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Identification and molecular characterization

of a receptor-like protein kinase gene from
Corchorus capsularis

Article in Turkish Journal of Biology · February 2013

DOI: 10.3906/biy-1202-22

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 Turkish Journal of Biology Turk J Biol
(2013) 37: 11-17
http://journals.tubitak.gov.tr/biology/
© TÜBİTAK
Research Article doi:10.3906/biy-1202-22

Identification and molecular characterization of a receptor-like protein kinase gene from

Corchorus capsularis
1, 1, 1 1
Kh. Ambareen REZA **, Sazia SHARMIN **, Mahdi Muhammad MOOSA , Niaz MAHMOOD ,
2 1 1,
Ajit GHOSH , Rifat Ara BEGUM , Haseena KHAN *
1
Molecular Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Dhaka, Bangladesh
2
International Centre for Genetic Engineering and Biotechnology, New Delhi, India

Received: 12.02.2012 Accepted: 01.07.2012 Published Online: 10.01.2013 Printed: 01.02.2013

Abstract: A leucine-rich repeat-containing protein kinase (LRR-PK) gene has been identified in Corchorus capsularis. This gene, named
CcLRR-RLK1, is 3032 bp long and encodes a protein composed of 958 amino acid residues. The deduced peptide contains 3 distinctive
domains: a transmembrane domain, 5 leucine-rich repeat-containing motifs, and a serine/threonine protein kinase domain. Expression
analysis indicated that the gene is reduced by several environmental stresses including high salt, fungus, and abscisic acid, suggesting its
possible involvement in multiple stress response pathways.

Key words: Corchorus capsularis, jute, leucine-rich repeat-containing protein kinase, expression analysis

1. Introduction To date, many plant LRR-RLK genes have been

In order to survive in ever-changing environmental
conditions, plants have developed several mechanisms to
perceive external signals and act accordingly. One such
mechanism involves the receptor-like kinases (RLKs),
which are involved in the perception and transmission
of external stimuli through signaling cascades to elicit
appropriate cellular responses (1). The largest group
of RLKs includes proteins with leucine-rich repeats
(LRRs) that are mainly involved in various protein–
protein interactions (2). Most of the LRR-RLKs have an
extracellular domain composed of tandem repeats of a
leucine-rich motif, a transmembrane domain, and an
intracellular kinase domain with serine/threonine kinase
activity (3).
The LRR, typically composed of around 20–30 amino
acids with a characteristic repetitive sequence pattern
rich in leucine, is a widespread structural motif found in
the primary structure of thousands of protein sequences
in all life forms, from viruses to eukaryotes (4,5). Apart
from their functions in pathogen recognition and disease
resistance in plants (6), proteins containing tandems of 2
or more LRRs also play a role in other biological processes
across different eukaryotic lineages. Examples include
RNA processing (7), cell adhesion and signaling (8),
platelet aggregation (9), neuronal development (10), and
immune response (11).
* Correspondence: haseena@univdhaka.edu
** These authors contributed equally to this study.
functionally characterized in different plant species (12–
14). Studies of plant LRR-RLKs revealed their function
in a wide array of cellular and signaling pathways, such
as pollen–pistil interaction by SRK (15) and hormone
perception by BRI1 (16).
Corchorus capsularis L. (white jute) is one of the most
widely cultivated jute species with an Indo-Burma origin
(17). In spite of its long history of cultivation and enormous
economic importance, studies of the molecular biology
of C. capsularis are relatively rare. As of December 2011,
only 696 expressed sequence tags and 13 partial coding
sequences of C. capsularis genes had been deposited in the
NCBI database. None of the coding sequences are of full
length, and only a few have been characterized. Here we
report on the first LRR-RLK gene of C. capsularis, which
we named CcLRR-RLK1. Expression analysis was also
performed to further characterize its role in jute.
2. Materials and methods
2.1. Plant materials and stress treatment
C. capsularis var. 2197 seeds were incubated in petri dishes
with water only at room temperature in the absence of
light for 2 days. Germinated plant seedlings were subjected
to fungus and low-temperature stress. Fungus treatment
was performed by spraying a suspension of Macrophomina
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 REZA et al. / Turk J Biol

Table 1. List of primers (with their sequences) used in this study.

Primer name Sequence (5′-> 3′)

LRPK up for1 ATG AAA TGG CAC CCA AAG CAG CTT C
UpGSP4 ACA TGG GGA AGT CAC CTC TGA AG
LRPK_Up_For3 CGT TAC GTG TCC TTG ACT TGT CTT A
LEU SEQ REV ACA TCG AAT TTA GCT TCT TTT GGT T
LEU SEQ FOR CTC AAT GTT CTT GAT CTT TCC AAC A
LRPK_DOWN_REV3 GTG GTA GAA TCT TTC CCT CCT GTA G
Ds GSP4 ACA GGA GGG AAA GAT TCT ACC AC
LRPK_DOWN_REV ACC TAA AAC TCC CCA TCA TAT ACG AC
J132 F TGC AGA ACA ATA AGG TTT CAG GT
J132 R GGG AGG TAC TGG GTG TTA CAA
Actin deg for TGG CAT CAY ACW TTC TAC AAT GA
Actin deg rev GGN RYA TTG AAV GTC TCA AAC AT

phaseolina onto the plate with the germinated seedlings
(18,19). For low-temperature treatment, 3-day-old
seedlings were kept at 16 °C for 2 days following 3 days
of normal growth at room temperature. For inducing salt
stress, 3-day-old seedlings were sprayed with 100 mM NaCl
(10 mL solution per day per petri dish) for 2 days and then
collected. In order to study the effect of exogenous abscisic
acid (ABA) on jute LRR-RLK expression, 100 µM ABA (15
mL per petri dish) was sprayed on 5-day-old seedlings 12
h prior to collection. Seedlings were then collected, frozen
in liquid nitrogen, and stored at –80 °C until DNA and
RNA isolation.
2.2. Isolation of DNA and RNA
Genomic DNA from C. capsularis was isolated using the
CTAB method (20). RNA was isolated according to the
protocol described by Mahmood et al. (21).
2.3. Identification of the full length LRR-RLK gene
Our group previously identified and characterized the
LRR-RLK gene (GenBank no. FJ207521) from a related
jute species, C. olitorius (19). Here, we used it as a
reference to design gene-specific primers to sequence the
LRR-RLK gene from C. capsularis. In this study a total
of 4 sets of primers (Table 1) were used to obtain the full
length sequence of the putative CcLRR-RLK gene from C.
capsularis (a combination of LRPK up for1 and UpGSP4,
LRPK_Up_For3 and LEU SEQ REV, LEU SEQ FOR and
LRPK_DOWN_REV3, and Ds GSP4 and LRPK_DOWN_
REV primers were used for amplifying 480-, 1335-, 925-,
and 656-bp regions, respectively).
2.4. Sequence assembly and phylogenetic analysis
Sequences from gel-extracted bands were assembled using
the CAP3 assembler (22). Secondary and tertiary structure
of the protein was predicted using the NPS@ web server
(23) and CPHmodels-3.0 server (http://www.cbs.dtu.dk/
services/CPHmodels), respectively. Multiple sequence
alignment was done with Clustal X version 2.0 (24), and
the phylogenetic tree was constructed using the neighbor-
joining method (25) with a bootstrap multiple alignment
resampling set at 10,000 using Molecular Evolutionary
Genetics Analysis (MEGA) software version 4.1 (26).
2.5. Semiquantitative RT-PCR
Expression analysis of a gene under various stress
conditions is canonically performed by semiquantitative
reverse transcriptase polymerase chain reaction (RT-
PCR) (27). Total RNA was isolated from jute seedlings
and quantified using NanoDrop (ND-1000). First-strand

Figure 1. Structure of the CcLRR-RLK1 protein as predicted by SMART. The region on the protein containing
signal peptides, as determined by the SignalP program, is shown with a red rectangle. The region containing
transmembrane segments, as predicted by the TMHMM2 program, is shown with a blue rectangle. LRR regions
are shown by rectangular boxes labeled LRR, and serine/threonine protein kinase domain-containing region is
shown by the pentagon.

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 REZA et al. / Turk J Biol

Table 2. Summary of predicted secondary structures from different prediction tools at NPS@ web server. The last row is for consensus
secondary structure.

Tool name Random coil (c) Alpha helix (h) Beta turn (t) Extended strand (e)

DPM 52.51% 6.58% 7.31% 33.61%

DSC 59.92% 34.86% 0.00% 5.22%
GOR1 10.02% 36.33% 12.00% 41.65%
GOR3 42.90% 37.79% 0.00% 19.31%
HNNC 47.81% 37.58% 0.00% 14.61%
PHD 53.44% 28.60% 0.00% 17.95%
Predator 63.99% 19.31% 0.00% 16.70%
SIMPA96 55.90% 28.63% 0.00% 15.46%
SOPM 36.12% 35.80% 9.08% 19.00%
SOPMA 45.82% 39.67% 3.44% 11.06%
Sec. cons. (consensus) 45.51% 28.91% 0.00% 16.81%

cDNA was synthesized from 50 ng of mRNA using gene
specific primer J132 R. PCR amplification of the cDNA
was carried out for 25 cycles using primers J132 F and
J132 R (95 °C for 40 s, 58 °C for 40 s, and 72 °C for 50 s).
The housekeeping gene β-actin was used as the internal
standard for RT-PCR. The entire process was repeated
twice to validate the reproducibility of the experiment.
3. Results and discussion
3.1. Deduction of full-length LRR-RLK sequence in C.
capsularis
Through a combination of 4 primers sets, the full-
length coding sequence of LRR-RLK gene CcLRR-RLK1
Figure 2. The 3-D structure of the CcLRR-RLK1 protein as
predicted by the CPHmodels-3.0 server. The α-helices are shown
in green and β-sheets are in blue.
was deduced. The gene sequence was submitted to the
GenBank database with accession number JN585827.
The open reading frame of the gene encodes a protein
composed of 958 amino acids. The molecular mass of the
protein is 106.18 kDa, as determined by Protein Calculator
v 3.3 (http://www.scripps.edu/~cdputnam/protcalc.html).
The BLAST-P of the CcLRR-RLK1 protein sequence
compared with other leucine-rich repeat receptor kinases
from different higher plants in the NCBI nonredundant
database showed similarity with the previously identified
C. olitorius LRR-RLK gene (GenBank accession no.
ACI42311). Although the protein sequences of the LRR-
RLK of C. capsularis and C. olitorius were almost identical,
there are some differences in their DNA sequences. Alam
et al. (19) previously reported an intron in C. olitorius that
is not present in C. capsularis. It is possible that during the
course of evolution C. capsularis lost this intron.
The NCBI  Conserved Domain Database  (CDD) (28)
was used to identify the conserved domains within the
CcLRR-RLK1 protein. The CDD detected the presence
of 2 highly conserved domains: the catalytic domain of
serine/threonine kinase protein (indicated as PKc) and the
LRR repeat-containing domains. There is also a potential
ATP binding site within the PKc domain of the CcLRR-
RLK1 protein.
The SignalP 4.0 Server indicated the presence of a
hydrophobic signal peptide at the N-terminus of the
protein with the most likely cleavage site located between
the 20th and 21st amino acids. Such hydrophobicity is
needed for the localization of the protein on the plasma
membrane, and the signal peptide could possibly be
removed after targeting.
The TMHMM2 program predicted the presence of a
transmembrane domain from 584 to 603 aa. Furthermore,

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 REZA et al. / Turk J Biol

N L G IP
3

L LDLS L
Bits
2
1 RV L S SL N
0 QNK
L
VD
E
G
M
I L YY
Y
Q
E I
N
G
R
V
F
H
K
Q FR H
T
N
D
Q

F L
E
K
M
H
S
E I
GM
GA
S
C
F
TM
R C
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
N C
weblogo.berkeley.edu

Figure 3. Consensus sequence of the LRR motifs in jute as represented by WebLogo.

SMART (http://smart.embl-heidelberg.de/) detected the
presence of 5 LRR repeats in the protein (Figure 1).
3.2. Secondary and tertiary structure prediction
Table 1 shows the summary of secondary structures
predicted for the CcLRR-RLK1 protein using the NPS@
web server. The predicted secondary structures may not
exactly reflect in vivo structure; however, it has been used
as a guide.
The predictions suggested that a significant portion
of the amino acids of CcLRR-RLK1 are most likely to
form random coils (Table 2). Random coils or more
specific coils add flexibility to the protein structure, and
there is a possible relationship between random coils and
dehydration response (29). The 3-D structure of jute LRR-
RLK as predicted by the CPHmodels-3.0 server is shown
in Figure 2.
3.3. Pattern of the LRR motif in Corchorus spp.
By retrieving the 5 LRR motifs identified in CcLRR-RLK1
along with the 5 motifs in the previously identified jute
LRR gene (GenBank no. FJ207521), a consensus sequence
for jute LRR motif was determined by Multiple Expectation
Maximization for Motif Elicitation (MEME) (30,31) and
visualized by the WebLogo program (32) (Figure 3). The
consensus sequence (LxxLxLSxNsssGxxPxxxxxL) has a
length of 22 amino acids, and database comparison (NCBI
and BLAST-P) of the MEME-generated total consensus
sequence of this motif matched multiple LRR genes of
other plant species (data not shown). This again validates
the fact that the LRR motif is conserved across different
plant species.
3.4. Phylogeny of CcLRR-RLK1 and other plant-specific
protein kinases (RLKs)
A phylogenetic tree was constructed from the alignments
of CcLRR-RLK1 with other RLK protein sequences of
plants in the NCBI database (Figures 4a and 4b). More
closely related species showed higher levels of sequence
identity and were grouped together. For example, the
CcLRR-RLK1 protein of C. capsularis was grouped with
the C. olitorius LRR-RLK gene, and Arabidopsis thaliana
NP_199777 protein was grouped with Arabidopsis lyrata
XP_002865749. In addition, the tree clustered the proteins
from monocotyledonous and dicotyledonous plants in 2
separate clusters.
3.5. Expression of CcLRR-RLK1 gene
Expression studies showed the differential expression of
this gene upon exposure to fungus, high salt, and ABA
(Figure 5). However, no significant change was observed
under low-temperature stress conditions. The expression
level was significantly reduced under fungal, salt, and ABA
treatment conditions. Plant hormones play major roles in
various cellular responses such as the regulation of many
plant genes. In this study we found that expression of the
CcLRR-RLK1 gene was greatly reduced 12 h after either
ABA treatment or high salt stress. High salt levels cause
osmotic stress by reducing water potential, and ABA is
also known to be involved in the osmotic stress response
that is caused by several environmental stressors (33).
Therefore, this gene may be involved in osmotic stress
response. However, low-temperature stress also causes
osmotic stress by reducing the water supply from the
roots to green tissues (34). However, in CcLRR-RLK1, the
change in expression level due to low-temperature stress is
insignificant. This could be due to the fact that 14 °C, the
low temperature used in our study, was not low enough to
elicit sufficient osmotic stress.
The change in expression level after fungal infection
indicates that CcLRR-RLK1 might also play a role in defense
pathways against fungal infection in jute. The rice Xa21
gene, which has a structure similar to CcLRR-RLK1 and
carries a leucine-rich repeat motif and a serine/threonine
kinase-like domain, is involved in the recognition of rice
leaf blight bacteria and confers resistance to Xanthomonas
oryzae (35). In addition, plant hormones such as ABA
have been effective in inducing defense responses in plants
(36). The change in CcLRR-RLK1 gene expression level
after fungal and hormone treatment further indicates that
crosstalk may exist among these pathways to activate the
gene in response to a pathogen attack. The expression
pattern of the CcLRR-RLK1 gene of C. capsularis shown
in this study is completely different from its structurally

14
 REZA et al. / Turk J Biol

A. thaliana LDVSENRLSGPLPAHVCKSGKLLYFLVLQNRFTGSIPETYGSCKTLIRFRVASNRLVGTI
A. lyrata LDVSENRLSGPLPAHVCKSGKLLYFLVLQNQFTGSIPETYGSCKTLIRFRVASNHLVGFI
CcLRR-RLK1 LDLSENNLTGLLPTEVCRGGKLLYFLVLDNMFSGKLPGSYANCKSLLRFRVSKNHLEGPI
C. olitorius LDLSENNLTGLLPTEVCRGGKLLYFLVLDNMFTGKLPASYANCKSLLRFRVSNNHLEGPI
P. trichocarpa VDLSENRLSGPLPSDVCRGGKLLYFLVLDNMFSGELPDSYAKCKTLLRFRLSHNHLEGSI
R. communis LDVSENRLSGPLPTEVCSGGKLLYFLVLDNMFSGGLPSSYAKCKTLLRFRVSHNRLEGSI
V. vinifera LDLSENHLSGELPTEVCKGGNLLYFLVLDNMFSGKLPENYAKCESLLRFRVSNNRLEGPI
S. bicolor IEVSENQLTGPLPPYACVNGKLQYILVLSNLLTGPIPPAYAECTPLIRFRVSNNHLEGDV
O. sativa LEVSENQLTGPLPPYACANGQLQYILVLSNLLTGAIPASYAACRPLLRFRVSNNHLDGDV

A. thaliana PQGVMSLPHVSIIDLAYNSLSGPIPNAIGNAWNLSELFMQSNRISGVIPHELSHSTNLVK
A. lyrata PQGVMSLPHVSIIDLAYNSLSGPIPNAIGNAWNLSELFMQGNRISGFLPHEISHATNLVK
CcLRR-RLK1 PEGLLGLPHVTIIDLAYNNFSGPFPNSVGNARNLSELFVQNNKLSGVIPPEISRARNLVK
C. olitorius PEGLLNLPHVSIIDLAYNNFSGTFPNEFGNARNLSELFMQNNKVSGVIPPEISRARNLVK
P. trichocarpa PEGILGLPRVSIIDLSYNNFSGPISNTIGTARNLSELFVQSNKISGVIPPEISRAINLVK
R. communis PEGLLGLPHVSIIDLGYNNFSGSISNTIRTARNLSELFLQSNKISGVLPPEISGAINLVK
V. vinifera PEGLLGLPRVSILDLGFNNLNGQIGKTIGTARNLSELFIQSNRISGALPPEISQATNLVK
S. bicolor PPGIFGLPHASIVDLNYNHFTGPVAATVAGATNLTSLFASNNRMSGVLPPDIAGASGLVK
O. sativa PAGIFALPHASIIDLSYNHLTGPVPATIAGATNLTSLFASNNRMSGVLPPEIAGAATLVK

A. thaliana LDLSNNQLSGPIPSEVGRLRKLNLLVLQGNHLDSSIPDSLSNLKSLNVLDLSSNLLTGRI
A. lyrata LDLSNNQLSGPIPSEIGRLRKLNLLVLQGNHLDSSIPESLSNLKSLNVLDLSSNLLTGRI
CcLRR-RLK1 IDLSNNVLSGPIPSEMGNLKYLNLLMLQGNQLSSSIPSSLSLLKLLNVLDLSNNLLTGNI
C. olitorius IDLSNNLLSGPIPSEMGNLKYLNLLMLQGNQLSSSIPSSLSLLKLLNVLDLSNNLLTGNI
P. trichocarpa IDLSSNLLYGPIPSEIGYLKKLNLLILQGNKLNSSIPKSLSLLRSLNVLDLSNNLLTGSI
R. communis IDVSNNLLSGPVPFQIGYLTKLNLLMLQGNMLNSSIPDSLSFLKSLNVLDLSNNLLTGNV
V. vinifera IDLSNNLLSGPIPSEIGNLNKLNLLLLQGNKFNSAIPKSLSSLKSVNVLDLSNNRLTGKI
S. bicolor IDLSNNLIAGPIPASVGLLSKLNQLSLQGNRLNGSIPETLAGLKTLNVLNLSDNALSGEI
O. sativa IDLSNNQIGGAIPEAVGRLSRLNQLSLQGNRLNGSIPATLADLHSLNVLNLSYNALAGEI

A. thaliana PENLSELLPTSINFSSNRLSGPIPVSLIRGGLVESFSDNPNLCIPPTAGSSDLKFPMCQE
A. lyrata PEDLSELLPTSINFSSNRLSGPIPVSLIRGGLVESFSDNPNLCVPPTAGSSDLKFPMCQE
CcLRR-RLK1 PESLSALLPNSINFSNNKLSGPIPLSLIKGGLVESFSGNPGLCVPVHVQN----FPICSH
C. olitorius PESLSALLPNSINFSNNKLSGPIPLSLIKGGLVESFSGNPGLCVPVHVQN----FPICSH
P. trichocarpa PESLSELLPNSINFSNNLLSGPIPLSLIKGGLVESFSGNPGLCVPVYVDSSDQSFPMCSH
R. communis PESLSVLLPNSIDFSNNRLSGPIPLPLIKGGLLESFSGNPGLCVPIYVVS-DQNFPVCSR
V. vinifera PESLSELLPNSINFTNNLLSGPIPLSLIQGGLAESFSGNPHLCVSVYVNSSDSNFPICSQ
S. bicolor PESLCKLLPNSLDFSNNNLSGPVPLQLIKEGLLESVAGNPGLCVAFRLNLTDPALPLCPR
O. sativa PEALCTLLPNSLDFSNNNLSGPVPLQLIREGLLESVAGNPGLCVAFRLNLTDPALPLCPK

A. thaliana PH---GKKKLSSIWAILVSVFILVLGVIMFYLRQRMSKNRAVIEQDE---TLASSFFSYD
A. lyrata PR---GKKKLSSIWAILVSVFILVLGGIMFYLRQRMSKNRAVIEQDE---TLASSFFSYD
CcLRR-RLK1 TY---NQKKLNSMWAIIISIIVITIG-ALLFLKRRFSKDRAIMEHDE---TLSSSFFSYD
C. olitorius TY---NQKKLNSMWAIIISIIVITIG-ALLFLKRRFSKDRAIMEHDE---TLSSSFFSYD
P. trichocarpa TY---NRKRLNSIWAIGISVAILTVG-ALLFLKRQFSKDRAVKQHDE---TTASSFFSYD
R. communis RY---NRKRLNSIWVIGISVVIFIVG-ALFFLKRKLSKD-KLTGRDE---TMSSSFFSYE
V. vinifera XD---NRKKLNCIWVIGASSVIVIVG-VVLFLKRWFSKQRAVMEHDE---NMSSSFFSYA
S. bicolor PS--LRRGLAGDVWVVGVCALVCAVA-MLALARRWVVRARRLAEQDGALATSPGSSASYD
O. sativa PARLRMRGLAGSVWVVAVCALVCVVA-TLALARRWVLRARQDGEHDG-LPTSPASSSSYD

(a)

95 Populus trichocarpa
82 Ricinus communis
100 Vitis vinifera
Dicot plants
CcLRR-RLK1
100 Corchorus olitorius
Arabidopsis thaliana
100 Arabidopsis lyrata
Sorghum bicolor
100 Oryza sativa Japonica Group Monocot plants

(b)

Figure 4. (a) Portion of the multiple sequence alignment (MSA) used for construction of the phylogenetic tree. Due to space limitations,
full alignment is not shown here; the MSA is labeled with species names. (b) Phylogenetic tree of CcLRR-RLK1 and other plant-specific
protein kinases (RLKs). GenBank accession numbers: Populus trichocarpa, XP_002301126; Ricinus communis, XP_002510008; Vitis
vinifera, CAN77413; Corchorus olitorius, ACI42311; Arabidopsis thaliana, NP_199777; Arabidopsis lyrata, XP_002865749; Sorghum
bicolor, XP_002442602; and Oryza sativa Japonica Group, NP_001067348.

15
 REZA et al. / Turk J Biol
N L F A S genes with different patterns of expression (37,38).
CcLRR-RLK1
β-actin
Figure 5. Semiquantitative RT-PCR of CcLRR-RLK1 (top)
and β-actin control (bottom) under different conditions. Jute
seedlings were exposed to various stresses as indicated here for
12 h. N, L, F, A, and S stand for normal, low-temperature, fungal,
ABA, and salt treatments, respectively.
similar counterpart in C. olitorius when compared with
results published by Alam et al. (19). However, this is not
an uncommon phenomenon. Previous studies of different
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16
species have shown the presence of structurally similar
The CcLRR-RLK1 gene is the first receptor-like
protein kinase gene of the C. capsularis species for which
the full-length sequence has been deduced. This study
demonstrates the involvement of the gene in a general
stress responsive pathway. Further studies are needed in
order to obtain greater insight into the signal transduction
pathway.
Acknowledgments
This research was supported by the United States
Department of Agriculture (USDA). We are thankful to the
Bangladesh Jute Research Institute (BJRI) for providing us
with the seeds of different jute species.
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