Islam Md Shohel Ul, Akter Nasrin, Zohra Fatema Tuz, Rashid Shuraya Beente, Hasan Naimul, Rahman Shaikh Mizanur, Sarkar Md Abdur Rauf
Laboratory of Functional Genomics and Proteomics, Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore, Bangladesh.
Department of Genetic Engineering and Biotechnology, Faculty of Biological Sciences, University of Rajshahi, Rajshahi, Bangladesh.
PLoS One. 2025 Jan 24;20(1):e0317008. doi: 10.1371/journal.pone.0317008. eCollection 2025.
The cation-proton antiporter (CPA) superfamily plays pivotal roles in regulating cellular ion and pH homeostasis in plants. To date, the regulatory functions of CPA family members in rice (Oryza sativa L.) have not been elucidated. In this study, we use rice public data and information techniques, 29 OsCPA candidate genes were identified in the rice japonica variety (referred to as OsCPA) and phylogenetically categorized into K+ efflux antiporter (KEA), Na+/H+ exchanger (NHX), and cation/H+ exchanger (CHX) groups containing 4, 7, and 18 OsCPA genes. The OsCPA proteins were predominantly localized in the plasma membrane and unevenly scattered on 11 chromosomes. The structural analysis of OsCPA proteins revealed higher similarities within groups. Prediction of selection pressure, collinearity, and synteny analysis indicated that all duplicated OsCPA genes had undergone strong purifying selection throughout their evolution. The cis-acting regulatory elements (CAREs) analysis identified 56 CARE motifs responsive to light, tissue, hormones, and stresses. Additionally, 124 miRNA families were identified in the gene promoters, and OsNHX7 was targeted by the highest number of miRNAs (43 miRNAs). Gene Ontology analysis demonstrated the numerous functions of OsCPA genes associated with biological processes (57.14%), cellular components (7.94%), and molecular functions (34.92%). A total of 12 transcription factor families (TFFs), including 40 TFs were identified in gene promoters, with the highest numbers of TFFs (5TFFs) linked to OsCHX13, and OsCHX15. Protein-protein interaction analysis suggested maximum functional similarities between rice and Arabidopsis CPA proteins. Based on expression analysis, OsKEA1, OsKEA2, OsNHX3, and OsNHX7 were frequently expressed in rice tissues. Furthermore, OsNHX3, OsNHX4, OsNHX6, OsNHX7, OsCHX8, and OsCHX17 in abscisic acid, OsKEA1, OsNHX3, and OsCHX8 in gibberellic acid, OsKEA1, OsKEA3, OsNHX1, and OsNHX3 in indole-3-acetic acid treatment were demonstrated as potential candidates in response to hormone. These findings highlight potential candidates for further characterization of OsCPA genes, which may aid in the development of rice varieties.
阳离子-质子反向转运体（CPA）超家族在调节植物细胞离子和pH稳态方面发挥着关键作用。迄今为止，CPA家族成员在水稻（Oryza sativa L.）中的调控功能尚未阐明。在本研究中，我们利用水稻公共数据和信息技术，在粳稻品种中鉴定出29个OsCPA候选基因（称为OsCPA），并通过系统发育分析将其分为K+外流反向转运体（KEA）、Na+/H+交换体（NHX）和阳离子/H+交换体（CHX）组，分别包含4个、7个和18个OsCPA基因。OsCPA蛋白主要定位于质膜，不均匀地分布在11条染色体上。OsCPA蛋白的结构分析表明，各亚组内具有较高的相似性。选择压力预测、共线性和同线性分析表明，所有重复的OsCPA基因在进化过程中都经历了强烈的纯化选择。顺式作用调控元件（CARE）分析确定了56个响应光、组织、激素和胁迫的CARE基序。此外，在基因启动子中鉴定出124个miRNA家族，其中OsNHX7受miRNA靶向的数量最多（43个miRNA）。基因本体分析表明，OsCPA基因具有与生物过程（57.14%）、细胞成分（7.94%）和分子功能（34.92%）相关的多种功能。在基因启动子中总共鉴定出12个转录因子家族（TFF），包括40个转录因子，其中与OsCHX13和OsCHX15相关的TFF数量最多（5个TFF）。蛋白质-蛋白质相互作用分析表明，水稻和拟南芥CPA蛋白之间具有最大的功能相似性。基于表达分析，OsKEA1、OsKEA2、OsNHX3和OsNHX7在水稻组织中频繁表达。此外，脱落酸处理下的OsNHX3、OsNHX4、OsNHX6、OsNHX7、OsCHX8和OsCHX17，赤霉素处理下的OsKEA1、OsNHX3和OsCHX8，吲哚-3-乙酸处理下的OsKEA1、OsKEA3、OsNHX1和OsNHX3被证明是响应激素的潜在候选基因。这些发现突出了进一步表征OsCPA基因的潜在候选基因，这可能有助于水稻品种的培育。
