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Evolutionary analysis of CBL-interacting protein kinase gene family in plants

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Abstract

Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) form the CBL-CIPK complexes, perceiving calcium signals and relaying the signals to downstream responses in plants. To further understand the CBL-CIPK signaling system, here we focused on the evolutionary analysis of CIPKs. We re-evaluated eight plant genomes and identified 146 CIPKs, providing several new CIPKs in rice and poplar. A phylogenetic tree was constructed, showing that these 146 CIPKs are grouped into intron-rich and intron-less clades. Furthermore, all the CIPKs from the non-angiosperm species were found in intron-rich clade. We identified 30 conserved protein motifs among these 146 CIPKs. Analysis of gene duplication showed that the expansion of CIPKs in both clades is partly contributed by segmental duplications, however, tandem duplicates were found only in intron-less clade. Ka/Ks ratios showed that CIPK genes have experienced purifying selective pressure. Additionally, clustering of gene expression revealed that some CIPK genes in two clades share similar expression patterns under abiotic stresses and four CIPKs in intron-less clade form a distinct cluster (i.e., different expression patterns), suggesting the complexity of CIPK gene expression under abiotic stresses. Taken together, our results provided some new insights into the evolution of CIPKs and the hint that the expansion of CIPKs in intron-less clade is adaptive to environmental stresses.

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Abbreviations

CBLs:

Calcineurin B-like proteins

CIPKs:

CBL-interacting protein kinases

HMM:

Hidden Markov model

CAMs:

Calmodulins

CDPKs:

Calcium-dependent protein kinases

SOS:

Salt overly sensitive

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Acknowledgments

This research was supported by grants from the Ministry of Science and Technology of China (2011BAD38B01, 2009CB119101), the National Natural Science Foundation of China (31070597, 31270656, and 31100492), Joint Programs of the Scientific Research and Graduate Training from BMEC (Stress Resistance Mechanism of Poplar), and Beijing Forestry University Technology Innovation Program (BLYJ200904).

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Authors and Affiliations

  1. College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Xinli Xia & Weilun Yin

  2. College of Forestry, Beijing Forestry University, Beijing, 100083, People’s Republic of China

    Chu-Yu Ye & Weilun Yin

  3. National Engineering Laboratory for Tree Breeding, Beijing Forestry University, No. 35, Tsinghua East Road, Beijing, 100083, People’s Republic of China

    Chu-Yu Ye, Xinli Xia & Weilun Yin

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  1. Chu-Yu Ye
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  2. Xinli Xia
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  3. Weilun Yin
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Correspondence to Xinli Xia or Weilun Yin.

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Ye, CY., Xia, X. & Yin, W. Evolutionary analysis of CBL-interacting protein kinase gene family in plants. Plant Growth Regul 71, 49–56 (2013). https://doi.org/10.1007/s10725-013-9808-5

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  • DOI: https://doi.org/10.1007/s10725-013-9808-5

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