The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress

Weihua Su,Yachun Su,Youxiong Que,Yongjuan Ren,Jingfang Feng,Mutian Shi,Liping Xu,Dongjiao Wang,Chang Zhang,Tingting Sun

doi:10.1186/s12864-021-07828-3

Abstract

BackgroundIn plants, Calcium (Ca2+) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes. The Ca2+/cation antiporter (CaCA) superfamily proteins play vital roles in the transport of Ca2+ and/or other cations. However, the characteristics of these superfamily members in Saccharum and their evolutionary and functional implications have remained unclear.ResultsA total of 34 CaCA genes in Saccharum spontaneum, 5 CaCA genes in Saccharum spp. R570, and 14 CaCA genes in Sorghum bicolor were identified and characterized. These genes consisted of the H+/cation exchanger (CAX), cation/Ca2+ exchanger (CCX), EF-hand / CAX (EFCAX), and Mg2+/H+ exchanger (MHX) families, among which the CCX and EFCAX could be classified into three groups while the CAX could be divided into two groups. The exon/intron structures and motif compositions suggested that the members in the same group were highly conserved. Synteny analysis of CaCAs established their orthologous and paralogous relationships among the superfamily in S. spontaneum, R570, and S. bicolor. The results of protein-protein interactions indicated that these CaCA proteins had direct or indirect interactions. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis demonstrated that most members of Saccharum CaCA genes exhibited a similar expression pattern in response to hormonal (abscisic acid, ABA) treatment but played various roles in response to biotic (Sporisorium scitamineum) and abiotic (cold) stresses. Furthermore, ScCAX4, a gene encoding a cytoplasm, plasma membrane and nucleus positioning protein, was isolated from sugarcane. This gene was constitutively expressed in different sugarcane tissues and its expression was only induced at 3 and 6 h time points after ABA treatment, however was inhibited and indued in the whole process under cold and S. scitamineum stresses, respectively.ConclusionsThis study systematically conducted comparative analyses of CaCA superfamily genes among S. spontaneum, R570, and S. bicolor, delineating their sequence and structure characteristics, classification, evolutionary history, and putative functions. These results not only provided rich gene resources for exploring the molecular mechanism of the CaCA superfamily genes but also offered guidance and reference for research on other gene families in Saccharum.

Highlights

In plants, Calcium (Ca2+) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes
Identification and sequence features of Ca2+/ cation antiporter (CaCA) genes in S. spontaneum, R570 and S. bicolor genomes Statistical results showed that 34 copies of CaCA genes were present in S. spontaneum, with 14 copies in S. bicolor, while R570 had only five CaCA genes
To reveal the taxonomic information of CaCA superfamily genes, a phylogenetic tree based on the amino acid homology among Arabidopsis, S. spontaneum, R570, and S. bicolor was constructed using the neighbor-joining (NJ) method (Fig. 1)

Summary

Introduction

Calcium (Ca2+) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes. Previous studies showed that three classes of membrane transporters, Ca2+-ATPases (PMCAs), Ca2+ permeable channels, and Ca2+/cation antiporters (CaCAs), act as “gatekeepers” to mediate Ca2+ flux across the membrane and to regulate cytosolic Ca2+ levels [3,4,5]. CaCA superfamily proteins are widespread in archaea, bacteria, fungi, plants and animals [6, 7]. They can enhance the efflux of Ca2+ across membranes against the concentration gradient by exchanging the influx of monovalent cations such as H+, Na+, or K+ to energize the process [6,7,8]. According to a study by Cai et al [7], the CaCA superfamily can be classified into six families, i.e., the YRBG, Na+/Ca2+ exchanger (NCX), Na+/Ca2+, K+ exchanger (NCKX), cation/Ca2+ exchanger (CCX), and H+/cation exchanger (CAX) families

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Discussion

Conclusion