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Zhao J, Yu X, Zhang C, Hou L, Wu N, Zhang W, Wang Y, Yao B, Delaplace P, Tian J. Harnessing microbial interactions with rice: Strategies for abiotic stress alleviation in the face of environmental challenges and climate change. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168847. [PMID: 38036127 DOI: 10.1016/j.scitotenv.2023.168847] [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: 08/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 12/02/2023]
Abstract
Rice, which feeds more than half of the world's population, confronts significant challenges due to environmental and climatic changes. Abiotic stressors such as extreme temperatures, drought, heavy metals, organic pollutants, and salinity disrupt its cellular balance, impair photosynthetic efficiency, and degrade grain quality. Beneficial microorganisms from rice and soil microbiomes have emerged as crucial in enhancing rice's tolerance to these stresses. This review delves into the multifaceted impacts of these abiotic stressors on rice growth, exploring the origins of the interacting microorganisms and the intricate dynamics between rice-associated and soil microbiomes. We highlight their synergistic roles in mitigating rice's abiotic stresses and outline rice's strategies for recruiting these microorganisms under various environmental conditions, including the development of techniques to maximize their benefits. Through an in-depth analysis, we shed light on the multifarious mechanisms through which microorganisms fortify rice resilience, such as modulation of antioxidant enzymes, enhanced nutrient uptake, plant hormone adjustments, exopolysaccharide secretion, and strategic gene expression regulation, emphasizing the objective of leveraging microorganisms to boost rice's stress tolerance. The review also recognizes the growing prominence of microbial inoculants in modern rice cultivation for their eco-friendliness and sustainability. We discuss ongoing efforts to optimize these inoculants, providing insights into the rigorous processes involved in their formulation and strategic deployment. In conclusion, this review emphasizes the importance of microbial interventions in bolstering rice agriculture and ensuring its resilience in the face of rising environmental challenges.
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Affiliation(s)
- Jintong Zhao
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium; Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiaoxia Yu
- School of Water Resources & Environmental Engineering, East China University of Technology, Nanchang, Jiangxi 330000, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Sanya Institute, Hainan, Academy of Agricultural Sciences, Sanya 572000, China
| | - Ligang Hou
- Rice Research Institute, Jilin Academy of Agricultural Sciences, Gongzhuling, Jilin 136100, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuan Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bin Yao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Pierre Delaplace
- Gembloux Agro-Bio Tech, University of Liege, TERRA - Teaching & Research Center, Plant Sciences, 5030 Gembloux, Belgium
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Zhao Y, Yin T, Ran X, Liu W, Shen Y, Guo H, Peng Y, Zhang C, Ding Y, Tang S. Stimulus-responsive proteins involved in multi-process regulation of storage substance accumulation during rice grain filling under elevated temperature. BMC PLANT BIOLOGY 2023; 23:547. [PMID: 37936114 PMCID: PMC10631114 DOI: 10.1186/s12870-023-04563-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The intensified global warming during grain filling deteriorated rice quality, in particular increasing the frequency of chalky grains which markedly impact market value. The formation of rice quality is a complex process influenced by multiple genes, proteins and physiological metabolic processes. Proteins responsive to stimulus can adjust the ability of plants to respond to unfavorable environments, which may be an important protein involved in the regulation of quality formation under elevated temperature. However, relatively few studies have hindered our further understanding of rice quality formation under elevated temperature. RESULTS We conducted the actual field elevated temperature experiment and performed proteomic analysis of rice grains at the early stage of grain filling. Starting with the response to stimulus in GO annotation, 22 key proteins responsive to stimulus were identified in the regulation of grain filling and response to elevated temperature. Among the proteins responsive to stimulus, during grain filling, an increased abundance of signal transduction and other stress response proteins, a decreased abundance of reactive oxygen species-related proteins, and an increased accumulation of storage substance metabolism proteins consistently contributed to grain filling. However, the abundance of probable indole-3-acetic acid-amido synthetase GH3.4, probable indole-3-acetic acid-amido synthetase GH3.8 and CBL-interacting protein kinase 9 belonged to signal transduction were inhibited under elevated temperature. In the reactive oxygen species-related protein, elevated temperature increased the accumulation of cationic peroxidase SPC4 and persulfide dioxygenase ETHE1 homolog to maintain normal physiological homeostasis. The increased abundance of alpha-amylase isozyme 3E and seed allergy protein RA5 was related to the storage substance metabolism, which regulated starch and protein accumulation under elevated temperature. CONCLUSION Auxin synthesis and calcium signal associated with signal transduction, other stress responses, protein transport and modification, and reactive oxygen species-related proteins may be key proteins responsive to stimulus in response to elevated temperature. Alpha-amylase isozyme 3E and seed allergy protein RA5 may be the key proteins to regulate grain storage substance accumulation and further influence quality under elevated temperature. This study enriched the regulatory factors involved in the response to elevated temperature and provided a new idea for a better understanding of grain response to temperature.
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Affiliation(s)
- Yufei Zhao
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Tongyang Yin
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Xuan Ran
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Wenzhe Liu
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yingying Shen
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Hao Guo
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yuxuan Peng
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Chen Zhang
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
| | - Yanfeng Ding
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, 210095, Nanjing, People's Republic of China
| | - She Tang
- College of Agronomy, Nanjing Agricultural University, 210095, Nanjing, People's Republic of China.
- Jiangsu Collaborative Innovation Center for Modern Crop Production, 210095, Nanjing, People's Republic of China.
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Habibpourmehraban F, Wu Y, Masoomi-Aladizgeh F, Amirkhani A, Atwell BJ, Haynes PA. Pre-Treatment of Rice Plants with ABA Makes Them More Tolerant to Multiple Abiotic Stress. Int J Mol Sci 2023; 24:ijms24119628. [PMID: 37298579 DOI: 10.3390/ijms24119628] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Multiple abiotic stress is known as a type of environmental unfavourable condition maximizing the yield and growth gap of crops compared with the optimal condition in both natural and cultivated environments. Rice is the world's most important staple food, and its production is limited the most by environmental unfavourable conditions. In this study, we investigated the pre-treatment of abscisic acid (ABA) on the tolerance of the IAC1131 rice genotype to multiple abiotic stress after a 4-day exposure to combined drought, salt and extreme temperature treatments. A total of 3285 proteins were identified and quantified across the four treatment groups, consisting of control and stressed plants with and without pre-treatment with ABA, with 1633 of those proteins found to be differentially abundant between groups. Compared with the control condition, pre-treatment with the ABA hormone significantly mitigated the leaf damage against combined abiotic stress at the proteome level. Furthermore, the application of exogenous ABA did not affect the proteome profile of the control plants remarkably, while the results were different in stress-exposed plants by a greater number of proteins changed in abundance, especially those which were increased. Taken together, these results suggest that exogenous ABA has a potential priming effect for enhancing the rice seedlings' tolerance against combined abiotic stress, mainly by affecting stress-responsive mechanisms dependent on ABA signalling pathways in plants.
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Affiliation(s)
- Fatemeh Habibpourmehraban
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Yunqi Wu
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Ardeshir Amirkhani
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW 2109, Australia
| | - Brian J Atwell
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- School of Natural Sciences, Macquarie University, North Ryde, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, North Ryde, NSW 2109, Australia
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Kausar R, Wang X, Komatsu S. Crop Proteomics under Abiotic Stress: From Data to Insights. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212877. [PMID: 36365330 PMCID: PMC9657731 DOI: 10.3390/plants11212877] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 10/09/2022] [Accepted: 10/22/2022] [Indexed: 06/09/2023]
Abstract
Food security is a major challenge in the present world due to erratic weather and climatic changes. Environmental stress negatively affects plant growth and development which leads to reduced crop yields. Technological advancements have caused remarkable improvements in crop-breeding programs. Proteins have an indispensable role in developing stress resilience and tolerance in crops. Genomic and biotechnological advancements have made the process of crop improvement more accurate and targeted. Proteomic studies provide the information required for such targeted approaches. The crosstalk among cellular components is being analyzed by subcellular proteomics. Additionally, the functional diversity of proteins is being unraveled by post-translational modifications during abiotic stress. The exploration of precise cellular responses and the networking among different cellular organelles help in the prediction of signaling pathways and protein-protein interactions. High-throughput mass-spectrometry-based protein studies are now possible due to incremental advancements in mass-spectrometry techniques, sample protocols, and bioinformatic tools as well as the increasing availability of plant genome sequence information for multiple species. In this review, the key role of proteomic analysis in identifying the abiotic-stress-responsive mechanisms in various crops was summarized. The development and availability of advanced computational tools were discussed in detail. The highly variable protein responses among different crops have provided a wide avenue for molecular-marker-assisted genetic buildup studies to develop smart, high-yielding, and stress-tolerant varieties to cope with food-security challenges.
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Affiliation(s)
- Rehana Kausar
- Department of Botany, University of Azad Jammu and Kashmir, Muzaffarabad 13100, Pakistan
| | - Xin Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan
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5
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Marques I, Rodrigues AP, Gouveia D, Lidon FC, Martins S, Semedo MC, Gaillard JC, Pais IP, Semedo JN, Scotti-Campos P, Reboredo FH, Partelli FL, DaMatta FM, Armengaud J, Ribeiro-Barros AI, Ramalho JC. High-resolution shotgun proteomics reveals that increased air [CO 2] amplifies the acclimation response of coffea species to drought regarding antioxidative, energy, sugar, and lipid dynamics. JOURNAL OF PLANT PHYSIOLOGY 2022; 276:153788. [PMID: 35944291 DOI: 10.1016/j.jplph.2022.153788] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 06/15/2023]
Abstract
As drought threatens crop productivity it is crucial to characterize the defense mechanisms against water deficit and unveil their interaction with the expected rise in the air [CO2]. For that, plants of Coffea canephora cv. Conilon Clone 153 (CL153) and C. arabica cv. Icatu grown under 380 (aCO2) or 700 μL L-1 (eCO2) were exposed to moderate (MWD) and severe (SWD) water deficits. Responses were characterized through the activity and/or abundance of a selected set of proteins associated with antioxidative (e.g., Violaxanthin de-epoxidase, Superoxide dismutase, Ascorbate peroxidases, Monodehydroascorbate reductase), energy/sugar (e.g., Ferredoxin-NADP reductase, NADP-dependent glyceraldehyde-3-phosphate dehydrogenase, sucrose synthase, mannose-6-phosphate isomerase, Enolase), and lipid (Lineolate 13S-lipoxygenase) processes, as well as with other antioxidative (ascorbate) and protective (HSP70) molecules. MWD caused small changes in both genotypes regardless of [CO2] level while under the single imposition to SWD, only Icatu showed a global reinforcement of most studied proteins supporting its tolerance to drought. eCO2 alone did not promote remarkable changes but strengthened a robust multi-response under SWD, even supporting the reversion of impacts already observed by CL153 at aCO2. In the context of climate changes where water constraints and [CO2] levels are expected to increase, these results highlight why eCO2 might have an important role in improving drought tolerance in Coffea species.
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Affiliation(s)
- Isabel Marques
- PlantStress & Biodiversity Lab., Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. da República, 2784-505 Oeiras, and Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Ana P Rodrigues
- PlantStress & Biodiversity Lab., Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. da República, 2784-505 Oeiras, and Tapada da Ajuda, 1349-017, Lisboa, Portugal.
| | - Duarte Gouveia
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-F-30200, Bagnols-sur-Cèze, France.
| | - Fernando C Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal.
| | - Sónia Martins
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal; Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.
| | - Magda C Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal; Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.
| | - Jean-Charles Gaillard
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-F-30200, Bagnols-sur-Cèze, France.
| | - Isabel P Pais
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal; Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Quinta do Marquês, Av. República, 2784-505, Oeiras, Portugal.
| | - José N Semedo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal; Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Quinta do Marquês, Av. República, 2784-505, Oeiras, Portugal.
| | - Paula Scotti-Campos
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal; Unid. Investigação em Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P. (INIAV), Quinta do Marquês, Av. República, 2784-505, Oeiras, Portugal.
| | - Fernando H Reboredo
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516, Caparica, Portugal.
| | - Fábio L Partelli
- Centro Univ. Norte do Espírito Santo (CEUNES), Dept. Ciências Agrárias e Biológicas (DCAB), Univ. Federal Espírito Santo (UFES), Rod. BR 101 Norte, Km. 60, Bairro Litorâneo, CEP: 29932-540, São Mateus, ES, Brazil.
| | - Fábio M DaMatta
- Dept. Biologia Vegetal, Univ. Federal Viçosa (UFV), 36570-000, Viçosa, MG, Brazil.
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, F-F-30200, Bagnols-sur-Cèze, France.
| | - Ana I Ribeiro-Barros
- PlantStress & Biodiversity Lab., Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. da República, 2784-505 Oeiras, and Tapada da Ajuda, 1349-017, Lisboa, Portugal; Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.
| | - José C Ramalho
- PlantStress & Biodiversity Lab., Centro de Estudos Florestais (CEF), Dept. Recursos Naturais, Ambiente e Território (DRAT), Instituto Superior de Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. da República, 2784-505 Oeiras, and Tapada da Ajuda, 1349-017, Lisboa, Portugal; Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007, Lisboa, Portugal.
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Masoomi‐Aladizgeh F, Kamath KS, Haynes PA, Atwell BJ. Genome survey sequencing of wild cotton (Gossypium robinsonii) reveals insights into proteomic responses of pollen to extreme heat. PLANT, CELL & ENVIRONMENT 2022; 45:1242-1256. [PMID: 35092006 PMCID: PMC9415111 DOI: 10.1111/pce.14268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Heat stress specifically affects fertility by impairing pollen viability but cotton wild relatives successfully reproduce in hot savannas where they evolved. An Australian arid-zone cotton (Gossypium robinsonii) was exposed to heat events during pollen development then mature pollen was subjected to deep proteomic analysis using 57 023 predicted genes from a genomic database we assembled for the same species. Three stages of pollen development, including tetrads (TEs), uninucleate microspores (UNs) and binucleate microspores (BNs) were exposed to 36°C or 40°C for 5 days and the resulting mature pollen was collected at anthesis (p-TE, p-UN and p-BN, respectively). Using the sequential windowed acquisition of all theoretical mass spectra proteomic analysis, 2704 proteins were identified and quantified across all pollen samples analysed. Proteins predominantly decreased in abundance at all stages in response to heat, particularly after exposure of TEs to 40°C. Functional enrichment analyses demonstrated that extreme heat increased the abundance of proteins that contributed to increased messenger RNA splicing via spliceosome, initiation of cytoplasmic translation and protein refolding in p-TE40. However, other functional categories that contributed to intercellular transport were inhibited in p-TE40, linked potentially to Rab proteins. We ascribe the resilience of reproductive processes in G. robinsonii at temperatures up to 40°C, relative to commercial cotton, to a targeted reduction in protein transport.
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Affiliation(s)
| | | | - Paul A. Haynes
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
| | - Brian J. Atwell
- School of Natural SciencesMacquarie UniversityNorth RydeNew South WalesAustralia
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7
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Multiple Abiotic Stresses Applied Simultaneously Elicit Distinct Responses in Two Contrasting Rice Cultivars. Int J Mol Sci 2022; 23:ijms23031739. [PMID: 35163659 PMCID: PMC8836074 DOI: 10.3390/ijms23031739] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
Rice crops are often subject to multiple abiotic stresses simultaneously in both natural and cultivated environments, resulting in yield reductions beyond those expected from single stress. We report physiological changes after a 4 day exposure to combined drought, salt and extreme temperature treatments, following a 2 day salinity pre-treatment in two rice genotypes—Nipponbare (a paddy rice) and IAC1131 (an upland landrace). Stomata closed after two days of combined stresses, causing intercellular CO2 concentrations and assimilation rates to diminish rapidly. Abscisic acid (ABA) levels increased at least five-fold but did not differ significantly between the genotypes. Tandem Mass Tag isotopic labelling quantitative proteomics revealed 6215 reproducibly identified proteins in mature leaves across the two genotypes and three time points (0, 2 and 4 days of stress). Of these, 987 were differentially expressed due to stress (cf. control plants), including 41 proteins that changed significantly in abundance in all stressed plants. Heat shock proteins, late embryogenesis abundant proteins and photosynthesis-related proteins were consistently responsive to stress in both Nipponbare and IAC1131. Remarkably, even after 2 days of stress there were almost six times fewer proteins differentially expressed in IAC1131 than Nipponbare. This contrast in the translational response to multiple stresses is consistent with the known tolerance of IAC1131 to dryland conditions.
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Zargar SM, Mir RA, Ebinezer LB, Masi A, Hami A, Manzoor M, Salgotra RK, Sofi NR, Mushtaq R, Rohila JS, Rakwal R. Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. FRONTIERS IN PLANT SCIENCE 2022; 12:803603. [PMID: 35154193 PMCID: PMC8829427 DOI: 10.3389/fpls.2021.803603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Drought differs from other natural disasters in several respects, largely because of the complexity of a crop's response to it and also because we have the least understanding of a crop's inductive mechanism for addressing drought tolerance among all abiotic stressors. Overall, the growth and productivity of crops at a global level is now thought to be an issue that is more severe and arises more frequently due to climatic change-induced drought stress. Among the major crops, rice is a frontline staple cereal crop of the developing world and is critical to sustaining populations on a daily basis. Worldwide, studies have reported a reduction in rice productivity over the years as a consequence of drought. Plants are evolutionarily primed to withstand a substantial number of environmental cues by undergoing a wide range of changes at the molecular level, involving gene, protein and metabolite interactions to protect the growing plant. Currently, an in-depth, precise and systemic understanding of fundamental biological and cellular mechanisms activated by crop plants during stress is accomplished by an umbrella of -omics technologies, such as transcriptomics, metabolomics and proteomics. This combination of multi-omics approaches provides a comprehensive understanding of cellular dynamics during drought or other stress conditions in comparison to a single -omics approach. Thus a greater need to utilize information (big-omics data) from various molecular pathways to develop drought-resilient crop varieties for cultivation in ever-changing climatic conditions. This review article is focused on assembling current peer-reviewed published knowledge on the use of multi-omics approaches toward expediting the development of drought-tolerant rice plants for sustainable rice production and realizing global food security.
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Affiliation(s)
- Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Biosciences and Biotechnology, BGSB University, Rajouri, India
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Ammarah Hami
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Najeebul Rehman Sofi
- Division of Plant Breeding and Genetics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Roohi Mushtaq
- Department of Biotechnology and Bioinformatics, SP College, Cluster University Srinagar, Srinagar, India
| | - Jai Singh Rohila
- Dale Bumpers National Rice Research Center, United States Department of Agriculture (USDA)-Agricultural Research Service (ARS), Stuttgart, AR, United States
| | - Randeep Rakwal
- Faculty of Health and Sport Sciences, University of Tsukuba, Ibaraki, Japan
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Pascual J, Kangasjärvi S. Targeted Mass Spectrometry Analysis of Protein Phosphorylation by Selected Ion Monitoring Coupled to Parallel Reaction Monitoring (tSIM/PRM). Methods Mol Biol 2022; 2526:227-240. [PMID: 35657524 DOI: 10.1007/978-1-0716-2469-2_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent developments in targeted mass spectrometry-based proteomics have provided new methodological solutions for accurate and quantitative analysis of proteins and their posttranslational control, which has significantly advanced our understanding of stress responses in different plant species. Instrumentation allowing high-resolution, accurate-mass (HR/AM) analysis has provided new acquisition strategies for targeted quantitative proteomic analysis by targeted selected ion monitoring (tSIM) and parallel reaction monitoring (PRM). Here we report a sensitive and accurate method for targeted analysis of protein phosphorylation by tSIM coupled to PRM (tSIM/PRM). The tSIM/PRM method takes advantage of HR/AM mass spectrometers and benefits from the combination of highly sensitive precursor ion quantification by tSIM and highly confident peptide identification by spectral library matching in PRM. The detailed protocol describes tSIM/PRM analysis of Arabidopsis thaliana foliar proteins, from the building of a spectral library to sample preparation, mass spectrometry, and data analysis, and provides a methodological approach for specifying the molecular mechanisms of interest.
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Affiliation(s)
- Jesús Pascual
- Molecular Plant Biology, Department of Biochemistry, University of Turku, Turku, Finland
| | - Saijaliisa Kangasjärvi
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, FIN-00014 University of Helsinki, Helsinki, Finland.
- Department of Agricultural Sciences, Faculty of Agriculture and Forestry, FIN-00014 University of Helsinki, Helsinki, Finland.
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10
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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11
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Hamzelou S, Melino VJ, Plett DC, Kamath KS, Nawrocki A, Larsen MR, Atwell BJ, Haynes PA. The phosphoproteome of rice leaves responds to water and nitrogen supply. Mol Omics 2021; 17:706-718. [PMID: 34291261 DOI: 10.1039/d1mo00137j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or excess nitrogen supply, plants employ complex systems for signalling and regulation of metabolic processes. There is limited information on the involvement of one of the most important post-translational modifications (PTMs), protein phosphorylation, in plant adaptation to long-term changes in resource supply. Oryza sativa cv. Nipponbare was grown under two regimes of nitrogen from the time of germination to final harvest. Twenty-five days after germination, water was withheld from half the pots in each nitrogen treatment and low water supply continued for an additional 26 days, while the remaining pots were well watered. Leaves from all four groups of plants were harvested after 51 days in order to test whether phosphorylation of leaf proteins responded to prior abiotic stress events. The dominant impact of these resources is exerted in leaves, where PTMs have been predicted to occur. Proteins were extracted and phosphopeptides were analysed by nanoLC-MS/MS analysis, coupled with label-free quantitation. Water and nitrogen regimes triggered extensive changes in phosphorylation of proteins involved in membrane transport, such as the aquaporin OsPIP2-6, a water channel protein. Our study reveals phosphorylation of several peptides belonging to proteins involved in RNA-processing and carbohydrate metabolism, suggesting that phosphorylation events regulate the signalling cascades that are required to optimize plant response to resource supply.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Vanessa J Melino
- King Abdullah University for Science and Technology, 2955-6990, Kingdom of Saudi Arabia
| | - Darren C Plett
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia. and Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Arkadiusz Nawrocki
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
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12
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Masoomi-Aladizgeh F, Najeeb U, Hamzelou S, Pascovici D, Amirkhani A, Tan DKY, Mirzaei M, Haynes PA, Atwell BJ. Pollen development in cotton (Gossypium hirsutum) is highly sensitive to heat exposure during the tetrad stage. PLANT, CELL & ENVIRONMENT 2021; 44:2150-2166. [PMID: 33047317 DOI: 10.1111/pce.13908] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 05/22/2023]
Abstract
The development of gametes in plants is acutely susceptible to heatwaves as brief as a few days, adversely affecting pollen maturation and reproductive success. Pollen in cotton (Gossypium hirsutum) was differentially affected when tetrad and binucleate stages were exposed to heat, revealing new insights into the interaction between heat and pollen development. Squares were tagged and exposed to 36/25°C (day/night, moderate heat) or 40/30°C (day/night, extreme heat) for 5 days. Mature pollen grains and leaves were collected for physiological and proteomic responses. While photosynthetic competence was not compromised even at 40°C, leaf tissues became leakier. In contrast, pollen grains were markedly smaller after the tetrad stage was exposed to 40°C and boll production was reduced by 65%. Sugar levels in pollen grains were elevated after exposure to heat, eliminating carbohydrate deficits as a likely cause of poor reproductive capacity. Proteomic analysis of pure pollen samples revealed a particularly high abundance of 70-kDa heat shock (Hsp70s) and cytoskeletal proteins. While short-term bursts of heat had a minor impact on leaves, male gametophyte development was profoundly damaged. Cotton acclimates to maxima of 36°C at both the vegetative and reproductive stages but 5-days exposure to 40°C significantly impairs reproductive development.
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Affiliation(s)
| | - Ullah Najeeb
- Queensland Alliance for Agriculture & Food Innovation, The University of Queensland, Toowoomba, Australia
| | - Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Ardeshir Amirkhani
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Daniel K Y Tan
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Plant Breeding Institute, Sydney Institute of Agriculture, Sydney, New South Wales, Australia
| | - Mehdi Mirzaei
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, New South Wales, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, New South Wales, Australia
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, New South Wales, Australia
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13
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Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
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Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
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14
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Hamzelou S, Kamath KS, Masoomi-Aladizgeh F, Johnsen MM, Atwell BJ, Haynes PA. Wild and Cultivated Species of Rice Have Distinctive Proteomic Responses to Drought. Int J Mol Sci 2020; 21:ijms21175980. [PMID: 32825202 PMCID: PMC7504292 DOI: 10.3390/ijms21175980] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/25/2022] Open
Abstract
Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Farhad Masoomi-Aladizgeh
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Matthew M. Johnsen
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
| | - Brian J. Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (F.M.-A.); (B.J.A.)
| | - Paul A. Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia; (S.H.); (K.S.K.); (M.M.J.)
- Correspondence:
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15
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Metabolomics: A Tool for Cultivar Phenotyping and Investigation of Grain Crops. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10060831] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The quality of plants is often enhanced for diverse purposes such as improved resistance to environmental pressures, better taste, and higher yields. Considering the world’s dependence on plants (nutrition, medicine, or biofuel), developing new cultivars with superior characteristics is of great importance. As part of the ‘omics’ approaches, metabolomics has been employed to investigate the large number of metabolites present in plant systems under well-defined environmental conditions. Recent advances in the metabolomics field have greatly expanded our understanding of plant metabolism, largely driven by potential application to agricultural systems. The current review presents the workflow for plant metabolome analyses, current knowledge, and future directions of such research as determinants of cultivar phenotypes. Furthermore, the value of metabolome analyses in contemporary crop science is illustrated. Here, metabolomics has provided valuable information in research on grain crops and identified significant biomarkers under different conditions and/or stressors. Moreover, the value of metabolomics has been redefined from simple biomarker identification to a tool for discovering active drivers involved in biological processes. We illustrate and conclude that the rapid advances in metabolomics are driving an explosion of information that will advance modern breeding approaches for grain crops and address problems associated with crop productivity and sustainable agriculture.
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