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Liu J, Li D, Wang J, Wang Q, Guo X, Fu Q, Kear P, Zhu G, Yang X. Genome-wide characterization of the CPA gene family in potato and a preliminary functional analysis of its role in NaCl tolerance. BMC Genomics 2024; 25:144. [PMID: 38317113 PMCID: PMC10840148 DOI: 10.1186/s12864-024-10000-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND The cation/proton antiporter (CPA) superfamily plays a crucial role in regulating ion homeostasis and pH in plant cells, contributing to stress resistance. However, in potato (Solanum tuberosum L.), systematic identification and analysis of CPA genes are lacking. RESULTS A total of 33 StCPA members were identified and classified into StNHX (n = 7), StKEA (n = 6), and StCHX (n = 20) subfamilies. StCHX owned the highest number of conserved motifs, followed by StKEA and StNHX. The StNHX and StKEA subfamilies owned more exons than StCHX. NaCl stress induced the differentially expression of 19 genes in roots or leaves, among which StCHX14 and StCHX16 were specifically induced in leaves, while StCHX2 and StCHX19 were specifically expressed in the roots. A total of 11 strongly responded genes were further verified by qPCR. Six CPA family members, StNHX1, StNHX2, StNHX3, StNHX5, StNHX6 and StCHX19, were proved to transport Na+ through yeast complementation experiments. CONCLUSIONS This study provides comprehensive insights into StCPAs and their response to NaCl stress, facilitating further functional characterization.
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Affiliation(s)
- Jintao Liu
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
- Southwest United Graduate School, Kunming, 650500, China
| | - Dianjue Li
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Jing Wang
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Qian Wang
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Xiao Guo
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan, 250100, China
| | - Qi Fu
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China
| | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific, Beijing, 100081, China
| | - Guangtao Zhu
- Key Lab for Potato Biology in Universities of Yunnan, School of Life Sciences, Yunnan Normal University, Kunming, 650500, China.
- Southwest United Graduate School, Kunming, 650500, China.
| | - Xiaohui Yang
- Institute of Vegetables, Shandong Academy of Agricultural Sciences/Molecular Biology Key Laboratory of Shandong Facility Vegetable/National Vegetable Improvement Center Shandong Sub-Center, Jinan, 250100, China.
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Sharma H, Taneja M, Upadhyay SK. Identification, characterization and expression profiling of cation-proton antiporter superfamily in Triticum aestivum L. and functional analysis of TaNHX4-B. Genomics 2019; 112:356-370. [PMID: 30818061 DOI: 10.1016/j.ygeno.2019.02.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/18/2019] [Accepted: 02/20/2019] [Indexed: 12/23/2022]
Abstract
The monovalent cation proton antiporter (CPA) superfamily comprises Na+/H+ exchanger (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) family proteins, which play vital functions in plants. A total of 107 TaCPA proteins were identified in Triticum aestivum, and phylogenetically classified into 35 TaNHX, 24 TaKEA and 48 TaCHX proteins. These families had representatives derived from all three sub-genomes. TaKEA genes consisted of higher number of exons, followed by TaNHXs and TaCHXs. The occurrence of about 10 transmembrane regions and higher composition of helices and coils support their membrane-bound and hydrophobic nature. Diverse expression in various tissues and modulated expression under stress conditions suggested their role in development and in response to stress. Co-expression analyses revealed their complex interaction networks. Expression of TaNHX4-B.1 and TaNHX4-B.4 facilitated differential abiotic stress tolerance to Escherichia coli. Our study provides comprehensive information about CPA genes, which would be useful in their future functional characterization.
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Affiliation(s)
- Himanshu Sharma
- Department of Botany, Panjab University, Sector 14, Chandigarh 160014, India
| | - Mehak Taneja
- Department of Botany, Panjab University, Sector 14, Chandigarh 160014, India
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Jia B, Sun M, DuanMu H, Ding X, Liu B, Zhu Y, Sun X. GsCHX19.3, a member of cation/H + exchanger superfamily from wild soybean contributes to high salinity and carbonate alkaline tolerance. Sci Rep 2017; 7:9423. [PMID: 28842677 PMCID: PMC5573395 DOI: 10.1038/s41598-017-09772-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 07/28/2017] [Indexed: 01/21/2023] Open
Abstract
Cation/H+ exchangers (CHX) are characterized to be involved in plant growth, development and stress responses. Although soybean genome sequencing has been completed, the CHX family hasn't yet been systematically analyzed, especially in wild soybean. Here, through Hidden Markov Model search against Glycine soja proteome, 34 GsCHXs were identified and phylogenetically clustered into five groups. Members within each group showed high conservation in motif architecture. Interestingly, according to our previous RNA-seq data, only Group IVa members exhibited highly induced expression under carbonate alkaline stress. Among them, GsCHX19.3 displayed the greatest up-regulation in response to carbonate alkaline stress, which was further confirmed by quantitative real-time PCR analysis. We also observed the ubiquitous expression of GsCHX19.3 in different tissues and its localization on plasma membrane. Moreover, we found that GsCHX19.3 expression in AXT4K, a yeast mutant lacking four ion transporters conferred resistance to low K+ at alkali pH, as well as carbonate stress. Consistently, in Arabidopsis, GsCHX19.3 overexpression increased plant tolerance both to high salt and carbonate alkaline stresses. Furthermore, we also confirmed that GsCHX19.3 transgenic lines showed lower Na+ concentration but higher K+/Na+ values under salt-alkaline stress. Taken together, our findings indicated that GsCHX19.3 contributed to high salinity and carbonate alkaline tolerance.
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Affiliation(s)
- Bowei Jia
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, P.R. China
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, P.R. China
| | - Mingzhe Sun
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, P.R. China
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, P.R. China
| | - Huizi DuanMu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, P.R. China
| | - Xiaodong Ding
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, P.R. China
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, Medicinaregatan, 9ES-413 90, Gothenburg, Sweden
| | - Yanming Zhu
- Key Laboratory of Agricultural Biological Functional Genes, Northeast Agricultural University, Harbin, 150030, P.R. China.
| | - Xiaoli Sun
- Crop Stress Molecular Biology Laboratory, Heilongjiang Bayi Agricultural University, Daqing, 163319, P.R. China.
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Zhou H, Qi K, Liu X, Yin H, Wang P, Chen J, Wu J, Zhang S. Genome-wide identification and comparative analysis of the cation proton antiporters family in pear and four other Rosaceae species. Mol Genet Genomics 2016; 291:1727-42. [DOI: 10.1007/s00438-016-1215-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 05/06/2016] [Indexed: 11/28/2022]
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Gene-expression profile of developing pollen tube of Pyrus bretschneideri. Gene Expr Patterns 2015; 20:11-21. [PMID: 26547040 DOI: 10.1016/j.gep.2015.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 10/28/2015] [Accepted: 10/30/2015] [Indexed: 11/23/2022]
Abstract
Pollen is an ideal model system for investigation of cell growth. In order to better understand the molecular biology mechanisms of the process of pear pollen tube development, RNA sequencing (RNA-Seq) technology was used to characterize the expression of genes during four development stages of pear pollen, including mature pollen grains (MP), hydrated pollen grains (HP), growing pollen tubes (PT) and stopped-growth pollen tubes (SPT). The four libraries generated a total of 47,072,151 clean reads that were mapped and assembled into 21,394 genes. Transcripts from the four stages were classified into 38 functional subcategories. Between MP and HP, 305 genes were differentially expressed, and 502 genes were differentially expressed between HP and PT. More importantly, we have observed that 2208 genes were differentially expressed between PT and SPT, and this is the first report of the gene expression comparison between the two development stages. Eight of the differentially expressed genes were randomly selected to confirm the RNA-Seq results by quantitative real-time PCR (qRT-PCR). Taken together, this research provides a platform for future research on pear pollen tube growth and growth cessation.
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Zhao J, Wang T, Wang M, Liu Y, Yuan S, Gao Y, Yin L, Sun W, Peng L, Zhang W, Wan J, Li X. DWARF3 Participates in an SCF Complex and Associates with DWARF14 to Suppress Rice Shoot Branching. ACTA ACUST UNITED AC 2014; 55:1096-109. [DOI: 10.1093/pcp/pcu045] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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