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Eysholdt-Derzsó E, Hause B, Sauter M, Schmidt-Schippers RR. Hypoxia reshapes Arabidopsis root architecture by integrating ERF-VII factor response and abscisic acid homoeostasis. PLANT, CELL & ENVIRONMENT 2024; 47:2879-2894. [PMID: 38616485 DOI: 10.1111/pce.14914] [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: 11/27/2023] [Revised: 04/02/2024] [Accepted: 04/04/2024] [Indexed: 04/16/2024]
Abstract
Oxygen limitation (hypoxia), arising as a key stress factor due to flooding, negatively affects plant development. Consequently, maintaining root growth under such stress is crucial for plant survival, yet we know little about the root system's adaptions to low-oxygen conditions and its regulation by phytohormones. In this study, we examine the impact of hypoxia and, herein, the regulatory role of group VII ETHYLENE-RESPONSE FACTOR (ERFVII) transcription factors on root growth in Arabidopsis. We found lateral root (LR) elongation to be actively maintained by hypoxia via ERFVII factors, as erfVII seedlings possess hypersensitivity towards hypoxia regarding their LR growth. Pharmacological inhibition of abscisic acid (ABA) biosynthesis revealed ERFVII-driven counteraction of hypoxia-induced inhibition of LR formation in an ABA-dependent manner. However, postemergence LR growth under hypoxia mediated by ERFVIIs was independent of ABA. In roots, ERFVIIs mediate, among others, the induction of ABA-degrading ABA 8'-hydroxylases CYP707A1 expression. RAP2.12 could activate the pCYC707A1:LUC reporter gene, indicating, combined with single mutant analyses, that this transcription factor regulates ABA levels through corresponding transcript upregulation. Collectively, hypoxia-induced adaptation of the Arabidopsis root system is shaped by developmental reprogramming, whereby ERFVII-dependent promotion of LR emergence, but not elongation, is partly executed through regulation of ABA degradation.
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Affiliation(s)
| | - Bettina Hause
- Department of Cell and Metabolic Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany
| | - Margret Sauter
- Plant Developmental Biology and Plant Physiology, University of Kiel, Kiel, Germany
| | - Romy R Schmidt-Schippers
- Department of Plant Biotechnology, University of Bielefeld, Institute of Biology, Bielefeld, Germany
- Center for Biotechnology, University of Bielefeld, Bielefeld, Germany
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2
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Triozzi PM, Brunello L, Novi G, Ferri G, Cardarelli F, Loreti E, Perales M, Perata P. Spatiotemporal oxygen dynamics in young leaves reveal cyclic hypoxia in plants. MOLECULAR PLANT 2024; 17:377-394. [PMID: 38243593 DOI: 10.1016/j.molp.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/15/2024] [Indexed: 01/21/2024]
Abstract
Oxygen is essential for plant growth and development. Hypoxia occurs in plants due to limited oxygen availability following adverse environmental conditions as well in hypoxic niches in otherwise normoxic environments. However, the existence and functional integration of spatiotemporal oxygen dynamics with plant development remains unknown. In animal systems dynamic fluctuations in oxygen availability are known as cyclic hypoxia. In this study, we demonstrate that cyclic fluctuations in internal oxygen levels occur in young emerging leaves of Arabidopsis plants. Cyclic hypoxia in plants is based on a mechanism requiring the ETHYLENE RESPONSE FACTORS type VII (ERFVII) that are central components of the oxygen-sensing machinery in plants. The ERFVII-dependent mechanism allows precise adjustment of leaf growth in response to carbon status and oxygen availability within plant cells. This study thus establishes a functional connection between internal spatiotemporal oxygen dynamics and developmental processes of plants.
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Affiliation(s)
- Paolo M Triozzi
- PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy; Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luca Brunello
- PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy
| | - Giacomo Novi
- PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy
| | | | - Francesco Cardarelli
- Laboratorio NEST, Scuola Normale Superiore, Istituto Nanoscienze-CNR, Piazza S. Silvestro, 12, 56127 Pisa, Italy
| | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, National Research Council, 56124 Pisa, Italy
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus de Montegancedo UPM, Pozuelo de Alarcón, 28223 Madrid, Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Pierdomenico Perata
- PlantLab, Center of Plant Sciences, Sant'Anna School of Advanced Studies, 56010 Pisa, Italy.
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3
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Koo D, Lee HG, Bae SH, Lee K, Seo PJ. Callus proliferation-induced hypoxic microenvironment decreases shoot regeneration competence in Arabidopsis. MOLECULAR PLANT 2024; 17:395-408. [PMID: 38297841 DOI: 10.1016/j.molp.2024.01.009] [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: 07/07/2023] [Revised: 12/10/2023] [Accepted: 01/23/2024] [Indexed: 02/02/2024]
Abstract
Plants are aerobic organisms that rely on molecular oxygen for respiratory energy production. Hypoxic conditions, with oxygen levels ranging between 1% and 5%, usually limit aerobic respiration and affect plant growth and development. Here, we demonstrate that the hypoxic microenvironment induced by active cell proliferation during the two-step plant regeneration process intrinsically represses the regeneration competence of the callus in Arabidopsis thaliana. We showed that hypoxia-repressed plant regeneration is mediated by the RELATED TO APETALA 2.12 (RAP2.12) protein, a member of the Ethylene Response Factor VII (ERF-VII) family. We found that the hypoxia-activated RAP2.12 protein promotes salicylic acid (SA) biosynthesis and defense responses, thereby inhibiting pluripotency acquisition and de novo shoot regeneration in calli. Molecular and genetic analyses revealed that RAP2.12 could bind directly to the SALICYLIC ACID INDUCTION DEFICIENT 2 (SID2) gene promoter and activate SA biosynthesis, repressing plant regeneration possibly via a PLETHORA (PLT)-dependent pathway. Consistently, the rap2.12 mutant calli exhibits enhanced shoot regeneration, which is impaired by SA treatment. Taken together, these findings uncover that the cell proliferation-dependent hypoxic microenvironment reduces cellular pluripotency and plant regeneration through the RAP2.12-SID2 module.
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Affiliation(s)
- Dohee Koo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Hong Gil Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
| | - Soon Hyung Bae
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Kyounghee Lee
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea; Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea; Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea.
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4
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Fagerstedt KV, Pucciariello C, Pedersen O, Perata P. Recent progress in understanding the cellular and genetic basis of plant responses to low oxygen holds promise for developing flood-resilient crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1217-1233. [PMID: 37991267 PMCID: PMC10901210 DOI: 10.1093/jxb/erad457] [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: 09/04/2023] [Accepted: 11/21/2023] [Indexed: 11/23/2023]
Abstract
With recent progress in active research on flooding and hypoxia/anoxia tolerance in native and agricultural crop plants, vast knowledge has been gained on both individual tolerance mechanisms and the general mechanisms of flooding tolerance in plants. Research on carbohydrate consumption, ethanolic and lactic acid fermentation, and their regulation under stress conditions has been accompanied by investigations on aerenchyma development and the emergence of the radial oxygen loss barrier in some plant species under flooded conditions. The discovery of the oxygen-sensing mechanism in plants and unravelling the intricacies of this mechanism have boosted this very international research effort. Recent studies have highlighted the importance of oxygen availability as a signalling component during plant development. The latest developments in determining actual oxygen concentrations using minute probes and molecular sensors in tissues and even within cells have provided new insights into the intracellular effects of flooding. The information amassed during recent years has been used in the breeding of new flood-tolerant crop cultivars. With the wealth of metabolic, anatomical, and genetic information, novel holistic approaches can be used to enhance crop species and their productivity under increasing stress conditions due to climate change and the subsequent changes in the environment.
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Affiliation(s)
- Kurt V Fagerstedt
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, PO Box 65, FI-00014, University of Helsinki, Finland
| | - Chiara Pucciariello
- PlantLab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, Pisa 56127, Italy
| | - Ole Pedersen
- The Freshwater Biological Laboratory, Department of Biology, University of Copenhagen, Universitetsparken 4, Copenhagen 2100, Denmark
- School of Biological Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, 6009 WA, Australia
| | - Pierdomenico Perata
- PlantLab, Center of Plant Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, Pisa 56127, Italy
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Yao S, Kim SC, Li J, Tang S, Wang X. Phosphatidic acid signaling and function in nuclei. Prog Lipid Res 2024; 93:101267. [PMID: 38154743 PMCID: PMC10843600 DOI: 10.1016/j.plipres.2023.101267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Membrane lipidomes are dynamic and their changes generate lipid mediators affecting various biological processes. Phosphatidic acid (PA) has emerged as an important class of lipid mediators involved in a wide range of cellular and physiological responses in plants, animals, and microbes. The regulatory functions of PA have been studied primarily outside the nuclei, but an increasing number of recent studies indicates that some of the PA effects result from its action in nuclei. PA levels in nuclei are dynamic in response to stimuli. Changes in nuclear PA levels can result from activities of enzymes associated with nuclei and/or from movements of PA generated extranuclearly. PA has also been found to interact with proteins involved in nuclear functions, such as transcription factors and proteins undergoing nuclear translocation in response to stimuli. The nuclear action of PA affects various aspects of plant growth, development, and response to stress and environmental changes.
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Affiliation(s)
- Shuaibing Yao
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Sang-Chul Kim
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Jianwu Li
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Shan Tang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA
| | - Xuemin Wang
- Department of Biology, University of Missouri-St. Louis, St. Louis, MO 63121, USA; Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
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6
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Yemelyanov VV, Puzanskiy RK, Shishova MF. Plant Life with and without Oxygen: A Metabolomics Approach. Int J Mol Sci 2023; 24:16222. [PMID: 38003412 PMCID: PMC10671363 DOI: 10.3390/ijms242216222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.
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Affiliation(s)
- Vladislav V. Yemelyanov
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Roman K. Puzanskiy
- Department of Plant Physiology and Biochemistry, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (R.K.P.); (M.F.S.)
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Maria F. Shishova
- Department of Plant Physiology and Biochemistry, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (R.K.P.); (M.F.S.)
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7
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Chi HY, Ou SL, Wang MC, Yang CY. Physiological responses and Ethylene-Response AP2/ERF Factor expression in Indica rice seedlings subjected to submergence and osmotic stress. BMC PLANT BIOLOGY 2023; 23:372. [PMID: 37501108 PMCID: PMC10373351 DOI: 10.1186/s12870-023-04380-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 07/12/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND The increased frequency of heavy rains in recent years has led to submergence stress in rice paddies, severely affecting rice production. Submergence causes not only hypoxic stress from excess water in the surrounding environment but also osmotic stress in plant cells. We assessed physiological responses and Ethylene-Response AP2/ERF Factor regulation under submergence conditions alone and with ionic or nonionic osmotic stress in submergence-sensitive IR64 and submergence-tolerant IR64-Sub1 Indica rice cultivars. RESULTS Our results indicate that both IR64 and IR64-Sub1 exhibited shorter plant heights and root lengths under submergence with nonionic osmotic stress than normal condition and submergence alone. IR64-Sub1 seedlings exhibited a significantly lower plant height under submergence conditions alone and with ionic or nonionic osmotic stress than IR64 cultivars. IR64-Sub1 seedlings also presented lower malondialdehyde (MDA) concentration and higher survival rates than did IR64 seedlings after submergence with ionic or nonionic osmotic stress treatment. Sub1A-1 affects reactive oxygen species (ROS) accumulation and antioxidant enzyme activity in rice. The results also show that hypoxia-inducible ethylene response factors (ERF)-VII group and alcohol dehydrogenase 1 (ADH1) and lactate dehydrogenase 1 (LDH1) genes exhibited different expression levels under nonionic or ionic osmotic stress during submergence on rice. CONCLUSIONS Together, these results demonstrate that complex regulatory mechanisms are involved in responses to the aforementioned forms of stress and offer new insights into the effects of submergence and osmotic stress on rice.
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Affiliation(s)
- Hsin-Yu Chi
- International Master Program of Agriculture, National Chung Hsing University, Taichung, 402, Taiwan
| | - Shang-Ling Ou
- Department of Agronomy, National Chung Hsing University, Taichung, 402, Taiwan
| | - Mao-Chang Wang
- Department of Accounting, Chinese Culture University, Taipei, 111, Taiwan
| | - Chin-Ying Yang
- Department of Agronomy, National Chung Hsing University, Taichung, 402, Taiwan.
- Smart Sustainable New Agriculture Research Center (SMARTer), National Chung Hsing University, Taichung, 402, Taiwan.
- Innovation and Development Center of Sustainable Agriculture (IDCSA), National Chung Hsing University, Taichung, 402, Taiwan.
- Advanced Plant and Food Biotechnology Center, National Chung Hsing University, Taichung, 402, Taiwan.
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8
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Shahid M, Singh UB, Khan MS, Singh P, Kumar R, Singh RN, Kumar A, Singh HV. Bacterial ACC deaminase: Insights into enzymology, biochemistry, genetics, and potential role in amelioration of environmental stress in crop plants. Front Microbiol 2023; 14:1132770. [PMID: 37180266 PMCID: PMC10174264 DOI: 10.3389/fmicb.2023.1132770] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/20/2023] [Indexed: 05/16/2023] Open
Abstract
Growth and productivity of crop plants worldwide are often adversely affected by anthropogenic and natural stresses. Both biotic and abiotic stresses may impact future food security and sustainability; global climate change will only exacerbate the threat. Nearly all stresses induce ethylene production in plants, which is detrimental to their growth and survival when present at higher concentrations. Consequently, management of ethylene production in plants is becoming an attractive option for countering the stress hormone and its effect on crop yield and productivity. In plants, ACC (1-aminocyclopropane-1-carboxylate) serves as a precursor for ethylene production. Soil microorganisms and root-associated plant growth promoting rhizobacteria (PGPR) that possess ACC deaminase activity regulate growth and development of plants under harsh environmental conditions by limiting ethylene levels in plants; this enzyme is, therefore, often designated as a "stress modulator." TheACC deaminase enzyme, encoded by the AcdS gene, is tightly controlled and regulated depending upon environmental conditions. Gene regulatory components of AcdS are made up of the LRP protein-coding regulatory gene and other regulatory components that are activated via distinct mechanisms under aerobic and anaerobic conditions. ACC deaminase-positive PGPR strains can intensively promote growth and development of crops being cultivated under abiotic stresses including salt stress, water deficit, waterlogging, temperature extremes, and presence of heavy metals, pesticides and other organic contaminants. Strategies for combating environmental stresses in plants, and improving growth by introducing the acdS gene into crop plants via bacteria, have been investigated. In the recent past, some rapid methods and cutting-edge technologies based on molecular biotechnology and omics approaches involving proteomics, transcriptomics, metagenomics, and next generation sequencing (NGS) have been proposed to reveal the variety and potential of ACC deaminase-producing PGPR that thrive under external stresses. Multiple stress-tolerant ACC deaminase-producing PGPR strains have demonstrated great promise in providing plant resistance/tolerance to various stressors and, therefore, it could be advantageous over other soil/plant microbiome that can flourish under stressed environments.
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Affiliation(s)
- Mohammad Shahid
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, India
- *Correspondence: Mohammad Shahid, ; Udai B. Singh, ; Prakash Singh,
| | - Udai B. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, India
- *Correspondence: Mohammad Shahid, ; Udai B. Singh, ; Prakash Singh,
| | - Mohammad Saghir Khan
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Prakash Singh
- Department of Plant Breeding and Genetics, Veer Kunwar Singh College of Agriculture, Bihar Agricultural University, Dumraon, India
- *Correspondence: Mohammad Shahid, ; Udai B. Singh, ; Prakash Singh,
| | - Ratan Kumar
- Krishi Vigyan Kendra, Rohtas, Bihar Agricultural University, Bikramganj, Bihar, India
| | - Raj Narian Singh
- Directorate of Extension Education, Bihar Agricultural University, Bhagalpur, Bihar, India
| | - Arun Kumar
- Swamy Keshwanand Rajasthan Agriculture University, Bikaner, Rajasthan, India
| | - Harsh V. Singh
- Plant-Microbe Interaction and Rhizosphere Biology Lab, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau, Uttar Pradesh, India
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9
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Weits DA, Zhou L, Giuntoli B, Carbonare LD, Iacopino S, Piccinini L, Lombardi L, Shukla V, Bui LT, Novi G, van Dongen JT, Licausi F. Acquisition of hypoxia inducibility by oxygen sensing N-terminal cysteine oxidase in spermatophytes. PLANT, CELL & ENVIRONMENT 2023; 46:322-338. [PMID: 36120894 PMCID: PMC10092093 DOI: 10.1111/pce.14440] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 08/23/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
N-terminal cysteine oxidases (NCOs) use molecular oxygen to oxidise the amino-terminal cysteine of specific proteins, thereby initiating the proteolytic N-degron pathway. To expand the characterisation of the plant family of NCOs (plant cysteine oxidases [PCOs]), we performed a phylogenetic analysis across different taxa in terms of sequence similarity and transcriptional regulation. Based on this survey, we propose a distinction of PCOs into two main groups. A-type PCOs are conserved across all plant species and are generally unaffected at the messenger RNA level by oxygen availability. Instead, B-type PCOs appeared in spermatophytes to acquire transcriptional regulation in response to hypoxia. The inactivation of two A-type PCOs in Arabidopsis thaliana, PCO4 and PCO5, is sufficient to activate the anaerobic response in young seedlings, whereas the additional removal of B-type PCOs leads to a stronger induction of anaerobic genes and impairs plant growth and development. Our results show that both PCO types are required to regulate the anaerobic response in angiosperms. Therefore, while it is possible to distinguish two clades within the PCO family, we conclude that they all contribute to restrain the anaerobic transcriptional programme in normoxic conditions and together generate a molecular switch to toggle the hypoxic response.
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Affiliation(s)
- Daan A. Weits
- Institute of Biology 1, Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Plant‐Environment Signaling, Institute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Lina Zhou
- Institute of Biology 1, Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
- School of Life SciencesLanzhou UniversityLanzhouChina
- School of Ecology and EnvironmentNorthwestern Polytechnical UniversityXi'anChina
| | - Beatrice Giuntoli
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Department of BiologyUniversity of PisaPisaItaly
| | | | - Sergio Iacopino
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Department of BiologyUniversity of PisaPisaItaly
- Department of Plant SciencesUniversity of OxfordOxfordUK
| | - Luca Piccinini
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
| | | | - Vinay Shukla
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
| | - Liem T. Bui
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Biotechnology Research and Development InstituteCan Tho UniversityCan ThoVietnam
| | - Giacomo Novi
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
| | - Joost T. van Dongen
- Institute of Biology 1, Aachen Biology and BiotechnologyRWTH Aachen UniversityAachenGermany
| | - Francesco Licausi
- Institute of Life SciencesScuola Superiore Sant'AnnaPisaItaly
- Department of BiologyUniversity of PisaPisaItaly
- Department of Plant SciencesUniversity of OxfordOxfordUK
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10
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Transcriptomic Analysis of Distal Parts of Roots Reveals Potentially Important Mechanisms Contributing to Limited Flooding Tolerance of Canola ( Brassica napus) Plants. Int J Mol Sci 2022; 23:ijms232415469. [PMID: 36555110 PMCID: PMC9779561 DOI: 10.3390/ijms232415469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Since most of the root metabolic activities as well as root elongation and the uptake of water and mineral nutrients take place in the distal parts of roots, we aimed to gain insight into the physiological and transcriptional changes induced by root hypoxia in the distal parts of roots in canola (Brassica napus) plants, which are relatively sensitive to flooding conditions. Plants were subject to three days of root hypoxia via lowering oxygen content in hydroponic medium, and various physiological and anatomical features were examined to characterize plant responses. Untargeted transcriptomic profiling approaches were also applied to investigate changes in gene expression that took place in the distal root tissues in response to hypoxia. Plants responded to three days of root hypoxia by reducing growth and gas exchange rates. These changes were accompanied by decreases in leaf water potential (Ψleaf) and root hydraulic conductivity (Lpr). Increased deposition of lignin and suberin was also observed in the root tissues of hypoxic plants. The transcriptomic data demonstrated that the effect of hypoxia on plant water relations involved downregulation of most BnPIPs in the root tissues with the exception of BnPIP1;3 and BnPIP2;7, which were upregulated. Since some members of the PIP1 subfamily of aquaporins are known to transport oxygen, the increase in BnPIP1;3 may represent an important hypoxia tolerance strategy in plants. The results also demonstrated substantial rearrangements of different signaling pathways and transcription factors (TFs), which resulted in alterations of genes involved in the regulation of Lpr, TCA (tricarboxylic acid) cycle-related enzymes, antioxidant enzymes, and cell wall modifications. An integration of these data enabled us to draft a comprehensive model of the molecular pathways involved in the responses of distal parts of roots in B. napus. The model highlights systematic transcriptomic reprogramming aimed at explaining the relative sensitivity of Brassica napus to root hypoxia.
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11
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Yang J, Mathew IE, Rhein H, Barker R, Guo Q, Brunello L, Loreti E, Barkla BJ, Gilroy S, Perata P, Hirschi KD. The vacuolar H+/Ca transporter CAX1 participates in submergence and anoxia stress responses. PLANT PHYSIOLOGY 2022; 190:2617-2636. [PMID: 35972350 PMCID: PMC9706465 DOI: 10.1093/plphys/kiac375] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/17/2022] [Indexed: 05/04/2023]
Abstract
A plant's oxygen supply can vary from normal (normoxia) to total depletion (anoxia). Tolerance to anoxia is relevant to wetland species, rice (Oryza sativa) cultivation, and submergence tolerance of crops. Decoding and transmitting calcium (Ca) signals may be an important component to anoxia tolerance; however, the contribution of intracellular Ca transporters to this process is poorly understood. Four functional cation/proton exchangers (CAX1-4) in Arabidopsis (Arabidopsis thaliana) help regulate Ca homeostasis around the vacuole. Our results demonstrate that cax1 mutants are more tolerant to both anoxic conditions and submergence. Using phenotypic measurements, RNA-sequencing, and proteomic approaches, we identified cax1-mediated anoxia changes that phenocopy changes present in anoxia-tolerant crops: altered metabolic processes, diminished reactive oxygen species production post anoxia, and altered hormone signaling. Comparing wild-type and cax1 expressing genetically encoded Ca indicators demonstrated altered cytosolic Ca signals in cax1 during reoxygenation. Anoxia-induced Ca signals around the plant vacuole are involved in the control of numerous signaling events related to adaptation to low oxygen stress. This work suggests that cax1 anoxia response pathway could be engineered to circumvent the adverse effects of flooding that impair production agriculture.
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Affiliation(s)
- Jian Yang
- Pediatrics-Nutrition, Children’s Nutrition Research, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Iny Elizebeth Mathew
- Pediatrics-Nutrition, Children’s Nutrition Research, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hormat Rhein
- Pediatrics-Nutrition, Children’s Nutrition Research, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Richard Barker
- Department of Botany, Birge Hall, University of Wisconsin, Wisconsin, USA
| | - Qi Guo
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Luca Brunello
- Plant Lab, Institute of Life Sciences, Scuola Superiore Sant'Anna, San Giuliano Terme, Pisa, Italy
| | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, National Research Council, 56124 Pisa, Italy
| | - Bronwyn J Barkla
- Southern Cross Plant Science, Southern Cross University, Lismore, New South Wales, Australia
| | - Simon Gilroy
- Department of Botany, Birge Hall, University of Wisconsin, Wisconsin, USA
| | - Pierdomenico Perata
- Plant Lab, Institute of Life Sciences, Scuola Superiore Sant'Anna, San Giuliano Terme, Pisa, Italy
| | - Kendal D Hirschi
- Pediatrics-Nutrition, Children’s Nutrition Research, Baylor College of Medicine, Houston, Texas 77030, USA
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12
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Pereira Neto LG, Rossini BC, Marino CL, Toorop PE, Silva EAA. Comparative Seeds Storage Transcriptome Analysis of Astronium fraxinifolium Schott, a Threatened Tree Species from Brazil. Int J Mol Sci 2022; 23:ijms232213852. [PMID: 36430327 PMCID: PMC9696909 DOI: 10.3390/ijms232213852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/12/2022] Open
Abstract
Astronium fraxinifolium Schott (Anacardiaceae), also known as a 'gonçalo-alves', is a tree of the American tropics, with distribution in Mexico, part of Central America, Argentina, Bolivia, Brazil and Paraguay. In Brazil it is an endangered species that occurs in the Cerrado, Caatinga and in the Amazon biomes. In support of ex situ conservation, this work aimed to study two accessions with different longevity (p50) of A. fraxinifolium collected from two different geographic regions, and to evaluate the transcriptome during aging of the seeds in order to identify genes related to seed longevity. Artificial ageing was performed at a constant temperature of 45 °C and 60% relative humidity. RNA was extracted from 100 embryonic axes exposed to control and aging conditions for 21 days. The transcriptome analysis revealed differentially expressed genes such as Late Embryogenesis Abundant (LEA) genes, genes involved in the photosystem, glycine rich protein (GRP) genes, and several transcription factors associated with embryo development and ubiquitin-conjugating enzymes. Thus, these results contribute to understanding which genes play a role in seed ageing, and may serve as a basis for future functional characterization of the seed aging process in A. fraxinifolium.
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Affiliation(s)
| | - Bruno Cesar Rossini
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Correspondence:
| | - Celso Luis Marino
- Biotechnology Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18607-440, Brazil
- Departament of Biological and Chemical Sciences, Biosciences Institute, São Paulo State University “Júlio de Mesquita Filho”, Botucatu 18618-689, Brazil
| | - Peter E. Toorop
- Department of Comparative Plant and Fungal Biology, Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN, UK
| | - Edvaldo Aparecido Amaral Silva
- Departamento de Produção Vegetal, Faculdade de Ciências Agronômicas, Universidade Estadual Paulista, Botucatu 18610-034, Brazil
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13
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Kumar P, Singh S, Pranaw K, Kumar S, Singh B, Poria V. Bioinoculants as mitigators of multiple stresses: A ray of hope for agriculture in the darkness of climate change. Heliyon 2022; 8:e11269. [DOI: 10.1016/j.heliyon.2022.e11269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/04/2022] [Accepted: 10/21/2022] [Indexed: 11/28/2022] Open
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14
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Agualongo DAP, Da-Silva CJ, Garcia N, de Oliveira FK, Shimoia EP, Posso DA, de Oliveira ACB, de Oliveira DDSC, do Amarante L. Waterlogging priming alleviates the oxidative damage, carbohydrate consumption, and yield loss in soybean ( Glycine max) plants exposed to waterlogging. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:1029-1042. [PMID: 35908797 DOI: 10.1071/fp22030] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
In this study, we tested whether waterlogging priming at the vegetative stage would mitigate a subsequent waterlogging event at the reproductive stage in soybean [Glycine max (L.) Merr.]. Plants (V3 stage) were subjected to priming for 7days and then exposed to waterlogging stress for 5days (R2 stage) with non-primed plants. Roots and leaves were sampled on the fifth day of waterlogging and the second and fifth days of reoxygenation. Overall, priming decreased the H2 O2 concentration and lipid peroxidation in roots and leaves during waterlogging and reoxygenation. Priming also decreased the activity of antioxidative enzymes in roots and leaves and increased the foliar concentration of phenols and photosynthetic pigments. Additionally, priming decreased fermentation and alanine aminotransferase activity during waterlogging and reoxygenation. Finally, priming increased the concentration of amino acids, sucrose, and total soluble sugars in roots and leaves during waterlogging and reoxygenation. Thus, primed plants were higher and more productive than non-primed plants. Our study shows that priming alleviates oxidative stress, fermentation, and carbohydrate consumption in parallel to increase the yield of soybean plants exposed to waterlogging and reoxygenation.
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Affiliation(s)
- Darwin Alexis Pomagualli Agualongo
- Departamento de Botânica, Universidade Federal de Pelotas, Capão do Leão 96160-000, Brazil; and State University of Bolívar, Guaranda 020150, Ecuador
| | | | - Natália Garcia
- Departamento de Botânica, Universidade Federal de Pelotas, Capão do Leão 96160-000, Brazil
| | | | | | - Douglas Antônio Posso
- Departamento de Botânica, Universidade Federal de Pelotas, Capão do Leão 96160-000, Brazil
| | | | | | - Luciano do Amarante
- Departamento de Botânica, Universidade Federal de Pelotas, Capão do Leão 96160-000, Brazil
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15
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Identification of Functional Genetic Variations Underlying Flooding Tolerance in Brazilian Soybean Genotypes. Int J Mol Sci 2022; 23:ijms231810611. [PMID: 36142529 PMCID: PMC9502317 DOI: 10.3390/ijms231810611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/23/2022] [Accepted: 09/05/2022] [Indexed: 11/21/2022] Open
Abstract
Flooding is a frequent environmental stress that reduces soybean (Glycine max) growth and grain yield in many producing areas in the world, such as, e.g., in the United States, Southeast Asia and Southern Brazil. In these regions, soybean is frequently cultivated in lowland areas by rotating with rice (Oryza sativa), which provides numerous technical, economic and environmental benefits. Given these realities, this work aimed to characterize physiological responses, identify genes differentially expressed under flooding stress in Brazilian soybean genotypes with contrasting flooding tolerance, and select SNPs with potential use for marker-assisted selection. Soybean cultivars TECIRGA 6070 (flooding tolerant) and FUNDACEP 62 (flooding sensitive) were grown up to the V6 growth stage and then flooding stress was imposed. Total RNA was extracted from leaves 24 h after the stress was imposed and sequenced. In total, 421 induced and 291 repressed genes were identified in both genotypes. TECIRGA 6070 presented 284 and 460 genes up- and down-regulated, respectively, under flooding conditions. Of those, 100 and 148 genes were exclusively up- and down-regulated, respectively, in the tolerant genotype. Based on the RNA sequencing data, SNPs in differentially expressed genes in response to flooding stress were identified. Finally, 38 SNPs, located in genes with functional annotation for response to abiotic stresses, were found in TECIRGA 6070 and absent in FUNDACEP 62. To validate them, 22 SNPs were selected for designing KASP assays that were used to genotype a panel of 11 contrasting genotypes with known phenotypes. In addition, the phenotypic and grain yield impacts were analyzed in four field experiments using a panel of 166 Brazilian soybean genotypes. Five SNPs possibly related to flooding tolerance in Brazilian soybean genotypes were identified. The information generated from this research will be useful to develop soybean genotypes adapted to poorly drained soils or areas subject to flooding.
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16
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Gao Y, Jiang Z, Shi M, Zhou Y, Huo L, Li X, Xu K. Comparative transcriptome provides insight into responding mechanism of waterlogging stress in Actinidia valvata Dunn. Gene 2022; 845:146843. [PMID: 36041594 DOI: 10.1016/j.gene.2022.146843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/20/2022] [Accepted: 08/23/2022] [Indexed: 11/04/2022]
Abstract
Kiwifruit is one of the most popular fruits, and the area of its cultivation in China has grown rapidly over the last decade. However, kiwifruit vines are vulnerable to waterlogging, especially in the extensive areas of south China where it is grown. This has become an important factor limiting yields. Therefore, it is necessary to clarify the responses of kiwifruit to waterlogging. Here, we have selected Actinidia valvata Dunn which is able to withstand waterlogging conditions and the waterlogging-susceptible Actinidia deliciosa to perform the RNA-seq of roots under waterlogging stress. Seedling roots of Actinidia valvata Dunn and Actinidia deliciosa presented distinct root phenotypes after waterlogging treatments. Genome mapping showed a large genome difference between Actinidia valvata Dunn and Actinidia deliciosa. Transcription factors MYB, MYB-related, AP2-EREBP, bHLH, WRKY, and NAC were identified as the key genes involved in the response to waterlogging stress of kiwifruit. Meanwhile, the MAPK signaling pathway and the glycolysis/gluconeogenesis pathway were identified as the vital pathways involved in the response to waterlogging, and key genes were identified from these two pathways. These results will broaden our understanding of transcriptional response of waterlogging stress and will provide new insights into the molecular mechanisms associated with waterlogging stress. Furthermore, identification of the genes responsible will assist in the breeding of kiwifruit tolerant of waterlogging.
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Affiliation(s)
- Yongbin Gao
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Zeyu Jiang
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Mengqi Shi
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Yifei Zhou
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Liuqing Huo
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China
| | - Xiaolong Li
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China.
| | - Kai Xu
- College of Horticulture Science, Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Zhejiang A & F University, Hangzhou, 311300, China.
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17
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Strawberry FaSnRK1α Regulates Anaerobic Respiratory Metabolism under Waterlogging. Int J Mol Sci 2022; 23:ijms23094914. [PMID: 35563305 PMCID: PMC9101944 DOI: 10.3390/ijms23094914] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Sucrose nonfermenting-1-related protein kinase 1 (SnRK1) is a central integrator of plant stress and energy starvation signalling pathways. We found that the FaSnRK1α-overexpression (OE) roots had a higher respiratory rate and tolerance to waterlogging than the FaSnRK1α-RNAi roots, suggesting that FaSnRK1α plays a positive role in the regulation of anaerobic respiration under waterlogging. FaSnRK1α upregulated the activity of anaerobic respiration-related enzymes including hexokinase (HK), phosphofructokinase (PFK), pyruvate kinase (PK), pyruvate decarboxylase (PDC), alcohol dehydrogenase (ADH) and lactate dehydrogenase (LDH). FaSnRK1α also enhanced the ability to quench reactive oxygen species (ROS) by increasing antioxidant enzyme activities. We sequenced the transcriptomes of the roots of both wild-type (WT) and FaSnRK1α-RNAi plants, and the differentially expressed genes (DEGs) were clearly enriched in the defence response, response to biotic stimuli, and cellular carbohydrate metabolic process. In addition, 42 genes involved in glycolysis and 30 genes involved in pyruvate metabolism were significantly regulated in FaSnRK1α-RNAi roots. We analysed the transcript levels of two anoxia-related genes and three ERFVIIs, and the results showed that FaADH1, FaPDC1, FaHRE2 and FaRAP2.12 were upregulated in response to FaSnRK1α, indicating that FaSnRK1α may be involved in the ethylene signalling pathway to improve waterlogging tolerance. In conclusion, FaSnRK1α increases the expression of ERFVIIs and further activates anoxia response genes, thereby enhancing anaerobic respiration metabolism in response to low-oxygen conditions during waterlogging.
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18
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Lei B, Chang W, Zhao H, Zhang K, Yu J, Yu S, Cai K, Zhang J, Lu K. Nitrogen application and differences in leaf number retained after topping affect the tobacco (Nicotiana tabacum) transcriptome and metabolome. BMC PLANT BIOLOGY 2022; 22:38. [PMID: 35045826 PMCID: PMC8767696 DOI: 10.1186/s12870-022-03426-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Agronomic treatments such as the application of nitrogen fertilizer and topping (removal of the inflorescence and top leaves) cause substantial changes in plant metabolism. To explore these changes, we conducted comparative transcriptomic and metabolomic analyses of leaves collected from four positions along the stem on plants exposed to two nitrogen doses and with different numbers of leaves retained after topping in tobacco (Nicotiana tabacum). RESULTS We identified 13,330 unique differentially expressed genes and 32 differentially abundant metabolites. Through RNA-seq and WGCNA analyze, we constructed 2 co-expression networks (green and blue) highly correlation to N application and leaf number retained, predicted a hub gene NtGER3 may play an important role in N metabolism related to amino acid (cysteine) through CK pathway in tobacco leaves, NtARFs may participated in modulating the auxin signal and N in bottom leaves and NtRAP2.12 as key gene involved in N regulation by ethylene pathway. What's more, our data prove C/N transformation and balance affect the "source - flow - sink" redistribution and remobilization in tobacco during growth and development process. CONCLUSIONS Overall, this comparative transcriptomics study provides novel insight into the complex molecular mechanisms underlying plant responses to different levels of nitrogen application and the number of leaves remaining after topping in plants.
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Affiliation(s)
- Bo Lei
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Wei Chang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Huina Zhao
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Kai Zhang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Jing Yu
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, China National Tobacco Corporation, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Kai Cai
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Jie Zhang
- Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China.
- Academy of Agricultural Sciences, Southwest University, Chongqing, 400715, China.
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, 400715, China.
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19
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León J. Protein Tyrosine Nitration in Plant Nitric Oxide Signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:859374. [PMID: 35360296 PMCID: PMC8963475 DOI: 10.3389/fpls.2022.859374] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 02/21/2022] [Indexed: 05/09/2023]
Abstract
Nitric oxide (NO), which is ubiquitously present in living organisms, regulates many developmental and stress-activated processes in plants. Regulatory effects exerted by NO lies mostly in its chemical reactivity as a free radical. Proteins are main targets of NO action as several amino acids can undergo NO-related post-translational modifications (PTMs) that include mainly S-nitrosylation of cysteine, and nitration of tyrosine and tryptophan. This review is focused on the role of protein tyrosine nitration on NO signaling, making emphasis on the production of NO and peroxynitrite, which is the main physiological nitrating agent; the main metabolic and signaling pathways targeted by protein nitration; and the past, present, and future of methodological and strategic approaches to study this PTM. Available information on identification of nitrated plant proteins, the corresponding nitration sites, and the functional effects on the modified proteins will be summarized. However, due to the low proportion of in vivo nitrated peptides and their inherent instability, the identification of nitration sites by proteomic analyses is a difficult task. Artificial nitration procedures are likely not the best strategy for nitration site identification due to the lack of specificity. An alternative to get artificial site-specific nitration comes from the application of genetic code expansion technologies based on the use of orthogonal aminoacyl-tRNA synthetase/tRNA pairs engineered for specific noncanonical amino acids. This strategy permits the programmable site-specific installation of genetically encoded 3-nitrotyrosine sites in proteins expressed in Escherichia coli, thus allowing the study of the effects of specific site nitration on protein structure and function.
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20
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Landi L, Peralta-Ruiz Y, Chaves-López C, Romanazzi G. Chitosan Coating Enriched With Ruta graveolens L. Essential Oil Reduces Postharvest Anthracnose of Papaya ( Carica papaya L.) and Modulates Defense-Related Gene Expression. FRONTIERS IN PLANT SCIENCE 2021; 12:765806. [PMID: 34858463 PMCID: PMC8632526 DOI: 10.3389/fpls.2021.765806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/05/2021] [Indexed: 06/13/2023]
Abstract
Anthracnose of papaya (Carica papaya L.) caused by the fungus Colletotrichum spp. is one of the most economically important postharvest diseases. Coating with chitosan (CS) and Ruta graveolens essential oil (REO) might represent a novel eco-friendly method to prevent postharvest anthracnose infection. These compounds show both antimicrobial and eliciting activities, although the molecular mechanisms in papaya have not been investigated to date. In this study, the effectiveness of CS and REO alone and combined (CS-REO) on postharvest anthracnose of papaya fruit during storage were investigated, along with the expression of selected genes involved in plant defense mechanisms. Anthracnose incidence was reduced with CS, REO, and CS-REO emulsions after 9 days storage at 25°C, by 8, 21, and 37%, respectively, with disease severity reduced by 22, 29, and 44%, respectively. Thus, McKinney's decay index was reduced by 22, 30, and 44%, respectively. A protocol based on reverse transcription quantitative real-time PCR (RT-qPCR) was validated for 17 papaya target genes linked to signaling pathways that regulate plant defense, pathogenesis-related protein, cell wall-degrading enzymes, oxidative stress, abiotic stress, and the phenylpropanoid pathway. CS induced gene upregulation mainly at 6 h posttreatment (hpt) and 48 hpt, while REO induced the highest upregulation at 0.5 hpt, which then decreased over time. Furthermore, CS-REO treatment delayed gene upregulation by REO alone, from 0.5 to 6 hpt, and kept that longer over time. This study suggests that CS stabilizes the volatile and/or hydrophobic substances of highly reactive essential oils. The additive effects of CS and REO were able to reduce postharvest decay and affect gene expression in papaya fruit.
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Affiliation(s)
- Lucia Landi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
| | - Yeimmy Peralta-Ruiz
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
- Facultad de Ingeniería, Programa de Ingeniería Agroindustrial, Universidad del Atlántico, Puerto Colombia, Colombia
| | - Clemencia Chaves-López
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, Teramo, Italy
| | - Gianfranco Romanazzi
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
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21
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Considine MJ, Foyer CH. Oxygen and reactive oxygen species-dependent regulation of plant growth and development. PLANT PHYSIOLOGY 2021; 186:79-92. [PMID: 33793863 PMCID: PMC8154071 DOI: 10.1093/plphys/kiaa077] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/29/2020] [Indexed: 05/04/2023]
Abstract
Oxygen and reactive oxygen species (ROS) have been co-opted during evolution into the regulation of plant growth, development, and differentiation. ROS and oxidative signals arising from metabolism or phytohormone-mediated processes control almost every aspect of plant development from seed and bud dormancy, liberation of meristematic cells from the quiescent state, root and shoot growth, and architecture, to flowering and seed production. Moreover, the phytochrome and phytohormone-dependent transmissions of ROS waves are central to the systemic whole plant signaling pathways that integrate root and shoot growth. The sensing of oxygen availability through the PROTEOLYSIS 6 (PRT6) N-degron pathway functions alongside ROS production and signaling but how these pathways interact in developing organs remains poorly understood. Considerable progress has been made in our understanding of the nature of hydrogen peroxide sensors and the role of thiol-dependent signaling networks in the transmission of ROS signals. Reduction/oxidation (redox) changes in the glutathione (GSH) pool, glutaredoxins (GRXs), and thioredoxins (TRXs) are important in the control of growth mediated by phytohormone pathways. Although, it is clear that the redox states of proteins involved in plant growth and development are controlled by the NAD(P)H thioredoxin reductase (NTR)/TRX and reduced GSH/GRX systems of the cytosol, chloroplasts, mitochondria, and nucleus, we have only scratched the surface of this multilayered control and how redox-regulated processes interact with other cell signaling systems.
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Affiliation(s)
- Michael J Considine
- The School of Molecular Sciences, The University of Western Australia, Perth, Western Australia 6009, Australia
| | - Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, B15 2TT, UK
- Author for communication:
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22
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Harada T, Horiguchi I, Ueyama S, Murai A, Tsuzuki C. Comprehensive analysis of sucrolytic enzyme gene families in carnation (Dianthus caryophyllus L.). PHYTOCHEMISTRY 2021; 185:112607. [PMID: 33774571 DOI: 10.1016/j.phytochem.2020.112607] [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: 03/05/2020] [Revised: 11/09/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Sucrose plays crucial roles in growth and responses of plants to the environment, including those in ornamental species. During post-harvest handling of cut flowers, sucrose degradation is an essential process of inter- and intra-cellular carbon partitioning affecting flower opening and senescence and, subsequently, flower quality. However, complete information about the molecular basis of sucrose degradation in ornamental flowers, which can be catalyzed by two kinds of sucrolytic enzymes, invertase (INV), and sucrose synthase (SUS), is not available from past reports. The present study shows that sucrose treatment of carnation (Dianthus caryophyllus L.) florets increased starch content in petals, accompanied by decreased vacuolar INV (VIN) activity and increased SUS activity. However, hypoxic treatment of carnation florets decreased sucrose content and cell-wall INV (CWIN) activity in petals. In silico analysis using the carnation genome database identified six CWIN, three VIN, eight cytoplasmic INV (CIN), and five SUS genes. Real-time RT-PCR analysis confirmed that these genes are differentially expressed in carnation petals in response to sucrose and hypoxic treatments, partially corresponding to the changes in enzyme activities. In contrast to DcSUS1 (Dca4507.1), a SUS gene already reported in carnation, which showed preferential expression under aerated conditions, the expression of DcSUS2 (Dca22218.1), an undescribed carnation SUS gene, was enhanced under hypoxia similarly to an alcohol dehydrogenase gene DcADH1 (Dca18671.1). These results suggest that sugar metabolism in carnation petals is regulated in response to environmental cues, accompanied by modulated activities and gene expression of a set of sucrolytic enzymes.
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Affiliation(s)
- Taro Harada
- Graduate School of Education, Okayama University, Okayama, 700-8530, Japan.
| | - Itsuku Horiguchi
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
| | - Sayaka Ueyama
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
| | - Ai Murai
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
| | - Chie Tsuzuki
- Department of Science Education, Faculty of Education, Okayama University, Okayama, 700-8530, Japan
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Kou SM, Jin R, Wu YY, Huang JW, Zhang QY, Sun NJ, Yang Y, Guan CF, Wang WQ, Zhu CQ, Zhu QG, Yin XR. Transcriptome Analysis Revealed the Roles of Carbohydrate Metabolism on Differential Acetaldehyde Production Capacity in Persimmon Fruit in Response to High-CO 2 Treatment. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:836-845. [PMID: 33416310 DOI: 10.1021/acs.jafc.0c06001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Persimmon (Diospyros kaki Thunb.) fruit is unique due to the continuous accumulation of soluble tannins during fruit development in most cultivars, which causes undesired astringency. High-CO2 treatment was the most effective widely used method for astringency removal. However, differential effects of high-CO2 treatment between cultivars were observed and the molecular basis remained inclusive. Previously, one cultivar ("Luoyangfangtianshengshi," LYFTSS) showed rapid deastringency, while two cultivars ("Shijiazhuanglianhuashi," SJZLHS; "Laopige," LPG) showed slow deastringency in response to high-CO2 (95% CO2) treatment. In this study, the metabolites (acetaldehyde and ethanol) related to deastringency were further analyzed and both acetaldehyde and ethanol were higher in SJZLHS and LYFTSS than that in LPG, where acetaldehyde was undetectable. Based on the RNA-seq data, the weighted gene coexpression network analysis (WGCNA) revealed that one module, comprised of 1773 unigenes, significantly correlated with the contents of acetaldehyde and ethanol (P < 0.001). Further analysis based on the acetaldehyde metabolism pathway indicated that the differentially expressed structural genes, including previously characterized DkADH and DkPDC and also their upstream members (e.g., PFK, phosphofructokinase), showed positive correlations with acetaldehyde production. Quantitative analysis of the precursor substances indicated that sucrose, glucose, and fructose exhibited limited differences between cultivar except for malic acid. However, the content of malic acid is much less than the total soluble sugar content. To verify the correlations between these genes and acetaldehyde production, the fruit from 14 more cultivars were collected and treated with high CO2. After the treatment, acetaldehyde contents in different cultivars ranked in 30.4-255.5 μg/g FW. Real-time polymerase chain reaction (PCR) and correlation analysis indicated that the EVM0002315 (PFK) gene, belonging to carbohydrate metabolism, was significantly correlated with acetaldehyde content in fruit. Thus, it could be proposed that the differentially expressed carbohydrate metabolism related genes (especially PFK) are the basis for the variance of acetaldehyde production among different persimmon cultivars.
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Affiliation(s)
- Su-Mei Kou
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Rong Jin
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- Agricultural Experiment Station, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Ying-Ying Wu
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Jing-Wen Huang
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Qiu-Yun Zhang
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Ning-Jing Sun
- College of Resources and Environment Sciences, Baoshan University, Baoshan 678000, Yunnan, P. R. China
| | - Yong Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, P. R. China
| | - Chang-Fei Guan
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, P. R. China
| | - Wen-Qiu Wang
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Chang-Qing Zhu
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
| | - Qing-Gang Zhu
- College of Horticulture, Northwest A&F University, Yangling 712100, Shannxi, P. R. China
| | - Xue-Ren Yin
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, Zhejiang, P. R. China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Department of Horticulture, Zhejiang University, Zijingang Campus, Hangzhou 310058, P. R. China
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24
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Cho HY, Loreti E, Shih MC, Perata P. Energy and sugar signaling during hypoxia. THE NEW PHYTOLOGIST 2021; 229:57-63. [PMID: 31733144 DOI: 10.1111/nph.16326] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
The major consequence of hypoxia is a dramatic reduction in energy production. At the onset of hypoxia, both oxygen and ATP availability decrease. Oxygen and energy sensing therefore converge to induce an adaptive response at both the transcriptional and translational levels. Oxygen sensing results in stabilization of the transcription factors that activate hypoxia-response genes, including enzymes required for efficient sugar metabolism, allowing plants to produce enough energy to ensure survival. The translation of the resulting mRNAs is mediated by SnRK1, acting as an energy sensor. However, as soon as the sugar availability decreases, a homeostatic mechanism, detecting sugar starvation, dampens the hypoxia-dependent transcription to reduce energy consumption and preserves carbon reserves for regrowth when oxygen availability is restored.
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Affiliation(s)
- Hsing-Yi Cho
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Elena Loreti
- Institute of Agricultural Biology and Biotechnology, CNR, National Research Council, Via Moruzzi 1, 56124, Pisa, Italy
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Pierdomenico Perata
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Via Giudiccioni 10, 56010, San Giuliano Terme, Pisa, Italy
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25
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Moenga SM, Gai Y, Carrasquilla-Garcia N, Perilla-Henao LM, Cook DR. Gene co-expression analysis reveals transcriptome divergence between wild and cultivated chickpea under drought stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1195-1214. [PMID: 32920943 DOI: 10.1111/tpj.14988] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 08/21/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
Ancestral adaptations in crop wild relatives can provide a genetic reservoir for crop improvement. Here we document physiological changes to mild and severe drought stress, and the associated transcriptome dynamics in both wild and cultivated chickpea. Over 60% of transcriptional changes were related to metabolism, indicating that metabolic plasticity is a core and conserved drought response. In addition, changes in RNA processing and protein turnover were predominant in the data, suggestive of broad restructuring of the chickpea proteome in response to drought. While 12% of the drought-responsive transcripts have similar dynamics in cultivated and wild accessions, numerous transcripts had expression patterns unique to particular genotypes, or that distinguished wild from cultivated genotypes and whose divergence may be a consequence of domestication. These and other comparisons provide a transcriptional correlate of previously described species' genetic diversity, with wild accessions well differentiated from each other and from cultivars, and cultivars essentially indistinguishable at the broad transcriptome level. We identified metabolic pathways such as phenylpropanoid metabolism, and biological processes such as stomatal development, which are differentially regulated across genotypes with potential consequences on drought tolerance. These data indicate that wild Cicer reticulatum may provide both conserved and divergent mechanisms as a resource in breeding for drought tolerance in cultivated chickpea.
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Affiliation(s)
- Susan M Moenga
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Yunpeng Gai
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
- Institute of Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Laura M Perilla-Henao
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
| | - Douglas R Cook
- Department of Plant Pathology and Plant Biology Graduate Group, University of California Davis, Davis, CA, 95616, USA
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26
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White MD, Dalle Carbonare L, Lavilla Puerta M, Iacopino S, Edwards M, Dunne K, Pires E, Levy C, McDonough MA, Licausi F, Flashman E. Structures of Arabidopsis thaliana oxygen-sensing plant cysteine oxidases 4 and 5 enable targeted manipulation of their activity. Proc Natl Acad Sci U S A 2020; 117:23140-23147. [PMID: 32868422 PMCID: PMC7502726 DOI: 10.1073/pnas.2000206117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
In higher plants, molecular responses to exogenous hypoxia are driven by group VII ethylene response factors (ERF-VIIs). These transcriptional regulators accumulate in the nucleus under hypoxia to activate anaerobic genes but are destabilized in normoxic conditions through the action of oxygen-sensing plant cysteine oxidases (PCOs). The PCOs catalyze the reaction of oxygen with the conserved N-terminal cysteine of ERF-VIIs to form cysteine sulfinic acid, triggering degradation via the Cys/Arg branch of the N-degron pathway. The PCOs are therefore a vital component of the plant oxygen signaling system, connecting environmental stimulus with cellular and physiological response. Rational manipulation of PCO activity could regulate ERF-VII levels and improve flood tolerance, but requires detailed structural information. We report crystal structures of the constitutively expressed PCO4 and PCO5 from Arabidopsis thaliana to 1.24 and 1.91 Å resolution, respectively. The structures reveal that the PCOs comprise a cupin-like scaffold, which supports a central metal cofactor coordinated by three histidines. While this overall structure is consistent with other thiol dioxygenases, closer inspection of the active site indicates that other catalytic features are not conserved, suggesting that the PCOs may use divergent mechanisms to oxidize their substrates. Conservative substitution of two active site residues had dramatic effects on PCO4 function both in vitro and in vivo, through yeast and plant complementation assays. Collectively, our data identify key structural elements that are required for PCO activity and provide a platform for engineering crops with improved hypoxia tolerance.
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Affiliation(s)
- Mark D White
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
- School of Chemistry, University of Sydney, Sydney NSW 2006, Australia
| | | | - Mikel Lavilla Puerta
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56010 Pisa, Italy
| | - Sergio Iacopino
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Martin Edwards
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Kate Dunne
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Elisabete Pires
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology, University of Manchester, M1 7DN Manchester, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom
| | - Francesco Licausi
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant'Anna, 56010 Pisa, Italy
- Department of Plant Sciences, University of Oxford, OX1 3RB Oxford, United Kingdom
| | - Emily Flashman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA Oxford, United Kingdom;
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27
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Juntawong P, Butsayawarapat P, Songserm P, Pimjan R, Vuttipongchaikij S. Overexpression of Jatropha curcas ERFVII2 Transcription Factor Confers Low Oxygen Tolerance in Transgenic Arabidopsis by Modulating Expression of Metabolic Enzymes and Multiple Stress-Responsive Genes. PLANTS 2020; 9:plants9091068. [PMID: 32825465 PMCID: PMC7570394 DOI: 10.3390/plants9091068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022]
Abstract
Enhancing crop tolerance to waterlogging is critical for improving food and biofuel security. In waterlogged soils, roots are exposed to a low oxygen environment. The group VII ethylene response factors (ERFVIIs) were recently identified as key regulators of plant low oxygen response. Oxygen-dependent N-end rule pathways can regulate the stability of ERFVIIs. This study aims to characterize the function of the Jatropha curcas ERFVIIs and the impact of N-terminal modification that stabilized the protein toward low oxygen response. This study revealed that all three JcERFVII proteins are substrates of the N-end rule pathway. Overexpression of JcERFVII2 conferred tolerance to low oxygen stress in Arabidopsis. In contrast, the constitutive overexpression of stabilized JcERFVII2 reduced low oxygen tolerance. RNA-seq was performed to elucidate the functional roles of JcERFVII2 and the impact of its N-terminal modification. Overexpression of both wildtype and stabilized JcERFVII2 constitutively upregulated the plant core hypoxia-responsive genes. Besides, overexpression of the stabilized JcERFVII2 further upregulated various genes controlling fermentative metabolic processes, oxidative stress, and pathogen responses under aerobic conditions. In summary, JcERFVII2 is an N-end rule regulated waterlogging-responsive transcription factor that modulates the expression of multiple stress-responsive genes; therefore, it is a potential candidate for molecular breeding of multiple stress-tolerant crops.
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Affiliation(s)
- Piyada Juntawong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Correspondence: or ; Tel.: +66-02-562-5555
| | - Pimprapai Butsayawarapat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
| | - Pattralak Songserm
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
| | - Ratchaneeporn Pimjan
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand; (P.B.); (P.S.); (R.P.); (S.V.)
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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28
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Shukla V, Lombardi L, Pencik A, Novak O, Weits DA, Loreti E, Perata P, Giuntoli B, Licausi F. Jasmonate Signalling Contributes to Primary Root Inhibition Upon Oxygen Deficiency in Arabidopsis thaliana. PLANTS 2020; 9:plants9081046. [PMID: 32824502 PMCID: PMC7464498 DOI: 10.3390/plants9081046] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/01/2022]
Abstract
Plants, including most crops, are intolerant to waterlogging, a stressful condition that limits the oxygen available for roots, thereby inhibiting their growth and functionality. Whether root growth inhibition represents a preventive measure to save energy or is rather a consequence of reduced metabolic rates has yet to be elucidated. In the present study, we gathered evidence for hypoxic repression of root meristem regulators that leads to root growth inhibition. We also explored the contribution of the hormone jasmonic acid (JA) to this process in Arabidopsis thaliana. Analysis of transcriptomic profiles, visualisation of fluorescent reporters and direct hormone quantification confirmed the activation of JA signalling under hypoxia in the roots. Further, root growth assessment in JA-related mutants in aerobic and anaerobic conditions indicated that JA signalling components contribute to active root inhibition under hypoxia. Finally, we show that the oxygen-sensing transcription factor (TF) RAP2.12 can directly induce Jasmonate Zinc-finger proteins (JAZs), repressors of JA signalling, to establish feedback inhibition. In summary, our study sheds new light on active root growth restriction under hypoxic conditions and on the involvement of the JA hormone in this process and its cross talk with the oxygen sensing machinery of higher plants.
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Affiliation(s)
- Vinay Shukla
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (V.S.); (D.A.W.); (P.P.); (B.G.)
| | - Lara Lombardi
- Department of Biology, University of Pisa, 56126 Pisa, Italy;
| | - Ales Pencik
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Ondrej Novak
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany, The Czech Academy of Sciences, CZ-783 71 Olomouc, Czech Republic; (A.P.); (O.N.)
| | - Daan A. Weits
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (V.S.); (D.A.W.); (P.P.); (B.G.)
| | - Elena Loreti
- The Institute of Agricultural Biology and Biotechnology, National Research Council, 20133 Milan, Italy;
| | - Pierdomenico Perata
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (V.S.); (D.A.W.); (P.P.); (B.G.)
| | - Beatrice Giuntoli
- Plantlab, Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy; (V.S.); (D.A.W.); (P.P.); (B.G.)
- Department of Biology, University of Pisa, 56126 Pisa, Italy;
| | - Francesco Licausi
- Department of Biology, University of Pisa, 56126 Pisa, Italy;
- Department of Plant Sciences, University of Oxford, Oxford OX1 3RB, UK
- Correspondence:
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29
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Ogden AJ, Wietsma TW, Winkler T, Farris Y, Myers GL, Ahkami AH. Dynamics of Global Gene Expression and Regulatory Elements in Growing Brachypodium Root System. Sci Rep 2020; 10:7071. [PMID: 32341392 PMCID: PMC7184759 DOI: 10.1038/s41598-020-63224-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022] Open
Abstract
Root systems are dynamic and adaptable organs that play critical roles in plant development. However, how roots grow and accumulate biomass during plant life cycle and in relation to shoot growth phenology remains understudied. A comprehensive time-dependent root morphological analysis integrated with molecular signatures is then required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root morphology, biomass production, and C/N ratios during developmental stages. To provide insight into gene regulation that accompanies root growth, we generated comprehensive transcript profiles of Brachypodium whole-root system at four developmental stages. Our data analysis revealed that multiple biological processes including trehalose metabolism and various families of transcription factors (TFs) were differentially expressed in root system during plant development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated as plant entered the booting/heading stage, while ARFs and GRFs were downregulated suggesting these TF families as important factors involved in specific phases of rooting, and possibly in regulation of transition to plant reproductive stages. We identified several Brachypodium candidate root biomass-promoting genes and cis-regulatory elements for further functional validations and root growth improvements in grasses.
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Affiliation(s)
- Aaron J Ogden
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Thomas W Wietsma
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Tanya Winkler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Yuliya Farris
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Gabriel L Myers
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington, USA.
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30
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Zhou W, Chen F, Meng Y, Chandrasekaran U, Luo X, Yang W, Shu K. Plant waterlogging/flooding stress responses: From seed germination to maturation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 148:228-236. [PMID: 31981875 DOI: 10.1016/j.plaphy.2020.01.020] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 05/27/2023]
Abstract
Global climate change is strongly associated with variations in precipitation and flooding events. Flooding usually causes submergence- or partial submergence stress in plants, which significantly has a negative influence on agricultural production, from seed germination to vegetative and reproductive growth. Flooding stress results in crop growth under low oxygen conditions and thus, negatively affects the developmental periods of plant lifecycle. The survival strategies of different plant species under this stressful condition are distinct, whereas the perception pathways associated with flooding stress are similar at the molecular level. Plants respond to flooding stress by mediating changes in their architecture, energy metabolism, photosynthesis, respiration and endogenous phytohormone biosynthesis/signaling, because aerobic respiration is inhibited under flooding stress, the decrease of energy metabolism further constrains plant development. Consequently, to acclimate under these unfavorable conditions, the anaerobic respiration cascade must be promoted. In this updated review, we primarily focus on recent advances in our understanding of the mechanisms underlying plant responses to flooding stress. We summarize the functions of the flooding response factors involved in energy metabolism and phytohormone biosynthesis/signaling cascades. Finally, the current understanding of how plants circumvent flooding stress, and the potential challenges for future research, are discussed.
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Affiliation(s)
- Wenguan Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China; Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Feng Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China; Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yongjie Meng
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | | | - Xiaofeng Luo
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China; Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Wenyu Yang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, 611130, China
| | - Kai Shu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, 710129, China.
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31
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Rauf M, Awais M, Ud-Din A, Ali K, Gul H, Rahman MM, Hamayun M, Arif M. Molecular Mechanisms of the 1-Aminocyclopropane-1-Carboxylic Acid (ACC) Deaminase Producing Trichoderma asperellum MAP1 in Enhancing Wheat Tolerance to Waterlogging Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:614971. [PMID: 33537050 PMCID: PMC7847992 DOI: 10.3389/fpls.2020.614971] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/17/2020] [Indexed: 05/18/2023]
Abstract
Waterlogging stress (WS) induces ethylene (ET) and polyamine (spermine, putrescine, and spermidine) production in plants, but their reprogramming is a decisive element for determining the fate of the plant upon waterlogging-induced stress. WS can be challenged by exploring symbiotic microbes that improve the plant's ability to grow better and resist WS. The present study deals with identification and application of 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase-producing fungal endophyte Trichoderma asperellum (strain MAP1), isolated from the roots of Canna indica L., on wheat growth under WS. MAP1 positively affected wheat growth by secreting phytohormones/secondary metabolites, strengthening the plant's antioxidant system and influencing the physiology through polyamine production and modulating gene expression. MAP1 inoculation promoted yield in comparison to non-endophyte inoculated waterlogged seedlings. Exogenously applied ethephon (ET synthesis inducer) and 1-aminocyclopropane carboxylic acid (ACC; ET precursor) showed a reduction in growth, compared to MAP1-inoculated waterlogged seedlings, while amino-oxyacetic acid (AOA; ET inhibitor) application reversed the negative effect imposed by ET and ACC, upon waterlogging treatment. A significant reduction in plant growth rate, chlorophyll content, and stomatal conductance was noticed, while H2O2, MDA production, and electrolyte leakage were increased in non-inoculated waterlogged seedlings. Moreover, in comparison to non-inoculated waterlogged wheat seedlings, MAP1-inoculated waterlogged wheat exhibited antioxidant-enzyme activities. In agreement with the physiological results, genes associated with the free polyamine (PA) biosynthesis were highly induced and PA content was abundant in MAP1-inoculated seedlings. Furthermore, ET biosynthesis/signaling gene expression was reduced upon MAP1 inoculation under WS. Briefly, MAP1 mitigated the adverse effect of WS in wheat, by reprogramming the PAs and ET biosynthesis, which leads to optimal stomatal conductance, increased photosynthesis, and membrane stability as well as reduced ET-induced leaf senescence.
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Affiliation(s)
- Mamoona Rauf
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Awais
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
- Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin-si, South Korea
| | - Aziz Ud-Din
- Department of Biotechnology and Genetic Engineering, Hazara University Mansehra, Mansehra, Pakistan
| | - Kazim Ali
- National Agricultural Research Center (NARC), National Institute for Genomics and Advanced Biotechnology, Islamabad, Pakistan
| | - Humaira Gul
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Mizanur Rahman
- Department of Biotechnology and Genetic Engineering, Islamic University, Kushtia, Bangladesh
| | - Muhammad Hamayun
- Department of Botany, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muhammad Arif
- Department of Biotechnology, Abdul Wali Khan University Mardan, Mardan, Pakistan
- *Correspondence: Muhammad Arif,
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Lee TA, Bailey-Serres J. Integrative Analysis from the Epigenome to Translatome Uncovers Patterns of Dominant Nuclear Regulation during Transient Stress. THE PLANT CELL 2019; 31:2573-2595. [PMID: 31519798 PMCID: PMC6881120 DOI: 10.1105/tpc.19.00463] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/21/2019] [Accepted: 09/12/2019] [Indexed: 05/19/2023]
Abstract
Gene regulation is a dynamic process involving changes ranging from the remodeling of chromatin to preferential translation. To understand integrated nuclear and cytoplasmic gene regulatory dynamics, we performed a survey spanning the epigenome to translatome of Arabidopsis (Arabidopsis thaliana) seedlings in response to hypoxia and reoxygenation. This included chromatin assays (examining histones, accessibility, RNA polymerase II [RNAPII], and transcription factor binding) and three RNA assays (nuclear, polyadenylated, and ribosome-associated). Dynamic patterns of nuclear regulation distinguished stress-induced and growth-associated mRNAs. The rapid upregulation of hypoxia-responsive gene transcripts and their preferential translation were generally accompanied by increased chromatin accessibility, RNAPII engagement, and reduced Histone 2A.Z association. Hypoxia promoted a progressive upregulation of heat stress transcripts, as evidenced by RNAPII binding and increased nuclear RNA, with polyadenylated RNA levels only elevated after prolonged stress or reoxygenation. Promoters of rapidly versus progressively upregulated genes were enriched for cis-elements of ethylene-responsive and heat shock factor transcription factors, respectively. Genes associated with growth, including many encoding cytosolic ribosomal proteins, underwent distinct histone modifications, yet retained RNAPII engagement and accumulated nuclear transcripts during the stress. Upon reaeration, progressively upregulated and growth-associated gene transcripts were rapidly mobilized to ribosomes. Thus, multilevel nuclear regulation of nucleosomes, transcript synthesis, accumulation, and translation tailor transient stress responses.plantcell;31/11/2573/FX1F1fx1.
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Affiliation(s)
- Travis A Lee
- Center for Plant Cell Biology and Botany and Plant Sciences Department, University of California, Riverside, California 92521
| | - Julia Bailey-Serres
- Center for Plant Cell Biology and Botany and Plant Sciences Department, University of California, Riverside, California 92521
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Premkumar A, Lindberg S, Lager I, Rasmussen U, Schulz A. Arabidopsis PLDs with C2-domain function distinctively in hypoxia. PHYSIOLOGIA PLANTARUM 2019; 167:90-110. [PMID: 30417386 DOI: 10.1111/ppl.12874] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/31/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Hypoxia (oxygen deprivation) causes metabolic disturbances at physiological, biochemical and genetic levels and results in decreased plant growth and development. Phospholipase D (PLD)-mediated signaling was reported for abiotic and biotic stress signaling events in plants. To investigate the participatory role of PLDs also in hypoxia signaling, we used wild type of Arabidopsis thaliana and 10 pld isoform mutants containing C2-domain. Hypoxia-induced changes in three major signaling players, namely, cytosolic free calcium (Ca2+ cyt ), reactive oxygen species (ROS) and phosphatidic acid (PA), were determined in mesophyll protoplasts. The Ca2+ cyt and ROS levels were monitored by fluorescence microscopy and confocal imaging, while PA levels were quantified by an enzymatic method. Our findings reveal that the elevations of cytosolic calcium and PA are reduced in all the 10 mutants dysfunctional in PLD isoforms. The hypoxia-related changes in both calcium and ROS show different kinetic patterns depending on the type of PLD studied. Pharmacological experiments confirm that both external and internal sources contribute to calcium and ROS accumulation under hypoxia. PLDα1-3, PLDβ1 and PLDγ1-3 are likely involved in calcium signaling under hypoxia as well as in PA production, while all investigated PLDs, except for PLDγ3, take part in ROS elevation.
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Affiliation(s)
- Albert Premkumar
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Sylvia Lindberg
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Ida Lager
- Department of Plant Breeding, Swedish University of Agricultural Sciences, SE-230 53 Alnarp, Sweden
| | - Ulla Rasmussen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Alexander Schulz
- Center for Advanced Bioimaging, Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Fredriksberg, Denmark
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Armstrong W, Beckett PM, Colmer TD, Setter TL, Greenway H. Tolerance of roots to low oxygen: 'Anoxic' cores, the phytoglobin-nitric oxide cycle, and energy or oxygen sensing. JOURNAL OF PLANT PHYSIOLOGY 2019; 239:92-108. [PMID: 31255944 DOI: 10.1016/j.jplph.2019.04.010] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 04/19/2019] [Accepted: 04/19/2019] [Indexed: 06/09/2023]
Abstract
Acclimation by plants to hypoxia and anoxia is of importance in various ecological systems, and especially for roots in waterlogged soil. We present evidence for acclimation by roots via 'anoxic' cores rather than being triggered by O2 sensors. The evidence for 'anoxic' cores comes from radial O2 profiles across maize roots and associated metabolic changes such as increases in the 'anaerobic enzymes' ADH and PDC in the 'anoxic' core, and inhibition of Cl- transport to the xylem. These cores are predicted to develop within 15-20 min after sudden transfer of a root to hypoxia, so that the cores are 'anoxically-shocked'. We suggest that 'anoxic' cores could emanate a signal(s), such as ACC the precursor of ethylene and/or propagation of a 'Ca2+ wave', to other tissue zones. There, the signalling would result in acclimation of the tissues to energy crisis metabolism. An O2 diffusion model for tissues with an 'anoxic' core, indicates that the phytoglobin-nitric oxide (Pgb-NO) cycle would only be engaged in a thin 'shell' (annulus) of tissue surrounding the 'anoxic' core, and so would only contribute small amounts of ATP on a whole organ basis (e.g. whole roots). A key feature within this annulus of tissue, where O2 is likely to be limiting, is that the ratio (ATP formed) / (O2 consumed) is 5-6, both when the NAD(P)H of glycolysis is converted to NAD(P)+ by the Pgb-NO cycle or by the TCA cycle linked to the electron transport chain. The main function of the Pgb-NO cycle may be the modulating of NO levels and O2 scavenging, thus preventing oxidative damage. We speculate that an 'anoxic' core in hypoxic plant organs may have a particularly high tolerance to anoxia because cells might receive a prolonged supply of carbohydrates and/or ATP from the regions still receiving sufficient O2 for oxidative phosphorylation. Severely hypoxic or 'anoxic' cores are well documented, but much research on responses of roots to hypoxia is still based on bulk tissue analyses. More research is needed on the interaction between 'anoxic' cores and tissues still receiving sufficient O2 for oxidative phosphorylation, both during a hypoxic exposure and during subsequent anoxia of the tissue/organ as a whole.
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Affiliation(s)
- William Armstrong
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, WA, Australia; Department of Biological Sciences, The University of Hull, Hull, UK
| | | | - Timothy D Colmer
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, WA, Australia.
| | - Timothy L Setter
- Agricultural and Environmental Consultant, P.O. Box 305, Bull Creek, 6149, WA, Australia
| | - Hank Greenway
- School of Agriculture and Environment, Faculty of Science, The University of Western Australia, 35 Stirling Highway, Crawley, 6009, Perth, WA, Australia
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Liu X, Wang T, Lu Y, Yang Q, Li Y, Deng X, Liu Y, Du X, Qiao L, Zheng J. Effect of high oxygen pretreatment of whole tuber on anti-browning of fresh-cut potato slices during storage. Food Chem 2019; 301:125287. [PMID: 31387048 DOI: 10.1016/j.foodchem.2019.125287] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/28/2019] [Accepted: 07/28/2019] [Indexed: 10/26/2022]
Abstract
The surface browning usually occurs on fresh-cut potato during storage. The effect of short-time high oxygen pretreatment on anti-browning of fresh-cut potato slices was investigated. The whole potato tubers were firstly immersed in the oxygen concentration of 21%, 60% and 80% for 20 min. Then, the potatoes were peeled, cut and stored at 4 °C for 8 days. The results showed that the short-time 80% oxygen pretreatment possessed significantly anti-browning effect by retarding the increase of polyphenol oxidase (PPO) activity and the accumulation of malondialdehyde (MDA) content, maintaining the cell integrity. Meanwhile, the 80% oxygen treatment could increase the activities of phenylalanine ammonia lyase (PAL) and peroxidase (POD), and the total phenolic content. Importantly, the 80% oxygen treatment could effectively improve the antioxidant capacity. Overall, all results suggest that the short-time high oxygen pretreatment holds great promise on anti-browning of fresh-cut potato.
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Affiliation(s)
- Xia Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China.
| | - Ting Wang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Yuzhuo Lu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Qian Yang
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Yuan Li
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Xudong Deng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Ying Liu
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Xinru Du
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Liping Qiao
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
| | - Jiaxuan Zheng
- State Key Laboratory of Food Nutrition and Safety, Key Laboratory of Food Nutrition and Safety, Ministry of Education of China, College of Food Engineering and Biotechnology, Tianjin University of Science &Technology, Tianjin 300457, PR China
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Zaffagnini M, Fermani S, Marchand CH, Costa A, Sparla F, Rouhier N, Geigenberger P, Lemaire SD, Trost P. Redox Homeostasis in Photosynthetic Organisms: Novel and Established Thiol-Based Molecular Mechanisms. Antioxid Redox Signal 2019; 31:155-210. [PMID: 30499304 DOI: 10.1089/ars.2018.7617] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Significance: Redox homeostasis consists of an intricate network of reactions in which reactive molecular species, redox modifications, and redox proteins act in concert to allow both physiological responses and adaptation to stress conditions. Recent Advances: This review highlights established and novel thiol-based regulatory pathways underlying the functional facets and significance of redox biology in photosynthetic organisms. In the last decades, the field of redox regulation has largely expanded and this work is aimed at giving the right credit to the importance of thiol-based regulatory and signaling mechanisms in plants. Critical Issues: This cannot be all-encompassing, but is intended to provide a comprehensive overview on the structural/molecular mechanisms governing the most relevant thiol switching modifications with emphasis on the large genetic and functional diversity of redox controllers (i.e., redoxins). We also summarize the different proteomic-based approaches aimed at investigating the dynamics of redox modifications and the recent evidence that extends the possibility to monitor the cellular redox state in vivo. The physiological relevance of redox transitions is discussed based on reverse genetic studies confirming the importance of redox homeostasis in plant growth, development, and stress responses. Future Directions: In conclusion, we can firmly assume that redox biology has acquired an established significance that virtually infiltrates all aspects of plant physiology.
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Affiliation(s)
- Mirko Zaffagnini
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | - Simona Fermani
- 2 Department of Chemistry Giacomo Ciamician, University of Bologna, Bologna, Italy
| | - Christophe H Marchand
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Alex Costa
- 4 Department of Biosciences, University of Milan, Milan, Italy
| | - Francesca Sparla
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
| | | | - Peter Geigenberger
- 6 Department Biologie I, Ludwig-Maximilians-Universität München, LMU Biozentrum, Martinsried, Germany
| | - Stéphane D Lemaire
- 3 Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, UMR8226, Centre National de la Recherche Scientifique, Institut de Biologie Physico-Chimique, Sorbonne Université, Paris, France
| | - Paolo Trost
- 1 Department of Pharmacy and Biotechnology and University of Bologna, Bologna, Italy
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Calvo-Polanco M, Ruiz-Lozano JM, Azcón R, Molina S, Beuzon CR, García JL, Cantos M, Aroca R. Phenotypic and molecular traits determine the tolerance of olive trees to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 139:521-527. [PMID: 31015091 DOI: 10.1016/j.plaphy.2019.04.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/28/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Olive trees are known for their capacity to adapt to drought through several phenotypic and molecular variations, although this can vary according to the different provenances of the same olive cultivar. We confronted the same olive cultivar from two different location in Spain: Freila, in the Granada province, with low annual precipitation, and Grazalema, in the Cadiz province, with high annual precipitation, and subjected them to five weeks of severe drought stress. We found distinctive physiological and developmental adaptations among the two provenances. Thus, trees from Freila subjected to drought stress exhibited increasing root dry weights and decreasing leaf numbers and relative stem heights. On the other hand, the treatment with drought in Grazalema trees reduced their leaf chlorophyll contents, but increased their relative stem diameter and their root hydraulic conductivity. The physiological responses of Freila tree roots to drought were linked to different molecular adaptations that involved the regulation of genes related to transcription factors induced by ABA, auxin and ethylene signaling, as well as, the action of a predicted membrane intrinsic protein (MIP). On the other hand, the responses of Grazalema trees were related with different root genes related to oxidation-reduction, ATP synthesis, transduction and posttranslational regulation, with a special mention to the cytokinins signaling through the transcript predicted as a histidine-containing phosphotransfer protein. Our results show that olive trees adapted to dry environments will adjust their growth and water uptake capacity through transcription factors regulation, and this will influence the different physiological responses to drought stress.
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Affiliation(s)
- Mónica Calvo-Polanco
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain.
| | - Juan Manuel Ruiz-Lozano
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Rosario Azcón
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Sonia Molina
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
| | - Carmen R Beuzon
- Department of Cellular Biology, Genetics and Physiology, Campus de Teatinos, University of Málaga, 29010, Málaga, Spain
| | - José Luis García
- Department of Cellular Biology, Genetics and Physiology, Campus de Teatinos, University of Málaga, 29010, Málaga, Spain
| | - Manuel Cantos
- Department of Plant Biotechnnology, Instituto de Recursos Naturales y Agrobiología (CSIC), Av. Reina Mercedes, 10 41012, Sevilla, Spain
| | - Ricardo Aroca
- Department of Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (CSIC), C/Profesor Albareda 1, 18008, Granada, Spain
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38
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Wei X, Xu H, Rong W, Ye X, Zhang Z. Constitutive expression of a stabilized transcription factor group VII ethylene response factor enhances waterlogging tolerance in wheat without penalizing grain yield. PLANT, CELL & ENVIRONMENT 2019; 42:1471-1485. [PMID: 30566765 DOI: 10.1111/pce.13505] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 12/13/2018] [Accepted: 12/16/2018] [Indexed: 05/24/2023]
Abstract
Waterlogging causes oxygen deprivation within plant roots and affects crop growth and yield. In crop wheat (Triticum aestivum), molecular responses to waterlogging are poorly understood. Here, we performed a genome-wide analysis of group VII ethylene response factor (ERFVII) genes in hexaploid wheat and identified 25 genes, which were induced by waterlogging with diverse manner. Among them, TaERFVII.1 exhibited differential expression patterns between waterlogging-tolerant wheat Nonglin46 and susceptible wheat Yangmai16 under waterlogging. Constitutive expression of TaERFVII.1 with an MYC-peptide tag at its N terminus in wheat enhanced tolerance to waterlogging as evidenced by increased grain weight per plant, survival rate, and chlorophyll content of leaves and by increased expression of waterlogging-responsive genes, while silencing of TaERFVII.1 compromised the expression of waterlogging-responsive genes. Notably, constitutive expression of the stabilized TaERFVII.1 did not negatively impact both plant development and grain yield under standard conditions. We further demonstrated that constitutive expression of stabilized TaERFVII.1 elevated the transcriptional level of TaSAB18.1, the ortholog of Arabidopsis HRA1 and rice SAB18, consequently reduced the expression of waterlogging-responsive genes under standard conditions. These results suggest that TaERFVII.1 plays an important role in wheat tolerance to waterlogging, and it could be a candidate for improving crop waterlogging tolerance.
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Affiliation(s)
- Xuening Wei
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huijun Xu
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei Rong
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xingguo Ye
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengyan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Key Laboratory of Biology and Genetic Improvement of Triticeae Crops, Ministry of Agriculture, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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39
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Shukla V, Lombardi L, Iacopino S, Pencik A, Novak O, Perata P, Giuntoli B, Licausi F. Endogenous Hypoxia in Lateral Root Primordia Controls Root Architecture by Antagonizing Auxin Signaling in Arabidopsis. MOLECULAR PLANT 2019; 12:538-551. [PMID: 30641154 DOI: 10.1016/j.molp.2019.01.007] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 05/27/2023]
Abstract
As non-photosynthesizing organs, roots are dependent on diffusion of oxygen from the external environment and, in some instances, from the shoot for their aerobic metabolism. Establishment of hypoxic niches in the developing tissues of plants has been postulated as a consequence of insufficient diffusion of oxygen to satisfy the demands throughout development. Here, we report that such niches are established at specific stages of lateral root primordia development in Arabidopsis thaliana grown under aerobic conditions. Using gain- and loss-of-function mutants, we show that ERF-VII transcription factors, which mediate hypoxic responses, control root architecture by acting in cells with a high level of auxin signaling. ERF-VIIs repress the expression of the auxin-induced genes LBD16, LBD18, and PUCHI, which are essential for lateral root development, by binding to their promoters. Our results support a model in which the establishment of hypoxic niches in the developing lateral root primordia contributes to the shutting down of key auxin-induced genes and regulates the production of lateral roots.
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Affiliation(s)
- Vinay Shukla
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | | | - Sergio Iacopino
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Ales Pencik
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS & Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | - Ondrej Novak
- Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Institute of Experimental Botany CAS & Faculty of Science, Palacký University, Šlechtitelů 27, 78371 Olomouc, Czech Republic
| | | | - Beatrice Giuntoli
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy; Biology Department, University of Pisa, Pisa, Italy.
| | - Francesco Licausi
- Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy; Biology Department, University of Pisa, Pisa, Italy.
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40
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Ruperti B, Botton A, Populin F, Eccher G, Brilli M, Quaggiotti S, Trevisan S, Cainelli N, Guarracino P, Schievano E, Meggio F. Flooding Responses on Grapevine: A Physiological, Transcriptional, and Metabolic Perspective. FRONTIERS IN PLANT SCIENCE 2019; 10:339. [PMID: 30972087 PMCID: PMC6443911 DOI: 10.3389/fpls.2019.00339] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Studies on model plants have shown that temporary soil flooding exposes roots to a significant hypoxic stress resulting in metabolic re-programming, accumulation of toxic metabolites and hormonal imbalance. To date, physiological and transcriptional responses to flooding in grapevine are poorly characterized. To fill this gap, we aimed to gain insights into the transcriptional and metabolic changes induced by flooding on grapevine roots (K5BB rootstocks), on which cv Sauvignon blanc (Vitis vinifera L.) plants were grafted. A preliminary experiment under hydroponic conditions enabled the identification of transiently and steadily regulated hypoxia-responsive marker genes and drafting a model for response to oxygen deprivation in grapevine roots. Afterward, over two consecutive vegetative seasons, flooding was imposed to potted vines during the late dormancy period, to mimick the most frequent waterlogging events occurring in the field. Untargeted transcriptomic and metabolic profiling approaches were applied to investigate early responses of grapevine roots during exposure to hypoxia and subsequent recovery after stress removal. The initial hypoxic response was marked by a significant increase of the hypoxia-inducible metabolites ethanol, GABA, succinic acid and alanine which remained high also 1 week after recovery from flooding with the exception of ethanol that leveled off. Transcriptomic data supported the metabolic changes by indicating a substantial rearrangement of primary metabolic pathways through enhancement of the glycolytic and fermentative enzymes and of a subset of enzymes involved in the TCA cycle. GO and KEGG pathway analyses of differentially expressed genes showed a general down-regulation of brassinosteroid, auxin and gibberellin biosynthesis in waterlogged plants, suggesting a general inhibition of root growth and lateral expansion. During recovery, transcriptional activation of gibberellin biosynthetic genes and down-regulation of the metabolic ones may support a role for gibberellins in signaling grapevine rootstocks waterlogging metabolic and hormonal changes to the above ground plant. The significant internode elongation measured upon budbreak during recovery in plants that had experienced flooding supported this hypothesis. Overall integration of these data enabled us to draft a first comprehensive view of the molecular and metabolic pathways involved in grapevine's root responses highlighting a deep metabolic and transcriptomic reprogramming during and after exposure to waterlogging.
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Affiliation(s)
- Benedetto Ruperti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- Interdepartmental Research Centre for Viticulture and Enology, University of Padova, Conegliano, Italy
- CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Alessandro Botton
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- Interdepartmental Research Centre for Viticulture and Enology, University of Padova, Conegliano, Italy
- CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Francesca Populin
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Giulia Eccher
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Matteo Brilli
- Department of Biosciences, University of Milan, Milan, Italy
| | - Silvia Quaggiotti
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- CRIBI Biotechnology Centre, University of Padova, Padova, Italy
| | - Sara Trevisan
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Nadia Cainelli
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
| | - Paola Guarracino
- Department of Chemical Sciences, University of Padova, Padova, Italy
| | | | - Franco Meggio
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, Legnaro, Italy
- Interdepartmental Research Centre for Viticulture and Enology, University of Padova, Conegliano, Italy
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Fukao T, Barrera-Figueroa BE, Juntawong P, Peña-Castro JM. Submergence and Waterlogging Stress in Plants: A Review Highlighting Research Opportunities and Understudied Aspects. FRONTIERS IN PLANT SCIENCE 2019; 10:340. [PMID: 30967888 PMCID: PMC6439527 DOI: 10.3389/fpls.2019.00340] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Accepted: 03/05/2019] [Indexed: 05/20/2023]
Abstract
Soil flooding creates composite and complex stress in plants known as either submergence or waterlogging stress depending on the depth of the water table. In nature, these stresses are important factors dictating the species composition of the ecosystem. On agricultural land, they cause economic damage associated with long-term social consequences. The understanding of the plant molecular responses to these two stresses has benefited from research studying individual components of the stress, in particular low-oxygen stress. To a lesser extent, other associated stresses and plant responses have been incorporated into the molecular framework, such as ion and ROS signaling, pathogen susceptibility, and organ-specific expression and development. In this review, we aim to highlight known or suspected components of submergence/waterlogging stress that have not yet been thoroughly studied at the molecular level in this context, such as miRNA and retrotransposon expression, the influence of light/dark cycles, protein isoforms, root architecture, sugar sensing and signaling, post-stress molecular events, heavy-metal and salinity stress, and mRNA dynamics (splicing, sequestering, and ribosome loading). Finally, we explore biotechnological strategies that have applied this molecular knowledge to develop cultivars resistant to flooding or to offer alternative uses of flooding-prone soils, like bioethanol and biomass production.
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Affiliation(s)
- Takeshi Fukao
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA, United States
| | | | - Piyada Juntawong
- Center for Advanced Studies in Tropical Natural Resources, National Research University – Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Julián Mario Peña-Castro
- Laboratorio de Biotecnología Vegetal, Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec, Mexico
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Pan DL, Wang G, Wang T, Jia ZH, Guo ZR, Zhang JY. AdRAP2.3, a Novel Ethylene Response Factor VII from Actinidia deliciosa, Enhances Waterlogging Resistance in Transgenic Tobacco through Improving Expression Levels of PDC and ADH Genes. Int J Mol Sci 2019; 20:E1189. [PMID: 30857203 PMCID: PMC6429156 DOI: 10.3390/ijms20051189] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 02/28/2019] [Accepted: 03/05/2019] [Indexed: 01/18/2023] Open
Abstract
APETALA2/ethylene-responsive factor superfamily (AP2/ERF) is a transcription factor involved in abiotic stresses, for instance, cold, drought, and low oxygen. In this study, a novel ethylene-responsive transcription factor named AdRAP2.3 was isolated from Actinidia deliciosa 'Jinkui'. AdRAP2.3 transcription levels in other reproductive organs except for the pistil were higher than those in the vegetative organs (root, stem, and leaf) in kiwi fruit. Plant hormones (Salicylic acid (SA), Methyl-jasmonate acid (MeJA), 1-Aminocyclopropanecarboxylic Acid (ACC), Abscisic acid (ABA)), abiotic stresses (waterlogging, heat, 4 °C and NaCl) and biotic stress (Pseudomonas Syringae pv. Actinidiae, Psa) could induce the expression of AdRAP2.3 gene in kiwi fruit. Overexpression of the AdRAP2.3 gene conferred waterlogging stress tolerance in transgenic tobacco plants. When completely submerged, the survival rate, fresh weight, and dry weight of transgenic tobacco lines were significantly higher than those of wile type (WT). Upon the roots being submerged, transgenic tobacco lines grew aerial roots earlier. Overexpression of AdRAP2.3 in transgenic tobacco improved the pyruvate decarboxylase (PDC) and alcohol dehydrogenase (ADH) enzyme activities, and improved the expression levels of waterlogging mark genes NtPDC, NtADH, NtHB1, NtHB2, NtPCO1, and NtPCO2 in roots under waterlogging treatment. Overall, these results demonstrated that AdRAP2.3 might play an important role in resistance to waterlogging through regulation of PDC and ADH genes in kiwi fruit.
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Affiliation(s)
- De-Lin Pan
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Gang Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Tao Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Zhan-Hui Jia
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Zhong-Ren Guo
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Ji-Yu Zhang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
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Wang L, Ma H, Lin J. Angiosperm-Wide and Family-Level Analyses of AP2/ ERF Genes Reveal Differential Retention and Sequence Divergence After Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2019; 10:196. [PMID: 30863419 PMCID: PMC6399210 DOI: 10.3389/fpls.2019.00196] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/05/2019] [Indexed: 05/21/2023]
Abstract
Plants are immobile and often face stressful environmental conditions, prompting the evolution of genes regulating environmental responses. Such evolution is achieved largely through gene duplication and subsequent divergence. One of the most important gene families involved in regulating plant environmental responses and development is the AP2/ERF superfamily; however, the evolutionary history of these genes is unclear across angiosperms and in major angiosperm families adapted to various ecological niches. Specifically, the impact on gene copy number of whole-genome duplication events occurring around the time of the origins of several plant families is unknown. Here, we present the first angiosperm-wide comparative study of AP2/ERF genes, identifying 75 Angiosperm OrthoGroups (AOGs), each derived from an ancestral angiosperm gene copy. Among these AOGs, 21 retain duplicates with increased copy number in many angiosperm lineages, while the remaining 54 AOGs tend to maintain low copy number. Further analyses of multiple species in the Brassicaceae family indicated that family-specific duplicates experienced differential selective pressures in coding regions, with some paralogs showing signs of positive selection. Further, cis regulatory elements also exhibit extensive divergence between duplicates in Arabidopsis. Moreover, comparison of expression levels suggested that AP2/ERF genes with frequently retained duplicates are enriched for broad expression patterns, offering increased opportunities for functional diversification via changes in expression patterns, and providing a mechanism for repeated duplicate retention in some AOGs. Our results represent the most comprehensive evolutionary history of the AP2/ERF gene family, and support the hypothesis that AP2/ERF genes with broader expression patterns are more likely to be retained as duplicates than those with narrower expression profiles, which could lead to a higher chance of duplicate gene subfunctionalization. The greater tendency of some AOGs to retain duplicates, allowing expression and functional divergence, may facilitate the evolution of complex signaling networks in response to new environmental conditions.
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Affiliation(s)
- Linbo Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
- Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, United States
| | - Juan Lin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Institute of Biodiversity Sciences, School of Life Sciences, Fudan University, Shanghai, China
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Eysholdt‐Derzsó E, Sauter M. Hypoxia and the group VII ethylene response transcription factor HRE2 promote adventitious root elongation in Arabidopsis. PLANT BIOLOGY (STUTTGART, GERMANY) 2019; 21 Suppl 1:103-108. [PMID: 29996004 PMCID: PMC6585952 DOI: 10.1111/plb.12873] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 07/09/2018] [Indexed: 05/17/2023]
Abstract
Soil water-logging and flooding are common environmental stress conditions that can impair plant fitness. Roots are the first organs to be confronted with reduced oxygen tension as a result of flooding. While anatomical and morphological adaptations of roots are extensively studied, the root system architecture is only now becoming a focus of flooding research. Adventitious root (AR) formation shifts the root system higher up the plant, thereby facilitating supply with oxygen, and thus improving root and plant survival. We used Arabidopsis knockout mutants and overexpressors of ERFVII transcription factors to study their role in AR formation under hypoxic conditions and in response to ethylene. Results show that ethylene inhibits AR formation. Hypoxia mainly promotes AR elongation rather than formation mediated by ERFVII transcription factors, as indicated by reduced AR elongation in erfVII seedlings. Overexpression of HRE2 induces AR elongation to the same degree as hypoxia, while ethylene overrides HRE2-induced AR elongation. The ERFVII transcription factors promote establishment of an AR system that is under negative control by ethylene. Inhibition of growth of the main root system and promotion of AR elongation under hypoxia strengthens the root system in upper soil layers where oxygen shortage may last for shorter time periods.
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Affiliation(s)
- E. Eysholdt‐Derzsó
- Plant Developmental Biology and Plant PhysiologyUniversity of KielKielGermany
| | - M. Sauter
- Plant Developmental Biology and Plant PhysiologyUniversity of KielKielGermany
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Low-oxygen response is triggered by an ATP-dependent shift in oleoyl-CoA in Arabidopsis. Proc Natl Acad Sci U S A 2018; 115:E12101-E12110. [PMID: 30509981 PMCID: PMC6304976 DOI: 10.1073/pnas.1809429115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
To control adaptive responses to the ever-changing environment that plants are continuously exposed to, plant cells must integrate a multitude of information to make optimal decisions. Here, we reveal how plants can link information about the cellular energy status with the actual oxygen concentration of the cell to trigger a response reaction to low-oxygen stress. We reveal that oleoyl-CoA has a moonlighting function in an energy (ATP)-dependent signal transduction pathway in plants, and we provide a model that explains how diminishing oxygen availability can initiate adaptive responses when it coincides with a decreased energy status of the cell. Plant response to environmental stimuli involves integration of multiple signals. Upon low-oxygen stress, plants initiate a set of adaptive responses to circumvent an energy crisis. Here, we reveal how these stress responses are induced by combining (i) energy-dependent changes in the composition of the acyl-CoA pool and (ii) the cellular oxygen concentration. A hypoxia-induced decline of cellular ATP levels reduces LONG-CHAIN ACYL-COA SYNTHETASE activity, which leads to a shift in the composition of the acyl-CoA pool. Subsequently, we show that different acyl-CoAs induce unique molecular responses. Altogether, our data disclose a role for acyl-CoAs acting in a cellular signaling pathway in plants. Upon hypoxia, high oleoyl-CoA levels provide the initial trigger to release the transcription factor RAP2.12 from its interaction partner ACYL-COA BINDING PROTEIN at the plasma membrane. Subsequently, according to the N-end rule for proteasomal degradation, oxygen concentration-dependent stabilization of the subgroup VII ETHYLENE-RESPONSE FACTOR transcription factor RAP2.12 determines the level of hypoxia-specific gene expression. This research unveils a specific mechanism activating low-oxygen stress responses only when a decrease in the oxygen concentration coincides with a drop in energy.
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He L, Yu L, Li B, Du N, Guo S. The effect of exogenous calcium on cucumber fruit quality, photosynthesis, chlorophyll fluorescence, and fast chlorophyll fluorescence during the fruiting period under hypoxic stress. BMC PLANT BIOLOGY 2018; 18:180. [PMID: 30180797 PMCID: PMC6122546 DOI: 10.1186/s12870-018-1393-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 08/27/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Plants often suffer from hypoxic stress during waterlogging and hydroponic culturing. This study investigated the response of cucumber (Cucumis sativus L.) plant growth parameters, leaf photosynthesis, chlorophyll fluorescence, fast chlorophyll a fluorescence transient (OJIP), and fruit quality parameters to hypoxic stress alleviated by exogenous calcium. During the fruiting period, cucumber plants were exposed to hypoxia and hypoxia + Ca2+ treatment (4 mM Ca2+) for 9 d. RESULT Exogenous calcium application enhanced the biomass and fruit quality of hypoxic stressed cucumber and also increased the net photosynthesis rate, stomatal conductance, intercellular CO2 concentration, maximum quantum efficiency of photosystem II photochemistry, actual photochemical efficiency of PSII, photochemical quenching coefficient, and non-photochemical quenching coefficient. Additionally, measurement of chlorophyll a fluorescence transients showed the positive K- and L-bands were more pronounced in leaves treated with hypoxia compared with those with hypoxia + Ca2+, indicating that hypoxic treatment induced uncoupling of the oxygen-evolving complex and inhibited electron transport beyond plastoquinone pool (Qa, Qb) including possible constraints on the reduction of end electron acceptors of photosystem I. Exogenous calcium can reduce these stress-induced damages in cucumber. CONCLUSION This research focused the effect of exogenous calcium on cucumber photosynthesis during the fruiting period under hypoxic stress. Hypoxic stress might impair the photosynthetic electron-transport chain from the donor side of PSII up to the reduction of end acceptors of PSI, and exogenous calcium enhanced electron transport capacity and reduced hypoxic damage of cucumber leaves.
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Affiliation(s)
- Lizhong He
- Shanghai Key Lab of Protected Horticulture Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Science, Shanghai, 201106 China
- Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agricultural, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Li Yu
- Shanghai Key Lab of Protected Horticulture Technology, Horticultural Research Institute, Shanghai Academy of Agricultural Science, Shanghai, 201106 China
- Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agricultural, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Bin Li
- Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agricultural, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- College of Horticulture Shanxi Agriculture University, Taigu, 030801 Shanxi China
| | - Nanshan Du
- Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agricultural, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Department of Horticulture, Henan Agricultural University, Zhengzhou, 450000 Henan China
| | - Shirong Guo
- Key Laboratory of Southern Vegetable Crop Genetic Improvement, Ministry of Agricultural, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
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Sun X, Yu G, Li J, Liu J, Wang X, Zhu G, Zhang X, Pan H. AcERF2, an ethylene-responsive factor of Atriplex canescens, positively modulates osmotic and disease resistance in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 274:32-43. [PMID: 30080618 DOI: 10.1016/j.plantsci.2018.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/02/2018] [Accepted: 05/05/2018] [Indexed: 05/02/2023]
Abstract
Ethylene-responsive factors (ERFs) comprise a large family of transcription factors in plants and play important roles in developmental processes and stress responses. Here, we characterized a novel AP2/ERF transcription factor, AcERF2, from the halophyte Atriplex canescens (four-wing saltbush, Chenopodiaceae). AcERF2 was proved to be a transcriptional activator in yeast and localized to the nucleus upon transient expression in Nicotiana benthamiana, indicating its potential role as a transcription factor. Overexpression of AcERF2 driven by a CaMV35S promoter led to decreased accumulation of reactive oxygen species (ROS) and malondialdehyde (MDA), and increased antioxidant enzymatic activities, as well as rapid stomatal closure under osmotic treatment in Arabidopsis. Arabidopsis plants overexpressing AcERF2 were hypersensitive to abscisic acid (ABA) during germination, seedling establishment, and primary root elongation, and exhibited significant tolerance to osmotic stress. Furthermore, overexpression of AcERF2 induced transcript accumulation of plant defense-related genes (PR1, PR2, PR5, ERF1 and ERF3) and increased Arabidopsis resistance to the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 and the necrotrophic fungal pathogen Botrytis cinerea. These results suggest that AcERF2 may play a positive modulation role in response to osmotic stress and pathogen infection in plants.
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Affiliation(s)
- Xinhua Sun
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Gang Yu
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Jingtao Li
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Jinliang Liu
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Xueliang Wang
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Genglin Zhu
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Xianghui Zhang
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
| | - Hongyu Pan
- College of Plant Sciences, Jilin University, Changchun, Jilin, 130062, PR China.
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Greenway H, Armstrong W. Energy-crises in well-aerated and anoxic tissue: does tolerance require the same specific proteins and energy-efficient transport? FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:877-894. [PMID: 32291053 DOI: 10.1071/fp17250] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/20/2018] [Indexed: 06/11/2023]
Abstract
Many of the profound changes in metabolism that are caused by O2 deficiency also occur in well-aerated tissues when oxidative phosphorylation is partially or wholly inhibited. For these well-aerated tissues, reduction in energy formation occurs during exposure to inhibitors of oxidative phosphorylation, cold/chilling and wounding, so we prefer the term 'energy crisis' metabolism over 'anaerobic' metabolism. In this review, we note that the overwhelming body of data on energy crises has been obtained by exposure to hypoxia-anoxia, which we will indicate when discussing the particular experiments. We suggest that even transient survival of an energy crisis requires a network of changes common to a large number of conditions, ranging from changes in development to various adverse conditions such as high salinity, drought and nutrient deficiency, all of which reduce growth. During an energy crisis this general network needs to be complemented by energy specific proteins, including the so called 'anaerobic proteins' and the group of ERFVII transcription factors, which induces the synthesis of these proteins. Crucially, the difference between anoxia-intolerant and -tolerant tissues in the event of a severe energy crisis would mainly depend on changes in some 'key' energy crisis proteins: we suggest these proteins would include phytoglobin, the V-H+PPiase and pyruvate decarboxylase. A second characteristic of a high tolerance to an energy crisis is engagement of energy efficient transport. This feature includes a sharp reduction in rates of solute transport and use of energy-efficient modifications of transport systems by primary H+ transport and secondary H+-solute transport systems. Here we also discuss the best choice of species to study an energy crisis. Further, we consider confounding of the acclimative response by responses to injury, be it due to the use of tissues intolerant to an energy crisis, or to faulty techniques.
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Affiliation(s)
- Hank Greenway
- School of Plant Biology, Faculty of Science, the University of Western Australia, Crawley, WA 6009, Australia
| | - William Armstrong
- School of Plant Biology, Faculty of Science, the University of Western Australia, Crawley, WA 6009, Australia
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Ali S, Kim WC. Plant Growth Promotion Under Water: Decrease of Waterlogging-Induced ACC and Ethylene Levels by ACC Deaminase-Producing Bacteria. Front Microbiol 2018; 9:1096. [PMID: 29887854 PMCID: PMC5981179 DOI: 10.3389/fmicb.2018.01096] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/08/2018] [Indexed: 12/13/2022] Open
Abstract
Some plant growth-promoting bacteria encode for 1-aminocyclopropane-1-carboxylate (ACC) deaminase, which facilitates plant growth and development by lowering the level of stress ethylene under waterlogged conditions. The substrate ACC is the immediate precursor for ethylene synthesis in plants; while bacterial ACC deaminase hydrolyzes this compound into α-ketobutyrate and ammonia to mitigate the adverse effects of the stress caused by ethylene exposure. Here, the structure and function of ACC deaminase, ethylene biosynthesis and waterlogging response, waterlogging and its consequences, role of bacterial ACC deaminase under waterlogged conditions, and effect of this enzyme on terrestrial and riparian plants are discussed.
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50
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Dubois M, Van den Broeck L, Inzé D. The Pivotal Role of Ethylene in Plant Growth. TRENDS IN PLANT SCIENCE 2018; 23:311-323. [PMID: 29428350 DOI: 10.1016/j.tplants.2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 05/27/2023]
Abstract
Being continuously exposed to variable environmental conditions, plants produce phytohormones to react quickly and specifically to these changes. The phytohormone ethylene is produced in response to multiple stresses. While the role of ethylene in defense responses to pathogens is widely recognized, recent studies in arabidopsis and crop species highlight an emerging key role for ethylene in the regulation of organ growth and yield under abiotic stress. Molecular connections between ethylene and growth-regulatory pathways have been uncovered, and altering the expression of ethylene response factors (ERFs) provides a new strategy for targeted ethylene-response engineering. Crops with optimized ethylene responses show improved growth in the field, opening new windows for future crop improvement. This review focuses on how ethylene regulates shoot growth, with an emphasis on leaves.
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Affiliation(s)
- Marieke Dubois
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium; Present address: Institut de Biologie Moléculaire des Plantes, Centre National de la Recherche Scientifique, 67000 Strasbourg, France
| | - Lisa Van den Broeck
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium. https://twitter.com/@InzeDirk
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