全 文 ：Received 10 Apr. 2003 Accepted 3 Dec. 2003
* Author for correspondence. E-mail：.
http://www.chineseplantscience.com
Acta Botanica Sinica
植 物 学 报 2004, 46 (6): 647-654
Phylogenetic Analysis of Receptor-like Kinases from Rice
DONG Yi1, ZHANG Jian-Guo2, WANG Yong-Jun1, ZHANG Jin-Song1, CHEN Shou-Yi1*
(1. Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, The Chinese Academy
of Sciences, Beijing 100101, China;
2. Beijing Genomics Institute, Beijing 101300, China)
Abstract: Plant receptor-like kinases (RLKs) have been shown to be critical components in plant cellular
processes. To provide a valid basis to evaluate the evolutionary relationships among RLKs from Arabidopsis
and rice, a genome-wide search for RLKs-related sequences was conducted. By doing BLASTP through the
database of rice (Oryza sativa L. subsp. indica) genome at Beijing Genomics Institute (BGI), we identified
267 putative RLK genes. All RLKs were classified into different structural groups based on their extracellular
structures. The phylogenetic analysis of RLKs in rice and Arabidopsis showed that the different groups of
RLKs had different characteristics of sequence conservation and of evolutionary relationship. The multi-
sequences alignment of rice RLKs and Arabidopsis Brassinosteroid-insensitive 1 (BRI1) suggested that the
putative autophosphorylation sites of rice RLKs were dissimilar to those in BRI1.
Key words: plant receptor-like kinases (RLKs); phylogenetic; autophosphorylation site; rice
Protein kinases are essential for the regulation of growth
and development in both prokaryotes and eukaryotes. The
protein kinases can be grouped into three distinct classes:
the serine/threonine protein kinases, the tyrosine protein
kinases, and the histidine kinases. The serine/threonine
protein kinases were predominantly found among eukary-
otes (Hanks and Hunter, 1995). The histidine kinases were
mainly involved in bacterial two-component signaling
pathways. In several eukaryotic organisms, histidine ki-
nase-like proteins were also identified and some exhibited
serine/threonine kinase activities (Loomis et al., 1997; Xie
et al., 2003; Zhang et al., 2003). Plant receptor-like kinases
(RLKs) form a protein kinase family, which is structurally
similar to the receptor tyrosine kinases (RTKs) in animals.
They both have an extracellular receptor domain, a trans-
membrane domain and a cytoplasmic kinase domain (Walker,
1994). In addition, within the superfamily of the eukaryotic
serine/threonine/tyrosine protein kinases, there is a close
relationship between members belonging to RLKs and RTKs
(Hanks and Hunter, 1995). The structural similarity of plant
RLKs with animal RTKs suggested a similar biological
mechanism for RLKs action. Nevertheless, there is a major
difference between the two families in that all plant RLKs
identified presently only have serine/threonine kinase ac-
tivity (Ulrich and Schlessinger, 1990).
The great variations in extracellular structure of differ-
ent RLKs suggest that these proteins may be involved in a
variety of cellular signaling processes, by responding to
diverse extracellular signals and have different physiologi-
cal functions. Several groups of plant RLKs are distin-
guished mainly based on their extracellular domains (Braun
and Walker, 1996) and described as follows: (1) The S-do-
main containing type, S-RLKs, with similarities to the S-
locus glycoprotein in Brassica. These proteins have ten or
more conserved cysteine residues and appear to be in-
volved in the self-incompatibility recognition system
(Nasrallah et al., 1985). The recent work also revealed that
a S-domain-containing receptor-like kinase was involved
in plant defense reaction (Pastuglia et al., 1997). (2) The
leucine-rich repeat (LRR) type, contains a tandemly repeated
(9-26) Leu-rich motif. It is the largest subfamily in RLKs
and involved in various cellular processes, including mor-
phogenesis (Torii et al., 1996), embryogenesis (Schmidt et
al., 1997), meristematic growth (Clark et al., 1997), and pol-
len self-incompatibility (Muschietti et al., 1998). Some regu-
late responses to environmental signals such as light
(Deeken and Kaldenhoff, 1997), hormones (van der Knaap
et al., 1996; Hong et al., 1997; Li and Chory, 1997), and
pathogens (Song et al., 1995). (3) The WAK (wall associ-
ated kinase)-like type, contains several epidermal growth
factor (EGF)-like repeats. This type of RLKs is involved in
the response to pathogens (He et al., 1998) and is required
for cell expansion (Lally et al., 2001; Wagner and Kohorn,
2001). (4) The tumor necrosis factor receptor (TNFR)-like
type mediates cellular differentiation responses (Becraft et
al., 1996). (5) The lectin-like type possesses an extracellular
Acta Botanica Sinica 植物学报 Vol.46 No.6 2004648
domain homologous to carbohydrate-binding protein of
the legume family (Herve et al., 1996) and may be involved
in perception of oligosaccharide-mediated signal
transduction.
In Arabidopsis, several RLKs and their functions have
been identified, such as Brassinosteroid-insensitive 1 (BRI1)
(Li and Chory, 1997), CLAVATA1 (Clark et al., 1997) and
HAESA (Jinn et al., 2000). The completion of Arabidopsis
genome sequence enables researchers to analyze RLKs in
more comprehensive ways. It is reported that there are at
least 610 RLK members, which represent nearly 2.5% of
Arabidopsis protein coding genes (Shiu and Bleecker, 2001).
As the sequencing of rice genome project at Beijing
Genomics Institute (BGI) was getting nearly completed (Yu
et al., 2002), the comparison of RLK-related sequences be-
tween the two genomes can help us to understand the evo-
lutionary relationships of RLK family in plants and to pre-
dict the functions and possible activation mechanisms of
rice RLKs.
In this report, we conducted a genome-wide search in
BGI databank and identified 267 putative RLK genes. These
genes were classified into several groups by their extracel-
lular configurations. The kinase domain amino acid se-
quences of every group were aligned respectively (all the
alignments were done using amino acid sequences), and
the alignments were used to generate phylogenetic trees
with the Neighbor-joining method. The conserved motifs
or residues in the kinase domains of some rice RLKs were
also compared with those from BRI1, which is a RLK and
involved in brassinolide signal transduction.
1 Materials and Methods
We used one rice receptor-like kinase sequence
(AF248493) from National Center for Biotechnology Infor-
mation (NCBI) to conduct BLASTP search in the rice ge-
nome database (up to September, 2002), with an E value
cutoff of 1×10-10 and found more than 750 related genes.
After removal of redundant sequences and sequences en-
coding less than 200 amino acid residues, we got 267 genes
for subsequent analysis. The structural domains were pre-
dicted according to SMART (Schultz et al., 2000) and Pfam
(Sonnhammer et al., 1998) programs. These genes were cat-
egorized into different classes based on their extracellular
domain structures.
The alignment of kinase domain sequences from all the
267 RLKs was carried out using CLUSTALX version 1.81
(Higgins et al., 1996) (data not shown). Pairwise alignment
parameters were set as follows: slow/accurate alignment;
gap opening penalty 10; gap extension penalty 0.20;
protein weight matrix PAM250 (Point Accepted Mutation).
Multiple alignment was performed with gap opening pen-
alty 10, gap extension penalty 0.20; delay divergent se-
quences 30% and protein weight matrix PAM series. In or-
der to investigate the phylogenetic relationship of RLKs
from rice and Arabidopsis genomes, we used 17 Arabidopsis
RLKs kinase domain as the representatives of all different
structural classes of Arabidopsis RLKs, to align with the
267 rice RLKs. These gene names and their accession num-
bers are as follows: At4g23200 (CAB79275), At1g52310
(AAG21563), CLV1 (AAD02501), At3g51990 (T49078),
At3g46290 (CAB90956), BRI1 (AAC49810), At1g25390
(AAG12740), At3g59740 (CAB75793), At5g56890
(BAB10581), At3g24550 (BAB02007), At3g21630
(BAB00013), At5g38260 (BAB11292), At1g16140
(AAF18509), At4g27300 (CAA19724), At2g42960
(AAD21713), At5g38280 (BAB11294) and At1g11050
(AAB65477). The kinase domain sequences from each
group of rice RLKs were aligned with the 17 sequences
respectively. The structural classes of these 17 Arabidopsis
RLKs genes represented are shown in Table 1.
The results of the S-domain group and the WAK-like
group were realigned respectively with additional 18 RLK
genes from rice and Arabidopsis. Their names or accession
numbers are as follows: eight representatives of rice S-
domam RLKs (OsSRLKs), AAO38825, T04124, RLK10
(AAM90697), RLK11 (AAM90696), RLK13 (AAM90695),
RLK14 (AAM90694), TMK (CAA69028), Xa21 (A57676);
six representatives of Arabidopsis WAK-like RLKs (AtWAK
Table 1 The structural classes of Arabidopsis plant receptor-
like kinases (RLKs) and the 17 representative proteins
Structural class
Gene name or
accession number
DUF (domain of unknown function) At4g23200
C-type lectin At1g52310
LRR CLV1
BRI1
Crinkly4-like At3g51990
CrRLK1 (catharanthus roseus RLK1) At3g46290
LRK10-like At1g25390
At5g38260
L-lectin (legume lectin) At3g59740
Extensin-like At5g56890
At3g24550
LysM (lysine motif) At3g21630
WAK-like At1g16140
S-RLK At4g27300
CK (cytoplasmic kinase) At2g42960
THN (thaumatin-like) At5g38280
MK (membrane kinase) At1g11050
DONG Yi et al.: Phylogenetic Analysis of Receptor-like Kinases from Rice 649
RLKs), At1g16110 (AAF18506), At1g16130 (AAF18508),
At1g16160 (AAF18511), WAK1 (AAF81356), WAK2
(CAB42872), WAK4 (AAF81361) and four representatives
of Arabidopsis S-domain RLKs (AtSRLKs), RKS1
(AAC95352), RKS2 (AAC95353), ARK1 (AAF23832) and
ARK3 (CAA20203).
The phylogenetic trees were inferred from the multiple
sequence alignment with PHYLIP 3.6 (PHYLIP (http://
evolution.genetics.washington.edu/phylip.html)). Pairwise
distances were determined with PROTDIST. Neighbor-join-
ing phylogenetic trees (Saitou and Nei, 1987) were calcu-
lated with NEIGHBOR program using standard parameters.
The kinase domain sequence alignments of BRI1 and 24
representative proteins from different rice RLK groups were
carried out with CLUSTALX using the same parameters as
above.
2 Results and Discussion
By using BLASTP to search throughout the BGI rice
genome database, 267 non-redundant RLK gene candidates
were identified. Of these 267 RLK proteins, 54 members
showed no transmembrane domains and were classified as
cytoplasmic kinase (CK) group (Fig.1). The rest can be cat-
egorized into five groups according to their extracellular
receptor structures (Fig.1). Ninety-seven RLKs have trans-
membrane domains but their extracellular structure domains
did not show homology to the known motifs. This group
was named as membrane kinase (MK) group. The LRR-like
group contains 24 members. The WAK-like group, which
has EGF-like repeat domain, contains 14 members. The S-
RLK group contains 74 members. At last, there are four
RLKs having TNFR-like domain and they are classified as
CR4-like group.
To study the evolutionary relationships of various RLK
gene groups between Arabidopsis and rice, the Neighbor-
joining phylogenetic trees of each group were constructed
and they showed different patterns. The CK, MK, CR4-like
and LRR-like groups had no clear pattern for their evolu-
tionary relationships. The phylogenetic analysis of S-do-
main group showed that all kinase domain sequences of 74
rice members separated from the Arabidopsis members and
formed a single clade. To verify this result, additional four
AtSRLKs from NCBI were pooled to do the re-alignment. In
this phylogenetic tree, the OsSRLK still formed a single
clade and the additional four AtSRLKs did not fall into the
same clade with the OsSRLK (Fig.2). It suggested that, al-
though the RLK gene sequences are conserved during eu-
karyotic protein kinase evolution, the S-domain RLKs in
rice and Arabidopsis may undergo divergent evolution pro-
cesses and may have differentiations in substrate recogni-
tion and functional mechanisms.
The WAK-like group showed a different pattern from
the S-domain group. Almost all OsWAK RLKs (12 out of
14) and the AtWAK RLKs (At1g16140) fell into a single
clade separated from other Arabidopsis RLKs (data not
shown). Moreover, when additional eight OsRLKs (not
WAK-like RLKs) and six AtWAK RLKs were re-aligned, it
was the seven AtWAK RLKs (At1g16140 plus six addi-
tional AtWAK RLKs) but not the eight OsRLKs that exhib-
ited a closer relationship with the OsWAK RLKs (Fig.3). It
suggested that, in contrast with other OsRLKs, OsWAK
RLKs had a closer evolutionary relationship with AtWAK
RLKs. We hypothesized that WAK-like RLKs were under
more restrict evolution forces and exhibited a high degree
of conservativity. Therefore, the WAK-like group RLKs
perhaps play the same roles in rice and Arabidopsis. At the
very least, OsWAK RLKs and AtWAK RLKs may also have
similar phosphorylation substrates and their signal trans-
duction mechanisms may be similar.
In previous studies, only a few phosphorylation sites in
RLK have been identified. In CRLK1 from Catharanthus
roseus, Thr-720 is responsible for its autophosphorylation
(Schulze-Muth et al., 1996). The BRI1 kinase domain has
two invariant Asp residues (Asp-1009 and Asp-1027), Asp-
1009 was thought to be required for catalytic activity and
Fig.1. The schematic diagram of receptor-like kinase (RLK)
structural groups. CK, cytoplasmic kinases; EGF, epidermal
growth factor; LRR, leucine rich repeat; MK, membrane kinases;
TM, transmembrane; TNFR, tumor necrosis factor receptor;
WAK, wall associate kinases.
Acta Botanica Sinica 植物学报 Vol.46 No.6 2004650
Asp-1027 indicated the beginning of the activation loop
(from Asp-1027 to Glu-1056 in BRI1). In this activation loop,
BRI1 autophosphorylates at least two residues and there
were four conserved Ser/Thr residues (Thr-1039, Ser-1042,
Ser-1044, and Thr-1049) in BRI1 that also occurred in other
49 related plant kinases (Oh et al., 2000). We aligned all the
267 genes kinase domain sequences with the BRI1 kinase
domain sequences. Due to space limitation, only the
Fig.2. The OsSRLKs form a single clade distinct from that of the AtSRLKs. Arrows indicate the Arabidopsis S-domain RLKs. The
phylogenetic tree was generated with the kinase domain sequences by using Neighbor-joining methods.
DONG Yi et al.: Phylogenetic Analysis of Receptor-like Kinases from Rice 651
alignment of 24 OsRLKs kinase domain sequences repre-
senting six structural groups was shown in Fig.4. In the
position corresponding to the Asp-1009, the frequency of
Asp residue appearance was 96% (257 out of 267 genes),
with deletions in 5 RLKs and residue substitution in the
other five RLKs. As to the position corresponding to Asp-
1027, there were 98% Asp residues (261 out of 267 genes),
with deletions in three RLKs and residue substitution in
the other three RLKs. It was interesting to note that in the
three RLKs, which did not have Asp residues correspond-
ing to Asp-1027, the Asp residues corresponding to Asp-
1009 were also absent.
The alignment of all the 267 RLKs with BRI1 kinase do-
m a i n s e q u e n c e s s h o we d t h a t t h e p u t a t i v e
autophosphorylation residues in OsRLKs were different
from those in BRI1. At the position corresponding to Thr-
1049 and Ser-1044 of BRI1, 96% (256/267) and 90% (240/
267) rice RLKs had Thr and Ser residues, respectively.
Whereas at the positions corresponding to Thr-1039 and
Ser-1042, there were only 48% and 27% rice RLKs (127/267,
72/267, respectively) that had Thr and Ser residues,
respect ive ly. This divergence in the putat ive
autophosphorylation residues may imply that the
autophosphorylation sites and signal transduction mecha-
nisms of different groups of OsRLKs were different.
However, due to the abundance of Thr or Ser residues in
this area and the evolutionary difference between rice and
Arabidopsis, there were still some ambiguities in the pre-
diction of putative autophosporylation sites. Further work
should be carr ied out to identify the specific
Fig.3. The OsWAK RLKs and the AtWAK RLKs (shaded area) kinase domain sequences fell into the same clade distinct from the other
OsRLKs and AtRLK kinase domain sequences. Arrows indicate the two exceptional OsWAK RLKs.
Acta Botanica Sinica 植物学报 Vol.46 No.6 2004652
autophosphorylation sites both in vitro and in vivo.
Plant receptor-like kinases are involved in many physi-
ological processes including growth and development,
embryogenesis, fertilization, abscission, disease resistance,
and response to light. As a result of the functional diversity,
the ligands, the structures of extracellular domain and the
activation mechanisms of cytoplasmic kinases are diverse.
The phylogenetic analysis of a gene family is a very useful
method in tracing the evolutionary relationships of homolo-
gous genes because it not only gives information about
gene’s evolutionary history, but also provides a rational
basis for genes structure-function relationships. Based on
the comparison of RLK kinase domain sequences in
Arabidopsis and O. sativa, we sought to reveal the evolu-
tionary relationships between RLKs of the two species.
The difference in the conservation of WAK-like RLKs and
S-domain RLKs suggested that the two RLK groups had
taken different processes during their evolution. Moreover,
the kinase domain sequence alignments of BRI1 and rice
RLKs can facilitate the future identification of putative
autophosphorylation sites in rice RLKs by using biochemi-
cal and molecular methods.
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