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Steward KF, Refai M, Dyer WE, Copié V, Lachowiec J, Bothner B. Acute stress reduces population-level metabolic and proteomic variation. BMC Bioinformatics 2023; 24:87. [PMID: 36882728 PMCID: PMC9993721 DOI: 10.1186/s12859-023-05185-4] [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: 04/18/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND Variation in omics data due to intrinsic biological stochasticity is often viewed as a challenging and undesirable feature of complex systems analyses. In fact, numerous statistical methods are utilized to minimize the variation among biological replicates. RESULTS We demonstrate that the common statistics relative standard deviation (RSD) and coefficient of variation (CV), which are often used for quality control or part of a larger pipeline in omics analyses, can also be used as a metric of a physiological stress response. Using an approach we term Replicate Variation Analysis (RVA), we demonstrate that acute physiological stress leads to feature-wide canalization of CV profiles of metabolomes and proteomes across biological replicates. Canalization is the repression of variation between replicates, which increases phenotypic similarity. Multiple in-house mass spectrometry omics datasets in addition to publicly available data were analyzed to assess changes in CV profiles in plants, animals, and microorganisms. In addition, proteomics data sets were evaluated utilizing RVA to identify functionality of reduced CV proteins. CONCLUSIONS RVA provides a foundation for understanding omics level shifts that occur in response to cellular stress. This approach to data analysis helps characterize stress response and recovery, and could be deployed to detect populations under stress, monitor health status, and conduct environmental monitoring.
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Affiliation(s)
- Katherine F Steward
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - Mohammed Refai
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA
| | - William E Dyer
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.,Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, USA
| | - Valérie Copié
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA.,Thermal Biology Institute, Montana State University, Bozeman, USA
| | - Jennifer Lachowiec
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, USA
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, 59717, USA. .,Thermal Biology Institute, Montana State University, Bozeman, USA.
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2
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Du W, Lu Y, Li Q, Luo S, Shen S, Li N, Chen X. TIR1/AFB proteins: Active players in abiotic and biotic stress signaling. FRONTIERS IN PLANT SCIENCE 2022; 13:1083409. [PMID: 36523629 PMCID: PMC9745157 DOI: 10.3389/fpls.2022.1083409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
The TIR1/AFB family of proteins is a group of functionally diverse auxin receptors that are only found in plants. TIR1/AFB family members are characterized by a conserved N-terminal F-box domain followed by 18 leucine-rich repeats. In the past few decades, extensive research has been conducted on the role of these proteins in regulating plant development, metabolism, and responses to abiotic and biotic stress. In this review, we focus on TIR1/AFB proteins that play crucial roles in plant responses to diverse abiotic and biotic stress. We highlight studies that have shed light on the mechanisms by which TIR1/AFB proteins are regulated at the transcriptional and post-transcriptional as well as the downstream in abiotic or biotic stress pathways regulated by the TIR1/AFB family.
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Affiliation(s)
- Wenchao Du
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Yang Lu
- Hebei University Characteristic sericulture Application Technology Research and Development Center, Institute of Sericulture, Chengde Medical University, Chengde, China
| | - Qiang Li
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuangxia Luo
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Shuxing Shen
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Na Li
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
| | - Xueping Chen
- Key Laboratory for Vegetable Germplasm Enhancement and Utilization of Hebei, Collaborative Innovation Center of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding, China
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Genomic regions associated with herbicide tolerance in a worldwide faba bean (Vicia faba L.) collection. Sci Rep 2022; 12:158. [PMID: 34996977 PMCID: PMC8741826 DOI: 10.1038/s41598-021-03861-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 12/09/2021] [Indexed: 01/18/2023] Open
Abstract
Weeds represent one of the major constraints for faba bean crop. The identification of molecular markers associated with key genes imparting tolerance to herbicides can facilitate and fasten the efficient and effective development of herbicide tolerant cultivars. We phenotyped 140 faba bean genotypes in three open field experiments at two locations in Lebanon and Morocco against three herbicide treatments (T1 metribuzin 250 g ai/ha; T2 imazethapyr 75 g ai/ha; T3 untreated) and one in greenhouse where T1 and T3 were applied. The same set was genotyped using genotyping by sequencing (GBS) which yield 10,794 high quality single nucleotide polymorphisms (SNPs). ADMIXTURE software was used to infer the population structure which revealed two ancestral subpopulations. To identify SNPs associated with phenological and yield related traits under herbicide treatments, Single-trait (ST) and Multi-trait (MT) Genome Wide Association Studies (GWAS) were fitted using GEMMA software, showing 10 and 14 highly significant associations, respectively. Genomic sequences containing herbicide tolerance associated SNPs were aligned against the NCBI database using BLASTX tool using default parameters to annotate candidate genes underlying the causal variants. SNPs from acidic endochitinase, LRR receptor-like serine/threonine-protein kinase RCH1, probable serine/threonine-protein kinase NAK, malate dehydrogenase, photosystem I core protein PsaA and MYB-related protein P-like were significantly associated with herbicide tolerance traits.
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Villette C, Maurer L, Delecolle J, Zumsteg J, Erhardt M, Heintz D. In situ localization of micropollutants and associated stress response in Populus nigra leaves. ENVIRONMENT INTERNATIONAL 2019; 126:523-532. [PMID: 30851483 DOI: 10.1016/j.envint.2019.02.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 06/09/2023]
Abstract
Micropollutants and emerging organic contaminants (EOCs) have been widely studied in terms of persistance, removal, human risk assessment, toxicology, etc. Mass spectrometry imaging (MSI) offers the possibility of following the fate of a single pesticide in a plant leaf or a drug in the whole body of an animal, organ by organ. However, the admissibility of chronic low doses of complex mixtures for the ecosystem has not been assessed. How do micropollutants diffuse in the environment? How do living organisms cope with chronic exposure to a low dose of diverse micropollutants? Is there a cocktail effect or a chance for hormesis? Combining mass spectrometry imaging (MSI) and targeted and nontargeted liquid chromatography coupled to mass spectrometry (LC-MS), we attempt to answer these questions. We investigate the diversity of micropollutants at the exit of a water treatment facility, their diffusion in sludge and black poplar (Populus nigra), and their impact on a living organism. We reveal a specific tissue localization of micropollutants in peripheral leaf tissues, and an associated stress response from the plant, with stress hormones and tissue degradation markers induced in the plant growing near the water efflux.
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Affiliation(s)
- C Villette
- Plant Imaging and Mass Spectrometry (PIMS), Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France.
| | - L Maurer
- Plant Imaging and Mass Spectrometry (PIMS), Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France; Département mécanique, ICube Laboratoire des sciences de l'ingénieur, de l'informatique et de l'imagerie, UNISTRA/CNRS/ENGEES/INSA, 2 rue Boussingault, 67000 Strasbourg, France
| | - J Delecolle
- Plant Imaging and Mass Spectrometry (PIMS), Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - J Zumsteg
- Plant Imaging and Mass Spectrometry (PIMS), Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - M Erhardt
- Microscopie et imagerie cellulaire, Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
| | - D Heintz
- Plant Imaging and Mass Spectrometry (PIMS), Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084 Strasbourg, France
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Huang B, Chen YE, Zhao YQ, Ding CB, Liao JQ, Hu C, Zhou LJ, Zhang ZW, Yuan S, Yuan M. Exogenous Melatonin Alleviates Oxidative Damages and Protects Photosystem II in Maize Seedlings Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2019; 10:677. [PMID: 31178885 PMCID: PMC6543012 DOI: 10.3389/fpls.2019.00677] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/06/2019] [Indexed: 05/18/2023]
Abstract
The protective role of melatonin in plants against various abiotic stresses have been widely demonstrated, but poorly explored in organ-specific responses and the transmission of melatonin signals across organs. In this study, the effects of melatonin with the root-irrigation method and the leaf-spraying method on the antioxidant system and photosynthetic machinery in maize seedlings under drought stress were investigated. The results showed that drought stress led to the rise in reactive oxygen species (ROS), severe cell death, and degradation of D1 protein, which were mitigated by the melatonin application. The application of melatonin improved the photosynthetic activities and alleviated the oxidative damages of maize seedlings under the drought stress. Compared with the leaf-spraying method, the root-irrigation method was more effective on enhancing drought tolerance. Moreover, maize seedlings made organ-specific physiological responses to the drought stress, and the physiological effects of melatonin varied with the dosage, application methods and plant organs. The signals of exogenous melatonin received by roots could affect the stress responses of leaves, and the melatonin signals perceived by leaves also led to changes in physiological metabolisms in roots under the stress. Consequently, the whole seedlings coordinated the different parts and made a systemic acclimation against the drought stress. Melatonin as a protective agent against abiotic stresses has a potential application prospect in the agricultural industry.
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Affiliation(s)
- Bo Huang
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Yang-Er Chen
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Yu-Qing Zhao
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Chun-Bang Ding
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Jin-Qiu Liao
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Chao Hu
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Li-Jun Zhou
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
| | - Zhong-Wei Zhang
- College of Resources Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Shu Yuan
- College of Resources Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ming Yuan
- College of Life Sciences, Sichuan Agricultural University, Ya’an, China
- *Correspondence: Ming Yuan,
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Dyer WE. Stress-induced evolution of herbicide resistance and related pleiotropic effects. PEST MANAGEMENT SCIENCE 2018; 74:1759-1768. [PMID: 29688592 DOI: 10.1002/ps.5043] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/13/2018] [Accepted: 04/14/2018] [Indexed: 05/11/2023]
Abstract
Herbicide-resistant weeds, especially those with resistance to multiple herbicides, represent a growing worldwide threat to agriculture and food security. Natural selection for resistant genotypes may act on standing genetic variation, or on a genetic and physiological background that is fundamentally altered because of stress responses to sublethal herbicide exposure. Stress-induced changes include DNA mutations, epigenetic alterations, transcriptional remodeling, and protein modifications, all of which can lead to herbicide resistance and a wide range of pleiotropic effects. Resistance selected in this manner is termed systemic acquired herbicide resistance, and the associated pleiotropic effects are manifested as a suite of constitutive transcriptional and post-translational changes related to biotic and abiotic stress adaptation, representing the evolutionary signature of selection. This phenotype is being investigated in two multiple herbicide-resistant populations of the hexaploid, self-pollinating weedy monocot Avena fatua that display such changes as well as constitutive reductions in certain heat shock proteins and their transcripts, which are well known as global regulators of diverse stress adaptation pathways. Herbicide-resistant populations of most weedy plant species exhibit pleiotropic effects, and their association with resistance genes presents a fertile area of investigation. This review proposes that more detailed studies of resistant A. fatua and other species through the lens of plant evolution under stress will inform improved resistant weed prevention and management strategies. © 2018 Society of Chemical Industry.
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Affiliation(s)
- William Edward Dyer
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, USA
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McConnell EW, Werth EG, Hicks LM. The phosphorylated redox proteome of Chlamydomonas reinhardtii: Revealing novel means for regulation of protein structure and function. Redox Biol 2018; 17:35-46. [PMID: 29673699 PMCID: PMC6006682 DOI: 10.1016/j.redox.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/16/2023] Open
Abstract
Post-translational modifications (PTMs) are covalent modifications to protein residues which may alter both conformation and activity, thereby modulating signaling and metabolic processes. While PTMs have been largely investigated independently, examination into how different modification interact, or crosstalk, will reveal a more complete understanding of the reciprocity of signaling cascades across numerous pathways. Combinatorial reversible thiol oxidation and phosphorylation in eukaryotes is largely recognized, but rigorous approaches for experimental discovery are underdeveloped. To begin meaningful interrogation of PTM crosstalk in systems biology research, knowledge of targeted proteins must be advanced. Herein, we demonstrate protein-level enrichment of reversibly oxidized proteoforms in Chlamydomonas reinhardtii with subsequent phosphopeptide analysis to determine the extent of phosphorylation in the redox thiol proteome. Label-free quantification was used to quantify 3353 oxidized Cys-sites on 1457 enriched proteins, where sequential phosphopeptide enrichment measured 1094 sites of phosphorylation on 720 proteins with 23% (172 proteins) also identified as reversibly oxidized. Proteins identified with both reversible oxidation and phosphorylation were involved in signaling transduction, ribosome and translation-related machinery, and metabolic pathways. Several redox-modified Calvin-Benson cycle proteins were found phosphorylated and many kinases/phosphatases involved in phosphorylation-dependent photosynthetic state transition and stress-response pathways had sites of reversible oxidation. Identification of redox proteins serves as a crucial element in understanding stress response in photosynthetic organisms and beyond, whereby knowing the ensemble of modifications co-occurring with oxidation highlights novel mechanisms for cellular control. Quantified reversible oxidation on protein cysteine residues. Sequential phosphopeptide enrichment to define the phosphorylated redox proteome. Found >3000 oxidized cysteines and >1000 phosphosites in Chlamydomonas reinhardtii. Co-modified proteins discovered across diverse metabolic and signaling pathways.
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Affiliation(s)
- Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Emily G Werth
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.
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