title: The Wall-associated Kinase gene family in rice genomes.
abstract: The environment is a dynamic system in which life forms adapt. Wall-Associated Kinases (WAK) are a subfamily of receptor-like kinases associated with the cell wall. These genes have been suggested as sensors of the extracellular environment and triggers of intracellular signals. They belong to the ePK superfamily with or without a conserved arginine before the catalytic subdomain VIB, which characterizes RD and non-RD WAKs. WAK is a large subfamily in rice. We performed an extensive comparison of WAK genes from A. thaliana (AtWAK), O. sativa japonica and indica subspecies (OsWAK). Phylogenetic studies and WAK domain characterization allowed for the identification of two distinct groups of WAK genes in Arabidopsis and rice. One group corresponds to a cluster containing only OsWAKs that most likely expanded after the monocot-dicot separation, which evolved into a non-RD kinase class. The other group comprises classical RD-kinases with both AtWAK and OsWAK representatives. Clusterization analysis using extracellular and kinase domains demonstrated putative functional redundancy for some genes, but also highlighted genes that could recognize similar extracellular stimuli and activate different cascades. The gene expression pattern of WAKs in response to cold suggests differences in the regulation of the OsWAK genes in the indica and japonica subspecies. Our results also confirm the hypothesis of functional diversification between A. thaliana and O. sativa WAK genes. Furthermore, we propose that plant WAKs constitute two evolutionarily related but independent subfamilies: WAK-RD and WAK-nonRD. Recognition of this structural division will further provide insights to understanding WAK functions and regulations.
authors.affiliation: Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Brazil; Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Brazil.
authors.forename: Luiz Felipe Valter
authors.initials: LFV
authors.lastname: de Oliveira
authors.affiliation: Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Brazil; Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Brazil.
authors.forename: Ana Paula
authors.initials: AP
authors.lastname: Christoff
authors.affiliation: Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Brazil; Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Brazil.
authors.forename: Júlio Cesar
authors.initials: JC
authors.lastname: de Lima
authors.affiliation: Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Brazil.
authors.forename: Bruno Comparsi Feijó
authors.initials: BCF
authors.lastname: de Ross
authors.affiliation: Departamento de Genética, Universidade Federal do Rio de Janeiro, Brazil.
authors.forename: Gilberto
authors.initials: G
authors.lastname: Sachetto-Martins
authors.affiliation: Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Brazil.
authors.forename: Marcia
authors.initials: M
authors.lastname: Margis-Pinheiro
authors.affiliation: Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul, Brazil; Centro de Biotecnologia e Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Brazil; Departamento de Biofísica, Universidade Federal do Rio Grande do Sul, Brazil. Electronic address: rogerio.margis@ufrgs.br.
authors.forename: Rogerio
authors.initials: R
authors.lastname: Margis
mesh_terms: D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001499:Bayes Theorem; D002473:Cell Wall / Q000201:enzymology* / Q000235:genetics*; D016000:Cluster Analysis; D003080:Cold Temperature; D020869:Gene Expression Profiling; D015971:Gene Expression Regulation, Enzymologic; D018506:Gene Expression Regulation, Plant; D020131:Genes, Duplicate; D017343:Genes, Plant; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D005810:Multigene Family; D012275:Oryza / Q000201:enzymology* / Q000235:genetics*; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011494:Protein Kinases / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D013312:Stress, Physiological
chemical_list: D010940:Plant Proteins; D011494:Protein Kinases
keywords: Oryza sativa; RLK; Rice; WAK; Wall-associated Kinase