Genome-wide cloning and sequence analysis of leucine-rich repeat receptor-like protein kinase genes in Arabidopsis thaliana

BackgroundTransmembrane receptor kinases play critical roles in both animal and plant signaling pathways regulating growth, development, differentiation, cell death, and pathogenic defense responses. In Arabidopsis thaliana, there are at least 223 Leucine-rich repeat receptor-like kinases (LRR-RLKs), representing one of the largest protein families. Although functional roles for a handful of LRR-RLKs have been revealed, the functions of the majority of members in this protein family have not been elucidated.ResultsAs a resource for the in-depth analysis of this important protein family, the complementary DNA sequences (cDNAs) of 194 LRR-RLKs were cloned into the GatewayR donor vector pDONR/ZeoR and analyzed by DNA sequencing. Among them, 157 clones showed sequences identical to the predictions in the Arabidopsis sequence resource, TAIR8. The other 37 cDNAs showed gene structures distinct from the predictions of TAIR8, which was mainly caused by alternative splicing of pre-mRNA. Most of the genes have been further cloned into GatewayR destination vectors with GFP or FLAG epitope tags and have been transformed into Arabidopsis for in planta functional analysis. All clones from this study have been submitted to the Arabidopsis Biological Resource Center (ABRC) at Ohio State University for full accessibility by the Arabidopsis research community.ConclusionsMost of the Arabidopsis LRR-RLK genes have been isolated and the sequence analysis showed a number of alternatively spliced variants. The generated resources, including cDNA entry clones, expression constructs and transgenic plants, will facilitate further functional analysis of the members of this important gene family.

[1]  Noriaki Tanabe,et al.  Differential expression of alternatively spliced mRNAs of Arabidopsis SR protein homologs, atSR30 and atSR45a, in response to environmental stress. , 2007, Plant & cell physiology.

[2]  S. Clough,et al.  Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. , 1998, The Plant journal : for cell and molecular biology.

[3]  C. Pikaard,et al.  Gateway-compatible vectors for plant functional genomics and proteomics. , 2006, The Plant journal : for cell and molecular biology.

[4]  John C. Walker,et al.  Relationship of a putative receptor protein kinase from maize to the S-locus glycoproteins of Brassica , 1990, Nature.

[5]  A Keith Dunker,et al.  Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[6]  F. Tax,et al.  Functional analysis of receptor-like kinases in monocots and dicots. , 2006, Current opinion in plant biology.

[7]  J. Cock,et al.  Receptor kinase signalling in plants and animals: distinct molecular systems with mechanistic similarities. , 2002, Current opinion in cell biology.

[8]  H. Fukuoka,et al.  GASSHO1 and GASSHO2 encoding a putative leucine-rich repeat transmembrane-type receptor kinase are essential for the normal development of the epidermal surface in Arabidopsis embryos. , 2007, The Plant journal : for cell and molecular biology.

[9]  A. Wood,et al.  Plant receptor-like serine threonine kinases: roles in signaling and plant defense. , 2008, Molecular plant-microbe interactions : MPMI.

[10]  B. Haas,et al.  Full-length messenger RNA sequences greatly improve genome annotation , 2002, Genome Biology.

[11]  P. Becraft.  First published online as a Review in Advance on June 26, 2002 RECEPTOR KINASE SIGNALING IN PLANT DEVELOPMENT , 2022 .

[12]  S. Shiu,et al.  Receptor-like kinases from Arabidopsis form a monophyletic gene family related to animal receptor kinases , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[13]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[14]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[15]  T. Boller,et al.  FLS2: an LRR receptor-like kinase involved in the perception of the bacterial elicitor flagellin in Arabidopsis. , 2000, Molecular cell.

[16]  M. Garcia-Blanco,et al.  Protein–protein interactions and 5'-splice-site recognition in mammalian mRNA precursors , 1994, Nature.

[17]  J. Manley,et al.  SR proteins and splicing control. , 1996, Genes & development.

[18]  A. Reddy,et al.  An SC35-like Protein and a Novel Serine/Arginine-rich Protein Interact with Arabidopsis U1-70K Protein* , 1999, The Journal of Biological Chemistry.

[19]  K. Torii.  Leucine-rich repeat receptor kinases in plants: structure, function, and signal transduction pathways. , 2004, International review of cytology.

[20]  A. Reddy,et al.  Alternative splicing of pre-mRNAs of Arabidopsis serine/arginine-rich proteins: regulation by hormones and stresses. , 2007, The Plant journal : for cell and molecular biology.

[21]  Xiaofeng Wang,et al.  Sequential transphosphorylation of the BRI1/BAK1 receptor kinase complex impacts early events in brassinosteroid signaling. , 2008, Developmental cell.

[22]  Nicole K Clay,et al.  VH1, a Provascular Cell–Specific Receptor Kinase That Influences Leaf Cell Patterns in Arabidopsis , 2002, The Plant Cell Online.

[23]  K. Shinozaki,et al.  Leucine-Rich Repeat Receptor-Like Kinase1 Is a Key Membrane-Bound Regulator of Abscisic Acid Early Signaling in Arabidopsisw⃞ , 2005, The Plant Cell Online.

[24]  H. Hirt,et al.  The BRI1-Associated Kinase 1, BAK1, Has a Brassinolide-Independent Role in Plant Cell-Death Control , 2007, Current Biology.

[25]  R. Dixon,et al.  Activation tagging in Arabidopsis. , 2000, Plant physiology.

[26]  Alexandra M. E. Jones,et al.  The receptor-like kinase SERK3/BAK1 is a central regulator of innate immunity in plants , 2007, Proceedings of the National Academy of Sciences.

[27]  Jia Li,et al.  BAK1, an Arabidopsis LRR Receptor-like Protein Kinase, Interacts with BRI1 and Modulates Brassinosteroid Signaling , 2002, Cell.

[28]  John C. Walker,et al.  HAESA, an Arabidopsis leucine-rich repeat receptor kinase, controls floral organ abscission. , 2000, Genes & development.

[29]  V. Brendel,et al.  Genomewide comparative analysis of alternative splicing in plants. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[30]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[31]  D. Becker,et al.  Binary vectors which allow the exchange of plant selectable markers and reporter genes , 1990, Nucleic Acids Res..

[32]  She Chen,et al.  Regulation of cell death and innate immunity by two receptor-like kinases in Arabidopsis. , 2009, Cell host & microbe.

[33]  R. Mache,et al.  COP1b, an isoform of COP1 generated by alternative splicing, has a negative effect on COP1 function in regulating light-dependent seedling development in Arabidopsis , 1998, Molecular and General Genetics MGG.

[34]  K. Feldmann,et al.  Brassinosteroid-insensitive dwarf mutants of Arabidopsis accumulate brassinosteroids. , 1999, Plant physiology.

[35]  S. D. de Vries,et al.  Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASE Proteins Serve Brassinosteroid-Dependent and -Independent Signaling Pathways1[C][W] , 2008, Plant Physiology.

[36]  F. Skoog,et al.  A revised medium for rapid growth and bio assays with tobacco tissue cultures , 1962 .

[37]  Robert W. Williams,et al.  The CLAVATA1 Gene Encodes a Putative Receptor Kinase That Controls Shoot and Floral Meristem Size in Arabidopsis , 1997, Cell.

[38]  K. Akiyama,et al.  Functional Annotation of a Full-Length Arabidopsis cDNA Collection , 2002, Science.

[39]  A. Diévart,et al.  LRR-containing receptors regulating plant development and defense , 2003, Development.

[40]  S. Turner,et al.  PXY, a Receptor-like Kinase Essential for Maintaining Polarity during Plant Vascular-Tissue Development , 2007, Current Biology.

[41]  A. Reddy,et al.  Structure and expression of a plant U1 snRNP 70K gene: alternative splicing of U1 snRNP 70K pre-mRNAs produces two different transcripts. , 1996, The Plant cell.

[42]  A Keith Dunker,et al.  Intrinsic disorder in scaffold proteins: getting more from less. , 2008, Progress in biophysics and molecular biology.

[43]  Jonathan D. G. Jones,et al.  A flagellin-induced complex of the receptor FLS2 and BAK1 initiates plant defence , 2007, Nature.

[44]  Masakazu Satou,et al.  Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. , 2004, Nucleic acids research.

[45]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[46]  Tom Maniatis,et al.  Specific interactions between proteins implicated in splice site selection and regulated alternative splicing , 1993, Cell.

[47]  J. Casacuberta,et al.  Regulation of the kinase activity of the MIK GCK-like MAP4K by alternative splicing , 2006, Plant Molecular Biology.

[48]  J. Chory,et al.  A Putative Leucine-Rich Repeat Receptor Kinase Involved in Brassinosteroid Signal Transduction , 1997, Cell.

[49]  Jianming Li,et al.  BRI1/BAK1, a Receptor Kinase Pair Mediating Brassinosteroid Signaling , 2002, Cell.

[50]  Tadao Asami,et al.  Identification and Functional Analysis of in Vivo Phosphorylation Sites of the Arabidopsis BRASSINOSTEROID-INSENSITIVE1 Receptor Kinase , 2005, The Plant Cell Online.

[51]  B. Mangin,et al.  ERECTA, an LRR receptor-like kinase protein controlling development pleiotropically affects resistance to bacterial wilt. , 2003, The Plant journal : for cell and molecular biology.

[52]  Hong Ma,et al.  The excess microsporocytes1 gene encodes a putative leucine-rich repeat receptor protein kinase that controls somatic and reproductive cell fates in the Arabidopsis anther. , 2002, Genes & development.

[53]  John C. Walker,et al.  Receptor-like protein kinases: the keys to response. , 2003, Current opinion in plant biology.

[54]  N. Mitsukawa,et al.  The Arabidopsis ERECTA gene encodes a putative receptor protein kinase with extracellular leucine-rich repeats. , 1996, The Plant cell.

[55]  S. D. de Vries,et al.  The Arabidopsis thaliana SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASES1 and 2 Control Male Sporogenesis , 2005, The Plant Cell Online.

[56]  Michael D. Nodine,et al.  RPK1 and TOAD2 are two receptor-like kinases redundantly required for arabidopsis embryonic pattern formation. , 2007, Developmental cell.

[57]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[58]  A. Reddy,et al.  The Plant U1 Small Nuclear Ribonucleoprotein Particle 70K Protein Interacts with Two Novel Serine/Arginine–Rich Proteins , 1998, Plant Cell.

[59]  Christopher J. Oldfield,et al.  The unfoldomics decade: an update on intrinsically disordered proteins , 2008, BMC Genomics.

[60]  R. Roca,et al.  The Direct Activation of MIK, a Germinal Center Kinase (GCK)-like Kinase, by MARK, a Maize Atypical Receptor Kinase, Suggests a New Mechanism for Signaling through Kinase-dead Receptors* , 2003, Journal of Biological Chemistry.

[61]  Christopher J. Oldfield,et al.  Intrinsically disordered proteins in human diseases: introducing the D2 concept. , 2008, Annual review of biophysics.

[62]  Jia Li,et al.  BAK1 and BKK1 Regulate Brassinosteroid-Dependent Growth and Brassinosteroid-Independent Cell-Death Pathways , 2007, Current Biology.

[63]  H. Nam,et al.  Identification of a Receptor-Like Protein Kinase Gene Rapidly Induced by Abscisic Acid, Dehydration, High Salt, and Cold Treatments in Arabidopsis thaliana , 1997, Plant physiology.

[64]  J. Schroeder,et al.  Arabidopsis SOMATIC EMBRYOGENESIS RECEPTOR KINASES1 and 2 Are Essential for Tapetum Development and Microspore Maturation[W][OA] , 2005, The Plant Cell Online.