Diversity, classification and function of the plant protein kinase superfamily

Abstract

Eukaryotic protein kinases belong to a large superfamily with hundreds to thousands of copies and are components of essentially all cellular functions. The goals of this study are to classify protein kinases from 25 plant species and to assess their evolutionary history in conjunction with consideration of their molecular functions. The protein kinase superfamily has expanded in the flowering plant lineage, in part through recent duplications. As a result, the flowering plant protein kinase repertoire, or kinome, is in general significantly larger than other eukaryotes, ranging in size from 600 to 2500 members. This large variation in kinome size is mainly due to the expansion and contraction of a few families, particularly the receptor-like kinase/Pelle family. A number of protein kinases reside in highly conserved, low copy number families and often play broadly conserved regulatory roles in metabolism and cell division, although functions of plant homologues have often diverged from their metazoan counterparts. Members of expanded plant kinase families often have roles in plant-specific processes and some may have contributed to adaptive evolution. Nonetheless, non-adaptive explanations, such as kinase duplicate subfunctionalization and insufficient time for pseudogenization, may also contribute to the large number of seemingly functional protein kinases in plants.

The Arabidopsis ZED1 pseudokinase is required for ZAR1-mediated immunity induced by the Pseudomonas syringae type III effector HopZ1a

“…S9), including seven highly similar protein kinases genomically clustered with ZED1 ( Fig. 4C) (31). The RLCK IXb subfamily is closely related to RLCK XII-2 subfamily, and we refer to members of both of these subfamilies as ZED1-related kinases (ZRKs; Fig.…”

“…ZED1 is part of the broad receptor-like kinase (RLK)/Pelle family of protein kinases, which has dramatically expanded in the land plant lineages (31). The RLK/Pelle family is composed of Ser/Thr kinases, and most are similar to transmembrane receptors with an extracellular domain, a transmembrane domain, and an intracellular kinase domain.…”

“…Homologs of the RLCK IXb subfamily are also found in other plant species, including the closely related A. lyrata as well as poplar (Populus trichocarpa) and grape (Vitis vinifera). Interestingly, this subfamily has only been identified in dicots and is absent from other vascular land plants unlike most other subfamilies of the RLK/Pelle family (31). The tandemly arrayed ZRKs are numbered according to the secondto-last digit of their ATG number (e.g., At3g57770 = ZRK7) with the exception of At3g57700, which we have numbered ZRK10.…”

Evolution of Gene Duplication in Plants

“…Although the proportion of familial genes in plant genomes is high, there can be dramatic differences in the size of gene families across species due to lineage-specific expansions (Lespinet et al, 2002). For example, one of the largest families in plants is the protein kinase superfamily, which has 426 members in the unicellular green alga C. reinhardtii and 2,532 in Eucalyptus grandis (Lehti- Shiu and Shiu, 2012). Another example illustrating the variation in plant gene family size is the large difference in the number of transcription factors, which can differ more than 10-fold among plant species (Jin et al, 2014).…”

Constitutively Elevated Salicylic Acid Levels Alter Photosynthesis and Oxidative State but Not Growth in Transgenic Populus

“…RLKs belong to the protein kinase superfamily with important functions in defense signaling (Morris and Walker, 2003;Lehti-Shiu and Shiu, 2012). Of the 308 RLKs captured in our network (i.e., with differential expression among genotypes or treatments), a majority of them (;77%) were associated with SA-correlated modules, especially the green (II) module where RLKs accounted for ;13% (132) of its nodes.…”