U.S. patent application number 11/687962 was filed with the patent office on 2007-07-12 for plant myb transcription factor homologs.
Invention is credited to Rebecca E. Cahoon, Yiwen Fang, Joan T. Odell, Zude Weng.
Application Number | 20070161035 11/687962 |
Document ID | / |
Family ID | 46280203 |
Filed Date | 2007-07-12 |
United States Patent
Application |
20070161035 |
Kind Code |
A1 |
Cahoon; Rebecca E. ; et
al. |
July 12, 2007 |
Plant Myb Transcription Factor Homologs
Abstract
This invention relates to an isolated nucleic acid fragment
encoding a Myb-related transcription factor. The invention also
relates to the construction of a chimeric gene encoding all or a
portion of the Myb-related transcription factor, in sense or
antisense orientation, wherein expression of the chimeric gene
results in production of altered levels of the Myb-related
transcription factor in a transformed host cell.
Inventors: |
Cahoon; Rebecca E.; (Webster
Grove, MO) ; Fang; Yiwen; (Los Angeles, CA) ;
Odell; Joan T.; (Unionville, PA) ; Weng; Zude;
(Vernon Hill, IL) |
Correspondence
Address: |
E I DU PONT DE NEMOURS AND COMPANY;LEGAL PATENT RECORDS CENTER
BARLEY MILL PLAZA 25/1128
4417 LANCASTER PIKE
WILMINGTON
DE
19805
US
|
Family ID: |
46280203 |
Appl. No.: |
11/687962 |
Filed: |
March 19, 2007 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10659869 |
Sep 11, 2003 |
7193132 |
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11687962 |
Mar 19, 2007 |
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10021811 |
Dec 14, 2001 |
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10659869 |
Sep 11, 2003 |
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09452244 |
Dec 1, 1999 |
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10021811 |
Dec 14, 2001 |
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60110609 |
Dec 2, 1998 |
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Current U.S.
Class: |
435/6.12 ;
435/189; 435/419; 435/468; 435/6.13; 435/69.1; 536/23.2 |
Current CPC
Class: |
C12N 15/8216 20130101;
C12Q 1/6895 20130101; C12Q 2600/158 20130101; C12Q 1/6876 20130101;
C12N 15/8241 20130101; C07K 14/415 20130101 |
Class at
Publication: |
435/006 ;
435/069.1; 435/189; 435/419; 435/468; 536/023.2 |
International
Class: |
C12Q 1/68 20060101
C12Q001/68; C07H 21/04 20060101 C07H021/04; C12P 21/06 20060101
C12P021/06; C12N 9/02 20060101 C12N009/02; C12N 5/04 20060101
C12N005/04 |
Claims
1. An isolated polynucleotide comprising a nucleotide sequence
selected from the group consisting of: (a) a first nucleotide
sequence encoding a polypeptide of at least 50 amino acids that has
at least 80% identity based on the Clustal method of alignment when
compared to a polypeptide selected from the group consisting of SEQ
ID NO: 2, SEQ ID NO: 12, and SEQ ID NO:56; (b) a second nucleotide
sequence encoding a polypeptide of at least 50 amino acids that has
at least 85% identity based on the Clustal method of alignment when
compared to a polypeptide selected from the group consisting of SEQ
ID NO: 8 and SEQ ID NO:28; (c) a third nucleotide sequence encoding
a polypeptide of at least 50 amino acids that has at least 90%
identity based on the Clustal method of alignment when compared to
a polypeptide of SEQ ID NO: 16; (d) a fourth nucleotide sequence
encoding a polypeptide of at least 50 amino acids that has at least
95% identity based on the Clustal method of alignment when compared
to polypeptide of SEQ ID NO: 52; (e) a fifth nucleotide sequence
encoding a polypeptide of at least 100 amino acids that has at
least 80% identity based on the Clustal method of alignment when
compared to a polypeptide selected from the group consisting of SEQ
ID NO: 6, SEQ ID NO: 14, SEQ ID NO:50, and SEQ ID NO:58; (f) a
sixth nucleotide sequence encoding a polypeptide of at least 100
amino acids that has at least 85% identity based on the Clustal
method of alignment when compared to SEQ ID NO: 60; (g) a seventh
nucleotide sequence encoding a polypeptide of at least 100 amino
acids that has at least 90% identity based on the Clustal method of
alignment when compared to a polypeptide selected from the group
consisting of SEQ ID NO: 4, SEQ ID NO:10, SEQ ID NO:22, SEQ ID
NO:24, and SEQ ID NO:62; (h) a eighth nucleotide sequence encoding
a polypeptide of at least 100 amino acids that has at least 95%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of SEQ ID NO: 18
and SEQ ID NO:20; (i) a ninth nucleotide sequence encoding a
polypeptide of at least 150 amino acids that has at least 80%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of SEQ ID NO: 26,
SEQ ID NO: 34, SEQ ID NO:38, SEQ ID NO:40, SEQ ID NO:42, SEQ ID
NO:48, and SEQ ID NO:54; (j) a tenth nucleotide sequence encoding a
polypeptide of at least 150 amino acids that has at least 85%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of SEQ ID NO: 32,
SEQ ID NO:44, and SEQ ID NO:46; (k) an eleventh nucleotide sequence
encoding a polypeptide of at least 200 amino acids that has at
least 80% identity based on the Clustal method of alignment when
compared to SEQ ID NO: 36; (l) a twelfth nucleotide sequence
encoding a polypeptide of at least 200 amino acids that has at
least 85% identity based on the Clustal method of alignment when
compared to SEQ ID NO: 30; and (m) a thirteenth nucleotide sequence
comprising the complement of (a), (b), (c), (d), (e), (f), (g),
(h), (i), (j), (k), or (l).
2-16. (canceled)
17. An isolated polynucleotide comprising: (a) a nucleotide
sequence encoding a polypeptide having Myb-related transcription
factor activity, wherein the polypeptide has an amino acid sequence
of at least 90% sequence identity when compared to SEQ ID NO:10,
based on the Clustal V method of alignment with pairwise alignment
default parameters of KTUPLE=1, GAP PENALTY=3, WINDOW=5 and
DIAGONALS SAVED=5, or (b) a full-length complement of the
nucleotide sequence of (a).
18. The polynucleotide of claim 17, wherein the amino acid sequence
of the polypeptide has at least 95% sequence identity when compared
to SEQ ID NO:10, based on the Clustal V method of alignment with
the pairwise alignment default parameters.
19. The polynucleotide of claim 17, wherein the amino acid sequence
of the polypeptide comprises SEQ ID NO:10.
20. The polynucleotide of claim 17 wherein the nucleotide sequence
comprises SEQ ID NO:9.
21. A vector comprising the polynucleotide of claim 17.
22. A recombinant DNA construct comprising the polynucleotide of
claim 17 operably linked to at least one regulatory sequence.
23. A method for transforming a cell, comprising transforming a
cell with the polynucleotide of claim 17.
24. A cell comprising the recombinant DNA construct of claim
22.
25. A method for producing a transgenic plant comprising
transforming a plant cell with the polynucleotide of claim 17 and
regenerating a transgenic plant from the transformed plant
cell.
26. A plant comprising the recombinant DNA construct of claim
22.
27. A seed comprising the recombinant DNA construct of claim 22.
Description
[0001] This application claims the benefit of U.S. Provisional
Application No. 60/110,609, filed Dec. 2, 1998.
FIELD OF THE INVENTION
[0002] This invention is in the field of plant molecular biology.
More specifically, this invention pertains to nucleic acid
fragments encoding Myb-related transcription factors in plants and
seeds.
BACKGROUND OF THE INVENTION
[0003] Improvement of crop plants for a variety of traits,
including disease and pest resistance, and grain quality
improvements such as oil, starch or protein composition, can be
achieved by introducing new or modified genes (transgenes) into the
plant genome. Transcriptional activation of genes, including
transgenes, is in general controlled by the promoter through a
complex set of protein/DNA and protein/protein interactions.
Promoters can impart patterns of expression that are either
constitutive or limited to specific tissues or times during
development.
[0004] Transcriptional activation is primarily mediated through
transcription factors that interact with enhancer and promoter
elements. Binding of transcription factors to such DNA elements
constitutes a crucial step in transcriptional initiation. Each
transcription factor binds to its specific binding sequence in a
promoter and activates expression of the linked coding region
through interactions with coactivators and/or proteins that are a
part of the transcription complex.
[0005] Several plant genes have been identified that appear to
encode transcription factors structurally related to the cMyb
protooncogene family of mammals. Central to the similarities shared
by these proteins is the Myb repeat DNA-binding domain containing
conserved tryptophan residues at certain positions, and a
helix-turn-helix-related domain. Generally, Myb-related proteins
from plants contain two of these repeats, R2 and R3 (Kranz et al.
(1998) Plant J 16:263-276), though proteins having only one repeat
have been identified (e.g., Feldbrugge et al. (1997) Plant J
11:1079-1093). These Myb-related genes appear to encode a large
family of plant transcription factors that are involved in a
diversity of gene regulation. For example, plant Myb-related genes
have been shown to regulate anthrocyanin biosynthesis in maize and
phenylpropanoid metabolism, disease resistance (WO9813486-A1),
expression of gibberellin-regulated genes (WO9700961-A1),
expression of stress-related genes (WO9916878-A1), active
carbohydrate secretion and flavonol metabolism in antirrhinum
flowers (Jackson et al. (1992) Plant Cell 3(2):115-125). The first
plant transcription activator gene described at the molecular level
was the maize c1 gene which encodes a Myb protein (Paz-Ares et al.
(1987) EMBO J 16:3553-3558) involved in regulating anthocyanin
biosynthesis by trans-activating genes such as c2, A1 and Bz1 which
encode enzymes involved in the pathway.
[0006] There is a great deal of interest in identifying the genes
that encode proteins involved in transcriptional regulation in
plants. These genes may be used in plant cells to control gene
expression constitutively, in specific tissues or at various times
during development. Accordingly, the availability of nucleic acid
sequences encoding all or a portion of a Myb-related transcription
factor would facilitate studies to better understand gene
regulation in plants and provide genetic tools to enhance or
otherwise alter the expression of genes controlled by Myb-related
transcription factors.
SUMMARY OF THE INVENTION
[0007] The present invention relates to isolated polynucleotides
comprising a nucleotide sequence encoding a first polypeptide of at
least 50 amino acids that has at least 80% identity based on the
Clustal method of alignment when compared to a polypeptide selected
from the group consisting of a corn Myb-related transcription
factor polypeptide of SEQ ID NO:2, a rice Myb-related transcription
factor polypeptide of SEQ ID NO:12, and a wheat Myb-related
transcription factor polypeptide of SEQ ID NO:56. The present
invention also relates to isolated polynucleotides comprising a
nucleotide sequence encoding a first polypeptide of at least 50
amino acids that has at least 85% identity based on the Clustal
method of alignment when compared to a polypeptide selected from
the group consisting of a corn Myb-related transcription factor
polypeptide of SEQ ID NO:8, and a soybean Myb-related transcription
factor polypeptide of SEQ ID NO:28. The present invention also
relates to isolated polynucleotides comprising a nucleotide
sequence encoding a first polypeptide of at least 50 amino acids
that has at least 90% identity based on the Clustal method of
alignment when compared to a rice Myb-related transcription factor
polypeptide of SEQ ID NO:16. The present invention also relates to
isolated polynucleotides comprising a nucleotide sequence encoding
a first polypeptide of at least 50 amino acids that has at least
95% identity based on the Clustal method of alignment when compared
to a soybean Myb-related transcription factor polypeptide of SEQ ID
NO:52. The present invention also relates to isolated
polynucleotides comprising a nucleotide sequence encoding a first
polypeptide of at least 100 amino acids that has at least 80%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of a corn
Myb-related transcription factor polypeptide of SEQ ID NO:6, a rice
Myb-related transcription factor polypeptide of SEQ ID NO:14, a
soybean Myb-related transcription factor polypeptide of SEQ ID
NO:50, and a wheat Myb-related transcription factor polypeptide of
SEQ ID NO:58. The present invention also relates to isolated
polynucleotides comprising a nucleotide sequence encoding a first
polypeptide of at least 100 amino acids that has at least 85%
identity based on the Clustal method of alignment when compared to
a wheat Myb-related transcription factor polypeptide of SEQ ID
NO:60. The present invention also relates to isolated
polynucleotides comprising a nucleotide sequence encoding a first
polypeptide of at least 100 amino acids that has at least 90%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of a corn
Myb-related transcription factor polypeptide of SEQ ID NO:4, a corn
Myb-related transcription factor polypeptide of SEQ ID NO:10, a
rice Myb-related transcription factor polypeptide of SEQ ID NO:22,
a rice Myb-related transcription factor polypeptide of SEQ ID
NO:24, and a wheat Myb-related transcription factor polypeptide of
SEQ ID NO:62. The present invention also relates to isolated
polynucleotides comprising a nucleotide sequence encoding a first
polypeptide of at least 100 amino acids that has at least 95%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of a rice
Myb-related transcription factor polypeptide of SEQ ID NO:18 and a
rice Myb-related transcription factor polypeptide of SEQ ID NO:20.
The present invention also relates to isolated polynucleotides
comprising a nucleotide sequence encoding a first polypeptide of at
least 150 amino acids that has at least 80% identity based on the
Clustal method of alignment when compared to a polypeptide selected
from the group consisting of a rice Myb-related transcription
factor polypeptide of SEQ ID NO:26, a soybean Myb-related
transcription factor polypeptide of SEQ ID NO:34, a soybean
Myb-related transcription factor polypeptide of SEQ ID NO:38, a
soybean Myb-related transcription factor polypeptide of SEQ ID
NO:40, a soybean Myb-related transcription factor polypeptide of
SEQ ID NO:42, a soybean Myb-related transcription factor
polypeptide of SEQ ID NO:48, and a soybean Myb-related
transcription factor polypeptide of SEQ ID NO:54. The present
invention also relates to isolated polynucleotides comprising a
nucleotide sequence encoding a first polypeptide of at least 150
amino acids that has at least 85% identity based on the Clustal
method of alignment when compared to a polypeptide selected from
the group consisting of a soybean Myb-related transcription factor
polypeptide of SEQ ID NO:32, a soybean Myb-related transcription
factor polypeptide of SEQ ID NO:44, and a soybean Myb-related
transcription factor polypeptide of SEQ ID NO:46. The present
invention also relates to isolated polynucleotides comprising a
nucleotide sequence encoding a first polypeptide of at least 200
amino acids that has at least 80% identity based on the Clustal
method of alignment when compared to a soybean Myb-related
transcription factor polypeptide of SEQ ID NO:36. The present
invention also relates to isolated polynucleotides comprising a
nucleotide sequence encoding a first polypeptide of at least 200
amino acids that has at least 85% identity based on the Clustal
method of alignment when compared to a soybean Myb-related
transcription factor polypeptide of SEQ ID NO:30. The present
invention also relates to an isolated polynucleotide comprising the
complement of the nucleotide sequences described above.
[0008] It is preferred that the isolated polynucleotides of the
claimed invention consist of a nucleic acid sequence selected from
the group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17,
19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51,
53, 55, 57, 59, and 61 that codes for the polypeptide selected from
the group consisting of SEQ ID NOs:2, 4, 6, 8, 10, 12, 14, 16, 18,
20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52,
54, 56, 58, 60, and 62. The present invention also relates to an
isolated polynucleotide comprising a nucleotide sequences of at
least one of 60 (preferably at least one of 40, most preferably at
one least of 30) contiguous nucleotides derived from a nucleotide
sequence selected from the group consisting of SEQ ID NOs: 1, 3, 5,
7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39,
41, 43, 45, 47, 49, 51, 53, 55, 57, 59, and 61 and the complement
of such nucleotide sequences.
[0009] The present invention relates to a chimeric gene comprising
an isolated polynucleotide of the present invention operably linked
to suitable regulatory sequences.
[0010] The present invention relates to an isolated host cell
comprising a chimeric gene of the present invention or an isolated
polynucleotide of the present invention. The host cell may be
eukaryotic, such as a yeast or a plant cell, or prokaryotic, such
as a bacterial cell. The present invention also relates to a virus,
preferably a baculovirus, comprising an isolated polynucleotide of
the present invention or a chimeric gene of the present
invention.
[0011] The present invention relates to a process for producing an
isolated host cell comprising a chimeric gene of the present
invention or an isolated polynucleotide of the present invention,
the process comprising either transforming or transfecting an
isolated compatible host cell with a chimeric gene or isolated
polynucleotide of the present invention.
[0012] The present invention relates to a Myb-related transcription
factor polypeptide of at least 50 amino acids that has at least 80%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of SEQ ID NOs:2,
12, and 56. The present invention also relates to a Myb-related
transcription factor polypeptide of at least 50 amino acids that
has at least 85% identity based on the Clustal method of alignment
when compared to a polypeptide selected from the group consisting
of SEQ ID NOs:8 and 28. The present invention also relates to a
Myb-related transcription factor polypeptide of at least 50 amino
acids that has at least 90% identity based on the Clustal method of
alignment when compared to a rice Myb-related transcription factor
polypeptide of SEQ ID NO:16. The present invention also relates to
a Myb-related transcription factor polypeptide of at least 50 amino
acids that has at least 95% identity based on the Clustal method of
alignment when compared to a soybean Myb-related transcription
factor polypeptide of SEQ ID NO:52. The present invention also
relates to a Myb-related transcription factor polypeptide of at
least 100 amino acids that has at least 80% identity based on the
Clustal method of alignment when compared to a polypeptide selected
from the group consisting of SEQ ID NOs:6, 14, 50, and 58. The
present invention also relates to a Myb-related transcription
factor polypeptide of at least 100 amino acids that has at least
85% identity based on the Clustal method of alignment when compared
to a wheat Myb-related transcription factor polypeptide of SEQ ID
NO:60. The present invention also relates a Myb-related
transcription factor polypeptide of at least 100 amino acids that
has at least 90% identity based on the Clustal method of alignment
when compared to a polypeptide selected from the group consisting
of SEQ ID NOs:4, 10, 22, 24, and 62. The present invention also
relates to a Myb-related transcription factor polypeptide of at
least 100 amino acids that has at least 95% identity based on the
Clustal method of alignment when compared to a polypeptide selected
from the group consisting of SEQ ID NOs:18 and 20. The present
invention also relates to a Myb-related transcription factor
polypeptide of at least 150 amino acids that has at least 80%
identity based on the Clustal method of alignment when compared to
a polypeptide selected from the group consisting of SEQ ID NOs:26,
34, 38, 40, 42, 48, and 54. The present invention also relates to a
Myb-related transcription factor polypeptide of at least 150 amino
acids that has at least 85% identity based on the Clustal method of
alignment when compared to a polypeptide selected from the group
consisting of SEQ ID NOs:32, 44, and 46. The present invention also
relates to a Myb-related transcription factor polypeptide of at
least 200 amino acids that has at least 80% identity based on the
Clustal method of alignment when compared to a soybean Myb-related
transcription factor polypeptide of SEQ ID NO:36. The present
invention also relates to a Myb-related transcription factor
polypeptide of at least 200 amino acids that has at least 85%
identity based on the Clustal method of alignment when compared to
a soybean Myb-related transcription factor polypeptide of SEQ ID
NO:30.
[0013] The present invention relates to a method of selecting an
isolated polynucleotide that affects the level of expression of a
Myb-related transcription factor polypeptide in a host cell,
preferably a plant cell, the method comprising the steps of: [0014]
constructing an isolated polynucleotide of the present invention or
an isolated chimeric gene of the present invention; [0015]
introducing the isolated polynucleotide or the isolated chimeric
gene into a host cell; [0016] measuring the level of a Myb-related
transcription factor polypeptide in the host cell containing the
isolated polynucleotide; and [0017] comparing the level of a
Myb-related transcription factor polypeptide in the host cell
containing the isolated polynucleotide with the level of a
Myb-related transcription factor polypeptide in a host cell that
does not contain the isolated polynucleotide.
[0018] The present invention relates to a method of obtaining a
nucleic acid fragment encoding a substantial portion of a
Myb-related transcription factor polypeptide gene, preferably a
plant Myb-related transcription factor polypeptide gene, comprising
the steps of: synthesizing an oligonucleotide primer comprising a
nucleotide sequence of at least one of 60 (preferably at least one
of 40, most preferably at least one of 30) contiguous nucleotides
derived from a nucleotide sequence selected from the group
consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23,
25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57,
59, and 61 and the complement of such nucleotide sequences; and
amplifying a nucleic acid fragment (preferably a cDNA inserted in a
cloning vector) using the oligonucleotide primer. The amplified
nucleic acid fragment preferably will encode all or a portion of a
Myb-related transcription factor amino acid sequence.
[0019] The present invention also relates to a method of obtaining
a nucleic acid fragment encoding all or a substantial portion of
the amino acid sequence encoding a Myb-related transcription factor
polypeptide comprising the steps of: probing a cDNA or genomic
library with an isolated polynucleotide of the present invention;
identifying a DNA clone that hybridizes with an isolated
polynucleotide of the present invention; isolating the identified
DNA clone; and sequencing the cDNA or genomic fragment that
comprises the isolated DNA clone.
BRIEF DESCRIPTION OF THE DRAWING AND SEQUENCE DESCRIPTIONS
[0020] The invention can be more fully understood from the
following detailed description and the accompanying drawing and
Sequence Listing which form a part of this application.
[0021] FIG. 1 depicts the amino acid alignment between the
Myb-related transcription factor encoded by the nucleotide
sequences derived from corn clone cta1n.pk0079.e9 (SEQ ID NO:10),
contig assembled from rice clones rr1.pk0027.g9 and rr1.pk077.n9
(SEQ ID NO:14), rice clone rl0n.pk082.c13 (SEQ ID NO:26), soybean
clone sfl1.pk0032.g4 (SEQ ID NO:30), soybean clone sfl1.pk0086.a9
(SEQ ID NO:32), soybean clone sfl1.pk0091.a2 (SEQ ID NO:34),
soybean clone sfl1.pk0091.a2 (SEQ ID NO:36), soybean clone
sfl1.pk0003.a3 (SEQ ID NO:42), soybean clone srr3c.pk002.k6 (SEQ ID
NO:44), soybean clone ses9c.pk002.o16 (SEQ ID NO:46), soybean clone
sl2.pk127.e14 (SEQ ID NO:48), soybean clone src3c.pk010.i22 (SEQ ID
NO:50), soybean clone sgs4c.pk04j24 (SEQ ID NO:54), and a
Myb-related transcription factor-encoding nucleic acid fragment
from Pisum sativum (NCBI General Identification No. 1841475) (SEQ
ID NO:63). Amino acids which are conserved among all and at least
two sequences with an amino acid at that position are indicated
with an asterisk (*) above them. Dashes are used by the program to
maximize alignment of the sequences.
[0022] Table 1 lists the polypeptides that are described herein,
the designation of the cDNA clones that comprise the nucleic acid
fragments encoding polypeptides representing all or a substantial
portion of these polypeptides, and the corresponding identifier
(SEQ ID NO:) as used in the attached Sequence Listing. Table 1 also
identifies the cDNA clones as individual ESTs ("EST"), the
sequences of the entire cDNA inserts comprising the indicated cDNA
clones ("FIS"), contigs assembled from two or more ESTs ("Contig"),
contigs assembled from an FIS and one or more ESTs ("Contig*"), or
sequences encoding the entire protein derived from an FIS, a
contig, or an FIS and PCR ("CGS"). Nucleotide SEQ ID NOs:7, 11, 23,
27, 51, and 55 correspond to nucleotide SEQ ID NOs:1, 3, 9, 5, 1 1,
and 7, respectively, presented in U.S. Provisional Application No.
60/110,609, filed Dec. 2, 1998. Amino acid SEQ ID NOs:8, 12, 24,
28, 52, and 56 correspond to amino acid SEQ ID NOs: 2, 4, 10, 6,
12, and 8, respectively presented in U.S. Provisional Application
No. 60/110,609, filed Dec. 2, 1998. The sequence descriptions and
Sequence Listing attached hereto comply with the rules governing
nucleotide and/or amino acid sequence disclosures in patent
applications as set forth in 37 C.F.R. .sctn.1.821-1.825.
TABLE-US-00001 TABLE 1 Myb-related Transcription Factors SEQ ID NO:
Protein Clone Designation Status (Nucleotide) (Amino Acid)
Myb-related Contig of: Contig 1 2 Transcription csi1n.pk0008.b5
Factor (Corn) csi1n.pk0028.h7 Myb-related Contig of: Contig 3 4
Transcription p0008.cb31d06r Factor (Corn) p0026.ccrbd36rb
Myb-related chpc8.pk0002.d9 EST 5 6 Transcription Factor (Corn)
Myb-related cta1n.pk0079.e9 EST 7 8 Transcription Factor (Corn)
Myb-related cta1n.pk0079.e9 CGS 9 10 Transcription Factor (Corn)
Myb-related rr1.pk077.n9 EST 11 12 Transcription Factor (Rice)
Myb-related Contig of: CGS 13 14 Transcription rr1.pk0027.g9 Factor
(Rice) rr1.pk077.n9 Myb-related rr1.pk088.p6 EST 15 16
Transcription Factor (Rice) Myb-related rr1.pk0037.g7 EST 17 18
Transcription Factor (Rice) Myb-related rds3c.pk002.c6 EST 19 20
Transcription Factor (Rice) Myb-related Contig of: Contig 21 22
Transcription r1r24.pk0090.f5 Factor (Rice) r1r48.pk0012.c11
Myb-related r10n.pk082.c13 EST 23 24 Transcription Factor (Rice)
Myb-related r10n.pk082.c13 CGS 25 26 Transcription Factor (Rice)
Myb-related sfl1.pk0032.g4 EST 27 28 Transcription Factor (Soybean)
Myb-related sfl1.pk0032.g4 CGS 29 30 Transcription Factor (Soybean)
Myb-related sfl1.pk0086.a9 CGS 31 32 Transcription Factor (Soybean)
Myb-related sfl1.pk0091.a2 CGS 33 34 Transcription Factor (Soybean)
Myb-related sfl1.pk0105.e6 CGS 35 36 Transcription Factor (Soybean)
Myb-related sfl1.pk125.p19 FIS 37 38 Transcription Factor (Soybean)
Myb-related se6.pk0048.a12 FIS 39 40 Transcription Factor (Soybean)
Myb-related sfl1.pk0003.a3 CGS 41 42 Transcription Factor (Soybean)
Myb-related srr3c.pk002.k6 CGS 43 44 Transcription Factor (Soybean)
Myb-related ses9c.pk002.o16 CGS 45 46 Transcription Factor
(Soybean) Myb-related sl2.pk127.e14 CGS 47 48 Transcription Factor
(Soybean) Myb-related src3c.pk010.i22 CGS 49 50 Transcription
Factor (Soybean) Myb-related sgs4c.pk004.j24 EST 51 52
Transcription Factor (Soybean) Myb-related sgs4c.pk004.j24 CGS 53
54 Transcription Factor (Soybean) Myb-related wr1.pk0139.g11 EST 55
56 Transcription Factor (Wheat) Myb-related wr1.pk0139.g11 FIS 57
58 Transcription Factor (Wheat) Myb-related wdk3c.pk006.n12 EST 59
60 Transcription Factor (Wheat) Myb-related wlm1.pk0027.a5 EST 61
62 Transcription Factor (Wheat)
[0023] The Sequence Listing contains the one letter code for
nucleotide sequence characters and the three letter codes for amino
acids as defined in conformity with the IUPAC-IUBMB standards
described in Nucleic Acids Res. 13:3021-3030 (1985) and in the
Biochemical J. 219 (No. 2):345-373 (1984) which are herein
incorporated by reference. The symbols and format used for
nucleotide and amino acid sequence data comply with the rules set
forth in 37 C.F.R. .sctn.1.822.
DETAILED DESCRIPTION OF THE INVENTION
[0024] In the context of this disclosure, a number of terms shall
be utilized. As used herein, a "polynucleotide" is a nucleotide
sequence such as a nucleic acid fragment. A polynucleotide may be a
polymer of RNA or DNA that is single- or double-stranded, that
optionally contains synthetic, non-natural or altered nucleotide
bases. A polynucleotide in the form of a polymer of DNA may be
comprised of one or more segments of cDNA, genomic DNA, synthetic
DNA, or mixtures thereof. An isolated polynucleotide of the present
invention may include at least one of 60 contiguous nucleotides,
preferably at least one of 40 contiguous nucleotides, most
preferably one of at least 30 contiguous nucleotides, of the
nucleic acid sequence of the SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15,
17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49,
51, 53, 55, 57, 59, 61, or the complement of such sequences.
[0025] As used herein, "contig" refers to a nucleotide sequence
that is assembled from two or more constituent nucleotide sequences
that share common or overlapping regions of sequence homology. For
example, the nucleotide sequences of two or more nucleic acid
fragments can be compared and aligned in order to identify common
or overlapping sequences. Where common or overlapping sequences
exist between two or more nucleic acid fragments, the sequences
(and thus their corresponding nucleic acid fragments) can be
assembled into a single contiguous nucleotide sequence.
[0026] As used herein, "substantially similar" refers to nucleic
acid fragments wherein changes in one or more nucleotide bases
results in substitution of one or more amino acids, but do not
affect the functional properties of the polypeptide encoded by the
nucleotide sequence. "Substantially similar" also refers to nucleic
acid fragments wherein changes in one or more nucleotide bases does
not affect the ability of the nucleic acid fragment to mediate
alteration of gene expression by gene silencing through for example
antisense or co-suppression technology. "Substantially similar"
also refers to modifications of the nucleic acid fragments of the
instant invention such as deletion or insertion of one or more
nucleotides that do not substantially affect the functional
properties of the resulting transcript vis-a-vis the ability to
mediate gene silencing or alteration of the functional properties
of the resulting protein molecule. It is therefore understood that
the invention encompasses more than the specific exemplary
nucleotide or amino acid sequences and includes functional
equivalents thereof.
[0027] Substantially similar nucleic acid fragments may be selected
by screening nucleic acid fragments representing subfragments or
modifications of the nucleic acid fragments of the instant
invention, wherein one or more nucleotides are substituted, deleted
and/or inserted, for their ability to affect the level of the
polypeptide encoded by the unmodified nucleic acid fragment in a
plant or plant cell. For example, a substantially similar nucleic
acid fragment representing at least one of 30 contiguous
nucleotides derived from the instant nucleic acid fragment can be
constructed and introduced into a plant or plant cell. The level of
the polypeptide encoded by the unmodified nucleic acid fragment
present in a plant or plant cell exposed to the substantially
similar nucleic fragment can then be compared to the level of the
polypeptide in a plant or plant cell that is not exposed to the
substantially similar nucleic acid fragment.
[0028] For example, it is well known in the art that antisense
suppression and co-suppression of gene expression may be
accomplished using nucleic acid fragments representing less than
the entire coding region of a gene, and by nucleic acid fragments
that do not share 100% sequence identity with the gene to be
suppressed. Moreover, alterations in a nucleic acid fragment which
result in the production of a chemically equivalent amino acid at a
given site, but do not effect the functional properties of the
encoded polypeptide, are well known in the art. Thus, a codon for
the amino acid alanine, a hydrophobic amino acid, may be
substituted by a codon encoding another less hydrophobic residue,
such as glycine, or a more hydrophobic residue, such as valine,
leucine, or isoleucine. Similarly, changes which result in
substitution of one negatively charged residue for another, such as
aspartic acid for glutamic acid, or one positively charged residue
for another, such as lysine for arginine, can also be expected to
produce a functionally equivalent product. Nucleotide changes which
result in alteration of the N-terminal and C-terminal portions of
the polypeptide molecule would also not be expected to alter the
activity of the polypeptide. Each of the proposed modifications is
well within the routine skill in the art, as is determination of
retention of biological activity of the encoded products.
Consequently, an isolated polynucleotide comprising a nucleotide
sequence of at least one of 60 (preferably at least one of 40, most
preferably at least one of 30) contiguous nucleotides derived from
a nucleotide sequence selected from the group consisting of SEQ ID
NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, and 61 and the
complement of such nucleotide sequences may be used in methods of
selecting an isolated polynucleotide that affects the expression of
a polypeptide in a plant cell. A method of selecting an isolated
polynucleotide that affects the level of expression of a
polypeptide (such as a Myb-related transcription factor)in a host
cell (eukaryotic, such as plant or yeast, prokaryotic such as
bacterial, or viral) may comprise the steps of: constructing an
isolated polynucleotide of the present invention or an isolated
chimeric gene of the present invention; introducing the isolated
polynucleotide or the isolated chimeric gene into a host cell;
measuring the level of a polypeptide in the host cell containing
the isolated polynucleotide; and comparing the level of a
polypeptide in the host cell containing the isolated polynucleotide
with the level of a polypeptide in a host cell that does not
contain the isolated polynucleotide.
[0029] Moreover, substantially similar nucleic acid fragments may
also be characterized by their ability to hybridize. Estimates of
such homology are provided by either DNA-DNA or DNA-RNA
hybridization under conditions of stringency as is well understood
by those skilled in the art (Hames and Higgins, Eds. (1985) Nucleic
Acid Hybridisation, IRL Press, Oxford, U.K.). Stringency conditions
can be adjusted to screen for moderately similar fragments, such as
homologous sequences from distantly related organisms, to highly
similar fragments, such as genes that duplicate functional enzymes
from closely related organisms. Post-hybridization washes determine
stringency conditions. One set of preferred conditions uses a
series of washes starting with 6.times.SSC, 0.5% SDS at room
temperature for 15 min, then repeated with 2.times.SSC, 0.5% SDS at
45.degree. C. for 30 min, and then repeated twice with
0.2.times.SSC, 0.5% SDS at 50.degree. C. for 30 min. A more
preferred set of stringent conditions uses higher temperatures in
which the washes are identical to those above except for the
temperature of the final two 30 min washes in 0.2.times.SSC, 0.5%
SDS was increased to 60.degree. C. Another preferred set of highly
stringent conditions uses two final washes in 0.1.times.SSC, 0.1%
SDS at 65.degree. C.
[0030] Substantially similar nucleic acid fragments of the instant
invention may also be characterized by the percent identity of the
amino acid sequences that they encode to the amino acid sequences
disclosed herein, as determined by algorithms commonly employed by
those skilled in this art. Suitable nucleic acid fragments
(isolated polynucleotides of the present invention) encode
polypeptides that are at least about 70% identical, most preferably
at least about 80% identical to the amino acid sequences reported
herein. Preferred nucleic acid fragments encode amino acid
sequences that are at least about 85% identical to the amino acid
sequences reported herein. More preferred nucleic acid fragments
encode amino acid sequences that are at least about 90% identical
to the amino acid sequences reported herein. Most preferred are
nucleic acid fragments that encode amino acid sequences that are at
least about 95% identical to the amino acid sequences reported
herein. Suitable nucleic acid fragments not only have the above
homologies but typically encode a polypeptide having at least about
50 amino acids, preferably at least about 100 amino acids, more
preferably at least about 150 amino acids, still more preferably at
least about 200 amino acids, and most preferably at least about 250
amino acids. Sequence alignments and percent identity calculations
were performed using the Megalign program of the LASERGENE
bioinformatics computing suite (DNASTAR Inc., Madison, Wis.).
Multiple alignment of the sequences was performed using the Clustal
method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153)
with the default parameters (GAP PENALTY=10, GAP LENGTH
PENALTY=10). Default parameters for pairwise alignments using the
Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS
SAVED=5.
[0031] A "substantial portion" of an amino acid or nucleotide
sequence comprises an amino acid or a nucleotide sequence that is
sufficient to afford putative identification of the protein or gene
that the amino acid or nucleotide sequence comprises. Amino acid
and nucleotide sequences can be evaluated either manually by one
skilled in the art, or by using computer-based sequence comparison
and identification tools that employ algorithms such as BLAST
(Basic Local Alignment Search Tool; Altschul et al. (1993) J. Mol.
Biol. 215:403-410; see also www.ncbi.nlm.nih.gov/BLAST/). In
general, a sequence of ten or more contiguous amino acids or thirty
or more contiguous nucleotides is necessary in order to putatively
identify a polypeptide or nucleic acid sequence as homologous to a
known protein or gene. Moreover, with respect to nucleotide
sequences, gene-specific oligonucleotide probes comprising 30 or
more contiguous nucleotides may be used in sequence-dependent
methods of gene identification (e.g., Southern hybridization) and
isolation (e.g., in situ hybridization of bacterial colonies or
bacteriophage plaques). In addition, short oligonucleotides of 12
or more nucleotides may be used as amplification primers in PCR in
order to obtain a particular nucleic acid fragment comprising the
primers. Accordingly, a "substantial portion" of a nucleotide
sequence comprises a nucleotide sequence that will afford specific
identification and/or isolation of a nucleic acid fragment
comprising the sequence. The instant specification teaches amino
acid and nucleotide sequences encoding polypeptides that comprise
one or more particular plant proteins. The skilled artisan, having
the benefit of the sequences as reported herein, may now use all or
a substantial portion of the disclosed sequences for purposes known
to those skilled in this art. Accordingly, the instant invention
comprises the complete sequences as reported in the accompanying
Sequence Listing, as well as substantial portions of those
sequences as defined above.
[0032] "Codon degeneracy" refers to divergence in the genetic code
permitting variation of the nucleotide sequence without effecting
the amino acid sequence of an encoded polypeptide. Accordingly, the
instant invention relates to any nucleic acid fragment comprising a
nucleotide sequence that encodes all or a substantial portion of
the amino acid sequences set forth herein. The skilled artisan is
well aware of the "codon-bias" exhibited by a specific host cell in
usage of nucleotide codons to specify a given amino acid.
Therefore, when synthesizing a nucleic acid fragment for improved
expression in a host cell, it is desirable to design the nucleic
acid fragment such that its frequency of codon usage approaches the
frequency of preferred codon usage of the host cell.
[0033] "Synthetic nucleic acid fragments" can be assembled from
oligonucleotide building blocks that are chemically synthesized
using procedures known to those skilled in the art. These building
blocks are ligated and annealed to form larger nucleic acid
fragments which may then be enzymatically assembled to construct
the entire desired nucleic acid fragment. "Chemically synthesized",
as related to nucleic acid fragment, means that the component
nucleotides were assembled in vitro. Manual chemical synthesis of
nucleic acid fragments may be accomplished using well established
procedures, or automated chemical synthesis can be performed using
one of a number of commercially available machines. Accordingly,
the nucleic acid fragments can be tailored for optimal gene
expression based on optimization of nucleotide sequence to reflect
the codon bias of the host cell. The skilled artisan appreciates
the likelihood of successful gene expression if codon usage is
biased towards those codons favored by the host. Determination of
preferred codons can be based on a survey of genes derived from the
host cell where sequence information is available.
[0034] "Gene" refers to a nucleic acid fragment that expresses a
specific protein, including regulatory sequences preceding (5'
non-coding sequences) and following (3' non-coding sequences) the
coding sequence. "Native gene" refers to a gene as found in nature
with its own regulatory sequences. "Chimeric gene" refers any gene
that is not a native gene, comprising regulatory and coding
sequences that are not found together in nature. Accordingly, a
chimeric gene may comprise regulatory sequences and coding
sequences that are derived from different sources, or regulatory
sequences and coding sequences derived from the same source, but
arranged in a manner different than that found in nature.
"Endogenous gene" refers to a native gene in its natural location
in the genome of an organism. A "foreign" gene refers to a gene not
normally found in the host organism, but that is introduced into
the host organism by gene transfer. Foreign genes can comprise
native genes inserted into a non-native organism, or chimeric
genes. A "transgene" is a gene that has been introduced into the
genome by a transformation procedure.
[0035] "Coding sequence" refers to a nucleotide sequence that codes
for a specific amino acid sequence. "Regulatory sequences" refer to
nucleotide sequences located upstream (5' non-coding sequences),
within, or downstream (3' non-coding sequences) of a coding
sequence, and which influence the transcription, RNA processing or
stability, or translation of the associated coding sequence.
Regulatory sequences may include promoters, translation leader
sequences, introns, and polyadenylation recognition sequences.
[0036] "Promoter" refers to a nucleotide sequence capable of
controlling the expression of a coding sequence or functional RNA.
In general, a coding sequence is located 3' to a promoter sequence.
The promoter sequence consists of proximal and more distal upstream
elements, the latter elements often referred to as enhancers.
Accordingly, an "enhancer" is a nucleotide sequence which can
stimulate promoter activity and may be an innate element of the
promoter or a heterologous element inserted to enhance the level or
tissue-specificity of a promoter. Promoters may be derived in their
entirety from a native gene, or be composed of different elements
derived from different promoters found in nature, or even comprise
synthetic nucleotide segments. It is understood by those skilled in
the art that different promoters may direct the expression of a
gene in different tissues or cell types, or at different stages of
development, or in response to different environmental conditions.
Promoters which cause a nucleic acid fragment to be expressed in
most cell types at most times are commonly referred to as
"constitutive promoters". New promoters of various types useful in
plant cells are constantly being discovered; numerous examples may
be found in the compilation by Okamuro and Goldberg (1989)
Biochemistry of Plants 15:1-82. It is further recognized that since
in most cases the exact boundaries of regulatory sequences have not
been completely defined, nucleic acid fragments of different
lengths may have identical promoter activity.
[0037] The "translation leader sequence" refers to a nucleotide
sequence located between the promoter sequence of a gene and the
coding sequence. The translation leader sequence is present in the
fully processed mRNA upstream of the translation start sequence.
The translation leader sequence may affect processing of the
primary transcript to mRNA, mRNA stability or translation
efficiency. Examples of translation leader sequences have been
described (Turner and Foster (1995) Mol. Biotechnol.
3:225-236).
[0038] The "3' non-coding sequences" refer to nucleotide sequences
located downstream of a coding sequence and include polyadenylation
recognition sequences and other sequences encoding regulatory
signals capable of affecting mRNA processing or gene expression.
The polyadenylation signal is usually characterized by affecting
the addition of polyadenylic acid tracts to the 3' end of the mRNA
precursor. The use of different 3' non-coding sequences is
exemplified by Ingelbrecht et al. (1989) Plant Cell 1:671-680.
[0039] "RNA transcript" refers to the product resulting from RNA
polymerase-catalyzed transcription of a DNA sequence. When the RNA
transcript is a perfect complementary copy of the DNA sequence, it
is referred to as the primary transcript or it may be a RNA
sequence derived from posttranscriptional processing of the primary
transcript and is referred to as the mature RNA. "Messenger RNA
(mRNA)" refers to the RNA that is without introns and that can be
translated into polypeptide by the cell. "cDNA" refers to a
double-stranded DNA that is complementary to and derived from mRNA.
"Sense" RNA refers to an RNA transcript that includes the mRNA and
so can be translated into a polypeptide by the cell. "Antisense
RNA" refers to an RNA transcript that is complementary to all or
part of a target primary transcript or mRNA and that blocks the
expression of a target gene (see U.S. Pat. No. 5,107,065,
incorporated herein by reference). The complementarity of an
antisense RNA may be with any part of the specific nucleotide
sequence, i.e., at the 5' non-coding sequence, 3' non-coding
sequence, introns, or the coding sequence. "Functional RNA" refers
to sense RNA, antisense RNA, ribozyme RNA, or other RNA that may
not be translated but yet has an effect on cellular processes.
[0040] The term "operably linked" refers to the association of two
or more nucleic acid fragments on a single nucleic acid fragment so
that the function of one is affected by the other. For example, a
promoter is operably linked with a coding sequence when it is
capable of affecting the expression of that coding sequence (i.e.,
that the coding sequence is under the transcriptional control of
the promoter). Coding sequences can be operably linked to
regulatory sequences in sense or antisense orientation.
[0041] The term "expression", as used herein, refers to the
transcription and stable accumulation of sense (mRNA) or antisense
RNA derived from the nucleic acid fragment of the invention.
Expression may also refer to translation of mRNA into a
polypeptide. "Antisense inhibition" refers to the production of
antisense RNA transcripts capable of suppressing the expression of
the target protein. "Overexpression" refers to the production of a
gene product in transgenic organisms that exceeds levels of
production in normal or non-transformed organisms.
"Underexpression" refers to the production of a gene product in
transgenic organisms at levels below that of levels of production
in normal or non-transformed organisms. "Co-suppression" refers to
the production of sense RNA transcripts capable of suppressing the
expression of identical or substantially similar foreign or
endogenous genes (U.S. Pat. No. 5,231,020, incorporated herein by
reference).
[0042] "Altered levels" refers to the production of gene product(s)
in transgenic organisms in amounts or proportions that differ from
that of normal or non-transformed organisms.
[0043] "Mature" protein refers to a post-translationally processed
polypeptide; i.e., one from which any pre- or propeptides present
in the primary translation product have been removed. "Precursor"
protein refers to the primary product of translation of mRNA; i.e.,
with pre- and propeptides still present. Pre- and propeptides may
be but are not limited to intracellular localization signals.
[0044] A "chloroplast transit peptide" is an amino acid sequence
which is translated in conjunction with a protein and directs the
protein to the chloroplast or other plastid types present in the
cell in which the protein is made. "Chloroplast transit sequence"
refers to a nucleotide sequence that encodes a chloroplast transit
peptide. A "signal peptide" is an amino acid sequence which is
translated in conjunction with a protein and directs the protein to
the secretory system (Chrispeels (1991) Ann. Rev. Plant Phys. Plant
Mol. Biol. 42:21-53). If the protein is to be directed to a
vacuole, a vacuolar targeting signal (supra) can further be added,
or if to the endoplasmic reticulum, an endoplasmic reticulum
retention signal (supra) may be added. If the protein is to be
directed to the nucleus, any signal peptide present should be
removed and instead a nuclear localization signal included (Raikhel
(1992) Plant Phys. 100:1627-1632).
[0045] "Transformation" refers to the transfer of a nucleic acid
fragment into the genome of a host organism, resulting in
genetically stable inheritance. Host organisms containing the
transformed nucleic acid fragments are referred to as "transgenic"
organisms. Examples of methods of plant transformation include
Agrobacterium-mediated transformation (De Blaere et al. (1987)
Meth. Enzymol. 143:277) and particle-accelerated or "gene gun"
transformation technology (Klein et al. (1987) Nature (London)
327:70-73; U.S. Pat. No. 4,945,050, incorporated herein by
reference).
[0046] Standard recombinant DNA and molecular cloning techniques
used herein are well known in the art and are described more fully
in Sambrook et al. Molecular Cloning: A Laboratory Manual; Cold
Spring Harbor Laboratory Press: Cold Spring Harbor, 1989
(hereinafter "Maniatis").
[0047] Nucleic acid fragments encoding at least a portion of
several Myb-related transcription factors have been isolated and
identified by comparison of random plant cDNA sequences to public
databases containing nucleotide and protein sequences using the
BLAST algorithms well known to those skilled in the art. The
nucleic acid fragments of the instant invention may be used to
isolate cDNAs and genes encoding homologous proteins from the same
or other plant species. Isolation of homologous genes using
sequence-dependent protocols is well known in the art. Examples of
sequence-dependent protocols include, but are not limited to,
methods of nucleic acid hybridization, and methods of DNA and RNA
amplification as exemplified by various uses of nucleic acid
amplification technologies (e.g., polymerase chain reaction, ligase
chain reaction).
[0048] For example, genes encoding other Myb-related transcription
factors, either as cDNAs or genomic DNAs, could be isolated
directly by using all or a portion of the instant nucleic acid
fragments as DNA hybridization probes to screen libraries from any
desired plant employing methodology well known to those skilled in
the art. Specific oligonucleotide probes based upon the instant
nucleic acid sequences can be designed and synthesized by methods
known in the art (Maniatis). Moreover, the entire sequences can be
used directly to synthesize DNA probes by methods known to the
skilled artisan such as random primer DNA labeling, nick
translation, or end-labeling techniques, or RNA probes using
available in vitro transcription systems. In addition, specific
primers can be designed and used to amplify a part or all of the
instant sequences. The resulting amplification products can be
labeled directly during amplification reactions or labeled after
amplification reactions, and used as probes to isolate full length
cDNA or genomic fragments under conditions of appropriate
stringency.
[0049] In addition, two short segments of the instant nucleic acid
fragments may be used in polymerase chain reaction protocols to
amplify longer nucleic acid fragments encoding homologous genes
from DNA or RNA. The polymerase chain reaction may also be
performed on a library of cloned nucleic acid fragments wherein the
sequence of one primer is derived from the instant nucleic acid
fragments, and the sequence of the other primer takes advantage of
the presence of the polyadenylic acid tracts to the 3' end of the
mRNA precursor encoding plant genes. Alternatively, the second
primer sequence may be based upon sequences derived from the
cloning vector. For example, the skilled artisan can follow the
RACE protocol (Frohman et al. (1988) Proc. Natl. Acad. Sci. USA
85:8998-9002) to generate cDNAs by using PCR to amplify copies of
the region between a single point in the transcript and the 3' or
5' end. Primers oriented in the 3' and 5' directions can be
designed from the instant sequences. Using commercially available
3' RACE or 5' RACE systems (BRL), specific 3' or 5' cDNA fragments
can be isolated (Ohara et al. (1989) Proc. Natl. Acad. Sci. USA
86:5673-5677; Loh et al. (1989) Science 243:217-220). Products
generated by the 3' and 5' RACE procedures can be combined to
generate full-length cDNAs (Frohman and Martin (1989) Techniques
1:165). Consequently, a polynucleotide comprising a nucleotide
sequence of at least one of 60 (preferably one of at least 40, most
preferably one of at least 30) contiguous nucleotides derived from
a nucleotide sequence selected from the group consisting of SEQ ID
NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33,
35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, and 61and the
complement of such nucleotide sequences may be used in such methods
to obtain a nucleic acid fragment encoding a substantial portion of
an amino acid sequence of a polypeptide (such as a Myb-related
transcription factor. The present invention relates to a method of
obtaining a nucleic acid fragment encoding a substantial portion of
a polypeptide of a gene (such as Myb-related transcription factor)
preferably a substantial portion of a plant polypeptide of a gene,
comprising the steps of: synthesizing an oligonucleotide primer
comprising a nucleotide sequence of at least one of 60 (preferably
at least one of 40, most preferably at least one of 30) contiguous
nucleotides derived from a nucleotide sequence selected from the
group consisting of SEQ ID NOs:1, 3, 5, 7, 9, 11, 13, 15, 17, 19,
21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53,
55, 57, 59, and 61 and the complement of such nucleotide sequences;
and amplifying a nucleic acid fragment (preferably a cDNA inserted
in a cloning vector) using the oligonucleotide primer. The
amplified nucleic acid fragment preferably will encode a portion of
a polypeptide.
[0050] Availability of the instant nucleotide and deduced amino
acid sequences facilitates immunological screening of cDNA
expression libraries. Synthetic peptides representing portions of
the instant amino acid sequences may be synthesized. These peptides
can be used to immunize animals to produce polyclonal or monoclonal
antibodies with specificity for peptides or proteins comprising the
amino acid sequences. These antibodies can be then be used to
screen cDNA expression libraries to isolate full-length cDNA clones
of interest (Lerner (1984) Adv. Immunol. 36:1-34; Maniatis).
[0051] The nucleic acid fragments of the instant invention may be
used to create transgenic plants in which the disclosed
polypeptides are present at higher or lower levels than normal or
in cell types or developmental stages in which they are not
normally found. This would have the effect of altering the level of
expression of Myb-regulated genes in those cells, and consequently
the phenotype affected by those Myb-regulated genes.
[0052] Overexpression of the proteins of the instant invention may
be accomplished by first constructing a chimeric gene in which the
coding region is operably linked to a promoter capable of directing
expression of a gene in the desired tissues at the desired stage of
development. For reasons of convenience, the chimeric gene may
comprise promoter sequences and translation leader sequences
derived from the same genes. 3' Non-coding sequences encoding
transcription termination signals may also be provided. The instant
chimeric gene may also comprise one or more introns in order to
facilitate gene expression.
[0053] Plasmid vectors comprising the instant chimeric gene can
then be constructed. The choice of plasmid vector is dependent upon
the method that will be used to transform host plants. The skilled
artisan is well aware of the genetic elements that must be present
on the plasmid vector in order to successfully transform, select
and propagate host cells containing the chimeric gene. The skilled
artisan will also recognize that different independent
transformation events will result in different levels and patterns
of expression (Jones et al. (1985) EMBO J. 4:2411-2418; De Almeida
et al. (1989) Mol. Gen. Genetics 218:78-86), and thus that multiple
events must be screened in order to obtain lines displaying the
desired expression level and pattern. Such screening may be
accomplished by Southern analysis of DNA, Northern analysis of mRNA
expression, Western analysis of protein expression, or phenotypic
analysis.
[0054] For some applications it may be useful to direct the instant
polypeptides to different cellular compartments, or to facilitate
its secretion from the cell. It is thus envisioned that the
chimeric gene described above may be further supplemented by
altering the coding sequence to encode the instant polypeptides
with appropriate intracellular targeting sequences such as transit
sequences (Keegstra (1989) Cell 56:247-253), signal sequences or
sequences encoding endoplasmic reticulum localization (Chrispeels
(1991) Ann. Rev. Plant Phys. Plant Mol. Biol. 42:21-53), or nuclear
localization signals (Raikhel (1992) Plant Phys. 100:1627-1632)
added and/or with targeting sequences that are already present
removed. While the references cited give examples of each of these,
the list is not exhaustive and more targeting signals of utility
may be discovered in the future.
[0055] It may also be desirable to reduce or eliminate expression
of genes encoding the instant polypeptides in plants for some
applications. In order to accomplish this, a chimeric gene designed
for co-suppression of the instant polypeptide can be constructed by
linking a gene or gene fragment encoding that polypeptide to plant
promoter sequences. Alternatively, a chimeric gene designed to
express antisense RNA for all or part of the instant nucleic acid
fragment can be constructed by linking the gene or gene fragment in
reverse orientation to plant promoter sequences. Either the
co-suppression or antisense chimeric genes could be introduced into
plants via transformation wherein expression of the corresponding
endogenous genes are reduced or eliminated.
[0056] Molecular genetic solutions to the generation of plants with
altered gene expression have a decided advantage over more
traditional plant breeding approaches. Changes in plant phenotypes
can be produced by specifically inhibiting expression of one or
more genes by antisense inhibition orcosuppression (U.S. Pat. Nos.
5,190,931, 5,107,065 and 5,283,323). An antisense or cosuppression
construct would act as a dominant negative regulator of gene
activity. While conventional mutations can yield negative
regulation of gene activity these effects are most likely
recessive. The dominant negative regulation available with a
transgenic approach may be advantageous from a breeding
perspective. In addition, the ability to restrict the expression of
specific phenotype to the reproductive tissues of the plant by the
use of tissue specific promoters may confer agronomic advantages
relative to conventional mutations which may have an effect in all
tissues in which a mutant gene is ordinarily expressed.
[0057] The person skilled in the art will know that special
considerations are associated with the use of antisense or
cosuppression technologies in order to reduce expression of
particular genes. For example, the proper level of expression of
sense or antisense genes may require the use of different chimeric
genes utilizing different regulatory elements known to the skilled
artisan. Once transgenic plants are obtained by one of the methods
described above, it will be necessary to screen individual
transgenics for those that most effectively display the desired
phenotype. Accordingly, the skilled artisan will develop methods
for screening large numbers of transformants. The nature of these
screens will generally be chosen on practical grounds, and is not
an inherent part of the invention. For example, one can screen by
looking for changes in gene expression by using antibodies specific
for the protein encoded by the gene being suppressed, or one could
establish assays that specifically measure enzyme activity. A
preferred method will be one which allows large numbers of samples
to be processed rapidly, since it will be expected that a large
number of transformants will be negative for the desired
phenotype.
[0058] The instant polypeptides (or portions thereof) may be
produced in heterologous host cells, particularly in the cells of
microbial hosts, and can be used to prepare antibodies to the these
proteins by methods well known to those skilled in the art. The
antibodies are useful for detecting the polypeptides of the instant
invention in situ in cells or in vitro in cell extracts. Preferred
heterologous host cells for production of the instant polypeptides
are microbial hosts. Microbial expression systems and expression
vectors containing regulatory sequences that direct high level
expression of foreign proteins are well known to those skilled in
the art. Any of these could be used to construct a chimeric gene
for production of the instant polypeptides. This chimeric gene
could then be introduced into appropriate microorganisms via
transformation to provide high level expression of the encoded
Myb-related transcription factors. An example of a vector for high
level expression of the instant polypeptides in a bacterial host is
provided (Example 6).
[0059] All or a substantial portion of the nucleic acid fragments
of the instant invention may also be used as probes for genetically
and physically mapping the genes that they are a part of, and as
markers for traits linked to those genes. Such information may be
useful in plant breeding in order to develop lines with desired
phenotypes. For example, the instant nucleic acid fragments may be
used as restriction fragment length polymorphism (RFLP) markers.
Southern blots (Maniatis) of restriction-digested plant genomic DNA
may be probed with the nucleic acid fragments of the instant
invention. The resulting banding patterns may then be subjected to
genetic analyses using computer programs such as MapMaker (Lander
et al. (1987) Genomics 1:174-181) in order to construct a genetic
map. In addition, the nucleic acid fragments of the instant
invention may be used to probe Southern blots containing
restriction endonuclease-treated genomic DNAs of a set of
individuals representing parent and progeny of a defined genetic
cross. Segregation of the DNA polymorphisms is noted and used to
calculate the position of the instant nucleic acid sequence in the
genetic map previously obtained using this population (Botstein et
al. (1980) Am. J. Hum. Genet. 32:314-331).
[0060] The production and use of plant gene-derived probes for use
in genetic mapping is described in Bematzky and Tanksley (1986)
Plant Mol. Biol. Reporter 4:37-41. Numerous publications describe
genetic mapping of specific cDNA clones using the methodology
outlined above or variations thereof For example, F2 intercross
populations, backcross populations, randomly mated populations,
near isogenic lines, and other sets of individuals may be used for
mapping. Such methodologies are well known to those skilled in the
art.
[0061] Nucleic acid probes derived from the instant nucleic acid
sequences may also be used for physical mapping (i.e., placement of
sequences on physical maps; see Hoheisel et al. In: Nonmammalian
Genomic Analysis: A Practical Guide, Academic press 1996, pp.
319-346, and references cited therein).
[0062] In another embodiment, nucleic acid probes derived from the
instant nucleic acid sequences may be used in direct fluorescence
in situ hybridization (FISH) mapping (Trask (1991) Trends Genet.
7:149-154). Although current methods of FISH mapping favor use of
large clones (several to several hundred KB; see Laan et al. (1995)
Genome Res. 5:13-20), improvements in sensitivity may allow
performance of FISH mapping using shorter probes.
[0063] A variety of nucleic acid amplification-based methods of
genetic and physical mapping may be carried out using the instant
nucleic acid sequences. Examples include allele-specific
amplification (Kazazian (1989) J. Lab. Clin. Med. 11:95-96),
polymorphism of PCR-amplified fragments (CAPS; Sheffield et al.
(1993) Genomics 16:325-332), allele-specific ligation (Landegren et
al. (1988) Science 241:1077-1080), nucleotide extension reactions
(Sokolov (1990) Nucleic Acid Res. 18:3671), Radiation Hybrid
Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy
Mapping (Dear and Cook (1989) Nucleic Acid Res. 1 7:6795-6807). For
these methods, the sequence of a nucleic acid fragment is used to
design and produce primer pairs for use in the amplification
reaction or in primer extension reactions. The design of such
primers is well known to those skilled in the art. In methods
employing PCR-based genetic mapping, it may be necessary to
identify DNA sequence differences between the parents of the
mapping cross in the region corresponding to the instant nucleic
acid sequence. This, however, is generally not necessary for
mapping methods.
[0064] Loss of function mutant phenotypes may be identified for the
instant cDNA clones either by targeted gene disruption protocols or
by identifying specific mutants for these genes contained in a
maize population carrying mutations in all possible genes
(Ballinger and Benzer (1989) Proc. Natl. Acad. Sci USA
86:9402-9406; Koes et al. (1995) Proc. Natl. Acad. Sci USA
92:8149-8153; Bensen et al. (1995) Plant Cell 7:75-84). The latter
approach may be accomplished in two ways. First, short segments of
the instant nucleic acid fragments may be used in polymerase chain
reaction protocols in conjunction with a mutation tag sequence
primer on DNAs prepared from a population of plants in which
Mutator transposons or some other mutation-causing DNA element has
been introduced (see Bensen, supra). The amplification of a
specific DNA fragment with these primers indicates the insertion of
the mutation tag element in or near the plant gene encoding the
instant polypeptide. Alternatively, the instant nucleic acid
fragment may be used as a hybridization probe against PCR
amplification products generated from the mutation population using
the mutation tag sequence primer in conjunction with an arbitrary
genomic site primer, such as that for a restriction enzyme
site-anchored synthetic adaptor. With either method, a plant
containing a mutation in the endogenous gene encoding the instant
polypeptide can be identified and obtained. This mutant plant can
then be used to determine or confirm the natural function of the
instant polypeptides disclosed herein.
EXAMPLES
[0065] The present invention is further defined in the following
Examples, in which all parts and percentages are by weight and
degrees are Celsius, unless otherwise stated. It should be
understood that these Examples, while indicating preferred
embodiments of the invention, are given by way of illustration
only. From the above discussion and these Examples, one skilled in
the art can ascertain the essential characteristics of this
invention, and without departing from the spirit and scope thereof,
can make various changes and modifications of the invention to
adapt it to various usages and conditions.
Example 1
Composition of cDNA Libraries; Isolation and Sequencing of cDNA
Clones
[0066] cDNA libraries representing mRNAs from various corn, rice,
soybean and wheat tissues were prepared. The characteristics of the
libraries are described below. TABLE-US-00002 TABLE 2 cDNA
Libraries from Corn, Rice, Soybean and Wheat Library Tissue Clone
chpc8 Corn (Zea mays L.) (MBS847) 8 Day Old Shoot Treated
chpc8.pk0002.d9 8 Hours With PDO Herbicide MK593* csi1n Corn (Zea
mays L.) Silk** csi1n.pk0008.b5 csi1n.pk0028.h7 cta1n Corn (Zea
mays L.) Tassel** cta1n.pk0079.e9 p0008 Corn (Zea mays L.) 3 Week
Old Leaf p0008.cb31d06r p0026 Corn (Zea mays L.) Regenerating
Callus (Hi-II 223a and p0026.ccrbd36rb 1129e), 5 Days After Auxin
Removal rds3c Rice (Oryza sativa) Developing Seed From Top of the
Plant rds3c.pk002.c6 rl0n Rice (Oryza sativa) 15 Day Old Leaf**
rl0n.pk082.c13 rlr24 Resistant Rice (Oryza sativa) Leaf 15 Days
After rlr24.pk0090.f5 Germination, 24 Hours After Infection of
Strain Magnaporthe grisea 4360-R-62 (AVR2-YAMO) rlr48 Resistant
Rice (Oryza sativa) Leaf 15 Days After rlr48.pk0012.c11
Germination, 48 Hours After Infection of Strain Magnaporthe grisea
4360-R-62 (AVR2-YAMO) rr1 Rice (Oryza sativa) Root of Two Week Old
Developing rr1.pk0027.g9 Seedling rr1.pk0037.g7 rr1.pk077.n9
rr1.pk088.p6 se6 Soybean (Glycine max L) Embryo, 26 Days After
Flowering se6.pk0048.a12 ses9c Soybean (Glycine max L) Embryogenic
Suspension ses9c.pk002.o16 sfl1 Soybean (Glycine max L) Immature
Flower sfl1.pk0003.a3 sfl1.pk0032.g4 sfl1.pk0086.a9 sfl1.pk0091.a2
sfl1.pk0105.e6 sfl1.pk125.p19 sgs4c Soybean (Glycine max L) Seed 2
Days After Germination sgs4c.pk004.j24 sl2 Soybean (Glycine max L)
Two-Week-Old Developing sl2.pk127.e14 Seedling Treated With 2.5 ppm
chlorimuron src3c Soybean (Glycine max L) 8 Day Old Root Infected
With src3c.pk010.i22 Cyst Nematode srr3c Soybean (Glycine max L) 8
Day Old Root srr3c.pk002.k6 wdk3c Wheat (Triticum aestivum L)
Developing Kernel, wdk3c.pk006.n12 14 Days After Anthesis wlm1
Wheat (Triticum aestivum L) Seedling 1 Hour After wlm1.pk0027.a5
Inoculation With Erysiphe graminis f. sp tritici wr1 Wheat
(Triticum aestivum L) Root From 7 Day Old wr1.pk0139.g11 Seedling
Light Grown *Application of
2-[(2,4-dihydro-2,6,9-trimethyl[1]benzothiopyrano[4,3-c]pyrazol-8-yl)carb-
onyl]-1,3-cyclohexanedione S,S-dioxide; synthesis and methods of
using this compound are described in WO 97/19087, incorporated
herein by reference. **These libraries were normalized essentially
as described in U.S. Pat. No. 5,482,845, incorporated herein by
reference.
[0067] cDNA libraries may be prepared by any one of many methods
available. For example, the cDNAs may be introduced into plasmid
vectors by first preparing the cDNA libraries in Uni-ZAP.TM. XR
vectors according to the manufacturer's protocol (Stratagene
Cloning Systems, La Jolla, Calif.). The Uni-ZAP.TM. XR libraries
are converted into plasmid libraries according to the protocol
provided by Stratagene. Upon conversion, cDNA inserts will be
contained in the plasmid vector pBluescript. In addition, the cDNAs
may be introduced directly into precut Bluescript II SK(+) vectors
(Stratagene) using T4 DNA ligase (New England Biolabs), followed by
transfection into DH10B cells according to the manufacturer's
protocol (GIBCO BRL Products). Once the cDNA inserts are in plasmid
vectors, plasmid DNAs are prepared from randomly picked bacterial
colonies containing recombinant pBluescript plasmids, or the insert
cDNA sequences are amplified via polymerase chain reaction using
primers specific for vector sequences flanking the inserted cDNA
sequences. Amplified insert DNAs or plasmid DNAs are sequenced in
dye-primer sequencing reactions to generate partial cDNA sequences
(expressed sequence tags or "ESTs"; see Adams et al., (1991)
Science 252:1651-1656). The resulting ESTs are analyzed using a
Perkin Elmer Model 377 fluorescent sequencer.
[0068] Determination of complete nucleotide sequence of cDNA
inserts may be accomplished by a number of methods well-known to
those skilled in the art (Maniatis). For example, this may be
accomplished stepwise, wherein oligonucleotides near the 5' or 3'
end of the sequence may be synthesized which can then serve as
primers for sequencing reactions that will extend the known
sequence. Another set of oligonucleotides near the 5' or 3' end of
the new sequence in the next round prime another set of sequencing
reactions to obtain more sequence information. These steps are
repeated until the complete nucleotide sequence is determined.
Example 2
Identification of cDNA Clones
[0069] cDNA clones encoding Myb-related transcription factors were
identified by conducting BLAST (Basic Local Alignment Search Tool;
Altschul et al. (1993) J. Mol. Biol. 215:403-410; see also
www.ncbi.nlm.nih.gov/BLAST/) searches for similarity to sequences
contained in the BLAST "nr" database (comprising all non-redundant
GenBank CDS translations, sequences derived from the 3-dimensional
structure Brookhaven Protein Data Bank, the last major release of
the SWISS-PROT protein sequence database, EMBL, and DDBJ
databases). The cDNA sequences obtained in Example 1 were analyzed
for similarity to all publicly available DNA sequences contained in
the "nr" database using the BLASTN algorithm provided by the
National Center for Biotechnology Information (NCBI). The DNA
sequences were translated in all reading frames and compared for
similarity to all publicly available protein sequences contained in
the "nr" database using the BLASTX algorithm (Gish and States
(1993) Nat. Genet. 3:266-272) provided by the NCBI. For
convenience, the P-value (probability) of observing a match of a
cDNA sequence to a sequence contained in the searched databases
merely by chance as calculated by BLAST are reported herein as
"pLog" values, which represent the negative of the logarithm of the
reported P-value. Accordingly, the greater the pLog value, the
greater the likelihood that the cDNA sequence and the BLAST "hit"
represent homologous proteins.
Example 3
Characterization of cDNA Clones Encoding Myb-related Transcription
Factors
[0070] The BLASTX search using the EST sequence from clone
cta1n.pk0079.e9 revealed similarity of the protein encoded by the
cDNA to a Myb-related transcription factor from Craterostigma
plantagineum (NCBI Identifier No. gi 1002800). The BLASTX search
using the EST sequence from clone rr1.pk077.n9 revealed similarity
of the protein encoded by the cDNA to a Myb-related transcription
factor from Arabidopsis thaliana (NCBI Identifier No. gi 1732513).
The BLASTX search using the EST sequence from clone sfl1.pk0032.g4
revealed similarity of the protein encoded by the cDNA to a
Myb-related transcription factor from Pisum sativum (NCBI
Identifier No. gi 1841475). The BLASTX search using the EST
sequence from clone wr1.pk0139.g11 revealed similarity of the
protein encoded by the cDNA to a Myb-related transcription factor
from Arabidopsis thaliana (NCBI Identifier No. gi 2832500). The
BLAST results for each of these ESTs are shown in Table 3:
TABLE-US-00003 TABLE 3 BLAST Results for Clones Encoding
Polypeptides Homologous to Plant Myb-related Transcription Factors
Clone BLAST pLog Score cta1n.pk0079.e9 39.00 rr1.pk077.n9 27.70
sfl1.pk0032.g4 38.50 wr1.pk0139.g11 16.00
[0071] The sequence of a portion of the cDNA insert from clone
cta1n.pk0079.e9 is shown in SEQ ID NO:7; the deduced amino acid
sequence of this cDNA is shown in SEQ ID NO:8. The sequence of a
portion of the cDNA insert from clone rr1.pk077.n9 is shown in SEQ
ID NO:11; the deduced amino acid sequence of this cDNA is shown in
SEQ ID NO:12. The sequence of a portion of the cDNA insert from
clone sfl1.pk0032.g4 is shown in SEQ ID NO:27; the deduced amino
acid sequence of this cDNA is shown in SEQ ID NO:28. The sequence
of a portion of the cDNA insert from clone wr1.pk0139.g11 is shown
in SEQ ID NO:55; the deduced amino acid sequence of this cDNA is
shown in SEQ ID NO:56. BLAST scores and probabilities indicate that
the instant nucleic acid fragments encode portions of a Myb-related
transcription factor protein.
[0072] The BLASTX search using the EST sequences from clones
rl0n.pk082.c13 and sgs4c.pk004j24 revealed similarity of the
proteins encoded by the cDNAs to a Myb-related transcription factor
protein from Pisum sativum (NCBI Identifier No. gi 82307). The
BLAST results for each of these ESTs are shown in Table 4:
TABLE-US-00004 TABLE 4 BLAST Results for Clones Encoding
Polypeptides Homologous to Plant Myb-related Transcription Factors
Clone BLAST pLog Score rl0n.pk082.c13 62.50 sgs4c.pk004.j24
47.50
[0073] The sequence of a portion of the cDNA insert from clone
rl0n.pk082.c13 is shown in SEQ ID NO:23; the deduced amino acid
sequence of this cDNA is shown in SEQ ID NO:24. The sequence of a
portion of the cDNA insert from clone sgs4c.pk004j24 is shown in
SEQ ID NO:51; the deduced amino acid sequence of this cDNA is shown
in SEQ ID NO:52. BLAST scores and probabilities indicate that the
instant nucleic acid fragments encode portions of a Myb-related
transcription factor protein.
[0074] The BLASTX search using the sequences from clones listed in
Table 5 revealed similarity of the polypeptides encoded by the
cDNAs to Myb-related transcription factors from different plant
species including Pisum sativum (NCBI General Identification No.
1841475), Arabidopsis thaliana (NCBI General Identification Nos.
3941480 and 3941528), Craterostigma plantagineum (NCBI General
Identification Nos. 1002796, 1002798, and 1002800), and Antirrhinum
majus (NCBI General Identification No. 82307). Shown in Table 5 are
the BLAST results for individual ESTs ("EST"), the sequences of the
entire cDNA inserts comprising the indicated cDNA clones ("FIS"),
contigs assembled from two or more ESTs ("Contig"), contigs
assembled from an FIS and one or more ESTs ("Contig*"), or
sequences encoding the entire protein derived from an FIS, a
contig, or an FIS and PCR ("CGS"): TABLE-US-00005 TABLE 5 BLAST
Results for Sequences Encoding Polypeptides Homologous to
Myb-related Transcription Factors BLAST Results NCBI General Clone
Status Identification No. pLog Score Contig of: Contig 1841475
54.40 csi1n.pk0008.b5 csi1n.pk0028.h7 Contig of: Contig 3941480
70.10 p0008.cb31d06r p0026.ccrbd36rb chpc8.pk0002.d9 EST 1002800
44.70 cta1n.pk0079.e9 CGS 1002800 68.52 Contig of: CGS 3941480
50.00 rr1.pk0027.g9 rr1.pk077.n9 rr1.pk088.p6 EST 3941480 22.52
rr1.pk0037.g7 EST 1002798 79.70 rds3c.pk002.c6 EST 1002798 62.00
Contig of: Contig 1002800 55.04 rlr24.pk0090.f5 rlr48.pk0012.c11
rl0n.pk082.c13 CGS 82307 84.22 sfl1.pk0032.g4 CGS 1841475 96.52
sfl1.pk0086.a9 CGS 1841475 92.22 sfl1.pk0091.a2 CGS 1841475 75.10
sfl1.pk0105.e6 CGS 1841475 96.40 sfl1.pk125.p19 FIS 1841475 90.52
se6.pk0048.a12 FIS 1002798 66.70 sfl1.pk0003.a3 CGS 1002796 59.70
srr3c.pk002.k6 CGS 1002798 77.40 ses9c.pk002.o16 CGS 1002798 73.70
sl2.pk127.e14 CGS 1002800 60.70 src3c.pk010.i22 CGS 1002800 57.05
sgs4c.pk004.j24 CGS 82307 90.52 wr1.pk0139.g11 FIS 3941480 48.52
wdk3c.pk006.n12 EST 1002796 43.70 wlm1.pk0027.a5 EST 3941528
73.70
[0075] FIG. 1 presents an alignment of the amino acid sequences set
forth in SEQ ID NOs:10, 14, 26, 30, 32, 34, 36, 42, 44, 46, 48, 50,
and 54 and the Pisum sativum sequence (NCBI General Identification
No. 1841475; SEQ ID NO:63). The data in Table 6 represents a
calculation of the percent identity of the amino acid sequences set
forth in SEQ ID NOs:10, 14, 26, 30, 32, 34, 36, 42, 44, 46, 48, 50,
and 54 and the Pisum sativum sequence (NCBI General Identification
No. 1841475; SEQ ID NO:63). TABLE-US-00006 TABLE 6 Percent Identity
of Amino Acid Sequences Deduced From the Nucleotide Sequences of
cDNA Clones Encoding Polypeptides Homologous to Myb-related
Transcription Factors Percent Identity to SEQ ID NO. NCBI General
Identification No. 1841475 10 43.8 14 33.2 26 30.9 30 75.6 32 74.1
34 64.1 36 77.7 42 43.8 44 48.5 46 46.5 48 45.6 50 46.1 54 31.8
[0076] Sequence alignments and percent identity calculations were
performed using the Megalign program of the LASERGENE
bioinformatics computing suite (DNASTAR Inc., Madison, Wis.).
Multiple alignment of the sequences was performed using the Clustal
method of alignment (Higgins and Sharp (1989) CABIOS. 5:151-153)
with the default parameters (GAP PENALTY=10, GAP LENGTH
PENALTY=10). Default parameters for pairwise alignments using the
Clustal method were KTUPLE 1, GAP PENALTY=3, WINDOW=5 and DIAGONALS
SAVED=5. Sequence alignments and BLAST scores and probabilities
indicate that the nucleic acid fragments comprising the instant
cDNA clones encode all or a substantial portion of a Myb-related
transcription factor. These sequences represent the first soybean
and wheat sequences encoding Myb-related transcription factors.
Nucleic acid fragments encoding Myb-related transcription factors
have previously been isolated from rice and corn (Marocco et al.
(1989) Mol Gen Genet 216:183-187; Pandolfi et al. (1997) Plant
Physiol 114:747).
Example 4
Expression of Chimeric Genes in Monocot Cells
[0077] A chimeric gene comprising a cDNA encoding the instant
polypeptide in sense orientation with respect to the maize 27 kD
zein promoter that is located 5' to the cDNA fragment, and the 10
kD zein 3' end that is located 3' to the cDNA fragment, can be
constructed. The cDNA fragment of this gene may be generated by
polymerase chain reaction (PCR) of the cDNA clone using appropriate
oligonucleotide primers. Cloning sites (NcoI or SmaI) can be
incorporated into the oligonucleotides to provide proper
orientation of the DNA fragment when inserted into the digested
vector pML103 as described below. Amplification is then performed
in a standard PCR. The amplified DNA is then digested with
restriction enzymes NcoI and SmaI and fractionated on an agarose
gel. The appropriate band can be isolated from the gel and combined
with a 4.9 kb NcoI-SmaI fragment of the plasmid pML103. Plasmid
pML103 has been deposited under the terms of the Budapest Treaty at
ATCC (American Type Culture Collection, 10801 University Blvd.,
Manassas, Va. 20110-2209), and bears accession number ATCC 97366.
The DNA segment from pML103 contains a 1.05 kb SalI-NcoI promoter
fragment of the maize 27 kD zein gene and a 0.96 kb SmaI-SalI
fragment from the 3' end of the maize 10 kD zein gene in the vector
pGem9Zf(+) (Promega). Vector and insert DNA can be ligated at
15.degree. C. overnight, essentially as described (Maniatis). The
ligated DNA may then be used to transform E. coli XL1-Blue
(Epicurian Coli XL-1 Blue.TM.; Stratagene). Bacterial transformants
can be screened by restriction enzyme digestion of plasmid DNA and
limited nucleotide sequence analysis using the dideoxy chain
termination method (Sequenase.TM. DNA Sequencing Kit; U.S.
Biochemical). The resulting plasmid construct would comprise a
chimeric gene encoding, in the 5' to 3' direction, the maize 27 kD
zein promoter, a cDNA fragment encoding the instant polypeptide,
and the 10 kD zein 3' region.
[0078] The chimeric gene described above can then be introduced
into corn cells by the following procedure. Immature corn embryos
can be dissected from developing caryopses derived from crosses of
the inbred corn lines H99 and LH132. The embryos are isolated 10 to
11 days after pollination when they are 1.0 to 1.5 mm long. The
embryos are then placed with the axis-side facing down and in
contact with agarose-solidified N6 medium (Chu et al. (1975) Sci.
Sin. Peking 18:659-668). The embryos are kept in the dark at
27.degree. C. Friable embryogenic callus consisting of
undifferentiated masses of cells with somatic proembryoids and
embryoids borne on suspensor structures proliferates from the
scutellum of these immature embryos. The embryogenic callus
isolated from the primary explant can be cultured on N6 medium and
sub-cultured on this medium every 2 to 3 weeks.
[0079] The plasmid, p35S/Ac (obtained from Dr. Peter Eckes, Hoechst
Ag, Frankfurt, Germany) may be used in transformation experiments
in order to provide for a selectable marker. This plasmid contains
the Pat gene (see European Patent Publication 0 242 236) which
encodes phosphinothricin acetyl transferase (PAT). The enzyme PAT
confers resistance to herbicidal glutamine synthetase inhibitors
such as phosphinothricin. The pat gene in p35S/Ac is under the
control of the 35S promoter from Cauliflower Mosaic Virus (Odell et
al. (1985) Nature 313:810-812) and the 3' region of the nopaline
synthase gene from the T-DNA of the Ti plasmid of Agrobacterium
tumefaciens.
[0080] The particle bombardment method (Klein et al. (1987) Nature
327:70-73) may be used to transfer genes to the callus culture
cells. According to this method, gold particles (1 .mu.m in
diameter) are coated with DNA using the following technique. Ten
.mu.g of plasmid DNAs are added to 50 .mu.L of a suspension of gold
particles (60 mg per mL). Calcium chloride (50 .mu.L of a 2.5 M
solution) and spermidine free base (20 .mu.L of a 1.0 M solution)
are added to the particles. The suspension is vortexed during the
addition of these solutions. After 10 minutes, the tubes are
briefly centrifuged (5 sec at 15,000 rpm) and the supernatant
removed. The particles are resuspended in 200 .mu.L of absolute
ethanol, centrifuged again and the supernatant removed. The ethanol
rinse is performed again and the particles resuspended in a final
volume of 30 .mu.L of ethanol. An aliquot (5 .mu.L) of the
DNA-coated gold particles can be placed in the center of a
Kapton.TM. flying disc (Bio-Rad Labs). The particles are then
accelerated into the corn tissue with a Biolistic.TM. PDS-1000/He
(Bio-Rad Instruments, Hercules Calif.), using a helium pressure of
1000 psi, a gap distance of 0.5 cm and a flying distance of 1.0
cm.
[0081] For bombardment, the embryogenic tissue is placed on filter
paper over agarose-solidified N6 medium. The tissue is arranged as
a thin lawn and covered a circular area of about 5 cm in diameter.
The petri dish containing the tissue can be placed in the chamber
of the PDS-1000/He approximately 8 cm from the stopping screen. The
air in the chamber is then evacuated to a vacuum of 28 inches of
Hg. The macrocarrier is accelerated with a helium shock wave using
a rupture membrane that bursts when the He pressure in the shock
tube reaches 1000 psi.
[0082] Seven days after bombardment the tissue can be transferred
to N6 medium that contains gluphosinate (2 mg per liter) and lacks
casein or proline. The tissue continues to grow slowly on this
medium. After an additional 2 weeks the tissue can be transferred
to fresh N6 medium containing gluphosinate. After 6 weeks, areas of
about 1 cm in diameter of actively growing callus can be identified
on some of the plates containing the glufosinate-supplemented
medium. These calli may continue to grow when sub-cultured on the
selective medium.
[0083] Plants can be regenerated from the transgenic callus by
first transferring clusters of tissue to N6 medium supplemented
with 0.2 mg per liter of 2,4-D. After two weeks the tissue can be
transferred to regeneration medium (Fromm et al. (1990)
Bio/Technology 8:833-839).
Example 5
Expression of Chimeric Genes in Dicot Cells
[0084] A seed-specific expression cassette composed of the promoter
and transcription terminator from the gene encoding the .beta.
subunit of the seed storage protein phaseolin from the bean
Phaseolus vulgaris (Doyle et al. (1986) J. Biol. Chem.
261:9228-9238) can be used for expression of the instant
polypeptides in transformed soybean. The phaseolin cassette
includes about 500 nucleotides upstream (5') from the translation
initiation codon and about 1650 nucleotides downstream (3') from
the translation stop codon of phaseolin. Between the 5' and 3'
regions are the unique restriction endonuclease sites Nco I (which
includes the ATG translation initiation codon), Sma I, Kpn I and
Xba I. The entire cassette is flanked by Hind III sites.
[0085] The cDNA fragment of this gene may be generated by
polymerase chain reaction (PCR) of the cDNA clone using appropriate
oligonucleotide primers. Cloning sites can be incorporated into the
oligonucleotides to provide proper orientation of the DNA fragment
when inserted into the expression vector. Amplification is then
performed as described above, and the isolated fragment is inserted
into a pUC18 vector carrying the seed expression cassette.
[0086] Soybean embryos may then be transformed with the expression
vector comprising sequences encoding the instant polypeptides. To
induce somatic embryos, cotyledons, 3-5 mm in length dissected from
surface sterilized, immature seeds of the soybean cultivar A2872,
can be cultured in the light or dark at 26.degree. C. on an
appropriate agar medium for 6-10 weeks. Somatic embryos which
produce secondary embryos are then excised and placed into a
suitable liquid medium. After repeated selection for clusters of
somatic embryos which multiplied as early, globular staged embryos,
the suspensions are maintained as described below.
[0087] Soybean embryogenic suspension cultures can maintained in 35
mL liquid media on a rotary shaker, 150 rpm, at 26.degree. C. with
florescent lights on a 16:8 hour day/night schedule. Cultures are
subcultured every two weeks by inoculating approximately 35 mg of
tissue into 35 mL of liquid medium.
[0088] Soybean embryogenic suspension cultures may then be
transformed by the method of particle gun bombardment (Klein et al.
(1987) Nature (London) 327:70-73, U.S. Pat. No. 4,945,050). A
DuPont Biolistic.TM. PDS1000/HE instrument (helium retrofit) can be
used for these transformations.
[0089] A selectable marker gene which can be used to facilitate
soybean transformation is a chimeric gene composed of the 35S
promoter from Cauliflower Mosaic Virus (Odell et al. (1985) Nature
313:810-812), the hygromycin phosphotransferase gene from plasmid
pJR225 (from E. coli; Gritz et al. (1983) Gene 25:179-188) and the
3' region of the nopaline synthase gene from the T-DNA of the Ti
plasmid of Agrobacterium tumefaciens. The seed expression cassette
comprising the phaseolin 5' region, the fragment encoding the
instant polypeptide and the phaseolin 3' region can be isolated as
a restriction fragment. This fragment can then be inserted into a
unique restriction site of the vector carrying the marker gene.
[0090] To 50 .mu.L of a 60 mg/mL 1 .mu.m gold particle suspension
is added (in order): 5 .mu.L DNA (1 .mu.g/.mu.L), 20 .mu.l
spermidine (0.1 M), and 50 .mu.L CaCl.sub.2 (2.5 M). The particle
preparation is then agitated for three minutes, spun in a microfuge
for 10 seconds and the supernatant removed. The DNA-coated
particles are then washed once in 400 .mu.L 70% ethanol and
resuspended in 40 .mu.L of anhydrous ethanol. The DNA/particle
suspension can be sonicated three times for one second each. Five
.mu.L of the DNA-coated gold particles are then loaded on each
macro carrier disk.
[0091] Approximately 300-400 mg of a two-week-old suspension
culture is placed in an empty 60.times.15 mm petri dish and the
residual liquid removed from the tissue with a pipette. For each
transformation experiment, approximately 5-10 plates of tissue are
normally bombarded. Membrane rupture pressure is set at 1100 psi
and the chamber is evacuated to a vacuum of 28 inches mercury. The
tissue is placed approximately 3.5 inches away from the retaining
screen and bombarded three times. Following bombardment, the tissue
can be divided in half and placed back into liquid and cultured as
described above.
[0092] Five to seven days post bombardment, the liquid media may be
exchanged with fresh media, and eleven to twelve days post
bombardment with fresh media containing 50 mg/mL hygromycin. This
selective media can be refreshed weekly. Seven to eight weeks post
bombardment, green, transformed tissue may be observed growing from
untransformed, necrotic embryogenic clusters. Isolated green tissue
is removed and inoculated into individual flasks to generate new,
clonally propagated, transformed embryogenic suspension cultures.
Each new line may be treated as an independent transformation
event. These suspensions can then be subcultured and maintained as
clusters of immature embryos or regenerated into whole plants by
maturation and germination of individual somatic embryos.
Example 6
Expression of Chimeric Genes in Microbial Cells
[0093] The cDNAs encoding the instant polypeptides can be inserted
into the T7 E. coli expression vector pBT430. This vector is a
derivative of pET-3a (Rosenberg et al. (1987) Gene 56:125-135)
which employs the bacteriophage T7 RNA polymerase/T7 promoter
system. Plasmid pBT430 was constructed by first destroying the EcoR
I and Hind III sites in pET-3a at their original positions. An
oligonucleotide adaptor containing EcoR I and Hind III sites was
inserted at the BamH I site of pET-3a. This created pET-3aM with
additional unique cloning sites for insertion of genes into the
expression vector. Then, the Nde I site at the position of
translation initiation was converted to an Nco I site using
oligonucleotide-directed mutagenesis. The DNA sequence of pET-3aM
in this region, 5'-CATATGG, was converted to 5'-CCCATGG in
pBT430.
[0094] Plasmid DNA containing a cDNA may be appropriately digested
to release a nucleic acid fragment encoding the protein. This
fragment may then be purified on a 1% NuSieve GTG.TM. low melting
agarose gel (FMC). Buffer and agarose contain 10 .mu.g/ml ethidium
bromide for visualization of the DNA fragment. The fragment can
then be purified from the agarose gel by digestion with GELase.TM.
(Epicentre Technologies) according to the manufacturer's
instructions, ethanol precipitated, dried and resuspended in 20
.mu.L of water. Appropriate oligonucleotide adapters may be ligated
to the fragment using T4 DNA ligase (New England Biolabs, Beverly,
Mass.). The fragment containing the ligated adapters can be
purified from the excess adapters using low melting agarose as
described above. The vector pBT430 is digested, dephosphorylated
with alkaline phosphatase (NEB) and deproteinized with
phenol/chloroform as described above. The prepared vector pBT430
and fragment can then be ligated at 16.degree. C. for 15 hours
followed by transformation into DH5 electrocompetent cells (GIBCO
BRL). Transformants can be selected on agar plates containing LB
media and 100 .mu.g/mL ampicillin. Transformants containing the
gene encoding the instant polypeptide are then screened for the
correct orientation with respect to the T7 promoter by restriction
enzyme analysis.
[0095] For high level expression, a plasmid clone with the cDNA
insert in the correct orientation relative to the T7 promoter can
be transformed into E. coli strain BL21(DE3) (Studier et al. (1986)
J. Mol. Biol. 189:113-130). Cultures are grown in LB medium
containing ampicillin (100 mg/L) at 25.degree. C. At an optical
density at 600 nm of approximately 1, IPTG
(isopropylthio-.beta.-galactoside, the inducer) can be added to a
final concentration of 0.4 mM and incubation can be continued for 3
h at 25.degree.. Cells are then harvested by centrifugation and
re-suspended in 50 .mu.L of 50 mM Tris-HCl at pH 8.0 containing 0.1
mM DTT and 0.2 mM phenyl methylsulfonyl fluoride. A small amount of
1 mm glass beads can be added and the mixture sonicated 3 times for
about 5 seconds each time with a microprobe sonicator. The mixture
is centrifuged and the protein concentration of the supernatant
determined. One .mu.g of protein from the soluble fraction of the
culture can be separated by SDS-polyacrylamide gel electrophoresis.
Gels can be observed for protein bands migrating at the expected
molecular weight.
Example 7
Assaying Myb-related Transcription Factor Activity
[0096] The polypeptides described herein may be produced using any
number of methods known to those skilled in the art. Such methods
include, but are not limited to, expression in bacteria as
described in Example 6, or expression in eukaryotic cell culture,
in planta, and using viral expression systems in suitably infected
organisms or cell lines. The instant -4B. In an alternate
embodiment, a thioredoxin fusion protein may be eluted using
dithiothreitol; however, elution may be accomplished using other
reagents which interact to displace the thioredoxin from the resin.
These reagents include .beta.-mercaptoethanol or other reduced
thiol. The eluted fusion protein may be subjected to further
purification by polypeptides may be expressed either as mature
forms of the proteins as observed in vivo or as fusion proteins by
covalent attachment to a variety of enzymes, proteins or affinity
tags. Common fusion protein partners include glutathione
S-transferase ("GST"), thioredoxin ("Trx"), maltose binding
protein, and C- and/or N-terminal hexahistidine polypeptide
("(His).sub.6"). The fusion proteins may be engineered with a
protease recognition site at the fusion point so that fusion
partners can be separated by protease digestion to yield intact
mature enzyme. Examples of such proteases include thrombin,
enterokinase and factor Xa. However, any protease can be used which
specifically cleaves the peptide connecting the fusion protein and
the enzyme.
[0097] Purification of the instant polypeptides, if desired, may
utilize any number of separation technologies familiar to those
skilled in the art of protein purification. Examples of such
methods include, but are not limited to, homogenization,
filtration, centrifugation, heat denaturation, ammonium sulfate
precipitation, desalting, pH precipitation, ion exchange
chromatography, hydrophobic interaction chromatography and affinity
chromatography, wherein the affinity ligand represents a substrate,
substrate analog or inhibitor. When the instant polypeptides are
expressed as fusion proteins, the purification protocol may include
the use of an affinity resin which is specific for the fusion
protein tag attached to the expressed enzyme or an affinity resin
containing ligands which are specific for the enzyme. For example,
the instant polypeptides may be expressed as a fusion protein
coupled to the C-terminus of thioredoxin. In addition, a
(His).sub.6 peptide may be engineered into the N-terminus of the
fused thioredoxin moiety to afford additional opportunities for
affinity purification. Other suitable affinity resins could be
synthesized by linking the appropriate ligands to any suitable
resin such as Sepharosetraditional means as stated above, if
desired. Proteolytic cleavage of the thioredoxin fusion protein and
the enzyme may be accomplished after the fusion protein is purified
or while the protein is still bound to the ThioBond.TM. affinity
resin or other resin.
[0098] Crude, partially purified or purified enzyme, either alone
or as a fusion protein, may be utilized in assays to verify over-
or underexpression of functional Myb-related transcription factor
protein in transgenic plants and transformed bacterial cells.
Assays may be conducted under well known experimental conditions
which permit optimal enzymatic activity. For example, assays for
Myb-related transcription factors are presented by Moyano et al.
(1996) Plant Cell 8:1519-1532.
[0099] Various modifications of the invention in addition to those
shown and described herein will be apparent to those skilled in the
art from the foregoing description. Such modifications are also
intended to fall within the scope of the appended claims.
[0100] The disclosure of each reference set forth above is
incorporated herein by reference in its entirety.
* * * * *
References