The Arabidopsis CDPK-SnRK Superfamily of Protein Kinases

Abstract

The CDPK-SnRK superfamily consists of seven types of serine-threonine protein kinases: calcium-dependent protein kinase (CDPKs), CDPK-related kinases (CRKs), phosphoenolpyruvate carboxylase kinases (PPCKs), PEP carboxylase kinase-related kinases (PEPRKs), calmodulin-dependent protein kinases (CaMKs), calcium and calmodulin-dependent protein kinases (CCaMKs), and SnRKs. Within this superfamily, individual isoforms and subfamilies contain distinct regulatory domains, subcellular targeting information, and substrate specificities. Our analysis of the Arabidopsis genome identified 34 CDPKs, eight CRKs, two PPCKs, two PEPRKs, and 38 SnRKs. No definitive examples were found for a CCaMK similar to those previously identified in lily (Lilium longiflorum) and tobacco (Nicotiana tabacum) or for a CaMK similar to those in animals or yeast. CDPKs are present in plants and a specific subgroup of protists, but CRKs, PPCKs, PEPRKs, and two of the SnRK subgroups have been found only in plants. CDPKs and at least one SnRK have been implicated in decoding calcium signals in Arabidopsis. Analysis of intron placements supports the hypothesis that CDPKs, CRKs, PPCKs and PEPRKs have a common evolutionary origin; however there are no conserved intron positions between these kinases and the SnRK subgroup. CDPKs and SnRKs are found on all five Arabidopsis chromosomes. The presence of closely related kinases in regions of the genome known to have arisen by genome duplication indicates that these kinases probably arose by divergence from common ancestors. The PlantsP database provides a resource of continuously updated information on protein kinases from Arabidopsis and other plants.In eukaryotes, protein kinases are involved in regulating key aspects of cellular function, including cell division, metabolism, and responses to external signals. The completed sequence of the Arabidopsis genome provides the first opportunity to identify all of the protein kinases present in a model plant. The Arabidopsis genome encodes 1,085 typical protein kinases (M. Gribskov, unpublished data), which is about 4% of the predicted 25,500 genes (Arabidopsis Article, publication date, and citation information can be found at www.plantphysiol.org/cgi

The calcium‐dependent protein kinase (CDPK) and CDPK‐related kinase gene families in Hevea brasiliensis—comparison with five other plant species in structure, evolution, and expression

“…This analysis identified a total of 161 CDPK genes and 45 CRK genes in the six plant species, including 39 H. brasiliensis CDPK and CRK genes ( HbCPK1 to 30, and HbCRK1 to 9 , Table 1a), 31 M. esculenta genes ( MeCPK1 to 22 , and MeCRK1 to 9 , Table 1b), 21 R. communis genes ( RcCPK1 to 16, and RcCRK1 to 5 , Table 1c), 42 A. thaliana genes ( AtCPK1 to 34, and AtCRK1 to 8, Table S1–4), 39 P. trichocarpa genes ( PtCDPK1 to 30, and PtCRK1 to 9 , Table S1–5), and 34 O. sativa genes ( OsCPK1 to 29, and OsCRK1 to 5 , Table S1–6). The gene numbers of CDPK and CRK families identified here for the three model plants agree well with those previously reported 12, 28, 41.…”

“…The latest genome and protein sequences of these species were downloaded from Phytozome v10. Local blast searches of the genomes were performed by using the published CDPK and CRK sequences of three model plants of A. thaliana , O. sativa, and P. trichocarpa as queries 12, 26, 28, 40. This analysis identified a total of 161 CDPK genes and 45 CRK genes in the six plant species, including 39 H. brasiliensis CDPK and CRK genes ( HbCPK1 to 30, and HbCRK1 to 9 , Table 1a), 31 M. esculenta genes ( MeCPK1 to 22 , and MeCRK1 to 9 , Table 1b), 21 R. communis genes ( RcCPK1 to 16, and RcCRK1 to 5 , Table 1c), 42 A. thaliana genes ( AtCPK1 to 34, and AtCRK1 to 8, Table S1–4), 39 P. trichocarpa genes ( PtCDPK1 to 30, and PtCRK1 to 9 , Table S1–5), and 34 O. sativa genes ( OsCPK1 to 29, and OsCRK1 to 5 , Table S1–6).…”

Dissecting the β-Aminobutyric Acid–Induced Priming Phenomenon in Arabidopsis

“…BLAST analysis of the IBS1 protein revealed 80% sequence identity with a cyclin-dependent kinase (CDK)-like protein (At1G74330) from Arabidopsis ( Figure 2). Furthermore, IBS1 has 48% sequence identity with the CDC2 protein from Arabidopsis, a CDK involved in meiotic and mitotic cell divisions (Moran and Walker, 1993), and 44% sequence identity with the CRK1 protein of Beta vulgaris, which belongs to the superfamily of calcium-dependent protein kinases (Hrabak et al, 2003).…”

“…Additionally, IBS1 shares 44% sequence identity with the CRK1 protein from B. vulgaris (Figure 2). This protein kinase belongs to the family of calcium-dependent protein kinases, which have functions in a wide array of developmental and stress-related responses in plants (Hrabak et al, 2003). The N-terminal part of IBS1 contains an N-terminal myristoylation sequence (Figure 2).…”

Genome-wide analysis and expression profiling of calcium-dependent protein kinases in potato (Solanum tuberosum)

“…Changes in calcium ion concentration are sensed, among others, by calcium-dependent protein kinases (CDPKs, also named CPKs). CDPKs are Ser/Thr protein kinases typically comprising five domains: an N-terminal variable domain, a catalytic domain (CD), an autoinhibitory junction domain (JD), a calmodulin-like domain (CLD), and a C-terminal domain (Hrabak et al 2003). The N-and C-terminal domains are variable, differing in length and amino-acid composition.…”