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Gouesbet G. Deciphering Macromolecular Interactions Involved in Abiotic Stress Signaling: A Review of Bioinformatics Analysis. Methods Mol Biol 2023; 2642:257-294. [PMID: 36944884 DOI: 10.1007/978-1-0716-3044-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Plant functioning and responses to abiotic stresses largely involve regulations at the transcriptomic level via complex interactions of signal molecules, signaling cascades, and regulators. Nevertheless, all the signaling networks involved in responses to abiotic stresses have not yet been fully established. The in-depth analysis of transcriptomes in stressed plants has become a relevant state-of-the-art methodology to study these regulations and signaling pathways that allow plants to cope with or attempt to survive abiotic stresses. The plant science and molecular biology community has developed databases about genes, proteins, protein-protein interactions, protein-DNA interactions and ontologies, which are valuable sources of knowledge for deciphering such regulatory and signaling networks. The use of these data and the development of bioinformatics tools help to make sense of transcriptomic data in specific contexts, such as that of abiotic stress signaling, using functional biological approaches. The aim of this chapter is to present and assess some of the essential online tools and resources that will allow novices in bioinformatics to decipher transcriptomic data in order to characterize the cellular processes and functions involved in abiotic stress responses and signaling. The analysis of case studies further describes how these tools can be used to conceive signaling networks on the basis of transcriptomic data. In these case studies, particular attention was paid to the characterization of abiotic stress responses and signaling related to chemical and xenobiotic stressors.
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Affiliation(s)
- Gwenola Gouesbet
- University of Rennes, CNRS, ECOBIO [(Ecosystèmes, Biodiversité, Evolution)] - UMR 6553, Rennes, France.
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Zhang NC, Hong ZF, Qiu RL, Chao YQ, Yu YF, A D. Removal pathway quantification and co-metabolic mechanism evaluation of alkylphenols from synthetic wastewater by phenolic root exudates in the rhizosphere of Phragmites australis. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127269. [PMID: 34607026 DOI: 10.1016/j.jhazmat.2021.127269] [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: 05/04/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Phenolic root exudates (PREs) released from wetland plants are potentially effective for accelerating the biodegradation of alkylphenols, yet the inherent behavior is still unclear. In this study, two representative root exudates (REs), namely p-coumaric acid (PREs) and oxalic acid (non-PREs) were exogenously added as specific and non-specific co-metabolic substrates, respectively, to elucidate the quantification of each removal pathway and degradation mechanism of co-metabolism for alkylphenols (i.e. p-tert-butylphenol (PTBP)) from synthetic wastewater. The results showed that soil adsorption (31-37%), microbial degradation (27-37%), and plant uptake (16-41%) are the main removal pathways of PTBP by PREs in the Phragmites australis rhizosphere. Both REs enriched anaerobic functional community (anaerobic ammonium oxidation bacteria and denitrifying bacteria) and promoted the usage of PTBP as carbon source and/or electron donor. The activity of non-specific enzyme (polyphenol oxidase) was enhanced by RE which owning a significant positive correlation with bacterial abundance, whereas only PREs strengthened the activity of specific enzyme (monophenol oxidase) catalyzing the phenolic ring hydroxylation of PTBP followed by a dehydrogenation route. Moreover, exogenous PREs significantly improved the growth of degrading-related bacteria (Sphingomonas and Gemmatimonas), especially in unplanted soils with high activity of dioxygenase catalyzing the cleavage pathway of PTBP, instead of plant presence.
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Affiliation(s)
- Ni-Chen Zhang
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Feng Hong
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Rong-Liang Qiu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Guangdong Laboratory for Lingnan Modern Agriculture, College of Natural Resources and Environment, South China Agricultural University, Guangzhou 510642, China
| | - Yuan-Qing Chao
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Ya-Fei Yu
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China
| | - Dan A
- School of Environmental Science and Engineering, Guangdong Provincial Key Lab for Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510006, China; Engineering and Technology Research Center for Agricultural Land Pollution Integrated Prevention and Control of Guangdong Higher Education Institute, College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China.
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Serra AA, Bittebière AK, Mony C, Slimani K, Pallois F, Renault D, Couée I, Gouesbet G, Sulmon C. Local-scale dynamics of plant-pesticide interactions in a northern Brittany agricultural landscape. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 744:140772. [PMID: 32711307 DOI: 10.1016/j.scitotenv.2020.140772] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 06/24/2020] [Accepted: 07/04/2020] [Indexed: 06/11/2023]
Abstract
Soil pollution by anthropogenic chemicals is a major concern for sustainability of crop production and of ecosystem functions mediated by natural plant biodiversity. Understanding the complex effects of soil pollution requires multi-level and multi-scale approaches. Non-target and agri-environmental plant communities of field margins and vegetative filter strips are confronted with agricultural xenobiotics through soil contamination, drift, run-off and leaching events that result from chemical applications. Plant-pesticide dynamics in vegetative filter strips was studied at field scale in the agricultural landscape of a long-term ecological research network in northern Brittany (France). Vegetative filter strips effected significant pesticide abatement between the field and riparian compartments. However, comparison of pesticide usage modalities and soil chemical analysis revealed the extent and complexity of pesticide persistence in fields and vegetative filter strips, and suggested the contribution of multiple sources (yearly carry-over, interannual persistence, landscape-scale contamination). In order to determine the impact of such persistence, plant dynamics was followed in experimentally-designed vegetative filter strips of identical initial composition (Agrostis stolonifera, Anthemis tinctoria/Cota tinctoria, Centaurea cyanus, Fagopyrum esculentum, Festuca rubra, Lolium perenne, Lotus corniculatus, Phleum pratense, Trifolium pratense). After homogeneous vegetation establishment, experimental vegetative filter strips underwent rapid changes within the following two years, with Agrostis stolonifera, Festuca rubra, Lolium perenne and Phleum pratense becoming dominant and with the establishment of spontaneous vegetation. Co-inertia analysis showed that plant dynamics and soil residual pesticides could be significantly correlated, with the triazole fungicide epoxiconazole, the imidazole fungicide prochloraz and the neonicotinoid insecticide thiamethoxam as strong drivers of the correlation. However, the correlation was vegetative-filter-strip-specific, thus showing that correlation between plant dynamics and soil pesticides likely involved additional factors, such as threshold levels of residual pesticides. This situation of complex interactions between plants and soil contamination is further discussed in terms of agronomical, environmental and health issues.
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Affiliation(s)
- Anne-Antonella Serra
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
| | - Anne-Kristel Bittebière
- Université de Lyon 1, CNRS, UMR 5023 LEHNA, 43 Boulevard du 11 novembre 1918, F-69622 Villeurbanne Cedex, France
| | - Cendrine Mony
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
| | - Kahina Slimani
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
| | - Frédérique Pallois
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
| | - David Renault
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
| | - Ivan Couée
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France.
| | - Gwenola Gouesbet
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
| | - Cécile Sulmon
- Univ Rennes, Université de Rennes 1, CNRS, ECOBIO [(Ecosystems-Biodiversity-Evolution)] - UMR 6553, Campus de Beaulieu, 263 avenue du Général Leclerc, F-35042 Rennes Cedex, France
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