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Momo J, Rawoof A, Kumar A, Islam K, Ahmad I, Ramchiary N. Proteomics of Reproductive Development, Fruit Ripening, and Stress Responses in Tomato. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:65-95. [PMID: 36584279 DOI: 10.1021/acs.jafc.2c06564] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The fruits of the tomato crop (Solanum lycopersicum L.) are increasingly consumed by humans worldwide. Due to their rich nutritional quality, pharmaceutical properties, and flavor, tomato crops have gained a salient role as standout crops among other plants. Traditional breeding and applied functional research have made progress in varying tomato germplasms to subdue biotic and abiotic stresses. Proteomic investigations within a span of few decades have assisted in consolidating the functional genomics and transcriptomic research. However, due to the volatility and dynamicity of proteins in the regulation of various biosynthetic pathways, there is a need for continuing research in the field of proteomics to establish a network that could enable a more comprehensive understanding of tomato growth and development. With this view, we provide a comprehensive review of proteomic studies conducted on the tomato plant in past years, which will be useful for future breeders and researchers working to improve the tomato crop.
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Affiliation(s)
- John Momo
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Abdul Rawoof
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ajay Kumar
- Department of Plant Sciences, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala 671316, India
| | - Khushbu Islam
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Ilyas Ahmad
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, Delhi 110067, India
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Borbély P, Poór P, Tari I. Changes in physiological and photosynthetic parameters in tomato of different ethylene status under salt stress: Effects of exogenous 1-aminocyclopropane-1-carboxylic acid treatment and the inhibition of ethylene signalling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:345-356. [PMID: 33002713 DOI: 10.1016/j.plaphy.2020.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 09/12/2020] [Indexed: 05/04/2023]
Abstract
Although ethylene (ET) is an important participant in plant responses to salt stress, its role in the early period of acclimation, especially in the case of photosynthesis has not been revealed in detail. In this study, the effects of tolerable (100 mM) or lethal (250 mM) NaCl concentrations were investigated in hydroponically grown tomato (Solanum lycopersicum L. cv. Ailsa Craig) plants of different ET status, in wild type (WT) plants, in WT plants pre-treated with the ET generator 1-aminocyclopropane-1-carboxylic acid (ACC) and in ET insensitive, Never ripe (Nr/Nr) mutants for 1-, 6- and 24 h. In the leaves ACC treatment reduced the osmotic effect of salt stress, while Nr mutation enhanced not only osmotic but ionic component of salt stress at 100 mM NaCl. ET insensitivity caused greater decline in stomatal conductance and photosynthetic CO2 assimilation rate than in the controls under tolerable salt stress, but both ACC treatment and Nr mutation helped to maintain positive carbon assimilation under lethal salt stress after 24 h. Nr mutant leaves showed highly enhanced regulated non-photochemical quenching (NPQ) and therefore lower quantum yield of photosystem II (PSII), due to more intensive cyclic electron flow around photosystem I (CEF-PSI), which was further increased under high salinity. Exogenous ACC treatment lowered CEF-PSI and enhanced PSII photochemistry after 6 h of lethal salt stress. Controlling PSI photoinhibition, ET is suggested to be an important regulator of CEF-PSI and photoprotection under salt stress. Furthermore, the altered ET status could cause contrasting effects under different stress severity.
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Affiliation(s)
- Péter Borbély
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép fasor 52., Hungary; Biological Doctoral School, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép fasor 52., Hungary; Department of Plant Molecular Biology, Agricultural Institute, Centre for Agricultural Research, 2462, Martonvásár, Brunszvik u. 2., Hungary.
| | - Péter Poór
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép fasor 52., Hungary
| | - Irma Tari
- Department of Plant Biology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép fasor 52., Hungary
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Zhang Z, Liu C, Guo Y. Wheat Transcription Factor TaSNAC11-4B Positively Regulates Leaf Senescence through Promoting ROS Production in Transgenic Arabidopsis. Int J Mol Sci 2020; 21:ijms21207672. [PMID: 33081330 PMCID: PMC7589474 DOI: 10.3390/ijms21207672] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/13/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
Senescence is the final stage of leaf development which is accompanied by highly coordinated and complicated reprogramming of gene expression. Genetic manipulation of leaf senescence in major crops including wheat has been shown to be able to increase stress tolerance and grain yield. NAC(No apical meristem (NAM), ATAF1/2, and cup-shaped cotyledon (CUC)) transcription factors (TFs) play important roles in regulating gene expression changes during leaf senescence and in response to abiotic stresses. Here, we report the characterization of TaSNAC11-4B (Uniprot: A0A1D5XI64), a wheat NAC family member that acts as a functional homolog of AtNAP, a key regulator of leaf senescence in Arabidopsis. The expression of TaSNAC11-4B was up-regulated with the progression of leaf senescence, in response to abscisic acid (ABA) and drought treatments in wheat. Ectopic expression of TaSNAC11-4B in Arabidopsis promoted ROS accumulation and significantly accelerated age-dependent as well as drought- and ABA-induced leaf senescence. Results from transcriptional activity assays indicated that the TaSNAC11-4B protein displayed transcriptional activation activities that are dependent on its C terminus. Furthermore, qRT-PCR and dual-Luciferase assay results suggested that TaSNAC11-4B could positively regulate the expression of AtrbohD and AtrbohF, which encode catalytic subunits of the ROS-producing NADPH oxidase. Further analysis of TaSNAC11-4B in wheat senescence and the potential application of this gene in manipulating leaf senescence with the purpose of yield increase and stress tolerance is discussed.
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Barrera NF, Melgarejo LM, Cruz-Gallego M, Cortés LJ, Guzmán F, Calvo JC. Conformationally Restricted Peptides from Rice Proteins Elicit Antibodies That Recognize the Corresponding Native Protein in ELISA Assays. Molecules 2018; 23:molecules23092262. [PMID: 30189617 PMCID: PMC6225240 DOI: 10.3390/molecules23092262] [Citation(s) in RCA: 2] [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: 08/07/2018] [Revised: 08/29/2018] [Accepted: 09/01/2018] [Indexed: 01/13/2023] Open
Abstract
The rice hoja blanca virus (RHBV), transmitted by the planthopper insect Tagosodes orizicolus, is a disease that attacks rice and generates significant production losses in Colombia. Fedearroz 2000 and Colombia I commercial rice varieties, which have different resistance levels to the disease, were selected in this study. To identify proteins associated to the insect and virus signaling, a comparative proteomics study was performed. By comparing proteomic profiles, between virus-infected and control group plants in two-dimensional electrophoresis, proteins exhibiting significant changes in abundance were found. In another test, peptide dendrimers containing sequences conformationally restricted to α-helix from four of those rice proteins were synthesized. In the experiment, sera from mice inoculated with peptide dendrimers could recognize the corresponding native protein in ELISA assays. Reported comparative proteomic results provide new insights into the molecular mechanisms of plant response to the RHBV and comprehensive tools for the analysis of new crop varieties. Besides, results from conformational peptide dendrimer approach are promising and show that it is feasible to detect proteins as markers, and may have biological applications by decreasing the susceptibility to proteolytic degradation.
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Affiliation(s)
- Nubia F Barrera
- Doctorado en Biotecnología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 224, Bogotá 110111, Colombia.
- Grupo Proteoma UD, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Carrera 4 No. 26B-54, Bogotá 110111, Colombia.
| | - Luz M Melgarejo
- Laboratorio de Fisiología y Bioquímica Vegetal, Departamento de Biología, Universidad Nacional de Colombia, Carrera 30 No. 45-03, Edificio 421, Bogotá 110111, Colombia.
| | - Maribel Cruz-Gallego
- Centro Internacional de Agricultura Tropical, CIAT, Fondo Latinoamericano para Arroz de Riego, FLAR, Palmira, Valle 763537, Colombia.
| | - Lina Jimena Cortés
- Núcleo de Biotecnología de Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Fanny Guzmán
- Núcleo de Biotecnología de Curauma, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Julio C Calvo
- Grupo Proteoma UD, Facultad de Ciencias y Educación, Universidad Distrital Francisco José de Caldas, Carrera 4 No. 26B-54, Bogotá 110111, Colombia.
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Peng Z, He S, Gong W, Xu F, Pan Z, Jia Y, Geng X, Du X. Integration of proteomic and transcriptomic profiles reveals multiple levels of genetic regulation of salt tolerance in cotton. BMC PLANT BIOLOGY 2018; 18:128. [PMID: 29925319 PMCID: PMC6011603 DOI: 10.1186/s12870-018-1350-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 06/12/2018] [Indexed: 05/19/2023]
Abstract
BACKGROUND Salinity is a major abiotic stress that limits upland cotton growth and reduces fibre production worldwide. To reveal genetic regulation via transcript and protein levels after salt stress, we comprehensively analysed the global changes in mRNA, miRNA, and protein profiles in response to salt stress in two contrasting salt-tolerant cotton genotypes. RESULTS In the current study, proteomic and mRNA-seq data were combined to reveal that some genes are differentially expressed at both the proteomic and mRNA levels. However, we observed no significant change in mRNA corresponding to most of the strongly differentially abundant proteins. This finding may have resulted from global changes in alternative splicing events and miRNA levels under salt stress conditions. Evidence was provided indicating that several salt stress-responsive proteins can alter miRNAs and modulate alternative splicing events in upland cotton. The results of the stringent screening of the mRNA-seq and proteomic data between the salt-tolerant and salt-sensitive genotypes identified 63 and 85 candidate genes/proteins related to salt tolerance after 4 and 24 h of salt stress, respectively, between the tolerant and sensitive genotype. Finally, we predicted an interaction network comprising 158 genes/proteins and then discovered that two main clusters in the network were composed of ATP synthase (CotAD_74681) and cytochrome oxidase (CotAD_46197) in mitochondria. The results revealed that mitochondria, as important organelles involved in energy metabolism, play an essential role in the synthesis of resistance proteins during the process of salt exposure. CONCLUSION We provided a plausible schematic for the systematic salt tolerance model; this schematic reveals multiple levels of gene regulation in response to salt stress in cotton and provides a list of salt tolerance-related genes/proteins. The information here will facilitate candidate gene discovery and molecular marker development for salt tolerance breeding in cotton.
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Affiliation(s)
- Zhen Peng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Wenfang Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Feifei Xu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiaoli Geng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000 Henan China
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Barkla BJ, Castellanos-Cervantes T, de León JLD, Matros A, Mock HP, Perez-Alfocea F, Salekdeh GH, Witzel K, Zörb C. Elucidation of salt stress defense and tolerance mechanisms of crop plants using proteomics--current achievements and perspectives. Proteomics 2014; 13:1885-900. [PMID: 23723162 DOI: 10.1002/pmic.201200399] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 04/12/2013] [Accepted: 04/24/2013] [Indexed: 12/18/2022]
Abstract
Salinity is a major threat limiting the productivity of crop plants. A clear demand for improving the salinity tolerance of the major crop plants is imposed by the rapidly growing world population. This review summarizes the achievements of proteomic studies to elucidate the response mechanisms of selected model and crop plants to cope with salinity stress. We also aim at identifying research areas, which deserve increased attention in future proteome studies, as a prerequisite to identify novel targets for breeding strategies. Such areas include the impact of plant-microbial communities on the salinity tolerance of crops under field conditions, the importance of hormone signaling in abiotic stress tolerance, and the significance of control mechanisms underlying the observed changes in the proteome patterns. We briefly highlight the impact of novel tools for future proteome studies and argue for the use of integrated approaches. The evaluation of genetic resources by means of novel automated phenotyping facilities will have a large impact on the application of proteomics especially in combination with metabolomics or transcriptomics.
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Abstract
Quantitative proteomics by LC-MS/MS is a widely used approach for quantifying a significant portion of any complex proteome. Among the different techniques used for this purpose, one is by use of Data Independent Acquisition (DIA). We present a descriptive protocol for label-free quantitation of proteins by one DIA method termed LC-MS(E), which facilitates large-scale quantification of proteins without the need for isotopic labelling and with no theoretical limit to the number of samples included in an experiment.
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Affiliation(s)
- Alon Savidor
- Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, 76100, Israel
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Jacoby RP, Millar AH, Taylor NL. Investigating the role of respiration in plant salinity tolerance by analyzing mitochondrial proteomes from wheat and a salinity-tolerant Amphiploid (wheat × Lophopyrum elongatum). J Proteome Res 2013; 12:4807-29. [PMID: 23895732 DOI: 10.1021/pr400504a] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The effect of salinity on mitochondrial properties was investigated by comparing the reference wheat variety Chinese Spring (CS) to a salt-tolerant amphiploid (AMP). The octoploid AMP genotype was previously generated by combining hexaploid bread wheat (CS) with the diploid wild wheatgrass adapted to salt marshes, Lophopyrum elongatum. Here we used a combination of physiological, biochemical, and proteomic analyses to explore the mitochondrial and respiratory response to salinity in these two genotypes. The AMP showed greater growth tolerance to salinity treatments and altered respiration rate in both roots and shoots. A proteomic workflow of 2D-DIGE and MALDI TOF/TOF mass spectrometry was used to compare the protein composition of isolated mitochondrial samples from roots and shoots of both genotypes, following control or salt treatment. A large set of mitochondrial proteins were identified as responsive to salinity in both genotypes, notably enzymes involved in detoxification of reactive oxygen species. Genotypic differences in mitochondrial composition were also identified, with AMP exhibiting a higher abundance of manganese superoxide dismutase, serine hydroxymethyltransferase, aconitase, malate dehydrogenase, and β-cyanoalanine synthase compared to CS. We present peptide fragmentation spectra derived from some of these AMP-specific protein spots, which could serve as biomarkers to track superior protein variants.
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Affiliation(s)
- Richard P Jacoby
- ARC Centre of Excellence in Plant Energy Biology & Centre for Comparative Analysis of Biomolecular Networks (CABiN), M316, The University of Western Australia , 35 Stirling Highway, Crawley, WA 6009, Australia
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Hakeem KR, Chandna R, Ahmad P, Iqbal M, Ozturk M. Relevance of Proteomic Investigations in Plant Abiotic Stress Physiology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012; 16:621-35. [DOI: 10.1089/omi.2012.0041] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Khalid Rehman Hakeem
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Ruby Chandna
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Parvaiz Ahmad
- Department of Botany, Amar Singh College, University of Kashmir, Srinagar, India
| | - Muhammad Iqbal
- Molecular Ecology Laboratory, Department of Botany, Jamia Hamdard, New Delhi, India
| | - Munir Ozturk
- Department of Botany, Ege University, Bornova, Izmir, Turkey
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