The CBL and CIPK Gene Family in Grapevine (Vitis vinifera): Genome-Wide Analysis and Expression Profiles in Response to Various Abiotic Stresses.

Zong-Ming (Max) Cheng,Jinyi Liu,Yue Xi,Chao Dong

doi:10.3389/fpls.2017.00978

Abstract

Calcium plays a central role in regulating signal transduction pathways. Calcineurin B-like proteins (CBLs), which harbor a crucial region consisting of EF hands that capture Ca2+, interact in a specific manner with CBL-interacting protein kinases (CIPKs). This two gene families or their interacting-complex widely respond to various environment stimuli and development processes. The genome-wide annotation and specific expression patterns of CBLs and CIPKs, however, in grapevine remain unclear. In the present study, eight CBL and 20 CIPK genes were identified in grapevine genome, and divided into four and five subfamilies, respectively, based on phylogenetic analysis, and validated by gene structure and the distribution of conserved protein motifs. Four (50%) out of eight VvCBLs and eight (40%) out of 20 VvCIPKs were found to be derived from tandem duplication, and five (25%) out of 20 VvCIPKs were derived from segmental duplication, indicating that the expansion of grapevine CBL and CIPK gene families were mainly contributed by gene duplication, and all duplication events between VvCIPK genes only detected in intron poor clade. Estimating of synonymous and non-synonymous substitution rates of both gene families suggested that VvCBL genes seems more conserved than VvCIPK genes, and were derived by positive selection pressure, whereas VvCIPK genes were mainly derived by purifying selection pressure. Expressional analyses of VvCBL and VvCIPK genes based on microarray and qRT-PCR data performed diverse expression patterns of VvCBLs and VvCIPKs in response to both various abiotic stimuli and at different development stages. Furthermore, the co-expression analysis of grapevine CBLs and CIPKs suggested that CBL-CIPK complex seems to be more responsive to abiotic stimuli than during different development stages. VvCBLs may play an important and special role in regulating low temperature stress. The protein interaction analysis suggested divergent mechanisms might exist between Arabidopsis and grapevine. Our results will facilitate the future functional characterization of individual VvCBLs and VvCIPKs.

Highlights

Calcium serves as a ubiquitous second messenger and plays a critical role in plant against various abiotic stresses
Much of the research into the function of Calcineurin B-like proteins (CBLs) and CBL-interacting protein kinases (CIPKs) families has been analyzed in model plants and major crops, such as Arabidopsis, rice, poplar, and other species (Qiu et al, 2002; Zhang et al, 2008; Kanwar et al, 2014), but research in grapevine is limited
8 CBL and 20 CIPK genes were identified in the grapevine genome using a comprehensive means

Summary

Introduction

Calcium serves as a ubiquitous second messenger and plays a critical role in plant against various abiotic stresses. A conserved NAF/FISL motif, required for interacting with CBLs, is present in the C-terminal regulatory domain of CIPKs, and is responsible for the activation role of CIPKs (Albrecht et al, 2001; Guo et al, 2001). Another protein-phosphatase interaction (PPI) domain present in the C-terminal of a few CIPKs can target several different phosphatase 2C (PP2C) proteins (Ohta et al, 2003)

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Results

Conclusion