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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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Jin T, An J, Xu H, Chen J, Pan L, Zhao R, Wang N, Gai J, Li Y. A soybean sodium/hydrogen exchanger GmNHX6 confers plant alkaline salt tolerance by regulating Na +/K + homeostasis. FRONTIERS IN PLANT SCIENCE 2022; 13:938635. [PMID: 36204047 PMCID: PMC9531905 DOI: 10.3389/fpls.2022.938635] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Alkaline soil has a high pH due to carbonate salts and usually causes more detrimental effects on crop growth than saline soil. Sodium hydrogen exchangers (NHXs) are pivotal regulators of cellular Na+/K+ and pH homeostasis, which is essential for salt tolerance; however, their role in alkaline salt tolerance is largely unknown. Therefore, in this study, we investigated the function of a soybean NHX gene, GmNHX6, in plant response to alkaline salt stress. GmNHX6 encodes a Golgi-localized sodium/hydrogen exchanger, and its transcript abundance is more upregulated in alkaline salt tolerant soybean variety in response to NaHCO3 stress. Ectopic expression of GmNHX6 in Arabidopsis enhanced alkaline salt tolerance by maintaining high K+ content and low Na+/K+ ratio. Overexpression of GmNHX6 also improved soybean tolerance to alkaline salt stress. A single nucleotide polymorphism in the promoter region of NHX6 is associated with the alkaline salt tolerance in soybean germplasm. A superior promoter of GmNHX6 was isolated from an alkaline salt tolerant soybean variety, which showed stronger activity than the promoter from an alkaline salt sensitive soybean variety in response to alkali stress, by luciferase transient expression assays. Our results suggested soybean NHX6 gene plays an important role in plant tolerance to alkaline salt stress.
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Solis CA, Yong MT, Zhou M, Venkataraman G, Shabala L, Holford P, Shabala S, Chen ZH. Evolutionary Significance of NHX Family and NHX1 in Salinity Stress Adaptation in the Genus Oryza. Int J Mol Sci 2022; 23:ijms23042092. [PMID: 35216206 PMCID: PMC8879705 DOI: 10.3390/ijms23042092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/28/2022] [Accepted: 02/07/2022] [Indexed: 02/06/2023] Open
Abstract
Rice (Oryza sativa), a staple crop for a substantial part of the world’s population, is highly sensitive to soil salinity; however, some wild Oryza relatives can survive in highly saline environments. Sodium/hydrogen antiporter (NHX) family members contribute to Na+ homeostasis in plants and play a major role in conferring salinity tolerance. In this study, we analyzed the evolution of NHX family members using phylogeny, conserved domains, tertiary structures, expression patterns, and physiology of cultivated and wild Oryza species to decipher the role of NHXs in salt tolerance in Oryza. Phylogenetic analysis showed that the NHX family can be classified into three subfamilies directly related to their subcellular localization: endomembrane, plasma membrane, and tonoplast (vacuolar subfamily, vNHX1). Phylogenetic and structural analysis showed that vNHX1s have evolved from streptophyte algae (e.g., Klebsormidium nitens) and are abundant and highly conserved in all major land plant lineages, including Oryza. Moreover, we showed that tissue tolerance is a crucial trait conferring tolerance to salinity in wild rice species. Higher Na+ accumulation and reduced Na+ effluxes in leaf mesophyll were observed in the salt-tolerant wild rice species O. alta, O. latifolia, and O. coarctata. Among the key genes affecting tissue tolerance, expression of NHX1 and SOS1/NHX7 exhibited significant correlation with salt tolerance among the rice species and cultivars. This study provides insights into the evolutionary origin of plant NHXs and their role in tissue tolerance of Oryza species and facilitates the inclusion of this trait during the development of salinity-tolerant rice cultivars.
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Affiliation(s)
- Celymar Angela Solis
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
| | - Miing-Tiem Yong
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600113, India;
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS 7001, Australia; (M.Z.); (L.S.)
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
- Correspondence: (S.S.); (Z.-H.C.); Tel.: +61-245-701-934 (Z.-H.C.)
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW 2751, Australia; (C.A.S.); (M.-T.Y.); (P.H.)
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW 2751, Australia
- Correspondence: (S.S.); (Z.-H.C.); Tel.: +61-245-701-934 (Z.-H.C.)
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Rajakani R, Sellamuthu G, Ishikawa T, Ahmed HAI, Bharathan S, Kumari K, Shabala L, Zhou M, Chen ZH, Shabala S, Venkataraman G. Reduced apoplastic barriers in tissues of shoot-proximal rhizomes of Oryza coarctata are associated with Na+ sequestration. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:998-1015. [PMID: 34606587 DOI: 10.1093/jxb/erab440] [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: 12/16/2020] [Accepted: 09/25/2021] [Indexed: 06/13/2023]
Abstract
Oryza coarctata is the only wild rice species with significant salinity tolerance. The present work examines the role of the substantial rhizomatous tissues of O. coarctata in conferring salinity tolerance. Transition to an erect phenotype (shoot emergence) from prostrate growth of rhizome tissues is characterized by marked lignification and suberization of supporting sclerenchymatous tissue, epidermis, and bundle sheath cells in aerial shoot-proximal nodes and internodes in O. coarctata. With salinity, however, aerial shoot-proximal internodal tissues show reductions in lignification and suberization, most probably related to re-direction of carbon flux towards synthesis of the osmporotectant proline. Concurrent with hypolignification and reduced suberization, the aerial rhizomatous biomass of O. coarctata appears to have evolved mechanisms to store Na+ in these specific tissues under salinity. This was confirmed by histochemical staining, quantitative real-time reverse transcription-PCR expression patterns of genes involved in lignification/suberization, Na+ and K+ contents of internodal tissues, as well as non-invasive microelectrode ion flux measurements of NaCl-induced net Na+, K+, and H+ flux profiles of aerial nodes were determined. In O. coarctata, aerial proximal internodes appear to act as 'traffic controllers', sending required amounts of Na+ and K+ into developing leaves for osmotic adjustment and turgor-driven growth, while more deeply positioned internodes assume a Na+ buffering/storage role.
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Affiliation(s)
- Raja Rajakani
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
| | - Gothandapani Sellamuthu
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
- Forest Molecular Entomology Laboratory, Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague-16500, Czech Republic
| | - Tetsuya Ishikawa
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
| | - Hassan Ahmed Ibraheem Ahmed
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
- Department of Botany, Faculty of Science, Port Said University, Port Said 42522, Egypt
| | - Subhashree Bharathan
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thirumalaisamudram, Thanjavur-613401, Tamil Nadu, India
| | - Kumkum Kumari
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
| | - Lana Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
| | - Zhong-Hua Chen
- School of Science, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, College of Science and Engineering, University of Tasmania, Private Bag 98, Hobart, Tas 7001, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M.S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai 600 113, India
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Rawat N, Wungrampha S, Singla-Pareek SL, Yu M, Shabala S, Pareek A. Rewilding staple crops for the lost halophytism: Toward sustainability and profitability of agricultural production systems. MOLECULAR PLANT 2022; 15:45-64. [PMID: 34915209 DOI: 10.1016/j.molp.2021.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/10/2021] [Accepted: 12/12/2021] [Indexed: 06/14/2023]
Abstract
Abiotic stress tolerance has been weakened during the domestication of all major staple crops. Soil salinity is a major environmental constraint that impacts over half of the world population; however, given the increasing reliance on irrigation and the lack of available freshwater, agriculture in the 21st century will increasingly become saline. Therefore, global food security is critically dependent on the ability of plant breeders to create high-yielding staple crop varieties that will incorporate salinity tolerance traits and account for future climate scenarios. Previously, we have argued that the current agricultural practices and reliance on crops that exclude salt from uptake is counterproductive and environmentally unsustainable, and thus called for a need for a major shift in a breeding paradigm to incorporate some halophytic traits that were present in wild relatives but were lost in modern crops during domestication. In this review, we provide a comprehensive physiological and molecular analysis of the key traits conferring crop halophytism, such as vacuolar Na+ sequestration, ROS desensitization, succulence, metabolic photosynthetic switch, and salt deposition in trichomes, and discuss the strategies for incorporating them into elite germplasm, to address a pressing issue of boosting plant salinity tolerance.
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Affiliation(s)
- Nishtha Rawat
- Stress Physiology and Molecular Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Silas Wungrampha
- Stress Physiology and Molecular Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology, New Delhi 110067, India
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000, China; Tasmanian Institute for Agriculture, University of Tasmania, Hobart Tas 7001, Australia.
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India; National Agri-Food Biotechnology Institute, Mohali 140306, India.
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6
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Solis CA, Yong MT, Venkataraman G, Milham P, Zhou M, Shabala L, Holford P, Shabala S, Chen ZH. Sodium sequestration confers salinity tolerance in an ancestral wild rice. PHYSIOLOGIA PLANTARUM 2021; 172:1594-1608. [PMID: 33619741 DOI: 10.1111/ppl.13352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 05/27/2023]
Abstract
Wild rice Oryza rufipogon, a progenitor of cultivated rice Oryza sativa L., possesses superior salinity tolerance and is a potential donor for breeding salinity tolerance traits in rice. However, a mechanistic basis of salinity tolerance in this donor species has not been established. Here, we examined salinity tolerance from the early vegetative stage to maturity in O. rufipogon in comparison with a salt-susceptible (Koshihikari) and a salt-tolerant (Reiziq) variety of O. sativa. We assessed their phylogeny and agronomical traits, photosynthetic performance, ion contents, as well as gene expression in response to salinity stress. Salt-tolerant O. rufipogon exhibited efficient leaf photosynthesis and less damage to leaf tissues during the course of salinity treatment. In addition, O. rufipogon showed a significantly higher tissue Na+ accumulation that is achieved by vacuolar sequestration compared to the salt tolerant O. sativa indica subspecies. These findings are further supported by the upregulation of genes involved with ion transport and sequestration (e.g. high affinity K+ transporter 1;4 [HKT1;4], Na+ /H+ exchanger 1 [NHX1] and vacuolar H+ -ATPase c [VHA-c]) in salt-tolerant O. rufipogon as well as by the close phylogenetic relationship of key salt-responsive genes in O. rufipogon to these in salt-tolerant wild rice species such as O. coarctata. Thus, the high accumulation of Na+ in the leaves of O. rufipogon acts as a cheap osmoticum to minimize the high energy cost of osmolyte biosynthesis and excessive reactive oxygen species production. These mechanisms demonstrated that O. rufipogon has important traits that can be used for improving salinity tolerance in cultivated rice.
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Affiliation(s)
- Celymar Angela Solis
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Miing-Tiem Yong
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Gayatri Venkataraman
- Plant Molecular Biology Laboratory, M. S. Swaminathan Research Foundation, III Cross Street, Taramani Institutional Area, Chennai, India
| | - Paul Milham
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Lana Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Paul Holford
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania, Australia
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, New South Wales, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
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Kong M, Luo M, Li J, Feng Z, Zhang Y, Song W, Zhang R, Wang R, Wang Y, Zhao J, Tao Y, Zhao Y. Genome-wide identification, characterization, and expression analysis of the monovalent cation-proton antiporter superfamily in maize, and functional analysis of its role in salt tolerance. Genomics 2021; 113:1940-1951. [PMID: 33895282 DOI: 10.1016/j.ygeno.2021.04.032] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 03/11/2021] [Accepted: 04/19/2021] [Indexed: 11/16/2022]
Abstract
Na+, K+ and pH homeostasis are important for plant life and they are controlled by the monovalent cation proton antiporter (CPA) superfamily. The roles of ZmCPAs in salt tolerance are not fully elucidated. In this study, we identified 35 ZmCPAs comprising 13 Na+/H+ exchangers (ZmNHXs), 16 cation/H+ exchanger (ZmCHXs), and 6 K+ efflux antiporters (ZmKEAs). All ZmCPAs have transmembrane domains and most of them were localized to plasma membrane or tonoplast. ZmCHXs were specifically highly expressed in anthers, while ZmNHXs and ZmKEAs showed high expression in various tissues. ZmNHX5 and ZmKEA2 were up-regulated in maize seedlings under both NaCl and KCl stresses. Yeast complementation experiments revealed the roles of ZmNHX5, ZmKEA2 in NaCl tolerance. Analysis of the maize mutants further validated the salt tolerance functions of ZmNHX5 and ZmKEA2. Our study highlights comprehensive information of ZmCPAs and provides new gene targets for salt tolerance maize breeding.
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Affiliation(s)
- Mengsi Kong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, Hebei, China; Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Meijie Luo
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Jingna Li
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Zhen Feng
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China; Plant Science and Technology College, Beijing University of Agriculture, Beijing 102206, China
| | - Yunxia Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Wei Song
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Ruyang Zhang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Ronghuan Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Yuandong Wang
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China
| | - Jiuran Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China.
| | - Yongsheng Tao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding 071001, Hebei, China.
| | - Yanxin Zhao
- Beijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing 100079, China.
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Ganie SA, Reddy ASN. Stress-Induced Changes in Alternative Splicing Landscape in Rice: Functional Significance of Splice Isoforms in Stress Tolerance. BIOLOGY 2021; 10:309. [PMID: 33917813 PMCID: PMC8068108 DOI: 10.3390/biology10040309] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/20/2022]
Abstract
Improvements in yield and quality of rice are crucial for global food security. However, global rice production is substantially hindered by various biotic and abiotic stresses. Making further improvements in rice yield is a major challenge to the rice research community, which can be accomplished through developing abiotic stress-resilient rice varieties and engineering durable agrochemical-independent pathogen resistance in high-yielding elite rice varieties. This, in turn, needs increased understanding of the mechanisms by which stresses affect rice growth and development. Alternative splicing (AS), a post-transcriptional gene regulatory mechanism, allows rapid changes in the transcriptome and can generate novel regulatory mechanisms to confer plasticity to plant growth and development. Mounting evidence indicates that AS has a prominent role in regulating rice growth and development under stress conditions. Several regulatory and structural genes and splicing factors of rice undergo different types of stress-induced AS events, and the functional significance of some of them in stress tolerance has been defined. Both rice and its pathogens use this complex regulatory mechanism to devise strategies against each other. This review covers the current understanding and evidence for the involvement of AS in biotic and abiotic stress-responsive genes, and its relevance to rice growth and development. Furthermore, we discuss implications of AS for the virulence of different rice pathogens and highlight the areas of further research and potential future avenues to develop climate-smart and disease-resistant rice varieties.
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Affiliation(s)
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA
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Isayenkov SV, Dabravolski SA, Pan T, Shabala S. Phylogenetic Diversity and Physiological Roles of Plant Monovalent Cation/H + Antiporters. FRONTIERS IN PLANT SCIENCE 2020; 11:573564. [PMID: 33123183 PMCID: PMC7573149 DOI: 10.3389/fpls.2020.573564] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/02/2020] [Indexed: 05/23/2023]
Abstract
The processes of plant nutrition, stress tolerance, plant growth, and development are strongly dependent on transport of mineral nutrients across cellular membranes. Plant membrane transporters are key components of these processes. Among various membrane transport proteins, the monovalent cation proton antiporter (CPA) superfamily mediates a broad range of physiological and developmental processes such as ion and pH homeostasis, development of reproductive organs, chloroplast operation, and plant adaptation to drought and salt stresses. CPA family includes plasma membrane-bound Na+/H+ exchanger (NhaP) and intracellular Na+/H+ exchanger NHE (NHX), K+ efflux antiporter (KEA), and cation/H+ exchanger (CHX) family proteins. In this review, we have completed the phylogenetic inventory of CPA transporters and undertaken a comprehensive evolutionary analysis of their development. Compared with previous studies, we have significantly extended the range of plant species, including green and red algae and Acrogymnospermae into phylogenetic analysis. Our data suggest that the multiplication and complexation of CPA isoforms during evolution is related to land colonisation by higher plants and associated with an increase of different tissue types and development of reproductive organs. The new data extended the number of clades for all groups of CPAs, including those for NhaP/SOS, NHE/NHX, KEA, and CHX. We also critically evaluate the latest findings on the biological role, physiological functions and regulation of CPA transporters in relation to their structure and phylogenetic position. In addition, the role of CPA members in plant tolerance to various abiotic stresses is summarized, and the future priority directions for CPA studies in plants are discussed.
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Affiliation(s)
- Stanislav V. Isayenkov
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics NAS of Ukraine, Kyiv, Ukraine
| | - Siarhei A. Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], Vitebsk, Belarus
| | - Ting Pan
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, Australia
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10
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Singh S, Geeta R, Das S. Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator. Gene Expr Patterns 2020; 38:119146. [PMID: 32947048 DOI: 10.1016/j.gep.2020.119146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/26/2020] [Accepted: 09/08/2020] [Indexed: 11/26/2022]
Abstract
Intra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, β-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress.
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Affiliation(s)
- Swati Singh
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - R Geeta
- Department of Botany, University of Delhi, Delhi, 110007, India
| | - Sandip Das
- Department of Botany, University of Delhi, Delhi, 110007, India.
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Subudhi PK, Garcia RS, Coronejo S, Tapia R. Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture. Int J Mol Sci 2020; 21:ijms21165759. [PMID: 32796695 PMCID: PMC7460981 DOI: 10.3390/ijms21165759] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/31/2020] [Accepted: 08/07/2020] [Indexed: 02/02/2023] Open
Abstract
The indiscriminate use of nitrogenous fertilizers continues unabated for commercial crop production, resulting in air and water pollution. The development of rice varieties with enhanced nitrogen use efficiency (NUE) will require a thorough understanding of the molecular basis of a plant’s response to low nitrogen (N) availability. The global expression profiles of root tissues collected from low and high N treatments at different time points in two rice genotypes, Pokkali and Bengal, with contrasting responses to N stress and contrasting root architectures were examined. Overall, the number of differentially expressed genes (DEGs) in Pokkali (indica) was higher than in Bengal (japonica) during low N and early N recovery treatments. Most low N DEGs in both genotypes were downregulated whereas early N recovery DEGs were upregulated. Of these, 148 Pokkali-specific DEGs might contribute to Pokkali’s advantage under N stress. These DEGs included transcription factors and transporters and were involved in stress responses, growth and development, regulation, and metabolism. Many DEGs are co-localized with quantitative trait loci (QTL) related to root growth and development, chlorate-resistance, and NUE. Our findings suggest that the superior growth performance of Pokkali under low N conditions could be due to the genetic differences in a diverse set of genes influencing N uptake through the regulation of root architecture.
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