Cation/Proton Antiporter Genes in Tomato: Genomic Characterization, Expression Profiling, and Co-Localization with Salt Stress-Related QTLs

Zahid Hussain,Emilie Widemann,Syed Shujait Ali,Arshad Iqbal,Sabir Hussain Shah,Muhammad Rizwan,Muhammad Imran,Sarfraz Shafiq,Habiba Khan,Shahid Ali,Muhammad Atif Muneer,Muhmmad Kashif Naeem

doi:10.3390/agronomy12020245

Abstract

The cation/proton antiporter (CPA) family represents a class of transmembrane transporter proteins that play a crucial role in plants during high salinity stress by maintaining the cell’s ionic balance and pH homeostasis. So far, the CPA genes have not been systematically characterized in tomato (Solanum lycopersicum). In this study, we identified and analyzed 33 putative CPA genes in tomato. Phylogenetic analysis showed that tomato CPAs could be classified into three subgroups, i.e., CHX (18 genes), KEA (8 genes), and NHX (7 genes). CPA genes within each subgroup shared similar motifs, conserved catalytic domains and gene structure. Further analysis revealed that the CPA genes were unevenly distributed on the chromosomes and segmental duplication events played a major role in the expansion of the CPA gene family in tomato. Gene expression analysis exhibited that CPA genes were differentially expressed in different tissues, various stages of fruit development, and differentially regulated in response to abiotic stresses, especially salt stress. Further, co-localization of tomato CPA genes with quantitative trait loci (QTL) of salt stress-related phenotypes revealed their broader functions in salt stress tolerance. Finally, predicted protein–protein interactions of tomato CPAs, gene ontology analysis, and the presence of putative cis-elements in the promoter further support the diverse role of tomato CPAs in plant development and plant stress tolerance. In brief, this study highlights the potential role of tomato CPAs in plant development and abiotic stress tolerance, especially in salt stress, and provides comprehensive information to explore new candidate genes for salt tolerance in tomato.

Highlights

The cation/proton antiporters (CPAs) are responsible for maintaining the pH homeostasis and ion concentrations in all living species, including plants and animals
Ion concentration and pH balance feat are accomplished with a diverse array of transporters, especially the CPA proteins [1] that are localized in the plasma membrane as well as organelle membranes such as endosomes, vacuoles, and chloroplasts [3,7,8]
Tomato CPAs are unevenly distributed on their chromosomes, and segmental duplication contributed to the evolution of the CPAs family

Summary

Introduction

The cation/proton antiporters (CPAs) are responsible for maintaining the pH homeostasis and ion concentrations in all living species, including plants and animals. The CPA superfamily is functionally involved in the exchange and transport of monovalent cations in plants [5], can be divided into two main types, i.e., transport of sodium ion (Na+) or potassium ion (K+) and a cation exchange for one or two protons [6]. Ion concentration and pH balance feat are accomplished with a diverse array of transporters, especially the CPA proteins [1] that are localized in the plasma membrane as well as organelle membranes such as endosomes, vacuoles, and chloroplasts [3,7,8]. The function of CPAs in tomato remains largely unknown

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Discussion

Conclusion