Genome-wide survey indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) calcium-dependent protein kinase genes

Wang, Qiuli; Yin, Xin; Chen, Qian; Xiang, Nan; Sun, Xudong; Yang, Yunqiang; Yang, Yongping

doi:10.1038/s41598-017-16102-0

Cited by 8 publications

(5 citation statements)

References 80 publications

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“…To dissect the evolutionary relationships of BdCDPK family members, all BdCDPK full-length amino acid sequences were used to construct an unrooted tree (Additional file 7). Based upon sequence homology, BdCDPK family members were clustered into four subgroup (I-IV), which was consistent with the previous works in Arabidopsis, rice, maize, and so on [9,38,40,47]. Subgroup IV contained the least members, with three members, in which, the BdCDPK12 showed distant relationship with other members in this subgroup.…”

Section: Resultssupporting

confidence: 86%

Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon

et al. 2020

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Background: Ca 2+ played as a ubiquitous secondary messenger involved in plant growth, development, and responses to various environmental stimuli. Calcium-dependent protein kinases (CDPK) were important Ca 2+ sensors, which could directly translate Ca 2+ signals into downstream phosphorylation signals. Considering the importance of CDPKs as Ca 2+ effectors for regulation of plant stress tolerance and few studies on Brachypodium distachyon were available, it was of interest for us to isolate CDPKs from B. distachyon. Results: A systemic analysis of 30 CDPK family genes in B. distachyon was performed. Results showed that all BdCDPK family members contained conserved catalytic Ser/Thr protein kinase domain, autoinhibitory domain, and EF-hand domain, and a variable N-terminal domain, could be divided into four subgroup (I-IV), based upon sequence homology. Most BdCDPKs had four EF-hands, in which EF2 and EF4 revealed high variability and strong divergence from EF-hand in AtCDPKs. Synteny results indicated that large number of syntenic relationship events existed between rice and B. distachyon, implying their high conservation. Expression profiles indicated that most of BdCDPK genes were involved in phytohormones signal transduction pathways and regulated physiological process in responding to multiple environmental stresses. Moreover, the co-expression network implied that BdCDPKs might be both the activator and the repressor involved in WRKY transcription factors or MAPK cascade genes mediated stress response processes, base on their complex regulatory network. Conclusions: BdCDPKs might play multiple function in WRKY or MAPK mediated abiotic stresses response and phytohormone signaling transduction in B. distachyon. Our genomics analysis of BdCDPKs could provide fundamental information for further investigation the functions of CDPKs in integrating Ca 2+ signalling pathways in response to environments stresses in B. distachyon.

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Section: Resultssupporting

confidence: 86%

Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon

et al. 2020

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“…We calculated this index for homologous gene pairs to explore the selection of DoCDPKs. Similar to the CDPKs in turnip and cucumber, those in D. officinale displayed a low Ka/Ks ratio (less than 1, Table 2), indicating that DoCDPKs had undergone negative selection [49,50]. The Ks values differed among gene pairs, indicating the evolution rate varied in homologous genes which could result in functional diversification.…”

Section: Discussionmentioning

confidence: 95%

Genome-Wide Survey Indicates Diverse Physiological Roles of Dendrobium officinale Calcium-Dependent Protein Kinase Genes

Chen

Yin

Wang

et al. 2022

IJMS

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Calcium-dependent protein kinases (CDPKs) are crucial calcium ions (Ca2+) sensors in plants with important roles in signal transduction, plant growth, development, and stress responses. Here, we identified 24 genes encoding CDPKs in Dendrobium officinale using genome-wide analysis. The phylogenetic analysis revealed that these genes formed four groups, with similar structures in the same group. The gene expression patterns following hormone treatments and yeast two-hybrid of homologous CDPK gene pairs with Rbohs showed differences, indicating functional divergence between homologous genes. In addition, the rapid accumulation of hydrogen peroxide (H2O2) and stomatal closure was observed in response to salicylic acid (SA)/jasmonic acid (JA) stress. Our data showed that CDPK9-2 and CDPK20-4 interacted with Rboh D and Rboh H, respectively, and were implicated in the generation of H2O2 and regulation of the stomatal aperture in response to salicylic acid/jasmonic acid treatment. We believe these results can provide a foundation for the functional divergence of homologous genes in D. officinale.

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“…CPK gene is a candidate gene for modifying plant stress resistance cations. Although there are some studies on CPKs of Brassica plants, such as turnip and canola (Zhang et al, 2014a;Wang et al, 2017), there are few studies on Brassica CPKs as a whole. Zhang et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…CPK gene is a candidate gene for modifying plant stress resistance cations. Although there are some studies on CPKs of Brassica plants, such as turnip and canola ( Zhang et al., 2014a ; Wang et al., 2017 ), there are few studies on Brassica CPKs as a whole. Additionally, most of the studies on CPKs are conducted in one type of plant, which cannot be accurately used for comparison between plants.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide survey of Calcium-Dependent Protein Kinases (CPKs) in five Brassica species and identification of CPKs induced by Plasmodiophora brassicae in B. rapa, B. oleracea, and B. napus

Yang

Zhu

et al. 2022

Front. Plant Sci.

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Calcium-dependent protein kinase (CPK) is a class of Ser/Thr protein kinase that exists in plants and some protozoa, possessing Ca2+ sensing functions and kinase activity. To better reveal the roles that Brassica CPKs played during plant response to stresses, five Brassica species, namely Brassica rapa (B. rapa), Brassica nigra (B. nigra), Brassica oleracea (B. oleracea), Brassica juncea (B. juncea), and Brassica napus (B. napus) were selected and analyzed. In total, 51 BraCPK, 56 BniCPK, 56 BolCPK, 88 BjuCPK, and 107 BnaCPK genes were identified genome wide and phylogenetics, chromosomal mapping, collinearity, promoter analysis, and biological stress analysis were conducted. The results showed that a typical CPK gene was constituted by a long exon and tandem short exons. They were unevenly distributed on most chromosomes except chromosome A08 in B. napus and B. rapa, and almost all CPK genes were located on regions of high gene density as non-tandem form. The promoter regions of BraCPKs, BolCPKs, and BnaCPKs possessed at least three types of cis-elements, among which the abscisic acid responsive-related accounted for the largest proportion. In the phylogenetic tree, CPKs were clustered into four primary groups, among which group I contained the most CPK genes while group IV contained the fewest. Some clades, like AT5G23580.1(CPK12) and AT2G31500.1 (CPK24) contained much more gene members than others, indicating a possibility that gene expansion occurred during evolution. Furthermore, 4 BraCPKs, 14 BolCPKs, and 31 BnaCPKs involved in the Plasmodiophora brassicae (P. brassicae) defense response in resistant (R) or susceptible (S) materials were derived from online databases, leading to the discovery that some R-specific induced CPKs, such as BnaC02g08720D, BnaA03g03800D, and BolC04g018270.2J.m1 might be ideal candidate genes for P. brassicae resistant research. Overall, these results provide valuable information for research on the function and evolution of CDK genes.

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Genome-wide survey indicates diverse physiological roles of the turnip (Brassica rapa var. rapa) calcium-dependent protein kinase genes

Cited by 8 publications

References 80 publications

Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon

Genome-wide survey and expression analysis of calcium-dependent protein kinase (CDPK) in grass Brachypodium distachyon

Genome-Wide Survey Indicates Diverse Physiological Roles of Dendrobium officinale Calcium-Dependent Protein Kinase Genes

Genome-wide survey of Calcium-Dependent Protein Kinases (CPKs) in five Brassica species and identification of CPKs induced by Plasmodiophora brassicae in B. rapa, B. oleracea, and B. napus

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