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      Integrative physiological, biochemical, and proteomic analysis of the leaves of two cotton genotypes under heat stress

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          Abstract

          Cotton ( Gossypium hirsutum L.), a crucial global fibre and oil seed crop faces diverse biotic and abiotic stresses. Among these, temperature stress strongly influences its growth, prompting adaptive physiological, biochemical, and molecular changes. In this study, we explored the proteomic changes underscoring the heat stress tolerance in the leaves of two locally developed cotton genotypes, i.e., heat tolerant (GH-Hamaliya H tol) and heat susceptible (CIM-789 H sus), guided by morpho-physiological and biochemical analysis. These genotypes were sown at two different temperatures, control (35°C) and stress (45°C), in a glasshouse, in a randomized complete block design (RCBD) in three replications. At the flowering stage, a label-free quantitative shotgun proteomics of cotton leaves revealed the differential expression of 701 and 1270 proteins in the tolerant and susceptible genotypes compared to the control, respectively. Physiological and biochemical analysis showed that the heat-tolerant genotype responded uniquely to stress by maintaining the net photosynthetic rate ( Pn) (25.2–17.5 μmolCO 2m -2S -1), chlorophyll (8.5–7.8mg/g FW), and proline contents (4.9–7.4 μmole/g) compared to control, supported by the upregulation of many proteins involved in several pathways, including photosynthesis, oxidoreductase activity, response to stresses, translation, transporter activities, as well as protein and carbohydrate metabolic processes. In contrast, the distinctive pattern of protein downregulation involved in stress response, oxidoreductase activity, and carbohydrate metabolism was observed in susceptible plants. To the best of our knowledge, this is the first proteomic study on cotton leaves that has identified more than 8000 proteins with an array of differentially expressed proteins responsive to the heat treatment that could serve as potential markers in the breeding programs after further experimentation.

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          The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

          The PRoteomics IDEntifications (PRIDE) database ( https://www.ebi.ac.uk/pride/ ) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) consortium and an ELIXIR core data resource. In this manuscript, we summarize the developments in PRIDE resources and related tools since the previous update manuscript was published in Nucleic Acids Research in 2019. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 500 datasets per month during 2021. In addition to continuous improvements in PRIDE Archive data pipelines and infrastructure, the PRIDE Spectra Archive has been developed to provide direct access to the submitted mass spectra using Universal Spectrum Identifiers. As a key point, the file format MAGE-TAB for proteomics has been developed to enable the improvement of sample metadata annotation. Additionally, the resource PRIDE Peptidome provides access to aggregated peptide/protein evidences across PRIDE Archive. Furthermore, we will describe how PRIDE has increased its efforts to reuse and disseminate high-quality proteomics data into other added-value resources such as UniProt, Ensembl and Expression Atlas.
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            Reactive oxygen species homeostasis and signalling during drought and salinity stresses.

            Water deficit and salinity, especially under high light intensity or in combination with other stresses, disrupt photosynthesis and increase photorespiration, altering the normal homeostasis of cells and cause an increased production of reactive oxygen species (ROS). ROS play a dual role in the response of plants to abiotic stresses functioning as toxic by-products of stress metabolism, as well as important signal transduction molecules. In this review, we provide an overview of ROS homeostasis and signalling in response to drought and salt stresses and discuss the current understanding of ROS involvement in stress sensing, stress signalling and regulation of acclimation responses.
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              Physiological, Biochemical, and Molecular Mechanisms of Heat Stress Tolerance in Plants

              High temperature (HT) stress is a major environmental stress that limits plant growth, metabolism, and productivity worldwide. Plant growth and development involve numerous biochemical reactions that are sensitive to temperature. Plant responses to HT vary with the degree and duration of HT and the plant type. HT is now a major concern for crop production and approaches for sustaining high yields of crop plants under HT stress are important agricultural goals. Plants possess a number of adaptive, avoidance, or acclimation mechanisms to cope with HT situations. In addition, major tolerance mechanisms that employ ion transporters, proteins, osmoprotectants, antioxidants, and other factors involved in signaling cascades and transcriptional control are activated to offset stress-induced biochemical and physiological alterations. Plant survival under HT stress depends on the ability to perceive the HT stimulus, generate and transmit the signal, and initiate appropriate physiological and biochemical changes. HT-induced gene expression and metabolite synthesis also substantially improve tolerance. The physiological and biochemical responses to heat stress are active research areas, and the molecular approaches are being adopted for developing HT tolerance in plants. This article reviews the recent findings on responses, adaptation, and tolerance to HT at the cellular, organellar, and whole plant levels and describes various approaches being taken to enhance thermotolerance in plants.
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                Author and article information

                Contributors
                Role: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draft
                Role: Formal analysisRole: InvestigationRole: Writing – original draft
                Role: Data curationRole: MethodologyRole: Writing – review & editing
                Role: Data curationRole: MethodologyRole: ResourcesRole: Writing – review & editing
                Role: InvestigationRole: MethodologyRole: SoftwareRole: VisualizationRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: SoftwareRole: ValidationRole: Writing – review & editing
                Role: MethodologyRole: ResourcesRole: SoftwareRole: VisualizationRole: Writing – review & editing
                Role: Data curationRole: MethodologyRole: Writing – review & editing
                Role: Funding acquisitionRole: ResourcesRole: VisualizationRole: Writing – original draft
                Role: Data curationRole: Writing – review & editing
                Role: Data curationRole: ResourcesRole: SoftwareRole: ValidationRole: VisualizationRole: Writing – review & editing
                Role: ConceptualizationRole: MethodologyRole: ResourcesRole: SupervisionRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS One
                PLoS One
                plos
                PLOS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                9 January 2025
                2025
                : 20
                : 1
                : e0316630
                Affiliations
                [1 ] Department of Biochemistry, Bahauddin Zakariya University, Multan, Pakistan
                [2 ] Department of Biochemistry and Molecular Biology, Federal University of Ceara, Fortaleza, Brazil
                [3 ] Department of Animal Science, Federal University of Ceara, Fortaleza, Brazil
                [4 ] Physiology/Chemistry Section, Central Cotton Research Institute, Multan, Pakistan
                [5 ] Faculty of Biological Sciences, Department of Plant Sciences, Quaid-i-Azam University, Islamabad, Pakistan
                [6 ] Department of Biochemistry, Proteomic Unit, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
                [7 ] Hainan International Joint Research Center of Marine Advanced Photoelectric Functional Materials, College of Chemistry and Chemical Engineering, Hainan Normal University, Haikou, PR China
                [8 ] Department of Chemistry, Kohat University of Science & Technology, Kohat, Pakistan
                [9 ] Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
                [10 ] Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
                University of Agriculture Faisalabad, PAKISTAN
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Author information
                https://orcid.org/0000-0001-6126-7102
                Article
                PONE-D-24-32920
                10.1371/journal.pone.0316630
                11717266
                39787180
                bae2dfbe-97db-4d80-8ca8-0d54b3f85c4f
                © 2025 Perveen et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 4 August 2024
                : 13 December 2024
                Page count
                Figures: 11, Tables: 1, Pages: 33
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/501100002383, King Saud University;
                Award ID: RSP2024R171
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/501100005283, Fundação Cearense de Apoio ao Desenvolvimento Científico e Tecnológico;
                Award ID: PVS-0215-00042.01.00/23
                Award Recipient :
                The authors thank Researchers Supporting Project Number (RSP2025R110) at King Saud University Riyadh Saudi Arabia for financial support awarded to R.U. We are also thankful to the Foundation for the Support of Scientific and Technological Development of the State of Ceará (FUNCAP; Project No. PVS-0215-00042.01.00/23) for providing a fellowship of visiting researcher/professor to Mohibullah Shah at the Department of Animal Science, Federal University of Ceará, Fortaleza, Brazil awarded to A.A.M.
                Categories
                Research Article
                Physical Sciences
                Physics
                Classical Mechanics
                Mechanical Stress
                Thermal Stresses
                Biology and Life Sciences
                Biochemistry
                Plant Biochemistry
                Photosynthesis
                Biology and Life Sciences
                Plant Science
                Plant Biochemistry
                Photosynthesis
                Biology and Life Sciences
                Organisms
                Eukaryota
                Plants
                Flowering Plants
                Cotton
                Biology and Life Sciences
                Physiology
                Plant Physiology
                Plant Defenses
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Physiology
                Plant Defenses
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Pathology
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Ecology and Environmental Sciences
                Ecology
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Ecology
                Plant-Environment Interactions
                Plant Resistance to Abiotic Stress
                Biology and Life Sciences
                Plant Science
                Plant Anatomy
                Leaves
                Biology and Life Sciences
                Cell Biology
                Cell Processes
                Cellular Stress Responses
                Heat Shock Response
                Biology and Life Sciences
                Molecular Biology
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Gene Expression and Vector Techniques
                Protein Expression
                Research and Analysis Methods
                Molecular Biology Techniques
                Molecular Biology Assays and Analysis Techniques
                Gene Expression and Vector Techniques
                Protein Expression
                Physical Sciences
                Chemistry
                Chemical Compounds
                Organic Compounds
                Amino Acids
                Cyclic Amino Acids
                Proline
                Physical Sciences
                Chemistry
                Organic Chemistry
                Organic Compounds
                Amino Acids
                Cyclic Amino Acids
                Proline
                Biology and Life Sciences
                Biochemistry
                Proteins
                Amino Acids
                Cyclic Amino Acids
                Proline
                Custom metadata
                The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD056003.

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                Uncategorized

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