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Jain R, Srivastava H, Kumar K, Sharma S, Singh A, Gaikwad K. Understanding the role of P-type ATPases in regulating pollen fertility and development in pigeonpea. Mol Genet Genomics 2024; 299:68. [PMID: 38980531 DOI: 10.1007/s00438-024-02155-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 06/08/2024] [Indexed: 07/10/2024]
Abstract
The P-type ATPase superfamily genes are the cation and phospholipid pumps that transport ions across the membranes by hydrolyzing ATP. They are involved in a diverse range of functions, including fundamental cellular events that occur during the growth of plants, especially in the reproductive organs. The present work has been undertaken to understand and characterize the P-type ATPases in the pigeonpea genome and their potential role in anther development and pollen fertility. A total of 59 P-type ATPases were predicted in the pigeonpea genome. The phylogenetic analysis classified the ATPases into five subfamilies: eleven P1B, eighteen P2A/B, fourteen P3A, fifteen P4, and one P5. Twenty-three pairs of P-type ATPases were tandemly duplicated, resulting in their expansion in the pigeonpea genome during evolution. The orthologs of the reported anther development-related genes were searched in the pigeonpea genome, and the expression profiling studies of specific genes via qRT-PCR in the pre- and post-meiotic anther stages of AKCMS11A (male sterile), AKCMS11B (maintainer) and AKPR303 (fertility restorer) lines of pigeonpea was done. Compared to the restorer and maintainer lines, the down-regulation of CcP-typeATPase22 in the post-meiotic anthers of the male sterile line might have played a role in pollen sterility. Furthermore, the strong expression of CcP-typeATPase2 in the post-meiotic anthers of restorer line and CcP-typeATPase46, CcP-typeATPase51, and CcP-typeATPase52 in the maintainer lines, respectively, compared to the male sterile line, clearly indicates their potential role in developing male reproductive organs in pigeonpea.
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Affiliation(s)
- Rishu Jain
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Harsha Srivastava
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, 208024, India
| | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Anandita Singh
- Department of Biotechnology, TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, 110070, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India.
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Zeng F, Feng Y, Wang T, Ma X, Jiao S, Yang S, Shao M, Ma Z, Mao J, Chen B. The asymmetric expression of plasma membrane H +-ATPase family genes in response to pulvinus-driven leaf phototropism movement in Vitis vinifera. PHYSIOLOGIA PLANTARUM 2024; 176:e14380. [PMID: 38894644 DOI: 10.1111/ppl.14380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 05/15/2024] [Accepted: 05/26/2024] [Indexed: 06/21/2024]
Abstract
Phototropism movement is crucial for plants to adapt to various environmental changes. Plant P-type H+-ATPase (HA) plays diverse roles in signal transduction during cell expansion, regulation of cellular osmotic potential and stomatal opening, and circadian movement. Despite numerous studies on the genome-wide analysis of Vitis vinifera, no research has been done on the P-type H+-ATPase family genes, especially concerning pulvinus-driven leaf movement. In this study, 55 VvHAs were identified and classified into nine distinct subgroups (1 to 9). Gene members within the same subgroups exhibit similar features in motif, intron/exon, and protein tertiary structures. Furthermore, four pairs of genes were derived by segmental duplication in grapes. Cis-acting element analysis identified numerous light/circadian-related elements in the promoters of VvHAs. qRT-PCR analysis showed that several genes of subgroup 7 were highly expressed in leaves and pulvinus during leaf movement, especially VvHA14, VvHA15, VvHA16, VvHA19, VvHA51, VvHA52, and VvHA54. Additionally, we also found that the VvHAs genes were asymmetrically expressed on both sides of the extensor and flexor cell of the motor organ, the pulvinus. The expression of VvHAs family genes in extensor cells was significantly higher than that in flexor cells. Overall, this study serves as a foundation for further investigations into the functions of VvHAs and contributes to the complex mechanisms underlying grapevine pulvinus growth and development.
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Affiliation(s)
- Fanwei Zeng
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Yongqing Feng
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Tian Wang
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Xiyuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Shuzhen Jiao
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Shangwen Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Miao Shao
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Zonghuan Ma
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Juan Mao
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
| | - Baihong Chen
- College of Horticulture, Gansu Agricultural University, Lanzhou, PR China
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Huang S, Shen Z, An R, Jia Q, Wang D, Wei S, Mu J, Zhang Y. Identification and characterization of the plasma membrane H +-ATPase genes in Brassica napus and functional analysis of BnHA9 in salt tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108566. [PMID: 38554537 DOI: 10.1016/j.plaphy.2024.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024]
Abstract
As a primary proton pump, plasma membrane (PM) H+-ATPase plays critical roles in regulating plant growth, development, and stress responses. PM H+-ATPases have been well characterized in many plant species. However, no comprehensive study of PM H+-ATPase genes has been performed in Brassica napus (rapeseed). In this study, we identified 32 PM H+-ATPase genes (BnHAs) in the rapeseed genome, and they were distributed on 16 chromosomes. Phylogenetical and gene duplication analyses showed that the BnHA genes were classified into five subfamilies, and the segmental duplication mainly contributed to the expansion of the rapeseed PM H+-ATPase gene family. The conserved domain and subcellular analyses indicated that BnHAs encoded canonical PM H+-ATPase proteins with 14 highly conserved domains and localized on PM. Cis-acting regulatory element and expression pattern analyses indicated that the expression of BnHAs possessed tissue developmental stage specificity. The 25 upstream open reading frames with the canonical initiation codon ATG were predicted in the 5' untranslated regions of 11 BnHA genes and could be used as potential target sites for improving rapeseed traits. Protein interaction analysis showed that BnBRI1.c associated with BnHA2 and BnHA17, indicating that the conserved activity regulation mechanism of BnHAs may be present in rapeseed. BnHA9 overexpression in Arabidopsis enhanced the salt tolerance of the transgenic plants. Thus, our results lay a foundation for further research exploring the biological functions of PM H+-ATPases in rapeseed.
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Affiliation(s)
- Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Zhen Shen
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Qingli Jia
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Daojie Wang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Shihao Wei
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China.
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China.
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4
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Chen W, Cui Y, He Y, Zhao L, Cui R, Liu X, Huang H, Zhang Y, Fan Y, Feng X, Ni K, Jiang T, Han M, Lei Y, Liu M, Meng Y, Chen X, Lu X, Wang D, Wang J, Wang S, Guo L, Chen Q, Ye W. Raffinose degradation-related gene GhAGAL3 was screened out responding to salinity stress through expression patterns of GhAGALs family genes. FRONTIERS IN PLANT SCIENCE 2023; 14:1246677. [PMID: 38192697 PMCID: PMC10773686 DOI: 10.3389/fpls.2023.1246677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024]
Abstract
A-galactosidases (AGALs), the oligosaccharide (RFO) catabolic genes of the raffinose family, play crucial roles in plant growth and development and in adversity stress. They can break down the non-reducing terminal galactose residues of glycolipids and sugar chains. In this study, the whole genome of AGALs was analyzed. Bioinformatics analysis was conducted to analyze members of the AGAL family in Gossypium hirsutum, Gossypium arboreum, Gossypium barbadense, and Gossypium raimondii. Meanwhile, RT-qPCR was carried out to analyze the expression patterns of AGAL family members in different tissues of terrestrial cotton. It was found that a series of environmental factors stimulated the expression of the GhAGAL3 gene. The function of GhAGAL3 was verified through virus-induced gene silencing (VIGS). As a result, GhAGAL3 gene silencing resulted in milder wilting of seedlings than the controls, and a significant increase in the raffinose content in cotton, indicating that GhAGAL3 responded to NaCl stress. The increase in raffinose content improved the tolerance of cotton. Findings in this study lay an important foundation for further research on the role of the GhAGAL3 gene family in the molecular mechanism of abiotic stress resistance in cotton.
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Affiliation(s)
- Wenhua Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Yupeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Yunxin He
- Hunan Institute of Cotton Science, Changde, Hunan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Ruifeng Cui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Xiaoyu Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Xixian Feng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Tiantian Jiang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Yuqian Lei
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Mengyue Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Yuan Meng
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences/Research Base, Anyang Institute of Technology, National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Anyang, Henan, China
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Urumqi, China
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5
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Luo S, Wang H, Wang Z, Xu W, Tian R, Zhou J. Internalization of myriocin involved in energy and affected expression of genes and proteins in the endocytosis pathway in Fusarium oxysporum f. sp. niveum. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2100721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Affiliation(s)
- Shiqi Luo
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Hengxu Wang
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Zhigang Wang
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Weihui Xu
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
| | - Renmao Tian
- Department of Food Safety, Institute for Food Safety and Health, Illinois Institute of Technology, Chicago, IL, USA
| | - Jiaxin Zhou
- Department of Horticulture, College of Life Science and Agroforestry, Qiqihar University, Qiqihar, Heilongjiang, PR China
- Department of Biology, Heilongjiang Provincial Technology Innovation Center of Agromicrobial Preparation Industrialization, Qiqihar, Heilongjiang, PR China
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Li J, Feng B, Yu P, Fu W, Wang W, Lin J, Qin Y, Li H, Chen T, Xu C, Tao L, Wu Z, Fu G. Oligomeric Proanthocyanidins Confer Cold Tolerance in Rice through Maintaining Energy Homeostasis. Antioxidants (Basel) 2022; 12:antiox12010079. [PMID: 36670941 PMCID: PMC9854629 DOI: 10.3390/antiox12010079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 12/23/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Oligomeric proanthocyanidins (OPCs) are abundant polyphenols found in foods and botanicals that benefit human health, but our understanding of the functions of OPCs in rice plants is limited, particularly under cold stress. Two rice genotypes, named Zhongzao39 (ZZ39) and its recombinant inbred line RIL82, were subjected to cold stress. More damage was caused to RIL82 by cold stress than to ZZ39 plants. Transcriptome analysis suggested that OPCs were involved in regulating cold tolerance in the two genotypes. A greater increase in OPCs content was detected in ZZ39 than in RIL82 plants under cold stress compared to their respective controls. Exogenous OPCs alleviated cold damage of rice plants by increasing antioxidant capacity. ATPase activity was higher and poly (ADP-ribose) polymerase (PARP) activity was lower under cold stress in ZZ39 than in RIL82 plants. Importantly, improvements in cold tolerance were observed in plants treated with the OPCs and 3-aminobenzamide (PARP inhibitor, 3ab) combination compared to the seedling plants treated with H2O, OPCs, or 3ab alone. Therefore, OPCs increased ATPase activity and inhibited PARP activity to provide sufficient energy for rice seedling plants to develop antioxidant capacity against cold stress.
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Affiliation(s)
- Juncai Li
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Baohua Feng
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Pinghui Yu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Weimeng Fu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Wenting Wang
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Jie Lin
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Yebo Qin
- Zhejiang Agricultural Technology Extension Center, Hangzhou 310020, China
| | - Hubo Li
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Tingting Chen
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Chunmei Xu
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Longxing Tao
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhihai Wu
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (Z.W.); (G.F.)
| | - Guanfu Fu
- Agronomy College, Jilin Agricultural University, Changchun 130118, China
- National Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
- Correspondence: (Z.W.); (G.F.)
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Sabir IA, Manzoor MA, Shah IH, Liu X, Jiu S, Wang J, Alam P, Abdullah M, Zhang C. Identification and Comprehensive Genome-Wide Analysis of Glutathione S-Transferase Gene Family in Sweet Cherry ( Prunus avium) and Their Expression Profiling Reveals a Likely Role in Anthocyanin Accumulation. FRONTIERS IN PLANT SCIENCE 2022; 13:938800. [PMID: 35903236 PMCID: PMC9315441 DOI: 10.3389/fpls.2022.938800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/16/2022] [Indexed: 05/08/2023]
Abstract
Glutathione S-transferases (GSTs) in plants are multipurpose enzymes that are involved in growth and development and anthocyanins transportation. However, members of the GST gene family were not identified in sweet cherry (Prunus avium). To identify the GST genes in sweet cherry, a genome-wide analysis was conducted. In this study, we identified 67 GST genes in P. avium genome and nomenclature according to chromosomal distribution. Phylogenetic tree analysis revealed that PavGST genes were classified into seven chief subfamily: TCHQD, Theta, Phi, Zeta, Lambda, DHAR, and Tau. The majority of the PavGST genes had a relatively well-maintained exon-intron and motif arrangement within the same group, according to gene structure and motif analyses. Gene structure (introns-exons) and conserved motif analysis revealed that the majority of the PavGST genes showed a relatively well-maintained motif and exons-introns configuration within the same group. The chromosomal localization, GO enrichment annotation, subcellular localization, syntenic relationship, Ka/Ks analysis, and molecular characteristics were accomplished using various bioinformatics tools. Mode of gene duplication showed that dispersed duplication might play a key role in the expansion of PavGST gene family. Promoter regions of PavGST genes contain numerous cis-regulatory components, which are involved in multiple stress responses, such as abiotic stress and phytohormones responsive factors. Furthermore, the expression profile of sweet cherry PavGSTs showed significant results under LED treatment. Our findings provide the groundwork for future research into induced LED anthocyanin and antioxidants deposition in sweet cherries.
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Affiliation(s)
- Irfan Ali Sabir
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | | | - Iftikhar Hussain Shah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Xunju Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Songtao Jiu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Jiyuan Wang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Muhammad Abdullah
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Caixi Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Caixi Zhang,
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8
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Manzoor MA, Li G, Abdullah M, Han W, Wenlong H, Yang Z, Xinya W, Yu Z, Xiaofeng F, Qing J, Shafique MS, Cai Y. Genome-wide investigation and comparative analysis of MATE gene family in Rosaceae species and their regulatory role in abiotic stress responses in Chinese pear (Pyrus bretschneideri). PHYSIOLOGIA PLANTARUM 2021; 173:1163-1178. [PMID: 34363225 DOI: 10.1111/ppl.13511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 06/18/2021] [Accepted: 07/21/2021] [Indexed: 05/12/2023]
Abstract
The Multidrug and Toxic Compound Extrusion (MATE) protein belongs to a secondary transporter gene family, which plays a primary role in transporting many kinds of substrates such as organic compounds, secondary metabolites, and phytohormones. MATE protein members exist in both prokaryotes and eukaryotes. However, evolution and comprehensive analysis of the MATE genes has not been performed in Rosaceae species. In the present study, a total of 404 MATEs genes were identified from six Rosaceae genomes (Prunus avium, Pyrus bretschneideri, Prunus persica, Fragaria vesca, Prunus mume, and Malus domestica) and classified into eight main subfamilies (I-VII) based on structural and phylogenetic analysis. Microcollinearity analysis showed that whole-genome duplication events might play a vital role in the expansion of the MATE genes family. The Ka/Ks analysis, chromosomal localization, subcellular localization, and molecular characteristics (length, weight, and pI) were performed using various bioinformatics tools. Furthermore, different subfamilies have different introns-exons structures, cis-acting elements, and conserved motifs analysis, indicating functional divergence in the MATE family. Subsequently, RNA-seq analysis and real-time qRT-PCR were conducted during Chinese pear fruit development. Moreover, PbMATE genes were significantly expressed under hormonal treatments of MeJA (methyl jasmonate), SA (salicylic acid), and ABA (abscisic acid). Overall, our results provide helpful insights into the functions, expansion complexity, and evolutions of the MATE genes in Chinese pear and five Rosaceae species.
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Affiliation(s)
| | - Guohui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wang Han
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Han Wenlong
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhang Yang
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Wang Xinya
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Zhao Yu
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Feng Xiaofeng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Jin Qing
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | | | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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9
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Gilbert KJ, Renner T. Acid or base? How do plants regulate the ecology of their phylloplane? AOB PLANTS 2021; 13:plab032. [PMID: 34285793 PMCID: PMC8286713 DOI: 10.1093/aobpla/plab032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/25/2021] [Indexed: 05/29/2023]
Abstract
Plants interface with and modify the external environment across their surfaces, and in so doing, can control or mitigate the impacts of abiotic stresses and also mediate their interactions with other organisms. Botanically, it is known that plant roots have a multi-faceted ability to modify rhizosphere conditions like pH, a factor with a large effect on a plant's biotic interactions with microbes. But plants can also modify pH levels on the surfaces of their leaves. Plants can neutralize acid rain inputs in a period of hours, and either acidify or alkalinize the pH of neutral water droplets in minutes. The pH of the phylloplane-that is, the outermost surface of the leaf-varies across species, from incredibly acidic (carnivorous plants: as low as pH 1) to exceptionally alkaline (species in the plant family, Malvaceae, up to pH 11). However, most species mildly acidify droplets on the phylloplane by 1.5 orders of magnitude in pH. Just as rhizosphere pH helps shape the plant microbiome and is known to influence belowground interactions, so too can phylloplane pH influence aboveground interactions in plant canopies. In this review, we discuss phylloplane pH regulation from the physiological, molecular, evolutionary, and ecological perspectives and address knowledge gaps and identify future research directions.
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Affiliation(s)
- Kadeem J Gilbert
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA 16802, USA
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA 16802, USA
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10
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Sun N, Xie YF, Wu Y, Guo N, Li DH, Gao JS. Genome-wide identification of ABCC gene family and their expression analysis in pigment deposition of fiber in brown cotton (Gossypium hirsutum). PLoS One 2021; 16:e0246649. [PMID: 33961624 PMCID: PMC8104370 DOI: 10.1371/journal.pone.0246649] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/25/2021] [Indexed: 11/20/2022] Open
Abstract
ABC (ATP-binding cassette) transporters are a class of superfamily transmembrane proteins that are commonly observed in natural organisms. The ABCC (ATP-binding cassette C subfamily) protein belongs to a subfamily of the ABC protein family and is a multidrug resistance-associated transporter that localizes to the tonoplast and plays a significant role in pathogenic microbial responses, heavy metal regulation, secondary metabolite transport, and plant growth. Recent studies have shown that the ABCC protein is also involved in the transport of anthocyanins/proanthocyanidins (PAs). To clarify the types and numbers of ABCC genes involved in PA transport in Gossypium hirsutum, the phylogenetic evolution, physical location, and structure of ABCC genes were classified by bioinformatic methods in the upland cotton genome, and the expression levels of these genes were analyzed at different developmental stages of the cotton fiber. The results showed that 42 ABCC genes were initially identified in the whole genome of upland cotton; they were designated GhABCC1-42. The gene structure and phylogenetic analysis showed that the closely related ABCC genes were structurally identical. The analysis of chromosomal localization demonstrated that there were no ABCC genes on the chromosomes of AD/At2, AD/At5, AD/At6, AD/At10, AD/At12, AD/At13, AD/Dt2, AD/Dt6, AD/Dt10, and AD/Dt13. Outside the genes, there were ABCC genes on other chromosomes, and gene clusters appeared on the two chromosomes AD/At11 and AD/Dt8. Phylogenetic tree analysis showed that some ABCC proteins in G. hirsutum were clustered with those of Arabidopsis thaliana, Vitis vinifera and Zea mays, which are known to function in anthocyanin/PA transport. The protein structure prediction indicated that the GhABCC protein structure is similar to the AtABCC protein in A. thaliana, and most of these proteins have a transmembrane domain. At the same time, a quantitative RT-PCR analysis of 42 ABCC genes at different developmental stages of brown cotton fiber showed that the relative expression levels of GhABCC24, GhABCC27, GhABCC28, GhABCC29 and GhABCC33 were consistent with the trend of PA accumulation, which may play a role in PA transport. These results provide a theoretical basis for further analysis of the function of the cotton ABCC genes and their role in the transport of PA.
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Affiliation(s)
- Na Sun
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
| | - Yong-Fei Xie
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
| | - Yong Wu
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
| | - Ning Guo
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
| | - Da-Hui Li
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
| | - Jun-Shan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, PR China
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11
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Plasma Membrane H +-ATPase SmPHA4 Negatively Regulates the Biosynthesis of Tanshinones in Salvia miltiorrhiza. Int J Mol Sci 2021; 22:ijms22073353. [PMID: 33805926 PMCID: PMC8037235 DOI: 10.3390/ijms22073353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 11/17/2022] Open
Abstract
Salvia miltiorrhiza Bunge has been widely used in the treatment of cardiovascular and cerebrovascular diseases, due to the pharmacological action of its active components such as the tanshinones. Plasma membrane (PM) H+-ATPase plays key roles in numerous physiological processes in plants. However, little is known about the PM H+-ATPase gene family in S. miltiorrhiza (Sm). Here, nine PM H+-ATPase isoforms were identified and named SmPHA1-SmPHA9. Phylogenetic tree analysis showed that the genetic distance of SmPHAs was relatively far in the S. miltiorrhiza PM H+-ATPase family. Moreover, the transmembrane structures were rich in SmPHA protein. In addition, SmPHA4 was found to be highly expressed in roots and flowers. HPLC revealed that accumulation of dihydrotanshinone (DT), cryptotanshinone (CT), and tanshinone I (TI) was significantly reduced in the SmPHA4-OE lines but was increased in the SmPHA4-RNAi lines, ranging from 2.54 to 3.52, 3.77 to 6.33, and 0.35 to 0.74 mg/g, respectively, suggesting that SmPHA4 is a candidate regulator of tanshinone metabolites. Moreover, qRT-PCR confirmed that the expression of tanshinone biosynthetic-related key enzymes was also upregulated in the SmPHA4-RNAi lines. In summary, this study highlighted PM H+-ATPase function and provided new insights into regulatory candidate genes for modulating secondary metabolism biosynthesis in S. miltiorrhiza.
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Zhang Y, Li Q, Xu L, Qiao X, Liu C, Zhang S. Comparative analysis of the P-type ATPase gene family in seven Rosaceae species and an expression analysis in pear (Pyrus bretschneideri Rehd.). Genomics 2020; 112:2550-2563. [PMID: 32057915 DOI: 10.1016/j.ygeno.2020.02.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 10/25/2022]
Abstract
P-type ATPases are integral membrane transporters that play important roles in transmembrane transport in plants. However, a comprehensive analysis of the P-type ATPase gene family has not been conducted in Chinese white pear (Pyrus bretschneideri) or other Rosaceae species. Here, we identified 419 P-type ATPase genes from seven Rosaceae species (Pyrus bretschneideri, Malus domestica, Prunus persica, Fragaria vesca, Prunus mume, Pyrus communis and Pyrus betulifolia). Structural and phylogenetic analyses revealed that P-type ATPase genes can be divided into five subfamilies. Different subfamilies have different conserved motifs and cis-acting elements, which may lead to functional divergence within one gene family. Dispersed duplication and whole-genome duplication may play critical roles in the expansion of the P-type ATPase family. Purifying selection was the primary force driving the evolution of P-type ATPase family genes. Based on the dynamic transcriptome analysis and transient transformation of Chinese white pear fruit, Pbr029767.1 in the P3A subfamily were found to be associated with malate accumulation during pear fruit development. Using a co-expression network, we identified several transcription factors that may have regulatory relationships with the P-type ATPase gene family. Overall, this study lays a solid foundation for understanding the evolution and functions of P-type ATPase genes in Chinese white pear and six other Rosaceae species.
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Affiliation(s)
- Yuxin Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qionghou Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Linlin Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xin Qiao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunxin Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
| | - Shaoling Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology Research, Nanjing Agricultural University, Nanjing 210095, China.
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13
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Abdullah M, Cheng X, Cao Y, Su X, Manzoor MA, Gao J, Cai Y, Lin Y. Zinc Finger-Homeodomain Transcriptional Factors (ZHDs) in Upland Cotton ( Gossypium hirsutum): Genome-Wide Identification and Expression Analysis in Fiber Development. Front Genet 2018; 9:357. [PMID: 30356782 PMCID: PMC6189526 DOI: 10.3389/fgene.2018.00357] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 08/20/2018] [Indexed: 11/13/2022] Open
Abstract
Zinc finger-homeodomain (ZHD) genes encode a family of plant-specific transcription factors that not only participate in the regulation of plant growth and development but also play an important role in the response to abiotic stress. The ZHD gene family has been studied in several model plants, including Solanum lycopersicum, Zea mays, Oryza sativa, and Arabidopsis thaliana. However, a comprehensive study of the genes of the ZHD family and their roles in fiber development and pigmentation in upland cotton has not been completed. To address this gap, we selected a brown fiber cultivar for our study; brown color in cotton is one of the most desired colors in the textile industry. The natural colored fibers require less processing and little dying, thereby eliminating dye costs and chemical residues. Using bioinformatics approaches, we identified 37 GhZHD genes from Gossypium hirsutum and then divided these genes into seven groups based on their phylogeny. The GhZHD genes were mostly conserved in each subfamily with minor variations in motif distribution and gene structure. These genes were largely distributed on 19 of the 26 upland cotton chromosomes. Among the Gossypium genomes, the paralogs and orthologs of the GhZHD genes were identified and further characterized. Furthermore, among the paralogs, we observed that the ZHD family duplications in Gossypium genomes (G. hirsutum, G. arboreum, and G. raimondii) were probably derived from segmental duplication or genome-wide duplication (GWD) events. Through a combination of qRT-PCR and proanthocyanidins (PA) accumulation analyses in brown cotton fibers, we concluded that the candidate genes involved in early fiber development and fiber pigment synthesis include the following: GhZHD29, GhZHD35, GhZHD30, GhZHD31, GhZHD11, GhZHD27, GhZHD18, GhZHD15, GhZHD16, GhZHD22, GhZHD6, GhZHD33, GhZHD13, GhZHD5, and GhZHD23. This study delivers insights into the evolution of the GhZHD genes in brown cotton, serves as a valuable resource for further studies, and identifies the conditions necessary for improving the quality of brown cotton fiber.
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Affiliation(s)
- Muhammad Abdullah
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xi Cheng
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yunpeng Cao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Xueqiang Su
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | | | - Junshan Gao
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Yi Lin
- School of Life Sciences, Anhui Agricultural University, Hefei, China
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