Phylogenetic Analysis of Receptor-like Kinases from Rice

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1 Acta Botanica Sinica 2004, 46 (6): Phylogenetic Analysis of Receptor-like Kinases from Rice DONG Yi 1, ZHANG Jian-Guo 2, WANG Yong-Jun 1, ZHANG Jin-Song 1, CHEN Shou-Yi 1* (1. Plant Biotechnology Laboratory, Institute of Genetics and Developmental Biology, The Chinese Academy of Sciences, Beijing , China; 2. Beijing Genomics Institute, Beijing , 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 multisequences 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 eukaryotes (Hanks and Hunter, 1995). The histidine kinases were mainly involved in bacterial two-component signaling pathways. In several eukaryotic organisms, histidine kinase-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 transmembrane 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 activity (Ulrich and Schlessinger, 1990). The great variations in extracellular structure of different RLKs suggest that these proteins may be involved in a variety of cellular signaling processes, by responding to diverse extracellular signals and have different physiological functions. Several groups of plant RLKs are distinguished mainly based on their extracellular domains (Braun and Walker, 1996) and described as follows: (1) The S-domain 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 involved 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 morphogenesis (Torii et al., 1996), embryogenesis (Schmidt et al., 1997), meristematic growth (Clark et al., 1997), and pollen self-incompatibility (Muschietti et al., 1998). Some regulate 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 associated 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 Received 10 Apr Accepted 3 Dec * Author for correspondence. <sychen@genetics.ac.cn>.

2 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 between the two genomes can help us to understand the evolutionary relationships of RLK family in plants and to predict 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 extracellular configurations. The kinase domain amino acid sequences 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 Information (NCBI) to conduct BLASTP search in the rice genome database (up to September, 2002), with an E value cutoff of and found more than 750 related genes. After removal of redundant sequences and sequences encoding less than 200 amino acid residues, we got 267 genes for subsequent analysis. The structural domains were predicted according to SMART (Schultz et al., 2000) and Pfam (Sonnhammer et al., 1998) programs. These genes were categorized 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 penalty 10, gap extension penalty 0.20; delay divergent sequences 30% and protein weight matrix PAM series. In order 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 numbers 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 receptorlike kinases (RLKs) and the 17 representative proteins Structural class DUF (domain of unknown function) C-type lectin LRR Crinkly4-like CrRLK1 (catharanthus roseus RLK1) LRK10-like L-lectin (legume lectin) Extensin-like LysM (lysine motif) WAK-like S-RLK CK (cytoplasmic kinase) THN (thaumatin-like) MK (membrane kinase) Gene name or accession number At4g23200 At1g52310 CLV1 BRI1 At3g51990 At3g46290 At1g25390 At5g38260 At3g59740 At5g56890 At3g24550 At3g21630 At1g16140 At4g27300 At2g42960 At5g38280 At1g11050

3 DONG Yi et al.: Phylogenetic Analysis of Receptor-like Kinases from Rice 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 ( evolution.genetics.washington.edu/phylip.html)). Pairwise distances were determined with PROTDIST. Neighbor-joining phylogenetic trees (Saitou and Nei, 1987) were calculated 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 categorized into five groups according to their extracellular receptor structures (Fig.1). Ninety-seven RLKs have transmembrane domains but their extracellular structure domains 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. 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 Neighborjoining 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 evolutionary relationships. The phylogenetic analysis of S-domain 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, although the RLK gene sequences are conserved during eukaryotic protein kinase evolution, the S-domain RLKs in rice and Arabidopsis may undergo divergent evolution processes and may have differentiations in substrate recognition 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 additional AtWAK RLKs) but not the eight OsRLKs that exhibited 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 transduction 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 was thought to be required for catalytic activity and

4 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. 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

5 DONG Yi et al.: Phylogenetic Analysis of Receptor-like Kinases from Rice 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. alignment of 24 OsRLKs kinase domain sequences representing 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 corresponding to Asp-1027, the Asp residues corresponding to Asp were also absent. The alignment of all the 267 RLKs with BRI1 kinase doma 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 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, respectively. This divergence in the putative autophosphorylation residues may imply that the autophosphorylation sites and signal transduction mechanisms 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 prediction of putative autophosporylation sites. Further work should be carried out to identify the specific

6 Fig.4. Multiple sequences alignment of BRI1 and 24 representatives of six groups. The invariant Asp residues (corresponding to Asp and Asp-1027 in BRI1) are in boxes. Arrows indicate residues corresponding to the autophosphorylated residues in BRI1 (Thr- 1039, Ser-1042, Ser-1044, Thr-1049) and the Thr or Ser residues are in shaded area. indicates positions which have a single, fully conserved residue; indicates positions which belong to a strong conserved group; indicates positions which belong to a weaker conserved group; dashes, gaps. autophosphorylation sites both in vitro and in vivo. Plant receptor-like kinases are involved in many physiological 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 homologous 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 evolutionary 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 biochemical and molecular methods. References: Becraft P W, Stinard P S, McCarty D R CRINKLY4: a TNFR-like receptor kinase involved in maize epidermal differentiation. Science, 273: Braun D M, Walker J C Plant transmembrane receptors: new pieces in the signaling puzzle. Trends Biochem Sci, 21: Clark S E, Williams R W, Meyerowitz E M The CLAVATA1 gene encodes a putative receptor kinase that controls shoot and floral meristem size in Arabidopsis. Cell, 89: Deeken R, Kaldenhoff R Light-repressible receptor protein kinase: a novel photo-regulated gene from Arabidopsis thaliana. Planta, 202: Hanks S K, Hunter T Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J, 9: He Z H, He D, Kohorn B D Requirement for the induced

7 DONG Yi et al.: Phylogenetic Analysis of Receptor-like Kinases from Rice expression of a cell wall associated receptor kinase for survival during the pathogen response. Plant J, 14: Herve C, Dabos P, Galaud J P, Rouge P, Lescure B Characterization of an Arabidopsis thaliana gene that defines a new class of putative plant receptor kinases with an extracellular lectin-like domain. J Mol Biol, 258: Higgins D G, Thompson J D, Gibson T J Using CLUSTAL for multiple sequence alignments. Methods Enzymol, 266: Hong S W, Jon J H, Kwak J M, Nam H G Identification of a receptor-like protein kinase gene rapidly induced by abscisic acid, dehydration, high salt, and cold treatments in Arabidopsis thaliana. Plant Physiol, 113: Hunter T Protein kinases and phosphatases: the yin and yang of protein phosphorylation and signaling. Cell, 80: Jinn T L, Stone J M, Walker J C HAESA, an Arabidopsis leucine-rich repeat receptor kinase, controls floral organ abscission. Genes Dev, 14: Lally D, Ingmire P, Tong H Y, He Z H Antisense expression of a cell wall-associated protein kinase, WAK4, inhibits cell elongation and alters morphology. Plant Cell, 13: Li J, Chory J A putative leucine-rich repeat receptor kinase involved in brassinosteroid signal transduction. Cell, 90: Loomis W F, Shaulsky G, Wang N Histidine kinases in signal transduction pathways of eukaryotes. J Cell Sci, 110: Muschietti J, Eyal Y, McCormick S Pollen tube localization implies a role in pollen-pistil interactions for the tomato receptor-like protein kinases LePRK1 and LePRK2. Plant Cell, 10: Nasrallah J B, Kao T H, Goldberg M L, Nasrallah M E A cdna clone encoding an S-locus specific glycoprotein from Brassica oleracea. Nature, 318: Oh M H, Ray W K, Huber S C, Asara J M, Gage D A, Clouse S D Clouse Recombinant brassinosteroid insensitive 1 receptor-like kinase autophosphorylates on Serine and Threonine residues and phosphorylates a conserved peptide motif in vitro. Plant Physiol, 124: Pastuglia M, Roby D, Dumas C, Cock J M Rapid induction by wounding and bacterial infection of an S gene family receptor-like kinase gene in Brassica oleracea. Plant Cell, 9: Saitou N, Nei M The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol, 4: Schmidt E D, Guzzo F, Toonen M A, de Vries S C A leucine-rich repeat containing receptor-like kinase marks somatic plant cells competent to form embryos. Development, 124: Schultz J, Copley R R, Doerks T, Ponting C P, Bork P SMART: a web-based tool for the study of genetically mobile domains. Nucleic Acids Res, 28: Schulze-Muth P, Irmler S, Schröder G, Schröder J Novel type of receptor-like protein kinase from a higher plant (Catharanthus roseus). J Biol Chem, 271: Shiu S H, Bleecker A B Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases. Proc Natl Acad Sci USA, 98: Song W Y, Wang G L, Chen L L, Kim H S, Pi L Y, Holsten T, Gardner J, Wang B, Zhai W X, Zhu L H A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science, 270: Sonnhammer E L, Eddy S R, Birney E, Bateman A, Durbin R Pfam: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res, 26: Torii K U, Mitsukawa N, Oosumi T, Matsuura Y, Yokoyama R, Whittier RF, Komeda Y The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats. Plant Cell, 8: Ulrich A, Schlessinger J Signal transduction by receptors with tyrosine kinase activity. Cell, 61: van der Knaap E, Sauter M, Wilford R, Kende H Identification of a gibberellin-induced receptor-like kinase in deepwater rice (accession no. Y07748) (PGR ). Plant Physiol, 112: Wagner T, Kohorn B Wall-associated kinases are expressed throughout plant development and are required for cell expansion. Plant Cell, 13: Walker J C Structure and function of the receptor-like protein kinases of higher plants. Plant Mol Biol, 26: Xie C, Zhang J S, Zhou H L, Li J, Zhang Z G, Wang D W, Chen S Y Serine/threonine kinase activity in the putative histidine kinase-like ethylene receptor NTHK1 from tobacco. Plant J, 33: Yu J, Hu S N, Wang J, Wong K S, Li S G, Liu B, Deng Y J, Dai L, Zhou Y, Zhang X Q, Cao M L, Liu J, Sun J D, Tang J B, Chen Y J, Huang X B, Lin W, Ye C, Tong W, Cong L J, Geng J N, Han Y J, Li L, Li W, Hu G Q, Huang X G, Li W J, Li J, Liu Z W, Li L, Liu J P, Qi Q H, Liu J S, Li L, Li T, Wang X G, Lu H, Wu T T, Zhu M, Ni P X, Han H, Dong W, Ren X Y, Feng X L, Cui P, Li X R, Wang H, Xu X, Zhai W X, Xu Z, Zhang J S, He S J, Zhang J G, Xu J C, Zhang K L, Zheng X W, Dong J H, Zeng W Y, Tao L, Ye J, Tan J, Ren X D, Chen X W, He J, Liu

8 D F, Tian W, Tian C G, Xia H A, Bao Q J, Li G, Gao H, Cao T, Wang J, Zhao W M, Li P, Chen W, Wang X D, Zhang Y, Hu J F, Wang J, Liu S, Yang J, Zhang G Y, Xiong Y Q, Li Z J, Mao L, Zhou C S, Zhu Z, Chen R S, Hao B L, Zheng W M, Chen S Y, Guo W, Li G J, Liu S Q, Tao M, Wang J, Zhu L H, Yuan L P, Yang H M A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science, 296: Zhang Z-G, Gong Y, He X-J, Wang Y-J, Sun Z-X, Zhang J-S ( ), Chen S-Y Cloning of the full-length gene for tobacco ethylene receptor NTHK2 and characterization of its kinase domain. Acta Bot Sin, 45: (Managing editor: ZHAO Li-Hui)

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