the teachings herein.
Oligonucleotide probes can be devised based on the known sequences
and used to probe genomic or cDNA libraries. The sequences can then
be further isolated using standard techniques and, e.g.,
restriction enzymes employed to truncate the gene at desired
portions of the full-length sequence. Similarly, sequences of
interest can be isolated directly from cells and tissues containing
the same, using known techniques, such as phenol extraction and the
sequence further manipulated to produce the desired truncations.
See, e.g., Sambrook et al., supra, for a description of techniques
used to obtain and isolate DNA.
[0122] The sequences encoding polypeptides can also be produced
synthetically, for example, based on the known sequences. The
nucleotide sequence can be designed with the appropriate codons for
the particular amino acid sequence desired. The complete sequence
is generally assembled from overlapping oligonucleotides prepared
by standard methods and assembled into a complete coding sequence.
See, e.g., Edge (1981) Nature 292:756; Nambair et al. (1984)
Science 223:1299; Jay et al. (1984) J. Biol. Chem. 259:6311;
Stemmer et al. (1995) Gene 164:49-53.
[0123] Recombinant techniques are readily used to clone sequences
encoding polypeptides useful in the claimed fusion proteins that
can then be mutagenized in vitro by the replacement of the
appropriate base pair(s) to result in the codon for the desired
amino acid. Such a change can include as little as one base pair,
effecting a change in a single amino acid, or can encompass several
base pair changes. Alternatively, the mutations can be effected
using a mismatched primer that hybridizes to the parent nucleotide
sequence (generally cDNA corresponding to the RNA sequence), at a
temperature below the melting temperature of the mismatched duplex.
The primer can be made specific by keeping primer length and base
composition within relatively narrow limits and by keeping the
mutant base centrally located. See, e.g., Innis et al, (1990) PCR
Applications: Protocols for Functional Genomics; Zoller and Smith,
Methods Enzymol. (1983) 100:468. Primer extension is effected using
DNA polymerase, the product cloned and clones containing the
mutated DNA, derived by segregation of the primer extended strand,
selected. Selection can be accomplished using the mutant primer as
a hybridization probe. The technique is also applicable for
generating multiple point mutations. See, e.g., Dalbie-McFarland et
al. Proc. Natl. Acad. Sci USA (1982) 79:6409.
[0124] Once coding sequences have been isolated and/or synthesized,
they can be cloned into any suitable vector or replicon for
expression. (See, also, Examples). As will be apparent from the
teachings herein, a wide variety of vectors encoding modified
polypeptides can be generated by creating expression constructs
which operably link, in various combinations, polynucleotides
encoding polypeptides having deletions or mutations therein.
[0125] Numerous cloning vectors are known to those of skill in the
art, and the selection of an appropriate cloning vector is a matter
of choice. Examples of re-combinant DNA vectors for cloning and
host cells which they can transform include the bacteriophage
.lamda. (E. coli), pBR322 (E. coli), pACYC177 (E. coli), pKT230
(gram-negative bacteria), pGV1106 (gram-negative bacteria), pLAFR1
(gram-negative bacteria), pME290 (non-E. coli gram-negative
bacteria), pHV14 (E. coli and Bacillus subtilis), pBD9 (Bacillus),
0.161 (Streptomyces), pUC6 (Streptomyces), YIp5 (Saccharomyces),
YCp19 (Saccharomyces) and bovine papilloma virus (mammalian cells).
See, generally, DNA Cloning: Vols. I & II, supra; Sambrook et
al., supra; B. Perbal, supra.
[0126] Insect cell expression systems, such as baculovirus systems,
can also be used and are known to those of skill in the art and
described in, e.g., Summers and Smith, Texas Agricultural
Experiment Station Bulletin No. 1555 (1987). Materials and methods
for baculovirus/insect cell expression systems are commercially
available in kit form from, inter alia, Invitrogen, San Diego
Calif. ("MaxBac" kit).
[0127] Plant expression systems can also be used to produce the
fusion proteins described herein. Generally, such systems use
virus-based vectors to transfect plant cells with heterologous
genes. For a description of such systems see, e.g., Porta et al.,
Mol. Biotech. (1996) 5:209-221; and Hackland et al., Arch. Virol.
(1994) 139:1-22.
[0128] Viral systems, such as a vaccinia based
infection/transfection system, as described in Tomei et al., J.
Virol. (1993) 67:4017-4026 and Selby et al., J. Gen. Virol. (1993)
74:1103-1113, will also find use with the present invention. In
this system, cells are first transfected in vitro with a vaccinia
virus recombinant that encodes the bacteriophage T7 RNA polymerase.
This polymerase displays exquisite specificity in that it only
transcribes templates bearing T7 promoters. Following infection,
cells are transfected with the DNA of interest, driven by a T7
promoter. The polymerase expressed in the cytoplasm from the
vaccinia virus recombinant transcribes the transfected DNA into RNA
that is then translated into protein by the host translational
machinery. The method provides for high level, transient,
cytoplasmic production of large quantities of RNA and its
translation product(s).
[0129] The gene can be placed under the control of a promoter,
ribosome binding site (for bacterial expression) and, optionally,
an operator (collectively referred to herein as "control"
elements), so that the DNA sequence encoding the desired
polypeptide is transcribed into RNA in the host cell transformed by
a vector containing this expression construction. The coding
sequence may or may not contain a signal peptide or leader
sequence. With the present invention, both the naturally occurring
signal peptides and heterologous sequences can be used. Leader
sequences can be removed by the host in post-translational
processing. See, e.g., U.S. Pat. Nos. 4,431,739; 4,425,437;
4,338,397. Such sequences include, but are not limited to, the TPA
leader, as well as the honey bee mellitin signal sequence.
[0130] Other regulatory sequences may also be desirable which allow
for regulation of expression of the protein sequences relative to
the growth of the host cell. Such regulatory sequences are known to
those of skill in the art, and examples include those which cause
the expression of a gene to be turned on or off in response to a
chemical or physical stimulus, including the presence of a
regulatory compound. Other types of regulatory elements may also be
present in the vector, for example, enhancer sequences.
[0131] The control sequences and other regulatory sequences may be
ligated to the coding sequence prior to insertion into a vector.
Alternatively, the coding sequence can be cloned directly into an
expression vector that already contains the control sequences and
an appropriate restriction site.
[0132] In some cases it may be necessary to modify the coding
sequence so that it may be attached to the control sequences with
the appropriate orientation; i.e., to maintain the proper reading
frame. Mutants or analogs may be prepared by the deletion of a
portion of the sequence encoding the protein, by insertion of a
sequence, and/or by substitution of one or more nucleotides within
the sequence. Techniques for modifying nucleotide sequences, such
as site-directed mutagenesis, are well known to those skilled in
the art. See, e.g., Sambrook et al., supra; DNA Cloning, Vols. I
and II, supra; Nucleic Acid Hybridization, supra.
[0133] The expression vector is then used to transform an
appropriate host cell. A number of mammalian cell lines are known
in the art and include immortalized cell lines available from the
American Type Culture Collection (ATCC), such as, but not limited
to, Chinese hamster ovary (CHO) cells, HeLa cells, baby hamster
kidney (BHK) cells, monkey kidney cells (COS), human hepatocellular
carcinoma cells (e.g., Hep G2), Vero293 cells, as well as others.
Similarly, bacterial hosts such as E. coli, Bacillus subtilis, and
Streptococcus spp., will find use with the present expression
constructs. Yeast hosts useful in the present invention include
inter alia, Saccharomyces cerevisiae, Candida albicans, Candida
maltosa, Hansenula polymorpha, Kluyveromyces fragilis,
Kluyveromyces lactis, Pichia guillerimondii, Pichia pastoris,
Schizosaccharomyces pombe and Yarrowia lipolytica. Insect cells for
use with baculovirus expression vectors include, inter alia, Aedes
aegypti, Autographa californica, Bombyx mori, Drosophila
melanogaster, Spodoptera frugiperda, and Trichoplusia ni.
[0134] Depending on the expression system and host selected, the
fusion proteins of the present invention are produced by growing
host cells transformed by an expression vector described above
under conditions whereby the protein of interest is expressed. The
selection of the appropriate growth conditions is within the skill
of the art.
[0135] In one embodiment, the transformed cells secrete the
polypeptide product into the surrounding media. Certain regulatory
sequences can be included in the vector to enhance secretion of the
protein product, for example using a tissue plasminogen activator
(TPA) leader sequence, an interferon (y or a) signal sequence or
other signal peptide sequences from known secretory proteins. The
secreted polypeptide product can then be isolated by various
techniques described herein, for example, using standard
purification techniques such as but not limited to, hydroxyapatite
resins, column chromatography, ion-exchange chromatography,
size-exclusion chromatography, electrophoresis, HPLC,
immunoadsorbent techniques, affinity chromatography,
immunoprecipitation, and the like.
[0136] Alternatively, the transformed cells are disrupted, using
chemical, physical or mechanical means, which lyse the cells yet
keep the recombinant polypeptides substantially intact.
Intracellular proteins can also be obtained by removing components
from the cell wall or membrane, e.g., by the use of detergents or
organic solvents, such that leakage of the polypeptides occurs.
Such methods are known to those of skill in the art and are
described in, e.g., Protein Purification Applications: A Practical
Approach, (Simon Roe, Ed., 2001).
[0137] For example, methods of disrupting cells for use with the
present invention include but are not limited to: sonication or
ultrasonication; agitation; liquid or solid extrusion; heat
treatment; freeze-thaw; desiccation; explosive decompression;
osmotic shock; treatment with lytic enzymes including proteases
such as trypsin, neuraminidase and lysozyme; alkali treatment; and
the use of detergents and solvents such as bile salts, sodium
dodecylsulphate, Triton, NP40 and CHAPS. The particular technique
used to disrupt the cells is largely a matter of choice and will
depend on the cell type in which the polypeptide is expressed,
culture conditions and any pre-treatment used.
[0138] Following disruption of the cells, cellular debris is
removed, generally by centrifugation, and the intracellularly
produced polypeptides are further purified, using standard
purification techniques such as but not limited to, column
chromatography, ion-exchange chromatography, size-exclusion
chromatography, electrophoresis, HPLC, immunoadsorbent techniques,
affinity chromatography, immunoprecipitation, and the like.
[0139] For example, one method for obtaining the intracellular
polypeptides of the present invention involves affinity
purification, such as by immunoaffinity chromatography using
antibodies (e.g., previously generated antibodies), or by lectin
affinity chromatography. Particularly preferred lectin resins are
those that recognize mannose moieties such as but not limited to
resins derived from Galanthus nivalis agglutinin (GNA), Lens
culinaris agglutinin (LCA or lentil lectin), Pisum sativum
agglutinin (PSA or pea lectin), Narcissus pseudonarcissus
agglutinin (NPA) and Allium ursinum agglutinin (AUA). The choice of
a suitable affinity resin is within the skill in the art. After
affinity purification, the polypeptides can be further purified
using conventional techniques well known in the art, such as by any
of the techniques described above.
[0140] C. Nucleic Acids Encoding Degron Fusion Proteins
[0141] Nucleic acids encoding degron fusion proteins can be used,
for example, to control production of a polypeptide of interest in
a cell, tissue, organ, organoid, or subject (e.g., invertebrate or
vertebrate animal) Upon delivery or expression of the fusion
protein in a cell, tissue, organ, organoid, or subject, the degron
is continuously cleaved from the fusion protein in the absence of a
protease inhibitor, thereby preventing the degron from directing
degradation of the polypeptide of interest. In the presence of a
protease inhibitor (e.g., a drug or small molecule), the degron
remains linked to the polypeptide of interest resulting in rapid
degradation of the polypeptide of interest in any fusion proteins
synthesized after the time of addition of the inhibitor. Thus,
production of the polypeptide of interest is readily
controlled.
[0142] The ability of constructs to produce degron fusion proteins
can be empirically determined (e.g., see Example 1 describing
detection of fusion proteins labeled with EGFP or AHA by
fluorescence microscopy or immunoblotting, respectively).
Additionally, production and degradation of the polypeptide of
interest in the presence and absence of protease inhibitors can be
monitored. Because the presence of a protease inhibitor prevents
accumulation of new protein copies without affecting old copies,
the overall levels of a polypeptide of interest after adding the
protease inhibitor depend on its degradation rate. Accordingly, the
half-life of the polypeptide of interest in a cell can be readily
calculated by monitoring its decay. Additionally, the turnover of
the polypeptide of interest can be determined by measuring amounts
of the polypeptide of interest in a transformed cell before and
after contacting the cell with a protease inhibitor and calculating
the turnover of the polypeptide of interest based on the amounts of
the polypeptide of interest in the cell before and after adding the
protease inhibitor. The amount of the polypeptide of interest in
the cell can be measured either continuously or periodically over a
period of time by any suitable method (e.g., immunoblotting or
microscopy).
[0143] Nucleic acids described herein can be inserted into an
expression vector to create an expression cassette capable of
producing the degron fusion proteins in a suitable host cell (e.g.
in a tissue, organ, organoid, or subject). Expression cassettes
typically include control elements operably linked to the coding
sequence, which allow for the expression of the gene in vivo in the
subject species. For example, typical promoters for mammalian cell
expression include the SV40 early promoter, a CMV promoter such as
the CMV immediate early promoter, the mouse mammary tumor virus LTR
promoter, the adenovirus major late promoter (Ad MLP), and the
herpes simplex virus promoter, among others. Other nonviral
promoters, such as a promoter derived from the murine
metallothionein gene, will also find use for mammalian expression.
Typically, transcription termination and polyadenylation sequences
will also be present, located 3' to the translation stop codon.
Preferably, a sequence for optimization of initiation of
translation, located 5' to the coding sequence, is also present.
Examples of transcription terminator/polyadenylation signals
include those derived from SV40, as described in Sambrook et al.,
supra, as well as a bovine growth hormone terminator sequence.
[0144] Enhancer elements may also be used herein to increase
expression levels of mammalian constructs. Examples include the
SV40 early gene enhancer, as described in Dijkema et al., EMPO J.
(1985) 4:761, the enhancer/promoter derived from the long terminal
repeat (LTR) of the Rous Sarcoma Virus, as described in Gorman et
al., Proc. Natl. Acad. Sci. USA (1982b) 79:6777 and elements
derived from human CMV, as described in Boshart et al., Cell (1985)
41:521, such as elements included in the CMV intron A sequence.
[0145] Constructs encoding degron fusion proteins can be
administered to a subject or introduced into cells, tissue, organs,
or organoids using standard gene delivery protocols. Methods for
gene delivery are known in the art. See, e.g., U.S. Pat. Nos.
5,399,346, 5,580,859, 5,589,466. Genes can be delivered either
directly to a subject or, alternatively, delivered ex vivo, to
cells derived from the subject and the cells reimplanted in the
subject.
[0146] A number of viral based systems have been developed for gene
transfer into mammalian cells. These include adenoviruses,
retroviruses (y-retroviruses and lentiviruses), poxviruses,
adeno-associated viruses, baculoviruses, and herpes simplex viruses
(see e.g., Warnock et al. (2011) Methods Mol. Biol. 737:1-25;
Walther et al. (2000) Drugs 60(2):249-271; and Lundstrom (2003)
Trends Biotechnol. 21(3):117-122; herein incorporated by
reference).
[0147] For example, retroviruses provide a convenient platform for
gene delivery systems. Selected sequences can be inserted into a
vector and packaged in retroviral particles using techniques known
in the art. The recombinant virus can then be isolated and
delivered to cells of the subject either in vivo or ex vivo. A
number of retroviral systems have been described (U.S. Pat. No.
5,219,740; Miller and Rosman (1989) BioTechniques 7:980-990;
Miller, A. D. (1990) Human Gene Therapy 1:5-14; Scarpa et al.
(1991) Virology 180:849-852; Burns et al. (1993) Proc. Natl. Acad.
Sci. USA 90:8033-8037; Boris-Lawrie and Temin (1993) Cur. Opin.
Genet. Develop. 3:102-109; and Ferry et al. (2011) Curr Pharm Des.
17(24):2516-2527). Lentiviruses are a class of retroviruses that
are particularly useful for delivering polynucleotides to mammalian
cells because they are able to infect both dividing and nondividing
cells (see e.g., Lois et al (2002) Science 295:868-872; Durand et
al. (2011) Viruses 3(2):132-159; herein incorporated by
reference).
[0148] A number of adenovirus vectors have also been described.
Unlike retroviruses which integrate into the host genome,
adenoviruses persist extrachromosomally thus minimizing the risks
associated with insertional mutagenesis (Haj-Ahmad and Graham, J.
Virol. (1986) 57:267-274; Bett et al., J. Virol. (1993)
67:5911-5921; Mittereder et al., Human Gene Therapy (1994)
5:717-729; Seth et al., J. Virol. (1994) 68:933-940; Barr et al.,
Gene Therapy (1994) 1:51-58; Berkner, K. L. BioTechniques (1988)
6:616-629; and Rich et al., Human Gene Therapy (1993) 4:461-476).
Additionally, various adeno-associated virus (AAV) vector systems
have been developed for gene delivery. AAV vectors can be readily
constructed using techniques well known in the art. See, e.g., U.S.
Pat. Nos. 5,173,414 and 5,139,941; International Publication Nos.
WO 92/01070 (published 23 January 1992) and WO 93/03769 (published
4 Mar.1993); Lebkowski et al., Molec. Cell. Biol. (1988)
8:3988-3996; Vincent et al., Vaccines 90 (1990) (Cold Spring Harbor
Laboratory Press); Carter, B. J. Current Opinion in Biotechnology
(1992) 3:533-539; Muzyczka, N. Current Topics in Microbiol. and
Immunol. (1992) 158:97-129; Kotin, R. M. Human Gene Therapy (1994)
5:793-801; Shelling and Smith, Gene Therapy (1994) 1:165-169; and
Zhou et al., J. Exp. Med. (1994) 179:1867-1875.
[0149] Another vector system useful for delivering the
polynucleotides of the present invention is the enterically
administered recombinant poxvirus vaccines described by Small, Jr.,
P. A., et al. (U.S. Pat. No. 5,676,950, issued Oct. 14, 1997,
herein incorporated by reference).
[0150] Additional viral vectors which will find use for delivering
the nucleic acid molecules encoding the degron fusion proteins
include those derived from the pox family of viruses, including
vaccinia virus and avian poxvirus. By way of example, vaccinia
virus recombinants expressing the fusion proteins can be
constructed as follows. The DNA encoding the particular fusion
protein coding sequence is first inserted into an appropriate
vector so that it is adjacent to a vaccinia promoter and flanking
vaccinia DNA sequences, such as the sequence encoding thymidine
kinase (TK). This vector is then used to transfect cells which are
simultaneously infected with vaccinia. Homologous recombination
serves to insert the vaccinia promoter plus the gene encoding the
coding sequences of interest into the viral genome. The resulting
TK-recombinant can be selected by culturing the cells in the
presence of 5-bromodeoxyuridine and picking viral plaques resistant
thereto.
[0151] Alternatively, avipoxviruses, such as the fowlpox and
canarypox viruses, can also be used to deliver the genes.
Recombinant avipox viruses, expressing immunogens from mammalian
pathogens, are known to confer protective immunity when
administered to non-avian species. The use of an avipox vector is
particularly desirable in human and other mammalian species since
members of the avipox genus can only productively replicate in
susceptible avian species and therefore are not infective in
mammalian cells. Methods for producing recombinant avipoxviruses
are known in the art and employ genetic recombination, as described
above with respect to the production of vaccinia viruses. See,
e.g., WO 91/12882; WO 89/03429; and WO 92/03545.
[0152] Molecular conjugate vectors, such as the adenovirus chimeric
vectors described in Michael et al., J. Biol. Chem. (1993)
268:6866-6869 and Wagner et al., Proc. Natl. Acad. Sci. USA (1992)
89:6099-6103, can also be used for gene delivery.
[0153] Members of the Alphavirus genus, such as, but not limited
to, vectors derived from the Sindbis virus (SIN), Semliki Forest
virus (SFV), and Venezuelan Equine Encephalitis virus (VEE), will
also find use as viral vectors for delivering the polynucleotides
of the present invention. For a description of Sindbis-virus
derived vectors useful for the practice of the instant methods,
see, Dubensky et al. (1996) J. Virol. 70:508-519; and International
Publication Nos. WO 95/07995, WO 96/17072; as well as, Dubensky,
Jr., T. W., et al., U.S. Pat. No. 5,843,723, issued Dec. 1, 1998,
and Dubensky, Jr., T. W., U.S. Pat. No. 5,789,245, issued Aug. 4,
1998, both herein incorporated by reference. Particularly preferred
are chimeric alphavirus vectors comprised of sequences derived from
Sindbis virus and Venezuelan equine encephalitis virus. See, e.g.,
Perri et al. (2003) J. Virol. 77: 10394-10403 and International
Publication Nos. WO 02/099035, WO 02/080982, WO 01/81609, and WO
00/61772; herein incorporated by reference in their entireties.
[0154] A vaccinia based infection/transfection system can be
conveniently used to provide for inducible, transient expression of
the coding sequences of interest (for example, a degron fusion
protein expression cassette) in a host cell. In this system, cells
are first infected in vitro with a vaccinia virus recombinant that
encodes the bacteriophage T7 RNA polymerase. This polymerase
displays exquisite specificity in that it only transcribes
templates bearing T7 promoters. Following infection, cells are
transfected with the polynucleotide of interest, driven by a T7
promoter. The polymerase expressed in the cytoplasm from the
vaccinia virus recombinant transcribes the transfected DNA into RNA
which is then translated into protein by the host translational
machinery. The method provides for high level, transient,
cytoplasmic production of large quantities of RNA and its
translation products. See, e.g., Elroy-Stein and Moss, Proc. Natl.
Acad. Sci. USA (1990) 87:6743-6747; Fuerst et al., Proc. Natl.
Acad. Sci. USA (1986) 83:8122-8126.
[0155] As an alternative approach to infection with vaccinia or
avipox virus recombinants, or to the delivery of genes using other
viral vectors, an amplification system can be used that will lead
to high level expression following introduction into host cells.
Specifically, a T7 RNA polymerase promoter preceding the coding
region for T7 RNA polymerase can be engineered. Translation of RNA
derived from this template will generate T7 RNA polymerase which in
turn will transcribe more template. Concomitantly, there will be a
cDNA whose expression is under the control of the T7 promoter.
Thus, some of the T7 RNA polymerase generated from translation of
the amplification template RNA will lead to transcription of the
desired gene. Because some T7 RNA polymerase is required to
initiate the amplification, T7 RNA polymerase can be introduced
into cells along with the template(s) to prime the transcription
reaction. The polymerase can be introduced as a protein or on a
plasmid encoding the RNA polymerase. For a further discussion of T7
systems and their use for transforming cells, see, e.g.,
International Publication No. WO 94/26911; Studier and Moffatt, J.
Mol. Biol. (1986) 189:113-130; Deng and Wolff, Gene (1994)
143:245-249; Gao et al., Biochem. Biophys. Res. Commun. (1994)
200:1201-1206; Gao and Huang, Nuc. Acids Res. (1993) 21:2867-2872;
Chen et al., Nuc. Acids Res. (1994) 22:2114-2120; and U.S. Pat. No.
5,135,855.
[0156] The synthetic expression cassette of interest can also be
delivered without a viral vector. For example, the synthetic
expression cassette can be packaged as DNA or RNA in liposomes
prior to delivery to the subject or to cells derived therefrom.
Lipid encapsulation is generally accomplished using liposomes which
are able to stably bind or entrap and retain nucleic acid. The
ratio of condensed DNA to lipid preparation can vary but will
generally be around 1:1 (mg DNA:micromoles lipid), or more of
lipid. For a review of the use of liposomes as carriers for
delivery of nucleic acids, see, e.g., Hug and Sleight, Biochim
Biophys. Acta (1991) 1097:1-17; Straubinger et al., in Methods of
Enzymology (1983), Vol. 101, pp. 512-527.
[0157] Liposomal preparations for use in the present invention
include cationic (positively charged), anionic (negatively charged)
and neutral preparations, with cationic liposomes particularly
preferred. Cationic liposomes have been shown to mediate
intracellular delivery of plasmid DNA (Feigner et al., Proc. Natl.
Acad. Sci. USA (1987) 84:7413-7416); mRNA (Malone et al., Proc.
Natl. Acad. Sci. USA (1989) 86:6077-6081); and purified
transcription factors (Debs et al., J. Biol. Chem. (1990)
265:10189-10192), in functional form.
[0158] Cationic liposomes are readily available. For example,
N[2,3-dioleyloxy)propyl]-N,N,N-triethylammonium (DOTMA) liposomes
are available under the trademark Lipofectin, from GIBCO BRL, Grand
Island, N.Y. (See, also, Felgner et al., Proc. Natl. Acad. Sci. USA
(1987) 84:7413-7416). Other commercially available lipids include
(DDAB/DOPE) and DOTAP/DOPE (Boerhinger). Other cationic liposomes
can be prepared from readily available materials using techniques
well known in the art. See, e.g., Szoka et al., Proc. Natl. Acad.
Sci. USA (1978) 75:4194-4198; PCT Publication No. WO 90/11092 for a
description of the synthesis of DOTAP
(1,2-bis(oleoyloxy)-3-(trimethylammonio)propane) liposomes.
[0159] Similarly, anionic and neutral liposomes are readily
available, such as, from Avanti Polar Lipids (Birmingham, Ala.), or
can be easily prepared using readily available materials. Such
materials include phosphatidyl choline, cholesterol, phosphatidyl
ethanolamine, dioleoylphosphatidyl choline (DOPC),
dioleoylphosphatidyl glycerol (DOPG), dioleoylphoshatidyl
ethanolamine (DOPE), among others. These materials can also be
mixed with the DOTMA and DOTAP starting materials in appropriate
ratios. Methods for making liposomes using these materials are well
known in the art.
[0160] The liposomes can comprise multilammelar vesicles (MLVs),
small unilamellar vesicles (SUVs), or large unilamellar vesicles
(LUVs). The various liposome-nucleic acid complexes are prepared
using methods known in the art. See, e.g., Straubinger et al., in
METHODS OF IMMUNOLOGY (1983), Vol. 101, pp. 512-527; Szoka et al.,
Proc. Natl. Acad. Sci. USA (1978) 75:4194-4198; Papahadjopoulos et
al., Biochim Biophys. Acta (1975) 394:483; Wilson et al., Cell
(1979) 17:77); Deamer and Bangham, Biochim Biophys. Acta (1976)
443:629; Ostro et al., Biochem. Biophys. Res. Commun. (1977)
76:836; Fraley et al., Proc. Natl. Acad. Sci. USA (1979) 76:3348);
Enoch and Strittmatter, Proc. Natl. Acad. Sci. USA (1979) 76:145);
Fraley et al., J. Biol. Chem. (1980) 255:10431; Szoka and
Papahadjopoulos, Proc. Natl. Acad. Sci. USA (1978) 75:145; and
Schaefer-Ridder et al., Science (1982) 215:166.
[0161] The DNA and/or peptide(s) can also be delivered in cochleate
lipid compositions similar to those described by Papahadjopoulos et
al., Biochem. Biophys. Acta (1975) 394:483-491. See, also, U.S.
Pat. Nos. 4,663,161 and 4,871,488.
[0162] The expression cassette of interest may also be
encapsulated, adsorbed to, or associated with, particulate
carriers. Examples of particulate carriers include those derived
from polymethyl methacrylate polymers, as well as microparticles
derived from poly(lactides) and poly(lactide-co-glycolides), known
as PLG. See, e.g., Jeffery et al., Pharm. Res. (1993) 10:362-368;
McGee J. P., et al., J Microencapsul. 14(2):197-210, 1997; O'Hagan
D. T., et al., Vaccine 11(2):149-54, 1993.
[0163] Furthermore, other particulate systems and polymers can be
used for the in vivo or ex vivo delivery of the nucleic acid of
interest. For example, polymers such as polylysine, polyarginine,
polyornithine, spermine, spermidine, as well as conjugates of these
molecules, are useful for transferring a nucleic acid of interest.
Similarly, DEAE dextran-mediated transfection, calcium phosphate
precipitation or precipitation using other insoluble inorganic
salts, such as strontium phosphate, aluminum silicates including
bentonite and kaolin, chromic oxide, magnesium silicate, talc, and
the like, will find use with the present methods. See, e.g.,
Feigner, P. L., Advanced Drug Delivery Reviews (1990) 5:163-187,
for a review of delivery systems useful for gene transfer. Peptoids
(Zuckerman, R. N., et al., U.S. Pat. No. 5,831,005, issued Nov. 3,
1998, herein incorporated by reference) may also be used for
delivery of a construct of the present invention.
[0164] Additionally, biolistic delivery systems employing
particulate carriers such as gold and tungsten are especially
useful for delivering synthetic expression cassettes of the present
invention. The particles are coated with the synthetic expression
cassette(s) to be delivered and accelerated to high velocity,
generally under a reduced atmosphere, using a gun powder discharge
from a "gene gun." For a description of such techniques, and
apparatuses useful therefore, see, e.g., U.S. Pat. Nos. 4,945,050;
5,036,006; 5,100,792; 5,179,022; 5,371,015; and 5,478,744. Also,
needle-less injection systems can be used (Davis, H. L., et al,
Vaccine 12:1503-1509, 1994; Bioject, Inc., Portland, Oreg.).
[0165] Recombinant vectors can be formulated into compositions for
delivery to a vertebrate subject. The compositions will generally
include one or more "pharmaceutically acceptable excipients or
vehicles" such as water, saline, glycerol, polyethyleneglycol,
hyaluronic acid, ethanol, etc. Additionally, auxiliary substances,
such as wetting or emulsifying agents, pH buffering substances,
surfactants and the like, may be present in such vehicles. Certain
facilitators of nucleic acid uptake and/or expression can also be
included in the compositions or coadministered.
[0166] Once formulated, the compositions of the invention can be
administered directly to the subject (e.g., as described above) or,
alternatively, delivered ex vivo, to cells derived from the
subject, using methods such as those described above. For example,
methods for the ex vivo delivery and reimplantation of transformed
cells into a subject are known in the art and can include, e.g.,
dextran-mediated transfection, calcium phosphate precipitation,
polybrene mediated transfection, lipofectamine and LT-1 mediated
transfection, protoplast fusion, electroporation, encapsulation of
the polynucleotide(s) in liposomes, and direct microinjection of
the DNA into nuclei.
[0167] Direct delivery of synthetic expression cassette
compositions in vivo will generally be accomplished with or without
viral vectors, as described above, by injection using either a
conventional syringe, needless devices such as Bioject.TM. or a
gene gun, such as the Accell gene delivery system (PowderMed Ltd,
Oxford, England).
[0168] D. Conditionally Replicating Viral Vectors Encoding Degron
Fusion Proteins
[0169] Conditionally replicating viral vectors controllable with
protease inhibitors can be designed by modifying a viral genome to
express a polypeptide required for efficient replication of the
virus as part of a degron fusion protein, as described herein. In
the presence of a protease inhibitor, the degron promotes
degradation of the polypeptide required for efficient replication
of the virus. In the absence of a protease inhibitor, cleavage of
the fusion protein by the protease releases the polypeptide
required for efficient replication of the virus from control of the
degron allowing the virus to replicate. Such conditionally
replicating viral vectors will be useful in any situation where
safety is a concern, for example, when using viruses engineered for
enhanced cytotoxicity or immune evasion or viruses for which no
inhibitors are currently available, and for treating
immunodeficient or immunosuppressed subjects.
[0170] For example, this method can be used to enhance the safety
of RNA virus-based therapies. There are currently no clinically
available inhibitors for most RNA viruses. The options for
controlling RNA viruses are limited because their life cycles
bypass DNA replication and transcription. Viral vectors, engineered
to encode degron fusion proteins, as described herein, can be used
to regulate protein production directly and provide a way to switch
off replication of viruses that would otherwise be difficult to
control.
[0171] In particular, this method can be used to enhance the safety
of oncolytic viruses. RNA viruses, such as measles virus and
vesicular stomatitis virus, which infect and lyse tumor cells, have
found use in cancer therapy. Such oncolytic viruses can be brought
under the control of a protease inhibitor by incorporating a
polypeptide required for efficient replication of the virus into a
degron fusion construct. For example, the viral phosphoprotein in
measles virus is needed for efficient replication. The
phosphoprotein brings the viral large protein, an RNA-dependent RNA
polymerase, to the nucleoprotein-encapsidated viral genome, a
critical step in viral replication. Engineering the measles virus
to express the viral phosphoprotein as a degron fusion protein
allows production of the phosphoprotein, and in turn viral
replication, to be controlled by protease inhibitors.
[0172] In one embodiment, a conditionally replicating measles viral
vector comprises the nucleotide sequence of SEQ ID NO:9, or a
variant thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, wherein
production of the virus can be inhibited with an HCV NS3 protease
inhibitor. An exemplary conditionally replicating measles virus
vector is described in Example 1.
[0173] Packaging of viral vectors into particles can be
accomplished by introducing the viral vector into cells (e.g., RNA
or DNA transfection, or particle infection) and culturing cells
under conditions suitable for production of virions. Conditionally
replicating viral vectors preferably are capable of providing
efficient production of virions in a host cell in the absence of a
protease inhibitor, comparable to the level of virions produced by
the wild-type viral genome. In certain embodiments, the level of
virions produced by a conditionally replicating viral vector in the
absence of a protease inhibitor is at least about 30%, 35%, 40%,
45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, or 100%, or
any amount in between as compared to levels of virions produced by
the wild-type viral genome.
[0174] Additionally, production of virions from a conditionally
replicating viral vector preferably can be nearly completely
suppressed in the presence of a protease inhibitor. For example, a
protease inhibitor may reduce production of virions by at least
80%, 90%, or 100%, or any amount in between as compared to levels
of virions in the absence of the protease inhibitor. In certain
embodiments, production of virions by the conditionally replicating
viral vector in the host cell in the presence of the protease
inhibitor is at least about 90% to 100% suppressed, including any
percent identity within this range, such as 90, 91, 92, 93, 94, 95,
96, 97, 98, or 99%.
[0175] E. Kits
[0176] Degron fusion proteins or nucleic acids encoding them as
well as conditionally replicating viral vectors can be provided in
kits with suitable instructions and other necessary reagents for
preparing or using them, as described above. The kit may contain in
separate containers fusion proteins, and/or recombinant constructs
for producing fusion proteins, and/or conditionally replicating
viral vectors, and/or cells (either already transfected or
separate). Additionally, instructions (e.g., written, tape, VCR,
CD-ROM, DVD, Blu-ray, flash drive, etc.) for using the fusion
proteins or viral vectors may be included in the kit. The kit may
further include a protease inhibitor, such as an HCV NS3 protease
inhibitor, including, for example, simeprevir, danoprevir,
asunaprevir, ciluprevir, boceprevir, sovaprevir, paritaprevir, or
telaprevir. The kit may also contain other packaged reagents and
materials (e.g., transfection reagents, buffers, media, and the
like).
[0177] In certain embodiments, the kit comprises a recombinant
polynucleotide encoding a degron fusion protein described herein.
In one embodiment, the kit comprises a recombinant polynucleotide
encoding a fusion protein comprising a sequence selected from the
group consisting of SEQ ID NO:7 and SEQ ID NO:8, or a variant
thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, wherein
the fusion protein comprises a degron operably linked to a
polypeptide of interest, which is capable of promoting degradation
of the polypeptide of interest, and a protease capable of cleaving
the fusion protein at a cleavage site.
[0178] In other embodiments, the kit comprises a conditionally
replicating viral vector as described herein. In one embodiment,
the kit comprises a conditionally replicating viral vector
comprising the nucleotide sequence of SEQ ID NO:9, or a variant
thereof comprising a sequence having at least about 80-100%
sequence identity thereto, including any percent identity within
this range, such as 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92,
93, 94, 95, 96, 97, 98, or 99% sequence identity thereto, wherein
production of the virus can be inhibited with a protease
inhibitor.
III. Experimental
[0179] Below are examples of specific embodiments for carrying out
the present invention. The examples are offered for illustrative
purposes only, and are not intended to limit the scope of the
present invention in any way. Efforts have been made to ensure
accuracy with respect to numbers used (e.g., amounts, temperatures,
etc.), but some experimental error and deviation should, of course,
be allowed for.
EXAMPLE 1
Small Molecule-Assisted Shutoff: A Widely Applicable Method for
Tunable and Reversible Control of Protein Production
Introduction
[0180] The ability to quickly control the production of specific
proteins would be useful in biomedical research and biotechnology.
An ideal method would feature 1) genetic specification of the
target protein, 2) a single genetic element for simplicity, 3)
minimal modification of the expressed protein, 4) generalizability
to many proteins and cell types, and 5) control by a drug with
proven safety and bioavailability at the required doses in mammals
While methods have been devised with some of these characteristics
(Table 1), none have encompassed all of them.
[0181] We envisaged that a degron that removes itself in a
drug-controllable manner could serve as the basis for a new method
with all the desired features. In particular, we reasoned that if a
site-specific drug-inhibitable protease and a degron were fused to
a protein of interest via an intervening protease site, then by
default the protease and degron would be removed by cis-cleavage
and the protein expressed in a minimally modified form. However, in
the presence of the protease inhibitor, the degron would remain
attached and lead to rapid degradation of the protein (FIG.
1A).
[0182] Here, we show that a system of this design using the
hepatitis C virus (HCV) nonstructural protein 3 (NS3) protease and
elements in the NS4A protein enables clinically tested HCV protease
inhibitors to effectively shut off expression. We termed this
method "small-molecule assisted shutoff", or SMASh. SMASh enabled
drug-induced inhibition of the production of various proteins in
multiple eukaryotic cell types. In contrast to other
single-component methods of post-translational regulation of
protein expression, SMASh functions robustly in yeast as well.
Finally, we used SMASh to confer HCV protease inhibitor sensitivity
onto an RNA virus currently in clinical trials for cancer but for
which no licensed drug inhibitor exists. SMASh thus enables
post-translational regulation of protein production with rapid
onset and minimal protein modification in a broad array of
experimental systems, while requiring only the fusion of a single
genetic element to the coding sequence of a protein of
interest.
[0183] Results
[0184] Development of the SMASh Tag, a Drug-Controllable
Self-Removing Degron
[0185] We had previously utilized HCV NS3 protease to control
protein tagging in a drug-dependent manner (Butko et al. (2012) Nat
Neurosci 15(12):1742-1751; Lin et al. (2008) Proc Natl Acad Sci USA
105:7744-7749) because it is monomeric and highly selective, and
because multiple non-toxic cell-permeable inhibitors are available,
such as simeprevir, danoprevir, asunaprevir, and ciluprevir (Jiang
et al. (2014) J Med Chem 57:1753-1769; Lamarre et al. (2003) Nature
426:186-189; McPhee et al. (2012) Antimicrob Agents Chemother
56(10):5387-5396; Talwani, et al. (2013) Drugs Today (Barc)
49:769-779). We hypothesized that we could use a NS3 protease fused
in cis to remove a degron from a protein of interest shortly after
translation by default, then apply a protease inhibitor to block
degron removal on subsequently synthesized copies. If the degron is
sufficiently strong, then the protease inhibitor would cause new
proteins to be rapidly degraded, in effect shutting off further
protein production. We refer to this strategy as Small
Molecule-Assisted Shutoff, or SMASh (FIG. 1A).
[0186] During the development of a tag for newly synthesized
proteins called TimeSTAMP2 (TS2) that incorporated the NS3 protease
domain (Butko et al. (2012) Nat Neurosci 15(12):1742-1751), we
cloned a sequence encoding the NS3 protease domain (hereafter
referred to as NS3pro) followed by the NS4A protein (FIG. 1B). We
noticed that when we fused the neuronal synaptic protein PSD95 to
NS3pro alone via a linker containing a cognate substrate sequence,
PSD95 was well expressed regardless of whether self-removal of
NS3pro was allowed to occur or was inhibited by asunaprevir (FIG.
1C, lanes 1 and 2). However, when we fused PSD95 via the same
linker to NS3pro followed by NS4A, PSD95 was well expressed when
self-removal of the NS3pro-NS4A cassette was allowed to occur, but
was poorly expressed when self-removal was inhibited by asunaprevir
(FIG. 1C, lanes 3 and 4).
[0187] To explain the above results, we surmised that the
arrangement of NS3pro and NS4A sequences in our construct had
created a functional degron. During normal HCV replication, the
free NS4A N-terminus forms a hydrophobic .alpha.-helix that is
inserted into the endoplasmic reticulum membrane (Brass et al.
(2008) Proc Natl Acad Sci USA 105:14545-14550) (FIG. 8A), while a
.beta.-strand C-terminal to this helix forms a complex with NS3pro,
enhancing its catalytic activity and tethering it to the membrane.
When the native full-length HCV nonstructural polypeptide is
expressed, the NS4A N-terminus is created by cleavage at the NS3/4A
junction (FIG. 8A). Despite NS3/4A not conforming to a consensus
NS3 protease substrate sequence, cleavage is believed to occur due
to its positioning in the NS3 protease active site by the adjacent
NS3 helicase domain (Yao et al. (1999) Structure 7:1353-1363).
However, as our engineered construct lacks the NS3 helicase domain,
NS3/4A cleavage may be disfavored, and the entire NS4A sequence may
remain fused to the NS3 protease without a free N-terminus (FIG.
8B). The hydrophobic sequences of NS4A, unable to insert into the
membrane, might then exhibit degron-like activity.
[0188] We tested the role of these putative destabilizing elements
in suppressing expression of a yellow fluorescent protein (YFP)
fused to the self-removing NS3pro-NS4A cassette. In the absence of
asunaprevir, a 30-kDa YFP fragment was released as expected (FIG.
1D, lane 1). In contrast, with asunaprevir, virtually no
full-length 64-kDa YFP-NS3pro-NS4A fusion was detected (FIG. 1D,
lane 2), similar to the earlier observations with PSD95. Mutation
of a 41-residue stretch comprising putatively unstructured sequence
from NS3 helicase and hydrophobic sequence from NS4A (dotted line
in FIG. 1B) to a glycine-serine linker of the same length rescued
expression of the full-length protein in cells treated with
asunaprevir to levels similar to YFP expressed in the absence of
asunaprevir (FIG. 1D, lanes 3-4), indicating this region is
essential for degron function. These results indicate that an
unstructured, hydrophobic sequence derived from NS3 helicase and
NS4A triggers rapid degradation of fused proteins.
[0189] To determine which cellular proteolytic pathways were
responsible for degrading NS3pro-NS4A fusions, we examined the
effect of inhibiting proteasomes or autophagosomes. We allowed
cells expressing YFP-NS3pro-NS4A to produce uncleaved
YFP-NS3pro-NS4A in asunaprevir while applying inhibitors of
proteasome or autophagosome degradation (FIG. 8C). Proteasome
inhibition (by MG132 or bortezomib) or autophagy inhibition (by
chloroquine or bafilomycin Al) each modestly increased
YFP-NS3pro-NS4A protein levels (FIG. 8C, lanes 2-6). However,
combined inhibition of the proteasome and the autophagosome (by
MG132 and chloroquine) rescued YFP-NS3pro-NS4A expression to the
same level as the mutant in which unstructured and hydrophobic
amino acids were replaced with a glycine-serine linker (FIG. 8C,
lanes 1 and 7). This effect was not restricted to YFP fusions, as a
PSD95-NS3pro-NS4A fusion exhibited the same selective sensitivity
to combined inhibition of the proteasome and autophagosome (FIG.
8D). The finding that only the combined blockade of both the
proteasome and autophagy is able to significantly impede
degradation suggests the strong possibility that the NS3pro-NS4A
cassette harbors a bifunctional degron.
[0190] To summarize our results so far, proteins fused to the NS3
protease-NSA cassette via an intervening NS3 protease substrate
sequence were well expressed in the absence of NS3 protease
inhibitor at the size expected for released protein. By contrast,
in the presence of NS3 inhibitor, steady-state levels of the fusion
protein were drastically reduced, indicating that degradation
occurred quickly enough to prevent the accumulation of newly
synthesized proteins. This implies that fusion of a NS3pro-NS4A
cassette with an intervening protease site would allow NS3 protease
inhibitor application to effectively stop further protein
production, as desired for our SMASh scheme (FIG. 1A). We thus
designated the cassette comprising the NS3 protease domain, the
NS4A protein, and a cis-cleavage site as a "SMASh tag".
[0191] Smash Functions on Either Terminus
[0192] In the above constructs, the NS3 protease-NS4A cassette was
fused at the C-termini of proteins and could remove itself via
cleavage of a protease cleavage sequence from NS4A/4B in the
linker. To create a self-removing degron that could be attached at
either end of a protein of interest, we optimized the ability of a
NS3 protease-NS4A cassette to remove itself from the N-terminus of
the synaptic protein Arc. The incorporation of additional linker
sequences and the use of the NS5A/5B protease cleavage site proved
optimal for self-removal of the tag while preserving drug
responsiveness (FIG. 9A). The final N-terminal SMASh tag (FIG. 2A)
regulated Arc production with similar efficacy to the original
C-terminal SMASh tag (FIG. 9B). To further confirm that the SMASh
tag confers robust control of protein expression by drug when
placed at either the N- or C-terminus of a protein, we coexpressed
SMASh-YFP or YFP-SMASh in HEK293 cells with a red fluorescent
protein (RFP) derived from mNeptune2 (Chu et al. (2014) Nat Methods
11:572-578) as a control. In the absence of NS3 protease inhibitor,
YFP was liberated as a single species of the expected size from
either N-terminal or C-terminal fusions, while both cleaved and
full-length protein were significantly reduced in the presence of
asunaprevir (FIG. 2B). Imaging of YFP fluorescence in living cells
confirmed this effect, as YFP was nearly undetectable in the
presence of asunaprevir (FIG. 2C). There was no difference in RFP
expression, showing the selectivity of asunaprevir for the
SMASh-tagged target protein.
[0193] SMASh Allows Tunable and Reversible Control of Protein
Expression with Rapid Onset
[0194] To determine whether SMASh allows tunable control of protein
levels, we treated cells expressing YFP-SMASh with asunaprevir at
various concentrations from 15 pM to 15 .mu.M. YFP levels were
regulated by asunaprevir in a clear dose-dependent manner (FIG.
3A), with YFP intensity related to the log of drug concentration
(FIG. 3B). The 50% effective concentration (EC.sub.50) of
asunaprevir as measured by YFP suppression was approximately 1 nM,
comparable to the EC.sub.50)in HCV replicon assays (McPhee et al,
supra), demonstrating that the SMASh construct design does not
significantly change asunaprevir binding to NS3 protease. Notably,
YFP was undetectable with asunaprevir at 1.5 .mu.M, a concentration
at which it exhibits no activity against a panel of cellular
proteases and is not cytotoxic (McPhee et al, supra). Asunaprevir
also achieved protein repression to 1.9% of undrugged levels at 150
nM, a concentration that can be maintained in plasma and organs for
hours following oral ingestion of therapeutic non-toxic doses in
humans, dogs, and rodents (McPhee et al, supra; Eley et al. (2013)
Clin Pharmacol Drug Dev 2(4):316-327; Yuan et al. (2013) J
Chromatogr B Analyt Technol Biomed Life Sci 921-922:81-86). Thus
SMASh-mediated repression is tunable across a dynamic range of
greater than 50-fold using drug concentrations that are non-toxic
and achievable in vivo in mammals by oral administration.
[0195] Because HCV protease inhibitor prevents accumulation of new
protein copies without affecting old copies, the overall levels of
a protein of interest following shutoff depend on its degradation
rate. Interestingly, SMASh allows for the easy measurement of
protein half-lives, as the liberated species is no longer produced
after addition of saturating amounts of drug, and its decay can
thus be followed by immunoblotting. We used this method to measure
the half-lives in HEK293 cells of the relatively long-lived and
short-lived proteins PSD95 and CYP21A2, respectively, as 12.4 hours
and 2.2 hours (FIGS. 10A, 11A). This procedure is similar to how
cycloheximide is often used to block all protein synthesis and
allow the measurement of protein half-lives by following their
decay, but in contrast to cycloheximide, SMASh-mediated shutoff is
specific to the tagged protein of interest. Next, we characterized
how quickly proteins with a retained SMASh tag are degraded
compared to their untagged state. Using a simple mathematical model
to relate observed relative abundances of protein species to their
measured synthesis and degradation rates (Methods), we found that
the SMASh tag reduced the half-life of PSD95 from 12.4 hours to 1.1
hours (FIG. 10B) and of CYP21A2 from 130 minutes to 15 minutes
(FIG. 11B).
[0196] As mRNA transcripts encoding SMASh-regulated proteins are
not expected to be affected by protease inhibitor treatment,
protein shutoff by SMASh should be readily reversible upon drug
removal. To test this, we incubated HeLa cells expressing YFP-SMASh
for 12 hours post-transfection in the presence of asunaprevir to
ensure total initial shutoff. Then, after drug washout, we followed
the appearance of YFP signal over time. By immunoblotting, YFP
signal appeared 1 hour after washout (FIG. 3C). By live-cell
fluorescence microscopy, YFP signal was visible at 2 hours after
washout, and by 6 hours fluorescence intensity approximated that of
cells cultured in parallel for 12 hours without asunaprevir (FIG.
3D). The delay in appearance of YFP signal in microscopy relative
to immunoblotting is attributable to the time course of maturation
of the YFP chromophore, whose time constant of maturation has been
measured to be 40 minutes (Iizuka et al. (2011) Anal Biochem
414:173-178).
[0197] Taken together, our results demonstrate that the SMASh
system can control protein expression in a dose-dependent and
reversible manner by causing rapid degradation of tagged proteins
synthesized in the presence of drug. Recovery of protein expression
after drug removal is rapid as mRNA pools are not depleted, which
can be beneficial when fast onset of protein production is
required.
[0198] Smash Functions on Multiple Protein Types and in Neurons
[0199] We next determined if SMASh can control production of a
variety of protein types. SMASh was able to control the production
of a multimeric enzyme, calcium/calmodulin activated protein kinase
II a (FIG. 4A), and of a multi-pass transmembrane protein, the
Drosophila GluRIIA glutamate receptor (FIG. 4B). Additionally,
SMASh is also capable of suppressing the expression of a
short-lived protein, CYP21A2 (half-life .about.2 hours, FIG. 4C).
Thus, for the six proteins of various sizes and structures which we
tested--PSD95, YFP, Arc, CaMKII.alpha., GluRIIA and CYP21A2--the
SMASh tag was able to confer robust drug inhibition of protein
production in all cases.
[0200] Synthesis of specific proteins is tightly regulated by
growth factors and synaptic activity in neurons, where it is
required for long-lasting cellular changes that support memory
formation. As our previous experiments using SMASh were only
performed in proliferating cell types, we therefore investigated
whether SMASh could function in post-mitotic neurons as well. We
indeed observed that SMASh conferred drug control over the
production of YFP in primary cultures of rat and mouse
cortical/hippocampal neurons (FIGS. 12A and 12B).
[0201] SMASh Functions in Yeast
[0202] We next investigated whether the SMASh tag could enable
pharmacological control of protein production in the budding yeast
S. cerevisiae. Yeast genes can be transcriptionally regulated by
substituting drug-responsive promoters for endogenous promoters,
but this requires expression of an exogenous transcription factor
from another gene and does not preserve endogenous patterns of
transcriptional regulation (Mnaimneh et al. (2004) Cell
118(1):31-44). Yeast protein stability can be regulated by a
temperature-sensitive degron, but this induces a heat shock
response and requires switching growth media (Morawska et al.
(2013) Yeast 30:341-351). Researchers have therefore also attempted
to regulate protein expression in yeast by controlling protein
stability with drugs. The only chemical assisted method that has
been successfully adapted to yeast is the auxin-induced degradation
(AID) method, which involves attaching proteins of interest to a
domain that recruits an ubiquitin ligase in an auxin-dependent
manner (Morawska et al., supra; Nishimura et al. (2009) Nat Methods
6:917-922). However, AID requires both permanent tagging of the
protein of interest and expression of a second transgene, and can
exhibit premature auxin-independent degradation or incomplete
auxin-dependent degradation (Morawska et al., supra). Thus, a
method for drug regulation of protein production that is both
simple and robust is still lacking in yeast.
[0203] When expressed in yeast from an episomal gene, we found the
C-terminal SMASh tag with a protease cleavage site of sequence
DEMEEC/S was able to confer drug repression on YFP expression,
similarly to its performance in mammalian cells (FIG. 5A, lane
4-6). However, the N-terminal SMASh tag and fast-cleaving site
(EDVVPC/S) used in mammalian cells allowed leaky expression of YFP
in yeast in the presence of drug (data not shown). Changing the
fast protease cleavage site to a slower-cleaving site, DEMEEC/S,
fixed this problem (FIG. 5A, lane 1-3), consistent with HCV
protease being more active at the lower temperatures of yeast
compared to mammalian cells. SMASh was able to repress YFP
expression to undetectable levels at 3 .mu.M asunaprevir (FIGS.
5A-5C). We also tested a strain lacking the Pdr1 and Pdr3
transcriptional activators of drug efflux pumps (Su et al. (2010)
Dis Model Mech 3:194-208) to see if drug doses can be further
lowered, but found no effect (FIG. 5A, lane 7-9). These results
demonstrate that SMASh confers drug-mediated control of protein
expression in yeast using micromolar concentrations of drug. To the
best of our knowledge, SMASh is the first method that uses a single
genetic element to impose drug control over the expression of
specific proteins in yeast.
[0204] We next determined whether SMASh can regulate the production
of proteins encoded by single-copy chromosomal genes in yeast.
First, we expressed YFP-SMASh from an integrated chromosomal
location and again observed robust suppression of protein levels by
a drug (FIGS. 6A and 6B). Next, we integrated the SMASh tag at the
ends of endogenous genes encoding essential proteins, such as SEC14
(a phosphatidylinositol/phosphatidylcholine transfer protein) and
YSH1 (an endoribonuclease). In the absence of asunaprevir,
SEC14-SMASh yeast grew similarly to wild-type yeast, whereas in the
presence of asunaprevir, SEC14-SMASh yeast showed complete growth
inhibition (FIG. 6C). YSH1-SMASh yeast strain growth was normal in
the absence of drug and suppressed in the presence of drug (FIG.
6D). As was the case with mammalian CYP21A2, the ability of SMASh
to control the expression in yeast of YSH1, a short-lived protein
with a half-life of 34-45 minutes (Belle et al. (2006) Proc Natl
Acad Sci USA 103:13004-13009), implies that degradation of
SMASh-fused proteins can be very fast.
[0205] SMASh Enables Pharmacological Control Over an RNA Virus
[0206] Many RNA viruses propagate and induce cell death more
efficiently in tumors than in normal cells (Miest et al. (2014) Nat
Rev Microbiol 12:23-34; Russell et al. (2012) Nat Biotechnol
30:658-670). These viruses, which include measles virus (MeV),
Newcastle disease virus, and stomatitis vesicular virus, are under
active clinical investigation as oncolytic agents (Miest et al.,
supra; Russell et al., supra). While currently tested agents cause
either no disease or mild self-limited disease, safety
considerations will become a concern if they are engineered for
enhanced cytotoxicity or immune evasion, as has been proposed
(Miest et al., supra; Russell et al., supra; Msaouel et al. (2013)
Expert Opin Biol Ther 13:483-502), or if they are used in
immunocompromised patients. It is thus important for the future
development of oncolytic RNA viruses to develop drug-responsive
off-switches for safety. However, there are no clinically available
inhibitors of these viruses to utilize in case of undesirable
toxicities. Furthermore, regulation through drug-dependent
transcription, a strategy used for DNA viruses such as adenovirus
or herpesvirus, is not possible with pure RNA viruses, as their
life cycles bypass host-mediated DNA replication and transcription.
As SMASh regulates protein production without involving DNA or RNA
modulation, we explored the possibility that it could be used as an
off-switch to enhance the safety of RNA virus-based therapies.
[0207] Among oncolytic RNA viruses, measles virus vaccine strain
(MeV) is one of the most advanced in clinical testing (Msaouel et
al., supra), so we chose to create a SMASh-controlled MeV as a
model for engineering drug control into viral therapies. MeV
phosphoprotein (P) functions to bring the viral large (L) protein,
a RNA-dependent RNA polymerase, to the nucleoprotein
(N)-encapsidated viral genome (FIG. 7A, top). We therefore
hypothesized that replacing the P gene in the MeV genome with
P-SMASh would enable inhibition of MeV replication by HCV NS3
protease inhibitor (FIG. 7A, bottom). To be a suitable off-switch
for an RNA virus, drug control of P expression should ideally be
rapid. To investigate the dynamics of P protein shutoff with SMASh,
we attached the SMASh tag to the C-terminus of P. The infectivity
factor C protein is translated from an overlapping open reading
frame beginning 19 nucleotides downstream from the P start codon
(Rima et al. (2009) Curr Top Microbiol Immunol 329:77-102), and
this seemed less likely to be affected by a C-terminal fusion. We
then assessed the effect of HCV protease inhibitor on P protein
production in cells transiently transfected with a plasmid encoding
P-SMASh. After allowing P-SMASh expression for 20 hours,
application of asunaprevir for 3 hours (FIG. 13A) caused a
noticeable drop in accumulated P protein levels relative to
control, indicating that P protein itself is relatively short-lived
(FIG. 13B, lanes 3-4). We also measured the tightness of shutoff by
specifically labeling protein synthesized after inhibitor addition
with the methionine analog azidohomoalanine (AHA), followed by
reaction with a biotin-conjugated alkyne and purification on
streptavidin-conjugated beads Immunoblotting revealed no
AHA-labeled P or P-SMASh from cells incubated with AHA and
asunaprevir simultaneously (FIG. 13B, lane 7), indicating that
inhibitor induced the rapid degradation of newly synthesized copies
of P to undetectable levels. AHA labeling and purification did
detect P in the absence of protease inhibitor (FIG. 13B, lane 6),
confirming the efficacy of the labeling and purification steps.
These data demonstrate that further production of SMASh-tagged P
protein can be robustly shut off by protease inhibitor.
[0208] Finally, to make MeV drug-controllable, we replaced the P
coding region with P-SMASh in MeV-EGFP, which contains an
additional transcriptional unit expressing enhanced green
fluorescent protein (EGFP) (Zuniga et al. (2007) Vaccine
25:2974-2983), creating MeV-EGFP-P-SMASh (FIG. 7B, FIG. 13A). In
the absence of asunaprevir, MeV-EGFP-P-SMASh replicated to a
similar titer as parental MeV-EGFP in the standard Vero host cell
line (MeV-EGFP-P-SMASh 1.5.times.10.sup.7 TCID50/ml vs. MeV-EGFP
3.8.times.10.sup.7 TCID50/ml, measured by end-point dilution),
indicating functionality of liberated P in viral replication.
MeV-EGFP-P-SMASh also expressed EGFP and induced formation of
syncytia in Vero cells as efficiently as parental MeV-EGFP in the
absence of drug (FIG. 7C). In contrast, in the presence of
asunaprevir, EGFP expression and formation of syncytia by
MeV-EGFP-P-SMASh was completely abolished, while parental MeV-EGFP
virus was unaffected by drug (FIG. 7C). Suppression was remarkably
tight, with drug suppressing 97.3% of EGFP fluorescence compared to
the untreated case 3 days post-transfection (FIG. 7D, FIG. 13B)
Immunoblotting confirmed that asunaprevir efficiently inhibited P
production in virus-infected cells (FIG. 7E). Thus, in summary,
SMASh allowed us to render MeV exquisitely sensitive to inhibition
by HCV NS3 protease inhibitors. Through the simple insertion of a
SMASh tag in one viral gene, we were able to create a
drug-regulatable version of this RNA virus for which no specific
clinically approved inhibitors previously existed.
[0209] Discussion
[0210] The ability to reversibly regulate protein production using
small molecules would be a valuable tool for biologists. Here we
present a new concept, SMASh, for regulating protein production
using a cell-permeable drug with rapid onset. Our system is based
on genetic fusion of a protein of interest to a degron that is
capable of self-removal via cis-cleavage by an internal HCV NS3
protease, so that the protein of interest is expressed by default
in a minimally modified state. After addition of one of several
clinically available small-molecule NS3 protease inhibitors, the
degron is retained on subsequently synthesized proteins, leading to
their rapid degradation and effectively shutting off further
protein production. We have shown that the SMASh tag functions on
either terminus of a protein and generalizes to various proteins
and multiple cell types. Moreover, our data raise the interesting
possibility that the SMASh degron is capable of eliciting
degradation through both major proteolysis pathways of the cell
(proteasome and autophagy), which could help to avert saturation of
either pathway, contributing to its generalizability for various
cell types and contexts. SMASh is unique in combining multiple
desirable features, including rapid onset, reversible and robust
drug regulation of protein expression, a requirement for only a
single genetic element, minimal modification to proteins of
interest, and the use of a non-toxic drug that is clinically
approved for use in humans.
[0211] Several approaches previously existed to control specific
protein levels via drug-dependent degradation or stabilization, but
these either require multiple components or substantially change
the structure of the target protein (Table 1). For example,
drug-induced ubiquitin fragment complementation can be used to
remove degradation signals (degrons) on proteins of interest (Pratt
et al. (2007) Proc Natl Acad Sci USA 104:11209-11214), but this
method requires the expression of multiple transgenes and shows
poor dynamic range, requiring an additional level of
transcriptional repression for tight shutoff (Lin et al. (2014)
Chembiochem 15:805-809). The AID system allows drug-induced
destabilization of a protein of interest, but requires addition of
a large tag to the protein of interest and expression of a second
protein (Morawska et al., supra). Single domains that are unstable
in the absence or presence of a drug can be attached to proteins of
interest to allow chemical control of protein stability, and this
approach is similar to SMASh in requiring only a single genetic tag
(Banaszynski et al. (2006) Cell 126:995-1004; Cho et al. (2013)
PLoS One 8:e72393; Iwamoto et al. (2010) Chem Biol 17:981-988;
Rakhit et al. (2011) Bioorg Med Chem Lett 21:4965-4968; Stankunas
et al. (2003) Mol Cell 12:1615-1624; Bonger et al. (2011) Nat Chem
Biol 7:531-537; Tae et al. (2012) Chembiochem 13:538-541). However,
the AID system and these latter methods all require the permanent
fusion of a lengthy polypeptide to the protein of interest, and the
possibility of a large attachment interfering with protein function
is always a concern. Therefore, a simple method for reversible drug
control of protein production with rapid onset that allows proteins
to be expressed with minimal perturbation has long been desired
(Lampson et al. (2006) Cell 126:827-829).
[0212] SMASh provides robust drug control of protein expression
with only minimal modification to the protein of interest,
appending only six amino acids of a protease recognition site when
the SMASh tag is fused at the C-terminus, or three amino acids when
fused at the N-terminus. Just as fusion to small peptides preserves
function in some cases where GFP does not (Andresen et al. (2004)
Mol Biol Cell 15:5616-5622), SMASh should be less likely to perturb
the function of proteins than methods requiring permanent
attachment of structured protein domains. The MeV P protein serves
as an example of the minimally disruptive nature of the SMASh tag.
Consistent with both termini of P protein being required for
interaction with N protein (Chen, et al. (2003) Virus Res
98:123-129; Harty et al. (1995) J Gen Virol 76:2863-2867; Shu et
al. (2012) J Biol Chem 287:11951-11967), the P-GFP fusion is
completely nonfunctional, and the GFP-P fusion severely hinders MeV
replication (Devaux et al. (2004) J Virol 78:11632-11640). Hence,
one would not expect a constitutively attached drug-controllable
degron system to be compatible with P function. By contrast, MeV
expressing P-SMASh replicated similarly to parental virus,
indicating the liberated P protein is functional. Minimal protein
modification may also be useful in yeast, as attachment of long
protein sequences may adversely affect a large percent of yeast
proteins. For instance, among 2086 yeast proteins whose
localization was studied by fusion to a 237-residue green
fluorescent protein (GFP) tag or a 93-residue tag containing
multiple hemagglutinin (HA) tags, a large proportion of proteins,
32%, showed different localizations with the two tags, suggesting
that at least one of the tags caused protein mislocalization (Huh
et al. (2003) Nature 425:686-691).
[0213] SMASh could also be useful where rapid increases in protein
levels are desired. Using SMASh, the experimenter can repress
expression of a protein of interest by treatment with drug, then
when protein expression is desired, the drug can be washed out.
Protein will then immediately accumulate from ongoing translation
of existing mRNAs. Upregulating proteins by reversal of SMASh
shutoff is expected to be faster than by induction of gene
transcription. The time course of protein accumulation following
pharmacological regulation of gene transcription is many hours in
mammalian systems even in systems optimized for speed (Shoulders et
al. (2013) J Am Chem Soc 135:8129-8132).
[0214] A notable feature of SMASh is that it allows regulation of
protein production by HCV protease inhibitors, a class of drugs
with high bioavailability and safety which have been approved for
long-term use in humans. SMASh-tagged proteins are regulated by
these drugs at the same low concentrations used for inhibiting HCV
replication (e.g. 1 nM for asunaprevir). SMASh would thus be
expected to be especially advantageous for in vivo use in mammals,
where most other methods of drug-regulated protein expression use
experimental chemical compounds that can be limited by poor
bioavailability, toxicity, or expense (Tae et al. (2012)
Chembiochem 13:538-541; Limenitakis et al. (2011) FEBS Lett
585:1579-1588). Our experiments also indicate that the HCV protease
inhibitor asunaprevir is able to cross the yeast cell wall. Even
when overexpressed from episomes using the strong GPD promoter,
expression of SMASh-tagged YFP was completely suppressed in 3 .mu.M
asunaprevir. In contrast, 1000 .mu.M auxin was required for AID to
degrade a target protein expressed from the approximately tenfold
weaker ADH promoter (Morawska et al., supra; Mumberg et al. (1995)
Gene 156:119-122).
[0215] Finally, SMASh differs from most other strategies for
regulating protein stability in that it selectively controls the
degradation of new copies of a protein of interest, and not
pre-existing copies. Cells respond rapidly to environmental stimuli
such as growth signals (Shimobayashi et al. (2014) Nat Rev Mol Cell
Biol 15:155-162) or, in the nervous system, synaptic activity
(Butko et al., supra), by synthesizing new proteins. SMASh can be
used to query the role of specific new protein species in such
biological responses, similarly to how cycloheximide or anisomycin
is used to suggest a role for synthesis of new proteins in general,
but without the toxicity of these broadly acting protein synthesis
inhibitors. SMASh can also be used to estimate half-lives of
proteins of interest, as the persistence of untagged protein copies
previously produced in the absence of drug can be measured over
time while further production is inhibited in the presence of drug.
Here, SMASh can again be used similarly to cycloheximide or
anisomycin in estimating protein half-lives (Zhou et al. (2004)
Methods Mol Biol 284:67-77), but with much less toxicity.
Cycloheximide and anisomycin, by inhibiting all protein synthesis
in the cell, can be expected to impair cell health after several
hours of treatment, and to generate erroneous half-life
calculations if levels of other proteins regulating the stability
of the protein of interest also drop. The SMASh system may thus be
especially advantageous for measuring half-lives of long-lived
proteins such as PSD95 (FIG. 10A).
[0216] RNA viruses that replicate more efficiently in certain
neoplastic cell types have long been considered as targeted cancer
treatments. However, only viruses that cause non-pathogenic or mild
disease, such as vaccine-strain MeV, are currently being tested in
clinical trials. As the self-limiting nature of these weak viruses
is likely to limit their oncolytic efficacy as well, researchers
have proposed arming viruses for enhanced cytotoxicity or modifying
them for improved immune evasion (Cattaneo et al. (2008) Nat Rev
Microbiol 6:529-540; Meng et al. (2010) Mol Ther 18:544-551). But
because such steps could lead to unexpected side effects (Chen et
al. (2011) Virology 409:328-337), it would be desirable to have
pharmacological methods for terminating replication of engineered
viruses (Russell et al. (2012) Nat Biotechnol 30:658-670). We found
that SMASh enabled robust control by HCV NS3 protease inhibitors
over MeV, a RNA virus in clinical trials as a replication-competent
oncolytic agent but for which no clinically available specific
inhibitors exist. Our results suggest the feasibility of
controlling related oncolytic single-strand enveloped RNA viruses
by tagging P protein orthologs (Fuentes et al. (2010) Future
Microbiol 5:9-13), and open up the possibility of controlling other
classes of viruses by tagging other viral proteins.
[0217] In summary, SMASh has advantages over other methods for
controlling levels of proteins of interest in minimizing
modification to the protein, in requiring only one genetically
encoded element, and in using a clinically available class of drugs
that are nontoxic and cell permeable. The combination of these
advantages has not been achieved by other post-translational
protein control methods so far. Furthermore, SMASh functions
robustly in mitotic and non-mitotic mammalian cells, and also in
yeast. Using SMASh, we have also engineered, for the first time, an
RNA virus that can be tightly regulated by a drug without the need
to develop new, virus-specific small molecule inhibitors. Thus,
with its ease of implementation and generalizability, the SMASh
technique can be applied to a variety of problems in biomedicine
and biotechnology, ranging from the study of gene function to the
engineering of drug-dependent features in cellular and viral
therapies.
[0218] Methods
[0219] DNA constructs. Plasmids encoding PSD95 or Arc fused to
TimeSTAMP cassettes (Yuan et al., supra; Iizuka et al., supra) were
modified by standard molecular biology techniques including PCR,
restriction enzyme digestion and ligation or In-Fusion enzyme
(Clontech) to create new TimeSTAMP variants or SMASh variants. All
subcloned fragments were sequenced in their entirety to confirm
successful construction. Full sequences of all plasmids used in
this study are available upon request.
[0220] Cell culture and transfection. HEK293, Vero, and HeLa cell
lines were cultured at 37.degree. C. in 5% CO.sub.2 in Dulbecco's
Modified Eagle's Medium (DMEM, HyClone) supplemented with 10% fetal
bovine serum (Gibco), 2 mM glutamine (Life Technologies) and 100
U/mL penicillin and 100 .mu.g/mL streptomycin (Life Technologies).
Cells were transfected using Lipofectamine 2000 (Life Technologies)
in Opti-MEM (Life Technologies) according to the manufacturer's
recommended protocol.
[0221] Chemical reagents. HCV NS3 inhibitors ciluprevir (CLV) and
asunaprevir (ASV) were obtained by custom synthesis (Acme
Bioscience) and dissolved in DMSO (Thermo) at 3 mM for medium-term
storage at -20.degree. C. These were then diluted into media to
achieve the desired final concentration (1-3 .mu.M) for treatment
of cells. Further serial dilutions were performed for the
dose-dependency experiment. For long-term CLV and ASV incubations,
drug was applied simultaneously with transfection media or 1-2
hours after transfection. MG132 (Sigma) was dissolved in DMSO for a
1000.times. working stock of 10 mM. Bortezomib (Adooq Biosci.) was
dissolved in DMSO for a 500.times. working stock of 33 .mu.M.
Chloroquine diphosphate salt (Sigma) was dissolved in H.sub.2O for
a 1000.times. (100 mM) working stock. Bafilomycin A1 (Santa Cruz)
was dissolved in DMSO for a 500.times. (100 .mu.M) working stock.
Azidohomoalanine (AHA) (Click-IT, Invitrogen) was dissolved in DMSO
for a 500X working stock of 25 mM. Alkyne-PEG4-biotin (Invitrogen)
was dissolved in DMSO for a 100.times. working stock of 4 mM.
L-cystine dihydrochloride (Sigma) was dissolved in H.sub.2O pH 2.0
for a working stock of 0.1 M.
[0222] Yeast strains and cell growth. All experiments were carried
out in the w303-1A ADE2+ strain background (Thomas et al. (1989)
Cell 56:619-630) and a pump-deficient w303-1A strain (MATa
cant-100, his3-11,15, leu2-3,112, trp1-1, ura3-1, ade2-1,
pdr1::kanMX, pdr3::kanMX) (Su et al. (2010) Dis Model Mech
3:194-208). SMASh strains were made by transformation of yeast
episomal plasmid (pAG426) and yeast integrating plasmid (pRS405),
expressing SMASh fused YFP under GPD promoter Yeastmaker DNA kit
(Clontech) was used for yeast Li-Acetate transformations. Cells
were grown at 30.degree. C. in SD media or YDP media. To generate
SMASh knock-in yeast, PCR fragments containing SMASh tag followed
by yeast ADH1 terminator and NatMX (clonNAT resistance gene) are
inserted before the termination codon of the protein of interest by
homologous recombination. To perform yeast spotting assay, YDP
plates were prepared with ASV or the same concentration of DMSO (1%
v/v).
[0223] Primary neuronal culture. All animal procedures were
approved by the Stanford University Administrative Panel on
Laboratory Animal Care, and were performed in accordance with the
applicable regulatory standards. Sprague-Dawley rat E15
cortico-hippocampal tissue and FVB mouse E18 cortical tissue were
dissected, incubated in RPMI (Life Technologies) with papain
(Worthington) and DNase I (Roche) for dissociation, triturated, and
electroporated using the Amaxa Rat or Mouse Neuron Nucleofector kit
(Lonza), before being plated on poly-L-lysine-coated 4-chamber 35
mm glass bottom dishes (In Vitro Scientific), in the presence of
5-10% FBS (Gibco), at a density of .about.150K neurons per
quadrant. Neurons were cultured in NeuroBasal media (Life
Technologies) supplemented with GlutaMAX, B-27, and Pen-strep (Life
Technologies) at 37.degree. C. with 5% CO.sub.2. Every 3 days, 50%
of media was refreshed.
[0224] Virus cloning, packaging and infection. To construct
p(+)-MeV-EGFP-PSMASh, DNA encoding the SMASh tag was added in frame
to the P open reading frame in p(+)-MeV-EGFP, the resulting
full-length clone corrected for the paramyxovirus rule-of-six, and
verified through sequencing. Recombinant MeV were recovered using a
modified rescue system (Brindley et al. (2013) J Virol
87:11693-11703). BSR-T7/5 cells (Buchholz et al. (1999) J Virol
73:251-259) were transfected with p(+)-MeV-EGFP or
p(+)-MeV-EGFP-PSMASh (SEQ ID NO:9), respectively, and plasmids
encoding the L, N, or P proteins derived from the MeV IC-B strain
(Krumm et al. (2013) J Biol Chem 288:29943-29953). All constructs
were under the control of the T7 promoter. 48 hours
post-transfection, BSR-T7/5 helper cells were overlaid on Vero
cells stably expressing human CD150 and SLAM (Ono et al. (2001) J
Virol 75:4399-4401), and overlay plates incubated at 32.degree. C.
until infectious centers became detectable. Virions from individual
centers were transferred to fresh Vero-SLAM cells for generation of
passage two virus stocks. To confirm integrity of recombinant
viruses, RNA was extracted from infected cells using the RNeasy
mini kit (Qiagen) and cDNAs created using random hexamer primers
and Superscript III reverse transcriptase (Life Technologies). PCR
was performed with primers 28-F: TAATCTCCAAGCTAGAATC (SEQ ID NO:10)
and 35-R: AGCCTGCCATCACTGTA (SEQ ID NO:11) and sequenced (FIG. 9A).
To prepare virus stocks, Vero cells were infected at an MOI of 0.01
TCID50/cell with the relevant virus and incubated at 32.degree. C.
until cytopathic effect (CPE) become detectable. Plates were then
moved to 37.degree. C. and incubated until 100% CPE. Cells were
scraped in OptiMEM (Life Technologies), and particles released by
two freeze-thaw cycles. Titers were determined by TCID50 titration
on Vero cells according to the Spearman-Karber method as
described.sup.61. Virus infection for drug controllability tests
was initiated through inoculation of Vero cells at an MOI of 0.1
and 1 TCID50/cell at 32.degree. C.
[0225] Microscopy. For imaging of MeV-infected cells, brightfield
and fluorescence microscopy was performed on a Nikon TE300 with a
10.times./0.25-numerical aperture (NA) objective. HEK293A cells
were imaged with a 20.times./0.15 NA objective on the same
microscope. The cells were cultured in 12-well plates (Greiner),
MeV-infected cells were imaged in culture media (10% FBS
supplemented phenol red free DMEM) and HEK293 were imaged in HBSS.
Brightfield and fluorescence microscopy of yeast was done with an
Olympus 100.times./1.4-NA oil immersion objective on Olympus IX80.
Yeast cells were imaged in SD media in a ConA (Sigma) coated TC
CU109 chamber (Chamlide). For HeLa and neurons, microscopy was
performed on a Zeiss Axiovert 200M with a 40.times./1.2-NA water
immersion objective. These cells were cultured in 4-chamber 35 mm
glass bottom dishes (In Vitro Scientific) and culture media were
replaced with HBSS during live imaging sessions. All microscopes
were connected to Hamamatsu ORCA-ER cameras and controlled by
Micro-Manager software Image processing was performed in
ImageJ.
[0226] Immunoblotting. After washing twice with PBS, cells were
lysed with 50-100 .mu.l of hot SDS lysis buffer (100 mM Tris HCl pH
8.0, 4% SDS, 20% glycerol, 0.2% bromo-phenol blue, 10%
2-mercaptoethanol) and DNA was sheared by sonication. After heating
to 80-90.degree. C. for several minutes, cell lysates were loaded
onto 4%-12% Bis-Tris gels (NuPAGE, Life Technologies) along with
Novex Sharp pre-stained protein standard (Life Technologies) or
Precision Plus Protein Dual Color Standards (Bio-Rad),
dry-transferred to nitrocellulose or PVDF membranes (iBlot system,
Life Technologies), probed with primary and secondary antibodies,
and imaged using LI-COR Odyssey imaging system. Quantification of
immunoblots was performed in ImageJ.
[0227] Antibodies. The following primary antibodies were used for
immunoblotting at the indicated dilutions: mouse monoclonal
anti-PSD95 (NeuroMab, clone K28/43), 1:2000; mouse monoclonal
anti-Arc (Santa Cruz, clone C7, sc-17839), 1:200; mouse monoclonal
anti-GFP (Pierce, clone GF28R, MA5-15256), 1:1000; rabbit
monoclonal anti-GFP (Abcam, clone E385, ab32146), 1:1000; rabbit
polyclonal anti-.beta.-actin (GeneTex, GTX124214) 1:10,000; mouse
monoclonal anti-GAPDH (Santa Cruz, clone G-9, sc-365062), 1:4000;
rabbit polyclonal anti-GAPDH (Santa Cruz, sc-25778), 1:4000; mouse
monoclonal anti-GAPDH (Pierce, clone GA1R, MA5-15738), 1:1000;
mouse monoclonal anti-measles phosphoprotein (P) (Novus, clone 9H4,
NB110-37247 or Abcam, clone 9H4, ab43820), 1:200; rabbit polyclonal
anti-CamKII.alpha. (Santa Cruz, sc-13082), 1:200; mouse monoclonal
anti-GluRIIA (DSHB, 8B4D2), 1:1000; antiCYP21A2 (Santa Cruz, clone
C-17, sc-48466), 1:200; and rabbit monoclonal anti-HA (Cell
Signaling, C29F4), 1:1000. Secondary antibodies were LI-COR 680RD
goat-anti-mouse, 680RD goat-anti-rabbit, 680RD donkey-anti-rabbit,
800CW donkey-anti-goat, 800CW goat-anti-mouse, and 800CW
goat-anti-rabbit, used at 1:5000.
[0228] Metabolic labeling, Click chemistry, and pulldown. HeLa
cells were cultured in 12-well plates (Greiner) in standard DMEM
supplemented with glutamine, pen-strep, and 10% FBS. 20 hours after
transfection, wells were washed 3.times. with HBSS, and cells were
methionine-depleted via 30 minutes incubation in metabolic label
DMEM [methionine/cystine-free DMEM (Corning Cellgro) supplemented
with glutamine, pen-strep, 0.2 mM L-cystine (Sigma), and 10%
dialyzed FBS (Thermo)]. Following depletion step, media were
replaced with either standard DMEM, metabolic label DMEM with 50
.mu.M AHA, or metabolic label DMEM with 50 .mu.M AHA and 2 .mu.M
ASV. Equivalent volumes of DMSO were used as vehicle controls in
negative wells. Labeling incubation lasted 3 hours, after which
each well was washed and lysed with 50 .mu.L gentle lysis buffer
[1% SDS, 50 mM Tris HCl pH 8.0, EDTA-free protease inhibitor
cocktail (Complete Mini, Roche), phosphatase inhibitor cocktail
(Halt, Pierce), 3 .mu.M ASV]. For each condition, lysates from 3
separate wells were pooled. Lysates were sonicated and clarified by
centrifugation. For pre-click/pulldown samples, 50 .mu.L of each
lysate was reserved and combined with 50 .mu.L of hot SDS lysis
buffer for SDS-PAGE analysis.
[0229] For click reactions, 50 .mu.L of each lysate was processed
using the Click-IT Protein Reaction Buffer kit (Invitrogen) with
alkyne-PEG4-biotin (Invitrogen) according to manufacturer's
recommendations. Following click labeling, methanol-chloroform
extracted protein pellets were resuspended by vortexing in 20 .mu.L
of gentle lysis buffer+80 .mu.L of nondenaturing buffer (1% Nonidet
P40, 50 mM Tris HCl pH 8.0, EDTA-free protease inhibitor cocktail).
Proteins were allowed to solubilize at 4.degree. C. overnight.
Biotin-labeled proteins were purified via a magnetic streptavidin
bead (PureProteome, Millipore) pulldown. Prior to binding
reactions, beads were blocked by incubating 1 hour with 5% BSA
solution in PBS, on a rotator at room temp, and washing 3.times. in
PBS-T (PBS plus 0.1% Tween-20). Beads were resuspended in PBS-T.
Binding reactions (200 .mu.L volume) proceeded for 1 hour on a
rotator at room temp, after which beads were washed 3.times. with
PBS-T. Proteins were eluted for SDS-PAGE by heating beads in 50
.mu.L SDS lysis buffer at 95.degree. C. for 10 minutes.
[0230] Calculating half-lives of SMASh-tagged proteins. To
calculate production rates of PSD95 and PSD95-SMASh, we assumed
that the protein production rate is constant between 24 and 28
hours post-transfection, and are the same for PSD95-SMASh protein
expressed from a PSD95-SMASh gene with ASV and PSD95 protein
expressed from a PSD95-SMASh gene without ASV. The rate of change
in protein concentrations can be modeled with the differential
equations:
d[PSD95](t)/dt=k.sub.syn,PSD-k.sub.deg,PSD95[PSD95](t) (1)
i
d[PSD95SMASh](t)/dt=k.sub.syn,PSDSMASh-k.sub.deg,PSD95SMAsh[PSD95SMASh-
](t) (2)
where [PSD95](t) is protein concentration of PSD95 at time t,
[PSD95SMASh](t) is protein concentration of PSD95-SMASh at time t,
k.sub.syn,PSD95 and k.sub.syn,PSD95SMASh are production rate
constants of PSD95 and PSD95-SMASh, and k.sub.deg,PSD95 and
k.sub.deg,PSD95SMASh are decay rate constants of PSD95 and
PSD95-SMASh. Integration of these equations yields:
[PSD95](t)=(k.sub.syn,PSD/k.sub.deg,PSD95)(1-ehu kdeg,PSD95t)
(3)
[PSD95SMASh](t)=(k.sub.syn,PSD95SMASh/k.sub.deg,PSD95SMASh)(1-e.sup.-kde-
g,PSD95SMASht) (4)
[0231] We measured PSD95 half-life (t.sub.1/2,PSD95) by fitting the
PSD95 band intensities of different time points to monoexponential
decay curves (n=3), obtaining 12.4 hours. We then determined the
decay rate constant of PSD95
(k.sub.deg,PSD95=ln2/t.sub.1/2,PSD95=0.056/hour). We defined 1
relative intensity unit (RIU) as the mean band density on
immunoblotting from net production of PSD95 in 4 hours. By
immunoblotting lysates from cells incubated for 24 hours with ASV
then for 4 hours without ASV, we obtained a protein amount of 1 RIU
for [PSD95](4 hours) (standard deviation 0.16, n=3). By
immunoblotting in parallel lysates from cells incubated for 24
hours without ASV then for 4 hours with ASV, we obtained a protein
amount of 0.419 RIU for [PSD95SMASh](4 hours) (standard deviation
0.07, n=3). With values for k.sub.deg,PSD95 and for [PSD95](4
hours), we then used equation (3) to solve numerically for
k.sub.syn,PSD95, obtaining 0.280 RIU/hour. Assuming
k.sub.syn,PSD95SMASh equals k.sub.syn,PSD95, we could then use
equation (4) to solve numerically for k.sub.deg,PSD95SMAsh,
obtaining 0.607/hour. The PSD95SMASh half-life t.sub.1/2,PSD95SMASh
was then calculated as 1.14 hours
(t.sub.1/2,PSD95SMASh=ln2/k.sub.deg,PSD95SMASh=1.14 hours).
[0232] The half-life of CYP21A2-SMASh was calculated from the same
equations, except CYP21A2 was substituted for PSD95. Values
obtained were: t.sub.1/2,CYP21A2=2.2 hours,
k.sub.deg,CYP21A2=0.312/hour, [CYP21A2](4 hours)=1 RIU (standard
deviation 0.019, n=3), [CYP21A2SMASh](4 h)=0.163 RIU (standard
deviation 0.025, n=3),
k.sub.syn,CYP21A2=k.sub.syn,CYP21A2SMASh=0.438/hour,
k.sub.deg,CYP21A2SMASh=2.688/hour, t.sub.1/2,CYP21A2SMASh=0.258
hours.
[0233] While the preferred embodiments of the invention have been
illustrated and described, it will be appreciated that various
changes can be made therein without departing from the spirit and
scope of the invention.
TABLE-US-00001 TABLE 1 Comparison of methods for drug regulation of
protein expression. Drug-induced protein expression systems
Drug-induced protein suppression systems MaRaP ddFKBP ecDHFR SURF
LID AID Halotag SMASh Drug C20-MaRap Shield-1 trimethoprim
rapamycin Shield-1 auxin hydrophobic HCV chloroalkane protease
inhibitor Expressed fused to fused to fused to minimally fused to
fused to fused to minimally form FRB*, ddFKBP, ecDHFR, modified LID
IAA17 Halotag modified bound to bound to bound to drug drug drug
Suppressed fused to fused to fused to fused to fused to fused to
fused to fused to form FRB* ddFKBP ecDHFR Ub.sup.C-FRB- LID, IAA17,
Halotag, SMASh tag, degron bound to bound to bound to bound to drug
drug drug drug Single- no yes yes no yes no yes yes component
Selective for no no no yes no no no yes new proteins Reference 38
34 36 32 39 21 40 this work
Sequence CWU 1
1
16142PRTArtificial SequenceDegron 1Pro Ile Thr Lys Ile Asp Thr Lys
Tyr Ile Met Thr Cys Met Ser Ala1 5 10 15Asp Leu Glu Val Val Thr Ser
Thr Trp Val Leu Val Gly Gly Val Leu 20 25 30Ala Ala Leu Ala Ala Tyr
Cys Leu Ser Thr 35 40210PRTArtificial SequenceHCV NS4A/4B protease
cleavage site 2Asp Glu Met Glu Glu Cys Ser Gln His Leu1 5
1039PRTArtificial SequenceHCV NS5A/5B protease cleavage site 3Glu
Asp Val Val Pro Cys Ser Met Gly1 54186PRTHepatitis C virus 4Ala Pro
Ile Thr Ala Tyr Ala Gln Gln Thr Arg Gly Leu Leu Gly Cys1 5 10 15Ile
Ile Thr Ser Leu Thr Gly Arg Asp Lys Asn Gln Val Glu Gly Glu 20 25
30Val Gln Ile Val Ser Thr Ala Thr Gln Thr Phe Leu Ala Thr Cys Ile
35 40 45Asn Gly Val Cys Trp Ala Val Tyr His Gly Ala Gly Thr Arg Thr
Ile 50 55 60Ala Ser Pro Lys Gly Pro Val Ile Gln Met Tyr Thr Asn Val
Asp Gln65 70 75 80Asp Leu Val Gly Trp Pro Ala Pro Gln Gly Ser Arg
Ser Leu Thr Pro 85 90 95Cys Thr Cys Gly Ser Ser Asp Leu Tyr Leu Val
Thr Arg His Ala Asp 100 105 110Val Ile Pro Val Arg Arg Arg Gly Asp
Ser Arg Gly Ser Leu Leu Ser 115 120 125Pro Arg Pro Ile Ser Tyr Leu
Lys Gly Ser Ser Gly Gly Pro Leu Leu 130 135 140Cys Pro Ala Gly His
Ala Val Gly Leu Phe Arg Ala Ala Val Cys Thr145 150 155 160Arg Gly
Val Ala Lys Ala Val Asp Phe Ile Pro Val Glu Asn Leu Glu 165 170
175Thr Thr Met Arg Ser Pro Val Phe Thr Asp 180 185533PRTArtificial
SequenceNS3 helicase domain with deletion 5Asn Ser Ser Pro Pro Ala
Val Thr Leu Thr His Pro Ile Thr Lys Ile1 5 10 15Asp Thr Lys Tyr Ile
Met Thr Cys Met Ser Ala Asp Leu Glu Val Val 20 25
30Thr645PRTHepatitis C virus 6Ser Thr Trp Val Leu Val Gly Gly Val
Leu Ala Ala Leu Ala Ala Tyr1 5 10 15Cys Leu Ser Thr Gly Cys Val Val
Ile Val Gly Arg Ile Val Leu Ser 20 25 30Gly Lys Pro Ala Ile Ile Pro
Asp Arg Glu Val Leu Tyr 35 40 457304PRTArtificial
SequenceC-terminal SMASh tag with NS4A/4B protease cleavage site
7Asp Glu Met Glu Glu Cys Ser Gln His Leu Pro Gly Ala Gly Ser Ser1 5
10 15Gly Asp Ile Met Asp Tyr Lys Asp Asp Asp Asp Lys Gly Ser Ser
Gly 20 25 30Thr Gly Ser Gly Ser Gly Thr Ser Ala Pro Ile Thr Ala Tyr
Ala Gln 35 40 45Gln Thr Arg Gly Leu Leu Gly Cys Ile Ile Thr Ser Leu
Thr Gly Arg 50 55 60Asp Lys Asn Gln Val Glu Gly Glu Val Gln Ile Val
Ser Thr Ala Thr65 70 75 80Gln Thr Phe Leu Ala Thr Cys Ile Asn Gly
Val Cys Trp Ala Val Tyr 85 90 95His Gly Ala Gly Thr Arg Thr Ile Ala
Ser Pro Lys Gly Pro Val Ile 100 105 110Gln Met Tyr Thr Asn Val Asp
Gln Asp Leu Val Gly Trp Pro Ala Pro 115 120 125Gln Gly Ser Arg Ser
Leu Thr Pro Cys Thr Cys Gly Ser Ser Asp Leu 130 135 140Tyr Leu Val
Thr Arg His Ala Asp Val Ile Pro Val Arg Arg Arg Gly145 150 155
160Asp Ser Arg Gly Ser Leu Leu Ser Pro Arg Pro Ile Ser Tyr Leu Lys
165 170 175Gly Ser Ser Gly Gly Pro Leu Leu Cys Pro Ala Gly His Ala
Val Gly 180 185 190Leu Phe Arg Ala Ala Val Cys Thr Arg Gly Val Ala
Lys Ala Val Asp 195 200 205Phe Ile Pro Val Glu Asn Leu Glu Thr Thr
Met Arg Ser Pro Val Phe 210 215 220Thr Asp Asn Ser Ser Pro Pro Ala
Val Thr Leu Thr His Pro Ile Thr225 230 235 240Lys Ile Asp Thr Lys
Tyr Ile Met Thr Cys Met Ser Ala Asp Leu Glu 245 250 255Val Val Thr
Ser Thr Trp Val Leu Val Gly Gly Val Leu Ala Ala Leu 260 265 270Ala
Ala Tyr Cys Leu Ser Thr Gly Cys Val Val Ile Val Gly Arg Ile 275 280
285Val Leu Ser Gly Lys Pro Ala Ile Ile Pro Asp Arg Glu Val Leu Tyr
290 295 3008303PRTArtificial SequenceN-terminal SMASh tag with
NS5A/5B protease cleavage site 8Met Asp Tyr Lys Asp Asp Asp Asp Lys
Gly Ser Ser Gly Thr Gly Ser1 5 10 15Gly Ser Gly Thr Ser Ala Pro Ile
Thr Ala Tyr Ala Gln Gln Thr Arg 20 25 30Gly Leu Leu Gly Cys Ile Ile
Thr Ser Leu Thr Gly Arg Asp Lys Asn 35 40 45Gln Val Glu Gly Glu Val
Gln Ile Val Ser Thr Ala Thr Gln Thr Phe 50 55 60Leu Ala Thr Cys Ile
Asn Gly Val Cys Trp Ala Val Tyr His Gly Ala65 70 75 80Gly Thr Arg
Thr Ile Ala Ser Pro Lys Gly Pro Val Ile Gln Met Tyr 85 90 95Thr Asn
Val Asp Gln Asp Leu Val Gly Trp Pro Ala Pro Gln Gly Ser 100 105
110Arg Ser Leu Thr Pro Cys Thr Cys Gly Ser Ser Asp Leu Tyr Leu Val
115 120 125Thr Arg His Ala Asp Val Ile Pro Val Arg Arg Arg Gly Asp
Ser Arg 130 135 140Gly Ser Leu Leu Ser Pro Arg Pro Ile Ser Tyr Leu
Lys Gly Ser Ser145 150 155 160Gly Gly Pro Leu Leu Cys Pro Ala Gly
His Ala Val Gly Leu Phe Arg 165 170 175Ala Ala Val Cys Thr Arg Gly
Val Ala Lys Ala Val Asp Phe Ile Pro 180 185 190Val Glu Asn Leu Glu
Thr Thr Met Arg Ser Pro Val Phe Thr Asp Asn 195 200 205Ser Ser Pro
Pro Ala Val Thr Leu Thr His Pro Ile Thr Lys Ile Asp 210 215 220Thr
Lys Tyr Ile Met Thr Cys Met Ser Ala Asp Leu Glu Val Val Thr225 230
235 240Ser Thr Trp Val Leu Val Gly Gly Val Leu Ala Ala Leu Ala Ala
Tyr 245 250 255Cys Leu Ser Thr Gly Cys Val Val Ile Val Gly Arg Ile
Val Leu Ser 260 265 270Gly Lys Pro Ala Gly Ser Ser Gly Ser Ser Ile
Ile Pro Asp Arg Glu 275 280 285Val Leu Tyr Gln Glu Phe Glu Asp Val
Val Pro Cys Ser Met Gly 290 295 300920722DNAArtificial
SequenceMeV-EGFP-P-SMASh plasmid 9gttgtaaaac gacggccagt gaattgtaat
acgactcact ataaccaaac aaagttgggt 60aaggatagtt caatcaatga tcatcttcta
gtgcacttag gattcaagat cctattatca 120gggacaagag caggattagg
gatatcccga cgcgtacgcc accatggtga gcaagggcga 180ggagctgttc
accggggtgg tgcccatcct ggtcgagctg gacggcgacg taaacggcca
240caagttcagc gtgtccggcg agggcgaggg cgatgccacc tacggcaagc
tgaccctgaa 300gttcatctgc accaccggca agctgcccgt gccctggccc
accctcgtga ccaccctgac 360ctacggcgtg cagtgcttca gccgctaccc
cgaccacatg aagcagcacg acttcttcaa 420gtccgccatg cccgaaggct
acgtccagga gcgcaccatc ttcttcaagg acgacggcaa 480ctacaagacc
cgcgccgagg tgaagttcga gggcgacacc ctggtgaacc gcatcgagct
540gaagggcatc gacttcaagg aggacggcaa catcctgggg cacaagctgg
agtacaacta 600caacagccac aacgtctata tcatggccga caagcagaag
aacggcatca aggtgaactt 660caagatccgc cacaacatcg aggacggcag
cgtgcagctc gccgaccact accagcagaa 720cacccccatc ggcgacggcc
ccgtgctgct gcccgacaac cactacctga gcacccagtc 780cgccctgagc
aaagacccca acgagaagcg cgatcacatg gtcctgctgg agttcgtgac
840cgccgccggg atcactctcg gcatggacga gctgtacaag tagactgacg
tctcgcgatc 900gcgtccgcct accctccatc attgttataa aaaacttagg
aaccaggtcc acacagccgc 960cagcccatca accatccact cccacgattg
gagatatccg agatggccac acttttaagg 1020agcttagcat tgttcaaaag
aaacaaggac aaaccaccca ttacatcagg atccggtgga 1080gccatcagag
gaatcaaaca cattattata gtaccaatcc ctggagattc ctcaattacc
1140actcgatcca gacttctgga ccggttggtc aggttaattg gaaacccgga
tgtgagcggg 1200cccaaactaa caggggcact aataggtata ttatccttat
ttgtggagtc tccaggtcaa 1260ttgattcaga ggatcaccga tgaccctgac
gttagcataa ggctgttaga ggttgtccag 1320agtgaccagt cacaatctgg
ccttaccttc gcatcaagag gtaccaacat ggaggatgag 1380gcggaccaat
acttttcaca tgatgatcca attagtagtg atcaatccag gttcggatgg
1440ttcgagaaca aggaaatctc agatattgaa gtgcaagacc ctgagggatt
caacatgatt 1500ctgggtacca tcctagccca aatttgggtc ttgctcgcaa
aggcggttac ggccccagac 1560acggcagctg attcggagct aagaaggtgg
ataaagtaca cccaacaaag aagggtagtt 1620ggtgaattta gattggagag
aaaatggttg gatgtggtga ggaacaggat tgccgaggac 1680ctctccttac
gccgattcat ggtcgctcta atcctggaca tcaagagaac acccggaaac
1740aaacccagga ttgctgaaat gatatgtgac attgatacat atatcgtaga
ggcaggatta 1800gccagtttta tcctgactat taagtttggg atagaaacta
tgtatcctgc tcttggactg 1860catgaatttg ctggtgagtt atccacactt
gagtccttga tgaaccttta ccagcaaatg 1920ggggaaactg caccctacat
ggtaatcctg gagaactcaa ttcagaacaa gttcagtgca 1980ggatcatacc
ctctgctctg gagctatgcc atgggagtag gagtggaact tgaaaactcc
2040atgggaggtt tgaactttgg ccgatcttac tttgatccag catattttag
attagggcaa 2100gagatggtaa ggaggtcagc tggaaaggtc agttccacat
tggcatctga actcggtatc 2160actgccgagg atgcaaggct tgtttcagag
attgcaatgc atactactga ggacaagatc 2220agtagagcgg ttggacccag
acaagcccaa gtatcatttc tacacggtga tcaaagtgag 2280aatgagctac
cgagattggg gggcaaggaa gataggaggg tcaaacagag tcgaggagaa
2340gccagggaga gctacagaga aaccgggccc agcagagcaa gtgatgcgag
agctgcccat 2400cttccaaccg gcacacccct agacattgac actgcatcgg
agtccagcca agatccgcag 2460gacagtcgaa ggtcagctga cgccctgctt
aggctgcaag ccatggcagg aatctcggaa 2520gaacaaggct cagacacgga
cacccctata gtgtacaatg acagaaatct tctagactag 2580gtgcgagagg
ccgaggacca gaacaacatc cgcctaccct ccatcattgt tataaaaaac
2640ttaggaacca ggtccacaca gccgccagcc catcaaccat ccactcccac
gattggagca 2700gatggcagaa gagcaggcac gccatgtcaa aaacggactg
gaatgcatcc gggctctcaa 2760ggccgagccc atcggctcac tggccatcga
ggaagctatg gcagcatggt cagaaatatc 2820agacaaccca ggacaggagc
gagccacctg cagggaagag aaggcaggca gttcgggtct 2880cagcaaacca
tgcctctcag caattggatc aactgaaggc ggtgcacctc gcatccgcgg
2940tcagggacct ggagagagcg atgacgacgc tgaaactttg ggaatccccc
caagaaatct 3000ccaggcatca agcactgggc tacagtgtca ttatgtttat
gatcacagcg gtgaagcggt 3060taagggaatc caagatgctg actctatcat
ggttcaatca ggccttgatg gtgatagcac 3120cctctcagga ggagacaatg
aatctgaaaa cagcgatgtg gatattggcg aacctgatac 3180cgagggatat
gctatcactg accggggatc tgctcccatc tctatggggt tcagggcttc
3240tgatgttgaa actgcagaag gaggggagat ccacgagctc ctgagactcc
aatccagagg 3300caacaacttt ccgaagcttg ggaaaactct caatgttcct
ccgcccccgg accccggtag 3360ggccagcact tccgggacac ccattaaaaa
gggcacagac gcgagattag cctcatttgg 3420aacggagatc gcgtcttcat
tgacaggtgg tgcaacccaa tgtgctcgaa agtcaccctc 3480ggaaccatca
gggccaggtg cacctgcggg gaacgtcccc gagtgtgtga gcaatgccgc
3540actgatacag gagtggacac ccgaatctgg caccacaatc tccccgagat
cccagaataa 3600tgaagaaggg ggagaccatt atgatgatga gctgttctct
gatgtccaag atattaaaac 3660agccttggcc aaaatacacg aggataatca
gaagataatc tccaagctag aatcactgct 3720gttattgaag ggagaagttg
agtcaattaa gaagcagatc aacaggcaaa atatcagcat 3780atccaccctg
gaaggacacc tctcaagcat catgatcgcc attcctggac ttgggaagga
3840tcccaacgac cccactgcag atgtcgaaat caatcccgac ttgaaaccca
tcataggcag 3900agattcaggc cgagcactgg ccgaagttct caagaaaccc
gttgccagcc gacaactcca 3960aggaatgaca aatggacgga ccagttccag
aggacagctg ctgaaggaat ttcagctaaa 4020gccgatcggg aaaaagatga
gctcagccgt cgggtttgtt cctgacaccg gccctgcatc 4080acgcagtgta
atccgctcca ttataaaatc cagccggcta gaggaggatc ggaagcgtta
4140cctgatgact ctccttgatg atatcaaagg agccaatgat cttgccaagt
tccaccagat 4200gctggtgaag ataataatga aggacgaaat ggaggaatgt
tcacagcact tacccggcgc 4260cggcagtagt ggcgatatca tggattacaa
ggatgacgac gataagggct cttccgggac 4320aggctccgga tccggcacta
gtgcgcccat cacggcgtac gcccagcaga cgagaggcct 4380cctagggtgt
ataatcacca gcctgactgg ccgggacaaa aaccaagtgg agggtgaggt
4440ccagatcgtg tcaactgcta cccaaacctt cctggcaacg tgcatcaatg
gggtatgctg 4500ggcagtctac cacggggccg gaacgaggac catcgcatca
cccaagggtc ctgtcatcca 4560gatgtatacc aatgtggacc aagaccttgt
gggctggccc gctcctcaag gttcccgctc 4620attgacaccc tgtacctgcg
gctcctcgga cctttacctg gtcacgaggc acgccgatgt 4680cattcccgtg
cgccggcgag gtgatagcag gggtagcctg ctttcgcccc ggcccatttc
4740ctacttgaaa ggctcctcgg ggggtccgct gttgtgcccc gcgggacacg
ccgtgggcct 4800attcagggcc gcggtgtgca cccgtggagt ggctaaagcg
gtggacttta tccctgtgga 4860gaacctagag acaaccatga gatccccggt
gttcacggac aactcctctc caccagcagt 4920caccctgacg cacccaatca
ccaaaatcga taccaaatac atcatgacat gcatgtcggc 4980cgacctggag
gtcgtcacga gcacctgggt gctcgttggc ggcgtcctgg ctgctctggc
5040cgcgtattgc ctgtcaacag gctgcgtggt catagtgggc aggatcgtct
tgtccgggaa 5100gccggcaatt atacctgaca gggaggttct ctaccaggag
ttcggcgcgc cttgactaca 5160gctcaactta cctgccaacc ccatgccagt
cgacccaact agtacaacct aaatccatta 5220taaaaaactt aggagcaaag
tgattgcctc ccaagttcca caatgacaga gatctacgac 5280ttcgacaagt
cggcatggga catcaaaggg tcgatcgctc cgatacaacc caccacctac
5340agtgatggca ggctggtgcc ccaggtcaga gtcatagatc ctggtctagg
cgacaggaag 5400gatgaatgct ttatgtacat gtttctgctg ggggttgttg
aggacagcga ttccctaggg 5460cctccaatcg ggcgagcatt tgggtccctg
cccttaggtg ttggcagatc cacagcaaag 5520cccgaaaaac tcctcaaaga
ggccactgag cttgacatag ttgttagacg tacagcaggg 5580ctcaatgaaa
aactggtgtt ctacaacaac accccactaa ctctcctcac accttggaga
5640aaggtcctaa caacagggag tgtcttcaac gcaaaccaag tgtgcaatgc
ggttaatctg 5700ataccgctcg ataccccgca gaggttccgt gttgtttata
tgagcatcac ccgtctttcg 5760gataacgggt attacaccgt tcctggaaga
atgctggaat tcagatcggt caatgcagtg 5820gccttcaacc tgctggtgac
ccttaggatt gacaaggcga taggccctgg gaagatcatc 5880gacaatacag
agcaacttcc tgaggcaaca tttatggtcc acatcgggaa cttcaggaga
5940aagaagagtg aagtctactc tgccgattat tgcaaaatga aaatcgaaaa
gatgggcctg 6000gtttttgcac ttggtgggat agggggcacc agtcttcaca
ttagaagcac aggcaaaatg 6060agcaagactc tccatgcaca actcgggttc
aagaagacct tatgttaccc gctgatggat 6120atcaatgaag accttaatcg
attactctgg aggagcagat gcaagatagt aagaatccag 6180gcagttttgc
agccatcagt tcctcaagaa ttccgcattt acgacgacgt gatcataaat
6240gatgaccaag gactattcaa agttctgtag accgtagtgc ccagcaatgc
ccgaaaacga 6300cccccctcac aatgacagcc agaaggcccg gacaaaaaag
ccccctccga aagactccac 6360ggaccaagcg agaggccagc cagcagccga
cggcaagcgc gaacaccagg cggccccagc 6420acagaacagc cctgacacaa
ggccaccacc agccacccca atctgcatcc tcctcgtggg 6480acccccgagg
accaaccccc aaggctgccc ccgatccaaa ccaccaaccg catccccacc
6540acccccggga aagaaacccc cagcaattgg aaggcccctc cccctcttcc
tcaacacaag 6600aactccacaa ccgaaccgca caagcgaccg aggtgaccca
accgcaggca tccgactccc 6660tagacagatc ctctctcccc ggcaaactaa
acaaaactta gggccaagga acatacacac 6720ccaacagaac ccagaccccg
gcccacggcg ccgcgccccc aacccccgac aaccagaggg 6780agcccccaac
caatcccgcc ggctcccccg gtgcccacag gcagggacac caacccccga
6840acagacccag cacccaacca tcgacaatcc aagacggggg ggccccccca
aaaaaaggcc 6900cccaggggcc gacagccagc accgcgagga agcccaccca
ccccacacac gaccacggca 6960accaaaccag aacccagacc accctgggcc
accagctccc agactcggcc atcaccccgc 7020agaaaggaaa ggccacaacc
cgcgcacccc agccccgatc cggcggggag ccacccaacc 7080cgaaccagca
cccaagagcg atccccgaag gacccccgaa ccgcaaagga catcagtatc
7140ccacagcctc tccaagtccc ccggtctcct cctcttctcg aagggaccaa
aagatcaatc 7200caccacaccc gacgacactc aactccccac ccctaaagga
gacaccggga atcccagaat 7260caagactcat ccaatgtcca tcatgggtct
caaggtgaac gtctctgcca tattcatggc 7320agtactgtta actctccaaa
cacccaccgg tcaaatccat tggggcaatc tctctaagat 7380aggggtggta
ggaataggaa gtgcaagcta caaagttatg actcgttcca gccatcaatc
7440attagtcata aaattaatgc ccaatataac tctcctcaat aactgcacga
gggtagagat 7500tgcagaatac aggagactac tgagaacagt tttggaacca
attagagatg cacttaatgc 7560aatgacccag aatataagac cggttcagag
tgtagcttca agtaggagac acaagagatt 7620tgcgggagta gtcctggcag
gtgcggccct aggcgttgcc acagctgctc agataacagc 7680cggcattgca
cttcaccagt ccatgctgaa ctctcaagcc atcgacaatc tgagagcgag
7740cctggaaact actaatcagg caattgaggc aatcagacaa gcagggcagg
agatgatatt 7800ggctgttcag ggtgtccaag actacatcaa taatgagctg
ataccgtcta tgaaccaact 7860atcttgtgat ttaatcggcc agaagctcgg
gctcaaattg ctcagatact atacagaaat 7920cctgtcatta tttggcccca
gcttacggga ccccatatct gcggagatat ctatccaggc 7980tttgagctat
gcgcttggag gagacatcaa taaggtgtta gaaaagctcg gatacagtgg
8040aggtgattta ctgggcatct tagagagcag aggaataaag gcccggataa
ctcacgtcga 8100cacagagtcc tacttcattg tcctcagtat agcctatccg
acgctgtccg agattaaggg 8160ggtgattgtc caccggctag agggggtctc
gtacaacata ggctctcaag agtggtatac 8220cactgtgccc aagtatgttg
caacccaagg gtaccttatc tcgaattttg atgagtcatc 8280gtgtactttc
atgccagagg ggactgtgtg cagccaaaat gccttgtacc cgatgagtcc
8340tctgctccaa gaatgcctcc gggggtccac caagtcctgt gctcgtacac
tcgtatccgg 8400gtcttttggg aaccggttca ttttatcaca agggaaccta
atagccaatt gtgcatcaat 8460cctttgcaag tgttacacaa caggaacgat
cattaatcaa gaccctgaca agatcctaac 8520atacattgct gccgatcact
gcccggtagt cgaggtgaac ggcgtgacca tccaagtcgg 8580gagcaggagg
tatccagacg ctgtgtactt gcacagaatt gacctcggtc ctcccatatc
8640attggagagg ttggacgtag ggacaaatct ggggaatgca attgctaagt
tggaggatgc 8700caaggaattg ttggagtcat cggaccagat attgaggagt
atgaaaggtt tatcgagcac 8760tagcatagtc tacatcctga ttgcagtgtg
tcttggaggg ttgataggga tccccgcttt 8820aatatgttgc tgcagggggc
gttgtaacaa aaagggagaa caagttggta tgtcaagacc 8880aggcctaaag
cctgatctta cgggaacatc aaaatcctat gtaaggtcgc tctgatcctc
8940tacaactctt gaaacacaaa tgtcccacaa gtctcctctt cgtcatcaag
caaccaccgc 9000acccagcatc
aagcccacct gaaattatct ccggtttcca agcggaagaa caatatcggt
9060agttaattaa aacttagggt gcaagatcat ccacaatgtc accacaacga
gaccggataa 9120atgccttcta caaagataac ccccatccca agggaagtag
gatagtcatt aacagagaac 9180atcttatgat tgatagacct tatgttttgc
tggctgttct gtttgtcatg tttctgagct 9240tgatcgggtt gctagccatt
gcaggcatta gacttcatcg ggcagccatc tacaccgcag 9300agatccataa
aagcctcagc accaatctag atgtaactaa ctcaatcgag catcaggtca
9360aggacgtgct gacaccactc ttcaaaatca tcggtgatga agtgggcctg
aggacacctc 9420agagattcac tgacctagtg aaattcatct ctgacaagat
taaattcctt aatccggata 9480gggagtacga cttcagagat ctcacttggt
gtatcaaccc gccagagaga atcaaattgg 9540attatgatca atactgtgca
gatgtggctg ctgaagagct catgaatgca ttggtgaact 9600caactctact
ggagaccaga acaaccaatc agttcctagc tgtctcaaag ggaaactgct
9660cagggcccac tacaatcaga ggtcaattct caaacatgtc gctgtccctg
ttagacttgt 9720atttaggtcg aggttacaat gtgtcatcta tagtcactat
gacatcccag ggaatgtatg 9780ggggaactta cctagtggaa aagcctaatc
tgagcagcaa aaggtcagag ttgtcacaac 9840tgagcatgta ccgagtgttt
gaagtaggtg ttatcagaaa tccgggtttg ggggctccgg 9900tgttccatat
gacaaactat cttgagcaac cagtcagtaa tgatctcagc aactgtatgg
9960tggctttggg ggagctcaaa ctcgcagccc tttgtcacgg ggaagattct
atcacaattc 10020cctatcaggg atcagggaaa ggtgtcagct tccagctcgt
caagctaggt gtctggaaat 10080ccccaaccga catgcaatcc tgggtcccct
tatcaacgga tgatccagtg atagacaggc 10140tttacctctc atctcacaga
ggtgttatcg ctgacaacca agcaaaatgg gctgtcccga 10200caacacgaac
agatgacaag ttgcgaatgg agacatgctt ccaacaggcg tgtaagggta
10260aaatccaagc actctgcgag aatcccgagt gggcaccatt gaaggataac
aggattcctt 10320catacggggt cttgtctgtt gatctgagtc tgacagttga
gcttaaaatc aaaattgctt 10380cgggattcgg gccattgatc acacacggtt
cagggatgga cctatacaaa tccaaccaca 10440acaatgtgta ttggctgact
atcccgccaa tgaagaacct agccttaggt gtaatcaaca 10500cattggagtg
gataccgaga ttcaaggtta gtccctacct cttcactgtc ccaattaagg
10560aagcaggcgg agactgccat gccccaacat acctacctgc ggaggtggat
ggtgatgtca 10620aactcagttc caatctggtg attctacctg gtcaagatct
ccaatatgtt ttggcaacct 10680acgatacttc cagggttgaa catgctgtgg
tttattacgt ttacagccca agccgctcat 10740tttcttactt ttatcctttt
aggttgccta taaagggggt ccccatcgaa ttacaagtgg 10800aatgcttcac
atgggaccaa aaactctggt gccgtcactt ctgtgtgctt gcggactcag
10860aatctggtgg acatatcact cactctggga tggtgggcat gggagtcagc
tgcacagtca 10920cccgggaaga tggaaccaat cgcagatagg gctgctagtg
aaccaatcac atgatgtcac 10980ccagacatca ggcataccca ctagtgtgaa
atagacatca gaattaagaa aaacgtaggg 11040tccaagtggt tccccgttat
ggactcgcta tctgtcaacc agatcttata ccctgaagtt 11100cacctagata
gcccgatagt taccaataag atagtagcca tcctggagta tgctcgagtc
11160cctcacgctt acagcctgga ggaccctaca ctgtgtcaga acatcaagca
ccgcctaaaa 11220aacggatttt ccaaccaaat gattataaac aatgtggaag
ttgggaatgt catcaagtcc 11280aagcttagga gttatccggc ccactctcat
attccatatc caaattgtaa tcaggattta 11340tttaacatag aagacaaaga
gtcaacgagg aagatccgtg aactcctcaa aaaggggaat 11400tcgctgtact
ccaaagtcag tgataaggtt ttccaatgct taagggacac taactcacgg
11460cttggcctag gctccgaatt gagggaggac atcaaggaga aagttattaa
cttgggagtt 11520tacatgcaca gctcccagtg gtttgagccc tttctgtttt
ggtttacagt caagactgag 11580atgaggtcag tgattaaatc acaaacccat
acttgccata ggaggagaca cacacctgta 11640ttcttcactg gtagttcagt
tgagttgcta atctctcgtg accttgttgc tataatcagt 11700aaagagtctc
aacatgtata ttacctgaca tttgaactgg ttttgatgta ttgtgatgtc
11760atagagggga ggttaatgac agagaccgct atgactattg atgctaggta
tacagagctt 11820ctaggaagag tcagatacat gtggaaactg atagatggtt
tcttccctgc actcgggaat 11880ccaacttatc aaattgtagc catgctggag
cctctttcac ttgcttacct gcagctgagg 11940gatataacag tagaactcag
aggtgctttc cttaaccact gctttactga aatacatgat 12000gttcttgacc
aaaacgggtt ttctgatgaa ggtacttatc atgagttaat tgaagctcta
12060gattacattt tcataactga tgacatacat ctgacagggg agattttctc
atttttcaga 12120agtttcggcc accccagact tgaagcagta acggctgctg
aaaatgttag gaaatacatg 12180aatcagccta aagtcattgt gtatgagact
ctgatgaaag gtcatgccat attttgtgga 12240atcataatca acggctatcg
tgacaggcac ggaggcagtt ggccaccgct gaccctcccc 12300ctgcatgctg
cagacacaat ccggaatgct caagcttcag gtgatgggtt aacacatgag
12360cagtgcgttg ataactggaa atcttttgct ggagtgaaat ttggctgctt
tatgcctctt 12420agcctggata gtgatctgac aatgtaccta aaggacaagg
cacttgctgc tctccaaagg 12480gaatgggatt cagtttaccc gaaagagttc
ctgcgttacg accctcccaa gggaaccggg 12540tcacggaggc ttgtagatgt
tttccttaat gattcgagct ttgacccata tgatgtgata 12600atgtatgttg
taagtggagc ttacctccat gaccctgagt tcaacctgtc ttacagcctg
12660aaagaaaagg agatcaagga aacaggtaga ctttttgcta aaatgactta
caaaatgagg 12720gcatgccaag tgattgctga aaatctaatc tcaaacggga
ttggcaaata ttttaaggac 12780aatgggatgg ccaaggatga gcacgatttg
actaaggcac tccacactct agctgtctca 12840ggagtcccca aagatctcaa
agaaagtcac aggggggggc cagtcttaaa aacctactcc 12900cgaagcccag
tccacacaag taccaggaac gtgagagcag caaaagggtt tatagggttc
12960cctcaagtaa ttcggcagga ccaagacact gatcatccgg agaatatgga
agcttacgag 13020acagtcagtg catttatcac gactgatctc aagaagtact
gccttaattg gagatatgag 13080accatcagct tgtttgcaca gaggctaaat
gagatttacg gattgccctc atttttccag 13140tggctgcata agaggcttga
gacctctgtc ctgtatgtaa gtgaccctca ttgccccccc 13200gaccttgacg
cccatatccc gttatataaa gtccccaatg atcaaatctt cattaagtac
13260cctatgggag gtatagaagg gtattgtcag aagctgtgga ccatcagcac
cattccctat 13320ctatacctgg ctgcttatga gagcggagta aggattgctt
cgttagtgca aggggacaat 13380cagaccatag ccgtaacaaa aagggtaccc
agcacatggc cctacaacct taagaaacgg 13440gaagctgcta gagtaactag
agattacttt gtaattctta ggcaaaggct acatgatatt 13500ggccatcacc
tcaaggcaaa tgagacaatt gtttcatcac atttttttgt ctattcaaaa
13560ggaatatatt atgatgggct acttgtgtcc caatcactca agagcatcgc
aagatgtgta 13620ttctggtcag agactatagt tgatgaaaca agggcagcat
gcagtaatat tgctacaaca 13680atggctaaaa gcatcgagag aggttatgac
cgttaccttg catattccct gaacgtccta 13740aaagtgatac agcaaattct
gatctctctt ggcttcacaa tcaattcaac catgacccgg 13800gatgtagtca
tacccctcct cacaaacaac gacctcttaa taaggatggc actgttgccc
13860gctcctattg gggggatgaa ttatctgaat atgagcaggc tgtttgtcag
aaacatcggt 13920gatccagtaa catcatcaat tgctgatctc aagagaatga
ttctcgcctc actaatgcct 13980gaagagaccc tccatcaggt aatgacacaa
caaccggggg actcttcatt cctagactgg 14040gctagcgacc cttactcagc
aaatcttgta tgtgtccaga gcatcactag actcctcaag 14100aacataactg
caaggtttgt cctgatccat agtccaaacc caatgttaaa aggattattc
14160catgatgaca gtaaagaaga ggacgaggga ctggcggcat tcctcatgga
caggcatatt 14220atagtaccta gggcagctca tgaaatcctg gatcatagtg
tcacaggggc aagagagtct 14280attgcaggca tgctggatac cacaaaaggc
ttgattcgag ccagcatgag gaaggggggt 14340ttaacctctc gagtgataac
cagattgtcc aattatgact atgaacaatt cagagcaggg 14400atggtgctat
tgacaggaag aaagagaaat gtcctcattg acaaagagtc atgttcagtg
14460cagctggcga gagctctaag aagccatatg tgggcgaggc tagctcgagg
acggcctatt 14520tacggccttg aggtccctga tgtactagaa tctatgcgag
gccaccttat tcggcgtcat 14580gagacatgtg tcatctgcga gtgtggatca
gtcaactacg gatggttttt tgtcccctcg 14640ggttgccaac tggatgatat
tgacaaggaa acatcatcct tgagagtccc atatattggt 14700tctaccactg
atgagagaac agacatgaag cttgccttcg taagagcccc aagtcgatcc
14760ttgcgatctg ctgttagaat agcaacagtg tactcatggg cttacggtga
tgatgatagc 14820tcttggaacg aagcctggtt gttggctagg caaagggcca
atgtgagcct ggaggagcta 14880agggtgatca ctcccatctc aacttcgact
aatttagcgc ataggttgag ggatcgtagc 14940actcaagtga aatactcagg
tacatccctt gtccgagtgg cgaggtatac cacaatctcc 15000aacgacaatc
tctcatttgt catatcagat aagaaggttg atactaactt tatataccaa
15060caaggaatgc ttctagggtt gggtgtttta gaaacattgt ttcgactcga
gaaagatacc 15120ggatcatcta acacggtatt acatcttcac gtcgaaacag
attgttgcgt gatcccgatg 15180atagatcatc ccaggatacc cagctcccgc
aagctagagc tgagggcaga gctatgtacc 15240aacccattga tatatgataa
tgcaccttta attgacagag atgcaacaag gctatacacc 15300cagagccata
ggaggcacct tgtggaattt gttacatggt ccacacccca actatatcac
15360attttagcta agtccacagc actatctatg attgacctgg taacaaaatt
tgagaaggac 15420catatgaatg aaatttcagc tctcataggg gatgacgata
tcaatagttt cataactgag 15480tttctgctca tagagccaag attattcact
atctacttgg gccagtgtgc ggccatcaat 15540tgggcatttg atgtacatta
tcatagacca tcagggaaat atcagatggg tgagctgttg 15600tcatcgttcc
tttctagaat gagcaaagga gtgtttaagg tgcttgtcaa tgctctaagc
15660cacccaaaga tctacaagaa attctggcat tgtggtatta tagagcctat
ccatggtcct 15720tcacttgatg ctcaaaactt gcacacaact gtgtgcaaca
tggtttacac atgctatatg 15780acctacctcg acctgttgtt gaatgaagag
ttagaagagt tcacatttct cttgtgtgaa 15840agcgacgagg atgtagtacc
ggacagattc gacaacatcc aggcaaaaca cttatgtgtt 15900ctggcagatt
tgtactgtca accagggacc tgcccaccaa ttcaaggtct aagaccggta
15960gagaaatgtg cagttctaac cgaccatatc aaggcagagg ctatgttatc
tccagcagga 16020tcttcgtgga acataaatcc aattattgta gaccattact
catgctccct gacttatctc 16080cggcgaggat cgatcaaaca gataagattg
agagttgatc caggattcat tttcgacgcc 16140ctcgctgagg taaatgtcag
tcagccaaag atcggcagca acaacatctc aaatatgagc 16200atcaaggctt
tcagaccccc acacgatgat gttgcaaaat tgctcaaaga tatcaacaca
16260agcaagcaca atcttcccat ttcagggggc aatctcgcca attatgaaat
ccatgctttc 16320cgcagaatcg ggttgaactc atctgcttgc tacaaagctg
ttgagatatc aacattaatt 16380aggagatgcc ttgagccagg ggaggacggc
ttgttcttgg gtgagggatc gggttctatg 16440ttgatcactt ataaggagat
acttaaacta agcaagtgct tctataatag tggggtttcc 16500gccaattcta
gatctggtca aagggaatta gcaccctatc cctccgaagt tggccttgtc
16560gaacacagaa tgggagtagg taatattgtc aaagtgctct ttaacgggag
gcccgaagtc 16620acgtgggtag gcagtgtaga ttgcttcaat ttcatagtta
gtaatatccc tacctctagt 16680gtggggttta tccattcaga tatagagacc
ttgcctgaca aagatactat agagaagcta 16740gaggaattgg cagccatctt
atcgatggct ctgctcctgg gcaaaatag