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Plant Physiology 132:530-543 (2003)
© 2003 American Society of Plant Biologists

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RESEARCH PAPERS ON SYSTEMS BIOLOGY/GENOMICS/BIOINFORMATICS

Expansion of the Receptor-Like Kinase/Pelle Gene Family and Receptor-Like Proteins in Arabidopsis1,[w]

Shin-Han Shiu and Anthony B. Bleecker*

Department of Ecology and Evolution, University of Chicago, Chicago, Illinois 60637 (S.-H.S.); and Department of Botany and Laboratory of Genetics, University of Wisconsin, Madison, Wisconsin 53706 (A.B.B.)

Receptor-like kinases (RLKs) are a family of transmembrane proteins with versatile N-terminal extracellular domains and C-terminal intracellular kinases. They control a wide range of physiological responses in plants and belong to one of the largest gene families in the Arabidopsis genome with more than 600 members. Interestingly, this gene family constitutes 60% of all kinases in Arabidopsis and accounts for nearly all transmembrane kinases in Arabidopsis. Analysis of four fungal, six metazoan, and two Plasmodium sp. genomes indicates that the family was represented in all but fungal genomes, indicating an ancient origin for the family with a more recent expansion only in the plant lineages. The RLK/Pelle family can be divided into several subfamilies based on three independent criteria: the phylogeny based on kinase domain sequences, the extracellular domain identities, and intron locations and phases. A large number of receptor-like proteins (RLPs) resembling the extracellular domains of RLKs are also found in the Arabidopsis genome. However, not all RLK subfamilies have corresponding RLPs. Several RLK/Pelle subfamilies have undergone differential expansions. More than 33% of the RLK/Pelle members are found in tandem clusters, substantially higher than the genome average. In addition, 470 of the RLK/Pelle family members are located within the segmentally duplicated regions in the Arabidopsis genome and 268 of them have a close relative in the corresponding regions. Therefore, tandem duplications and segmental/whole-genome duplications represent two of the major mechanisms for the expansion of the RLK/Pelle family in Arabidopsis.

Article, publication date, and citation information can be found at www.plantphysiol.org/cgi/doi/10.1104/pp.103.021964.

1 The work was supported by a National Institutes of Health National Research Service Award (grant no. 1F32GM066554–01 to S.-H.S.) and by the Department of Energy (grant no. DE–FG02–91ER20029 to A.B.B.).

[w] The online version of this article contains Web-only data. The supplemental material is available at http://www.plantphysiol.org.

* Corresponding author; e-mail bleecker{at}facstaff.wisc.edu; fax 608–262–7509.

Received February 10, 2003; returned for revision March 4, 2003; accepted March 17, 2003.




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