Genome-wide identification and transcriptional expression analysis of mitogen-activated protein kinase and mitogen-activated protein kinase kinase genes in Capsicum annuum.

Zhiqin Liu,Jinsen Cai,Youquan Lin,Cailing Liu,Sheng Yang,Yanyan Liu,Rongzhang Wang,Lanping Shi,Huanxin Yu,Qian Tang,Jiayu Wen,Lei Shen,Jiong Hu,Yangwen Zhang,Shaoliang Mou,Shuilin He

doi:10.3389/fpls.2015.00780

Abstract

The tripartite mitogen-activated protein kinase (MAPK) signaling cascades have been implicated in plant growth, development, and environment adaptation, but a comprehensive understanding of MAPK signaling at genome-wide level is limited in Capsicum annuum. Herein, genome-wide identification and transcriptional expression analysis of MAPK and MAPK kinase (MAPKK) were performed in pepper. A total of 19 pepper MAPK (CaMAPKs) genes and five MAPKK (CaMAPKKs) genes were identified. Phylogenetic analysis indicated that CaMAPKs and CaMAPKKs could be classified into four groups and each group contains similar exon-intron structures. However, significant divergences were also found. Notably, five members of the pepper MAPKK family were much less conserved than those found in Arabidopsis, and 9 Arabidopsis MAPKs did not have orthologs in pepper. Additionally, 7 MAPKs in Arabidopsis had either two or three orthologs in the pepper genome, and six pepper MAPKs and one MAPKK differing in sequence were found in three pepper varieties. Quantitative real-time RT-PCR analysis showed that the majority of MAPK and MAPKK genes were ubiquitously expressed and transcriptionally modified in pepper leaves after treatments with heat, salt, and Ralstonia solanacearum inoculation as well as exogenously applied salicylic acid, methyl jasmonate, ethephon, and abscisic acid. The MAPKK-MAPK interactome was tested by yeast two-hybrid assay, the results showed that one MAPKK might interact with multiple MAPKs, one MAPK might also interact with more than one MAPKKs, constituting MAPK signaling networks which may collaborate in transmitting upstream signals into appropriate downstream cellular responses and processes. These results will facilitate future functional characterization of MAPK cascades in pepper.

Highlights

Plant growth, development, and response to environmental cues are tightly and coordinately regulated by sophisticated signaling networks
Genome-wide analyses of gene families of mitogen-activated protein kinase (MAPK), MAPK kinase (MAPKK), and MAPK kinase kinase (MAPKKK) have been performed in several plant species; these analyses have provided insights into the mechanisms underlying the regulation of MAPK modules, laying an important foundation for further functional characterization (Liu et al, 2010; Yin et al, 2013; Zhang et al, 2013; Wu et al, 2014)
These numbers were similar to the numbers of MAPKs and MAPKKs identified in other plant species, such as Arabidopsis (20/10), Oryza (17/8), Populus (21/11), tomato (16/5), apple (19/7), Medicago (18/4); (Ovecka et al, 2014), Phaseolus (15/9); (Neupane et al, 2013a), and soybean (38/11); (Neupane et al, 2013b)

Summary

Introduction

Development, and response to environmental cues are tightly and coordinately regulated by sophisticated signaling networks. One of the most important protein-kinasebased amplification cascades is the mitogen-activated protein kinase (MAPK) cascade, typically comprising the hierarchically organized MAPK kinase kinase (MAPKKK)-MAPK kinase (MAPKK)-MAPK, all encoded by multiple genes (Smékalová et al, 2014) In this cascade, MAPKs phosphorylate specific substrate proteins such as transcription factors and enzymes and subsequently trigger cellular responses. MAPKs are activated when both tyrosine and threonine residues in the TEY/TDY motif are phosphorylated by dual-specificity kinases (MAPKKs), which in turn are activated by MAPKKKs via phosphorylation of the conserved Thr/Ser motif (Group, 2002; Ishihama et al, 2011; Janitza et al, 2012) These cascades of activations rapidly transform upstream signals into appropriate intracellular responses (Group, 2002). The precise regulation mechanisms mediated by MAPK modules remain to be elucidated

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