U.S. patent application number 10/282287 was filed with the patent office on 2009-05-14 for isolated staphylococcus dnax subunit and use thereof.
Invention is credited to Michael E. O'Donnell, Richard Whipple, Dan Zhang.
Application Number | 20090123911 10/282287 |
Document ID | / |
Family ID | 26755761 |
Filed Date | 2009-05-14 |
United States Patent
Application |
20090123911 |
Kind Code |
A9 |
O'Donnell; Michael E. ; et
al. |
May 14, 2009 |
ISOLATED STAPHYLOCOCCUS DNAX SUBUNIT AND USE THEREOF
Abstract
The duplex DNA of chromosomes is replicated in a multicomponent
process. A helicase unwinds the DNA, a replicase synthesizes new
DNA, and primase repeatedly synthesizes new primed starts on the
lagging strand. The present invention is directed to the genes from
Gram positive bacterium encoding these proteins, and their
characterization.
Inventors: |
O'Donnell; Michael E.;
(Hastings-on-Hudson, NY) ; Zhang; Dan; (Forest
Hills, NY) ; Whipple; Richard; (Elizabeth,
NJ) |
Correspondence
Address: |
Michael L. Goldman;NIXON PEABODY LLP
1100 Clinton Square
Rochester
NY
14604
US
|
Prior
Publication: |
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Document Identifier |
Publication Date |
|
US 20030129633 A1 |
July 10, 2003 |
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Family ID: |
26755761 |
Appl. No.: |
10/282287 |
Filed: |
October 28, 2002 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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09235245 |
Jan 22, 1999 |
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10282287 |
Oct 28, 2002 |
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60074522 |
Jan 27, 1998 |
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60093727 |
Jul 22, 1998 |
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Current U.S.
Class: |
435/6.16 ;
435/199; 435/252.3; 435/320.1; 435/69.3; 536/23.7 |
Current CPC
Class: |
C12N 9/1241 20130101;
C07K 14/31 20130101; C12N 9/90 20130101; C12N 9/1252 20130101 |
Class at
Publication: |
435/006 ;
435/069.3; 435/199; 435/252.3; 435/320.1; 536/023.7 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; C07H 21/04 20060101 C07H021/04; C12N 9/22 20060101
C12N009/22; C12P 21/02 20060101 C12P021/02; C12N 1/21 20060101
C12N001/21; C12N 15/74 20060101 C12N015/74 |
Goverment Interests
[0002] The present invention was made with funding from National
Institutes of Health Grant No. GM38839. The United Stated
Government may have certain rights in this invention.
Claims
1. An isolated Staphylococcus DNA molecule comprising a nucleotide
sequence encoding a protein or polypeptide of SEQ ID NO: 2.
2. The isolated Staphylococcus DNA molecule according to claim 1,
wherein the DNA molecule comprises a nucleotide sequence of SEQ ID
NO: 1.
3. An expression system containing the DNA molecule according to
claim 1.
4. A host cell transformed with the DNA molecule according to claim
1.
5. An isolated Staphylococcus aureus DNA molecule encoding a dnaE
polypeptide.
6. An expression system containing the DNA molecule according to
claim 5.
7. A host cell transformed with the DNA molecule according to claim
5.
8. An isolated Staphylococcus protein or polypeptide comprising an
amino acid sequence according to SEQ ID NO: 2.
9. An isolated Staphylococcus aureus dnaE protein or
polypeptide.
10. An isolated Staphylococcus DNA molecule comprising a nucleotide
sequence encoding a protein or polypeptide of SEQ ID NO: 4.
11. The isolated Staphylococcus DNA molecule according to claim 10,
wherein the DNA molecule comprises a nucleotide sequence of SEQ ID
NO: 3.
12. An expression system containing the DNA molecule according to
claim 10.
13. A host cell transformed with the DNA molecule according to
claim 10.
14. An isolated Staphylococcus aureus DNA molecule encoding a dnaX
polypeptide.
15. An expression system containing the DNA molecule according to
claim 14.
16. A host cell transformed with the DNA molecule according to
claim 14.
17. An isolated Staphylococcus protein or polypeptide comprising an
amino acid sequence according to SEQ ID NO: 4.
18. An isolated Staphylococcus aureus dnaX protein or
polypeptide.
19. An isolated Staphylococcus DNA molecule comprising a nucleotide
sequence encoding a protein or polypeptide of SEQ ID NO: 6.
20. The isolated Staphylococcus DNA molecule according to claim 19,
wherein the DNA molecule comprises a nucleotide sequence of SEQ ID
NO: 5.
21. An expression system containing the DNA molecule according to
claim 19.
22. A host cell transformed with the DNA molecule according to
claim 19.
23. An isolated Staphylococcus aureus DNA molecule encoding a dnaB
protein or polypeptide.
24. An expression system containing the DNA molecule according to
claim 23.
25. A host cell transformed with the DNA molecule according to
claim 23.
26. An isolated Staphylococcus protein or polypeptide comprising an
amino acid sequence according to SEQ ID NO: 6.
27. An isolated Staphylococcus aureus dnaB protein or
polypeptide.
28. An isolated polypeptide comprising at least one functionally
active subunit of a Staphylococcus aureus DNA polymerase III
enzyme, wherein said subunit is selected from the group consisting
of dnaX protein, dnaE protein, dnaB protein, and combinations
thereof.
29. An isolated nucleic acid molecule encoding at least one
functionally active subunit of a Staphylococcus aureus DNA
polymerase III enzyme, wherein said subunit is selected from the
group consisting of dnaX protein, dnaE protein, dnaB protein, and
combinations thereof.
30. The isolated nucleic acid molecule of claim 29, wherein the
nucleotide sequence is DNA.
31. An expression system containing the nucleic acid molecule
according to claim 29.
32. A host cell transformed with the nucleic acid molecule
according to claim 29.
Description
[0001] This application is a continuation of U.S. patent
application Ser. No. 09/235,245 filed Jan. 22, 1999, which claims
benefit of U.S. Provisional Patent Application Nos. 60/074,572 and
60/093,727, filed Jan. 27, 1998, and Jul. 22, 1998,
respectively.
FIELD OF THE INVENTION
[0003] This invention relates to genes and proteins that replicate
the chromosome of Gram positive bacteria. These proteins can be
used in drug discovery to screen large libraries of chemicals for
identification of compounds with antibiotic activity.
BACKGROUND OF THE INVENTION
[0004] All forms of life must duplicate the genetic material to
propagate the species. The process by which the DNA in a chromosome
is duplicated is called replication. The replication process is
performed by numerous proteins that coordinate their actions to
smoothly duplicate the DNA. The main protein actors are as follows
(reviewed in Kornberg, et al., DNA Replication, Second Edition, New
York: W. H. Freeman and Company, pp. 165-194 (1992)). A helicase
uses the energy of ATP hydrolysis to unwind the two DNA strands of
the double helix. Two copies of the DNA polymerase use each
"daughter" strand as a template to convert them into two new
duplexes. The DNA polymerase acts by polymerizing the four monomer
unit building blocks of DNA (the 4 dNTPs, or deoxynucleoside
triphosphates are: dATP, dCTP, dGTP, dTTP). The polymerase rides
along one strand of DNA using it as a template that dictates the
sequence in which the monomer blocks are to be polymerized.
Sometimes the DNA polymerase makes a mistake and includes an
incorrect nucleotide (e.g., A instead of G). A proofreading
exonuclease examines the polymer as it is made and excises building
blocks that have been improperly inserted in the polymer.
[0005] Duplex DNA is composed of two strands that are oriented
antiparallel to one another, one being oriented 3'-5' and the other
5' to 3'. As the helicase unwinds the duplex, the DNA polymerase
moves continuously forward with the helicase on one strand (called
the leading strand). However, due to the fact that DNA polymerases
can only extend the DNA forward from a 3' terminus, the polymerase
on the other strand extends DNA in the opposite direction of DNA
unwinding (called the lagging strand). This necessitates a
discontinuous ratcheting motion on the lagging strand in which the
DNA is made as a series of Okazaki fragments. DNA polymerases
cannot initiate DNA synthesis de novo, but require a primed site
(i.e. a short duplex region). This job is fulfilled by primase, a
specialized RNA polymerase, that synthesizes short RNA primers on
the lagging strand. The primed sites are extended by DNA
polymerase. A single stranded DNA binding protein (SSB) is also
needed; it operates on the lagging strand. The function of SSB is
to coat single stranded DNA (ssDNA), thereby melting short hairpin
duplexes that would otherwise impede DNA synthesis by DNA
polymerase.
[0006] The replication process is best understood for the Gram
negative bacterium, Escherichia coli, and its bacteriophages T4 and
T7 (reviewed in Kelman, et al., "DNA Polymerase III Holoenzyme:
Structure and Function of Chromosomal Replicating Machine," Annu.
Rev. Biochem., 64:171-200 (1995); Marians, K. J., "Prokaryotic DNA
Replication," Annu. Rev. Biochem., 61:673-719 (1992); McHenry, C.
S., "DNA Polymerase III Holoenzyme: Components, Structure, and
Mechanism of a True Replicative Complex," J. Bio. Chem.,
266:19127-19130 (1991); Young et. al., "Structure and Function of
the Bacteriophage T4 DNA Polymerase Holoenzyme," Am. Chem. Soc.,
31:8675-8690 (1992)). The eukaryotic systems of yeast
(Saccharomyces cerevisae) (Morrison et. al., "A Third Essential DNA
Polymerase in S. cerevisiae," Cell, 62:1143-51 (1990) and humans
(Bambara, et al., "Reconstitution of Mammalian DNA Replication,"
Prog. Nuc. Acid Res., " 51:93-123 (1995)) have also been
characterized in some detail as has herpes virus (Boehmer, et al.,
"Herpes Simplex Virus DNA Replication," Annu. Rev. Biochem.,
66:347-384 (1997)) and vaccinia virus (McDonald, et. al.,
"Characterization of a Processive Form of the Vaccinia Virus DNA
Polymerase," Virology, 234:168-175 (1997)). The helicase of E. coli
is encoded by the dnaB gene and is called the DnaB-helicase. In
phage T4, the helicase is the product of the gene 41, and, in T7,
it is the product of gene 4. Generally, the helicase contacts the
DNA polymerase, in E. coli. This contact is necessary for the
helicase to achieve the catalytic efficiency needed to replicate a
chromosome (Kim, et. al., "Coupling of a Replicative Polymerase and
Helicase: A tau-DnaB Interaction Mediates Rapid Replication Fork
Movement," Cell, 84:643-650 (1996)). The identity of the helicase
that acts at the replication fork in a eukaryotic cellular system
is still not firm.
[0007] The primase of E. coli (product of the dnaG gene), phage T4
(product of gene 61), and T7 (gene 4) require the presence of their
cognate helicase for activity. The primase of eukaryotes, called
DNA polymerase alpha, looks and behaves differently. DNA polymerase
alpha is composed of 4 subunits. The primase activity is associated
with the two smaller subunits, and the largest subunit is the DNA
polymerase which extends the product of the priming subunits. DNA
polymerase alpha does not need a helicase for priming activity.
[0008] The chromosomal replicating DNA polymerase of all these
systems, prokaryotic and eukaryotic, share the feature that they
are processive, meaning they remain continuously associated with
the DNA template as they link monomer units (dNTPs) together. This
catalytic efficiency can be manifest in vitro by their ability to
extend a single primer around a circular single stranded DNA
(ssDNA) of over 5,000 nucleotide units in length. Chromosomal DNA
polymerases will be referred to here as replicases to distinguish
them from DNA polymerases that function in other DNA metabolic
processes and are far less processive.
[0009] There are three types of replicases known thus far that
differ in how they achieve processivity, and how their subunits are
organized. These will be referred to here as Types I-III. The Type
I is exemplified by the phage T5 replicase, which is composed of
only one subunit yet is highly processive (Das, et al., "Mechanism
of Primer-template Dependent Conversion of dNTP-dNMP by T7 DNA
Polymerase," J. Biol. Chem., 255:7149-7154 (1980)). It is possible
that the T5 enzyme achieves processivity by having a cavity within
it for binding DNA, and that a domain of the protein acts as a lid
that opens to accept the DNA, and closes to trap the DNA inside,
thereby keeping the polymerase on DNA during polymerization of
dNTPs. Type II is exemplified by the replicases of phage T7, herpes
simplex virus, and vaccinia virus. In these systems, the replicase
is composed of two subunits, the DNA polymerase and an "accessory
protein" which is needed for the polymerase to become highly
efficient. It is presumed that the DNA polymerase binds the DNA in
a groove and that the accessory protein forms a cap over the groove
trapping the DNA inside for processive action. Type III is
exemplified by the replicases of E. coli, phage T4, yeast, and
humans in which there are three separate components, a sliding
clamp protein, a clamp loader protein complex, and the DNA
polymerase. In these systems, the sliding clamp protein is an
oligomer in the shape of a ring. The clamp loader is a multiprotein
complex which uses ATP to assemble the clamp around DNA. The DNA
polymerase then binds the clamp which tethers the polymerase to DNA
for high processivity. The replicase of the E. coli system contains
a fourth component called tau that acts as a glue to hold two
polymerases and one clamp loader together into one structure called
Pol III*. In this application, any replicase that uses a minimum of
three components (i.e. clamp, clamp loader, and DNA polymerase)
will be referred to as either a type III enzyme or as a DNA
polymerase III-type replicase.
[0010] The E. coli replicase is also called DNA polymerase III
holoenzyme. The holoenzyme is a single multiprotein particle that
contains all the components and therefore is composed of 10
different proteins. This holoenzyme is suborganized into four
functional components called: 1) Pol III core (DNA polymerase); 2)
gamma complex (clamp loader); 3) beta subunit (sliding clamp); and
4) tau (glue protein). The DNA polymerase III "core" is a tightly
associated complex containing one each of the following three
subunits: 1) the alpha subunit is the actual DNA polymerase (129
kDa); 2) the epsilon subunit (28 kDa) contains the proofreading
3'-5' exonuclease activity; and 3) the theta subunit has an unknown
function. The gamma complex is the clamp loader and contains the
following subunits: gamma, delta, delta prime, chi and psi (U.S.
Pat. No. 5,583,026 to O'Donnell). The beta subunit is a homodimer
and forms the ring shaped sliding clamp. These components associate
to form the holoenzyme and the entire holoenzyme can be assembled
in vitro from 10 isolated pure subunits (U.S. Pat. No. 5,583,026 to
O'Donnell; U.S. Pat. No. 5,668,004 to O'Donnell). The tau subunit,
encoded by the same gene that encodes gamma (dnaX), acts as a glue
to hold two cores together with one gamma complex. This subassembly
is called DNA polymerase III star (Pol III*). One beta ring
interacts with each core in Pol III* to form DNA polymerase III
holoenzyme.
[0011] During replication, the two cores in the holoenzyme act
coordinately to synthesize both strands of DNA in a duplex
chromosome. At the replication fork, DNA polymerase III holoenzyme
physically interacts with the DnaB helicase through the tau subunit
to form a yet larger protein complex termed the "replisome" (Kim,
et. al., "Coupling of a Replicative Polymerase and Helicase: A
tau-DnaB Interaction Mediates Rapid Replication Fork Movement,"
Cell, 84:643-650 (1996); Yuzhakov, et. al., "Replisome Assembly
Reveals the Basis for Asymmetric Function in Leading and Lagging
Strand Replication," Cell, 86:877-886 (1996)). The primase
repeatedly contacts the helicase during replication fork movement
to synthesize RNA primers on the lagging strand (Marians, K. J.,
"Prokaryotic DNA Replication," Annu. Rev. Biochem., 61:673-719
(1992)).
[0012] In the present invention, new genes from Gram positive
bacteria (e.g., S. aureus) are identified. Although their homology
with E. coli proteins is often weak, they will be assigned names
based on their nearest homology to subunits in the E. coli system.
The gene of E. coli replication proteins are as follows: alpha
(dnaE); epsilon (dnaQ); theta (holE); tau (dnaX); gamma (dnaX);
delta (holA); delta prime (holB); chi (holC); psi (holD); beta
(dnaN); DnaB; helicase (dnaB); and primase (dnaG).
[0013] The dnaX gene encodes both tau and gamma. Tau is the product
of the full gene. Gamma is the product of the first 2/3 of the
gene; it is truncated by an efficient translational frameshift that
results in incorporation of one unique residue followed by a stop
codon.
[0014] Although there are many studies of replication mechanisms in
eukaryotes, and the Gram negative bacterium, E. coli and its
bacteriophages, there is very little information about how Gram
positive organisms replicate. The evolutionary split between Gram
positive bacteria and Gram negative bacteria occurred approximately
1.2 billion years ago. The Gram positive class of bacteria includes
some of the worst human pathogens such as Staphylococcus aureus,
Streptococcus pneumoniae, Streptococcus pyogenes, Enterococcus
faecalis, and Mycobacterium tuberculosis (Youmans, et. al., The
Biological and Clinical Basis of Infectious Disease (1985)).
[0015] Currently, the best characterized Gram positive organism for
DNA synthesis is Bacillus subtilis. Fractionation of B. subtitis
has identified three DNA polymerases. Gass, et al., "Further
Genetic and Enzymological Characterization of the Three Bacillus
subtilis Deoxyribonucleic Acid Polymerases," J. Bio. Chem.,
248:7688-7700 (1973); Ganesan, et. al.; "DNA Replication in a
Polymerase I Deficient Mutant and the Identification of DNA
Polymerases II and III in Bacillus subtilis," Biochem. And Biophy.
Res. Commun., 50:155-163 (1973)). These polymerases are thought to
be analogous to the three DNA polymerases of E. coli (DNA
polymerases I, II and III). Studies in B. subtilis have identified
a polymerase that appears to be involved in chromosome replication
and is termed Pol III (Ott, et. al.; "Cloning and Characterization
of the PolC Region of Bacillus subtilis," J. Bacteriol.,
165:951-957 (1986); Barnes, et. al., "Localization of the
Exonuclease and Polymerase Domains of Bacillus subtilis DNA
Polymerase III," Gene, 111:43-49 (1992); Barnes, et. al., "The
3'-5' Exonuclease Site of DNA Polymerase III From Gram-positive
Bacteria: Definition of a Novel Motif Structure," Gene" 165:45-50
(1995) or Barnes, et al., "Purification of DNA Polymerase III of
Gram-positive Bacteria," Methods in Enzy., 262:35-42 (1995)). The
B. subtilis Pol III (called PolC) is larger (about 165 kDa) than
the E. coli alpha subunit (about 129 kDa) and exhibits 3'-5'
exonuclease activity. The PolC gene encoding this Pol III shows
weak homology to the genes encoding E. coli alpha and the E. coli
epsilon subunit. Hence, this long form of the B. subtilis Pol III
(herein referred to as Pol III-L) essentially comprises both the
alpha and epsilon subunits of the E. coli core polymerase. The S.
aureus Pol III-L has also been sequenced, expressed in E. coli and
purified; it contains polymerase and 3'-5' exonuclease activity
(Pacitti, et. al., "Characterization and Overexpression of the Gene
Encoding Staphylococcus aureus DNA Polymerase III," Gene, 165:51-56
(1995)). Although this Pol III-L is essential to cell growth
(Clements, et. al., "Inhibition of Bacillus subtilis
Deoxyribonucleic Acid Polymerase III by Phenylhydrazinopyrimidines:
Demonstration of a Drug-induced Deoxyribonucleic Acid-Enzyme
Complex," J. Biol. Chem., 250:522-526 (1975); Cozzarelli, et al.,
"Mutational Alteraction of Bacillus subtilis DNA Polymerase III to
Hydroxyphenylazopyrimidine Resistance: Polymerase III is Necessary
for DNA Replication," Biochem. And Biophy. Res. Commun., 51:151-157
(1973); Low, et. al., "Mechanism of Inhibition of Bacillus subtilis
DNA Polymerase III by the Arylhydrazinopyrimidine Antimicrobial
Agents," Proc. Natl. Acad. Sci. USA, 71:2973-2977 (1974)), there
could still be another DNA polymerase(s) that is essential to the
cell, such as occurs in yeast (Morrison, et. al., "A Third
Essential DNA Polymerase in S. cerevisiae," Cell, 62:1143-1151
(1990)).
[0016] Purification of Pol III-L from B. subtilis results in only
this single protein without associated proteins Barnes, et. al.,
"Localization of the Exonuclease and Polymerase Domains of Bacillus
subtilis DNA Polymerase III," Gene, 111:43-49 (1992); Barnes, et.
al., "The 3'-5' Exonuclease Site of DNA Polymerase III From
Gram-positive Bacteria: Definition of a Novel Motif Structure,"
Gene" 165:45-50 (1995) or Barnes, et al., "Purification of DNA
Polymerase III of Gram-positive Bacteria," Methods in Enzy.,
262:35-42 (1995)). Hence, it is possible that Pol III-L is a member
of the Type I replicase (like T5) in which it is processive on its
own without accessory proteins. B. subtilis and S. aureus also have
a gene encoding a protein that has approximately 30% homology to
the beta subunit of E. coli; however the protein product has not
been purified or characterized (Alonso, et al., "Nucleotide
Sequence of the recF Gene Cluster From Staphylococcus aureus and
Complementation Analysis in Bacillus subtilis recF Mutants," Mol.
Gen. Genet., 246:680-686 (1995); Alonso, et al., "Nucleotide
Sequence of the recF Gene Cluster From Staphylococcus aureus and
Complementation Analysis in Bacillus subtilis recF Mutants," Mol.
Gen. Genet., 248:635-636 (1995)). Whether this beta subunit has a
function in replication, a ring shape, or functions as a sliding
clamp is not known. Even if this beta homolog is involved in
replication, it is not known whether it is functional with Pol
III-L or another polymerase.
[0017] There remains a need to understand the process of DNA
replication in Gram positive cells at a molecular level. It is
possible that a more detailed understanding of replication proteins
will lead to discovery of new antibiotics. Therefore, a deeper
understanding of replication proteins of Gram positive bacteria,
particularly members of the Staphylococcus genus is especially
important given the emergence of drug resistant strains of these
organisms. For example, Staphylococcus aureus has successfully
mutated to become resistant to all common antibiotics.
[0018] The "target" protein(s) of an antibiotic drug is generally
involved in a critical cell function, such that blocking its action
with a drug causes the pathogenic cell to die or no longer
proliferate. Current antibiotics are directed to very few targets.
These include membrane synthesis proteins (e.g. vancomycin,
penicillin, and its derivatives such as ampicillin, amoxicillin,
and cephalosporin), the ribosome machinery (tetracycline,
chloramphenicol, azithromycin, and the aminoglycosides: kanamycin,
neomycin, gentamicin, streptomycin), RNA polymerase (rifampimycin),
and DNA topoisomerases (novobiocin, quinolones, and
fluoroquinolones). The DNA replication apparatus is a crucial life
process, and, thus, the proteins involved in this process are also
good targets for antibiotics.
[0019] A powerful approach to discovery of a new drug is to obtain
a target protein, characterize it, and develop in vitro assays of
its cellular function. Large chemical libraries are then screened
in the functional assays to identify compounds that inhibit the
target protein. These candidate pharmaceuticals are then chemically
modified to optimize their potency, breadth of antibiotic spectrum,
performance in animal models, non toxicity, and, finally, clinical
trials. The screening of large chemical libraries requires a
plentiful source of the target protein. An abundant supply of
protein generally requires overproduction techniques using the gene
encoding the protein. This is especially true for replication
proteins as they are present in low abundance in the cell.
[0020] Selective and robust assays are needed to screen reliably a
large chemical library. The assay should be insensitive to most
chemicals in the concentration range normally used in the drug
discovery process. These assays should also be selective and not
show inhibition by antibiotics known to target proteins in
processes outside of replication. The present invention is directed
to overcoming these deficiencies in the art.
SUMMARY OF THE INVENTION
[0021] The present invention relates to various isolated DNA
molecules from Gram positive bacteria. These include dnaE, dnaX,
dnaB, PolC, dnaN, beta, and dnaG DNA molecules for Gram positive
bacteria. These DNA molecules can be inserted into an expression
system or used to transform host cells. The isolated proteins
encoded by these DNA molecules are also disclosed.
[0022] The present invention aims to understand the structure and
mechanism of the chromosomal replicase of Gram positive bacteria
and how it functions with a helicase and primase. This knowledge
and the enzymes involved in the replication process can be used for
the purpose of screening for potential antibiotic drugs. Further,
information about chromosomal replicases may be useful in DNA
sequencing, polymerase chain reaction, and other DNA polymerase
related techniques.
[0023] The present invention identifies the type of replicase that
Gram positive bacteria employ for chromosome replication. Rather
than use a DNA polymerase that attains high efficiency on its own,
or with one other subunit, the Gram positive bacteria replicase is
the Pol III-type of replicase (class III) that uses a sliding clamp
protein. The Gram positive bacteria replicase also uses a clamp
loader component that assembles the sliding clamp onto DNA.
[0024] The present invention identifies two DNA polymerases (both
of Pol III type) in Gram positive bacteria that utilize the sliding
clamp and clamp loader. The invention also identifies a gene with
homology to the alpha subunit of E. coli DNA polymerase III
holoenzyme, the chromosomal replicase of E. coli. These DNA
polymerases can extend a primer around a large circular natural
template when the beta clamp has been assembled onto the primed
ssDNA by the clamp loader or a primer on a linear DNA where the
beta clamp may assemble by itself by sliding over an end.
[0025] The present invention shows that the clamp and clamp loader
components of Gram negative cells can be exchanged for those of
Gram positive cells in that the clamp, once assembled onto DNA,
will function with Pol III obtained from either Gram positive and
Gram negative sources. This result implies that important contacts
between the polymerase and clamp have been conserved during
evolution. Therefore, these "mixed systems" may provide assays for
an inhibitor of this conserved interaction. Such an inhibitor may
be expected to shut down replication, and since the interaction is
apparently conserved across the evolutionary spectrum from Gram
positive and Gram negative cells, the inhibitor may exhibit a broad
spectrum of antibiotic activity. Further, these "mixed" systems are
composed of all overexpressed and purified proteins (8 total; 1
from S. aureus and 7 from E. coli) making possible large quantities
of protein needed for high throughput screening of hundreds of
thousands of chemicals.
[0026] The present invention demonstrates that Gram positive
bacteria contain a beta subunit that behaves as a sliding clamp
that encircles DNA. A dnaX gene sequence encoding a protein homolog
of the gamma/tau subunit of the clamp loader (gamma complex) E.
coli DNA polymerase III holoenzyme is also identified. The presence
of this gene confirms the presence of a clamp loading apparatus in
Gram positive bacteria that will assemble beta clamps onto DNA for
the DNA polymerases.
[0027] A new gene sequence encoding a DNA polymerase homologous to
the alpha subunit of DNA polymerase III holoenzyme of E. coli
(referred to herein as dnaE homolog) is also identified.
[0028] Also identified is a new gene sequence encoding a homolog of
the replicative dnaB helicase of E. coli.
[0029] This application also outlines methods and assays for use of
these replication proteins in drug screening processes.
BRIEF DESCRIPTION OF THE DRAWINGS
[0030] FIG. 1 shows the construction of the S. aureus Pol III-L
expression vector. The gene encoding Pol III-L was cloned into a
pT11 expression vector in a three step cloning scheme as
illustrated.
[0031] FIGS. 2A-C describe the expression and purification of S.
aureus Pol III-L. FIG. 2A compares E. coli cells that contain the
pET11PolC expression vector that are either induced or uninduced
for protein expression. The gel is stained with Coomassie Blue. The
induced band corresponds to the expected molecular weight of the S.
aureus Pol III-L, and is indicated to the right of the gel. FIG. 2B
shows the results of the MonoQ chromatography of a lysate of E.
coli (pET11PolC-L) induced for Pol III-L. The fractions were
analyzed in a Coomassie Blue stained gel (top) and for DNA
synthesis (bottom). Fractions containing Pol III-L are indicated.
In FIG. 2C, fractions containing Pol III-L from the MonoQ column
were pooled and chromatographed on a phosphocellulose column. This
shows an analysis of the column fractions from the phosphocellulose
column in a Coomassie Blue stained polyacrylamide gel. The position
of Pol III-L is indicated to the right.
[0032] FIG. 3 shows the S. aureus beta expression vector. The dnaN
gene was amplified from S. aureus genomic DNA and cloned into the
pET16 expression vector.
[0033] FIGS. 4A-C describe the expression and purification of S.
aureus beta. FIG. 4A compares E. coli cells that contain the
pET16beta expression vector that are either induced or uninduced
for protein expression. The gel is stained with Coomassie Blue. The
induced band corresponds to the expected molecular weight of the S.
aureus beta, and is indicated to the right of the gel. The
migration position of size standards are indicated to the left.
FIG. 4B shows the results of MonoQ chromatography of an E. coli
(pET16beta) lysate induced for beta. The fractions were analyzed in
a Coomassie Blue stained gel, and fractions containing beta are
indicated. In FIG. 4C, fractions containing beta from the MonoQ
column were pooled and chromatographed on a phosphocellulose
column. This shows an analysis of the column fractions from the
phosphocellulose column in a Coomassie Blue stained polyacrylamide
gel. The position of beta is indicated to the right.
[0034] FIGS. 5A-B demonstrate that the S. aureus beta stimulates S.
aureus Pol III-L and E. coli Pol III core on linear DNA, but not
circular DNA. In FIG. 5A, the indicated proteins were added to
replication reactions containing polydA-oligodT as described in the
Examples supra. Amounts of proteins added, when present, were:
lanes 1,2: S. aureus Pol III-L, 7.5 ng; S. aureus b, 6.2 ug; Lanes
3,4: E. coli Pol III core, 45 ng; S. aureus b, 9.3 ug; Lanes 5,6:
E. coli Pol III core, 45 ng; E. coli b, 5 .mu.g. Total DNA
synthesis was: Lanes 1-6: 4.4, 30.3, 5.1, 35.5, 0.97, 28.1 pmol,
respectively. In FIG. 5B, Lanes 1-3, the indicated proteins were
added to replication reactions containing circular singly primed
M13mp18 ssDNA as described in the Example supra. S. aureus b, 0.8
ug; S. aureus Pol III-L, 300 ng (purified through MonoQ); E. coli
gamma complex, 1.7 .mu.g. Results in the E. coli system are shown
in Lanes 4-6. Total DNA synthesis was: Lanes 1-6: 0.6, 0.36, 0.99,
2.7, 3.5, 280 pmol, respectively.
[0035] FIG. 6 shows that S. aureus Pol III-L functions with E. coli
beta and gamma complex on circular primed DNA. It also shows that
S. aureus beta does not convert Pol III-L with sufficient
processivity to extend the primer all the way around a circular
DNA. Replication reactions were performed on the circular singly
primed M13mp18 ssDNA. Proteins added to the assay were as indicated
in this figure. The amount of each protein, when present, was: S.
aureus beta, 800 ng; S. aureus Pol III-L, 1500 ng (MonoQ fraction
64); E. coli Pol III core, 450 ng; E. coli beta, 100 ng; E. coli
gamma complex, 1720 ng. Total DNA synthesis in each assay is
indicated at the bottom of the figure.
[0036] FIGS. 7A-B show that S. aureus contains four distinct DNA
polymerases. Four different DNA polymerases were partially purified
from S. aureus cells. S. aureus cell lysate was separated from DNA
and, then, chromatographed on a MonoQ column. Fractions were
analyzed for DNA polymerase activity. Three peaks of activity were
observed. The second peak was the largest and was expected to be a
mixture of two DNA polymerases based on early studies in B.
subtilis. Chromatography of the second peak on phosphocellulose
(FIG. 7B) resolved two DNA polymerases from one another.
[0037] FIGS. 8A-B show that S. aureus has two DNA Pol III's. The
four DNA polymerases partially purified from S. aureus extract,
designated peaks I-IV in FIG. 7, were assayed on circular singly
primed M13mp18 ssDNA coated with E. coli SSB either in the presence
or absence of E. coli beta (50 ng) and gamma complex (50 ng). Each
reaction contained 2 .mu.l of the partially pure polymerase (Peak 1
was Mono Q fraction 24 (1.4 ug), Peak 2 was phosphocellulose
fraction 26 (0.016 mg/ml), Peak 3 was phosphocellulose fraction 46
(0.18 mg/ml), and Peak 4 was MonoQ fraction 50 (1 ug). FIG. 8A
shows the product analysis in an agarose gel. FIG. 8B shows the
extent of DNA synthesis in each assay.
[0038] FIG. 9 compares the homology between the polypeptide encoded
by dnaE of S. aureus and other organisms. An alignment is shown for
the amino acid sequence of the S. aureus dnaE product with the dnaE
products (alpha subunits) of E. coli and Salmonella
typhimurium.
[0039] FIG. 10 compares the homology between the N-terminal regions
of the gamma/tau polypeptides of S. aureus, B. subtilis, and E.
coli. The conserved ATP site and the cystines forming the zinc
finger are indicated above the sequence. The organisms used in the
alignment were: E. coli (GenBank); and B. subtilis.
[0040] FIG. 11 compares the homology between the DnaB polypeptide
of S. aureus and other organisms. The organisms used in the
alignment were: E. coli (GenBank); B. subtilis; Sal. Typ.,
(Salmonella typhimurium).
DETAILED DESCRIPTION OF THE INVENTION
[0041] The present invention relates to various isolated DNA
molecules from Gram positive bacteria. These include dnaE, dnaX,
dnaB, PolC, dnaN, and dnaG DNA molecules from Gram positive
bacteria. These DNA molecules can be inserted into an expression
system or used to transform host cells. The isolated proteins
encoded by these DNA molecules are also disclosed.
[0042] These DNA molecules and proteins can be derived from any
Gram positive bacteria, including Staphylococcus, Streptococcus,
Enterococcus, and Mycobacterium. It is particularly directed to
such DNA molecules and proteins derived from Staphylococcus
bacteria, particularly Staphylococcus aureus.
[0043] One aspect of the present invention relates to a newly
discovered Pol III gene of S. aureus cells (herein identified as
dnaE) that is homologous to E. coli alpha (product of dnaE gene).
The partial DNA sequence of the S. aureus dnaE gene is as follows
(SEQ. ID. No. 1): TABLE-US-00001 GATATAGATA TGGACTGGGA AGATACACGC
CGAGAAAAGG TCATTCAGTA CGTCCAAGAA 60 AAATATGGCG AGCTACATGT
ATCTGGAATT GTGACTTTCG GTCATCTGCT TGCAAAAGCG 120 GTTGCTAAAG
ATGTTGGACG AATTATGGGG TTTGATGAAG TTACATTAAA TGAAATTTCA 180
AGTTTAATCC CACATAAATT AGGAATTACA CTTGATGAAG CATATCAAAT TGACGATTTT
240 AAAAAGTTTG TACATCGAAA CCATCGACAT CAACGCTGGT TCAGTATTTG
TAAAAAGTTA 300 GAAGGTTTAC CAAGACATAC ATCTACACAT GCGGCAGGAA
TTATTATTAA TGACCATCCA 360 TTATATGAAT ATGCCCCTTT AACGAAAGGC
CATACAGGAT TATTAACGCA ATGGACAATG 420 ACTGAAGCCG AACGTATTGG
TTTATTAAAA ATAGATTTTC TAGGGTTACG AAATTTATCA 480 ATTATCCATC
AAATTTTGAC TCGAGTCGAA AAAGATTTAG GTTTTAATAT TGATATTGAA 540
AAAATTCCAT TTGATGATCA AAAAGTGTTT GAATTGTTGT CGCAAGGAGA TACGACTGGC
600 ATATTTCAAT TAGAGTCTGA CGGTGTTAGA AGTGTATTAA AAAAATTAAA
GCCGGAACAC 660 TTTGAGGATA TTGTTGCTGT AACTTCTTTG TATAGACCAG
GTCCAATGGA AGAAATTCCA 720 ACTTACATTA CAAGAAGACA TGATCCAAGC
AAAGTTCAAT ATTTACATCC CCATTTAGAA 780 CCTATATTAA AAAATACTTA
CGGTGTTATT ATTTATCAAG AACAAATTAT GCAAATAGCG 840 AGCACTTTTG
CAAACTTCAG TTATGGTGAA GCGGATATTT TAAGAAGAGC AATGAGTAAA 900
AAAAATAGAG CTGTTCTTGA AAGAGACGCT CAACATTTTA TAGAAGGTAC AAAGCAAAAT
960 GGTTATCACG AAGACTTAGT AAGTAAGCAG ATATTTGATT TGATTCTGAA
ATTTGCTGAT 1020 GATGGATTTC CTAGAGCACA TGCTGTCAGC TATTCTAAAA
TTGCATACAT TATGAGCTTT 1080 TTAAAAGTCC ATTATCCAAA TTATTTTTAC
GCAAATATTT TAAGTAATGT TATTGGAAGT 1140 GAGAAGAAAA CTGCTCAAAT
GATAGAAGAA GCAAAAAAAC AAGGTATCAC TATATTGCCA 1200 CCGAACATTA
ACGAAAGTCA TTGGTTTTAT AAACCTTCCC AAGAAGGCAT TTATTTATCA 1260
ATTGGTACAA TTAAAGGTGT AGGTTATCAA AGTGTGAAAG TGATTGTTGA AGAACGTTTT
1320 CAGAACGGCA AATTTAAAGA TTTCTTTGAT TCTGCTAGAC GTATACCGAA
GAGAGTCAAA 1380 ACGAGAAAGT TACTTGAAGC ATTGATTTTA GTGGGAGCGT
TTGATGCTTT TGGTAAAACA 1440 CGTTCAACGT TGTTGCAAGC TATTGATCAA
GTGTTGGATG GTGATTTAAA CATTGAACAA 1500 GATGGTTTTT TATTTGATAT
TTTAACGCCA AAACAGATGT ATGAAGATAA AGAAGAATTG 1560 CCTGATGCAC
TTATTAGTCA GTATGAAAAA GAATATTTAG GATTTTATGT TTCGCAACAC 1620
CCAGTAGATA AGAAGTTTGT TGCCAAACAA TATTTAACGA TATTTTCTTG CGAAAACGTT
1680 GCTAAAGATG TTCGACGAAT TATGGGGTTT GATGAAGTTA AACAAA 1726
[0044] The S. aureus dnaE encoded protein has a partial amino acid
sequence as follows (SEQ. ID. No. 2): TABLE-US-00002 Asp Ile Asp
Met Asp Trp Glu Asp Thr Arg Arg Glu Lys Val Ile Gln 1 5 10 15 Tyr
Val Gln Glu Lys Tyr Gly Glu Leu His Val Ser Gly Ile Val Thr 20 25
30 Phe Gly His Leu Leu Ala Lys Ala Val Ala Lys Asp Val Gly Arg Ile
35 40 45 Met Gly Phe Asp Glu Val Thr Leu Asn Glu Ile Ser Ser Leu
Ile Pro 50 55 60 His Lys Leu Gly Ile Thr Leu Asp Glu Ala Tyr Gln
Ile Asp Asp Phe 65 70 75 80 Lys Lys Phe Val His Arg Asn His Arg His
Gln Arg Trp Phe Ser Ile 85 90 95 Cys Lys Lys Leu Glu Gly Leu Pro
Arg His Thr Ser Thr His Ala Ala 100 105 110 Gly Ile Ile Ile Asn Asp
His Pro Leu Tyr Glu Tyr Ala Pro Leu Thr 115 120 125 Lys Gly Asp Thr
Gly Leu Leu Thr Gln Trp Thr Met Thr Glu Ala Glu 130 135 140 Arg Ile
Gly Leu Leu Lys Ile Asp Phe Leu Gly Leu Arg Asn Leu Ser 145 150 155
160 Ile Ile His Gln Ile Leu Thr Arg Val Glu Lys Asp Leu Gly Phe Asn
165 170 175 Ile Asp Ile Glu Lys Ile Pro Phe Asp Asp Gln Lys Val Phe
Glu Leu 180 185 190 Leu Ser Gln Gly Asp Thr Thr Gly Ile Phe Gln Leu
Glu Ser Asp Gly 195 200 205 Val Arg Ser Val Leu Lys Lys Leu Lys Pro
Glu His Phe Glu Asp Ile 210 215 220 Val Ala Val Thr Ser Leu Tyr Arg
Pro Gly Pro Met Glu Glu Ile Pro 225 230 235 240 Thr Tyr Ile Thr Arg
Arg His Asp Pro Ser bys Val Gln Tyr Leu His 245 250 255 Pro His Leu
Glu Pro Ile Leu Lys Asn Thr Tyr Gly Val Ile Ile Tyr 260 265 270 Gln
Glu Gln Ile Met Gln Ile Ala Ser Thr Phe Ala Asn Phe Ser Tyr 275 280
285 Gly Glu Ala Asp Ile Leu Arg Arg Ala Met Ser Lys Lys Asn Arg Ala
290 295 300 Val Leu Glu Arg Asp Ala Gln His Phe Ile Glu Gly Thr Lys
Gln Asn 305 310 315 320 Gly Tyr His Glu Asp Ile Her Lys Gln Ile Phe
Asp Leu Ile Leu Lys 325 330 335 Phe Ala Asp Gly Phe Pro Arg Ala His
Ala Val Ser Tyr Ser Lys Ile 340 345 350 Ala Tyr Ile Met Her Phe Leu
Lys Val His Tyr Pro Asn Tyr Phe Tyr 355 360 365 Ala Asn Ile Leu Ser
Asn Val Ile Gly Ser Glu Lys Lys Thr Ala Gln 370 375 380 Met Ile Glu
Glu Ala Lys Lys Gln Gly Ile Thr Ile Leu Pro Pro Asn 385 390 395 400
Ile Asn Glu Her His Trp Phe Tyr Lys Pro Her Gln Glu Gly Ile Tyr 405
410 415 Leu Ser Ile Gly Thr Ile Lys Gly Val Gly Tyr Gln Her Val Lys
Val 420 425 430 Ile Val Glu Glu Arg Phe Gln Asn Gly Lys Phe Lys Asp
Phe Phe Asp 435 440 445 Ser Ala Arg Arg Ile Pro Lys Arg Val Lys Thr
Arg Lys Leu Leu Glu 450 455 460 Ala Leu Ile Leu Val Gly Ala Phe Asp
Ala Phe Gly Lys Thr Arg Ser 465 470 475 480 Thr Leu Leu Gln Ala Ile
Asp Gln Val Leu Asp Gly Asp Leu Asn Ile 485 490 495 Glu Gln Asp Gly
Phe Leu Phe Asp Ile Leu Thr Pro Lys Gln Met Tyr 500 505 510 Glu Asp
Lys Glu Glu Leu Pro Asp Ala Leu Ile Ser Gln Tyr Glu Lys 515 520 525
Glu Tyr Leu Gly Phe Tyr Val Her Gln His Pro Val Asp Lys Lys Phe 530
535 540 Val Ala Lys Gln Tyr Leu Thr Ile Phe Her Cys Glu Asn Val Ala
Lys 545 550 555 560 Asp Val Arg Arg Ile Met Gly Phe Asp Glu Val Lys
Gln 565 570
[0045] The present invention also relates to the S. aureus dnaX
gene. This S. aureus dnaX gene has a partial nucleotide sequence as
follows (SEQ. ID. No. 3): TABLE-US-00003 TTGAATTATC AAGCCTTATA
TCGTATGTAC AGACCCCAAA GTTTCGAGGA TCTCGTCGGA 60 CAAGAACATG
TCACGAAGAC ATTGCGCAAT GCGATTTCGA AAGAAAAACA GTCGGATGCA 120
TATATTTTTA GTGGTCCGAG AGGTACGGGG AAAACGAGTA TTGCCAAAGT GTTTGCTAAA
180 GCAATCAACT GTTTAAATAG CACTGATGGA GAACCTTGTA ATGAATGTCA
TATTTGTAAA 240 GGCATTACGC AGGGGACTAA TTCAGATGTG ATAGAAATTG
ATGCTCCTAC TAATAATGGC 300 GTTGATGAAA TAAGAAATAT TAGAGACAAA
GTTAAATATG CACCAAGTGA ATCGAAATAT 360 AAAGTTTATA TTATAGATGA
GGTGCACATG CTAACAACAG GTGCTTTTAA TGCCCTTTTA 420 AAGACGTTAG
AAGAACCTCC AGCACACGCT ATTTTTATAT TGGCAACGAC AGAACCACAT 480
AAAATCCCTC CAACAATCAT TTCTAGGGCA CAACGTTTTG ATTTTAAAGC AATTAGCCTA
540 CATCAAATTG TTCAACGTTT AAAATTTGTA GCAGATGCAC AACAAATTGA
ATGTGAAGAT 600 GAAGCCTTGG CATTTATCGC TAAAGCGTCT GAAGGGGGTA
TGCGTGATGC ATTAAGTATT 660 ATGGATCAGG CTATTGCTTT CGGCGATGGC
ACATTGACAT TACAAGATGC CCTAAATGTT 720 ACGGGTAGCG TTCATGATGA
AGCGTTGGAT CACTTGTTTG ATGATATTGT ACAAGGTGAC 780 GTACAAGCAT
CTTTTAAAAA ATACCATCAG TTTATAACAG AAGGTAAAGA AGTGAATCGC 840
CTAATAAATG ATATGATTTA TTTTGTCAGA GATACGATTA TGAATAAAAC ATCTGAGAAA
900 GATACTGAGT ATCGAGCACT GATGAACTTA GAATTAGATA TGTTATATCA
AATCATTGAT 960 CTTATTAATG ATACATTAGT GTCGATTCGT TTTAGTGTGA
ATCAAAACGT TCATTTTGAA 1020 GTATTGTTAG TAAAATTAGC TGAGCAGATT
AAGGGTCAAC CACAAGTGAT TGCGAATGTA 1080 GCTGAACCAG CACAAATTGC
TTCATCGCCA AACACAGATG TATTGTTGCA ACGTATGGAA 1140 CAGTTACAGC
AAGAACTAAA AACACTAAAA GCACAAGGAG TGAGTGTTGC TCCTACTCAA 1200
AAATCTTCGA AAAAGCCTGC GAGAGGTATA CAAAAATCTA AAAATGCATT TTCAATGCAA
1260 CAAATTGCAA AAGTGCTAGA TAAACCGAAT AAGGCAGATA TCAAATTGTT
GAAAGATCAT 1320 TGGCAAGAAG TGATTGACCA TGCCCAAAAC AATGATAAAA
AATCACTCGT TAGTTTATTG 1380 CAAAATTCGG AACCTGTGGC GGCAAGTGAA
GATCACGTCC TTGTGAAATT TGAGGAAGAG 1440 ATCCATTGTG AAATCGTCAA
TAAAGACGAC GACAAACGTA GTAGTATAGA AAGTGTTGTA 1500 TGTAATATCG
TTAATAAAAA CGTTAAAGTT GTTGGTGTAC CATCAGATCA ATCGCAAAGA 1560
GTTCGAACGG AGTATTTACA AAATCGTAAA AACGAAGGCG ATGATATGCC AAAGCAACAA
1620 GCACAACAAA CAGATATTGC TCAAAAAGCA AAAGATCTTT TCGGTGAAGA
AACTGTACAT 1680 GTGATAGATG AAGAGTGA 1698
[0046] The S. aureus dnaX protein (i.e. the gamma subunit/tau
subunit) has a partial amino acid sequence as follows (SEQ. ID. No.
4): TABLE-US-00004 Leu Asn Tyr Gln Ala Leu Tyr Arg Met Tyr Arg Pro
Gln Ser Phe Glu 1 5 10 15 Asp Val Val Gly Gln Glu His Val Thr Lys
Thr Leu Arg Asn Ala Ile 20 25 30 Ser Lys Glu Lys Gln Ser His Ala
Tyr Ile Phe Ser Gly Pro Arq Gly 35 40 45 Thr Gly Lys Thr Ser Ile
Ala Lys Val Phe Ala Lys Ala Ile Asn Cys 50 55 60 Leu Asn Ser Thr
Asp Gly Glu Pro Cys Asn Glu Cys His Ile Cys Lys 65 70 75 80 Gly Ile
Thr Gln Gly Thr Asn Ser Asp Val Ile Glu Ile Asp Ala Ala 85 90 95
Ser Asn Asn Gly Val Asp Glu Ile Arg Asn Ile Arg Asp Lys Val Lys 100
105 110 Tyr Ala Pro Ser Glu Ser Lys Tyr Lys Val Tyr Ile Ile Asp Glu
Val 115 120 125 His Met Leu Thr Thr Gly Ala Phe Asn Ala Leu Leu Lys
Thr Leu Glu 130 135 140 Glu Pro Pro Ala His Ala Ile Phe Ile Leu Ala
Thr Thr Glu Pro His 145 150 155 160 Lys Ile Pro Pro Thr Ile Ile Ser
Arg Ala Gln Arg Phe Asp Phe Lys 165 170 175 Ala Ile Ser Leu Asp Gln
Ile Val Glu Arg Leu Lys Phe Val Ala Asp 180 185 190 Ala Gln Gln Ile
Glu Cys Glu Asp Glu Ala Leu Ala Phe Ile Ala Lys 195 200 205 Ala Ser
Glu Gly Gly Met Arg Asp Ala Leu Ser Ile Met Asp Gln Ala 210 215 220
Ile Ala Phe Gly Asp Gly Thr Leu Thr Leu Gln Asp Ala Leu Asn Val 225
230 235 240 Thr Gly Ser Val His Asp Glu Ala Leu Asp His Leu Phe Asp
Asp Ile 245 250 255 Val Gln Gly Asp Val Gln Ala Ser Phe Lys Lys Tyr
His Gln Phe Ile 260 265 270 Thr Glu Gly Lys Glu Val Asn Arg Leu Ile
Asn Asp Met Ile Tyr Phe 275 280 285 Val Arg Asp Thr Ile Met Asn Lys
Thr Ser Glu Lys Asp Thr Glu Tyr 290 295 300 Arg Ala Leu Met Asn Leu
Glu Leu Asp Met Leu Tyr Gln Met Ile Asp 305 310 315 320 Leu Ile Asn
Asp Thr Leu Val Ser Ile Arg Phe Ser Val Asn Gln Asn 325 330 335 Val
His Phe Glu Val Leu Leu Val Lys Leu Ala Glu Gln Ile Lys Gly 340 345
350 Gln Pro Gln Val Ile Ala Asn Val Ala Glu Pro Ala Gln Ile Ala Ser
355 360 365 Ser Pro Asn Thr Asp Val Leu Leu Gln Arg Met Glu Gln Leu
Glu Gln 370 375 380 Glu Leu Lys Thr Leu Lys Ala Gln Gly Val Ser Val
Ala Pro Thr Gln 385 390 395 400 Lys Ser Ser Lys Lys Pro Aia Arg Gly
Ile Gln Lys Ser Lys Asn Ala 405 410 415 Phe Ser Met Gln Gln Ile Ala
Lys Val Leu Asp Lys Ala Asn Lys Ala 420 425 430 Asp Ile Lys Leu Leu
Lys Asp His Trp Gln Glu Val Ile Asp His Ala 435 440 445 Gln Asn Asn
Asp Lys Lys Ser Leu Val Ser Leu Leu Gln Asn Ser Glu 450 455 460 Pro
Val Ala Ala Ser Glu Asp His Val Leu Val Lys Phe Glu Glu Glu 465 470
475 480 Ile His Cys Glu Ile Val Asn Lys Asp Asp Glu Lys Arg Ser Ser
Ile 485 490 495 Glu Ser Val Val Cys Asn Ile Val Asn Lys Asn Val Lys
Val Val Gly 500 505 510 Val Pro Ser Asp Gln Trp Gln Arg Val Arg Thr
Glu Tyr Leu Gln Asn 515 520 525 Arg Lys Asn Glu Gly Asp Asp Met Pro
Lys Gln Gln Ala Gln Gln Thr 530 535 540 Asp Ile Ala Gln Lys Ala Lys
Asp Leu Phe Gly Glu Glu Thr Val His 545 550 555 560 Val Ile Asp Glu
Glu Glx 565
[0047] This invention also relates to the partial nucleotide
sequence of the S. aureus dnaB gene as follows (SEQ. ID. No. 5):
TABLE-US-00005 ATGGATAGAA TGTATGAGCA AAATCAAATG CCGCATAACA
ATGAAGCTGA ACAGTCTGTC 60 TTAGGTTCAA TTATTATAGA TCCAGAATTG
ATTAATACTA CTCAGGAAGT TTTGCTTCCT 120 GAGTCGTTTT ATAGGGGTGC
CCATCAACAT ATTTTCCGTG CAATGATGCA CTTAAATGAA 180 CATAATAAAG
AAATTGATGT TGTAACATTG ATGGATCAAT TATCGACGGA AGGTACGTTG 240
AATGAAGCGC GTGGCCCGCA ATATCTTGCA GAGTTATCTA CAAATGTACC AACGACGCGA
300 AATGTTCAGT ATTATACTGA TATCGTTTCT AAGCATGCAT TAAAACGTAG
ATTGATTCAA 360 ACTGCAGATA GTATTGCCAA TGATGGATAT AATGATCAAC
TTGAACTAGA TGCGATTTTA 420 AGTGATGCAG AACGTCGAAT TTTAGAGCTA
TCATCTTCTC GTGAAAGCGA TGGCTTTAAA 480 GACATTCGAG ACGTCTTAGC
ACAAGTGTAT GAAACACCTG AAGAGCTTGA TCAAAATAGT 540 GGTCAAACAC
CAGCTATACC TACAGGATAT CGAGATTTAG ACCAAATGAC AGCAGGGTTC 600
AACCGAAATG ATTTAATTAT CCTTGCAGCG CGTCCATCTG TAGGTAAGAC TGCGTTCCCA
660 CTTAATATTG CACAAAAAGT TGCAACGCAT GAAGATATGT ATACAGTTAA
AAGCAACAGG 720 AAGTTTCTGA AATCTCTCGT ACATTAAAAG CATTAGCCCG
TGAATTAAAA TGTCCACTTA 780 TCGCATTAAG TCAGTTATCT CGTGGTGTTG
AACAACGACA AGATAAACGT CCAATGATGA 840 GTGATATTCG TGAATCTGGT
TCGATTGAGC AAGATGCCGA TATCGTTGCA TTCTTATACC 900 GTGATGATTA
CTATAACCGT GGCGGCGATG AAGATGATGA CGATGATGGT GGTTTCGAGC 960
CACAAACGAA TGATGAAAAC GGTGAAATTG AAATTATCAT TGTTAACCAA CGTAACGGTC
1020 CAACAGGCAC AGTTAAGTTA CATTTTATGA AACAATATAA TAAATTTTAG
AGCTATCATC 1080 TTTTCGTGAA AGCGATGGCT TTAAAGACAT TCGAGACGTC
TTAGGACAAG TGTATGAAAC 1140 AGCTGAAGAG CTTGATCAAA ATAGTGGTGA
AACACCAGGT ATACCTACAG GATATCGAGA 1200 TTTAGACCAA ATOACAGGAG
GGTTCAACCG AAATGATTTA ATTATCCTTG CAGCGCGTCC 1260 ATCTGTAGGT
AAGACTGCGT TCGCACTTAA TATTGCACAA AAAGTTGCAA CGCATCCGCA 1320
CTTAATATTG CCAATAAGTT GGAACGCATG AAGATATATC TAGCAGTTGG TATTTTCTCA
1380 CTAGAGATGG GTGCTGATCA GTTAACCACA CGTATGATTT GTAGTTCTGG
TAATGTTGAC 1440 TCAAACCGCT TAAGAACCGG TACTATGACT GAGGAAGATT
GGAGTCGTTT TACTATAGCG 1500 CTTGCTAAAT TATCACGTAC GAAGATTTTT
ATTGATGATA CACCGGGTAT TCGAATTAAT 1560 GATTTACGTT CTAAATGTCG
TCGATTAAAG CAAGAACATG GCTTAGACAT CATTGTGATT 1620 GACTACTTAC
AGTTGATTCA AGGTAGTGGT TCACGTGCGT CCGATAACAC ACAACAGGAA 1680
GTTTCTGAAA TCTCTCGTAC ATTAAAAGCA TTAGCCCGTG AATTAAAATG TCCAGTTATC
1740 GCATTAAGTC AGTTATCTCG TGGTGTTGAA CAACGACAAG ATAAACGTCC
AATGATGAGT 1800 GATATTCGTG AATCTGGTTC GATTGAGCAA GATGCCGATA
TCGTTGCATT CTTATACCGT 1860 GATGATTACT ATAACCGTGG CGGCGATGAA
GATGATGACG ATGATGGTGG TTTCGAGCCC 1920 CAAACGAATG ATGAAAACGG
TGAAATTGAA ATTATCATTG CTAAGCAACG TTACGGTCCA 1980 ACAGGCACAG
TTAAGTTACT TTTTATGAAA CAATATGGTA AATTTACCGA TATC 2034
[0048] The amino acid sequence of S. aureus DnaB encoded by the
dnaB gene is as follows (SEQ. ID. No. 6): TABLE-US-00006 Met Asp
Arg Met Tyr Glu Gln Asn Gln Met Pro His Asn Asn Glu Ala 1 5 10 15
Glu Gln Ser Val Leu Gly Ser Ile Ile Ile Asp Pro Glu Leu Ile Asn 20
25 30 Thr Thr Gln Glu Val Leu Leu Pro Glu Ser Phe Tyr Arg Gly Ala
His 35 40 45 Gln His Ile Phe Arg Ala Met Met His Leu Asn Glu Asp
Asn Lys Glu 50 55 60 Ile Asp Val Val Thr Leu Met Asp Gln Leu Ser
Thr Glu Gly Thr Leu 65 70 75 80 Asn Glu Ala Gly Gly Pro Gln Tyr Leu
Ala Glu Leu Ser Thr Asn Val 85 90 95 Pro Thr Thr Arg Asn Val Gln
Tyr Tyr Thr Asp Ile Val Ser Lys His 100 105 110 Ala Leu Lys Arg Arg
Leu Ile Gln Thr Ala Asp Ser Ile Ala Asn Asp 115 120 125 Gly Tyr Asn
Asp Glu Leu Glu Leu Asp Ala Ile Leu Ser Asp Ala Glu 130 135 140 Arg
Arg Ile Leu Glu Leu Ser Ser Ser Arg Glu Ser Asp Gly Phe Lys 145 150
155 160 Asp Ile Arq Asp Val Leu Gly Gln Val Tyr Glu Thr Ala Glu Glu
Leu 165 170 175 Asp Gln Asn Ser Gly Gln Thr Pro Gly Ile Pro Thr Gly
Tyr Arg Asp 180 185 190 Leu Asp Gln Met Thr Ala Gly Phe Asn Arg Asn
Asp Leu Ile Ile Leu 195 200 205 Ala Ala Arg Pro Ser Val Gly Lys Thr
Ala Phe Ala Leu Asn Ile Ala 210 215 220 Gln Lys Leu Glu Arg Met Lys
Ile Tyr Leu Ala Val Gly Ile Phe Ser 225 230 235 240 Leu Glu Met Gly
Ala Asp Gln Leu Thr Thr Arg Met Ile Cys Ser Ser 245 250 255 Gly Asn
Val Asp Ser Asn Arg Leu Arg Thr Gly Thr Met Thr Glu Glu 260 265 270
Asp Trp Ser Arg Phe Thr Ile Ala Val Gly Lys Leu Ser Arg Thr Lys 275
280 285 Ile Phe Ile Asp Asp Thr Pro Gly Ile Arg Ile Asn Asp Leu Arg
Ser 290 295 300 Lys Cys Arg Arg Leu Lys Gln Glu His Gly Leu Asp Met
Ile Val Ile 305 310 315 320 Asp Tyr Leu Gln Leu Ile Gln Gly Ser Gly
Ser Arg Aia Ser Asp Asn 325 330 335 Arg Gln Gln Glu Val Ser Glu Ile
Ser Arg Thr Leu Lys Ala Leu Ala 340 345 350 Arg Glu Leu Lys Cys Pro
Val Ile Ala Leu Ser Gln Leu Ser Arg Gly 355 360 365 Val Glu Gln Arg
Gln Asp Lys Arg Pro Met Met Ser Asp Ile Arg Glu 370 375 380 Ser Gly
Ser Ile Glu Gln Asp Aia Asp Ile Val Ala Phe Leu Tyr Arg 385 390 395
400 Asp Asp Tyr Tyr Asn Arg Gly Gly Asp Glu Asp Asp Asp Asp Asp Gly
405 410 415 Gly Phe Glu Pro Gln Thr Asn Asp Glu Asn Gly Glu Ile Glu
Ile Ile 420 425 430 Ile Ala Lys Gln Arg Tyr Gly Pro Gly Thr Val Lys
Leu Leu Phe Met 435 440 445 Lys Gln Tyr Gly Lys Phe Thr Asp Ile 450
455
[0049] The present invention also uses the gene sequence of S.
aureus PolC (encoding Pol III-L). The nucleotide sequence is as
follows (SEQ. ID. No. 7): TABLE-US-00007 ATGACAGAGC AACAAAAATT
TAAAGTGCTT GCTGATCAAA TTAAAATTTC AAATCAATTA 60 GATGCTGAAA
TTTTAAATTC ACGTGAACTG ACACGTATAG ATGTTTCTAA CAAAAACAGA 120
ACATGGCAAT TTCATATTAC ATTACCACAA TTCTTAGCTC ATCAAGATTA TTTATTATTT
180 ATAAATGCAA TAGAGCAAGA GTTTAAACAT ATCGCCAACG TTACATGTCG
TTTTACGGTA 240 ACAAATGGCA CGAATCAAGA TGAACATGCA ATTAAATACT
TTGGGCACTG TATTGACCAA 300 ACAGCTTTAT CTCCAAAACT TAAAGGTCAA
TTGAAACAGA AAAAGCTTAT TATCTCTGGA 360 AAAGTATTAA AAGTAATGGT
ATCAAATGAC ATTGAACGTA ATCATTTTGA TAAGGCATGT 420 AATGGAAGTC
TTATCAAAGC GTTTAGAAAT TGTGGTTTTG ATATCGATAA AATCATATTC 480
GAAACAAATG ATAATGATCA AGAACAAAAC TTAGCTTCTT TACAAGCACA TATTCAAGAA
540 CAAGACGAAC AAAGTGCACC ATTGGCAACA GAGAAACTTC AAAAAATGAA
AGCTGAAAAA 600 GCGAAACAAC AAGATAACAA GCAAAGTGCT GTCCATAAGT
GTCAAATTGG TAAGCCGATT 660 CAAATTGAAA ATATTAAACC AATTGAATCT
ATTATTGAGG AAGAGTTTAA AGTTGCAATA 720 GAGGGTGTCA TTTTTGATAT
AAACTTAAAA GAACTTAAAA GTGGTCGCCA TATCGTAGAA 780 ATTAAAGTGA
CTGACTATAC GGACTCTTTA GTTTTAAAAA TGTTTACTCG TAAAAACAAA 840
GATGATTTAC AACATTTTAA AGCGCTAAGT GTTGGTAAAT GGGTTAGGGC TCAAGGTCGT
900 ATTGAAGAAG ATACATTTAT TAGAGATTTA GTTATGATGA TGTCTGATAT
TGAAGAGATT 960 AAAAAAGCGA CAAAAAAAGA TAAGCCTGAA GAAAAGCGAG
TAGAATTCCA CTTGCATACT 1020 GCAATGAGCC AAATGGATGG TATACCCAAT
ATTGGTGCGT ATGTTAAACA GGCAGCACAC 1080 TGGGGACATC CAGCCATTGC
GGTTACAGAC CATAATGTGG TGCAAGCATT TCCAGATGCT 1140 CACGCAGCAG
CGGAAAAACA TGGCATTAAA ATGATATACG GTATGGAAGG TATGTTAGTT 1200
GATGATGGTG TTCCGATTGC ATACAAACCA CAAGATGTCG TATTAAAAGA TGCTACTTAT
1260 GTTGTGTTCG ACGTTGAGAC AACTGGTTTA TCAAATCAGT ATGATAAAAT
CATCGAGCTT 1320 GCAGCTGTGA AAGTTCATAA CGGTGAAATC ATCGATAAGT
TTGAAAGGTT TAGTAATCCG 1380 CATCAACGAT TATCGGAAAC GATTATCAAT
TTGACGCATA TTACTGATGA TATGTTAGTA 1440 GATGCCCCTG AGATTGAAGA
AGTACTTACA GAGTTTAAAG AATGGGTTGG CGATGCGATA 1500 TTCGTAGCGC
ATAATGCTTC GTTTGATATG GGCTTCATCG ATACGGGATA TGAACGTCTT 1560
GGGTTTGGAC CATCAACGAA TGGTGTTATC GATACTTTAG AATTATCTCG TACGATTAAT
1620 ACTGAATATG GTAAACATGG TTTGAATTTC TTGGCTAAAA AATATGGCGT
AGAATTAACG 1680 CAACATCACC GTGCCATTTA TGATACAGAA GCAACAGCTT
ACATTTTCAT AAAAATGGTT 1740 CAACAAATGA AAGAATTAGG CGTATTAAAT
CATAACGAAA TCAACAAAAA ACTCAGTAAT 1800 GAAGATGCAT ATAAACGTGC
AAGACCTAGT CATGTCACAT TAATTGTACA AAACCAACAA 1860 GGTCTTAAAA
ATCTATTTAA AATTGTAAGT GCATCATTGG TGAAGTATTT CTACCGTACA 1920
CCTCGAATTC CACGTTCATT GTTAGATGAA TATCGTGAGG GATTATTGGT AGGTACAGCG
1980 TGTGATGAAG GTGAATTATT TACGGCAGTT ATGCAGAAGG ACCAGAGTCA
AGTTGAAAAA 2040 ATTGCCAAAT ATTATGATTT TATTGAAATT CAACCACCGG
CACTTTATCA AGATTTAATT 2100 GATAGAGAGC TTATTAGAGA TACTGAAACA
TTACATGAAA TTTATCAACG TTTAATACAT 2160 GCAGGTGACA CAGCGGGTAT
ACCTGTTATT GCGACAGGAA ATGCACACTA TTTGTTTGAA 2220 CATGATGGTA
TCGCACGTAA AATTTTAATA GCATCACAAC CCGGCAATCC ACTTAATCGC 2280
TCAACTTTAC CGGAAGCACA TTTTAGAACT ACAGATGAAA TGTTAAACGA GTTTCATTTT
2340 TTAGGTGAAG AAAAAGCGCA TGAAATTGTT GTGAAAAATA CAAACGAATT
AGCAGATCGA 2400 ATTGAACGTG TTGTTCCTAT TAAAGATGAA TTATACACAC
CGCGTATGGA AGGTGCTAAC 2460 GAAGAAATTA CAGAACTAAG TTATGCAAAT
GCGCGTAAAC TGTATGGTGA AGACCTGCCT 2520 CAAATCGTAA TTGATCGATT
AGAAAAAGAA TTAAAAAGTA TTATCGCTAA TGCATTTGCG 2580 GTAATTTACT
TAATTTCGCA ACGTTTAGTT AAAAAATCAT TAGATGATGG ATACTTAGTT 2640
GGTTCCCGTG GTTCAGTAGG TTCTAGTTTT CTAGCGACAA TGACTGAGAT TACTGAAGTA
2700 AACCCGTTAC CGCCACACTA TATTTGTCCG AACTGTAAAA CGAGTGAATT
TTTCAATGAT 2760 GGTTCAGTAG GATCAGCATT TGATTTACCT GATAAGACGT
GTGAAACTTG TGGACCGCCA 2820 CTTATTAAAG AAGGACAAGA TATTCCGTTT
GAAAAATTTT TAGGATTTAA GGGAGATAAA 2880 GTTCCTGATA TCGACTTAAA
CTTTAGTGGT GAATATCAAC CGAATGCCCA TAACTACACA 2940 AAAGTATTAT
TTGGTGAGGA TAAAGTATTC CGTGCAGGTA CAATTGGTAC TGTTGCTGAA 3000
AAGACTGCTT TTGGTTATGT TAAAGGTTAT TTGAATGATC AACGTATCCA CAAAAGAGGT
3060 GCTGAAATAG ATCGACTCGT TAAAGGATGT ACAGGTGTAC CTGATTACAT
GGATATTTAT 3120 GATTTTACGC CGATACAATA TCCTGCCGAT GATCAAAATT
CAGCATGGAT GACGACACAT 3180 TTTGATTTCC ATTCTATTCA TGATAATGTA
TTAAAACTTG ATATACTTGG ACACGATCAT 3240 CCAACAATGA TTCGTATGCT
TCAAGATTTA TCAGCAATTG ATCCAAAAAC AATACCTGTA 3300 GATGATAAAG
AAGTTATGCA GATATTTAGT ACACCTGAAA GTTTGGGTCT TACTGAAGAT 3360
GAAATTTTAT GTAAAACAGG TACATTTCGG GTACCGAATT CGGACAGGAT TCGTCGTCAA
3420 ATGTTAGAAG ATACAAAGCC AACAACATTT TCTGAATTAG TTCAAATCTC
AGGATTATCT 3480 CATGGTACAC ATGTGTGGTT AGGCAATGCT CAAGAATTAA
TTAAAACCGG TATATGTGAT 3540 TTATCAAGTG TAATTGGTTG TCGTGATGAT
ATCATGGTTT ATTTAATGTA TGCTGGTTTA 3600 GAACCATCAA TGGCTTTTAA
AATAATGGAG TCAGTACGTA AAGGTAAACG TTTAACTGAA 3660 GAAATGATTG
AAACGATGAA AGAAAATGAA GTGCCAGATT GGTATTTACA TTCATGTCTT 3720
AAAATTAAGT ACATATTCCC TAAAGCCCAT GCAGCAGCAT ACGTTTTAAT GGCAGTACCT
3780 ATCGCATATT TCAAAGTACA TCATCCACTT TATTACTATG CATCTTACTT
TACAATTCGT 3840 GCGTCAGACT TTGATTTAAT CACGATGATT AAAGATAAAA
CAAGCATTCG AAATACTGTA 3900 AAAGACATGT ATTCTCGCTA TATGGATCTA
GGTAAAAAAG AAAAAGACGT ATTAACAGTC 3960 TTGGAAATTA TGAATGAAAT
GGCGCATCGA GGTTATCGAA TGCAACCGAT TAGTTTAGAA 4020 AAGAGTCAGG
CGTTCGAATT TATCATTGAA GGCGATACAC TTATTCCGCC GTTCATATCA 4080
GTGCCTGGGC TTGGCGAAAA CGTTGCGAAA CGAATTGTTG AAGCTCGTGA CGATGGCCCA
4140 TTTTTATCAA AAGAAGATTT AAACAAAAAA GCTGGATTAT ATCAGAAAAT
TATTGAGTAT 4200 TTAGATGAGT TAGGCTCATT ACCGAATTTA CCAGATPAAC
CTCAACTTTC GATATTTGAT 4260 ATGTAA 4266
[0050] The amino acid sequence of the S. aureus PolC gene product,
Pol III-L is as follows (SEQ. ID. No. 8): TABLE-US-00008 Met Thr
Glu Gln Gln Lys Phe Lys Val Leu Ala Asp Gln Ile Lys Ile 1 5 10 15
Ser Asn Gln Leu Asp Ala Glu Ile Leu Asn Ser Gly Glu Leu Thr Arg 20
25 30 Ile Asp Val Ser Asn Lys Asn Arg Thr Trp Glu Phe His Ile Thr
Leu 35 40 45 Pro Gln Phe Leu Ala His Glu Asp Tyr Leu Leu Phe Ile
Asn Ala Ile 50 55 60 Glu Gln Glu Phe Lys Asp Ile Ala Asn Val Thr
Cys Arg Phe Thr Val 65 70 75 80 Thr Asn Gly Thr Asn Gln Asp Glu His
Ala Ile Lys Tyr Phe Gly His 85 90 95 Cys Ile Asp Gln Thr Ala Leu
Ser Pro Lys Val Lys Gly Gln Leu Lys 100 105 110 Gln Lys Lys Leu Ile
Met Ser Gly Lys Val Leu Lys Val Met Val Ser 115 120 125 Asn Asp Ile
Glu Arg Asn His Phe Asp Lys Ala Cys Asn Gly Ser Leu 130 135 140 Ile
Lys Ala Phe Arg Asn Cys Gly Phe Asp Ile Asp Lys Ile Ile Phe 145 150
155 160 Glu Thr Asn Asp Asn Asp Gln Glu Gln Asn Leu Ala Ser Leu Glu
Ala 165 170 175 His Ile Gln Glu Glu Asp Glu Gln Ser Ala Arg Leu Ala
Thr Glu Lys 180 185 190 Leu Glu Lys Met Lys Ala Glu Lys Ala Lys Gln
Gln Asp Asn Lys Gln 195 200 205 Ser Ala Val Asp Lys Cys Gln Ile Gly
Lys Pro Ile Gln Ile Glu Asn 210 215 220 Ile Lys Pro Ile Glu Ser Ile
Ile Glu Glu Glu Phe Lys Val Ala Ile 225 230 235 240 Glu Gly Val Ile
Phe Asp Ile Asn Leu Lys Glu Leu Lys Ser Gly Arg 245 250 255 His Ile
Val Glu Ile Lys Val Thr Asp Tyr Thr Asp Ser Leu Val Leu 260 265 270
Lys Met Phe Thr Arg Lys Asn Lys Asp Asp Leu Glu His Phe Lys Ala 275
280 285 Leu Ser Val Gly Lys Trp Val Arg Ala Gln Gly Arg Ile Glu Glu
Asp 290 295 300 Thr Phe Ile Arg Asp Leu Val Met Met Met Ser Asp Ile
Glu Glu Ile 305 310 315 320 Lys Lys Ala Thr Lys Lys Asp Lys Ala Glu
Glu Lys Arg Val Glu Phe 325 330 335 His Leu His Thr Ala Met Ser Gln
Met Asp Gly Ile Pro Asn Ile Gly 340 345 350 Ala Tyr Val Lys Gln Ala
Ala Asp Trp Gly His Pro Ala Ile Ala Val 355 360 365 Thr Asp His Asn
Val Val Gln Ala Phe Pro Asp Ala His Ala Ala Ala 370 375 380 Glu Lys
His Gly Ile Lys Met Ile Tyr Gly Met Glu Gly Met Leu Val 385 390 395
400 Asp Asp Gly Val Pro Ile Ala Tyr Lys Pro Gln Asp Val Val Leu Lys
405 410 415 Asp Ala Thr Tyr Val Val Phe Asp Val Glu Thr Thr Gly Leu
Ser Asn 420 425 430 Gln Tyr Asp Lys Ile Ile Glu Leu Ala Ala Val Lys
Val His Asn Gly 435 440 445 Glu Ile Ile Asp Lys Phe Glu Arg Phe Ser
Asn Pro His Glu Arg Leu 450 455 460 Ser Glu Thr Ile Ile Asn Leu Thr
His Ile Thr Asp Asp Met Leu Val 465 470 475 480 Asp Ala Pro Glu Ile
Glu Glu Val Leu Thr Glu Phe Lys Glu Trp Val 485 490 495 Gly Asp Ala
Ile Phe Val Ala His Asn Ala Ser Phe Asp Met Gly Phe 500 505 510 Ile
Asp Thr Gly Tyr Glu Arg Leu Gly Phe Gly Pro Ser Thr Asn Gly 515 520
525 Val Ile Asp Thr Leu Glu Leu Ser Arg Thr Ile Asn Thr Glu Tyr Gly
530 535 540 Lys His Gly Leu Asn Phe Leu Ala Lys Lys Tyr Gly Val Glu
Leu Thr 545 550 555 560 Gln His His Arg Ala Ile Tyr Asp Thr Glu Ala
Thr Ala Tyr Ile Phe 565 570 575 Ile Lys Met Val Gln Gln Met Lys Glu
Leu Gly Val Leu Asn His Asn 580 585 590 Glu Ile Asn Lys Lys Leu Ser
Asn Glu Asp Ala Tyr Lys Arg Ala Arg 595 600 605 Pro Ser His Val Thr
Leu Ile Val Gln Asn Gln Gln Gly Leu Lys Asn 610 615 620 Leu Phe Lys
Ile Val Ser Ala Ser Leu Val Lys Tyr Phe Tyr Arg Thr 625 630 635 640
Pro Arg Ile Pro Arg Ser Leu Leu Asp Glu Tyr Arg Glu Gly Leu Leu 645
650 655 Val Gly Thr Ala Cys Asp Glu Gly Glu Leu Phe Thr Ala Val Met
Gln 660 665 670 Lys Asp Gln Ser Gln Val Glu Lys Ile Ala Lys Tyr Tyr
Asp Phe Ile 675 680 685 Glu Ile Gln Pro Pro Ala Leu Tyr Gln Asp Leu
Ile Asp Arg Glu Leu 690 695 700 Ile Arg Asp Thr Glu Thr Leu His Glu
Ile Tyr Gln Arg Leu Ile His 705 710 715 720 Ala Gly Asp Thr Ala Gly
Ile Pro Val Ile Ala Thr Gly Asn Ala His 725 730 735 Tyr Leu Phe Glu
His Asp Gly Ile Ala Arg Lys Ile Leu Ile Ala Ser 740 745 750 Gln Pro
Gly Asn Pro Leu Asn Arg Ser Thr Leu Pro Glu Ala His Phe 755 760 765
Arg Thr Thr Asp Glu Met Leu Asn Glu Phe His Phe Leu Gly Glu Glu 770
775 780 Lys Ala His Glu Ile Val Val Lys Asn Thr Asn Glu Leu Ala Asp
Arg 785 790 795 800 Ile Glu Arg Val Val Pro Ile Lys Asp Glu Leu Tyr
Thr Pro Arg Met 805 810 815 Glu Gly Ala Asn Glu Glu Ile Arg Glu Leu
Ser Tyr Ala Asn Ala Arg 820 825 830 Lys Leu Tyr Gly Glu Asp Leu Pro
Gln Ile Val Ile Asp Arg Leu Glu 835 840 845 Lys Glu Leu Lys Ser Ile
Ile Gly Asn Gly Phe Ala Val Ile Tyr Leu 850 855 860 Ile Ser Gln Arg
Leu Val Lys Lys Ser Leu Asp Asp Gly Tyr Leu Val 865 870 875 880 Gly
Ser Arg Gly Ser Val Gly Ser Ser Phe Val Ala Thr Met Thr Glu 885 890
895 Ile Thr Glu Val Asn Pro Leu Pro Pro His Tyr Ile Cys Pro Asn Cys
900 905 910 Lys Thr Ser Glu Phe Phe Asn Asp Gly Ser Val Gly Ser Gly
Phe Asp 915 920 925 Leu Pro Asp Lys Thr Cys Glu Thr Cys Gly Ala Pro
Leu Ile Lys Glu 930 935 940 Gly Gln Asp Ile Pro Phe Glu Lys Phe Leu
Gly Phe Lys Gly Asp Lys 945 950 955 960 Val Pro Asp Ile Asp Leu Asn
Phe Ser Gly Glu Tyr Gln Pro Asn Ala 965 970 975 His Asn Tyr Thr Lys
Val Leu Phe Gly Glu Asp Lys Val Phe Arg Ala 980 985 990 Gly Thr Ile
Gly Thr Val Ala Glu Lys Thr Ala Phe Gly Tyr Val Lys 995 1000 1005
Gly Tyr Leu Asn Asp Gln Gly Ile His Lys Arg Gly Ala Glu Ile Asp
1010 1015 1020 Arg Leu Val Lys Gly Cys Thr Gly Val Arg Ala Thr Thr
Gly Gln His 1025 1030 1035 1040 Pro Gly Gly Ile Ile Val Val Pro Asp
Tyr Met Asp Ile Tyr Asp Phe 1045 1050 1055 Thr Pro Ile Gln Tyr Pro
Ala Asp Asp Gln Asn Ser Ala Trp Met Thr 1060 1065 1070 Thr His Phe
Asp Phe His Ser Ile His Asp Asn Val Leu Lys Leu Asp 1075 1080 1085
Ile Leu Gly His Asp Asp Pro Thr Met Ile Arg Met Leu Gln Asp Leu
1090 1095 1100 Ser Gly Ile Asp Pro Lys Thr Ile Pro Val Asp Asp Lys
Glu Val Met 1105 1110 1115 1120 Gln Ile Phe Ser Thr Pro Glu Ser Leu
Gly Val Thr Glu Asp Glu Ile 1125 1130 1135 Leu Cys Lys Thr Gly Thr
Phe Gly Val Pro Asn Ser Asp Arg Ile Arg 1140 1145 1150 Arg Gln Met
Leu Glu Asp Thr Lys Pro Thr Thr Phe Ser Glu Leu Val 1155 1160 1165
Gln Ile Ser Gly Leu Ser His Gly Thr Asp Val Trp Leu Gly Asn Ala
1170 1175 1180 Gln Glu Leu Ile Lys Thr Gly Ile Cys Asp Leu Ser Ser
Val Ile Gly 1185 1190 1195 1200 Cys Arg Asp Asp Ile Met Val Tyr Leu
Met Tyr Ala Gly Leu Glu Pro 1205 1210 1215 Ser Met Ala Phe Lys Ile
Met Gln Ser Val Arg Lys Gly Lys Gly Leu 1220 1225 1230 Thr Glu Glu
Met Ile Glu Thr Met Lys Glu Asn Glu Val Pro Asp Trp 1235 1240 1245
Tyr Leu Asp Ser Cys Leu Lys Ile Lys Tyr Ile Phe Pro Lys Ala His
1250 1255 1260 Ala Ala Ala Tyr Val Leu Met Ala Val Arg Ile Ala Tyr
Phe Lys Val 1265 1270 1275 1280 His His Pro Leu Tyr Tyr Tyr Ala Ser
Tyr Phe Thr Ile Arg Ala Ser 1285 1290 1295 Asp Phe Asp Leu Ile Thr
Met Ile Lys Asp Lys Thr Ser Ile Arg Asn 1300 1305 1310 Thr Val Lys
Asp Met Tyr Ser Arg Tyr Met Asp Leu Gly Lys Lys Glu 1315 1320
1325
Lys Asp Val Leu Thr Val Leu Glu Ile Met Asn Glu Met Ala His Arg
1330 1335 1340 Gly Tyr Arg Met Gln Pro Ile Ser Leu Glu Lys Ser Gln
Ala Phe Glu 1345 1350 1355 1360 Phe Ile Ile Glu Gly Asp Thr Leu Ile
Pro Pro Phe Ile Ser Val Pro 1365 1370 1375 Gly Leu Gly Glu Asn Val
Ala Lys Arg Ile Val Glu Ala Arg Asp Asp 1380 1385 1390 Gly Pro Phe
Leu Ser Lys Glu Asp Leu Asn Lys Lys Ala Gly Leu Tyr 1395 1400 1405
Gln Lys Ile Ile Glu Tyr Leu Asp Glu Leu Gly Ser Leu Pro Asn Leu
1410 1415 1420 Pro Asp Lys Ala Gln Leu Ser Ile Phe Asp Met 1425
1430 1435
[0051] This invention also relates to the sequence of the S. aureus
dnaN gene encoding the beta subunit. The nucleotide sequence is as
follows (SEQ. ID. No.9): TABLE-US-00009 ATGATGGAAT TCACTATTAA
AAGAGATTAT TTTATTACAC AATTAAATGA CACATTAAAA 60 CCTATTTCAC
CAAGAACAAC ATTACCTATA TTAACTGGTA TCAAAATCGA TGCGAAAGAA 120
CATGAAGTTA TATTAACTGG TTCAGACTCT GAAATTTCAA TAGAAATCAC TATTCCTAAA
180 ACTGTAGATG GCGAAGATAT TGTCAATATT TCAGAAACAG GCTCAGTAGT
ACTTCCTGGA 240 CGATTCTTTG TTGATATTAT AAAAAAATTA CCTGGTAAAG
ATGTTAAATT ATCTACAAAT 300 GAACAATTCC AGACATTAAT TACATCAGGT
CATTCTGAAT TTAATTTGAG TGGCTTAGAT 360 CCAGATCAAT ATCCTTTATT
ACCTCAAGTT TCTAGAGATG ACGCAATTCA ATTGTCGGTA 420 AAAGTACTTA
AAAACGTGAT TGCACAAACG AATTTTGCAG TGTCCACCTC AGAAACACGC 480
CCAGTACTAA CTGGTGTGAA CTGGCTTATA CAAGAAAATC AATTAATATG CACAGCGACT
540 GATTCACACC GCTTGGCTGT AAGAAAGTTG CAGTTAGAAG ATGTTTCTGA
AAACAAAAAT 600 GTCATCATTC CAGGTAAGGC TTTAGCTCAA TTAAATAAAA
TTATGTCTGA CAATGAAGAA 660 GACATTGATA TCTTCTTTGC TTCAAACCAA
GTTTTATTTA AAGTTGGAAA TGTGAACTTT 720 ATTTCTCGAT TATTAGAAGG
ACATTATCCT GATACAACAC GTTTATTCCC TGAAAACTAT 780 GAAATTAAAT
TAAGTATAGA CAATCGGGAG TTTTATCATG CGATTGATCG TGCCTCTTTA 840
TTAGCACGTG AAGGTGCTAA TAACGTTATT AAATTAAGTA CAGGTGATGA CGTTGTTGAA
900 TTATCTTCTA CATCACCAGA AATTGGTACT GTAAAAGAAG AAGTTGATGC
AAACGATGTT 960 GAAGGTGGTA GCCTGAAAAT TTCATTCAAC TCTAAATATA
TGATGGATGC TTTAAAAGCA 1020 ATCGATAATG ATGAGGTTGA AGTTGAATTC
TTCGGTACAA TGAAACCATT TATTCTAAAA 1080 CCAAAAGGTG ACGACTCGGT
AACGCAATTA ATTTTACCAA TCAGAACTTA CTAA 1134
[0052] This amino acid sequence of S. aureus beta subunit is as
follows (SEQ. ID. No. 10): TABLE-US-00010 Met Met GILu Phe Thr Ile
Lys Arg Asp Tyr Phe Ile Thr Gln Leu Asn 1 5 10 15 Asp Thr Leu Lys
Ala Ile Ser Pro Arg Thr Thr Leu Pro Ile Leu Thr 20 25 30 Gly Ile
Lys Ile Asp Ala Lys Glu His Glu Val Ile Leu Thr Gly Ser 35 40 45
Asp Ser Glu Ile Ser Ile Glu Ile Thr Ile Pro Lys Thr Val Asp Gly 50
55 60 Glu Asp Ile Val Asn Ile Ser Glu Thr Gly Ser Val Val Leu Pro
Gly 65 70 75 80 Arg Phe Phe Val Asp Ile Ile Lys Lys Leu Pro Gly Lys
Asp Val Lys 85 90 95 Leu Ser Thr Asn Glu Gln Phe Gln Thr Leu Ile
Thr Ser Gly His Ser 100 105 110 Glu Phe Asn Leu Ser Gly Leu Asp Pro
Asp Gln Tyr Pro Leu Leu Pro 115 120 125 Gln Val Ser Arg Asp Asp Ala
Ile Gln Leu Ser Val Lys Val Leu Lys 130 135 140 Asn Val Ile Ala Gln
Thr Asn Phe Aia Val Ser Thr Ser Glu Thr Arg 145 150 155 160 Pro Val
Leu Thr Gly Val Asn Trp Leu Ile Gln Glu Asn Glu Leu Ile 165 170 175
Cys Thr Ala Thr Asp Ser His Arg Leu Ala Val Arg Lys Leu Gln Leu 180
185 190 Glu Asp Val Ser Glu Aso Lys Asn Val Ile Ile Pro Gly Lys Ala
Leu 195 200 205 Ala Glu Leu Asn Lys Ile Met Ser Asp Asn Glu Glu Asp
Ile Asp Ile 210 215 220 Phe Phe Ala Ser Asn Gln Val Leu Phe Lys Val
Gly Asn Val Asn Phe 225 230 235 240 Ile Ser Arg Leu Leu Glu Gly His
Tyr Pro Asp Thr Thr Arg Leu Phe 245 250 255 Pro Glu Asn Tyr Glu Ile
Lys Leu Ser Ile Asp Asn Gly Glu Phe Tyr 260 265 270 His Ala Ile Asp
Arg Ala Ser Leu Leu Ala Arg Glu Gly Gly Asn Asn 275 280 285 Val Ile
Lys Leu Ser Thr Gly Asp Asp Val Val Glu Leu Ser Ser Thr 290 295 300
Ser Pro Glu Ile Gly Thr Val Lys Glu Glu Val Asp Ala Asn Asp Val 305
310 315 320 Glu Gly Gly Ser Leu Lys Ile Ser Phe Asn Ser Lys Tyr Met
Met Asp 325 330 335 Ala Leu Lys Ala Ile Asp Asn Asp Glu Val Glu Val
Gln Phe Phe Gly 340 345 350 Thr Met Lys Pro Phe Ile Leu Lys Pro Lys
Cly Asp Asp Ser Val Thr 355 360 365 Gln Leu Ile Leu Pro Ile Arg Thr
Tyr 370 375
[0053] This invention also relates to the sequence of the S. aureus
dnaG gene encoding a primase. The nucleotide sequence is as follows
(SEQ. ID. No. 11): TABLE-US-00011 ATGATAGGTT TGTGTCCTTT TCATGATGAA
AAGACACCTT CATTTACAGT TTCTGAAGAT 60 AAACAAATCT GTCATTGTTT
TGGTTGTAAA AAAGGTGGCA ATGTTTTTCA ATTTACTCAA 120 GAAATTAAAG
ACATATCATT TGTTGAAGCG GTTAAAGAAT TAGGTGATAG ACTTAATGTT 180
GCTGTAGATA TTGAGGCAAC ACAATCTAAC TCAAATGTTC AAATTGCTTC TGATGATTTA
240 CAAATGATTG AAATGCATGA GTTAATACAA GAATTTTATT ATTACGCTTT
AACAAAGACA 300 GTCGAAGGCG AACAAGCATT AACATACTTA CAAGAACGTG
GTTTTACACA TGCGCTTATT 360 AAAGAGCGAG GCATTGGCTT TGCACCCGAT
AGCTCACATT TTTGTCATGA TTTTCTTCAA 420 AAAAAGGGTT ACGATATTGA
ATTAGCATAT GAAGCCGGAT TATTATCACG TAACGAAGAA 480 AATTTCAGTT
ATTACGATAG ATTTCGAAAT CGTATTATGT TTCCTTTGAA AAATGCGCAA 540
GGAAGAATTG TTGGATATTC AGGTCGAACA TATACCGGTC AAGAACCAAA ATACCTAAAT
600 AGTCCTGAAA CGCCTATCTT TCAAAAAAGA AAGTTGTTAT ATAACTTAGA
TAAAGCACGT 660 AAATCAATTA GAAAATTAGA TGAAATTGTA TTACTAGAAG
GTTTTATGGA TGTTATAAAA 720 TCTGATACTG CTGGCTTGAA AAACGTTGTT
GCAACAATGG GTACACAGTT GTCAGATGAA 780 CATATTACCT TTATACGAAA
GTTAACATCA AATATAACAT TAATGTTTGA TGGGGATTTT 840 CCGGGTAGTG
AAGCAACACT TAAAACAGGT CAACATTTGT TACAGCAAGG GCTAAATGTA 900
TTTGTTATAC AATTGCCATC TGGCATGCAT CCGGATGAAT ACATTGGTAA GTATGGCAAC
960 GACGCATTTA CTACTTTTGT AAAAAATCAC AAAAAGTCAT TTGCACATTA
TAAAGTAAGT 1020 ATATTAAAAG ATGAAATTGC ACATAATGAC CTTTCATATG
AACGTTATTT GAAAGAACTG 1080 AGTCATGACA TTTCACTTAT GAAGTCATCA
ATTCTGCAAC AAAAGGCTAT AAATGATGTT 1140 GCGCCATTTT TCAATGTTAG
TCCTGAGCAG TTAGCTAACG AAATACAATT CAATCAAGCA 1200 CCAGCCAATT
ATTATCCAGA AGATGAGTAT GGCGGTTATG ATGAGTATGG CGGTTATATT 1260
GAACCTGAGC CAATTGGTAT GGCACAATTT GACAATTTGA GCCGTCGAGA AAAAGCGGAG
1320 CGAGCATTTT TAAAACATTT AATGAGAGAT AAAGATACAT TTTTAAATTA
TTATGAAAGT 1380 GTTGATAAGG ATAACTTCAC AAATCAGCAT TTTAAATATG
TATTCGAAGT CTTACATGAT 1440 TTTTATGCGG AAAATGATCA ATATAATATC
AGTGATGCTG TGCAGTATGT TAATTCAAAT 1500 GAGTTGAGAG AAACACTAAT
TAGCTTAGAA CAATATAATT TGAATGGCGA ACCATATGAA 1560 AATGAAATTG
ATGATTATGT CAATGTTATT AATGAAAAAG GACAAGAAAC AATTGAGTCA 1620
TTGAATCATA AATTAAGGGA AGCTACAAGG ATTGGCGATG TAGAATTACA AAAATACTAT
1680 TTACAGCAAA TTGTTGCTAA GAATAAAGAA CGCATGTAG 1719
[0054] The amino acid sequence of primase encoded by S. aureus dnaG
is as follows (SEQ. ID. No. 12): TABLE-US-00012 Met Ile Gly Leu Cys
Pro Phe His Asp Glu Lys Thr Pro Ser Phe Thr 1 5 10 15 Val Ser Glu
Asp Lys Gln Tie Cys His Cys Phe Gly Cys Lys Lys Gly 20 25 30 Gly
Asn Val Phe Gln Phe Thr Gln Glu Ile Lys Asp Ile Ser Phe Val 35 40
45 Glu Ala Val Lys Glu Leu Gly Asp Arg Val Asn Val Ala Val Asp Ile
50 55 60 Glu Ala Thr Gln Ser Asn Ser Asn Val Gln Ile Ala Ser Asp
Asp Leu 65 70 75 80 Gln Met Ile Glu Met His Glu Leu Ile Gln Glu Phe
Tyr Tyr Tyr Ala 85 90 95 Len Thr Lys Thr Val Glu Gly Glu Gln Ala
Leu Thr Tyr Leu Gln Gln 100 105 110 Arg Gly Phe Thr Asp Ala Leu Ile
Lys Glu Arg Gly Ile Gly Phe Ala 115 120 125 Pro Asp Ser Ser His Phe
Cys His Asp Phe Leu Gln Lys Lys Gly Tyr 130 135 140 Asp Ile Glu Len
Ala Tyr Glu Ala Gly Leu Leu Ser Arg Asn Glu Glu 145 150 155 160 Asn
Phe Ser Tyr Tyr Asp Arg Phe Arg Asn Arg Ile Met Phe Pro Leu 165 170
175 Lys Asn Ala Gln Gly Arg Ile Val Gly Tyr Ser Gly Arg Thr Tyr Thr
180 185 190 Gly Gln Glu Pro Lys Tyr Leu Asn Ser Pro Glu Thr Pro Ile
Phe Gln 195 200 205 Lys Arg Lys Leu Leu Tyr Asn Leu Asp Lys Ala Arg
Lys Ser Ile Arg 210 215 220 Lys Leu Asp Glu Ile Val Leu Leu Gln Gly
Phe Met Asp Val Ile Lys 225 230 235 240 Ser Asp Thr Ala Gly Leu Lys
Asn Val Val Ala Thr Met Gly Thr Gln 245 250 255 Leu Ser Asp Gln His
Ile Thr Phe Ile Arg Lys Leu Thr Ser Asn Ile 260 265 270 Thr Leu Met
Phe Asp Gly Asp Phe Ala Gly Ser Gln Ala Thr Leu Lys 275 280 285 Thr
Gly Gln His Leu Leu Gln Gln Gly Leu Asn Val Phe Val Ile Gln 290 295
300 Leu Pro Ser Gly Met Asp Pro Asp Glu Tyr Ile Gly Lys Tyr Gly Asn
305 310 315 320 Asp Ala Phe Thr Thr Phe Val Lys Asn Asp Lys Lys Ser
Phe Ala His 325 330 335 Tyr Lys Val Ser Ile Leu Lys Asp Glu Ile Ala
His Asn Asp Leu Ser 340 345 350 Tyr Glu Arg Tyr Leu Lys Glu Leu Ser
His Asp Ile Ser Leu Met Lys 355 360 365 Ser Ser Ile Leu Gln Gln Lys
Ala Ile Asn Asp Val Ala Pro Phe Phe 370 375 380 Asn Val Ser Pro Glu
Gln Leu Ala Asn Glu Ile Gln Phe Asn Gln Ala 385 390 395 400 Pro Ala
Aso Tyr Tyr Pro Glu Asp Glu Tyr Gly Gly Tyr Asp Glu Tyr 405 410 415
Gly Gly Tyr Ile Glu Pro Glu Pro Ile Gly Met Ala Gln Phe Asp Asn 420
425 430 Leu Ser Arg Arg Glu Lys Ala Glu Arg Ala Phe Leu Lys His Leu
Met 435 440 445 Arg Asp Lys Asp Thr Phe Leu Asn Tyr Tyr Glu Ser Val
Asp Lys Asp 450 455 460 Asn Phe Thr Asn Gln His Phe Lys Tyr Val Phe
Glu Val Leu His Asp 465 470 475 480 Phe Tyr Ala Glu Asn Asp Gln Tyr
Asn Ile Ser Asp Ala Val Gln Tyr 485 490 495 Val Asn Ser Asn Glu Leu
Arg Glu Thr Leu Ile Ser Leu Glu Gln Tyr 500 505 510 Asn Leu Asn Gly
Glu Pro Tyr Glu Asn Glu Ile Asp Asp Tyr Val Asn 515 520 525 Val Ile
Asn Glu Lys Gly Gln Glu Thr Ile Glu Ser Leu Asn His Lys 530 535 540
Leu Arg Glu Ala Thr Arg Ile Gly Asp Val Glu Leu Gln Lys Tyr Tyr 545
550 555 560 Leu Gln Gln Ile Val Ala Lys Asn Lys Glu Arg Met 565
570
[0055] Fragments of the above polypeptides or proteins are also
encompassed by the present invention.
[0056] Suitable fragments can be produced by several means. In the
first, subclones of the gene encoding the protein of the present
invention are produced by conventional molecular genetic
manipulation by subcloning gene fragments. The subclones then are
expressed in vitro or in vivo in bacterial cells to yield a smaller
protein or peptide that can be tested for activity according to the
procedures described below.
[0057] As an alternative, fragments of replication proteins can be
produced by digestion of a full-length replication protein with
proteolytic enzymes like chymotrypsin or Staphylococcus proteinase
A, or trypsin. Different proteolytic enzymes are likely to cleave
replication proteins at different sites based on the amino acid
sequence of the protein. Some of the fragments that result from
proteolysis may be active.
[0058] In another approach, based on knowledge of the primary
structure of the protein, fragments of a replication protein gene
may be synthesized by using the PCR technique together with
specific sets of primers chosen to represent particular portions of
the protein. These then would be cloned into an appropriate vector
for increased expression of a truncated peptide or protein.
[0059] Chemical synthesis can also be used to make suitable
fragments. Such a synthesis is carried out using known amino acid
sequences of replication proteins being produced. Alternatively,
subjecting a full length replication protein to high temperatures
and pressures will produce fragments. These fragments can then be
separated by conventional procedures (e.g., chromatography,
SDS-PAGE).
[0060] Variants may also (or alternatively) be modified by, for
example, the deletion or addition of amino acids that have minimal
influence on the properties, secondary structure, and hydropathic
nature of the polypeptide. For example, a polypeptide may be
conjugated to a signal (or leader) sequence at the N-terminal end
of the protein which cotranslationally or post-translationally
directs transfer of the protein. The polypeptide may also be
conjugated to a linker or other sequence for ease of synthesis,
purification, or identification of the polypeptide.
[0061] Suitable DNA molecules are those that hybridize to a DNA
molecule comprising a nucleotide sequence of 50 continuous bases of
SEQ. ID. Nos. 1, 3, 5, 7, 9, or 11 under stringent conditions such
as those characterized by a hybridization buffer comprising 0.9M
sodium citrate ("SSC") buffer at a temperature of 37.degree. C. and
remaining bound when subject to washing the SSC buffer at a
temperature of 37.degree. C.; and preferably in a hybridization
buffer comprising 20% formamide in 0.9M SSC buffer at a temperature
of 42.degree. C. and remaining bound when subject to washing at
42.degree. C. with 0.2.times.SSC buffer at 42.degree. C.
[0062] The proteins or polypeptides of the present invention are
preferably produced in purified form (preferably at least 80%, more
preferably 90%, pure) by conventional techniques. Typically, the
proteins or polypeptides of the present invention is secreted into
the growth medium of recombinant host cells. Alternatively, the
proteins or polypeptides of the present invention are produced but
not secreted into growth medium. In such cases, to isolate the
protein, the host cell (e.g., E. coli) carrying a recombinant
plasmid is propagated, lysed by sonication, heat, or chemical
treatment, and the homogenate is centrifuged to remove bacterial
debris. The supernatant is then subjected to purification
procedures such as ammonium sulfate precipitation, gel filtration,
ion exchange chromatography, FPLC, and HPLC.
[0063] The DNA molecule encoding replication polypeptides or
proteins derived from Gram positive bacteria can be incorporated in
cells using conventional recombinant DNA technology. Generally,
this involved inserting the DNA molecule into an expression system
to which the DNA molecule is heterologous (i.e. not normally
present). The heterologous DNA molecule is inserted into the
expression system or vector in proper sense orientation and correct
reading frame. The vector contains the necessary elements for the
transcription and translation of the inserted protein-coding
sequences.
[0064] U.S. Pat. No. 4,237,224 to Cohen and Boyer, which is hereby
incorporated by reference, describes the production of expression
systems in the form of recombinant plasmids using restriction
enzyme cleavage and ligation with DNA ligase. These recombinant
plasmids are then introduced by means of transformation and
replicated in unicellular cultures including procaryotic organisms
and eucaryotic cells grown in tissue culture.
[0065] Recombinant genes may also be introduced into viruses, such
as vaccina virus. Recombinant viruses can be generated by
transfection of plasmids into cells infected with virus.
[0066] Suitable vectors include, but are not limited to, the
following viral vectors such as lambda vector system gt11, gt
WES.tB, Charon 4, and plasmid vectors such as pBR322, pBR325,
pACYC177, pACYC1084, pUC8, pUC9, pUC18, pUC19, pLG339, pR290,
pKC37, pKC101, SV 40, pBluescript II SK+/- or KS+/- (see
"Stratagene Cloning Systems" Catalog (1993) from Stratagene, La
Jolla, Calif, which is hereby incorporated by reference), pQE,
pIH821, pGEX, pET series (see F. W. Studier et. al., "Use of T7 RNA
Polymerase to Direct Expression of Cloned Genes," Gene Expression
Technology vol. 185 (1990), which is hereby incorporated by
reference), and any derivatives thereof. Recombinant molecules can
be introduced into cells via transformation, particularly
transduction, conjugation, mobilization, or electroporation. The
DNA sequences are cloned into the vector using standard cloning
procedures in the art, as described by Sambrook, et al., Molecular
Cloning: A Laboratory Manual, Cold Springs Laboratory, Cold Springs
Harbor, N.Y. (1989), which is hereby incorporated by reference.
[0067] A variety of host-vector systems may be utilized to express
the protein-encoding sequence(s). Primarily, the vector system must
be compatible with the host cell used. Host-vector systems include
but are not limited to the following: bacteria transformed with
bacteriophage DNA, plasmid DNA, or cosmid DNA; microorganisms such
as yeast containing yeast vectors; mammalian cell systems infected
with virus (e.g., vaccinia virus, adenovirus, etc.); insect cell
systems infected with virus (e.g., baculovirus); and plant cells
infected by bacteria. The expression elements of these vectors vary
in their strength and specificities. Depending upon the host-vector
system utilized, any one of a number of suitable transcription and
translation elements can be used.
[0068] Different genetic signals and processing events control many
levels of gene expression (e.g., DNA transcription and messenger
RNA (mRNA) translation).
[0069] Transcription of DNA is dependent upon the presence of a
promotor which is a DNA sequence that directs the binding of RNA
polymerase and thereby promotes mRNA synthesis. The DNA sequences
of eucaryotic promoters differ from those of procaryotic promoters.
Furthermore, eucaryotic promoters and accompanying genetic signals
may not be recognized in or may not function in a procaryotic
system, and, further procaryotic promoters are not recognized and
do not function in eucaryotic cells.
[0070] Similarly, translation of mRNA in procaryotes depends upon
the presence of the proper procaryotic signals which differ from
those of eukaryotes. Efficient translation of mRNA in procaryotes
requires a ribosome binding site called the Shine-Dalgarno ("SD")
sequence on the mRNA. This sequence is a short nucleotide sequence
of mRNA that is located before the same codon, usually AUG, which
encodes the amino-terminal methionine of the protein. The SD
sequences are complementary to the 3'-end of the 16S rRNA
(ribosomal RNA) and probably promote binding of mRNA to ribosomes
by duplexing with the rRNA to allow correct positioning of the
ribosome. For a review on maximizing gene expression, see Roberts
and Lauer, Methods in Enzymology, 68:473 (1979), which is hereby
incorporated by reference.
[0071] Promoters vary in their "strength" (i.e. their ability to
promote transcription). For the purposes of expressing a cloned
gene, it is desirable to use strong promoters in order to obtain a
high level of transcription and, hence, expression of the gene.
Depending upon the host cell system utilized, any one of a number
of suitable promoters may be used. For instance, when cloning in E.
coli, its bacteriophages, or plasmids, promoters such as the T7
phage promoter, lac promotor, trp promotor, recA promotor,
ribosomal RNA promotor, the P.sub.R and P.sub.L promoters of
coliphage lambda and others, including but not limited, to lacUV5,
ompF, bla, lpp, and the like, may be used to direct high levels of
transcription of adjacent DNA segments. Additionally, a hybrid
trp-lacUV5 (tac) promotor or other E. coli promoters produced by
recombinant DNA or other synthetic DNA techniques may be used to
provide for transcription of the inserted gene.
[0072] Bacterial host cell strains and expression vectors may be
chosen which inhibit the action of the promotor unless specifically
induced. In certain operations, the addition of specific inducers
is necessary for efficient transcription of the inserted DNA. For
example, the lac operon is induced by the addition of lactose or
IPTG (isopropylthio-beta-D-galactoside). A variety of other
operons, such as trp, pro, etc., are under different controls.
Additionally, the cell may carry the gene for a heterologous RNA
polymerase such as from phage T7. Thus, a promoter specific for T7
RNA polymerase is used. The T7 RNA polymerase may be under
inducible control.
[0073] Specific initiation signals are also required for efficient
gene transcription and translation in procaryotic cells. These
transcription and translation initiation signals may vary in
"strength" as measured by the quantity of gene specific messenger
RNA and protein synthesized, respectively. The DNA expression
vector, which contains a promotor, may also contain any combination
of various "strong" transcription and/or translation initiation
signals. For instance, efficient translation in E. coli requires an
SD sequence about 7-9 bases 5' to the initiation codon ("ATG") to
provide a ribosome binding site. Thus, an SD-ATG combination that
can be utilized by host cell ribosomes may be employed. Such
combinations include but are not limited to the SD-ATG combination
from the cro gene or the N gene of coliphage lambda, or from the E.
coli tryptophan E, D, C, B or A genes. Additionally, any SD-ATG
combination produced by recombinant DNA or other techniques
involving incorporation of synthetic nucleotides may be used.
[0074] Once the isolated DNA molecule encoding a replication
polypeptide or protein has been cloned into an expression system,
it is ready to be incorporated into a host cell. Such incorporation
can be carried out by the various forms of transformation noted
above, depending upon the vector/host cell system. Suitable host
cells include, but are not limited to, bacteria, viruses, yeast,
mammalian cells, insects, plants, and the like.
[0075] The invention provides efficient methods of identifying
pharmacological agents or lead compounds for agents active at the
level of a replication protein function, particularly DNA
replication. Generally, these screening methods involve assaying
for compounds which interfere with the replication activity. The
methods are amenable to automated, cost-effective high throughput
screening of chemical libraries for lead compounds. Identified
reagents find use in the pharmaceutical industries for animal and
human trials; for example, the reagents may be derivatized and
rescreened in in vitro and in vivo assays to optimize activity and
minimize toxicity for pharmaceutical development. Target
therapeutic indications are limited only in that the target
cellular function be subject to modulation, usually inhibition, by
disruption of a replication activity or the formation of a complex
comprising a replication protein and one or more natural
intracellular binding targets. Target indications may include
arresting cell growth or causing cell death resulting in recovery
from the bacterial infection in animal studies.
[0076] A wide variety of assays for activity and binding agents are
provided, including DNA synthesis, ATPase, clamp loading onto DNA,
protein-protein binding assays, immunoassays, cell based assays,
etc. The replication protein compositions, used to identify
pharmacological agents, are in isolated, partially pure or pure
form and are typically recombinantly produced. The replication
protein may be part of a fusion product with another peptide or
polypeptide (e.g., a polypeptide that is capable of providing or
enhancing protein-protein binding, stability under assay conditions
(e.g., a tag for detection or anchoring), etc.). The assay mixtures
comprise a natural intracellular replication protein binding target
such as DNA, another protein, NTP, or dNTP. For binding assays,
while native binding targets may be used, it is frequently
preferred to use portions (e.g., peptides, nucleic acid fragments)
thereof so long as the portion provides binding affinity and
avidity to the subject replication protein conveniently measurable
in the assay. The assay mixture also comprises a candidate
pharmacological agent. Generally, a plurality of assay mixtures are
run in parallel with different agent concentrations to obtain a
differential response to the various concentrations. Typically, one
of these concentrations serves as a negative control (i.e. at zero
concentration or below the limits of assay detection). Additional
controls are often present such as a positive control, a dose
response curve, use of known inhibitors, use of control
heterologous proteins, etc. Candidate agents encompass numerous
chemical classes, though typically they are organic compounds;
preferably they are small organic compounds and are obtained from a
wide variety of sources, including libraries of synthetic or
natural compounds. A variety of other reagents may also be included
in the mixture. These include reagents like salts, buffers, neutral
proteins (e.g., albumin, detergents, etc.), which may be used to
facilitate optimal binding and/or reduce nonspecific or background
interactions, etc. Also reagents that otherwise improve the
efficiency of the assay (e.g., protease inhibitors, nuclease
inhibitors, antimicrobial agents, etc.) may be used.
[0077] The invention provides replication protein specific assays
and the binding agents including natural intracellular binding
targets such as other replication proteins, etc., and methods of
identifying and making such agents, and their use in a variety of
diagnostic and therapeutic applications, especially where disease
is associated with excessive cell growth. Novel replication
protein-specific binding agents include replication
protein-specific antibodies and other natural intracellular binding
agents identified with assays such as one- and two-hybrid screens,
non-natural intracellular binding agents identified in screens of
chemical libraries, etc.
[0078] Generally, replication protein-specificity of the binding
agent is shown by binding equilibrium constants. Such agents are
capable of selectively binding a replication protein (i.e., with an
equilibrium constant at least about 10.sup.7 M.sup.-1, preferably,
at least about 10.sup.8 M.sup.-1, more preferably, at least about
10.sup.9 M.sup.-1). A wide variety of cell-based and cell-free
assays may be used to demonstrate replication protein-specific
activity, binding, gel shift assays, immunoassays, etc.
[0079] The resultant mixture is incubated under conditions whereby,
but for the presence of the candidate pharmacological agent, the
replication protein specifically binds the cellular binding target,
portion, or analog. The mixture of components can be added in any
order that provides for the requisite bindings. Incubations may be
performed at any temperature which facilitates optimal binding,
typically between 4 and 40.degree. C., more commonly between
15.degree. and 40.degree. C. Incubation periods are likewise
selected for optimal binding but also minimized to facilitate
rapid, high-throughput screening, and are typically between 0.1 and
10 hours, preferably less than 5 hours, more preferably less than 2
hours.
[0080] After incubation, the presence or absence of activity or
specific binding between the replication protein and one or more
binding targets is detected by any convenient way. For cell-free
activity and binding type assays, a separation step may be used to
separate the activity product or the bound from unbound components.
Separation may be effected by precipitation (e.g.,
immunoprecipitation), immobilization (e.g., on a solid substrate
such as a microtiter plate), etc., followed by washing. Many assays
that do not require separation are also possible such as use of
europium conjugation in proximity assays or a detection system that
is dependent on a product or loss of substrate.
[0081] Detection may be effected in any convenient way. For
cell-free activity and binding assays, one of the components
usually comprises or is coupled to a label. A wide variety of
labels may be employed--essentially any label that provides for
detection of DNA product, loss of DNA substrate, conversion of a
nucleotide substrate, or bound protein is useful. The label may
provide for direct detection such as radioactivity, fluorescence,
luminescence, optical, or electron density, etc. or indirect
detection such as an epitope tag, an enzyme, etc. The label may be
appended to the protein (e.g., a phosphate group comprising a
radioactive isotope of phosphorous), or incorporated into the DNA
substrate or the protein structure (e.g., a methionine residue
comprising a radioactive isotope of sulfur.) A variety of methods
may be used to detect the label depending on the nature of the
label and other assay components. For example, the label may be
detected bound to the solid substrate, or a portion of the bound
complex containing the label may be separated from the solid
substrate, and thereafter the label detected. Labels may be
directly detected through optical or electron density, radioactive
emissions, nonradiative energy transfer, fluorescence emission,
etc. or indirectly detected with antibody conjugates, etc. For
example, in the case of radioactive labels, emissions may be
detected directly (e.g., with particle counters) or indirectly
(e.g., with scintillation cocktails and counters).
[0082] The present invention identifies the type of replication
system that Gram positive bacteria utilize. Specifically, the
replicase is comprised of a DNA polymerase III-type enzyme and it
is made functional by other components that are needed for
processive function. These components include a sliding clamp and a
clamp loader. Hence, Gram negative bacteria do not utilize the
replication strategies exemplified by one and two component
processive replicases.
[0083] The present invention also identifies, partially purifies,
and characterizes a second Pol III-type replicase. The polymerase
of the second Pol III-type enzyme, termed Pol III-2, behaves like
Pol III-L in that it also functions with the clamp and clamp loader
components.
[0084] This invention also expresses and purifies a protein from a
Gram positive bacteria that is homologous to the E. coli beta
subunit. The invention demonstrates that it behaves like a circular
protein. Further, this invention shows that the beta subunit from a
Gram positive bacteria is functional with both Pol III-L from a
Gram positive bacteria and with DNA polymerase III from a Gram
negative bacteria. This result can be explained by an interaction
between the clamp and the polymerase that has been conserved during
the evolutionary divergence of Gram positive and Gram negative
cells. A chemical inhibitor that would disrupt this interaction
would be predicted to have a broad spectrum of antibiotic activity,
shutting down replication in gram negative and gram positive cells
alike. This assay, and others based on this interaction, can be
devised to screen chemicals for such inhibition. Further, since all
the proteins in this assay are highly overexpressed through
recombinant techniques, sufficient quantities of the protein
reagents can be obtained for screening hundreds of thousands of
compounds.
[0085] The present invention provides methods by which replication
proteins from a Gram positive bacteria are used to discover new
pharmaceutical agents. The function of replication proteins is
quantified in the presence of different chemical compounds. A
chemical compound that inhibits the function is a candidate
antibiotic. Some replication proteins from a Gram positive bacteria
and from a Gram negative bacteria can be interchanged for one
another. Hence, they can function as mixtures. Reactions that assay
for the function of enzyme mixtures consisting of proteins from
Gram positive bacteria and from Gram negative bacteria can also be
used to discover drugs. Suitable E. coli replication proteins are
the subunits of its Pol III holoenzyme which are described in U.S.
Pat. Nos. 5,583,026 and 5,668,004, which are hereby incorporated by
reference.
[0086] The methods described here to obtain genes, and the assays
demonstrating activity behavior of S. aureus are likely to
generalize to all members of the Staphylococcus genus and to all
Gram positive bacteria.
[0087] The present invention describes a method to identify
chemicals that inhibit the activity of the Pol III-2 and/or Pol
III-L. This method involves contacting primed DNA with the DNA
polymerase in the presence of the candidate pharmaceutical, and
dNTPs (or modified dNTPs) to form a reaction mixture. The reaction
mixture is subjected to conditions effective to achieve nucleic
acid polymerization in the absence of the candidate pharmaceutical
and the presence or absence of the extension product in the
reaction mixture is analyzed. The candidate pharmaceutical is
detected by the absence of product.
[0088] The present invention describes a method to identify
chemicals that inhibit the ability of a beta subunit to stimulate
Pol III-2 and/or Pol III-L. This method involves contacting a
linear primed DNA with a beta subunit and a DNA polymerase in the
presence of the candidate compound, and dNTPs (or modified dNTPs)
to form a reaction mixture. The reaction mixture is subjected to
conditions which, in the absence of the candidate compound, would
affect nucleic acid polymerization and the presence or absence of
the extension product in the reaction mixture is analyzed. The
candidate pharmaceutical is detected by the absence of product. The
beta subunit and/or the DNA polymerase are derived from a Gram
positive bacterium.
[0089] The present invention also describes a method to identify
candidate pharmaceuticals that inhibit the activity of a gamma
complex (or a subunit or subassembly of the gamma complex) and a
beta subunit in stimulating either Pol III-2 or Pol III-L. The
method includes contacting a primed DNA (which may be coated with
SSB) with a DNA polymerase, a beta subunit, and a gamma complex (or
subunit or subassembly of the gamma complex) in the presence of the
candidate pharmaceutical, and dNTPs (or modified dNTPs) to form a
reaction mixture. The reaction mixture is subjected to conditions
which in the absence of the candidate pharmaceutical would effect
nucleic acid polymerization and the presence or absence of the
extension product in the reaction mixture is analyzed. The
candidate pharmaceutical is detected by the absence of product. The
DNA polymerase, the beta subunit, and/or the gamma complex or
subunit(s) thereof are derived from a Gram positive bacterium.
[0090] The present invention describes a method to identify
chemicals that inhibit the ability of a beta subunit and a DNA
polymerase to interact physically. This method involves contacting
the beta subunit with the DNA polymerase in the presence of the
candidate pharmaceutical to form a reaction mixture. The reaction
mixture is subjected to conditions under which the DNA polymerase
and the beta subunit would interact in the absence of the candidate
pharmaceutical. The reaction mixture is then analyzed for
interaction between the beta unit and the DNA polymerase. The
candidate pharmaceutical is detected by the absence of interaction
between the beta subunit and the DNA polymerase. The DNA polymerase
and/or the beta subunit are derived from a Gram positive
bacterium.
[0091] The present invention describes a method to identify
chemicals that inhibit the ability of a beta subunit and a gamma
complex (or a subunit or subassembly of the gamma complex) to
interact. This method includes contacting the beta subunit with the
gamma complex (or subunit or subassembly of the gamma complex) in
the presence of the candidate pharmaceutical to form a reaction
mixture. The reaction mixture is subjected to conditions under
which the gamma complex (or the subunit or subassembly of the gamma
complex) and the beta subunit would interact in the absence of the
candidate pharmaceutical. The reaction mixture is then analyzed for
interaction between the beta subunit and the gamma complex (or the
subunit or subassembly of the gamma complex). The candidate
pharmaceutical is detected by the absence of interaction between
the beta subunit and the gamma complex (or the subunit or
subassembly of the gamma complex). The beta subunit and/or the
gamma complex or subunit thereof is derived from a Gram positive
bacterium.
[0092] The present invention describes a method to identify
chemicals that inhibit the ability of a gamma complex (or a
subassembly of the gamma complex) to assemble a beta subunit onto a
DNA molecule. This method involves contacting a circular primed DNA
molecule (which may be coated with SSB) with the gamma complex (or
the subassembly thereof) and the beta subunit in the presence of
the candidate pharmaceutical, and ATP or dATP to form a reaction
mixture. The reaction mixture is subjected to conditions under
which the gamma complex (or subassembly) assembles the beta subunit
on the DNA molecule absent the candidate pharmaceutical. The
presence or absence of the beta subunit on the DNA molecule in the
reaction mixture is analyzed. The candidate pharmaceutical is
detected by the absence of the beta subunit on the DNA molecule.
The beta subunit and/or the gamma complex are derived from a Gram
positive bacterium.
[0093] The present invention describes a method to identify
chemicals that inhibit the ability of a gamma complex (or a
subunit(s) of the gamma complex) to disassemble a beta subunit from
a DNA molecule. This method comprises contacting a DNA molecule
onto which the beta subunit has been assembled in the presence of
the candidate pharmaceutical, to form a reaction mixture. The
reaction mixture is subjected to conditions under which the gamma
complex (or a subunit(s) or subassembly of the gamma complex)
disassembles the beta subunit from the DNA molecule absent the
candidate pharmaceutical. The presence or absence of the beta
subunit on the DNA molecule in the reaction mixture is analyzed.
The candidate pharmaceutical is detected by the presence of the
beta subunit on the DNA molecule. The beta subunit and/or the gamma
complex are derived from a Gram positive bacterium.
[0094] The present invention describes a method to identify
chemicals that dissassemble a beta subunit from a DNA molecule.
This method involves contacting a circular primed DNA molecule
(which may be coated with SSB) upon which the beta subunit has been
assembled (e.g., by action of the gamma complex) with the candidate
pharmaceutical. The presence or absence of the beta subunit on the
DNA molecule in the reaction mixture is analyzed. The candidate
pharmaceutical is detected by the absence of the beta subunit on
the DNA molecule. The beta subunit is derived from a Gram positive
bacterium.
[0095] The present invention describes a method to identify
chemicals that inhibit the dATP/ATP binding activity of a gamma
complex or a gamma complex subunit (e.g., gamma subunit). This
method includes contacting the gamma complex (or the gamma complex
subunit) with dATP/ATP either in the presence or absence of a DNA
molecule and/or the beta subunit in the presence of the candidate
pharmaceutical to form a reaction. The reaction mixture is
subjected to conditions in which the gamma complex (or the subunit
of gamma complex) interacts with dATP/ATP in the absence of the
candidate pharmaceutical. The reaction is analyzed to determine if
dATP/ATP is bound to the gamma complex (or the subunit of gamma
complex) in the presence of the candidate pharmaceutical. The
candidate pharmaceutical is detected by the absence of hydrolysis.
The gamma complex and/or the beta subunit is derived from a Gram
positive bacterium.
[0096] The present invention describes a method to identify
chemicals that inhibit the dATP/ATPase activity of a gamma complex
or a gamma complex subunit (e.g., the gamma subunit). This method
involves contacting the gamma complex (or the gamma complex
subunit) with dATP/ATP either in the presence or absence of a DNA
molecule and/or a beta subunit in the presence of the candidate
pharmaceutical to form a reaction mixture. The reaction mixture is
subjected to conditions in which the gamma subunit (or complex)
hydrolyzes dATP/ATP in the absence of the candidate pharmaceutical.
The reaction is analyzed to determine if dATP/ATP was hydrolyzed.
Suitable candidate pharmaceuticals are identified by the absence of
hydrolysis. The gamma complex and/or the beta subunit is derived
from a Gram positive bacterium.
[0097] The present invention describes methods to identify
chemicals that inhibit the activity of a DNA polymerase encoded by
either the dnaE gene or PolC gene. These methods are as
follows.
[0098] 1) Contacting a primed DNA molecule with the encoded product
of the dnaE gene or PolC gene in the presence of the candidate
pharmaceutical, and dNTPs (or modified dNTPs) to form a reaction
mixture. The reaction mixture is subjected to conditions, which in
the absence of the candidate pharmaceutical, affect nucleic acid
polymerization and the presence or absence of the extension product
in the reaction mixture is analyzed. The candidate pharmaceutical
is detected by the absence of extension product. The protein
encoded by the dnaE gene and PolC gene is derived from a Gram
positive bacterium.
[0099] 2) Contacting a linear primed DNA molecule with a beta
subunit and the encoded product of dnaE or PolC in the presence of
the candidate pharmaceutical, and dNTPs (or modified dNTPs) to form
a reaction mixture. The reaction mixture is subjected to
conditions, which in the absence of the candidate pharmaceutical,
affect nucleic acid polymerization, and the presence or absence of
the extension product in the reaction mixture is analyzed. The
candidate pharmaceutical is detected by the absence of extension
product. The protein encoded by the dnaE gene and PolC gene is
derived from a Gram positive bacterium.
[0100] 3) Contacting a circular primed DNA molecule (may be coated
with SSB) with a gamma complex, a beta subunit and the encoded
product of a dnaE gene or PolC gene in the presence of the
candidate pharmaceutical, and dNTPs (or modified dNTPs) to form a
reaction mixture. The reaction mixture is subjected to conditions,
which in the absence of the candidate pharmaceutical, affect
nucleic acid polymerization, and the presence or absence of the
extension product in the reaction mixture is analyzed. The
candidate pharmaceutical is detected by the absence of product. The
protein encoded by the dnaE gene and PolC gene, the beta subunit,
and/or the gamma complex are derived from a Gram positive
bacterium.
[0101] 4) Contacting a beta subunit with the product encoded by a
dnaE gene or PolC gene in the presence of the candidate
pharmaceutical to form a reaction mixture. The reaction mixture is
then analyzed for interaction between the beta subunit and the
product encoded by the dnaE gene or PolC gene. The candidate
pharmaceutical is detected by the absence of interaction between
the beta subunit and the product encoded by the dnaE gene or PolC
gene. The beta subunit and/or the protein encoded by the dnaE gene
and PolC gene is derived from a Gram positive bacterium.
[0102] The present invention discloses a method to identify
chemicals that inhibit a DnaB helicase. The method includes
contacting the DnaB helicase with a DNA molecule substrate that has
a duplex region in the presence of a nucleoside or deoxynucleoside
triphosphate energy source and a candidate pharmaceutical to form a
reaction mixture. The reaction mixture is subjected to conditions
that support helicase activity in the absence of the candidate
pharmaceutical. The DNA duplex molecule in the reaction mixture is
analyzed for whether it is converted to ssDNA. The candidate
pharmaceutical is detected by the absence of conversion of the
duplex DNA molecule to the ssDNA molecule. The DnaB helicase is
derived from a Gram positive bacterium.
[0103] The present invention describes a method to identify
chemicals that inhibit the nucleoside or deoxynucleoside
triphosphatase activity of a DnaB helicase. The method includes
contacting the DnaB helicase with a DNA molecule substrate that has
a duplex region in the presence of a nucleoside or deoxynucleoside
triphosphate energy source and the candidate pharmaceutical to form
a reaction mixture. The reaction mixture is subjected to conditions
that support nucleoside or deoxynucleoside triphosphatase activity
of the DnaB helicase in the absence of the candidate
pharmaceutical. The candidate pharmaceutical is detected by the
absence of conversion of nucleoside or deoxynucleoside triphosphate
to nucleoside or deoxynucleoside diphosphate. The DnaB helicase is
derived from a Gram positive bacterium.
[0104] The present invention describes a method to identify
chemicals that inhibit a primase. The method includes contacting
primase with a ssDNA molecule in the presence of a candidate
pharmaceutical to form a reaction mixture. The reaction mixture is
subjected to conditions that support primase activity (e.g., the
presence of nucleoside or deoxynucleoside triphosphates,
appropriate buffer, presence or absence of DnaB protein) in the
absence of the candidate pharmaceutical. Suitable candidate
pharmaceuticals are identified by the absence of primer formation
detected either directly or indirectly. The primase is derived from
a Gram positive bacterium.
[0105] The present invention describes a method to identify
chemicals that inhibit the ability of a primase and the protein
encoded by a DnaB gene to interact. This method includes contacting
the primase with the protein encoded by the DnaB gene in the
presence of the candidate pharmaceutical to form a reaction
mixture. The reaction mixture is subjected to conditions under
which the primase and the protein encoded by the DnaB gene interact
in the absence of the candidate pharmaceutical. The reaction
mixture is then analyzed for interaction between the primase and
the protein encoded by the DnaB gene. The candidate pharmaceutical
is detected by the absence of interaction between the primase and
the protein encoded by the DnaB gene. The primase and/or the DnaB
gene are derived from a Gram positive bacterium.
[0106] The present invention describes a method to identify
chemicals that inhibit the ability of a protein encoded by a DnaB
gene to interact with a DNA molecule. This method includes
contacting the protein encoded by the DnaB gene with the DNA
molecule in the presence of the candidate pharmaceutical to form a
reaction mixture. The reaction mixture is subjected to conditions
under which the DNA molecule and the protein encoded by the DnaB
gene interact in the absence of the candidate pharmaceutical. The
reaction mixture is then analyzed for interaction between the
protein encoded by the DnaB gene and the DNA molecule. The
candidate pharmaceutical is detected by the absence of interaction
between the DNA molecule and the protein encoded by the DnaB gene.
The DnaB gene is derived from a Gram positive bacterium.
EXAMPLES
Example 1
Materials
[0107] Labeled deoxy- and ribonucleoside triphosphates were from
Dupont--New England Nuclear; unlabelled deoxy- and ribonucleoside
triphosphates were from Pharmacia-LKB; E. coli replication proteins
were purified as described, alpha, epsilon, gamma, and tau
(Studwell, et al., "Processive Replication is Contingent on the
Exonuclease Subunit of DNA Polymerase III Holoenzyme," J. Biol.
Chem. 265:1171-1178 (1990), which is hereby incorporated by
reference), beta (Kong, et. al, "Three Dimensional Structure of the
Beta Subunit of Escherichia coli DNA Polymerase III Holoenzyme: A
Sliding DNA Clamp," Cell, 69:425-437 (1992), which is hereby
incorporated by reference), delta and delta prime (Dong, et. al.,
"DNA Polymerase III Accessory Proteins. I. HolA and holB Encoding
.delta. and .delta.'," J. Biol. Chem., 268:11758-11765 (1993),
which is hereby incorporated by reference), chi and psi (Xiao, et.
al., "DNA Polymerase III Accessory Proteins. III. HolC and holD
Encoding chi and psi," J. Biol. Chem., 268:11773-11778 (1993),
which is hereby incorporated by reference), theta
(Studwell-Vaughan, et al., "DNA Polymerase III Accessory Proteins.
V. Theta Encoded by holE," J. Biol. Chem., 268:11785-11791 (1993),
which is hereby incorporated by reference), and SSB (Weiner, et.
al., "The Deoxyribonucleic Acid Unwinding Protein of Escherichia
coli," J. Biol. Chem., 250:1972-1980 (1975), which is hereby
incorporated by reference). E. coli Pol III core, and gamma complex
(composed of subunits: gamma, delta, delta prime, chi, and psi)
were reconstituted as described in Onrust, et. al., "Assembly of a
Chromosomal Replication Machine: Two DNA Polymerases, a Clamp
Loader and Sliding Clamps in One Holoenzyme Particle. I.
Organization of the Clamp Loader," J. Biol. Chem., 270:13348-13357
(1995), which is hereby incorporated by reference. Pol III* was
reconstituted and purified as described in Onrust, et. al.,
"Assembly of a Chromosomal Replication Machine: Two DNA
Polymerases, a Clamp Loader and Sliding Clamps in One Holoenzyme
Particle. III. Interface Between Two Polymerases and the Clamp
Loader," J. Biol. Chem., 270:13366-13377 (1995), which is hereby
incorporated by reference. Protein concentrations were quantitated
by the Protein Assay (Bio-Rad) method using bovine serum albumin
(BSA) as a standard. DNA oligonucleotides were synthesized by
Oligos etc. Calf thymus DNA was from Sigma. Buffer A is 20 mM
Tris-HCl (pH=7.5), 0.5 mM EDTA, 2 mM DTT, and 20% glycerol.
Replication buffer is 20 mM Tris-Cl (pH 7.5), 8 mM MgCl.sub.2, 5 mM
DTT, 0.5 mM EDTA, 40 .mu.g/ml BSA, 4% glycerol, 0.5 mM ATP, 3 mM
each dCTP, dGTP, dATP, and 20 .mu.M [.alpha.-.sup.32P]dTTP. P-cell
buffer was 50 mM potassium phosphate (pH 7.6), 5 mM DTT, 0.3 mM
EDTA, 20% glycerol. T.E. buffer is 10 mM Tris-HCl (pH 7.5), 1 mM
EDTA. Cell lysis buffer was 50 mM Tris-HCl (pH 8.0) 10% sucrose, 1
M NaCl, 0.3 mM spermidine.
Example 2
Calf Thymus DNA Replication Assays
[0108] These assays were used in the purification of DNA
polymerases from S. aureus cell extracts. Assays contained 2.5
.mu.g activated calf thymus DNA in a final volume of 25 .mu.l
replication buffer. An aliquot of the fraction to be assayed was
added to the assay mixture on ice followed by incubation at
37.degree. C. for 5 min. DNA synthesis was quantitated using DE81
paper as described in Rowen, et al., "Primase, the DnaG Protein of
Escherichia coli. An Enzyme Which Starts DNA Chains," J. Biol.
Chem., 253:758-764 (1979), which is hereby incorporated by
reference.
Example 3
PolydA-oligodT Replication Assays
[0109] PolydA-oligodT was prepared as follows. PolydA of average
length 4500 nucleotides was purchased from SuperTecs. OligodT35 was
synthesized by Oligos etc. 145 ul of 5.2 mM (as nucleotide) polydA
and 22 .mu.l of 1.75 mM (as nucleotide) oligodT were mixed in a
final volume of 2100 .mu.l T.E. buffer (ratio as nucleotide was
21:1 polydA to oligodT). The mixture was heated to boiling in a 1
ml eppindorf tube, then removed and allowed to cool to room
temperature. Assays were performed in a final volume of 25 .mu.l 20
mM Tris-Cl (pH 7.5), 8 mM MgCl.sub.2, 5 mM DTT, 0.5 mM EDTA, 40
.mu.g/ml BSA, 4% glycerol, containing 20 .mu.M
[.alpha.-.sup.32P]dTTP and 0.36 .mu.g polydA-oligodT. Proteins were
added to the reaction on ice, then shifted to 37.degree. C. for 5
min. DNA synthesis was quantitated using DE81 paper as described in
Rowen, et al., "Primase, the DnaG Protein of Escherichia coli. An
Enzyme Which Starts DNA Chains," J. Biol. Chem., 253:758-764
(1979), which is hereby incorporated by reference.
Example 4
Singly Primed M13mp18 ssDNA Replication Assays
[0110] M13mp18 was phenol extracted from phage and purified by two
successive bandings (one downward and one upward) in cesium
chloride gradients. M13mp18 ssDNA was singly primed with a DNA
30mer (map position 6817-6846) as described in Studwell, et al.
"Processive Replication is Contingent on the Exonuclease Subunit of
DNA Polymerase III Holoenzyme," J. Biol. Chem., 265:1171-1178
(1990), which is hereby incorporated by reference. Replication
assays contained 72 ng of singly primed M13mp18 ssDNA in a final
volume of 25 .mu.l of replication buffer. Other proteins added to
the assay, and their amounts, are indicated in the Brief
Description of the Drawings. Reactions were incubated for 5 min. at
37.degree. C. and then were quenched upon adding an equal volume of
1% SDS and 40 mM EDTA. DNA synthesis was quantitated using DE81
paper as described in Rowen, et al., "Primase, the DnaG Protein of
Escherichia coli. An Enzyme Which Starts DNA Chains," J. Biol.
Chem., 253:758-764 (1979), which is hereby incorporated by
reference, and product analysis was performed in a 0.8% native
agarose gel followed by autoradiography.
Example 5
Genomic Staphylococcus aureus DNA
[0111] Two strains of S. aureus were used. For PCR of the first
fragment of the dnaX gene sequence, the strain was ATCC 25923. For
all other work the strain was strain 4220 (a gift of Dr. Pat
Schlievert, University of Minnisota). This strain lacks a gene
needed for producing toxic shock (Kreiswirth, et al., "The Toxic
Shock Syndrome Exotoxin Structural Gene is Not Detectably
Transmitted by a Prophage," Nature, 305:709-712 (1996) and Balan,
et al., "Autocrine Regulation of Toxin Synthesis by Staphylococcus
aureus," Proc. Natl. Acad. Sci. USA, 92:1619-1623 (1995), which are
hereby incorporated by reference). S. aureus cells were grown
overnight at 37.degree. C. in LB containing 0.5% glucose. Cells
were collected by centrifugation (24 g wet weight). Cells were
resuspended in 80 ml solution 1 (50 mM glucose, 10 mM EDTA, 25 mM
Tris-HCL (pH 8.0)). Then, SDS and NaOH were added to 1% and 0.2 N,
respectively, followed by incubation at 65.degree. C. for 30 min.
to lyse the cells. 68.5 ml of 3 M sodium acetate (pH 5.0) was added
followed by centrifugation at 12,000 rpm for 30 min. The
supernatant was discarded and the pellet was washed twice with 50
ml of 6M urea, 10 mM Tris-HCL (pH 7.5), 1 mM EDTA) using a dounce
homogenizer. After each wash, the resuspended pellet was collected
by centrifugation (12,000 rpm for 20 min.). After the second wash,
the pellet was resuspended in 50 ml 10 mM T.E. buffer using a
dounce homogenizer and then incubated for 30 min. at 65.degree. C.
The solution was centrifuged at 12,000 rpm for 20 min., and the
viscous supernatant was collected. 43.46 g CsCl.sub.2 was added to
the 50 ml of supernatant (density between 1.395-1.398) and poured
into two 35 ml quick seal ultracentrifuge tubes (tubes were
completely filled using the same density of CsCl.sub.2 in T.E.). To
each tube was added 0.5 ml of a 10 mg/ml stock of ethidium bromide.
Tubes were spun at 55,000 rpm for 18 h at 18.degree. C. in a
Sorvall TV860 rotor. The band of genomic DNA was extracted using a
syringe and needle. Ethidium bromide was removed using two butanol
extractions and then dialyzed against 4 l of T.E. at pH 8.0
overnight. The DNA was recovered by ethanol precipitation and then
resuspended in T.E. buffer (1.7 mg total) and stored at -20.degree.
C.
Example 6
Cloning and Purification of S. aureus Pol III-L Holoenzyme
[0112] To further characterize the mechanism of DNA replication in
S. aureus, large amounts of its replication proteins were produced
through use of the genes. The PolC gene encoding S. aureus Pol
III-L holoenzyme has been sequenced and expressed in E. coli
(Pacitti, et. al., "Characterization and Overexpression of the Gene
Encoding Staphylococcus aureus DNA Polymerase III," Gene, 165:51-56
(1995), which is hereby incorporated by reference). The previous
work utilized a pBS[KS] vector for expression in which the E. coli
RNA polymerase is used for gene transcription. In the earlier
study, the S. aureus Pol III gene was precisely cloned at the 5'
end encoding the N-terminus, but the amount of the gene that
remained past the 3' end was not disclosed and the procedure for
subcloning the gene into the expression vector was only briefly
summarized. Furthermore, the previous study does not show the level
of expression of the S. aureus Pol III, nor the amount of S. aureus
Pol III-L that is obtained from the induced cells. Since the
previously published procedure could not be repeated and the
efficiency of the expression vector could not be assessed, another
strategy outlined below had to be developed.
[0113] The isolated Pol III gene was cloned into a vector that
utilizes T7 RNA polymerase for transcription as this process
generally expresses a large amount of protein. Hence, the S. aureus
PolC gene was cloned precisely into the start codon at the NdeI
site downstream of the T7 promotor in a pET vector. As the PolC
gene contains an internal NdeI site, the entire gene could not be
amplified and placed it into the NdeI site of a pET vector. Hence,
a three step cloning strategy that yielded the desired clone was
devised (See FIG. 1). These attempts were quite frustrating
initially as no products of cloning in standard E. coli strains
such as DH5alpha, a typical laboratory strain for preparation of
DNA, could be obtained. Finally, a cell that was mutated in several
genes affecting DNA stability was useful in obtaining the desired
products of cloning.
[0114] In brief, the cloning strategy required use of another
expression vector (called pET1137 kDa) in which the 37 kDa subunit
of human RFC, the clamp loader of the human replication system, had
been cloned into the pET11 vector. The gene encoding the 37 kDa
subunit contains an internal NsiI site, which was needed for the
precise cloning of the isolated PolC gene. This three step strategy
is shown in FIG. 1. In the first step, an approximately 2.3 kb
section of the 5' section of the gene (encoding the N-terminus of
Pol III-L) was amplified using the polymerase chain reaction (PCR).
Primers were: upstream 5'-GGTGGTAATTGTCTTGCATATGACAGAGC-3' (SEQ.
ID. No. 13); downstream 5'-AGCGATTAAGTGGATTGCCGGGTTGTGATG C-3'
(SEQ. ID. No. 14). Amplification was performed using 500 ng genomic
DNA, 0.5 mM EDTA, 1 .mu.M of each primer, 1 mM MgSO.sub.4, 2 units
vent DNA polymerase (New England Biolabs) in 100 .mu.l of vent
buffer (New England Biolabs). Forty cycles were performed using the
following cycling scheme: 94.degree. C., 1 min; 60.degree. C., 1
min.; 72.degree. C., 2.5 min. The product was digested with NdeI
(underlined in the upstream primer) and NsiI (an internal site in
the product) and the approximately 1.8 kb fragment was gel
purified. A pET11 vector containing as an insert the 37 kDa subunit
of human replication factor C (pET1137 kDa) was digested with NdeI
and NsiI and gel purified. The PCR fragment was ligated into the
digested pET1137 kDa vector and the ligation reaction was
transformed into Epicurean coli supercompetent SURE 2 cells
(Stratagene) and colonies were screened for the correct chimera
(pET11PolC1) by examining minipreps for proper length and correct
digestion products using NdeI and NsiI. In the second step, an
approximately 2076 bp fragment containing the DNA encoding the
C-terminus of Pol III-L holoenzyme was amplified using as primers:
upstream 5'-AGCATCACAACCCGGCAATCCACTTAATCG C-3' (SEQ. ID. No. 15);
downstream, 5'-GACTACGCCATGGGCATTAAATAAATACC-3' (SEQ. ID. No. 16).
The amplification cycling scheme was as described above except the
elongation step at 72.degree. C. was for 2 min. The product was
digested with BamHI (underlined in the downstream primer) and NsiI
(internal to the product) and the approximately 480 bp product was
gel purified and ligated into the pET11PolC1 that had been digested
with NsiI/BamHI and gel purified (ligated product is pET11PolC2).
To complete the expression vector, an approximately 2080 bp PCR
product was amplified over the two NsiI sites internal to the gene
using the following primers: upstream 5'-GAAGAT GCA TATAAACGTGCA
AGACCTAGT C-3' (SEQ. ID. No. 17), downstream
5'-GTCTGACGCACGAATTGTAAAGTAAGATGCATA G-3' (SEQ. ID. No. 18). The
amplification cycling scheme was as described above except the
72.degree. C. elongation step was 2 min. The PCR product, and the
pET11PolC2 vector, were digested with NsiI and gel purified. The
ligation mixture was transformed as described above and colonies
were screened for the correct chimera (pET11PolC).
[0115] To express Pol III-L holoenzyme, the pET11PolC plasmid was
transformed into E. coli strain BL21 (DE3). 24 L of E. coli BL21
(DE3)pET11PolC were grown in LB media containing 50 .mu.g/ml
ampicillin at 37.degree. C. to an OD of 0.7 and then the
temperature was lowered to 15.degree. C. Cells were then induced
for Pol III-L expression upon addition of 1 mM IPTG to produce the
T7 RNA polymerase needed to transcribe PolC holoenzyme. This step
was followed by further incubation at 15.degree. C. for 18 h.
Expression of S. aureus Pol III-L holoenzyme was so high that it
could easily be visualized by Coomassie staining of a SDS
polyacrylamide gel of whole cells (FIG. 2A). The expressed protein
migrated in the SDS polyacrylamide gel in a position expected for a
165 kDa polypeptide. In this procedure, it is important that cells
are induced at 15.degree. C., as induction at 37.degree. C.
produces a truncated version of Pol III-L holoenzyme, of
approximately 130 kDa.
[0116] Cells were collected by centrifugation at 5.degree. C. Cells
(12 g wet weight) were stored at -70.degree. C. The following steps
were performed at 4.degree. C. Cells were thawed and lysed in cell
lysis buffer as described (final volume=50 ml) and were passed
through a French Press (Amico) at a minimum of 20,000 psi. PMSF (2
mM) was added to the lysate as the lysate was collected from the
French Press. DNA was removed and the lysate was clarified by
centrifugation. The supernatent was dialyzed for 1 h against Buffer
A containing 50 mM NaCl. The final conductivity was equivalent to
190 mM NaCl. Supernatent (24 ml, 208 mg) was diluted to 50 ml using
Buffer A to bring the conductivity to 96 MM MgCl.sub.2, and then
was loaded onto an 8 ml MonoQ column equilibrated in Buffer A
containing 50 mM NaCl. The column was eluted with a 160 ml linear
gradient of Buffer A from 50 mM NaCl to 500 mM NaCl. Seventy five
fractions (1.3 ml each) were collected (see FIG. 2B). Aliquots were
analyzed for their ability to synthesize DNA, and 20 .mu.l of each
fraction was analyzed by Coomassie staining of an SDS
polyacrylamide gel. Based on the DNA synthetic capability, and the
correct size band in the gel, fractions 56-65 containing Pol III-L
holoenzyme were pooled (22 ml, 31 mg). The pooled fractions were
dialyzed overnight at 4.degree. C. against 50 mM phosphate (pH
7.6), 5 mM DTT, 0.1 mM EDTA, 2 mM PMSF, and 20% glycerol (P-cell
buffer). The dialyzed pool was loaded onto a 4.5 ml
phosphocellulose column equilibrated in P-cell buffer, and then
eluted with a 25 ml linear gradient of P-cell buffer from 0 M NaCl
to 0.5 M NaCl. Fractions of 1 ml were collected and analyzed in a
SDS polyacrylamide gel stained with Coomassie Blue (see FIG. 2C).
Fractions 20-36 contained the majority of the Pol III-large at a
purity of greater than 90% (5 mg).
Example 7
S. aureus Pol III-L is Not Processive on its Own
[0117] The Pol III-L holoenzyme purifies from B. subtilis as a
single subunit without accessory factors (Barnes, et al.,
"Purification of DNA Polymerase III of Gram-positive Bacteria,"
Methods in Enzy., 262:35-42 (1995), which is hereby incorporated by
reference). Hence, it seemed possible that it may be a Type I
replicase (e.g., like T5 polymerase) and, thus, be capable of
extending a single primer full length around a long singly primed
template. To perform this experiment, a template M13mp18 ssDNA
primed with a single DNA oligonucleotide either in the presence or
absence of SSB was used. DNA products were analyzed in a neutral
agarose gel which resolved products by size. The results showed
that Pol III-L holoenzyme was incapable of extending the primer
around the DNA (to form a completed duplex circle referred to as
replicative form II (RFII)) whether SSB was present or not. This
experiment has been repeated using more enzyme and longer times,
but no full length RFII products are produced. Hence, Pol III-L
would appear not to follow the paradigm of the T5 system (Type I
replicase) in which the polymerase is efficient in synthesis in the
absence of any other protein(s).
Example 8
Cloning and Purification of S. aureus Beta Subunit
[0118] The sequence of an S. aureus homolog of the E. coli dnaN
gene (encoding the beta subunit) was obtained in a study in which
the large recF region of DNA was sequenced (Alonso, et al.,
"Nucleotide Sequence of the recF Gene Cluster From Staphylococcus
aureus and Complementation Analysis in Bacillus subtilis recF
Mutants," Mol. Gen. Genet., 246:680-686 (1995), Alonso, et al.,
"Nucleotide Sequence of the recF Gene Cluster From Staphylococcus
aureus and Complementation Analysis in Bacillus subtilis recF
Mutants," Mol. Gen. Genet., 248:635-636 (1995), which are hereby
incorporated by reference). Sequence alignment of the S. aureus
beta and E. coli beta show approximately 30% identity. Overall this
level of homology is low and makes it uncertain that S. aureus beta
will have the same shape and function as the E. coli beta
subunit.
[0119] To obtain S. aureus beta protein, the dnaN gene was isolated
and precisely cloned into a pET vector for expression in E. coli.
S. aureus genomic DNA was used as template to amplify the homolog
of the dnaN gene (encoding the putative beta). The upstream and
downstream primers were designed to isolate the dnaN gene by PCR
amplification from genomic DNA. Primers were: upstream
5'-CGACTGGAAGGAGTTTTAACATATGATGGAATTCAC-3' (SEQ. ID. No. 19); the
NdeI site used for cloning into pET16b is underlined. The
downstream primer was 5'-TTATATGGATCCTTAGTAAGTTCTGATTGG-3' (SEQ.
ID. No. 20); where the BamHI site used for cloning into pET16b
(Novagen) is underlined. The NdeI and BamHI sites were used for
directional cloning into pET16 (FIG. 3). Amplification was
performed using 500 ng genomic DNA, 0.5 mM dNTPs, 1 .mu.M of each
primer, 1 mM MgSO.sub.4, 2 units vent DNA polymerase in 100 ul of
vent buffer. Forty cycles were performed using the following
cycling scheme: 94.degree. C., 1 min; 60.degree. C., 1 min.;
72.degree. C., 1 min. 10 s. The 1167 bp product was digested with
NdeI and BamHI and purified in a 0.7% agarose gel. The pure
digested fragment was ligated into the pET16b vector which had been
digested with NdeI and BamHI and gel purified in a 0.7% agarose
gel. Ligated products were transformed into E. coli competent SURE
II cells (Stratagene) and colonies were screened for the correct
chimera by examining minipreps for proper length and correct
digestion products using NdeI and BamHI.
[0120] 24 L of of BL21 (DE3)pETheta cells were grown in LB
containing 50 .mu.g/ml ampicillin at 37.degree. C. to an O.D. of
0.7, and, then, the temperature was lowered to 15.degree. C. IPTG
was added to a concentration of 2 mM and after a further 18 h at
15.degree. C. to induce expression of S. aureus beta (FIG. 4A). It
is interesting to note that the beta subunit, when induced at
37.degree. C., was completely insoluble. However, induction of
cells at 15.degree. C. provided strong expression of beta and, upon
cell lysis, over 50% of the beta was present in the soluble
fraction.
[0121] Cells were harvested by centrifugation (44 g wet weight) and
stored at -70.degree. C. The following steps were performed at
4.degree. C. Cells (44 g wet weight) were thawed and resuspended in
45 ml 1.times.binding buffer (5 mM imidizole, 0.5 M NaCl, 20 mM
Tris HCl (final pH 7.5)) using a dounce homogenizer. Cells were
lysed using a French Pressure cell (Aminco) at 20,000 psi, and then
4.5 ml of 10% polyamine P (Sigma) was added. Cell debris and DNA
was removed by centrifugation at 13,000 rpm for 30 min. at
4.degree. C. The pET16beta vector places a 20 residue leader
containing 10 histidine residues at the N-terminus of beta. Hence,
upon lysing the cells, the S. aureus beta was greatly purified by
chromatography on a nickel chelate resin (FIG. 4B). The supernatant
(890 mg protein) was applied to a 10 ml HiTrap Chelating Separose
column (Pharmacia-LKB) equilibrated in binding buffer. The column
was washed with binding buffer, then eluted with a 100 ml linear
gradient of 60 mM imidazole to 1 M imidazole in binding buffer.
Fractions of 1.35 ml were collected. Fractions were analyzed for
the presence of beta in an SDS polyacrylamide gel stained with
Coomassie Blue. Fractions 28-52, containing most of the beta
subunit, were pooled (35 ml, 82 mg). Remaining contaminating
protein was removed by chromatography on MonoQ. The S. aureus beta
becomes insoluble as the ionic strength is lowered, and, thus, the
pool of beta was dialyzed overnight against Buffer A containing 400
mM NaCl. The dialyzed pool became slightly turbid indicating it was
at its solubility limit at these concentrations of protein and
NaCl. The insoluble material was removed by centrifugation (64 mg
remaining) and, then, diluted 2-fold with Buffer A to bring the
conductivity to 256. The protein was then applied to an 8 ml MonoQ
column equilibrated in Buffer A plus 250 mM NaCl and then eluted
with a 100 ml linear gradient of Buffer A from 0.25M NaCl to 0.75 M
NaCl; fractions of 1.25 ml were collected (FIG. 4C). Under these
conditions, approximately 27 mg of the beta flowed through the
column and the remainder eluted in fractions 1-18 (24 mg).
Example 9
The S. aureus Beta Subunit Protein Stimulates S. aureus Pol III-L
and E. coli Core
[0122] The experiment of FIG. 5A, tests the ability of S. aureus
beta to stimulate S. aureus Pol III-L on a linear polydA-oligodT
template. Reactions are also performed with E. coli beta and Pol
III core. The linear template was polydA of average length of 4500
nucleotides primed with a 30mer oligonucleotide of T residues. The
first two lanes show the activity of Pol III-L either without (lane
1) or with S. aureus beta (lane 2). The result shows that the S.
aureus beta stimulates Pol III-L approximately 5-6 fold. Lanes 5
and 6 show the corresponding experiment using E. coli core with
(lane 6) or without (lane 5) E. coli beta. The core is stimulated
over 10-fold by the beta subunit under the conditions used.
[0123] Although gram positive and gram negative cells diverged from
one another long ago and components of one polymerase machinery
would not be expected to be interchangable, it was decided to test
the activity of the S. aureus beta with E. coli Pol III core. Lanes
3 and 4 shows that the S. aureus beta also stimulates E. coli core
about 5-fold. This result can be explained by an interaction
between the clamp and the polymerase that has been conserved during
the evolutionary divergence of gram positive and gram negative
cells. A chemical inhibitor that would disrupt this interaction
would be predicted to have a broad spectrum of antibiotic activity,
shutting down replication in gram negative and gram positive cells
alike. This assay, and others based on this interaction, can be
devised to screen chemicals for such inhibition. Further, since all
the proteins in this assay are highly overexpressed through
recombinant techniques, sufficient quantities of the protein
reagents can be obtained for screening hundreds of thousands of
compounds.
[0124] In summary, the results show that S. aureus beta, produced
in E. coli, is indeed an active protein (i.e. it stimulates
polymerase activity). Furthermore, the results shows that Pol III-L
functions with a second protein (i.e. S. aureus beta). Before this
experiment, there was no assurance that Pol III-L, which is
significantly different in structure from E. coli alpha, would
function with another protein. For example, unlike E. coli alpha,
which copurifies with several accessory proteins, Pol III-L
purified from B. subtilis purifies as a single protein with no
other subunits attached (Barnes, et al., "Purification of DNA
Polymerase III of Gram-positive Bacteria," Methods in Enzy.
262:35-42 (1995), which is hereby incorporated by reference).
Finally, if one were to assume that S. aureus beta would function
with a polymerase, the logical candidate would have been the
product of the dnaE gene instead of PolC (Pol III-L) since the dnaE
product is more homologous to E. coli alpha subunit than Pol
III-L.
Example 10
The S. aureus Beta Subunit Behaves as a Circular Sliding Clamp
[0125] The ability of S. aureus beta to stimulate Pol III-L could
be explained by formation of a 2-protein complex between Pol III-L
and beta to form a processive replicase similar to the Type II
class (e.g. T7 type). Alternatively, the S. aureus replicase is
organized as the Type III replicase which operates with a circular
sliding clamp and a clamp loader. In this case, the S. aureus beta
would be a circular protein and would require a clamp loading
apparatus to load it onto DNA. The ability of the beta subunit to
stimulate Pol III-L in FIG. 5A could be explained by the fact that
the polydA-oligodT template is a linear DNA and a circular protein
could thread itself onto the DNA over an end. Such "end threading"
has been observed with PCNA and explains its ability to stimulate
DNA polymerase delta in the absence of the RFC clamp loader
(Burgers, et al., "ATP-Independent Loading of the Proliferating
Cell Nuclear Antigen Requires DNA Ends," J. Biol. Chem.,
268:19923-19926 (1993), which is hereby incorporated by
reference).
[0126] To distinguish between these possibilities, S. aureus beta
was examined for ability to stimulate Pol III-L on a circular
primed template. In FIG. 5B, assays were performed using circular
M13mp18 ssDNA coated with E. coli SSB and primed with a single
oligonucleotide to test the activity of beta on circular DNA. Lane
1 shows the extent of DNA synthesis using Pol III-L alone. In lane
2, Pol III-L was supplemented with S. aureus beta. The S. aureus
beta did not stimulate the activity of Pol III-L on this circular
DNA (nor in the absence of SSB). Inability of S. aureus beta to
stimulate Pol III-L is supported by the results of FIG. 6, lane 1
that analyzes the product of Pol III-L action on the circular DNA
in an agarose gel in the presence of S. aureus beta. In summary,
these results show that S. aureus beta only stimulates Pol III-L on
linear DNA, not circular DNA. Hence, the S. aureus beta subunit
behaves as a circular protein.
[0127] Lane 3 shows the result of adding both S. aureus beta and E.
coli gamma complex to Pol III-L. Again, no stimulation was observed
(compare with lane 1). This result indicates that the functional
contacts between the clamp and clamp loader were not conserved
during evolution of gram positive and gram negative cells.
[0128] Controls for these reactions on circular DNA are shown for
the E. coli system in Lanes 4-6. Addition of only beta to E. coli
Pol III core did not result in stimulating the polymerase (compare
lanes 4 and 5). However, when gamma complex was included with beta
and core, a large stimulation of synthesis was observed (lane 6).
In summary, stimulation of synthesis is only observed when both
beta and gamma complex were present, consistent with inability of
the circular beta ring to assemble onto circular DNA by itself.
Example 11
Pol III-L Functions as a Pol III-Type Replicase with Beta and Gamma
Complex to Become Processive
[0129] Next, it was determined whether S. aureus Pol III-L requires
two components (beta and gamma complex) to extend a primer full
length around a circular primed template. In FIG. 6, a template
circular M13mp18 ssDNA primed with a single DNA oligonucleotide was
used. DNA products were analyzed in a neutral agarose gel which
resolves starting materials (labeled ssDNA in FIG. 6) from
completed duplex circles (labelled RFII for replicative form II).
The first two lanes show, as demonstrated in other examples, that
Pol III-L is incapable of extending the primer around the circular
DNA in the presence of only S. aureus beta. In lane 4 of FIG. 6, E.
coli gamma complex and beta subunit were mixed with S. aureus Pol
III-L in the assay containing singly primed M13mp18 ssDNA coated
with SSB. If the beta clamp, assembled on DNA by gamma complex,
provides processivity to S. aureus Pol III-L, the ssDNA circle
should be converted into a fully duplex circle (RFII) which would
be visible in an agarose gel analysis. The results of the
experiment showed that the E. coli beta and gamma complex did
indeed provide Pol III-L with ability to fully extend the primer
around the circular DNA to form the RFII (lane 4). The negative
control using only E. coli gamma complex and beta is shown in lane
3. For comparison, lane 6 shows the result of mixing the three
components of the E. coli system (Pol III core, beta and gamma
complex). This reaction gives almost exclusively full length RFII
product. The qualitatively different product profile that Pol III-L
gives in the agarose gel analysis compared to E. coli Pol III core
with beta and gamma complex shows that the products observed using
Pol III-L is not due to a contaminant of E. coli Pol III core in
the S. aureus Pol III-L preparation (compare lanes 4 and 6).
[0130] It is generally thought that the polymerase of one system is
specific for its SSB. However, these reactions are performed on
ssDNA coated with the E. coli SSB protein. Hence, the S. aureus Pol
III-L appears capable of utilizing E. coli SSB and the E. coli
beta. It would appear that the only component that is not
interchangeable between the gram positive and gram negative systems
is the gamma complex.
[0131] Thus, the S. aureus Pol III-L functions as a Pol III type
replicase with the E. coli beta clamp assembled onto DNA by gamma
complex.
Example 12
Purification of Two DNA Polymerase III-Type Enzymes From S. aureus
Cells
[0132] The MonoQ resin by Pharmacia has very high resolution which
would resolve the three DNA polymerases of S. aureus. Hence, S.
aureus cells were lysed, DNA was removed from the lysate, and the
clarified lysate was applied onto a MonoQ column. The details of
this procedure are: 300 L of S. aureus (strain 4220 (a gift of Dr.
Pat Schlievert, University of Minnisota)) was grown in 2.times.LB
media at 37.degree. C. to an OD of approximately 1.5 and then were
collected by centrifugation. Approximately 2 kg of wet cell paste
was obtained and stored at -70.degree. C. 122 g of cell paste was
thawed and resuspended in 192 ml of cell lysis buffer followed by
passage through a French Press cell (Aminco) at 40,000 psi. The
resultant lysate was clarified by high speed centrifugation (1.3 g
protein in 120 ml). A 20 ml aliquot of the supernatant was dialyzed
2 h against 2 L of buffer A containing 50 mM NaCl. The dialyzed
material (148 mg, conductivity=101 mM NaCl) was diluted 2-fold with
Buffer A containing 50 mM NaCl and then loaded onto an 8 ml MonoQ
column equilibrated in Buffer A containing 50 mM NaCl. The column
was washed with Buffer A containing 50 mM NaCl, and then eluted
with a 160 ml linear gradient of 0.05 M NaCl to 0.5 M NaCl in
Buffer A. Fractions of 2.5 ml (64 total) were collected, followed
by analysis in an SDS polyacrylamide gel and for their replication
activity in assays using calf thymus DNA.
[0133] Three peaks of DNA polymerase activity were identified (FIG.
7). Previous studies of cell extracts prepared from the gram
positive organism, Bacillus subtilis, identified only two peaks of
activity off a DEAE column (similar charged resin to MonoQ). The
first peak was Pol II, and the second peak was a combination of DNA
polymerases I and III. The DNA polymerases I and III were then
separated on a subsequent phosphocellulose column. The middle peak
in FIG. 7 is much larger than the other two peaks, and, thus, it
was decided to chromatograph this peak on a phosphocellulose
column. The second peak of DNA synthetic activity was pooled
(fractions 37-43; 28 mg in 14 ml) and dialyzed against 1.5 L P-cell
buffer for 2.5 h. Then, the sample (ionic strength equal to 99 mM
NaCl) was applied to a 5 ml phosphocellulose column equilibrated in
P-cell buffer. After washing the column in 10 ml P-cell buffer, the
column was eluted with a 60 ml gradient of 0-0.5 M NaCl in P-cell
buffer. 70 fractions were collected. Fractions were analyzed for
DNA synthesis using calf thymus DNA as template.
[0134] This column resolved the polymerase activity into two
distinct peaks (FIG. 7B). Hence, there appear to be four DNA
polymerases in Staphylococcus aureus, which was designated here as
peaks 1 (first peak off MonoQ), peak 2 (first peak off
phosphocellulose), peak 3 (second peak of phosphocellulose), and
peak 4 (last peak off Mono Q) (see FIG. 7). Peak 4 was presumably
Pol III-L, as it elutes from MonoQ in a similar position as the Pol
III-L expressed in E. coli (compare FIG. 7A with FIG. 2).
[0135] To test which peak contained a Pol III-type of polymerase,
an assay was used in which the E. coli gamma complex and beta
support formation of full length RFII product starting from E. coli
SSB coated circular M13mp18 ssDNA primed with a single
oligonucleotide. In FIG. 8, both Peaks 1 and 2 are stimulated by
the E. coli gamma complex and beta subunit, and, in fact, Peaks 2
and 3 are inhibited by these proteins (the quantitation is shown
below the gel in the figure). Further, the product analysis in the
agarose gel shows full length RFII duplex DNA circles only for
peaks 1 and 4. These results, combined with the NEM, pCMB and KCl
characteristics in Table 1 below, suggests that there are two Pol
III-type DNA polymerases in S. aureus, and that these are partially
purified in peaks 1 and 4.
[0136] Next, it was determined which of these peaks of DNA
polymerase activity correspond to DNA polymerases I, II, and III,
and which peak is the unidentified DNA polymerase. In the gram
postive bacterium B. subtilis, Pol III is inhibited by pCMB, NEM,
and 0.15 M NaCl, Pol II is inhibited by KCl, but not NEM or 0.15 M
KCL, and Pol I is not inhibited by any of these treatments (Gass,
et al., "Further Genetic and Enzymological Characterization of the
Three Bacillus subtilis Deoxyribonucleic Acid Polymerases," J.
Biol. Chem., 248:7688-7700 (1973), which is hereby incorporated by
reference). Hence, assays were performed in the presence or absence
of pCMB, NEM, and 0.15 M KCl (see Table 1 below). Peak 3 clearly
corresponded to Pol I, because it was not inhibited by NEM, pCMB,
or 0.15 M NaCl. Peak 2 correspond to Pol II, because it was not
inhibited by NEM, but was inhibited by pCMB and 0.15 M NaCl. Peaks
1 and 4 both had characteristics that mimic Pol III; however, peak
4 elutes on MonoQ at a similar position as Pol III-L expressed in
E. coli (see FIG. 2B). Hence, peak 4 is likely Pol III-L, and peak
1 is likely the unknown polymerase. TABLE-US-00013 TABLE 1 Expected
Characteristics Polymerase pCMB NEM 0.15M KCl Pol I not not
inhibited not inhibited inhibited* Pol II inhibited** not inhibited
not inhibited Pol III-L inhibited inhibited not inhibited Observed
Characteristics 0.15M KCL Peak PCMB NEM assignment peak 1 inhibited
inhibited new polymerase Peak 2 inhibited not inhibited Pol II Peak
3 not inhibited not inhibited Pol I Peak 4 inhibited inhibited Pol
III-L *Not inhibited is defined as greater than 75% remaining
activity **Inhibited is defined as less than 40% remaining
activity
Example 13
Demonstration That Peak 1 (Pol 111-2) Functions as a Pol III-Type
Replicase With E. coli Beta Assembled on DNA by E. coli Gamma
Complex
[0137] It is interesting to note that the characteristics of peak 1
are similar to those of a Pol III-type of DNA polymerase. To test
whether peak 1 contained a Pol III type of polymerase, an assay in
which the E. Coli gamma complex and beta support formation of full
length RFII product starting from E. coli SSB coated circular
M13mp18 ssDNA primed with a single oligonucleotide was carried out.
In FIG. 8, both Peaks 1 and 2 are stimulated by the E. coli gamma
complex and beta subunit, and, in fact, Peaks 2 and 3 are inhibited
by these proteins (the quantitation is shown below the gel in the
FIG. 8). Further, the product analysis in the agarose gel shows
full length RFII duplex DNA circles only for peaks 1 and 4. These
results, combined with the NEM, pCMB, and KCl characteristics in
the Table above, suggests that there are two Pol III-type DNA
polymerases in S. aureus, and that these are partially purified in
peaks 1 and 4.
Example 14
Identification and Cloning of S. aureus dnaE
[0138] This invention describes the finding of two DNA polymerases
that function with a sliding clamp assembled onto DNA by a clamp
loader. One of these DNA polymerases is likely Pol III-L, but the
other has not been identified previously. Presumably the
chromatographic resins used in earlier studies did not have the
resolving power to separate the enzyme from other polymerases. This
would be compounded by the low activity of Pol III-2. To identify a
gene encoding a second Pol III, the amino acid sequences of the Pol
III alpha subunit of Escherichia coli, Salmonella typhimurium,
Vibrio cholerae, Haemophilis influenzae, and Helicobacter pylori
were aligned using Clustal W (1.5). Two regions about 400 residues
apart were conserved and primers were designed for the following
amino acid sequences: upstream, LLFERFLNPERVSMP (SEQ. ID. No. 21)
(corresponds in E. coli to residues 385-399); downstream
KFAGYGFNKSHSAAY (SEQ. ID. No. 22) (corresponds in E. coli to
residues 750-764). The following primers were designed to these two
peptide regions using codon preferences for S. aureus: upstream,
5'CTTCTTTTTGAAAGATTTCTAAATAAAGAACGTTATTCAATGCC 3' (SEQ. ID. No.
23); downstream, 5' ATAAGCTGCAGCATGACTTTTATTAAAACCATAACCTGCAAATTT
3' (SEQ. ID. No. 24). Amplification was performed using 2.5 units
of Taq DNA Polymerase (Gibco, BRL), 100 ng S. aureus genomic DNA, 1
mM of each of the four dNTPs, 1 .mu.M of each primer, and 3 mM
MgCl.sub.2 in 100 .mu.l of Taq buffer. Thirty-five cycles of the
following scheme were repeated: 94.degree. C., 1 min; 55.degree.
C., 1 min; 72.degree. C., 90 sec. The PCR product (approximately
1.1 kb) was electrophoresed in a 0.8% agarose gel, and purified
using a Geneclean III kit (Bio 101). The product was then divided
equally into ten separate aliquots, and used as a template for PCR
reactions, according to the above protocol, to reamplify the
fragment for sequencing. The final PCR product was purified using a
Quiagen Quiaquick PCR Purification kit, quantitated via optical
density at 260 nM, and sequenced by the Protein/DNA Technology
Center at Rockefeller University. The same primers used for PCR
were used to prime the sequencing reactions.
[0139] Next, additional PCR primers were designed to obtain more
sequence information 3' to the amplified section of the sequnce of
dnaE. The upstream primer was: 5'
AGTTAAAAATGCCATATTTTGACGTGTTTTAGTTCTAAT 3' (SEQ. ID. No. 25), and
the downstream primer was, 5'
CTTGCAAAAGCGGTTGCTAAAGATGTTGGACGAATTATGGGG 3' (SEQ. ID. No.
26).
[0140] These primers were used in a PCR reaction using 2.5 units of
Taq DNA Polymerase (Gibco, BRL) with 100 ng. S. aureus genomic DNA
as a template, 1 mM dNTP's, 1.quadrature.M of each prmer, 3 mM
MgCl.sub.2 in 100 l of Taq buffer. Thirty-five cycles of the
following scheme were repeated: 94.degree. C., 1 min; 55.degree.
C., 1 min; 72.degree. C., 2 min 30 seconds. The 1.6 Kb product was
then divided into 5 aliquots, and used as a template in a set of 5
PCR reactions, as described above, to amplify the product for
sequencing. The products of these reactions were purified using a
Qiagen Qiaquick PCR Purification kit, quantitated via optical
density at 260 nm, and sequenced by the Protein/DNA Technology
Center at Rockefeller University. The sequence of this product
yielded about 740 bp of new sequence 3' of the first sequence. As
this gene shows better homology to gram negative pol III subunit
compared to gram positive Pol III-L, it will be designated the dnaE
gene.
[0141] As this gene shows better homology to the gram negative Pol
III .alpha. subunit compared to gram positive Pol III-L, it will be
designated the dnaE gene.
Example 15
Identification and Cloning of S. aureus dnaX
[0142] The fact that the S. aureus beta stimulates Pol III-L and
has a ring shape suggests that the gram postive replication
machinery is of the three component type. This implies the presence
of a clamp loader complex. This is not a simple determination to
make as the B. subtilis genome shows homologs to only two of the
five subunits of the E. coli clamp loader (dnaX encoding gamma, and
holB encoding delta prime). On the basis of the experiments in this
application, which suggests that there is a clamp loader, we now
presume these two subunit homologues are part of the clamp loader
for the S. aureus beta.
[0143] As a start in obtaining the clamp loading apparatus, a
strategy was devised to obtain the gene encoding the tau/gamma
subunit of S. aureus. In E. coli, these two subunits are derived
from the same gene. Tau is the full length product, and gamma is
about 2/3 the length of tau. Gamma is derived from the dnaX gene by
an efficient translational frameshift mechanism that after it
occurs incorporates only one unique C-terminal reside before
encountering a stop codon. To identify the dnaX gene of S. aureus
by PCR analysis, the dnaX genes of B. subtilis, E. coli, and H.
influenzae were aligned. Upon comparison of the amino acid sequence
encoded by these dnaX genes, two areas of high homology were used
to predict the amino acid sequence of the S. aureus dnaX gene
product. PCR primers were designed to these sequences, and a PCR
product of the expected size was indeed produced. DNA primers were
designed to two regions of high similarity for use in PCR that were
about 100 residues apart. The amino acid sequences of these regions
were: upstream, HAYLFSGPRG (SEQ. ID. No. 27) (corresponds to
residues 39-48 of E. coli), and downstream, ALLKTLEEPPE (SEQ. ID.
No. 28) (corresponds to residues 138-148 of E. coli). The DNA
sequence of the PCR primers was based upon the codon usage of S.
aureus. The upstream 38mer was
5'-CGCGGATCCCATGCATATTTATTTTCAGGTCCAAGAGG-3' (SEQ. ID. No. 29). The
first 9 nucleotides contain a BamHI site and do not correspond to
amino acid codons; the 3' 29 nucleotides correspond to the amino
acids: HAYLFSGPRG (SEQ. ID. No.30). The downstream 39 mer was
5'-CCGGAATTCTGGTGGTTCTTCTAATGTTTTTAATAATGC-3' (SEQ. ID. No. 31).
The EcoRI site is underlined and the 3' 33 nucleotides correspond
to the amino acid sequence: ALLKTLEEPPE (SEQ. ID. No. 32). The
expected PCR product, based on the alignment, is approximately 268
bp between the primer sequences. Amplification was performed using
500 ng genomic DNA, 0.5 mM dNTPs, 1 .mu.M of each primer, 1 mM
MgSO.sub.4, 2 units vent DNA polymerase in 100 .mu.l of vent
buffer. Forty cycles were performed using the following cycling
scheme: 94.degree. C., 1 min; 60.degree. C., 1 min.; 72.degree. C.,
30s. The approximately 300 bp product was digested with EcoRI and
BamHI and purified in a 0.7% agarose gel. The pure digested
fragment was ligated into pUC18 which had been digested with EcoRI
and BamHI and gel purified in a 0.7% agarose gel. Ligated products
were transformed into E. coli competent DH5a cells (Stratagene),
and colonies were screened for the correct chimera by examining
minipreps for proper length and correct digestion products using
EcoRI and BamHI. The sequence of the insert was determined and was
found to have high homology to the dnaX genes of several bacteria.
This sequence was used to design circular PCR primers. Two new
primers were designed for circular PCR based on this sequence.
[0144] A circular PCR product of approximately 1.6 kb was obtained
from a HincII digest of chromosomal DNA that was recircularized
with ligase. This first circular PCR yielded most of the remaining
dnaX gene. The rightward directed primer was 5'-TTT GTA AAG GCA TTA
CGC AGG GGA CTA ATT CAG ATG TG-3' (SEQ. ID. No. 33); the sequence
of the leftward primer was 5'-TAT GAC ATT CAT TAC AAG GTT CTC CAT
CAG TGC-3' (SEQ. ID. No. 34). Genomic DNA (3 .mu.g) was digested
with HincII, purified with phenol/chloroform extraction, ethanol
precipitated and redissolved in 70 .mu.l T.E. buffer. The genomic
DNA was recircularized upon adding 4000 units T4 ligase (New
England Biolabs) in a final volume of 100 .mu.l T4 ligase buffer
(New England Biolabs) at 16.degree. C. overnight. The PCR reaction
consisted of 90 ng recircularized genomic DNA, 0.5 mM each dNTP,
100 pmol of each primer, 1.4 mM magnesium sulfate, and 1 unit of
elongase (GIBCO) in a final volume of 100 .mu.l elongase buffer
(GIBCO). 40 cycles were performed using the following scheme:
94.degree. C., 1 min., 55.degree. C., 1 min., and 68.degree. C., 2
min. The resulting PCR product was approximately 1.6 kb. The PCR
product was purified from a 0.7% agarose gel and sequenced
directly. A stretch of approximately 750 nucleotides was obtained
using the rightward primer used in the circular PCR reaction. To
obtain the rest of the sequence, other sequencing primers were
designed in succession based on the information of each new
sequencing run.
[0145] This sequence, when spliced together with the previous 300
bp PCR sequence, contained the complete N-terminus of the gene
product (stop codons are present upstream) and possibly lacked only
about 50 residues of the C-terminus. The amino terminal region of
E. coli gamma/tau shares appears the most conserved region of the
gene as this area shares homology with RFC subunit of the human
clamp loader and with the gene 44 protein of the phage T4 clamp
loader. An alignment of the N-terminal region of the S. aureus
gamma/tau protein with that of B. subtilis and E. coli is shown in
FIG. 10. Among the highly conserved residues are the ATP binding
site consensus sequence and the four cystine residues that form a
Zn++ finger.
[0146] After obtaining 1 kb of sequence in the 5' region of dnaX,
it was sought to determine the remaining 3' end of the gene.
Circular PCR products of approximately 800 bps, 600 bps, and 1600
bps were obtained from Apo I, or Nsi I or Ssp I digest of
chromosomal DNA that were recircularized with ligase. The rightward
directed primer was 5'-GAGCACTGATGAACTTAGAATTAGATATG-3' (SEQ. ID.
No. 35); the sequence of the leftward primer was
5'-GATACTCAGTATCTTTCTCAGATGTTTTATTC-3' (SEQ. ID. No. 36). Genomic
DNA (3 g) was digested with, Apo I, or Nsi I or Ssp I, purified
with phenol/chloroform extraction, ethanol precipitated, and
redissolved in 70 l T.E. buffer. The genomic DNA was recircularized
upon adding 4000 units of T4 ligase (New England Biolabs) in a
final volume of 100 I T4 ligase buffer (New England Biolabs) at
16.degree. C. overnight. The PCR reaction consisted of 90 ng
recircularized genomic DNA, 0.5 mM each dNTP, 100 pmol of each
primer, 1.4 mM magnesium sulfate, and 1 unit of elongase (GIBCO) in
a final volume of 100 l elongase buffer (GIBCO). 40 cycles were
performed using the following scheme: 94.degree. C., 1 min.;
55.degree. C., 1 min.; 68.degree. C., 2 min. The PCR products were
directly cloned into pCR II TOPO vector using the TOPO TA cloning
kit (Invitrogen Corporation) for obtaining the rest of the C
terminal vector using the TOPO TA cloning kit (Invitrogen
Corporation) for obtaining the rest of the C terminal sequence of
S. aureus dnaX. DNA sequencing was performed by the Rockefeller
University sequencing facility.
Example 16
Identification and Cloning of S. aureus dnaB
[0147] In E. coli, the DnaB helicase assembles with the DNA
polymerase III holoenzyme to form a replisome assembly. The DnaB
helicase also interacts directly with the primase to complete the
machinery needed to duplicate a double helix. As a first step in
studying how the S. aureus helicase acts with the replicase and
primase, S. aureus was examined for presence of a dnaB gene.
[0148] The amino acid sequences of the DnaB helicase of Escherichia
coli, Salmonella typhimurium, Haemophilis influenzae, and
Helicobacter pylori were aligned using Clustal W (1.5). Two regions
about 200 residues apart showed good homology. These peptide
sequences were: upstream, DLIIVAARPSMGKT (SEQ. ID. No. 37)
(corresponds to residues 225-238 of E. coli DnaB), and downstream,
EIIIGKQRNGPIGTV (SEQ. ID. No. 38) (corresponds to residues 435-449
of E. coli). The following primers were designed from regions which
contained conserved sequences using codon preferences for S.
aureus: The upstream primer was 5' GACCTTATAATTGTAGCTGCACGTCC
TTCTAT GGGAAAAAC 3' (SEQ. ID. No. 39); the dowstream primer was 5'
AACATTATTAAGTCAGCATCTTGT TCTATTGATCCAGATTCAACGAAG 3' (SEQ. ID. No.
40). A PCR reaction was carried out using 2.5 units of Taq DNA
Polymerase (Gibco, BRL) with 100 ng. S. aureus genomic DNA as
template, 1 mM dNTP's, 1 .mu.M of each primer, 3 mM MgCl.sub.2 in
100 .mu.l of Taq buffer. Thirty-five cycles of the following scheme
were repeated: 94.degree. C., 1 min.; 55.degree. C., 1 min.; and
72.degree. C., 1 min. Two PCR products were produced, one was about
1.1 kb, and another was 0.6 kb. The smaller one was the size
expected. The 0.6 kb product was gel purified and used as a
template for a second round of PCR as follows. The 0.6 kb PCR
product was purified from a 0.8% agarose gel using a Geneclean III
kit (Bio 101) and then divided equally into five separate aliquots,
as a template for PCR reactions. The final PCR product was purified
using a Quiagen Quiaquick PCR Purification kit, quantitated via
optical density at 260 nM, and sequenced by the Protein/DNA
Technology Center at Rockefeller University. The same primers used
for PCR were used to prime the sequencing reaction. The amino acid
sequence was determined by translation of the DNA sequence in all
three reading frames, and selecting the longest open reading frame.
The PCR product contained an open reading frame over its entire
length. The predicted amino acid sequence shares homology to the
amino acid sequences encoded by dnaB gene of other organisms.
[0149] Additional sequence information was determined using the
circular PCR technique. Briefly, S. aureus genomic DNA was digested
with various endonucleases, then religated with T4 DNA ligase to
form circular templates. To perform PCR, two primers were designed
from the initial sequence. The first primer, 5'
GATTTGTAGTTCTGGTAATGTTGACTCAAACCGCTTAAGAACCGG 3' (SEQ ID. No. 41),
matches the coding strand; the second primer, 5'
ATACGTGTGGTTAACTGATCAGCAACCCATCTCTAGTGAGAAAATACC 3' (SEQ ID. No.
42), matches the sequence of the complementary strand. These two
primers are directed outwards from a central point, and allow
determination of new sequence information up to the ligated
endonuclease site. A PCR product of approximately 900 bases in
length was produced using the above primers and template derived
from the ligation of S. aureus genomic DNA which had been cut with
the restriction endonuclease Apo I. This PCR product was
electrophoresed in a 0.8% agarose gel, eluted with a Qiagen gel
elution kit, divided into five separate aliquots, and used as a
template for reamplification by PCR using the same primers as
described above. The final product was electrophoresed in an 0.8%
agarose gel, visualized via staining with ethidium bromide under
ultraviolet light, and excised from the gel. The excised gel slice
was frozen, and centrifuged at 12,000 rpm for 15 minutes. The
supernatant was extracted with phenol/chloroform to remove ethidium
bromide, and was then cleaned using a Qiagen PCR purification kit.
The material was then quantitated from its optical density at 260
nm and sequenced by the Protein/DNA Technology Center at the
Rockefeller University.
[0150] The nucleotide sequence contained an open reading frame over
its length, up to a sequence which corresponded to the consensus
sequence of a cleavage site of the enzyme Apo I. Following this
point, a second open reading frame encoded a different reading
frame up to the end of the product. The inital sequence information
was found to match the inital sequence and to extend it yet further
towards the C-terminus of the protein. The second reading frame was
found to end in a sequence which matched the 5'-terminus of the
previously determined sequence and, thus, represents an extension
of the sequence towards the N-terminus of the protein.
[0151] Additional sequence information was obtained using the above
primers and a template generated using S. aureus genomic DNA
circularized via ligation with T4 ligase following digestion with
Cla I. The PCR product was generated using 35 cycles of the
following program: denaturation at 94.degree. C. for 1 min.;
annealing at 55.degree. C. for 1 min.; and extension at 68.degree.
C. for 3 minutes and 30 s. The PCR products were electrophoresed in
a 0.8% agarose gel, eluted with a Qiagen gel elution kit, divided
into five separate aliquots, and used as a template reamplification
via PCR with the same primers described above. The final product
was electrophoresed in an 0.8% agarose gel, visualized via staining
with ethidium bromide under ultraviolet light, and excised from the
gel. The excised gel slice was frozen, and centrifuged at 12,000
rpm for 15 min. The supernatant was cleaned using a Qiagen PCR
purification kit. The material was then quantitated via optical
density at 260 nm and sequenced by the Protein/DNA Technology
Center at Rockefeller University. The open reading frames continued
past 500 bases. Therefore, the following additional sequencing
primers were designed from the sequence to obtain further
information: TABLE-US-00014 (SEQ. ID No. 43) 5'
CGTTTTAATGCATGCTTAGAAACGATATCAG 3'and, +TL,32 (SEQ. ID No. 44) 5'
CATTGCTAAGCAACGTTACGGTCCAACAGGC 3'.
[0152] The N-terminal and C-terminal nucleotide sequence extensions
generated using this circular PCR product completed the 5' region
of the gene (encoding the N-terminus of DnaB); however, a stop
codon was not reached in the 3' region and, thus, a small amount of
sequence is still needed to complete this gene.
[0153] The alignment of the S. aureus dnaB with E. coli dnaB and
the dnaB genes of B. subtilis and S. typhimurium is shown in FIG.
11.
[0154] Although the invention has been described in detail for the
purpose of illustration, it is understood that such detail is
solely for that purpose, and variations can be made therein by
those skilled in the art without departing from the spirit and
scope of the invention which is defined by the following claims.
Sequence CWU 1
1
44 1 1726 DNA Staphylococcus aureus 1 gatatagata tggactggga
agatacacgc cgagaaaagg tcattcagta cgtccaagaa 60 aaatatggcg
agctacatgt atctggaatt gtgactttcg gtcatctgct tgcaaaagcg 120
gttgctaaag atgttggacg aattatgggg tttgatgaag ttacattaaa tgaaatttca
180 agtttaatcc cacataaatt aggaattaca cttgatgaag catatcaaat
tgacgatttt 240 aaaaagtttg tacatcgaaa ccatcgacat caacgctggt
tcagtatttg taaaaagtta 300 gaaggtttac caagacatac atctacacat
gcggcaggaa ttattattaa tgaccatcca 360 ttatatgaat atgccccttt
aacgaaaggg gatacaggat tattaacgca atggacaatg 420 actgaagccg
aacgtattgg tttattaaaa atagattttc tagggttacg aaatttatca 480
attatccatc aaattttgac tcgagtcgaa aaagatttag gttttaatat tgatattgaa
540 aaaattccat ttgatgatca aaaagtgttt gaattgttgt cgcaaggaga
tacgactggc 600 atatttcaat tagagtctga cggtgttaga agtgtattaa
aaaaattaaa gccggaacac 660 tttgaggata ttgttgctgt aacttctttg
tatagaccag gtccaatgga agaaattcca 720 acttacatta caagaagaca
tgatccaagc aaagttcaat atttacatcc ccatttagaa 780 cctatattaa
aaaatactta cggtgttatt atttatcaag aacaaattat gcaaatagcg 840
agcacttttg caaacttcag ttatggtgaa gcggatattt taagaagagc aatgagtaaa
900 aaaaatagag ctgttcttga aagagacgct caacatttta tagaaggtac
aaagcaaaat 960 ggttatcacg aagacttagt aagtaagcag atatttgatt
tgattctgaa atttgctgat 1020 gatggatttc ctagagcaca tgctgtcagc
tattctaaaa ttgcatacat tatgagcttt 1080 ttaaaagtcc attatccaaa
ttatttttac gcaaatattt taagtaatgt tattggaagt 1140 gagaagaaaa
ctgctcaaat gatagaagaa gcaaaaaaac aaggtatcac tatattgcca 1200
ccgaacatta acgaaagtca ttggttttat aaaccttccc aagaaggcat ttatttatca
1260 attggtacaa ttaaaggtgt aggttatcaa agtgtgaaag tgattgttga
agaacgtttt 1320 cagaacggca aatttaaaga tttctttgat tctgctagac
gtataccgaa gagagtcaaa 1380 acgagaaagt tacttgaagc attgatttta
gtgggagcgt ttgatgcttt tggtaaaaca 1440 cgttcaacgt tgttgcaagc
tattgatcaa gtgttggatg gtgatttaaa cattgaacaa 1500 gatggttttt
tatttgatat tttaacgcca aaacagatgt atgaagataa agaagaattg 1560
cctgatgcac ttattagtca gtatgaaaaa gaatatttag gattttatgt ttcgcaacac
1620 ccagtagata agaagtttgt tgccaaacaa tatttaacga tattttcttg
cgaaaacgtt 1680 gctaaagatg ttcgacgaat tatggggttt gatgaagtta aacaaa
1726 2 573 PRT Staphylococcus aureus 2 Asp Ile Asp Met Asp Trp Glu
Asp Thr Arg Arg Glu Lys Val Ile Gln 1 5 10 15 Tyr Val Gln Glu Lys
Tyr Gly Glu Leu His Val Ser Gly Ile Val Thr 20 25 30 Phe Gly His
Leu Leu Ala Lys Ala Val Ala Lys Asp Val Gly Arg Ile 35 40 45 Met
Gly Phe Asp Glu Val Thr Leu Asn Glu Ile Ser Ser Leu Ile Pro 50 55
60 His Lys Leu Gly Ile Thr Leu Asp Glu Ala Tyr Gln Ile Asp Asp Phe
65 70 75 80 Lys Lys Phe Val His Arg Asn His Arg His Gln Arg Trp Phe
Ser Ile 85 90 95 Cys Lys Lys Leu Glu Gly Leu Pro Arg His Thr Ser
Thr His Ala Ala 100 105 110 Gly Ile Ile Ile Asn Asp His Pro Leu Tyr
Glu Tyr Ala Pro Leu Thr 115 120 125 Lys Gly Asp Thr Gly Leu Leu Thr
Gln Trp Thr Met Thr Glu Ala Glu 130 135 140 Arg Ile Gly Leu Leu Lys
Ile Asp Phe Leu Gly Leu Arg Asn Leu Ser 145 150 155 160 Ile Ile His
Gln Ile Leu Thr Arg Val Glu Lys Asp Leu Gly Phe Asn 165 170 175 Ile
Asp Ile Glu Lys Ile Pro Phe Asp Asp Gln Lys Val Phe Glu Leu 180 185
190 Leu Ser Gln Gly Asp Thr Thr Gly Ile Phe Gln Leu Glu Ser Asp Gly
195 200 205 Val Arg Ser Val Leu Lys Lys Leu Lys Pro Glu His Phe Glu
Asp Ile 210 215 220 Val Ala Val Thr Ser Leu Tyr Arg Pro Gly Pro Met
Glu Glu Ile Pro 225 230 235 240 Thr Tyr Ile Thr Arg Arg His Asp Pro
Ser Lys Val Gln Tyr Leu His 245 250 255 Pro His Leu Glu Pro Ile Leu
Lys Asn Thr Tyr Gly Val Ile Ile Tyr 260 265 270 Gln Glu Gln Ile Met
Gln Ile Ala Ser Thr Phe Ala Asn Phe Ser Tyr 275 280 285 Gly Glu Ala
Asp Ile Leu Arg Arg Ala Met Ser Lys Lys Asn Arg Ala 290 295 300 Val
Leu Glu Arg Asp Ala Gln His Phe Ile Glu Gly Thr Lys Gln Asn 305 310
315 320 Gly Tyr His Glu Asp Ile Ser Lys Gln Ile Phe Asp Leu Ile Leu
Lys 325 330 335 Phe Ala Asp Gly Phe Pro Arg Ala His Ala Val Ser Tyr
Ser Lys Ile 340 345 350 Ala Tyr Ile Met Ser Phe Leu Lys Val His Tyr
Pro Asn Tyr Phe Tyr 355 360 365 Ala Asn Ile Leu Ser Asn Val Ile Gly
Ser Glu Lys Lys Thr Ala Gln 370 375 380 Met Ile Glu Glu Ala Lys Lys
Gln Gly Ile Thr Ile Leu Pro Pro Asn 385 390 395 400 Ile Asn Glu Ser
His Trp Phe Tyr Lys Pro Ser Gln Glu Gly Ile Tyr 405 410 415 Leu Ser
Ile Gly Thr Ile Lys Gly Val Gly Tyr Gln Ser Val Lys Val 420 425 430
Ile Val Glu Glu Arg Phe Gln Asn Gly Lys Phe Lys Asp Phe Phe Asp 435
440 445 Ser Ala Arg Arg Ile Pro Lys Arg Val Lys Thr Arg Lys Leu Leu
Glu 450 455 460 Ala Leu Ile Leu Val Gly Ala Phe Asp Ala Phe Gly Lys
Thr Arg Ser 465 470 475 480 Thr Leu Leu Gln Ala Ile Asp Gln Val Leu
Asp Gly Asp Leu Asn Ile 485 490 495 Glu Gln Asp Gly Phe Leu Phe Asp
Ile Leu Thr Pro Lys Gln Met Tyr 500 505 510 Glu Asp Lys Glu Glu Leu
Pro Asp Ala Leu Ile Ser Gln Tyr Glu Lys 515 520 525 Glu Tyr Leu Gly
Phe Tyr Val Ser Gln His Pro Val Asp Lys Lys Phe 530 535 540 Val Ala
Lys Gln Tyr Leu Thr Ile Phe Ser Cys Glu Asn Val Ala Lys 545 550 555
560 Asp Val Arg Arg Ile Met Gly Phe Asp Glu Val Lys Gln 565 570 3
1698 DNA Staphylococcus aureus 3 ttgaattatc aagccttata tcgtatgtac
agaccccaaa gtttcgagga tgtcgtcgga 60 caagaacatg tcacgaagac
attgcgcaat gcgatttcga aagaaaaaca gtcgcatgca 120 tatattttta
gtggtccgag aggtacgggg aaaacgagta ttgccaaagt gtttgctaaa 180
gcaatcaact gtttaaatag cactgatgga gaaccttgta atgaatgtca tatttgtaaa
240 ggcattacgc aggggactaa ttcagatgtg atagaaattg atgctgctag
taataatggc 300 gttgatgaaa taagaaatat tagagacaaa gttaaatatg
caccaagtga atcgaaatat 360 aaagtttata ttatagatga ggtgcacatg
ctaacaacag gtgcttttaa tgccctttta 420 aagacgttag aagaacctcc
agcacacgct atttttatat tggcaacgac agaaccacat 480 aaaatccctc
caacaatcat ttctagggca caacgttttg attttaaagc aattagccta 540
gatcaaattg ttgaacgttt aaaatttgta gcagatgcac aacaaattga atgtgaagat
600 gaagccttgg catttatcgc taaagcgtct gaagggggta tgcgtgatgc
attaagtatt 660 atggatcagg ctattgcttt cggcgatggc acattgacat
tacaagatgc cctaaatgtt 720 acgggtagcg ttcatgatga agcgttggat
cacttgtttg atgatattgt acaaggtgac 780 gtacaagcat cttttaaaaa
ataccatcag tttataacag aaggtaaaga agtgaatcgc 840 ctaataaatg
atatgattta ttttgtcaga gatacgatta tgaataaaac atctgagaaa 900
gatactgagt atcgagcact gatgaactta gaattagata tgttatatca aatgattgat
960 cttattaatg atacattagt gtcgattcgt tttagtgtga atcaaaacgt
tcattttgaa 1020 gtattgttag taaaattagc tgagcagatt aagggtcaac
cacaagtgat tgcgaatgta 1080 gctgaaccag cacaaattgc ttcatcgcca
aacacagatg tattgttgca acgtatggaa 1140 cagttagagc aagaactaaa
aacactaaaa gcacaaggag tgagtgttgc tcctactcaa 1200 aaatcttcga
aaaagcctgc gagaggtata caaaaatcta aaaatgcatt ttcaatgcaa 1260
caaattgcaa aagtgctaga taaagcgaat aaggcagata tcaaattgtt gaaagatcat
1320 tggcaagaag tgattgacca tgcccaaaac aatgataaaa aatcactcgt
tagtttattg 1380 caaaattcgg aacctgtggc ggcaagtgaa gatcacgtcc
ttgtgaaatt tgaggaagag 1440 atccattgtg aaatcgtcaa taaagacgac
gagaaacgta gtagtataga aagtgttgta 1500 tgtaatatcg ttaataaaaa
cgttaaagtt gttggtgtac catcagatca atggcaaaga 1560 gttcgaacgg
agtatttaca aaatcgtaaa aacgaaggcg atgatatgcc aaagcaacaa 1620
gcacaacaaa cagatattgc tcaaaaagca aaagatcttt tcggtgaaga aactgtacat
1680 gtgatagatg aagagtga 1698 4 566 PRT Staphylococcus aureus 4 Leu
Asn Tyr Gln Ala Leu Tyr Arg Met Tyr Arg Pro Gln Ser Phe Glu 1 5 10
15 Asp Val Val Gly Gln Glu His Val Thr Lys Thr Leu Arg Asn Ala Ile
20 25 30 Ser Lys Glu Lys Gln Ser His Ala Tyr Ile Phe Ser Gly Pro
Arg Gly 35 40 45 Thr Gly Lys Thr Ser Ile Ala Lys Val Phe Ala Lys
Ala Ile Asn Cys 50 55 60 Leu Asn Ser Thr Asp Gly Glu Pro Cys Asn
Glu Cys His Ile Cys Lys 65 70 75 80 Gly Ile Thr Gln Gly Thr Asn Ser
Asp Val Ile Glu Ile Asp Ala Ala 85 90 95 Ser Asn Asn Gly Val Asp
Glu Ile Arg Asn Ile Arg Asp Lys Val Lys 100 105 110 Tyr Ala Pro Ser
Glu Ser Lys Tyr Lys Val Tyr Ile Ile Asp Glu Val 115 120 125 His Met
Leu Thr Thr Gly Ala Phe Asn Ala Leu Leu Lys Thr Leu Glu 130 135 140
Glu Pro Pro Ala His Ala Ile Phe Ile Leu Ala Thr Thr Glu Pro His 145
150 155 160 Lys Ile Pro Pro Thr Ile Ile Ser Arg Ala Gln Arg Phe Asp
Phe Lys 165 170 175 Ala Ile Ser Leu Asp Gln Ile Val Glu Arg Leu Lys
Phe Val Ala Asp 180 185 190 Ala Gln Gln Ile Glu Cys Glu Asp Glu Ala
Leu Ala Phe Ile Ala Lys 195 200 205 Ala Ser Glu Gly Gly Met Arg Asp
Ala Leu Ser Ile Met Asp Gln Ala 210 215 220 Ile Ala Phe Gly Asp Gly
Thr Leu Thr Leu Gln Asp Ala Leu Asn Val 225 230 235 240 Thr Gly Ser
Val His Asp Glu Ala Leu Asp His Leu Phe Asp Asp Ile 245 250 255 Val
Gln Gly Asp Val Gln Ala Ser Phe Lys Lys Tyr His Gln Phe Ile 260 265
270 Thr Glu Gly Lys Glu Val Asn Arg Leu Ile Asn Asp Met Ile Tyr Phe
275 280 285 Val Arg Asp Thr Ile Met Asn Lys Thr Ser Glu Lys Asp Thr
Glu Tyr 290 295 300 Arg Ala Leu Met Asn Leu Glu Leu Asp Met Leu Tyr
Gln Met Ile Asp 305 310 315 320 Leu Ile Asn Asp Thr Leu Val Ser Ile
Arg Phe Ser Val Asn Gln Asn 325 330 335 Val His Phe Glu Val Leu Leu
Val Lys Leu Ala Glu Gln Ile Lys Gly 340 345 350 Gln Pro Gln Val Ile
Ala Asn Val Ala Glu Pro Ala Gln Ile Ala Ser 355 360 365 Ser Pro Asn
Thr Asp Val Leu Leu Gln Arg Met Glu Gln Leu Glu Gln 370 375 380 Glu
Leu Lys Thr Leu Lys Ala Gln Gly Val Ser Val Ala Pro Thr Gln 385 390
395 400 Lys Ser Ser Lys Lys Pro Ala Arg Gly Ile Gln Lys Ser Lys Asn
Ala 405 410 415 Phe Ser Met Gln Gln Ile Ala Lys Val Leu Asp Lys Ala
Asn Lys Ala 420 425 430 Asp Ile Lys Leu Leu Lys Asp His Trp Gln Glu
Val Ile Asp His Ala 435 440 445 Gln Asn Asn Asp Lys Lys Ser Leu Val
Ser Leu Leu Gln Asn Ser Glu 450 455 460 Pro Val Ala Ala Ser Glu Asp
His Val Leu Val Lys Phe Glu Glu Glu 465 470 475 480 Ile His Cys Glu
Ile Val Asn Lys Asp Asp Glu Lys Arg Ser Ser Ile 485 490 495 Glu Ser
Val Val Cys Asn Ile Val Asn Lys Asn Val Lys Val Val Gly 500 505 510
Val Pro Ser Asp Gln Trp Gln Arg Val Arg Thr Glu Tyr Leu Gln Asn 515
520 525 Arg Lys Asn Glu Gly Asp Asp Met Pro Lys Gln Gln Ala Gln Gln
Thr 530 535 540 Asp Ile Ala Gln Lys Ala Lys Asp Leu Phe Gly Glu Glu
Thr Val His 545 550 555 560 Val Ile Asp Glu Glu Glx 565 5 2034 DNA
Staphylococcus aureus 5 atggatagaa tgtatgagca aaatcaaatg ccgcataaca
atgaagctga acagtctgtc 60 ttaggttcaa ttattataga tccagaattg
attaatacta ctcaggaagt tttgcttcct 120 gagtcgtttt ataggggtgc
ccatcaacat attttccgtg caatgatgca cttaaatgaa 180 gataataaag
aaattgatgt tgtaacattg atggatcaat tatcgacgga aggtacgttg 240
aatgaagcgg gtggcccgca atatcttgca gagttatcta caaatgtacc aacgacgcga
300 aatgttcagt attatactga tatcgtttct aagcatgcat taaaacgtag
attgattcaa 360 actgcagata gtattgccaa tgatggatat aatgatgaac
ttgaactaga tgcgatttta 420 agtgatgcag aacgtcgaat tttagagcta
tcatcttctc gtgaaagcga tggctttaaa 480 gacattcgag acgtcttagg
acaagtgtat gaaacagctg aagagcttga tcaaaatagt 540 ggtcaaacac
caggtatacc tacaggatat cgagatttag accaaatgac agcagggttc 600
aaccgaaatg atttaattat ccttgcagcg cgtccatctg taggtaagac tgcgttcgca
660 cttaatattg cacaaaaagt tgcaacgcat gaagatatgt atacagttaa
aagcaacagg 720 aagtttctga aatctctcgt acattaaaag cattagcccg
tgaattaaaa tgtccagtta 780 tcgcattaag tcagttatct cgtggtgttg
aacaacgaca agataaacgt ccaatgatga 840 gtgatattcg tgaatctggt
tcgattgagc aagatgccga tatcgttgca ttcttatacc 900 gtgatgatta
ctataaccgt ggcggcgatg aagatgatga cgatgatggt ggtttcgagc 960
cacaaacgaa tgatgaaaac ggtgaaattg aaattatcat tgttaagcaa cgtaacggtc
1020 caacaggcac agttaagtta cattttatga aacaatataa taaattttag
agctatcatc 1080 ttttcgtgaa agcgatggct ttaaagacat tcgagacgtc
ttaggacaag tgtatgaaac 1140 agctgaagag cttgatcaaa atagtggtca
aacaccaggt atacctacag gatatcgaga 1200 tttagaccaa atgacagcag
ggttcaaccg aaatgattta attatccttg cagcgcgtcc 1260 atctgtaggt
aagactgcgt tcgcacttaa tattgcacaa aaagttgcaa cgcatccgca 1320
cttaatattg ccaataagtt ggaacgcatg aagatatatc tagcagttgg tattttctca
1380 ctagagatgg gtgctgatca gttaaccaca cgtatgattt gtagttctgg
taatgttgac 1440 tcaaaccgct taagaaccgg tactatgact gaggaagatt
ggagtcgttt tactatagcg 1500 gttggtaaat tatcacgtac gaagattttt
attgatgata caccgggtat tcgaattaat 1560 gatttacgtt ctaaatgtcg
tcgattaaag caagaacatg gcttagacat gattgtgatt 1620 gactacttac
agttgattca aggtagtggt tcacgtgcgt ccgataacag acaacaggaa 1680
gtttctgaaa tctctcgtac attaaaagca ttagcccgtg aattaaaatg tccagttatc
1740 gcattaagtc agttatctcg tggtgttgaa caacgacaag ataaacgtcc
aatgatgagt 1800 gatattcgtg aatctggttc gattgagcaa gatgccgata
tcgttgcatt cttataccgt 1860 gatgattact ataaccgtgg cggcgatgaa
gatgatgacg atgatggtgg tttcgagccc 1920 caaacgaatg atgaaaacgg
tgaaattgaa attatcattg ctaagcaacg ttacggtcca 1980 acaggcacag
ttaagttact ttttatgaaa caatatggta aatttaccga tatc 2034 6 457 PRT
Staphylococcus aureus 6 Met Asp Arg Met Tyr Glu Gln Asn Gln Met Pro
His Asn Asn Glu Ala 1 5 10 15 Glu Gln Ser Val Leu Gly Ser Ile Ile
Ile Asp Pro Glu Leu Ile Asn 20 25 30 Thr Thr Gln Glu Val Leu Leu
Pro Glu Ser Phe Tyr Arg Gly Ala His 35 40 45 Gln His Ile Phe Arg
Ala Met Met His Leu Asn Glu Asp Asn Lys Glu 50 55 60 Ile Asp Val
Val Thr Leu Met Asp Gln Leu Ser Thr Glu Gly Thr Leu 65 70 75 80 Asn
Glu Ala Gly Gly Pro Gln Tyr Leu Ala Glu Leu Ser Thr Asn Val 85 90
95 Pro Thr Thr Arg Asn Val Gln Tyr Tyr Thr Asp Ile Val Ser Lys His
100 105 110 Ala Leu Lys Arg Arg Leu Ile Gln Thr Ala Asp Ser Ile Ala
Asn Asp 115 120 125 Gly Tyr Asn Asp Glu Leu Glu Leu Asp Ala Ile Leu
Ser Asp Ala Glu 130 135 140 Arg Arg Ile Leu Glu Leu Ser Ser Ser Arg
Glu Ser Asp Gly Phe Lys 145 150 155 160 Asp Ile Arg Asp Val Leu Gly
Gln Val Tyr Glu Thr Ala Glu Glu Leu 165 170 175 Asp Gln Asn Ser Gly
Gln Thr Pro Gly Ile Pro Thr Gly Tyr Arg Asp 180 185 190 Leu Asp Gln
Met Thr Ala Gly Phe Asn Arg Asn Asp Leu Ile Ile Leu 195 200 205 Ala
Ala Arg Pro Ser Val Gly Lys Thr Ala Phe Ala Leu Asn Ile Ala 210 215
220 Gln Lys Leu Glu Arg Met Lys Ile Tyr Leu Ala Val Gly Ile Phe Ser
225 230 235 240 Leu Glu Met Gly Ala Asp Gln Leu Thr Thr Arg Met Ile
Cys Ser Ser 245 250 255 Gly Asn Val Asp Ser Asn Arg Leu Arg Thr Gly
Thr Met Thr Glu Glu 260 265 270 Asp Trp Ser Arg Phe Thr Ile Ala Val
Gly Lys Leu Ser Arg Thr Lys 275 280 285 Ile Phe Ile Asp Asp Thr Pro
Gly Ile Arg Ile Asn Asp Leu Arg Ser 290 295 300 Lys Cys Arg Arg Leu
Lys Gln Glu His Gly Leu Asp Met Ile Val Ile 305 310 315 320 Asp Tyr
Leu Gln Leu Ile Gln Gly Ser Gly Ser Arg Ala Ser Asp Asn 325 330 335
Arg Gln Gln Glu Val Ser Glu Ile Ser Arg Thr Leu Lys Ala Leu Ala 340
345 350 Arg Glu Leu Lys Cys Pro Val Ile Ala Leu Ser Gln Leu Ser Arg
Gly 355 360 365 Val Glu Gln Arg Gln Asp Lys Arg Pro Met Met Ser Asp
Ile Arg Glu 370 375 380 Ser Gly Ser Ile Glu
Gln Asp Ala Asp Ile Val Ala Phe Leu Tyr Arg 385 390 395 400 Asp Asp
Tyr Tyr Asn Arg Gly Gly Asp Glu Asp Asp Asp Asp Asp Gly 405 410 415
Gly Phe Glu Pro Gln Thr Asn Asp Glu Asn Gly Glu Ile Glu Ile Ile 420
425 430 Ile Ala Lys Gln Arg Tyr Gly Pro Gly Thr Val Lys Leu Leu Phe
Met 435 440 445 Lys Gln Tyr Gly Lys Phe Thr Asp Ile 450 455 7 4266
DNA Staphylococcus aureus 7 atgacagagc aacaaaaatt taaagtgctt
gctgatcaaa ttaaaatttc aaatcaatta 60 gatgctgaaa ttttaaattc
aggtgaactg acacgtatag atgtttctaa caaaaacaga 120 acatgggaat
ttcatattac attaccacaa ttcttagctc atgaagatta tttattattt 180
ataaatgcaa tagagcaaga gtttaaagat atcgccaacg ttacatgtcg ttttacggta
240 acaaatggca cgaatcaaga tgaacatgca attaaatact ttgggcactg
tattgaccaa 300 acagctttat ctccaaaagt taaaggtcaa ttgaaacaga
aaaagcttat tatgtctgga 360 aaagtattaa aagtaatggt atcaaatgac
attgaacgta atcattttga taaggcatgt 420 aatggaagtc ttatcaaagc
gtttagaaat tgtggttttg atatcgataa aatcatattc 480 gaaacaaatg
ataatgatca agaacaaaac ttagcttctt tagaagcaca tattcaagaa 540
gaagacgaac aaagtgcacg attggcaaca gagaaacttg aaaaaatgaa agctgaaaaa
600 gcgaaacaac aagataacaa gcaaagtgct gtcgataagt gtcaaattgg
taagccgatt 660 caaattgaaa atattaaacc aattgaatct attattgagg
aagagtttaa agttgcaata 720 gagggtgtca tttttgatat aaacttaaaa
gaacttaaaa gtggtcgcca tatcgtagaa 780 attaaagtga ctgactatac
ggactcttta gttttaaaaa tgtttactcg taaaaacaaa 840 gatgatttag
aacattttaa agcgctaagt gttggtaaat gggttagggc tcaaggtcgt 900
attgaagaag atacatttat tagagattta gttatgatga tgtctgatat tgaagagatt
960 aaaaaagcga caaaaaaaga taaggctgaa gaaaagcgag tagaattcca
cttgcatact 1020 gcaatgagcc aaatggatgg tatacccaat attggtgcgt
atgttaaaca ggcagcagac 1080 tggggacatc cagccattgc ggttacagac
cataatgtgg tgcaagcatt tccagatgct 1140 cacgcagcag cggaaaaaca
tggcattaaa atgatatacg gtatggaagg tatgttagtt 1200 gatgatggtg
ttccgattgc atacaaacca caagatgtcg tattaaaaga tgctacttat 1260
gttgtgttcg acgttgagac aactggttta tcaaatcagt atgataaaat catcgagctt
1320 gcagctgtga aagttcataa cggtgaaatc atcgataagt ttgaaaggtt
tagtaatccg 1380 catgaacgat tatcggaaac gattatcaat ttgacgcata
ttactgatga tatgttagta 1440 gatgcccctg agattgaaga agtacttaca
gagtttaaag aatgggttgg cgatgcgata 1500 ttcgtagcgc ataatgcttc
gtttgatatg ggcttcatcg atacgggata tgaacgtctt 1560 gggtttggac
catcaacgaa tggtgttatc gatactttag aattatctcg tacgattaat 1620
actgaatatg gtaaacatgg tttgaatttc ttggctaaaa aatatggcgt agaattaacg
1680 caacatcacc gtgccattta tgatacagaa gcaacagctt acattttcat
aaaaatggtt 1740 caacaaatga aagaattagg cgtattaaat cataacgaaa
tcaacaaaaa actcagtaat 1800 gaagatgcat ataaacgtgc aagacctagt
catgtcacat taattgtaca aaaccaacaa 1860 ggtcttaaaa atctatttaa
aattgtaagt gcatcattgg tgaagtattt ctaccgtaca 1920 cctcgaattc
cacgttcatt gttagatgaa tatcgtgagg gattattggt aggtacagcg 1980
tgtgatgaag gtgaattatt tacggcagtt atgcagaagg accagagtca agttgaaaaa
2040 attgccaaat attatgattt tattgaaatt caaccaccgg cactttatca
agatttaatt 2100 gatagagagc ttattagaga tactgaaaca ttacatgaaa
tttatcaacg tttaatacat 2160 gcaggtgaca cagcgggtat acctgttatt
gcgacaggaa atgcacacta tttgtttgaa 2220 catgatggta tcgcacgtaa
aattttaata gcatcacaac ccggcaatcc acttaatcgc 2280 tcaactttac
cggaagcaca ttttagaact acagatgaaa tgttaaacga gtttcatttt 2340
ttaggtgaag aaaaagcgca tgaaattgtt gtgaaaaata caaacgaatt agcagatcga
2400 attgaacgtg ttgttcctat taaagatgaa ttatacacac cgcgtatgga
aggtgctaac 2460 gaagaaatta gagaactaag ttatgcaaat gcgcgtaaac
tgtatggtga agacctgcct 2520 caaatcgtaa ttgatcgatt agaaaaagaa
ttaaaaagta ttatcggtaa tggatttgcg 2580 gtaatttact taatttcgca
acgtttagtt aaaaaatcat tagatgatgg atacttagtt 2640 ggttcccgtg
gttcagtagg ttctagtttt gtagcgacaa tgactgagat tactgaagta 2700
aacccgttac cgccacacta tatttgtccg aactgtaaaa cgagtgaatt tttcaatgat
2760 ggttcagtag gatcaggatt tgatttacct gataagacgt gtgaaacttg
tggagcgcca 2820 cttattaaag aaggacaaga tattccgttt gaaaaatttt
taggatttaa gggagataaa 2880 gttcctgata tcgacttaaa ctttagtggt
gaatatcaac cgaatgccca taactacaca 2940 aaagtattat ttggtgagga
taaagtattc cgtgcaggta caattggtac tgttgctgaa 3000 aagactgctt
ttggttatgt taaaggttat ttgaatgatc aaggtatcca caaaagaggt 3060
gctgaaatag atcgactcgt taaaggatgt acaggtgtac ctgattacat ggatatttat
3120 gattttacgc cgatacaata tcctgccgat gatcaaaatt cagcatggat
gacgacacat 3180 tttgatttcc attctattca tgataatgta ttaaaacttg
atatacttgg acacgatgat 3240 ccaacaatga ttcgtatgct tcaagattta
tcaggaattg atccaaaaac aatacctgta 3300 gatgataaag aagttatgca
gatatttagt acacctgaaa gtttgggtgt tactgaagat 3360 gaaattttat
gtaaaacagg tacatttggg gtaccgaatt cggacaggat tcgtcgtcaa 3420
atgttagaag atacaaagcc aacaacattt tctgaattag ttcaaatctc aggattatct
3480 catggtacag atgtgtggtt aggcaatgct caagaattaa ttaaaaccgg
tatatgtgat 3540 ttatcaagtg taattggttg tcgtgatgat atcatggttt
atttaatgta tgctggttta 3600 gaaccatcaa tggcttttaa aataatggag
tcagtacgta aaggtaaagg tttaactgaa 3660 gaaatgattg aaacgatgaa
agaaaatgaa gtgccagatt ggtatttaga ttcatgtctt 3720 aaaattaagt
acatattccc taaagcccat gcagcagcat acgttttaat ggcagtacgt 3780
atcgcatatt tcaaagtaca tcatccactt tattactatg catcttactt tacaattcgt
3840 gcgtcagact ttgatttaat cacgatgatt aaagataaaa caagcattcg
aaatactgta 3900 aaagacatgt attctcgcta tatggatcta ggtaaaaaag
aaaaagacgt attaacagtc 3960 ttggaaatta tgaatgaaat ggcgcatcga
ggttatcgaa tgcaaccgat tagtttagaa 4020 aagagtcagg cgttcgaatt
tatcattgaa ggcgatacac ttattccgcc gttcatatca 4080 gtgcctgggc
ttggcgaaaa cgttgcgaaa cgaattgttg aagctcgtga cgatggccca 4140
tttttatcaa aagaagattt aaacaaaaaa gctggattat atcagaaaat tattgagtat
4200 ttagatgagt taggctcatt accgaattta ccagataaag ctcaactttc
gatatttgat 4260 atgtaa 4266 8 1435 PRT Staphylococcus aureus 8 Met
Thr Glu Gln Gln Lys Phe Lys Val Leu Ala Asp Gln Ile Lys Ile 1 5 10
15 Ser Asn Gln Leu Asp Ala Glu Ile Leu Asn Ser Gly Glu Leu Thr Arg
20 25 30 Ile Asp Val Ser Asn Lys Asn Arg Thr Trp Glu Phe His Ile
Thr Leu 35 40 45 Pro Gln Phe Leu Ala His Glu Asp Tyr Leu Leu Phe
Ile Asn Ala Ile 50 55 60 Glu Gln Glu Phe Lys Asp Ile Ala Asn Val
Thr Cys Arg Phe Thr Val 65 70 75 80 Thr Asn Gly Thr Asn Gln Asp Glu
His Ala Ile Lys Tyr Phe Gly His 85 90 95 Cys Ile Asp Gln Thr Ala
Leu Ser Pro Lys Val Lys Gly Gln Leu Lys 100 105 110 Gln Lys Lys Leu
Ile Met Ser Gly Lys Val Leu Lys Val Met Val Ser 115 120 125 Asn Asp
Ile Glu Arg Asn His Phe Asp Lys Ala Cys Asn Gly Ser Leu 130 135 140
Ile Lys Ala Phe Arg Asn Cys Gly Phe Asp Ile Asp Lys Ile Ile Phe 145
150 155 160 Glu Thr Asn Asp Asn Asp Gln Glu Gln Asn Leu Ala Ser Leu
Glu Ala 165 170 175 His Ile Gln Glu Glu Asp Glu Gln Ser Ala Arg Leu
Ala Thr Glu Lys 180 185 190 Leu Glu Lys Met Lys Ala Glu Lys Ala Lys
Gln Gln Asp Asn Lys Gln 195 200 205 Ser Ala Val Asp Lys Cys Gln Ile
Gly Lys Pro Ile Gln Ile Glu Asn 210 215 220 Ile Lys Pro Ile Glu Ser
Ile Ile Glu Glu Glu Phe Lys Val Ala Ile 225 230 235 240 Glu Gly Val
Ile Phe Asp Ile Asn Leu Lys Glu Leu Lys Ser Gly Arg 245 250 255 His
Ile Val Glu Ile Lys Val Thr Asp Tyr Thr Asp Ser Leu Val Leu 260 265
270 Lys Met Phe Thr Arg Lys Asn Lys Asp Asp Leu Glu His Phe Lys Ala
275 280 285 Leu Ser Val Gly Lys Trp Val Arg Ala Gln Gly Arg Ile Glu
Glu Asp 290 295 300 Thr Phe Ile Arg Asp Leu Val Met Met Met Ser Asp
Ile Glu Glu Ile 305 310 315 320 Lys Lys Ala Thr Lys Lys Asp Lys Ala
Glu Glu Lys Arg Val Glu Phe 325 330 335 His Leu His Thr Ala Met Ser
Gln Met Asp Gly Ile Pro Asn Ile Gly 340 345 350 Ala Tyr Val Lys Gln
Ala Ala Asp Trp Gly His Pro Ala Ile Ala Val 355 360 365 Thr Asp His
Asn Val Val Gln Ala Phe Pro Asp Ala His Ala Ala Ala 370 375 380 Glu
Lys His Gly Ile Lys Met Ile Tyr Gly Met Glu Gly Met Leu Val 385 390
395 400 Asp Asp Gly Val Pro Ile Ala Tyr Lys Pro Gln Asp Val Val Leu
Lys 405 410 415 Asp Ala Thr Tyr Val Val Phe Asp Val Glu Thr Thr Gly
Leu Ser Asn 420 425 430 Gln Tyr Asp Lys Ile Ile Glu Leu Ala Ala Val
Lys Val His Asn Gly 435 440 445 Glu Ile Ile Asp Lys Phe Glu Arg Phe
Ser Asn Pro His Glu Arg Leu 450 455 460 Ser Glu Thr Ile Ile Asn Leu
Thr His Ile Thr Asp Asp Met Leu Val 465 470 475 480 Asp Ala Pro Glu
Ile Glu Glu Val Leu Thr Glu Phe Lys Glu Trp Val 485 490 495 Gly Asp
Ala Ile Phe Val Ala His Asn Ala Ser Phe Asp Met Gly Phe 500 505 510
Ile Asp Thr Gly Tyr Glu Arg Leu Gly Phe Gly Pro Ser Thr Asn Gly 515
520 525 Val Ile Asp Thr Leu Glu Leu Ser Arg Thr Ile Asn Thr Glu Tyr
Gly 530 535 540 Lys His Gly Leu Asn Phe Leu Ala Lys Lys Tyr Gly Val
Glu Leu Thr 545 550 555 560 Gln His His Arg Ala Ile Tyr Asp Thr Glu
Ala Thr Ala Tyr Ile Phe 565 570 575 Ile Lys Met Val Gln Gln Met Lys
Glu Leu Gly Val Leu Asn His Asn 580 585 590 Glu Ile Asn Lys Lys Leu
Ser Asn Glu Asp Ala Tyr Lys Arg Ala Arg 595 600 605 Pro Ser His Val
Thr Leu Ile Val Gln Asn Gln Gln Gly Leu Lys Asn 610 615 620 Leu Phe
Lys Ile Val Ser Ala Ser Leu Val Lys Tyr Phe Tyr Arg Thr 625 630 635
640 Pro Arg Ile Pro Arg Ser Leu Leu Asp Glu Tyr Arg Glu Gly Leu Leu
645 650 655 Val Gly Thr Ala Cys Asp Glu Gly Glu Leu Phe Thr Ala Val
Met Gln 660 665 670 Lys Asp Gln Ser Gln Val Glu Lys Ile Ala Lys Tyr
Tyr Asp Phe Ile 675 680 685 Glu Ile Gln Pro Pro Ala Leu Tyr Gln Asp
Leu Ile Asp Arg Glu Leu 690 695 700 Ile Arg Asp Thr Glu Thr Leu His
Glu Ile Tyr Gln Arg Leu Ile His 705 710 715 720 Ala Gly Asp Thr Ala
Gly Ile Pro Val Ile Ala Thr Gly Asn Ala His 725 730 735 Tyr Leu Phe
Glu His Asp Gly Ile Ala Arg Lys Ile Leu Ile Ala Ser 740 745 750 Gln
Pro Gly Asn Pro Leu Asn Arg Ser Thr Leu Pro Glu Ala His Phe 755 760
765 Arg Thr Thr Asp Glu Met Leu Asn Glu Phe His Phe Leu Gly Glu Glu
770 775 780 Lys Ala His Glu Ile Val Val Lys Asn Thr Asn Glu Leu Ala
Asp Arg 785 790 795 800 Ile Glu Arg Val Val Pro Ile Lys Asp Glu Leu
Tyr Thr Pro Arg Met 805 810 815 Glu Gly Ala Asn Glu Glu Ile Arg Glu
Leu Ser Tyr Ala Asn Ala Arg 820 825 830 Lys Leu Tyr Gly Glu Asp Leu
Pro Gln Ile Val Ile Asp Arg Leu Glu 835 840 845 Lys Glu Leu Lys Ser
Ile Ile Gly Asn Gly Phe Ala Val Ile Tyr Leu 850 855 860 Ile Ser Gln
Arg Leu Val Lys Lys Ser Leu Asp Asp Gly Tyr Leu Val 865 870 875 880
Gly Ser Arg Gly Ser Val Gly Ser Ser Phe Val Ala Thr Met Thr Glu 885
890 895 Ile Thr Glu Val Asn Pro Leu Pro Pro His Tyr Ile Cys Pro Asn
Cys 900 905 910 Lys Thr Ser Glu Phe Phe Asn Asp Gly Ser Val Gly Ser
Gly Phe Asp 915 920 925 Leu Pro Asp Lys Thr Cys Glu Thr Cys Gly Ala
Pro Leu Ile Lys Glu 930 935 940 Gly Gln Asp Ile Pro Phe Glu Lys Phe
Leu Gly Phe Lys Gly Asp Lys 945 950 955 960 Val Pro Asp Ile Asp Leu
Asn Phe Ser Gly Glu Tyr Gln Pro Asn Ala 965 970 975 His Asn Tyr Thr
Lys Val Leu Phe Gly Glu Asp Lys Val Phe Arg Ala 980 985 990 Gly Thr
Ile Gly Thr Val Ala Glu Lys Thr Ala Phe Gly Tyr Val Lys 995 1000
1005 Gly Tyr Leu Asn Asp Gln Gly Ile His Lys Arg Gly Ala Glu Ile
Asp 1010 1015 1020 Arg Leu Val Lys Gly Cys Thr Gly Val Arg Ala Thr
Thr Gly Gln His 1025 1030 1035 1040 Pro Gly Gly Ile Ile Val Val Pro
Asp Tyr Met Asp Ile Tyr Asp Phe 1045 1050 1055 Thr Pro Ile Gln Tyr
Pro Ala Asp Asp Gln Asn Ser Ala Trp Met Thr 1060 1065 1070 Thr His
Phe Asp Phe His Ser Ile His Asp Asn Val Leu Lys Leu Asp 1075 1080
1085 Ile Leu Gly His Asp Asp Pro Thr Met Ile Arg Met Leu Gln Asp
Leu 1090 1095 1100 Ser Gly Ile Asp Pro Lys Thr Ile Pro Val Asp Asp
Lys Glu Val Met 1105 1110 1115 1120 Gln Ile Phe Ser Thr Pro Glu Ser
Leu Gly Val Thr Glu Asp Glu Ile 1125 1130 1135 Leu Cys Lys Thr Gly
Thr Phe Gly Val Pro Asn Ser Asp Arg Ile Arg 1140 1145 1150 Arg Gln
Met Leu Glu Asp Thr Lys Pro Thr Thr Phe Ser Glu Leu Val 1155 1160
1165 Gln Ile Ser Gly Leu Ser His Gly Thr Asp Val Trp Leu Gly Asn
Ala 1170 1175 1180 Gln Glu Leu Ile Lys Thr Gly Ile Cys Asp Leu Ser
Ser Val Ile Gly 1185 1190 1195 1200 Cys Arg Asp Asp Ile Met Val Tyr
Leu Met Tyr Ala Gly Leu Glu Pro 1205 1210 1215 Ser Met Ala Phe Lys
Ile Met Glu Ser Val Arg Lys Gly Lys Gly Leu 1220 1225 1230 Thr Glu
Glu Met Ile Glu Thr Met Lys Glu Asn Glu Val Pro Asp Trp 1235 1240
1245 Tyr Leu Asp Ser Cys Leu Lys Ile Lys Tyr Ile Phe Pro Lys Ala
His 1250 1255 1260 Ala Ala Ala Tyr Val Leu Met Ala Val Arg Ile Ala
Tyr Phe Lys Val 1265 1270 1275 1280 His His Pro Leu Tyr Tyr Tyr Ala
Ser Tyr Phe Thr Ile Arg Ala Ser 1285 1290 1295 Asp Phe Asp Leu Ile
Thr Met Ile Lys Asp Lys Thr Ser Ile Arg Asn 1300 1305 1310 Thr Val
Lys Asp Met Tyr Ser Arg Tyr Met Asp Leu Gly Lys Lys Glu 1315 1320
1325 Lys Asp Val Leu Thr Val Leu Glu Ile Met Asn Glu Met Ala His
Arg 1330 1335 1340 Gly Tyr Arg Met Gln Pro Ile Ser Leu Glu Lys Ser
Gln Ala Phe Glu 1345 1350 1355 1360 Phe Ile Ile Glu Gly Asp Thr Leu
Ile Pro Pro Phe Ile Ser Val Pro 1365 1370 1375 Gly Leu Gly Glu Asn
Val Ala Lys Arg Ile Val Glu Ala Arg Asp Asp 1380 1385 1390 Gly Pro
Phe Leu Ser Lys Glu Asp Leu Asn Lys Lys Ala Gly Leu Tyr 1395 1400
1405 Gln Lys Ile Ile Glu Tyr Leu Asp Glu Leu Gly Ser Leu Pro Asn
Leu 1410 1415 1420 Pro Asp Lys Ala Gln Leu Ser Ile Phe Asp Met 1425
1430 1435 9 1134 DNA Staphylococcus aureus 9 atgatggaat tcactattaa
aagagattat tttattacac aattaaatga cacattaaaa 60 gctatttcac
caagaacaac attacctata ttaactggta tcaaaatcga tgcgaaagaa 120
catgaagtta tattaactgg ttcagactct gaaatttcaa tagaaatcac tattcctaaa
180 actgtagatg gcgaagatat tgtcaatatt tcagaaacag gctcagtagt
acttcctgga 240 cgattctttg ttgatattat aaaaaaatta cctggtaaag
atgttaaatt atctacaaat 300 gaacaattcc agacattaat tacatcaggt
cattctgaat ttaatttgag tggcttagat 360 ccagatcaat atcctttatt
acctcaagtt tctagagatg acgcaattca attgtcggta 420 aaagtactta
aaaacgtgat tgcacaaacg aattttgcag tgtccacctc agaaacacgc 480
ccagtactaa ctggtgtgaa ctggcttata caagaaaatg aattaatatg cacagcgact
540 gattcacacc gcttggctgt aagaaagttg cagttagaag atgtttctga
aaacaaaaat 600 gtcatcattc caggtaaggc tttagctgaa ttaaataaaa
ttatgtctga caatgaagaa 660 gacattgata tcttctttgc ttcaaaccaa
gttttattta aagttggaaa tgtgaacttt 720 atttctcgat tattagaagg
acattatcct gatacaacac gtttattccc tgaaaactat 780 gaaattaaat
taagtataga caatggggag ttttatcatg cgattgatcg tgcctcttta 840
ttagcacgtg aaggtggtaa taacgttatt aaattaagta caggtgatga cgttgttgaa
900 ttatcttcta catcaccaga aattggtact gtaaaagaag aagttgatgc
aaacgatgtt 960 gaaggtggta gcctgaaaat ttcattcaac tctaaatata
tgatggatgc tttaaaagca 1020 atcgataatg atgaggttga agttgaattc
ttcggtacaa tgaaaccatt tattctaaaa 1080 ccaaaaggtg acgactcggt
aacgcaatta attttaccaa tcagaactta ctaa 1134 10 377 PRT
Staphylococcus aureus 10 Met Met Glu Phe Thr Ile Lys Arg Asp Tyr
Phe Ile Thr Gln Leu Asn 1 5 10 15 Asp Thr Leu Lys Ala Ile Ser Pro
Arg Thr Thr Leu Pro Ile Leu Thr 20
25 30 Gly Ile Lys Ile Asp Ala Lys Glu His Glu Val Ile Leu Thr Gly
Ser 35 40 45 Asp Ser Glu Ile Ser Ile Glu Ile Thr Ile Pro Lys Thr
Val Asp Gly 50 55 60 Glu Asp Ile Val Asn Ile Ser Glu Thr Gly Ser
Val Val Leu Pro Gly 65 70 75 80 Arg Phe Phe Val Asp Ile Ile Lys Lys
Leu Pro Gly Lys Asp Val Lys 85 90 95 Leu Ser Thr Asn Glu Gln Phe
Gln Thr Leu Ile Thr Ser Gly His Ser 100 105 110 Glu Phe Asn Leu Ser
Gly Leu Asp Pro Asp Gln Tyr Pro Leu Leu Pro 115 120 125 Gln Val Ser
Arg Asp Asp Ala Ile Gln Leu Ser Val Lys Val Leu Lys 130 135 140 Asn
Val Ile Ala Gln Thr Asn Phe Ala Val Ser Thr Ser Glu Thr Arg 145 150
155 160 Pro Val Leu Thr Gly Val Asn Trp Leu Ile Gln Glu Asn Glu Leu
Ile 165 170 175 Cys Thr Ala Thr Asp Ser His Arg Leu Ala Val Arg Lys
Leu Gln Leu 180 185 190 Glu Asp Val Ser Glu Asn Lys Asn Val Ile Ile
Pro Gly Lys Ala Leu 195 200 205 Ala Glu Leu Asn Lys Ile Met Ser Asp
Asn Glu Glu Asp Ile Asp Ile 210 215 220 Phe Phe Ala Ser Asn Gln Val
Leu Phe Lys Val Gly Asn Val Asn Phe 225 230 235 240 Ile Ser Arg Leu
Leu Glu Gly His Tyr Pro Asp Thr Thr Arg Leu Phe 245 250 255 Pro Glu
Asn Tyr Glu Ile Lys Leu Ser Ile Asp Asn Gly Glu Phe Tyr 260 265 270
His Ala Ile Asp Arg Ala Ser Leu Leu Ala Arg Glu Gly Gly Asn Asn 275
280 285 Val Ile Lys Leu Ser Thr Gly Asp Asp Val Val Glu Leu Ser Ser
Thr 290 295 300 Ser Pro Glu Ile Gly Thr Val Lys Glu Glu Val Asp Ala
Asn Asp Val 305 310 315 320 Glu Gly Gly Ser Leu Lys Ile Ser Phe Asn
Ser Lys Tyr Met Met Asp 325 330 335 Ala Leu Lys Ala Ile Asp Asn Asp
Glu Val Glu Val Glu Phe Phe Gly 340 345 350 Thr Met Lys Pro Phe Ile
Leu Lys Pro Lys Gly Asp Asp Ser Val Thr 355 360 365 Gln Leu Ile Leu
Pro Ile Arg Thr Tyr 370 375 11 1719 DNA Staphylococcus aureus 11
atgataggtt tgtgtccttt tcatgatgaa aagacacctt catttacagt ttctgaagat
60 aaacaaatct gtcattgttt tggttgtaaa aaaggtggca atgtttttca
atttactcaa 120 gaaattaaag acatatcatt tgttgaagcg gttaaagaat
taggtgatag agttaatgtt 180 gctgtagata ttgaggcaac acaatctaac
tcaaatgttc aaattgcttc tgatgattta 240 caaatgattg aaatgcatga
gttaatacaa gaattttatt attacgcttt aacaaagaca 300 gtcgaaggcg
aacaagcatt aacatactta caagaacgtg gttttacaga tgcgcttatt 360
aaagagcgag gcattggctt tgcacccgat agctcacatt tttgtcatga ttttcttcaa
420 aaaaagggtt acgatattga attagcatat gaagccggat tattatcacg
taacgaagaa 480 aatttcagtt attacgatag atttcgaaat cgtattatgt
ttcctttgaa aaatgcgcaa 540 ggaagaattg ttggatattc aggtcgaaca
tataccggtc aagaaccaaa atacctaaat 600 agtcctgaaa cgcctatctt
tcaaaaaaga aagttgttat ataacttaga taaagcacgt 660 aaatcaatta
gaaaattaga tgaaattgta ttactagaag gttttatgga tgttataaaa 720
tctgatactg ctggcttgaa aaacgttgtt gcaacaatgg gtacacagtt gtcagatgaa
780 catattacct ttatacgaaa gttaacatca aatataacat taatgtttga
tggggatttt 840 gcgggtagtg aagcaacact taaaacaggt caacatttgt
tacagcaagg gctaaatgta 900 tttgttatac aattgccatc tggcatggat
ccggatgaat acattggtaa gtatggcaac 960 gacgcattta ctacttttgt
aaaaaatgac aaaaagtcat ttgcacatta taaagtaagt 1020 atattaaaag
atgaaattgc acataatgac ctttcatatg aacgttattt gaaagaactg 1080
agtcatgaca tttcacttat gaagtcatca attctgcaac aaaaggctat aaatgatgtt
1140 gcgccatttt tcaatgttag tcctgagcag ttagctaacg aaatacaatt
caatcaagca 1200 ccagccaatt attatccaga agatgagtat ggcggttatg
atgagtatgg cggttatatt 1260 gaacctgagc caattggtat ggcacaattt
gacaatttga gccgtcgaga aaaagcggag 1320 cgagcatttt taaaacattt
aatgagagat aaagatacat ttttaaatta ttatgaaagt 1380 gttgataagg
ataacttcac aaatcagcat tttaaatatg tattcgaagt cttacatgat 1440
ttttatgcgg aaaatgatca atataatatc agtgatgctg tgcagtatgt taattcaaat
1500 gagttgagag aaacactaat tagcttagaa caatataatt tgaatggcga
accatatgaa 1560 aatgaaattg atgattatgt caatgttatt aatgaaaaag
gacaagaaac aattgagtca 1620 ttgaatcata aattaaggga agctacaagg
attggcgatg tagaattaca aaaatactat 1680 ttacagcaaa ttgttgctaa
gaataaagaa cgcatgtag 1719 12 572 PRT Staphylococcus aureus 12 Met
Ile Gly Leu Cys Pro Phe His Asp Glu Lys Thr Pro Ser Phe Thr 1 5 10
15 Val Ser Glu Asp Lys Gln Ile Cys His Cys Phe Gly Cys Lys Lys Gly
20 25 30 Gly Asn Val Phe Gln Phe Thr Gln Glu Ile Lys Asp Ile Ser
Phe Val 35 40 45 Glu Ala Val Lys Glu Leu Gly Asp Arg Val Asn Val
Ala Val Asp Ile 50 55 60 Glu Ala Thr Gln Ser Asn Ser Asn Val Gln
Ile Ala Ser Asp Asp Leu 65 70 75 80 Gln Met Ile Glu Met His Glu Leu
Ile Gln Glu Phe Tyr Tyr Tyr Ala 85 90 95 Leu Thr Lys Thr Val Glu
Gly Glu Gln Ala Leu Thr Tyr Leu Gln Glu 100 105 110 Arg Gly Phe Thr
Asp Ala Leu Ile Lys Glu Arg Gly Ile Gly Phe Ala 115 120 125 Pro Asp
Ser Ser His Phe Cys His Asp Phe Leu Gln Lys Lys Gly Tyr 130 135 140
Asp Ile Glu Leu Ala Tyr Glu Ala Gly Leu Leu Ser Arg Asn Glu Glu 145
150 155 160 Asn Phe Ser Tyr Tyr Asp Arg Phe Arg Asn Arg Ile Met Phe
Pro Leu 165 170 175 Lys Asn Ala Gln Gly Arg Ile Val Gly Tyr Ser Gly
Arg Thr Tyr Thr 180 185 190 Gly Gln Glu Pro Lys Tyr Leu Asn Ser Pro
Glu Thr Pro Ile Phe Gln 195 200 205 Lys Arg Lys Leu Leu Tyr Asn Leu
Asp Lys Ala Arg Lys Ser Ile Arg 210 215 220 Lys Leu Asp Glu Ile Val
Leu Leu Glu Gly Phe Met Asp Val Ile Lys 225 230 235 240 Ser Asp Thr
Ala Gly Leu Lys Asn Val Val Ala Thr Met Gly Thr Gln 245 250 255 Leu
Ser Asp Glu His Ile Thr Phe Ile Arg Lys Leu Thr Ser Asn Ile 260 265
270 Thr Leu Met Phe Asp Gly Asp Phe Ala Gly Ser Glu Ala Thr Leu Lys
275 280 285 Thr Gly Gln His Leu Leu Gln Gln Gly Leu Asn Val Phe Val
Ile Gln 290 295 300 Leu Pro Ser Gly Met Asp Pro Asp Glu Tyr Ile Gly
Lys Tyr Gly Asn 305 310 315 320 Asp Ala Phe Thr Thr Phe Val Lys Asn
Asp Lys Lys Ser Phe Ala His 325 330 335 Tyr Lys Val Ser Ile Leu Lys
Asp Glu Ile Ala His Asn Asp Leu Ser 340 345 350 Tyr Glu Arg Tyr Leu
Lys Glu Leu Ser His Asp Ile Ser Leu Met Lys 355 360 365 Ser Ser Ile
Leu Gln Gln Lys Ala Ile Asn Asp Val Ala Pro Phe Phe 370 375 380 Asn
Val Ser Pro Glu Gln Leu Ala Asn Glu Ile Gln Phe Asn Gln Ala 385 390
395 400 Pro Ala Asn Tyr Tyr Pro Glu Asp Glu Tyr Gly Gly Tyr Asp Glu
Tyr 405 410 415 Gly Gly Tyr Ile Glu Pro Glu Pro Ile Gly Met Ala Gln
Phe Asp Asn 420 425 430 Leu Ser Arg Arg Glu Lys Ala Glu Arg Ala Phe
Leu Lys His Leu Met 435 440 445 Arg Asp Lys Asp Thr Phe Leu Asn Tyr
Tyr Glu Ser Val Asp Lys Asp 450 455 460 Asn Phe Thr Asn Gln His Phe
Lys Tyr Val Phe Glu Val Leu His Asp 465 470 475 480 Phe Tyr Ala Glu
Asn Asp Gln Tyr Asn Ile Ser Asp Ala Val Gln Tyr 485 490 495 Val Asn
Ser Asn Glu Leu Arg Glu Thr Leu Ile Ser Leu Glu Gln Tyr 500 505 510
Asn Leu Asn Gly Glu Pro Tyr Glu Asn Glu Ile Asp Asp Tyr Val Asn 515
520 525 Val Ile Asn Glu Lys Gly Gln Glu Thr Ile Glu Ser Leu Asn His
Lys 530 535 540 Leu Arg Glu Ala Thr Arg Ile Gly Asp Val Glu Leu Gln
Lys Tyr Tyr 545 550 555 560 Leu Gln Gln Ile Val Ala Lys Asn Lys Glu
Arg Met 565 570 13 29 DNA Staphylococcus aureus 13 ggtggtaatt
gtcttgcata tgacagagc 29 14 30 DNA Staphylococcus aureus 14
agcgattaag tggattgccg ggttgtgatg 30 15 31 DNA Staphylococcus aureus
15 agcatcacaa cccggcaatc cacttaatcg c 31 16 29 DNA Staphylococcus
aureus 16 gactacgcca tgggcattaa ataaatacc 29 17 31 DNA
Staphylococcus aureus 17 gaagatgcat ataaacgtgc aagacctagt c 31 18
34 DNA Staphylococcus aureus 18 gtctgacgca cgaattgtaa agtaagatgc
atag 34 19 36 DNA Staphylococcus aureus 19 cgactggaag gagttttaac
atatgatgga attcac 36 20 30 DNA Staphylococcus aureus 20 ttatatggat
ccttagtaag ttctgattgg 30 21 15 PRT Staphylococcus aureus 21 Leu Leu
Phe Glu Arg Phe Leu Asn Pro Glu Arg Val Ser Met Pro 1 5 10 15 22 15
PRT Staphylococcus aureus 22 Lys Phe Ala Gly Tyr Gly Phe Asn Lys
Ser His Ser Ala Ala Tyr 1 5 10 15 23 44 DNA Staphylococcus aureus
23 cttctttttg aaagatttct aaataaagaa cgttattcaa tgcc 44 24 45 DNA
Staphylococcus aureus 24 ataagctgca gcatgacttt tattaaaacc
ataacctgca aattt 45 25 39 DNA Staphylococcus aureus 25 agttaaaaat
gccatatttt gacgtgtttt agttctaat 39 26 42 DNA Staphylococcus aureus
26 cttgcaaaag cggttgctaa agatgttgga cgaattatgg gg 42 27 10 PRT
Staphylococcus aureus 27 His Ala Tyr Leu Phe Ser Gly Pro Arg Gly 1
5 10 28 11 PRT Staphylococcus aureus 28 Ala Leu Leu Lys Thr Leu Glu
Glu Pro Pro Glu 1 5 10 29 38 DNA Staphylococcus aureus 29
cgcggatccc atgcatattt attttcaggt ccaagagg 38 30 10 PRT
Staphylococcus aureus 30 His Ala Tyr Leu Phe Ser Gly Pro Arg Gly 1
5 10 31 39 DNA Staphylococcus aureus 31 ccggaattct ggtggttctt
ctaatgtttt taataatgc 39 32 11 PRT Staphylococcus aureus 32 Ala Leu
Leu Lys Thr Leu Glu Glu Pro Pro Glu 1 5 10 33 38 DNA Staphylococcus
aureus 33 tttgtaaagg cattacgcag gggactaatt cagatgtg 38 34 33 DNA
Staphylococcus aureus 34 tatgacattc attacaaggt tctccatcag tgc 33 35
29 DNA Staphylococcus aureus 35 gagcactgat gaacttagaa ttagatatg 29
36 32 DNA Staphylococcus aureus 36 gatactcagt atctttctca gatgttttat
tc 32 37 14 PRT Staphylococcus aureus 37 Asp Leu Ile Ile Val Ala
Ala Arg Pro Ser Met Gly Lys Thr 1 5 10 38 15 PRT Staphylococcus
aureus 38 Glu Ile Ile Ile Gly Lys Gln Arg Asn Gly Pro Ile Gly Thr
Val 1 5 10 15 39 41 DNA Staphylococcus aureus 39 gaccttataa
ttgtagctgc acgtccttct atgggaaaaa c 41 40 48 DNA Staphylococcus
aureus 40 aacattatta agtcagcatc ttgttctatt gatccagatt caacgaag 48
41 45 DNA Staphylococcus aureus 41 gatttgtagt tctggtaatg ttgactcaaa
ccgcttaaga accgg 45 42 48 DNA Staphylococcus aureus 42 atacgtgtgg
ttaactgatc agcaacccat ctctagtgag aaaatacc 48 43 31 DNA
Staphylococcus aureus 43 cgttttaatg catgcttaga aacgatatca g 31 44
31 DNA Staphylococcus aureus 44 cattgctaag caacgttacg gtccaacagg c
31
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