Genome-wide analysis of the apple CaCA superfamily reveals that MdCAX proteins are involved in the abiotic stress response as calcium transporters

Abstract

Background Calcium (Ca2+) plays an important role in plant growth and development, and the maintenance of calcium homeostasis is necessary for the survival of all plant species. Ca2+/H+ exchangers (CAXs) are a subgroup of the CaCA (Ca2+/cation antiporter) superfamily. In general, CAX proteins mediate cytosolic Ca2+ entry into vacuoles to prevent excessive accumulation of Ca2+ in the cytosol. The CaCA superfamily has been identified and characterised in many plant species; however, characterisation of the CaCA superfamily and functional study of apple CAX proteins have yet to be conducted in apple (Malus × domestica Borkh.). Results Here, we identified 21 CaCA family proteins in apple for the first time. Phylogenetic and gene structure analysis, as well as prediction of conserved motifs, suggested that these proteins could be classified into four groups: CAX, CCX, NCL, and MHX. Expression analysis showed that the 10 MdCAX genes we cloned strongly responded to calcium and abiotic stress treatments. Collinearity analysis and characterisation of calcium transport capacity resulted in the identification of a pair of segmental duplication genes: MdCAX3L-1 and MdCAX3L-2; MdCAX3L-2 showed strong calcium transport capacity, whereas MdCAX3L-1 showed no calcium transport capacity. Yeast two-hybrid (Y2H) assays showed that these two proteins could interact with each other. The high sequence similarity (94.6%) makes them a good model for studying the crucial residues and structural basis of the calcium transport of CAX proteins. Prediction of the protein interaction network revealed several proteins that may interact with CAX proteins and play important roles in plant stress responses, such as SOS2, CXIP1, MHX, NRAMP3, and MTP8. Conclusions Our analysis indicated that MdCAX proteins have strong calcium transport capacity and are involved in the abiotic stress response in apple. These findings provide new insight and rich resources for future studies of MdCAX proteins in apple.

Genome-Wide Analysis of the Apple CBL Family Reveals That Mdcbl10.1 Functions Positively in Modulating Apple Salt Tolerance

“…In this study, 11 MdCBL genes were identified from apples (Table 1), only one more than that from Arabidopsis, suggesting that the CBL family in apples had not expanded significantly during evolution. This was different from other gene families that were previously identified in apple, such as the bHLH [37], Lhc [51], and CaCA [38] families. Tandem and segmental duplication events are fundamental mechanisms of gene family expansion.…”

“…Ca 2+ is an essential element for plant growth and survival, and Ca 2+ signals are an important regulator of growth, development, and biotic and abiotic stresses in plants [7,38,42]. Studies in various fruit tree crops also have shown that Ca 2+ plays an important role in regulating fruit development, ripening, quality, and storage [43][44][45][46][47].…”

“…The online MEME software (version 5.3.3; https://meme-suite.org/ meme/tools/meme, accessed on 26 April 2021) was used to identify conserved motifs in the protein sequences of these MdCBLs. Detailed methods refer to previous studies [37,38].…”

Cation/Ca2+ Exchanger 1 (MdCCX1), a Plasma Membrane-Localized Na+ Transporter, Enhances Plant Salt Tolerance by Inhibiting Excessive Accumulation of Na+ and Reactive Oxygen Species

“…In our recent study, the gene MD12G1011500 was identified as the AtCCX1 ortholog in apple (Mao et al, 2021). Gene specific primers were designed based on MD12G1011500 and used to amplify the full-length coding sequence (CDS) of MdCCX1.…”

“…Proteins in the CaCA superfamily usually facilitate the Ca 2+ efflux against the concentration gradient across the membrane and promotes an influx of monovalent cations like H + , Na + , or K + in exchange (Amagaya et al, 2019). Based on their function and evolutionary relationships, the CaCA proteins are divided into five different families: YRBG, Na + /Ca 2+ exchanger (NCX), Na + /Ca 2+ , K + exchanger (NCKX), cation/Ca 2+ exchanger (CCX), and H + /cation exchanger (CAX) (Taneja et al, 2016;Amagaya et al, 2019;Mao et al, 2021). Although these proteins have a common conserved Na_Ca_ex structural domain (PF01699), diverse structural and functional characteristics differentiate them from one another.…”