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Leszczuk A, Kutyrieva-Nowak N, Nowak A, Nosalewicz A, Zdunek A. Low oxygen environment effect on the tomato cell wall composition during the fruit ripening process. BMC PLANT BIOLOGY 2024; 24:503. [PMID: 38840061 PMCID: PMC11155102 DOI: 10.1186/s12870-024-05226-x] [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: 10/13/2023] [Accepted: 05/30/2024] [Indexed: 06/07/2024]
Abstract
BACKGROUND Oxygen concentration is a key characteristic of the fruit storage environment determining shelf life and fruit quality. The aim of the work was to identify cell wall components that are related to the response to low oxygen conditions in fruit and to determine the effects of such conditions on the ripening process. Tomato (Solanum lycopersicum) fruits at different stages of the ripening process were stored in an anoxic and hypoxic environment, at 0% and 5% oxygen concentrations, respectively. We used comprehensive and comparative methods: from microscopic immunolabelling and estimation of enzymatic activities to detailed molecular approaches. Changes in the composition of extensin, arabinogalactan proteins, rhamnogalacturonan-I, low methyl-esterified homogalacturonan, and high methyl-esterified homogalacturonan were analysed. RESULTS In-depth molecular analyses showed that low oxygen stress affected the cell wall composition, i.e. changes in protein content, a significantly modified in situ distribution of low methyl-esterified homogalacturonan, appearance of callose deposits, disturbed native activities of β-1,3-glucanase, endo-β-1,4-glucanase, and guaiacol peroxidase (GPX), and disruptions in molecular parameters of single cell wall components. Taken together, the data obtained indicate that less significant changes were observed in fruit in the breaker stage than in the case of the red ripe stage. The first symptoms of changes were noted after 24 h, but only after 72 h, more crucial deviations were visible. The 5% oxygen concentration slows down the ripening process and 0% oxygen accelerates the changes taking place during ripening. CONCLUSIONS The observed molecular reset occurring in tomato cell walls in hypoxic and anoxic conditions seems to be a result of regulatory and protective mechanisms modulating ripening processes.
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Affiliation(s)
- Agata Leszczuk
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, 20-290, Poland.
| | | | - Artur Nowak
- Department of Industrial and Environmental Microbiology, Institute of Biological Sciences, Maria Curie- Skłodowska University, Akademicka 19, Lublin, 20-033, Poland
| | - Artur Nosalewicz
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, 20-290, Poland
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, Lublin, 20-290, Poland
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Rovere M, Pucciariello C, Castella C, Berger A, Forgia M, Guyet TA, Bosseno M, Pacoud M, Brouquisse R, Perata P, Boscari A. Group VII ethylene response factors, MtERF74 and MtERF75, sustain nitrogen fixation in Medicago truncatula microoxic nodules. PLANT, CELL & ENVIRONMENT 2023; 46:607-620. [PMID: 36479691 DOI: 10.1111/pce.14505] [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: 07/12/2022] [Revised: 12/02/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
Group VII ethylene response factors (ERF-VII) are plant-specific transcription factors (TFs) known for their role in the activation of hypoxia-responsive genes under low oxygen stress but also in plant endogenous hypoxic niches. However, their function in the microaerophilic nitrogen-fixing nodules of legumes has not yet been investigated. We investigated regulation and the function of the two Medicago truncatula ERF-VII TFs (MtERF74 and MtERF75) in roots and nodules, MtERF74 and MtERF75 in response to hypoxia stress and during the nodulation process using an RNA interference strategy and targeted proteolysis of MtERF75. Knockdown of MtERF74 and MtERF75 partially blocked the induction of hypoxia-responsive genes in roots exposed to hypoxia stress. In addition, a significant reduction in nodulation capacity and nitrogen fixation activity was observed in mature nodules of double knockdown transgenic roots. Overall, the results indicate that MtERF74 and MtERF75 are involved in the induction of MtNR1 and Pgb1.1 expression for efficient Phytogb-nitric oxide respiration in the nodule.
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Affiliation(s)
- Martina Rovere
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Claude Castella
- INRAE, UR1115 Plantes et Systèmes de culture Horticoles (PSH), Site Agroparc, Avignon, France
| | - Antoine Berger
- Agroécologie, AgroSup Dijon, CNRS, INRAE, University of Bourgogne Franche-Comté, Dijon, France
| | - Marco Forgia
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Tran A Guyet
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Marc Bosseno
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | - Marie Pacoud
- Université Côte d'Azur, INRAE, CNRS, ISA, Sophia Antipolis, France
| | | | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
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3
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Tata HL, Nuroniah HS, Ahsania DA, Anggunira H, Hidayati SN, Pratama M, Istomo I, Chimner RA, van Noordwijk M, Kolka R. Flooding tolerance of four tropical peatland tree species in a nursery trial. PLoS One 2022; 17:e0262375. [PMID: 35385481 PMCID: PMC8985972 DOI: 10.1371/journal.pone.0262375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
In order to facilitate hydrological restoration, initiatives have been conducted to promote tree growth in degraded and rewetted peatlands in Indonesia. For these initiatives to be successful, tree seedlings need to be able to survive flooding episodes, with or without shade. We investigated the survival rates and the formation of adventitious roots in the case of four tree species exposed to combinations of different shading and water levels under controlled conditions in a nursery, with artificial rainwater and with peat soil as the medium. The research focused on the following questions (i) whether trees can grow on flooded peat soils; and (ii) which plant traits allow plants to cope with inundation, with or without shade. The four tree species compared (Shorea balangeran, Cratoxylum arborescens, Nephelium lappaceum and Durio zibethinus) include two natural pioneer and two farmer-preferred fruit trees. The experiment used a split-split plot design with 48 treatment combinations and at least 13 tree-level replicates. The study found that S. balangeran and C. arborescens had relatively high survival rates and tolerated saturated condition for 13 weeks, while N. lappaceum and D. zibethinus required non-saturated peat conditions. S. balangeran and C. arborescens developed adventitious roots to adapt to the inundated conditions. D. zibethinus, S. balangeran and N. lappaceum grew best under moderate (30%) shading levels, while C. arborescent grew best in full sunlight.
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Affiliation(s)
- Hesti L. Tata
- Center for Standardization Instrument of Sustainable Forest Management (formerly known as Forest Research and Development Agency), Bogor, Indonesia
| | - Hani S. Nuroniah
- Center for Standardization Instrument of Sustainable Forest Management (formerly known as Forest Research and Development Agency), Bogor, Indonesia
| | - Diandra A. Ahsania
- Silviculture Department, Faculty of Forestry and Environment, IPB University, Bogor, Indonesia
| | - Haning Anggunira
- Silviculture Department, Faculty of Forestry and Environment, IPB University, Bogor, Indonesia
| | - Siti N. Hidayati
- Silviculture Department, Faculty of Forestry and Environment, IPB University, Bogor, Indonesia
| | - Meydina Pratama
- Silviculture Department, Faculty of Forestry and Environment, IPB University, Bogor, Indonesia
| | - Istomo Istomo
- Silviculture Department, Faculty of Forestry and Environment, IPB University, Bogor, Indonesia
| | - Rodney A. Chimner
- College of Forest Resources and Environmental Sciences, Michigan Technological University, Houghton, Michigan, United States of America
| | - Meine van Noordwijk
- Plant Production Systems Department, Wageningen University and Research Center, Wageningen, The Netherlands
- World Agroforestry (ICRAF), Bogor, Indonesia
| | - Randall Kolka
- USDA Forest Service, Northern Research Station, Grand Rapids, Minnesota, United States of America
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Waterlogging-Stress-Responsive LncRNAs, Their Regulatory Relationships with miRNAs and Target Genes in Cucumber ( Cucumis sativus L.). Int J Mol Sci 2021; 22:ijms22158197. [PMID: 34360961 PMCID: PMC8348067 DOI: 10.3390/ijms22158197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/19/2021] [Accepted: 07/23/2021] [Indexed: 12/13/2022] Open
Abstract
Low oxygen level is a phenomenon often occurring during the cucumber cultivation period. Genes involved in adaptations to stress can be regulated by non-coding RNA. The aim was the identification of long non-coding RNAs (lncRNAs) involved in the response to long-term waterlogging stress in two cucumber haploid lines, i.e., DH2 (waterlogging tolerant—WL-T) and DH4 (waterlogging sensitive—WL-S). Plants, at the juvenile stage, were waterlogged for 7 days (non-primed, 1xH), and after a 14-day recovery period, plants were stressed again for another 7 days (primed, 2xH). Roots were collected for high-throughput RNA sequencing. Implementation of the bioinformatic pipeline made it possible to determine specific lncRNAs for non-primed and primed plants of both accessions, highlighting differential responses to hypoxia stress. In total, 3738 lncRNA molecules were identified. The highest number (1476) of unique lncRNAs was determined for non-primed WL-S plants. Seventy-one lncRNAs were depicted as potentially being involved in acquiring tolerance to hypoxia in cucumber. Understanding the mechanism of gene regulation under long-term waterlogging by lncRNAs and their interactions with miRNAs provides sufficient information in terms of adaptation to the oxygen deprivation in cucumber. To the best of our knowledge, this is the first report concerning the role of lncRNAs in the regulation of long-term waterlogging tolerance by priming application in cucumber.
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Benkeblia N. Physiological and Biochemical Response of Tropical Fruits to Hypoxia/Anoxia. FRONTIERS IN PLANT SCIENCE 2021; 12:670803. [PMID: 34335647 PMCID: PMC8322732 DOI: 10.3389/fpls.2021.670803] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Aerobic respiration and oxygen consumption are indicators of routine metabolic rate, and dissolved oxygen in plant tissues is one of the most important environmental factors affecting their survival. The reduction of available O2 leads to hypoxia which causes a limitation of the oxidative phosphorylation; when O2 is absent, tissues generate ATP by activating the fermentative glycolysis to sustain glycolysis in the absence of mitochondrial respiration, which results in the production of lactate. Overall, hypoxia was reported to often decrease the respiration rate (O2 uptake) and delay the climacteric rise of ethylene in climacteric fruits by inhibiting action, thus delaying their ripening. Much research has been done on the application of postharvest hypoxia and anoxia treatment to temperate fresh crops (controlled or modified atmosphere), however, very few reported on tropical commodities. Indeed, the physiological mode of action of low or absence of oxygen in fresh crops is not well understood; and the physiological and biochemical bases of the effects low or absence of O2 are also yet to be clarified. Recent investigations using omics technologies, however, have provided useful information on the response of fresh fruits and vegetables to this abiotic stress. The aims of this review are to (i) report on the oxygen exchange in the crops tissue, (ii) discuss the metabolic responses to hypoxia and anoxia, and (iii) report the physiological and biochemical responses of crops tissues to these abiotic stresses and the potential benefits of these environmental conditions.
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Hou Y, Jiang F, Zheng X, Wu Z. Identification and analysis of oxygen responsive microRNAs in the root of wild tomato (S. habrochaites). BMC PLANT BIOLOGY 2019; 19:100. [PMID: 30866807 PMCID: PMC6416974 DOI: 10.1186/s12870-019-1698-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/27/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND MicroRNA (miRNA) are key players in regulating expression of target genes at post-transcriptional level. A number of miRNAs are implicated in modulating tolerance to various abiotic stresses. Waterlogging is an abiotic stress that deters plant growth and productivity by hypoxia. Dozens of reports mention about the miRNAs expressed in response to waterlogging and hypoxia. Despite the fact that tomato is a model vegetable but waterlogging sensitive crop, the role of miRNAs in hypoxia tolerance is poorly understood in tomato. RESULTS In this study, we investigated the differentially expressed miRNAs between hypoxia-treated and untreated wild tomato root by using high-throughput sequencing technology. A total of 33 known miRNAs were lowly expressed, whereas only 3 miRNAs showed higher expression in hypoxia-treated wild tomato root compared with untreated wild tomato root. Then two conserved and lowly expressed miRNAs, miR171 and miR390, were deactivated by Short Tandem Target Mimic (STTM) technology in Arabidopsis. As the results, the number and length of lateral roots were more in STTM171 and STTM390 transgenic lines compared with that of wild type plant, which partly phenocopy the increase root number and shortening the root length in hypoxia-treated wild tomato root. CONCLUSIONS The differentially expressed miRNAs between hypoxia-treated wild tomato and control root, which contribute to the auxin homeostasis, morphologic change, and stress response, might result in reduction in the biomass and length of the root in hypoxiated conditions.
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Affiliation(s)
- Yabing Hou
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Fangling Jiang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Xiaolan Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou, 450002 China
| | - Zhen Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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Shamakhi L, Zibaee A, Karimi-Malati A, Hoda H. Simultaneous effects of thermal stress and fungal infection on lipid peroxidation and antioxidant system of rice-striped stem borer, Chilo suppressalis Walker (Lepidoptera: Crambidae). BIOL RHYTHM RES 2018. [DOI: 10.1080/09291016.2018.1526500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Leila Shamakhi
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Arash Zibaee
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Azadeh Karimi-Malati
- Department of Plant Protection, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Hassan Hoda
- Iranian Research Institute of plant protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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8
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Diab H, Limami AM. Reconfiguration of N Metabolism upon Hypoxia Stress and Recovery: Roles of Alanine Aminotransferase (AlaAT) and Glutamate Dehydrogenase (GDH). PLANTS (BASEL, SWITZERLAND) 2016; 5:E25. [PMID: 27258319 PMCID: PMC4931405 DOI: 10.3390/plants5020025] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/24/2016] [Accepted: 05/26/2016] [Indexed: 11/16/2022]
Abstract
In the context of climatic change, more heavy precipitation and more frequent flooding and waterlogging events threaten the productivity of arable farmland. Furthermore, crops were not selected to cope with flooding- and waterlogging-induced oxygen limitation. In general, low oxygen stress, unlike other abiotic stresses (e.g., cold, high temperature, drought and saline stress), received little interest from the scientific community and less financial support from stakeholders. Accordingly, breeding programs should be developed and agronomical practices should be adapted in order to save plants' growth and yield-even under conditions of low oxygen availability (e.g., submergence and waterlogging). The prerequisite to the success of such breeding programs and changes in agronomical practices is a good knowledge of how plants adapt to low oxygen stress at the cellular and the whole plant level. In the present paper, we summarized the recent knowledge on metabolic adjustment in general under low oxygen stress and highlighted thereafter the major changes pertaining to the reconfiguration of amino acids syntheses. We propose a model showing (i) how pyruvate derived from active glycolysis upon hypoxia is competitively used by the alanine aminotransferase/glutamate synthase cycle, leading to alanine accumulation and NAD⁺ regeneration. Carbon is then saved in a nitrogen store instead of being lost through ethanol fermentative pathway. (ii) During the post-hypoxia recovery period, the alanine aminotransferase/glutamate dehydrogenase cycle mobilizes this carbon from alanine store. Pyruvate produced by the reverse reaction of alanine aminotransferase is funneled to the TCA cycle, while deaminating glutamate dehydrogenase regenerates, reducing equivalent (NADH) and 2-oxoglutarate to maintain the cycle function.
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Affiliation(s)
- Houssein Diab
- University of Angers, UMR 1345 IRHS, SFR 4207 QUASAV, 2 Bd Lavoisier, F-49045 Angers, France.
| | - Anis M Limami
- University of Angers, UMR 1345 IRHS, SFR 4207 QUASAV, 2 Bd Lavoisier, F-49045 Angers, France.
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Zhu QG, Wang MM, Gong ZY, Fang F, Sun NJ, Li X, Grierson D, Yin XR, Chen KS. Involvement of DkTGA1 Transcription Factor in Anaerobic Response Leading to Persimmon Fruit Postharvest De-Astringency. PLoS One 2016; 11:e0155916. [PMID: 27196670 PMCID: PMC4873192 DOI: 10.1371/journal.pone.0155916] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 05/06/2016] [Indexed: 12/27/2022] Open
Abstract
Persimmon fruit are unique in accumulating proanthocyanidins (tannins) during development, which cause astringency in mature fruit. In ‘Mopanshi’ persimmon, astringency can be removed by treatment with 95% CO2, which increases the concentrations of ethanol and acetaldehyde by glycolysis, and precipitates the soluble tannin. A TGA transcription factor, DkTGA1, belonging to the bZIP super family, was isolated from an RNA-seq database and real-time quantitative PCR indicated that DkTGA1 was up-regulated by CO2 treatment, in concert with the removal of astringency from persimmon fruit. Dual-luciferase assay revealed that DkTGA1 had a small (less than 2-fold), but significant effect on the promoters of de-astringency-related genes DkADH1, DkPDC2 and DkPDC3, which encode enzymes catalyzing formation of acetaldehyde and ethanol. A combination of DkTGA1 and a second transcription factor, DkERF9, shown previously to be related to de-astringency, showed additive effects on the activation of the DkPDC2 promoter. Yeast one-hybrid assay showed that DkERF9, but not DkTGA1, could bind to the DkPDC2 promoter. Thus, although DkTGA1 expression is positively associated with persimmon fruit de-astringency, trans-activation analyses with DkPDC2 indicates it is likely to act by binding indirectly DkPDC2 promoter, might with helps of DkERF9.
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Affiliation(s)
- Qing-gang Zhu
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, PR China
| | - Miao-miao Wang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
| | - Zi-yuan Gong
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
| | - Fang Fang
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
| | - Ning-jing Sun
- Department of Horticultural Sciences, College of Agriculture, Guangxi University, Nanning, PR China
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, PR China
| | - Donald Grierson
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
- Plant & Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, United Kingdom
| | - Xue-ren Yin
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, PR China
- * E-mail:
| | - Kun-song Chen
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, PR China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou, PR China
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Saithong T, Saerue S, Kalapanulak S, Sojikul P, Narangajavana J, Bhumiratana S. Gene Co-Expression Analysis Inferring the Crosstalk of Ethylene and Gibberellin in Modulating the Transcriptional Acclimation of Cassava Root Growth in Different Seasons. PLoS One 2015; 10:e0137602. [PMID: 26366737 PMCID: PMC4569563 DOI: 10.1371/journal.pone.0137602] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 08/20/2015] [Indexed: 12/21/2022] Open
Abstract
Cassava is a crop of hope for the 21st century. Great advantages of cassava over other crops are not only the capacity of carbohydrates, but it is also an easily grown crop with fast development. As a plant which is highly tolerant to a poor environment, cassava has been believed to own an effective acclimation process, an intelligent mechanism behind its survival and sustainability in a wide range of climates. Herein, we aimed to investigate the transcriptional regulation underlying the adaptive development of a cassava root to different seasonal cultivation climates. Gene co-expression analysis suggests that AP2-EREBP transcription factor (ERF1) orthologue (D142) played a pivotal role in regulating the cellular response to exposing to wet and dry seasons. The ERF shows crosstalk with gibberellin, via ent-Kaurene synthase (D106), in the transcriptional regulatory network that was proposed to modulate the downstream regulatory system through a distinct signaling mechanism. While sulfur assimilation is likely to be a signaling regulation for dry crop growth response, calmodulin-binding protein is responsible for regulation in the wet crop. With our initiative study, we hope that our findings will pave the way towards sustainability of cassava production under various kinds of stress considering the future global climate change.
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Affiliation(s)
- Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Thakham, Bangkhunthian, Bangkok, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Thakham, Bangkhunthian, Bangkok, Thailand
| | - Samorn Saerue
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Thakham, Bangkhunthian, Bangkok, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut’s University of Technology Thonburi, Thakham, Bangkhunthian, Bangkok, Thailand
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Thakham, Bangkhunthian, Bangkok, Thailand
| | - Punchapat Sojikul
- Center for Cassava Molecular Biotechnology, Faculty of Science, Mahidol University, Thungphayathai, Ratchathewi, Bangkok, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Thungphayathai, Ratchathewi, Bangkok, Thailand
| | - Jarunya Narangajavana
- Center for Cassava Molecular Biotechnology, Faculty of Science, Mahidol University, Thungphayathai, Ratchathewi, Bangkok, Thailand
- Department of Biotechnology, Faculty of Science, Mahidol University, Thungphayathai, Ratchathewi, Bangkok, Thailand
| | - Sakarindr Bhumiratana
- Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut’s University of Technology Thonburi, Thakham, Bangkhunthian, Bangkok, Thailand
- Department of Chemical Engineering, Faculty of Engineering, King Mongkut’s University of Technology Thonburi, Bangkok, Thungkhru, Bangmod, Bangkok, Thailand
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11
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Yang W, Catalanotti C, Wittkopp TM, Posewitz MC, Grossman AR. Algae after dark: mechanisms to cope with anoxic/hypoxic conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:481-503. [PMID: 25752440 DOI: 10.1111/tpj.12823] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 02/28/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Chlamydomonas reinhardtii is a unicellular, soil-dwelling (and aquatic) green alga that has significant metabolic flexibility for balancing redox equivalents and generating ATP when it experiences hypoxic/anoxic conditions. The diversity of pathways available to ferment sugars is often revealed in mutants in which the activities of specific branches of fermentative metabolism have been eliminated; compensatory pathways that have little activity in parental strains under standard laboratory fermentative conditions are often activated. The ways in which these pathways are regulated and integrated have not been extensively explored. In this review, we primarily discuss the intricacies of dark anoxic metabolism in Chlamydomonas, but also discuss aspects of dark oxic metabolism, the utilization of acetate, and the relatively uncharacterized but critical interactions that link chloroplastic and mitochondrial metabolic networks.
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Affiliation(s)
- Wenqiang Yang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Claudia Catalanotti
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Tyler M Wittkopp
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Matthew C Posewitz
- Department of Chemistry and Geochemistry, Colorado School of Mines, Golden, CO, 80401, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
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12
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Abstract
Oxygen is an indispensable substrate for many biochemical reactions in plants, including energy metabolism (respiration). Despite its importance, plants lack an active transport mechanism to distribute oxygen to all cells. Therefore, steep oxygen gradients occur within most plant tissues, which can be exacerbated by environmental perturbations that further reduce oxygen availability. Plants possess various responses to cope with spatial and temporal variations in oxygen availability, many of which involve metabolic adaptations to deal with energy crises induced by low oxygen. Responses are induced gradually when oxygen concentrations decrease and are rapidly reversed upon reoxygenation. A direct effect of the oxygen level can be observed in the stability, and thus activity, of various transcription factors that control the expression of hypoxia-induced genes. Additional signaling pathways are activated by the impact of oxygen deficiency on mitochondrial and chloroplast functioning. Here, we describe the molecular components of the oxygen-sensing pathway.
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Affiliation(s)
- Joost T van Dongen
- Institute of Biology I, Aachen Biology and Biotechnology, RWTH Aachen University, 52074 Aachen, Germany;
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Tsai KJ, Chou SJ, Shih MC. Ethylene plays an essential role in the recovery of Arabidopsis during post-anaerobiosis reoxygenation. PLANT, CELL & ENVIRONMENT 2014; 37:2391-405. [PMID: 24506560 DOI: 10.1111/pce.12292] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 01/09/2014] [Accepted: 01/20/2014] [Indexed: 05/05/2023]
Abstract
Ethylene is known to play an essential role in mediating hypoxic responses in plants. Here, we show that in addition to regulating hypoxic responses, ethylene also regulates cellular responses in the reoxygenation stage after anoxic treatment in Arabidopsis. We found that expression of several ethylene biosynthetic genes and ethylene-responsive factors, including ERF1 and ERF2, was induced during reoxygenation. Compared with the wild type, two ethylene-insensitive mutants (ein2-5 and ein3eil1) were more sensitive to reoxygenation and displayed damaged phenotypes during reoxygenation. To characterize the role of ethylene, we applied microarray analysis to Col-0, ein2-5 and ein3eil1 under reoxygenation conditions. Our results showed that gene transcripts involved in reactive oxygen species (ROS) detoxification, dehydration response and metabolic processes were regulated during reoxygenation. Moreover, ethylene signalling may participate in regulating these responses and maintaining the homeostasis of different phytohormones. Our work presents evidence that ethylene has distinct functions in recovery after anoxia and provides insight into the reoxygenation signalling network.
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Affiliation(s)
- Kuen-Jin Tsai
- Institute of Plant Biology, National Taiwan University, Taipei, 115, Taiwan; Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
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14
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Reeksting BJ, Coetzer N, Mahomed W, Engelbrecht J, van den Berg N. De novo sequencing, assembly, and analysis of the root transcriptome of Persea americana (Mill.) in response to Phytophthora cinnamomi and flooding. PLoS One 2014; 9:e86399. [PMID: 24563685 PMCID: PMC3919710 DOI: 10.1371/journal.pone.0086399] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 12/09/2013] [Indexed: 12/21/2022] Open
Abstract
Avocado is a diploid angiosperm containing 24 chromosomes with a genome estimated to be around 920 Mb. It is an important fruit crop worldwide but is susceptible to a root rot caused by the ubiquitous oomycete Phytophthora cinnamomi. Phytophthora root rot (PRR) causes damage to the feeder roots of trees, causing necrosis. This leads to branch-dieback and eventual tree death, resulting in severe losses in production. Control strategies are limited and at present an integrated approach involving the use of phosphite, tolerant rootstocks, and proper nursery management has shown the best results. Disease progression of PRR is accelerated under high soil moisture or flooding conditions. In addition, avocado is highly susceptible to flooding, with even short periods of flooding causing significant losses. Despite the commercial importance of avocado, limited genomic resources are available. Next generation sequencing has provided the means to generate sequence data at a relatively low cost, making this an attractive option for non-model organisms such as avocado. The aims of this study were to generate sequence data for the avocado root transcriptome and identify stress-related genes. Tissue was isolated from avocado infected with P. cinnamomi, avocado exposed to flooding and avocado exposed to a combination of these two stresses. Three separate sequencing runs were performed on the Roche 454 platform and produced approximately 124 Mb of data. This was assembled into 7685 contigs, with 106 448 sequences remaining as singletons. Genes involved in defence pathways such as the salicylic acid and jasmonic acid pathways as well as genes associated with the response to low oxygen caused by flooding, were identified. This is the most comprehensive study of transcripts derived from root tissue of avocado to date and will provide a useful resource for future studies.
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Affiliation(s)
- Bianca J Reeksting
- Department of Genetics, University of Pretoria, Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Nanette Coetzer
- Bioinformatics and Computational Biology Unit, Department of Biochemistry, University of Pretoria, Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Waheed Mahomed
- Department of Genetics, University of Pretoria, Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Juanita Engelbrecht
- Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Noëlani van den Berg
- Department of Genetics, University of Pretoria, Pretoria, South Africa ; Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
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15
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New Insights into the Metabolic and Molecular Mechanism of Plant Response to Anaerobiosis. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 311:231-64. [DOI: 10.1016/b978-0-12-800179-0.00005-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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16
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Oxidative Stress Components Explored in Anoxic and Hypoxic Global Gene Expression Data. LOW-OXYGEN STRESS IN PLANTS 2014. [DOI: 10.1007/978-3-7091-1254-0_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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17
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Yin D, Ni D, Song L, Zhang Z. Isolation of an alcohol dehydrogenase cDNA from and characterization of its expression in chrysanthemum under waterlogging. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2013; 212:48-54. [PMID: 24094053 DOI: 10.1016/j.plantsci.2013.05.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Revised: 05/21/2013] [Accepted: 05/31/2013] [Indexed: 06/02/2023]
Abstract
A PCR strategy was used to isolate a full-length CgADH (alcohol dehydrogenase) cDNA from chrysanthemum. The gene putatively encodes a 378 residue polypeptides, which shares 95% homology with tomato alcohol dehydrogenase class III. Endogenous ethylene generated in waterlogged Chrysanthemum zawadskii was enhanced by exogenous ethylene but decreased by 1-methylcyclopropene (1-MCP), an inhibitor of ethylene action. In waterlogged roots, the transcription of the gene encoding alcohol dehydrogenase (ADH, EC 1.1.1.1) increased rapidly but transiently, peaking at 7.5 fold the non-waterlogged level after 2h of stress. Waterlogging elevated ADH activity after a prolonged episode of stress. The exogenous supply of 40μLL(-1) ethylene suppressed the production of ethanol, while that of 4μLL(-1) 1-MCP enhanced it. Ethylene appeared to suppress an acceleration of both CgADH expression and fermentation, and alleviates ethanolic fermentation probably through by as a signal to acceleration of waterlogging-induced aerenchyma formation. This supports the previously observed phenomenon that the expression level of ADH gene is regulated by the local level of physiologically active ethylene. The relevance of the CgADH gene in relation to chrysanthemum waterlogging was discussed as well.
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Affiliation(s)
- Dongmei Yin
- School of Ecological Technology and Enginneering, Shanghai Institute of Technology, Shanghai 201418, China
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18
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Voesenek LACJ, Bailey-Serres J. Flooding tolerance: O2 sensing and survival strategies. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:647-653. [PMID: 23830867 DOI: 10.1016/j.pbi.2013.06.008] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 06/11/2013] [Accepted: 06/11/2013] [Indexed: 05/28/2023]
Abstract
The investigation of flooding survival strategies in model, crop and wild plant species has yielded insights into molecular, physiological and developmental mechanisms of soil flooding (waterlogging) and submergence survival. The antithetical flooding escape and quiescence strategies of deepwater and submergence tolerant rice (Oryza sativa), respectively, are regulated by members of a clade of ethylene responsive factor transcriptional activators. This knowledge paved the way for the discovery that these proteins are targets of a highly conserved O2-sensing protein turnover mechanism in Arabidopsis thaliana. Further examples of genes that regulate transcription, root and shoot metabolism or development during floods have emerged. With the rapid advancement of genomic technologies, the mining of natural genetic variation in flooding tolerant wild species may ultimately benefit crop production.
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Affiliation(s)
- L A C J Voesenek
- Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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19
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Hemschemeier A, Casero D, Liu B, Benning C, Pellegrini M, Happe T, Merchant SS. Copper response regulator1-dependent and -independent responses of the Chlamydomonas reinhardtii transcriptome to dark anoxia. THE PLANT CELL 2013; 25:3186-211. [PMID: 24014546 PMCID: PMC3809527 DOI: 10.1105/tpc.113.115741] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Anaerobiosis is a stress condition for aerobic organisms and requires extensive acclimation responses. We used RNA-Seq for a whole-genome view of the acclimation of Chlamydomonas reinhardtii to anoxic conditions imposed simultaneously with transfer to the dark. Nearly 1.4 × 10(3) genes were affected by hypoxia. Comparing transcript profiles from early (hypoxic) with those from late (anoxic) time points indicated that cells activate oxidative energy generation pathways before employing fermentation. Probable substrates include amino acids and fatty acids (FAs). Lipid profiling of the C. reinhardtii cells revealed that they degraded FAs but also accumulated triacylglycerols (TAGs). In contrast with N-deprived cells, the TAGs in hypoxic cells were enriched in desaturated FAs, suggesting a distinct pathway for TAG accumulation. To distinguish transcriptional responses dependent on copper response regulator1 (CRR1), which is also involved in hypoxic gene regulation, we compared the transcriptomes of crr1 mutants and complemented strains. In crr1 mutants, ~40 genes were aberrantly regulated, reaffirming the importance of CRR1 for the hypoxic response, but indicating also the contribution of additional signaling strategies to account for the remaining differentially regulated transcripts. Based on transcript patterns and previous results, we conclude that nitric oxide-dependent signaling cascades operate in anoxic C. reinhardtii cells.
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Affiliation(s)
- Anja Hemschemeier
- Ruhr Universität Bochum, Fakultät für Biologie und Biotechnologie, Arbeitsgruppe Photobiotechnologie, 44801 Bochum, Germany
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20
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Licausi F. Molecular elements of low-oxygen signaling in plants. PHYSIOLOGIA PLANTARUM 2013; 148:1-8. [PMID: 23167298 DOI: 10.1111/ppl.12011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2012] [Revised: 10/28/2012] [Accepted: 11/05/2012] [Indexed: 05/07/2023]
Abstract
Oxygen and its limitation are emerging as a crucial factor in plant fitness, growth and development. Recent studies revealed the mechanisms by which oxygen is perceived by plant cells. This sensory system partly relies on an oxygen-mediated branch of the N-end rule pathway for protein degradation acting on a specific clade of ethylene responsive transcription factors (ERF-VII). A complementary regulative step is provided by aerobic sequestration of an ERF-VII protein at the plasma membrane and its timely release when hypoxia occurs. Complete absence of oxygen triggers the transient accumulation of reactive hydrogen peroxide and induces an additional set of reactive oxygen species-related genes involved in both signaling and attenuation of oxidative stress. Moreover, temporary hypoxic environments that are built up as consequence of dense cell packing have been demonstrated to trigger cell-fate determination in maize anthers. Similarly, limited oxygen delivery in bulky fruit or tuber tissues growing in aerobic conditions were shown to stimulate anaerobic-like responses. These advances in low-oxygen signaling and its effect on cell development highlight the importance of taking hypoxia into account in agronomical practices as well as in breeding programs.
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21
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Matilla AJ, Rodríguez-Gacio MDC. Non-symbiotic hemoglobins in the life of seeds. PHYTOCHEMISTRY 2013; 87:7-15. [PMID: 23286879 DOI: 10.1016/j.phytochem.2012.11.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Revised: 11/13/2012] [Accepted: 11/21/2012] [Indexed: 06/01/2023]
Abstract
Non-symbiotic hemoglobins (nsHbs), ancestors of symbiotic-Hbs, are hexacoordinated dimeric proteins, for which the crystal structure is well described. According to the extent of hexacoordination, nsHbs are classified as belonging to class-1 (nsHbs1) or class-2 (nsHbs2). The nsHbs1 show weak hexacoordination, moderate rates of O(2)-binding, very small rates of O(2) dissociation, and a remarkably high affinity for O(2), all suggesting a function involving O(2) scavenging. In contrast, the nsHbs2 exhibit strong hexacoordination, low rates of O(2)-binding and moderately low O(2) dissociation and affinity, suggesting a sensing role for sustained low (μM) levels of O(2). The existence of spatial and specific expression of nsHbs1 suggests that nsHbs play tissue-specific rather than housekeeping functions. The permeation of O(2) into seeds is usually prevented during the desiccation phase and early imbibition, generating an internal hypoxic environment that leads to ATP limitation. During evolution, the seed has acquired mechanisms to prevent or reduce this hypoxic stress. The nsHbs1/NO cycle appear to be involved in modulating the redox state in the seed and in maintaining an active metabolism. Under O(2) deficit, NADH and NO are synthesized in the seed and nsHbs1 scavenges O(2), which is used to transform NO into NO(3)(-) with concomitant formation of Fe(3+)-nsHbs1. Expression of nsHbs1 is not detectable in dry viable seeds. However, in the seeds cross-talk occurs between nsHbs1 and NO during germination. This review considers the current status of our knowledge of seed nsHbs and considers key issues of further work to better understand their role in seed physiology.
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Affiliation(s)
- Angel J Matilla
- Department of Plant Physiology, University of Santiago de Compostela, 15782 Santiago de Compostela, A Coruña, Spain.
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22
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Licausi F, Pucciariello C, Perata P. New role for an old rule: N-end rule-mediated degradation of ethylene responsive factor proteins governs low oxygen response in plants(F). JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2013; 55:31-9. [PMID: 23164408 DOI: 10.1111/jipb.12011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The N-end rule pathway regulates protein degradation, which depends on exposed N-terminal sequences in prokaryotes and eukaryotes. In plants, conserved and specific enzymes stimulate selective proteolysis. Although a number of developmental and growth phenotypes have been reported for mutants in the N-end rule, its function has remained unrelated to specific physiological pathways. The first report of the direct involvement of the N-end rule in stress responses focused on hypoxic signaling and how the oxygen-dependent oxidation of cystein promotes the N-end rule-mediated degradation of ethylene responsive factor (ERF)-VII proteins, the master regulators of anaerobic responses. It has been suggested that plants have evolved specific mechanisms to tune ERF-VII availability in the nucleus. In this review, we speculate that ERF-VII proteins are reversibly protected from degradation via membrane sequestration. The oxidative response in plants subjected to anoxic conditions suggests that reactive oxygen and nitrogen species (reactive oxygen species and reactive nitrogen species) may interact or interfere with the N-end rule pathway-mediated response to hypoxia.
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Affiliation(s)
- Francesco Licausi
- Plant Lab, Institute of Life Sciences, Scuola Superiore Sant' Anna, Pisa 56124, Italy
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23
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Pucciariello C, Banti V, Perata P. ROS signaling as common element in low oxygen and heat stresses. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 59:3-10. [PMID: 22417734 DOI: 10.1016/j.plaphy.2012.02.016] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2011] [Accepted: 02/17/2012] [Indexed: 05/09/2023]
Abstract
The activation of the oxidative metabolism in plants under low oxygen conditions has prompted controversial views. The presence of a ROS component in the transcriptome in response to low oxygen has been observed and an overlap with heat stress has been proved. It has been also demonstrated that ROS are produced during both anoxia and heat, but the site of their production remain contentious. Membrane NADPH oxidase and mitochondrial electron transport flow have been indicated as possible ROS generation systems. Both anoxia and heat have been shown to induce the transcription of Heat Shock Factors (HSFs) and Heat Shock Proteins (HSPs), among which HSFA2 and some of its targets. HSFA2 over-expressing plant has been shown to be more tolerant to anoxia, while the knockout hsfa2 lose the capability of wild type plants to cross-acclimate to anoxia through mild heat pre-treatment. The production of ROS seems to be an integral part of the anoxia and heat response, where HSFs likely play a central role in activating the HSP pathway. This mechanism is suggested to result in enhanced plant tolerance to both anoxia and heat.
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Affiliation(s)
- Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127 Pisa, Italy.
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24
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Zhao Y, Wei T, Yin KQ, Chen Z, Gu H, Qu LJ, Qin G. Arabidopsis RAP2.2 plays an important role in plant resistance to Botrytis cinerea and ethylene responses. THE NEW PHYTOLOGIST 2012; 195:450-460. [PMID: 22530619 DOI: 10.1111/j.1469-8137.2012.04160.x] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
• Ethylene plays a crucial role in plant resistance to necrotrophic pathogens, in which ETHYLENE RESPONSE FACTORs (ERFs) are often involved. • Here, we evaluated the role of an ERF transcription factor, RELATED TO AP2 2 (RAP2.2), in Botrytis resistance and ethylene responses in Arabidopsis. We analyzed the resistance of transgenic plants overexpressing RAP2.2 and the T-DNA insertion mutant to Botrytis cinerea. We assessed its role in the ethylene signaling pathway by molecular and genetic approaches. • RAP2.2-overexpressing transgenic plants showed increased resistance to B. cinerea, whereas its T-DNA insertion mutant rap2.2-3 showed decreased resistance. Overexpression of RAP2.2 in ethylene insensitive 2 (ein2) and ein3 ein3-like 1 (eil1) mutants restored their resistance to B. cinerea. Both ethylene and Botrytis infection induced the expression of RAP2.2 and the induction was disrupted in ein2 and ein3 eil1 mutants. We identified rap2.12-1 as a T-DNA insertion mutant of RAP2.12, the closest homolog of RAP2.2. The hypocotyls of rap2.2-3 rap2.12-1 double mutants showed ethylene insensitivity. The constitutive triple response in constitutive triple response1 (ctr1) was partially released in the rap2.2-3 rap2.12-1 ctr1 triple mutants. • Our findings demonstrate that RAP2.2 functions as an important regulator in Botrytis resistance and ethylene responses.
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Affiliation(s)
- Yang Zhao
- College of Agriculture and Biotechnology, China Agricultural University, Beijing 100094, China
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Tong Wei
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Kang-Quan Yin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Zhangliang Chen
- College of Agriculture and Biotechnology, China Agricultural University, Beijing 100094, China
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
| | - Hongya Gu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- The National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Li-Jia Qu
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- The National Plant Gene Research Center (Beijing), Beijing 100101, China
| | - Genji Qin
- State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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25
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Abstract
The recent identification of the oxygen-sensing mechanism in plants is a breakthrough in plant physiology. The presence of a conserved N-terminal motif on some ethylene responsive factors (ERFs), targets the protein for post-translational modifications finally leading to degradation under normoxia and thus providing a mechanism for sensing the presence of oxygen. The stabilization of the N-terminus under low oxygen activates these ERFs, which regulate low oxygen core genes that enable plants to tolerate abiotic stress such as flooding. Additional mechanisms that signal low-oxygen probably also exist, and the production of reactive oxygen species (ROS) has been observed under low oxygen, suggesting that ROS might be part of the network involved in plant acclimation. Here, we review the most recent findings related to oxygen sensing.
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26
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Tiwari SB, Belachew A, Ma SF, Young M, Ade J, Shen Y, Marion CM, Holtan HE, Bailey A, Stone JK, Edwards L, Wallace AD, Canales RD, Adam L, Ratcliffe OJ, Repetti PP. The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 70:855-65. [PMID: 22321262 DOI: 10.1111/j.1365-313x.2012.04935.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In plants, the ERF/EREBP family of transcriptional regulators plays a key role in adaptation to various biotic and abiotic stresses. These proteins contain a conserved AP2 DNA-binding domain and several uncharacterized motifs. Here, we describe a short motif, termed 'EDLL', that is present in AtERF98/TDR1 and other clade members from the same AP2 sub-family. We show that the EDLL motif, which has a unique arrangement of acidic amino acids and hydrophobic leucines, functions as a strong activation domain. The motif is transferable to other proteins, and is active at both proximal and distal positions of target promoters. As such, the EDLL motif is able to partly overcome the repression conferred by the AtHB2 transcription factor, which contains an ERF-associated amphiphilic repression (EAR) motif. We further examined the activation potential of EDLL by analysis of the regulation of flowering time by NF-Y (nuclear factor Y) proteins. Genetic evidence indicates that NF-Y protein complexes potentiate the action of CONSTANS in regulation of flowering in Arabidopsis; we show that the transcriptional activation function of CONSTANS can be substituted by direct fusion of the EDLL activation motif to NF-YB subunits. The EDLL motif represents a potent plant activation domain that can be used as a tool to confer transcriptional activation potential to heterologous DNA-binding proteins.
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Affiliation(s)
- Shiv B Tiwari
- Mendel Biotechnology Inc., 3935 Point Eden Way, Hayward, CA 94545, USA
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27
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Pucciariello C, Parlanti S, Banti V, Novi G, Perata P. Reactive oxygen species-driven transcription in Arabidopsis under oxygen deprivation. PLANT PHYSIOLOGY 2012; 159:184-96. [PMID: 22415514 PMCID: PMC3375960 DOI: 10.1104/pp.111.191122] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 03/12/2012] [Indexed: 05/17/2023]
Abstract
Reactive oxygen species (ROS) play an important role as triggers of gene expression during biotic and abiotic stresses, among which is low oxygen (O(2)). Previous studies have shown that ROS regulation under low O(2) is driven by a RHO-like GTPase that allows tight control of hydrogen peroxide (H(2)O(2)) production. H(2)O(2) is thought to regulate the expression of heat shock proteins, in a mechanism that is common to both O(2) deprivation and to heat stress. In this work, we used publicly available Arabidopsis (Arabidopsis thaliana) microarray datasets related to ROS and O(2) deprivation to define transcriptome convergence pattern. Our results show that although Arabidopsis response to anoxic and hypoxic treatments share a common core of genes related to the anaerobic metabolism, they differ in terms of ROS-related gene response. We propose that H(2)O(2) production under O(2) deprivation is a trait present in a very early phase of anoxia, and that ROS are needed for the regulation of a set of genes belonging to the heat shock protein and ROS-mediated groups. This mechanism, likely not regulated via the N-end rule pathway for O(2) sensing, is probably mediated by a NADPH oxidase and it is involved in plant tolerance to the stress.
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Affiliation(s)
| | | | | | | | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
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28
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Ren Y, Chen L, Zhang Y, Kang X, Zhang Z, Wang Y. Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress. Funct Integr Genomics 2012; 12:327-39. [PMID: 22415631 DOI: 10.1007/s10142-012-0271-6] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Revised: 02/14/2012] [Accepted: 02/21/2012] [Indexed: 12/31/2022]
Abstract
MicroRNAs (miRNAs) are a class of small, non-coding RNAs that play important downregulation roles in plants growth, development, and stress responses. To better identify Populus tomentosa miRNAs and understand the functions of miRNAs in response to water stress (drought and flooding), 152 conserved miRNAs belonging to 36 miRNA families, 8 known but non-conserved miRNAs and 64 candidate novel miRNAs belonging to 54 miRNA families were identified and analyzed from three small RNA (sRNA) libraries (drought treatment, flooding treatment, and control) by high-throughput sequencing combined with qRT-PCR. Significant changes in the expression of 17 conserved miRNA families and nine novel miRNAs were observed in response to drought stress, and in seven conserved miRNA families and five novel miRNAs in response to flooding stress. Both miRNA and miRNA*s were involved in the regulation of plant stress responses. The annotation of the potential targets of miRNAs with differential expression indicate that many types of genes encoding transcription factors, enzymes, and signal transduction components are implicated in the abiotic stress response..
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Affiliation(s)
- Yuanyuan Ren
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, 100083 Beijing, People's Republic of China.
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29
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Bailey-Serres J, Fukao T, Gibbs DJ, Holdsworth MJ, Lee SC, Licausi F, Perata P, Voesenek LACJ, van Dongen JT. Making sense of low oxygen sensing. TRENDS IN PLANT SCIENCE 2012; 17:129-38. [PMID: 22280796 DOI: 10.1016/j.tplants.2011.12.004] [Citation(s) in RCA: 289] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2011] [Revised: 12/06/2011] [Accepted: 12/13/2011] [Indexed: 05/21/2023]
Abstract
Plant-specific group VII Ethylene Response Factor (ERF) transcription factors have emerged as pivotal regulators of flooding and low oxygen responses. In rice (Oryza sativa), these proteins regulate contrasting strategies of flooding survival. Recent studies on Arabidopsis thaliana group VII ERFs show they are stabilized under hypoxia but destabilized under oxygen-replete conditions via the N-end rule pathway of targeted proteolysis. Oxygen-dependent sequestration at the plasma membrane maintains at least one of these proteins, RAP2.12, under normoxia. Remarkably, SUB1A, the rice group VII ERF that enables prolonged submergence tolerance, appears to evade oxygen-regulated N-end rule degradation. We propose that the turnover of group VII ERFs is of ecological relevance in wetland species and might be manipulated to improve flood tolerance of crops.
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Affiliation(s)
- Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, USA.
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30
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Woodward FI, Hetherington AM. The New Phytologist Tansley Medal 2010. THE NEW PHYTOLOGIST 2011; 190:509. [PMID: 21496025 DOI: 10.1111/j.1469-8137.2011.03728.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
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