The grapevine kinome: annotation, classification and expression patterns in developmental processes and stress responses

Abstract

Protein kinases (PKs) have evolved as the largest family of molecular switches that regulate protein activities associated with almost all essential cellular functions. Only a fraction of plant PKs, however, have been functionally characterized even in model plant species. In the present study, the entire grapevine kinome was identified and annotated using the most recent version of the grapevine genome. A total of 1168 PK-encoding genes were identified and classified into 20 groups and 121 families, with the RLK-Pelle group being the largest, with 872 members. The 1168 kinase genes were unevenly distributed over all 19 chromosomes, and both tandem and segmental duplications contributed to the expansion of the grapevine kinome, especially of the RLK-Pelle group. Ka/Ks values indicated that most of the tandem and segmental duplication events were under purifying selection. The grapevine kinome families exhibited different expression patterns during plant development and in response to various stress treatments, with many being coexpressed. The comprehensive annotation of grapevine kinase genes, their patterns of expression and coexpression, and the related information facilitate a more complete understanding of the roles of various grapevine kinases in growth and development, responses to abiotic stress, and evolutionary history.

The sugarcane and sorghum kinomes: insights into evolutionary expansion and diversification

“…We also performed several in silico analyses to evaluate the molecular characteristics of the PKs identified in the two species. As reported for grapevine (Zhu et al, 2018b), the pIs and MWs of the PKs were generally similar within subfamilies in Ssp and Sbi; these results were expected, as these properties are estimated based on the protein sequence. We observed, however, that Ssp contained many more PK subfamilies with significant variation in the MW than did Sbi, possibly indicating a broader diversity of kinases in Ssp.…”

“…In both these Sbi and Ssp networks and those constructed in other kinome studies Zhu et al, 2018b), different members of the RLK-Pelle group (mostly those in the LRR and RLCK families) were identified as hubs. Considering the described abundance of these families, their tandem duplications, and related functional implications, the strong influence of such nodes on the correlations among kinase subfamilies was expected.…”

“…Even though multikinase domains were found in both Sbi and Ssp, Ssp contained more than Sbi, and more repetitions were found in some PKs. Similar to the soybean and grapevine kinomes (Liu et al, 2015;Zhu et al, 2018b), the Sbi kinome contained PKs with only 2 or 3 kinase domains, in contrast to the Ssp kinome, which contained PKs with between 2 and 5 kinase domains. Interestingly, the AGC_RSK-2 subfamily was found to have the largest number of multikinase domains in both Sbi and Ssp, accounting for a very high percentage of members of this subfamily, which is explained by the fusion of two PKs in the evolutionary history of the RSK family (Carriere et al, 2008).…”

“…Segmental duplication events were also the major contributors to PK expansion in other species; in the soybean kinome, these events accounted for the origin of more than 70% of the PKs (Liu et al, 2015); in grapevine, they were estimated to be responsible for the origin of ∼30% of the kinases and were thought to be especially relevant in the expansion of the RLK-Pelle family (Zhu et al, 2018b). The most striking duplication-related difference between the Ssp and Sbi kinomes was the distribution of the rate of nonsynonymous mutations (Ks), which was used to estimate the time of occurrence of these segmental duplications.…”

“…This expansion likely resulted from segmental, whole-genome, and tandem duplication events (Hanada et al, 2008). Arabidopsis thaliana was the first plant to have its kinome compiled (Champion et al, 2004), followed by of several other economically important species such as rice, soybean, and grapevine (Dardick et al, 2007;Liu et al, 2015;Zhu et al, 2018b). The kinome of Sbi was compiled shortly after the genome sequencing (Lehti-Shiu and Shiu, 2012).…”