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Khawula S, Gokul A, Niekerk LA, Basson G, Keyster M, Badiwe M, Klein A, Nkomo M. Insights into the Effects of Hydroxycinnamic Acid and Its Secondary Metabolites as Antioxidants for Oxidative Stress and Plant Growth under Environmental Stresses. Curr Issues Mol Biol 2023; 46:81-95. [PMID: 38275667 PMCID: PMC10814621 DOI: 10.3390/cimb46010007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/28/2023] [Accepted: 12/11/2023] [Indexed: 01/27/2024] Open
Abstract
Plant immobility renders plants constantly susceptible to various abiotic and biotic stresses. Abiotic and biotic stresses are known to produce reactive oxygen species (ROS), which cause comparable cellular secondary reactions (osmotic or oxidative stress), leading to agricultural productivity constraints worldwide. To mitigate the challenges caused by these stresses, plants have evolved a variety of adaptive strategies. Phenolic acids form a key component of these strategies, as they are predominantly known to be secreted by plants in response to abiotic or biotic stresses. Phenolic acids can be divided into different subclasses based on their chemical structures, such as hydroxybenzoic acids and hydroxycinnamic acids. This review analyzes hydroxycinnamic acids and their derivatives as they increase under stressful conditions, so to withstand environmental stresses they regulate physiological processes through acting as signaling molecules that regulate gene expression and biochemical pathways. The mechanism of action used by hydroxycinnamic acid involves minimization of oxidative damage to maintain cellular homeostasis and protect vital cellular components from harm. The purpose of this review is to highlight the potential of hydroxycinnamic acid metabolites/derivatives as potential antioxidants. We review the uses of different secondary metabolites associated with hydroxycinnamic acid and their contributions to plant growth and development.
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Affiliation(s)
- Sindiswa Khawula
- Plant Biotechnology Laboratory, Department of Agriculture, University of Zululand, Main Road, Kwa-Dlangezwa 3886, South Africa;
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of Free State, Phuthadithaba 9866, South Africa;
| | - Lee-Ann Niekerk
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (G.B.); (M.K.)
| | - Gerhard Basson
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (G.B.); (M.K.)
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa; (L.-A.N.); (G.B.); (M.K.)
| | - Mihlali Badiwe
- Department of Plant Pathology, Stellenbosch University, Stellenbosch 7435, South Africa;
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa;
| | - Mbukeni Nkomo
- Plant Biotechnology Laboratory, Department of Agriculture, University of Zululand, Main Road, Kwa-Dlangezwa 3886, South Africa;
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2
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Chao H, Zhang S, Hu Y, Ni Q, Xin S, Zhao L, Ivanisenko VA, Orlov YL, Chen M. Integrating omics databases for enhanced crop breeding. J Integr Bioinform 2023; 20:jib-2023-0012. [PMID: 37486120 PMCID: PMC10777369 DOI: 10.1515/jib-2023-0012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
Crop plant breeding involves selecting and developing new plant varieties with desirable traits such as increased yield, improved disease resistance, and enhanced nutritional value. With the development of high-throughput technologies, such as genomics, transcriptomics, and metabolomics, crop breeding has entered a new era. However, to effectively use these technologies, integration of multi-omics data from different databases is required. Integration of omics data provides a comprehensive understanding of the biological processes underlying plant traits and their interactions. This review highlights the importance of integrating omics databases in crop plant breeding, discusses available omics data and databases, describes integration challenges, and highlights recent developments and potential benefits. Taken together, the integration of omics databases is a critical step towards enhancing crop plant breeding and improving global food security.
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Affiliation(s)
- Haoyu Chao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Shilong Zhang
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Yueming Hu
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Qingyang Ni
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Saige Xin
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Liang Zhao
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
| | - Vladimir A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk630090, Russia
| | - Yuriy L. Orlov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk630090, Russia
- Agrarian and Technological Institute, Peoples’ Friendship University of Russia, Moscow117198, Russia
- The Digital Health Institute, I.M. Sechenov First Moscow State Medical University of the Russian Ministry of Health (Sechenov University), Moscow119991, Russia
| | - Ming Chen
- Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou310058, China
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3
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Hamzelou S, Belobrajdic D, Broadbent JA, Juhász A, Lee Chang K, Jameson I, Ralph P, Colgrave ML. Utilizing proteomics to identify and optimize microalgae strains for high-quality dietary protein: a review. Crit Rev Biotechnol 2023:1-16. [PMID: 38035669 DOI: 10.1080/07388551.2023.2283376] [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: 04/16/2023] [Accepted: 10/17/2023] [Indexed: 12/02/2023]
Abstract
Algae-derived protein has immense potential to provide high-quality protein foods for the expanding human population. To meet its potential, a broad range of scientific tools are required to identify optimal algal strains from the hundreds of thousands available and identify ideal growing conditions for strains that produce high-quality protein with functional benefits. A research pipeline that includes proteomics can provide a deeper interpretation of microalgal composition and biochemistry in the pursuit of these goals. To date, proteomic investigations have largely focused on pathways that involve lipid production in selected microalgae species. Herein, we report the current state of microalgal proteome measurement and discuss promising approaches for the development of protein-containing food products derived from algae.
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Affiliation(s)
| | | | | | - Angéla Juhász
- School of Science, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, Joondalup, Australia
| | | | - Ian Jameson
- CSIRO Ocean and Atmosphere, Hobart, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology Sydney, Ultimo, Australia
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, St Lucia, Australia
- School of Science, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, Edith Cowan University, Joondalup, Australia
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4
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Xu X, Fonseca de Lima CF, Vu LD, De Smet I. When drought meets heat - a plant omics perspective. FRONTIERS IN PLANT SCIENCE 2023; 14:1250878. [PMID: 37674736 PMCID: PMC10478009 DOI: 10.3389/fpls.2023.1250878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/07/2023] [Indexed: 09/08/2023]
Abstract
Changes in weather patterns with emerging drought risks and rising global temperature are widespread and negatively affect crop growth and productivity. In nature, plants are simultaneously exposed to multiple biotic and abiotic stresses, but most studies focus on individual stress conditions. However, the simultaneous occurrence of different stresses impacts plant growth and development differently than a single stress. Plants sense the different stress combinations in the same or in different tissues, which could induce specific systemic signalling and acclimation responses; impacting different stress-responsive transcripts, protein abundance and modifications, and metabolites. This mini-review focuses on the combination of drought and heat, two abiotic stress conditions that often occur together. Recent omics studies indicate common or independent regulators involved in heat or drought stress responses. Here, we summarize the current research results, highlight gaps in our knowledge, and flag potential future focus areas.
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Affiliation(s)
- Xiangyu Xu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cassio Flavio Fonseca de Lima
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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5
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Graska J, Fidler J, Gietler M, Prabucka B, Nykiel M, Labudda M. Nitric Oxide in Plant Functioning: Metabolism, Signaling, and Responses to Infestation with Ecdysozoa Parasites. BIOLOGY 2023; 12:927. [PMID: 37508359 PMCID: PMC10376146 DOI: 10.3390/biology12070927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023]
Abstract
Nitric oxide (NO) is an important signaling molecule that is involved in a wide range of physiological processes in plants, including responses to biotic and abiotic stresses. Changes in endogenous NO concentration lead to activation/deactivation of NO signaling and NO-related processes. This paper presents the current state of knowledge on NO biosynthesis and scavenging pathways in plant cells and highlights the role of NO in post-translational modifications of proteins (S-nitrosylation, nitration, and phosphorylation) in plants under optimal and stressful environmental conditions. Particular attention was paid to the interactions of NO with other signaling molecules: reactive oxygen species, abscisic acid, auxins (e.g., indole-3-acetic acid), salicylic acid, and jasmonic acid. In addition, potential common patterns of NO-dependent defense responses against attack and feeding by parasitic and molting Ecdysozoa species such as nematodes, insects, and arachnids were characterized. Our review definitely highlights the need for further research on the involvement of NO in interactions between host plants and Ecdysozoa parasites, especially arachnids.
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Affiliation(s)
- Jakub Graska
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.F.); (M.G.); (B.P.); (M.N.)
| | | | | | | | | | - Mateusz Labudda
- Department of Biochemistry and Microbiology, Institute of Biology, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland; (J.F.); (M.G.); (B.P.); (M.N.)
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6
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Du L, Ma Z, Mao H. Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2465. [PMID: 37447026 DOI: 10.3390/plants12132465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 07/15/2023]
Abstract
Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications.
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Affiliation(s)
- Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Zhenbing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, China
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7
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Yadav BG, Aakanksha, Kumar R, Yadava SK, Kumar A, Ramchiary N. Understanding the Proteomes of Plant Development and Stress Responses in Brassica Crops. J Proteome Res 2023; 22:660-680. [PMID: 36786770 DOI: 10.1021/acs.jproteome.2c00684] [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: 02/15/2023]
Abstract
Brassica crops have great economic value due to their rich nutritional content and are therefore grown worldwide as oilseeds, vegetables, and condiments. Deciphering the molecular mechanisms associated with the advantageous phenotype is the major objective of various Brassica improvement programs. As large technological advancements have been achieved in the past decade, the methods to understand molecular mechanisms underlying the traits of interest have also taken a sharp upturn in plant breeding practices. Proteomics has emerged as one of the preferred choices nowadays along with genomics and other molecular approaches, as proteins are the ultimate effector molecules responsible for phenotypic changes in living systems, and allow plants to resist variable environmental stresses. In the last two decades, rapid progress has been made in the field of proteomics research in Brassica crops, but a comprehensive review that collates the different studies is lacking. This review provides an inclusive summary of different proteomic studies undertaken in Brassica crops for cytoplasmic male sterility, oil content, and proteomics of floral organs and seeds, under different biotic and abiotic stresses including post-translational modifications of proteins. This comprehensive review will help in understanding the role of different proteins in controlling plant phenotypes, and provides information for initiating future studies on Brassica breeding and improvement programs.
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Affiliation(s)
- Bal Govind Yadav
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Aakanksha
- Department of Genetics, University of Delhi South Campus, New Delhi 110021, Delhi, India
| | - Rahul Kumar
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Satish Kumar Yadava
- Centre for Genetic Manipulation of Crop Plants, University of Delhi South Campus, New Delhi 110021, Delhi, India
| | - Ajay Kumar
- Department of Plant Science, School of Biological Sciences, Central University of Kerala, Kasaragod 671316, Kerala, India
| | - Nirala Ramchiary
- School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, Delhi, India
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8
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Genomics, Proteomics, and Metabolomics Approaches to Improve Abiotic Stress Tolerance in Tomato Plant. Int J Mol Sci 2023; 24:ijms24033025. [PMID: 36769343 PMCID: PMC9918255 DOI: 10.3390/ijms24033025] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
To explore changes in proteins and metabolites under stress circumstances, genomics, proteomics, and metabolomics methods are used. In-depth research over the previous ten years has gradually revealed the fundamental processes of plants' responses to environmental stress. Abiotic stresses, which include temperature extremes, water scarcity, and metal toxicity brought on by human activity and urbanization, are a major cause for concern, since they can result in unsustainable warming trends and drastically lower crop yields. Furthermore, there is an emerging reliance on agrochemicals. Stress is responsible for physiological transformations such as the formation of reactive oxygen, stomatal opening and closure, cytosolic calcium ion concentrations, metabolite profiles and their dynamic changes, expression of stress-responsive genes, activation of potassium channels, etc. Research regarding abiotic stresses is lacking because defense feedbacks to abiotic factors necessitate regulating the changes that activate multiple genes and pathways that are not properly explored. It is clear from the involvement of these genes that plant stress response and adaptation are complicated processes. Targeting the multigenicity of plant abiotic stress responses caused by genomic sequences, transcripts, protein organization and interactions, stress-specific and cellular transcriptome collections, and mutant screens can be the first step in an integrative approach. Therefore, in this review, we focused on the genomes, proteomics, and metabolomics of tomatoes under abiotic stress.
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Zhang K, Li Y, Huang T, Li Z. Potential application of TurboID-based proximity labeling in studying the protein interaction network in plant response to abiotic stress. FRONTIERS IN PLANT SCIENCE 2022; 13:974598. [PMID: 36051300 PMCID: PMC9426856 DOI: 10.3389/fpls.2022.974598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stresses are major environmental conditions that reduce plant growth, productivity and quality. Protein-protein interaction (PPI) approaches can be used to screen stress-responsive proteins and reveal the mechanisms of protein response to various abiotic stresses. Biotin-based proximity labeling (PL) is a recently developed technique to label proximal proteins of a target protein. TurboID, a biotin ligase produced by directed evolution, has the advantages of non-toxicity, time-saving and high catalytic efficiency compared to other classic protein-labeling enzymes. TurboID-based PL has been successfully applied in animal, microorganism and plant systems, particularly to screen transient or weak protein interactions, and detect spatially or temporally restricted local proteomes in living cells. This review concludes classic PPI approaches in plant response to abiotic stresses and their limitations for identifying complex network of regulatory proteins of plant abiotic stresses, and introduces the working mechanism of TurboID-based PL, as well as its feasibility and advantages in plant abiotic stress research. We hope the information summarized in this article can serve as technical references for further understanding the regulation of plant adaptation to abiotic stress at the protein level.
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Affiliation(s)
- Kaixin Zhang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yinyin Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Tengbo Huang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
| | - Ziwei Li
- Guangdong Provincial Key Laboratory for Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, China
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10
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Wang J, Yang J, Lei C, Sun X, Hu J. Phosphorylation of the Autographa californica multiple nucleopolyhedrovirus polyhedron envelope protein plays an important role in the formation of the occlusion body envelope. J Gen Virol 2022; 103. [PMID: 35737520 DOI: 10.1099/jgv.0.001759] [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: 11/18/2022] Open
Abstract
During the life cycle of a baculovirus, a crystallized protein matrix, formed by polyhedrin (POLH), is produced. The protein matrix is surrounded by a multilayered protein/carbohydrate envelope, and matrix and envelope together form a mature occlusion body (OB). The polyhedron envelope plays an important role in resistance against adverse external environments. The polyhedron envelope protein (PEP) is the main protein that forms the polyhedron envelope, but the mechanism of formation of the polyhedron envelope is unclear. Here, through immunofluorescence localization observations, we found that PEP interacted with both POLH and P10 during formation of the polyhedron envelope in the late stages of infection, and PEP was also required for P10 incorporation on the surface of OBs. In this process, the phosphorylation of PEP played an important role. PEP was determined to be a phosphorylated protein using the Phos-tag technique, and PK1 was determined to be the phosphokinase of PEP by co-immunoprecipitation and in vitro phosphorylation. Immunofluorescence localization revealed that PEP was continuously phosphorylated by PK1 after PEP entered the nucleus until PEP was correctly packaged on the OB surface. Multi-point mutations of PEP conservative potential phosphorylation sites showed that the simultaneous mutation of S85, T86 and Y92 caused changes in the location of PEP and P10 in the late stages of infection, and resulted in an OB surface that lacked the polyhedron envelope. These data suggested that the phosphorylation of PEP at particular sites, i.e. S85, T86 and Y92, plays an important role in the formation of the polyhedron envelope.
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Affiliation(s)
- Jia Wang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Jian Yang
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China.,University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Chengfeng Lei
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Xiulian Sun
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
| | - Jia Hu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, PR China
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Muthuramalingam P, Shin H, Adarshan S, Jeyasri R, Priya A, Chen JT, Ramesh M. Molecular Insights into Freezing Stress in Peach Based on Multi-Omics and Biotechnology: An Overview. PLANTS 2022; 11:plants11060812. [PMID: 35336695 PMCID: PMC8954506 DOI: 10.3390/plants11060812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 03/15/2022] [Indexed: 11/21/2022]
Abstract
In nature or field conditions, plants are frequently exposed to diverse environmental stressors. Among abiotic stresses, the low temperature of freezing conditions is a critical factor that influences plants, including horticultural crops, decreasing their growth, development, and eventually quality and productivity. Fortunately, plants have developed a mechanism to improve the tolerance to freezing during exposure to a range of low temperatures. In this present review, current findings on freezing stress physiology and genetics in peach (Prunus persica) were refined with an emphasis on adaptive mechanisms for cold acclimation, deacclimation, and reacclimation. In addition, advancements using multi-omics and genetic engineering approaches unravel the molecular physiological mechanisms, including hormonal regulations and their general perceptions of freezing tolerance in peach were comprehensively described. This review might pave the way for future research to the horticulturalists and research scientists to overcome the challenges of freezing temperature and improvement of crop management in these conditions.
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Affiliation(s)
- Pandiyan Muthuramalingam
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea;
- Department of Biotechnology, Sri Shakthi Institute of Engineering and Technology, Coimbatore 641062, Tamil Nadu, India
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (R.J.); (A.P.); (M.R.)
| | - Hyunsuk Shin
- Department of Horticultural Science, Gyeongsang National University, Jinju 52725, Korea;
- Correspondence:
| | - Sivakumar Adarshan
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (R.J.); (A.P.); (M.R.)
| | - Rajendran Jeyasri
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (R.J.); (A.P.); (M.R.)
| | - Arumugam Priya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (R.J.); (A.P.); (M.R.)
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan;
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India; (S.A.); (R.J.); (A.P.); (M.R.)
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12
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Kosová K, Vítámvás P, Prášil IT, Klíma M, Renaut J. Plant Proteoforms Under Environmental Stress: Functional Proteins Arising From a Single Gene. FRONTIERS IN PLANT SCIENCE 2021; 12:793113. [PMID: 34970290 PMCID: PMC8712444 DOI: 10.3389/fpls.2021.793113] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 11/16/2021] [Indexed: 05/30/2023]
Abstract
Proteins are directly involved in plant phenotypic response to ever changing environmental conditions. The ability to produce multiple mature functional proteins, i.e., proteoforms, from a single gene sequence represents an efficient tool ensuring the diversification of protein biological functions underlying the diversity of plant phenotypic responses to environmental stresses. Basically, two major kinds of proteoforms can be distinguished: protein isoforms, i.e., alterations at protein sequence level arising from posttranscriptional modifications of a single pre-mRNA by alternative splicing or editing, and protein posttranslational modifications (PTMs), i.e., enzymatically catalyzed or spontaneous modifications of certain amino acid residues resulting in altered biological functions (or loss of biological functions, such as in non-functional proteins that raised as a product of spontaneous protein modification by reactive molecular species, RMS). Modulation of protein final sequences resulting in different protein isoforms as well as modulation of chemical properties of key amino acid residues by different PTMs (such as phosphorylation, N- and O-glycosylation, methylation, acylation, S-glutathionylation, ubiquitinylation, sumoylation, and modifications by RMS), thus, represents an efficient means to ensure the flexible modulation of protein biological functions in response to ever changing environmental conditions. The aim of this review is to provide a basic overview of the structural and functional diversity of proteoforms derived from a single gene in the context of plant evolutional adaptations underlying plant responses to the variability of environmental stresses, i.e., adverse cues mobilizing plant adaptive mechanisms to diminish their harmful effects.
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Affiliation(s)
- Klára Kosová
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Ilja Tom Prášil
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Miroslav Klíma
- Division of Crop Genetics and Plant Breeding, Crop Research Institute, Prague, Czechia
| | - Jenny Renaut
- Biotechnologies and Environmental Analytics Platform (BEAP), Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology (LIST), Esch-Sur-Alzette, Luxembourg
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13
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Mustafa G, Komatsu S. Plant proteomic research for improvement of food crops under stresses: a review. Mol Omics 2021; 17:860-880. [PMID: 34870299 DOI: 10.1039/d1mo00151e] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Crop improvement approaches have been changed due to technological advancements in traditional plant-breeding methods. Abiotic and biotic stresses limit plant growth and development, which ultimately lead to reduced crop yield. Proteins encoded by genomes have a considerable role in the endurance and adaptation of plants to different environmental conditions. Biotechnological applications in plant breeding depend upon the information generated from proteomic studies. Proteomics has a specific advantage to contemplate post-translational modifications, which indicate the functional effects of protein modifications on crop production. Subcellular proteomics helps in exploring the precise cellular responses and investigating the networking among subcellular compartments during plant development and biotic/abiotic stress responses. Large-scale mass spectrometry-based plant proteomic studies with a more comprehensive overview are now possible due to dramatic improvements in mass spectrometry, sample preparation procedures, analytical software, and strengthened availability of genomes for numerous plant species. Development of stress-tolerant or resilient crops is essential to improve crop productivity and growth. Use of high throughput techniques with advanced instrumentation giving efficient results made this possible. In this review, the role of proteomic studies in identifying the stress-response processes in different crops is summarized. Advanced techniques and their possible utilization on plants are discussed in detail. Proteomic studies accelerate marker-assisted genetic augmentation studies on crops for developing high yielding stress-tolerant lines or varieties under stresses.
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Affiliation(s)
- Ghazala Mustafa
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Setsuko Komatsu
- Faculty of Environment and Information Sciences, Fukui University of Technology, Fukui 910-8505, Japan.
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Zenda T, Liu S, Dong A, Li J, Wang Y, Liu X, Wang N, Duan H. Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. FRONTIERS IN PLANT SCIENCE 2021; 12:774994. [PMID: 34925418 PMCID: PMC8672198 DOI: 10.3389/fpls.2021.774994] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Songtao Liu
- Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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15
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Rodriguez MC, Mehta D, Tan M, Uhrig RG. Quantitative Proteome and PTMome Analysis of Arabidopsis thaliana Root Responses to Persistent Osmotic and Salinity Stress. PLANT & CELL PHYSIOLOGY 2021; 62:1012-1029. [PMID: 34059891 DOI: 10.1093/pcp/pcab076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 05/12/2021] [Accepted: 05/31/2021] [Indexed: 06/12/2023]
Abstract
Abiotic stresses such as drought result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter but instead must adapt to survive. Studies investigating plant responses to osmotic and/or salt stress have largely focused on short-term systemic responses, leaving our understanding of intermediate to longer-term adaptation (24 h to d) lacking. In addition to protein abundance and phosphorylation changes, evidence suggests reversible lysine acetylation may also be important for abiotic stress responses. Therefore, to characterize the protein-level effects of osmotic and salt stress, we undertook a label-free proteomic analysis of Arabidopsis thaliana roots exposed to 300 mM mannitol and 150 mM NaCl for 24 h. We assessed protein phosphorylation, lysine acetylation and changes in protein abundance, detecting significant changes in 245, 35 and 107 total proteins, respectively. Comparison with available transcriptome data indicates that transcriptome- and proteome-level changes occur in parallel, while post-translational modifications (PTMs) do not. Further, we find significant changes in PTMs, and protein abundance involve different proteins from the same networks, indicating a multifaceted regulatory approach to prolonged osmotic and salt stress. In particular, we find extensive protein-level changes involving sulfur metabolism under both osmotic and salt conditions as well as changes in protein kinases and transcription factors that may represent new targets for drought stress signaling. Collectively, we find that protein-level changes continue to occur in plant roots 24 h from the onset of osmotic and salt stress and that these changes differ across multiple proteome levels.
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Affiliation(s)
- Maria C Rodriguez
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Devang Mehta
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
- These authors contributed equally to the work
| | - Maryalle Tan
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
| | - Richard G Uhrig
- Department of Biological Sciences, University of Alberta, 11455 Saskatchewan Drive, Edmonton, AB T6G 2E9, Canada
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16
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Arabia S, Sami AA, Akhter S, Sarker RH, Islam T. Comprehensive in silico Characterization of Universal Stress Proteins in Rice ( Oryza sativa L.) With Insight Into Their Stress-Specific Transcriptional Modulation. FRONTIERS IN PLANT SCIENCE 2021; 12:712607. [PMID: 34394169 PMCID: PMC8355530 DOI: 10.3389/fpls.2021.712607] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 07/07/2021] [Indexed: 06/10/2023]
Abstract
In a world where climate change is real and its consequences are unprecedented, understanding of the plant adaptive capacity and native stress-responsive machinery is crucial. In recent years, universal stress proteins (USPs) have received much attention in the field of plant science due to their stress-specific transcriptional regulation. This study focuses on the extensive characterization of the USP gene family members in the monocot crop rice (Oryza sativa L. var. japonica). Here, we report a total of 44 USP genes in the rice genome. In silico characterization of these genes showed that domain architecture played a major role in the functional diversification of the USP gene family which holds for all plant USPs. On top of that, a higher conservation of OsUSP members has been exhibited with a monocot genome (Zea mays L.) as compared to a dicot genome (Arabidopsis thaliana L.). Expression profiling of the identified genes led to the discovery of multiple OsUSP genes that showed pronounced transcript alteration under various abiotic stress conditions, indicating their potential role as multi-functional stress-specific modules. Furthermore, expression validation of OsUSP genes using qRT-PCR provided a strong evidence for the utility OsUSP genes in building multi-stress tolerant plants. Altogether, this study provides leads to suitable USP candidates that could be targeted for plant breeding and genetic engineering experiments to develop stress resilient crop species.
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17
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Hamzelou S, Melino VJ, Plett DC, Kamath KS, Nawrocki A, Larsen MR, Atwell BJ, Haynes PA. The phosphoproteome of rice leaves responds to water and nitrogen supply. Mol Omics 2021; 17:706-718. [PMID: 34291261 DOI: 10.1039/d1mo00137j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The scarcity of freshwater is an increasing concern in flood-irrigated rice, whilst excessive use of nitrogen fertilizers is costly and contributes to environmental pollution. To co-ordinate growth adaptation under prolonged exposure to limited water or excess nitrogen supply, plants employ complex systems for signalling and regulation of metabolic processes. There is limited information on the involvement of one of the most important post-translational modifications (PTMs), protein phosphorylation, in plant adaptation to long-term changes in resource supply. Oryza sativa cv. Nipponbare was grown under two regimes of nitrogen from the time of germination to final harvest. Twenty-five days after germination, water was withheld from half the pots in each nitrogen treatment and low water supply continued for an additional 26 days, while the remaining pots were well watered. Leaves from all four groups of plants were harvested after 51 days in order to test whether phosphorylation of leaf proteins responded to prior abiotic stress events. The dominant impact of these resources is exerted in leaves, where PTMs have been predicted to occur. Proteins were extracted and phosphopeptides were analysed by nanoLC-MS/MS analysis, coupled with label-free quantitation. Water and nitrogen regimes triggered extensive changes in phosphorylation of proteins involved in membrane transport, such as the aquaporin OsPIP2-6, a water channel protein. Our study reveals phosphorylation of several peptides belonging to proteins involved in RNA-processing and carbohydrate metabolism, suggesting that phosphorylation events regulate the signalling cascades that are required to optimize plant response to resource supply.
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Affiliation(s)
- Sara Hamzelou
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
| | - Vanessa J Melino
- King Abdullah University for Science and Technology, 2955-6990, Kingdom of Saudi Arabia
| | - Darren C Plett
- The Plant Accelerator, Australian Plant Phenomics Facility, The University of Adelaide, PMB 1, Glen Osmond, SA 5064, Australia
| | - Karthik Shantharam Kamath
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia. and Australian Proteome Analysis Facility, Macquarie University, North Ryde, NSW 2109, Australia
| | - Arkadiusz Nawrocki
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Martin R Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, DK 5230 Odense M, Denmark
| | - Brian J Atwell
- Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia
| | - Paul A Haynes
- Department of Molecular Sciences, Macquarie University, North Ryde, NSW 2109, Australia.
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18
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Bonilla JO, Callegari EA, Paez MD, Gil RA, Villegas LB. Characterization of copper stress response in Fusarium tricinctum M6: A metal-resistant microorganism isolated from an acid mine drainage-affected environment. JOURNAL OF HAZARDOUS MATERIALS 2021; 412:125216. [PMID: 33951861 PMCID: PMC8108702 DOI: 10.1016/j.jhazmat.2021.125216] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 05/30/2023]
Abstract
Acid mine drainage-affected environments are interesting microbial niches for the isolation of metal-resistant microorganisms. In this sense, the aim of the present work is to isolate and characterize metal-resistant microorganisms from sediments of an abandoned gold mine located in San Luis (Argentina). For these purposes, the metal removal capacity and the microelemental composition of the biomass exposed to metals were evaluated. Likewise, proteomic techniques were applied to understand the removal and resistance mechanisms. Fusarium tricinctum M6 was isolated and identified as tolerant to Cu(II), Fe(II) and Cr(VI). When faced with 40 µg mL-1 Cu(II), the growth was affected by 60% and the removal capacity was 30-35%. Copper was found uniformly distributed in the biomass (5.23% w/w) and variations in the proportion of other biomass constituent elements were detected. When exposed to Cu(II), F. tricinctum M6 showed differential expression of intra and extracellular proteins involved in different metabolic processes. A large number of proteins with metal ion binding sites were detected both at intra and extracellular levels. The results obtained in the present work indicated bioadsorption of the metal on the cell surface and an important readjustment of the protein expression to counteract the stress produced by Cu(II).
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Affiliation(s)
- José Oscar Bonilla
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | - Eduardo Alberto Callegari
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - María Daniela Paez
- Division of Basic Biomedical Sciences Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA
| | - Raúl Andrés Gil
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina
| | - Liliana Beatriz Villegas
- Instituto de Química San Luis (INQUISAL), CONICET, Chacabuco 917, 5700 San Luis, Argentina; Facultad de Química, Bioquímica y Farmacia, Universidad Nacional de San Luis, Chacabuco 917, 5700 San Luis, Argentina.
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19
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Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L. Int J Mol Sci 2021; 22:ijms22115879. [PMID: 34070927 PMCID: PMC8198124 DOI: 10.3390/ijms22115879] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 05/25/2021] [Accepted: 05/26/2021] [Indexed: 01/27/2023] Open
Abstract
Citric acid (CA), as an organic chelator, plays a vital role in alleviating copper (Cu) stress-mediated oxidative damage, wherein a number of molecular mechanisms alter in plants. However, it remains largely unknown how CA regulates differentially abundant proteins (DAPs) in response to Cu stress in Brassica napus L. In the present study, we aimed to investigate the proteome changes in the leaves of B. L. seedlings in response to CA-mediated alleviation of Cu stress. Exposure of 21-day-old seedlings to Cu (25 and 50 μM) and CA (1.0 mM) for 7 days exhibited a dramatic inhibition of overall growth and considerable increase in the enzymatic activities (POD, SOD, CAT). Using a label-free proteome approach, a total of 6345 proteins were identified in differentially treated leaves, from which 426 proteins were differentially expressed among the treatment groups. Gene ontology (GO) and KEGG pathways analysis revealed that most of the differential abundance proteins were found to be involved in energy and carbohydrate metabolism, photosynthesis, protein metabolism, stress and defense, metal detoxification, and cell wall reorganization. Our results suggest that the downregulation of chlorophyll biosynthetic proteins involved in photosynthesis were consistent with reduced chlorophyll content. The increased abundance of proteins involved in stress and defense indicates that these DAPs might provide significant insights into the adaptation of Brassica seedlings to Cu stress. The abundances of key proteins were further verified by monitoring the mRNA expression level of the respective transcripts. Taken together, these findings provide a potential molecular mechanism towards Cu stress tolerance and open a new route in accelerating the phytoextraction of Cu through exogenous application of CA in B. napus.
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20
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Smythers AL, Hicks LM. Mapping the plant proteome: tools for surveying coordinating pathways. Emerg Top Life Sci 2021; 5:203-220. [PMID: 33620075 PMCID: PMC8166341 DOI: 10.1042/etls20200270] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 12/14/2022]
Abstract
Plants rapidly respond to environmental fluctuations through coordinated, multi-scalar regulation, enabling complex reactions despite their inherently sessile nature. In particular, protein post-translational signaling and protein-protein interactions combine to manipulate cellular responses and regulate plant homeostasis with precise temporal and spatial control. Understanding these proteomic networks are essential to addressing ongoing global crises, including those of food security, rising global temperatures, and the need for renewable materials and fuels. Technological advances in mass spectrometry-based proteomics are enabling investigations of unprecedented depth, and are increasingly being optimized for and applied to plant systems. This review highlights recent advances in plant proteomics, with an emphasis on spatially and temporally resolved analysis of post-translational modifications and protein interactions. It also details the necessity for generation of a comprehensive plant cell atlas while highlighting recent accomplishments within the field.
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Affiliation(s)
- Amanda L Smythers
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
| | - Leslie M Hicks
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U.S.A
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21
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Fan W, Zheng H, Wang G. Proteomic analysis of ubiquitinated proteins in maize immature kernels. J Proteomics 2021; 243:104261. [PMID: 33984506 DOI: 10.1016/j.jprot.2021.104261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 11/17/2022]
Abstract
Protein ubiquitination is a dynamic post-translational modification involved in various biological processes in eukaryotes. To understand the function of ubiquitinated proteins in maize kernels, we used the specific K-GG antibody coupled with high-resolution LC-MS/MS to identify the ubiquitinated proteins in maize immature kernels. A total of 1999 lysine ubiquitination sites in 881 proteins were identified in maize kernels. Eight conserved ubiquitination motifs included KubD, GKub, EKub, KubXXXE, AKub, NXKub, KubXXXXXN, and KKub were found in ubiquitinated peptides. The ubiquitinated lysine neighborhoods are more frequently presented in ordered structures. Go and KEGG analysis showed the proteins involved in carbohydrate metabolism and protein processing were identified to be the targets of lysine ubiquitination. Other proteins, which related to RNA transport, spliceosome, endocytosis, ubiquitin-mediated proteolysis, proteasome, and MAPK signaling, were also found to be ubiquitinated. Protein-protein interaction network and KEGG analysis indicated that protein ubiquitination plays a major role in regulating many cellular processes and modulating diverse interactions in maize kernel development. The identification of the 881 ubiquitinated proteins in maize kernels provides a foundation for understanding the physiological roles of these ubiquitinated proteins. Our finding also provides a new insight view into the function of ubiquitinated proteins involved in maize kernel development. SIGNIFICANCE: We reported here the comprehensive proteomic analysis of the ubiquitin-modified proteome in maize kernel. We found that there are some new characteristics of them in ubiquitome of maize immature kernels. The results suggested that protein ubiquitination, as a post-translation modification, plays an essential role in regulating many cellular processes in maize kernel development. This study expands our knowledge on the regulatory roles and mechanisms of protein ubiquitination in maize. and other plants.
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Affiliation(s)
- Wei Fan
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 201100, China
| | - Hongjian Zheng
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences/CIMMYT-China Specialty Maize Research Center, Shanghai 201100, China
| | - Gang Wang
- School of Agriculture and Biology, Shanghai Jiao Tong University, 800 Dongchuan Road, Minhang District, Shanghai 201100, China.
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22
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Vo KTX, Rahman MM, Rahman MM, Trinh KTT, Kim ST, Jeon JS. Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update. RICE (NEW YORK, N.Y.) 2021; 14:30. [PMID: 33721115 PMCID: PMC7960847 DOI: 10.1186/s12284-021-00461-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 01/28/2021] [Indexed: 05/19/2023]
Abstract
Biotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.
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Affiliation(s)
- Kieu Thi Xuan Vo
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mizanor Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Md Mustafizur Rahman
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Kieu Thi Thuy Trinh
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang, 50463 South Korea
| | - Jong-Seong Jeon
- Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104 South Korea
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23
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Choi J, Lee W, An G, Kim SR. OsCBE1, a Substrate Receptor of Cullin4-Based E3 Ubiquitin Ligase, Functions as a Regulator of Abiotic Stress Response and Productivity in Rice. Int J Mol Sci 2021; 22:ijms22052487. [PMID: 33801226 PMCID: PMC7957871 DOI: 10.3390/ijms22052487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/22/2021] [Accepted: 02/24/2021] [Indexed: 01/03/2023] Open
Abstract
Ubiquitination is an important environmental stress response, and E3 ubiquitin ligases play a major role in the process. T-DNA insertion mutants of rice, Oscbe1-1, and Oscbe1-2, were identified through the screening of cold stress tolerance at seedling stage. Oscbe1 mutants showed a significantly higher cold stress tolerance in the fresh weight, chlorophyll content, and photosynthetic efficiency than wild type. Molecular prediction showed that OsCBE1 (Oryza sativa Cullin4-Based E3 ubiquitin ligase1) encoded a novel substrate receptor of Cullin4-based E3 ubiquitin ligase complex (C4E3). Whereas Oscbe1 mutants had fewer panicles and grains than wild type in the paddy field, the overexpression lines of OsCBE1 had more panicles and grains, suggesting that OsCBE1 is involved in the regulation of both abiotic stress response and development. Oscbe1 mutants also showed ABA hypersensitivity during seed germination, suggesting OsCBE1 function for the stress response via ABA signaling. In silico analysis of OsCBE1 activity predicted a CCCH-type transcription factor, OsC3H32, as a putative substrate. Co-IP (Co-immunoprecipitation) study showed that OsCBE1 interacts with OsDDB1, an expected binding component of OsCBE1 and OsC3H32. Additionally, expression of OsOLE16, OsOLE18, and OsBURP5 were negatively related with expression of OsCBE1. These results suggest that OsCBE1 functions as a regulator of the abiotic stress response via CCCH as a member of the C4E3.
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Affiliation(s)
- Juyoung Choi
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
| | - Wonkyung Lee
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
| | - Gynheung An
- Department of Plant Molecular Systems Biotechnology, Kyung Hee University, Yongin 17104, Korea;
| | - Seong-Ryong Kim
- Department of Life Science, Sogang University, Seoul 04107, Korea; (J.C.); (W.L.)
- Correspondence:
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24
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Li D, Sun Q, Zhang G, Zhai L, Li K, Feng Y, Wu T, Zhang X, Xu X, Wang Y, Han Z. MxMPK6-2-bHLH104 interaction is involved in reactive oxygen species signaling in response to iron deficiency in apple rootstock. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:1919-1932. [PMID: 33216933 DOI: 10.1093/jxb/eraa547] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 11/15/2020] [Indexed: 05/16/2023]
Abstract
Iron (Fe) is a trace element necessary for plant growth. Many land plants have evolved a set of mechanisms associated with the Fe absorption process to deal with the problem of insufficient Fe supply in the soil. During Fe absorption, reactive oxygen species (ROS) can be used as a signal to initiate a response to stress caused by Fe deficiency. However, the molecular mechanisms underlying the involvement of ROS in the Fe deficiency stress response remains unclear. In this study, we have identified a kinase, MxMPK6-2, from Malus xiaojinensis, an apple rootstock that is highly efficient at Fe absorption. MxMPK6-2 has been shown to be responsive to ROS signals during Fe deficiency, and MxMPK6-2 overexpression in apple calli enhanced its tolerance to Fe deficiency. We further screened for proteins in the Fe absorption pathway and identified MxbHLH104, a transcription factor which interacts with MxMPK6-2. MxbHLH104 can be phosphorylated by MxMPK6-2 in vivo, and we confirmed that its phosphorylation increased Fe absorption in apple calli under Fe deficiency, with the presence of ROS promoting this process. Overall, we have demonstrated that MxMPK6-2 is responsive to ROS signaling during Fe deficiency, and is able to control its response by regulating MxbHLH104.
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Affiliation(s)
- Duyue Li
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Qiran Sun
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Guifen Zhang
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Keting Li
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Yi Feng
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Xuefeng Xu
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, P. R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Nutrition and Physiology), Ministry of Agriculture, Beijing, P. R. China
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25
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Li P, Liu J. Protein Phosphorylation in Plant Cell Signaling. Methods Mol Biol 2021; 2358:45-71. [PMID: 34270045 DOI: 10.1007/978-1-0716-1625-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Owing to their sessile nature, plants have evolved sophisticated sensory mechanisms to respond quickly and precisely to the changing environment. The extracellular stimuli are perceived and integrated by diverse receptors, such as receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), and then transmitted to the nucleus by complex cellular signaling networks, which play vital roles in biological processes including plant growth, development, reproduction, and stress responses. The posttranslational modifications (PTMs) are important regulators for the diversification of protein functions in plant cell signaling. Protein phosphorylation is an important and well-characterized form of the PTMs, which influences the functions of many receptors and key components in cellular signaling. Protein phosphorylation in plants predominantly occurs on serine (Ser) and threonine (Thr) residues, which is dynamically and reversibly catalyzed by protein kinases and protein phosphatases, respectively. In this review, we focus on the function of protein phosphorylation in plant cell signaling, especially plant hormone signaling, and highlight the roles of protein phosphorylation in plant abiotic stress responses.
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Affiliation(s)
- Ping Li
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China
| | - Junzhong Liu
- State Key Laboratory of Conservation and Utilization of Bio-Resources in Yunnan and Center for Life Science, School of Life Sciences, Yunnan University, Kunming, China.
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26
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Bose U, Juhász A, Broadbent JA, Komatsu S, Colgrave ML. Multi-Omics Strategies for Decoding Smoke-Assisted Germination Pathways and Seed Vigour. Int J Mol Sci 2020; 21:E7512. [PMID: 33053786 PMCID: PMC7593932 DOI: 10.3390/ijms21207512] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/02/2023] Open
Abstract
The success of seed germination and the successful establishment of seedlings across diverse environmental conditions depends on seed vigour, which is of both economic and ecologic importance. The smoke-derived exogenous compound karrikins (KARs) and the endogenous plant hormone strigolactone (SL) are two classes of butanolide-containing molecules that follow highly similar signalling pathways to control diverse biological activities in plants. Unravelling the precise mode-of-action of these two classes of molecules in model species has been a key research objective. However, the specific and dynamic expression of biomolecules upon stimulation by these signalling molecules remains largely unknown. Genomic and post-genomic profiling approaches have enabled mining and association studies across the vast genetic diversity and phenotypic plasticity. Here, we review the background of smoke-assisted germination and vigour and the current knowledge of how plants perceive KAR and SL signalling and initiate the crosstalk with the germination-associated hormone pathways. The recent advancement of 'multi-omics' applications are discussed in the context of KAR signalling and with relevance to their adoption for superior agronomic trait development. The remaining challenges and future opportunities for integrating multi-omics datasets associated with their application in KAR-dependent seed germination and abiotic stress tolerance are also discussed.
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Affiliation(s)
- Utpal Bose
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; (U.B.); (J.A.B.)
| | - Angéla Juhász
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia;
| | - James A. Broadbent
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; (U.B.); (J.A.B.)
| | - Setsuko Komatsu
- Department of Environmental and Food Sciences, Fukui University of Technology, Fukui 910-8505, Japan
| | - Michelle L. Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia; (U.B.); (J.A.B.)
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, School of Science, Edith Cowan University, Joondalup, WA 6027, Australia;
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27
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Janni M, Gullì M, Maestri E, Marmiroli M, Valliyodan B, Nguyen HT, Marmiroli N. Molecular and genetic bases of heat stress responses in crop plants and breeding for increased resilience and productivity. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3780-3802. [PMID: 31970395 PMCID: PMC7316970 DOI: 10.1093/jxb/eraa034] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 01/20/2020] [Indexed: 05/21/2023]
Abstract
To ensure the food security of future generations and to address the challenge of the 'no hunger zone' proposed by the FAO (Food and Agriculture Organization), crop production must be doubled by 2050, but environmental stresses are counteracting this goal. Heat stress in particular is affecting agricultural crops more frequently and more severely. Since the discovery of the physiological, molecular, and genetic bases of heat stress responses, cultivated plants have become the subject of intense research on how they may avoid or tolerate heat stress by either using natural genetic variation or creating new variation with DNA technologies, mutational breeding, or genome editing. This review reports current understanding of the genetic and molecular bases of heat stress in crops together with recent approaches to creating heat-tolerant varieties. Research is close to a breakthrough of global relevance, breeding plants fitter to face the biggest challenge of our time.
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Affiliation(s)
- Michela Janni
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Amendola, Bari, Italy
- Institute of Materials for Electronics and Magnetism (IMEM), National Research Council (CNR), Parco Area delle Scienze, Parma, Italy
| | - Mariolina Gullì
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Elena Maestri
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Marta Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
| | - Babu Valliyodan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
- Lincoln University, Jefferson City, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze, Parma, Italy
- CINSA Interuniversity Consortium for Environmental Sciences, Parma/Venice, Italy
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28
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Calleja-Cabrera J, Boter M, Oñate-Sánchez L, Pernas M. Root Growth Adaptation to Climate Change in Crops. FRONTIERS IN PLANT SCIENCE 2020; 11:544. [PMID: 32457782 PMCID: PMC7227386 DOI: 10.3389/fpls.2020.00544] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 04/09/2020] [Indexed: 05/05/2023]
Abstract
Climate change is threatening crop productivity worldwide and new solutions to adapt crops to these environmental changes are urgently needed. Elevated temperatures driven by climate change affect developmental and physiological plant processes that, ultimately, impact on crop yield and quality. Plant roots are responsible for water and nutrients uptake, but changes in soil temperatures alters this process limiting crop growth. With the predicted variable climatic forecast, the development of an efficient root system better adapted to changing soil and environmental conditions is crucial for enhancing crop productivity. Root traits associated with improved adaptation to rising temperatures are increasingly being analyzed to obtain more suitable crop varieties. In this review, we will summarize the current knowledge about the effect of increasing temperatures on root growth and their impact on crop yield. First, we will describe the main alterations in root architecture that different crops undergo in response to warmer soils. Then, we will outline the main coordinated physiological and metabolic changes taking place in roots and aerial parts that modulate the global response of the plant to increased temperatures. We will discuss on some of the main regulatory mechanisms controlling root adaptation to warmer soils, including the activation of heat and oxidative pathways to prevent damage of root cells and disruption of root growth; the interplay between hormonal regulatory pathways and the global changes on gene expression and protein homeostasis. We will also consider that in the field, increasing temperatures are usually associated with other abiotic and biotic stresses such as drought, salinity, nutrient deficiencies, and pathogen infections. We will present recent advances on how the root system is able to integrate and respond to complex and different stimuli in order to adapt to an increasingly changing environment. Finally, we will discuss the new prospects and challenges in this field as well as the more promising pathways for future research.
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Affiliation(s)
| | | | | | - M. Pernas
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Madrid, Spain
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29
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Righetti PG, Boschetti E. Low-abundance plant protein enrichment with peptide libraries to enlarge proteome coverage and related applications. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 290:110302. [PMID: 31779915 DOI: 10.1016/j.plantsci.2019.110302] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/15/2019] [Accepted: 10/05/2019] [Indexed: 06/10/2023]
Abstract
In plant tissues proteins are present in low amounts but in a very large number. To this peculiar situation many complex foreign components render protein extraction and purification very difficult. In the last several years interesting technologies have been described to improve the technical situation to the point that some methodologies allow reaching very low-abundance proteins and minor allergens. Among enrichment methods the one documented in this report is based on combinatorial peptide ligand libraries (CPLLs) that emerged in the last decade by contributing to largely improve the knowledge in plant proteomics. It is the aim of this review to describe how this technology allows detecting low-abundance proteins from various plant tissues and to report the dynamics of the proteome components in response to environmental changes and biotic attacks. Typical documented examples with the description of their scientific interest are reported. The described technical approach and selected applications are considered as one of the most advanced approaches for plant proteomics investigations with possibilities not only to enlarge the knowledge of plant proteomes but also to discover novel allergens as well as plant biomarkers subsequent to stressful situations.
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Affiliation(s)
- Pier Giorgio Righetti
- Department of Chemistry Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Egisto Boschetti
- Scientific Consultant, JAM Conseil, 92200, Neuilly-sur-Seine, France
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30
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Méndez AAE, Pena LB, Curto LM, Fernández MM, Malchiodi EL, Garza-Aguilar SM, Vázquez-Ramos JM, Gallego SM. Oxidation of proline from the cyclin-binding motif in maize CDKA;1 results in lower affinity with its cyclin regulatory subunit. PHYTOCHEMISTRY 2020; 169:112165. [PMID: 31610323 DOI: 10.1016/j.phytochem.2019.112165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 10/01/2019] [Accepted: 10/07/2019] [Indexed: 06/10/2023]
Abstract
Cyclin dependent kinase A; 1 (CDKA; 1) is essential in G1/S transition of cell cycle and its oxidation has been implicated in cell cycle arrest during plant abiotic stress. In the present study, an evaluation at the molecular level was performed to find possible sites of protein oxidative modifications. In vivo studies demonstrated that carbonylation of maize CDKA,1 is associated with a decrease in complex formation with maize cyclin D (CycD). Control and in vitro oxidized recombinant CDKA; 1 were sequenced by mass spectrometry. Proline at the PSTAIRE cyclin-binding motif was identified as the most susceptible oxidation site by comparative analysis of the resulted peptides. The specific interaction between CDKA; 1 and CycD6; 1, measured by surface plasmon resonance (SPR), demonstrated that the affinity and the kinetic of the interaction depended on the reduced-oxidized state of the CDKA; 1. CDKA; 1 protein oxidative modification would be in part responsible for affecting cell cycle progression, and thus producing plant growth inhibition under oxidative stress.
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Affiliation(s)
- Andrea A E Méndez
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas "Profesor Alejandro C. Paladini" (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Liliana B Pena
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas "Profesor Alejandro C. Paladini" (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina.
| | - Lucrecia M Curto
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas "Profesor Alejandro C. Paladini" (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Marisa M Fernández
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Estudios de la Inmunidad Humoral "Profesor Ricardo A. Margni" (IDEHU), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Emilio L Malchiodi
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Estudios de la Inmunidad Humoral "Profesor Ricardo A. Margni" (IDEHU), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
| | - Sara M Garza-Aguilar
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico
| | - Jorge M Vázquez-Ramos
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Mexico
| | - Susana M Gallego
- Universidad de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química y Fisicoquímica Biológicas "Profesor Alejandro C. Paladini" (IQUIFIB), Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina.
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31
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Abstract
The third edition of "Plant Proteomics Methods and Protocols," with the title "Advances in Proteomics Techniques, Data Validation, and Integration with Other Classic and -Omics Approaches in the Systems Biology Direction," was conceived as being based on the success of the previous editions, and the continuous advances and improvements in proteomic techniques, equipment, and bioinformatics tools, and their uses in basic and translational plant biology research that has occurred in the past 5 years (in round figures, of around 22,000 publications referenced in WoS, 2000 were devoted to plants).The monograph contains 29 chapters with detailed proteomics protocols commonly employed in plant biology research. They present recent advances at all workflow stages, starting from the laboratory (tissue and cell fractionation, protein extraction, depletion, purification, separation, MS analysis, quantification) and ending on the computer (algorithms for protein identification and quantification, bioinformatics tools for data analysis, databases and repositories). At the end of each chapter there are enough explanatory notes and comments to make the protocols easily applicable to other biological systems and/or studies, discussing limitations, artifacts, or pitfalls. For that reason, as with the previous editions, it would be especially useful for beginners or novices.Out of the 29 chapters, six are devoted to descriptive proteomics, with a special emphasis on subcellular protein profiling (Chapters 5 - 10 ), six to PTMs (Chapters 11 , and 14 - 18 ), three to protein interactions (Chapters 19 - 21 ), and two to specific proteins, peroxidases (Chapter 24 ) and proteases and protease inhibitors (Chapter 26 ). The book reflects the new trajectory in MS-based protein identification and quantification, moving from the classic gel-based approaches to the most recent labeling (Chapters 10 , 11 , 29 ), shotgun (Chapters 5 , 7 , 12 , 15 ), parallel reaction monitoring (Chapter 16 ), and targeted data acquisition (Chapter 13 ). MS imaging (Chapter 25 ), the only in vivo MS-based proteomics strategy, is far from being fully optimized and exploited in plant biology research. A confident protein identification and quantitation, especially in orphan species, of low-abundance proteins, is still a challenging task (Chapters 4 , 28 ).What is really new is the use of different techniques for proteomics data validation and their integration into other classic and -omics approaches in the systems biology direction. Chapter 2 reports on multiple extractions in a single experiment of the different biomolecules, nucleic acids, proteins, and metabolites. Chapter 27 describes how metabolic pathways can be reconstructed from multiple -omics data, and Chapter 3 network building. Finally, Chapters 22 and 23 deal with, respectively, the search for allele-specific proteins and proteogenomics.Around 200 groups were, almost 1 year ago, invited to take part in this edition. Unfortunately, only 10% of them kindly accepted. My gratitude to those who accepted our invitation but also to those who did not, as all of them have contributed to the plant proteomics field. I will enlist, in this introductory chapter, following my own judgment, some of the relevant papers published in the past 5 years, those that have shown us how to enhance and exploit the potential of proteomics in plant biology research, without aiming at giving a too exhaustive list.
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Affiliation(s)
- Jesus V Jorrin-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, Cordoba, Spain.
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32
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The functional diversity of structural disorder in plant proteins. Arch Biochem Biophys 2019; 680:108229. [PMID: 31870661 DOI: 10.1016/j.abb.2019.108229] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 12/05/2019] [Accepted: 12/17/2019] [Indexed: 12/29/2022]
Abstract
Structural disorder in proteins is a widespread feature distributed in all domains of life, particularly abundant in eukaryotes, including plants. In these organisms, intrinsically disordered proteins (IDPs) perform a diversity of functions, participating as integrators of signaling networks, in transcriptional and post-transcriptional regulation, in metabolic control, in stress responses and in the formation of biomolecular condensates by liquid-liquid phase separation. Their roles impact the perception, propagation and control of various developmental and environmental cues, as well as the plant defense against abiotic and biotic adverse conditions. In this review, we focus on primary processes to exhibit a broad perspective of the relevance of IDPs in plant cell functions. The information here might help to incorporate this knowledge into a more dynamic view of plant cells, as well as open more questions and promote new ideas for a better understanding of plant life.
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33
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Wang H, Wang M, Xia Z. The Maize Class-I SUMO Conjugating Enzyme ZmSCE1d Is Involved in Drought Stress Response. Int J Mol Sci 2019; 21:ijms21010029. [PMID: 31861556 PMCID: PMC6982253 DOI: 10.3390/ijms21010029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 11/21/2022] Open
Abstract
Post-translational modification of cellular proteins by sumoylation plays a vital role in stress responses of plants. However, the mechanisms underlying the sumoylation’s involvement in stress responses in crop species remain largely unknown. Herein, a maize class-I SUMO conjugating enzyme gene (ZmSCE1d) was identified, whose expression was upregulated upon drought stress. Over-expression of ZmSCE1d in transgenic Arabidopsis plants increased SUMO conjugates and improved drought tolerance. The ZmSCE1d-transgenic plants showed higher antioxidant enzyme activities, but lower reactive oxygen species and lipid peroxidation upon drought stress. Furthermore, transcripts of several drought-responsive genes were significantly elevated, as revealed by qPCR in the transgenic lines. Taken together, these data have demonstrated that ZmSCE1d overexpression improved drought tolerance likely by regulating sumoylation levels, antioxidant capability, and drought-responsive gene expression in transgenic plants. This study may facilitate our understanding of the mechanisms underlying SCE-mediated sumoylation under drought stress and accelerate genetic improvement of crop plants tolerant to drought stress by manipulating the SUMO system.
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Affiliation(s)
- Huanyan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
| | - Meiping Wang
- Library, Henan Agricultural University, Zhengzhou 450002, China
| | - Zongliang Xia
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, China
- Collaborative Innovation Center of Henan Grain Crops and Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence: ; Tel./Fax: +86-371-6355-5790
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34
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Liu Y, Lu S, Liu K, Wang S, Huang L, Guo L. Proteomics: a powerful tool to study plant responses to biotic stress. PLANT METHODS 2019; 15:135. [PMID: 31832077 PMCID: PMC6859632 DOI: 10.1186/s13007-019-0515-8] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/29/2019] [Indexed: 05/08/2023]
Abstract
In recent years, mass spectrometry-based proteomics has provided scientists with the tremendous capability to study plants more precisely than previously possible. Currently, proteomics has been transformed from an isolated field into a comprehensive tool for biological research that can be used to explain biological functions. Several studies have successfully used the power of proteomics as a discovery tool to uncover plant resistance mechanisms. There is growing evidence that indicates that the spatial proteome and post-translational modifications (PTMs) of proteins directly participate in the plant immune response. Therefore, understanding the subcellular localization and PTMs of proteins is crucial for a comprehensive understanding of plant responses to biotic stress. In this review, we discuss current approaches to plant proteomics that use mass spectrometry, with particular emphasis on the application of spatial proteomics and PTMs. The purpose of this paper is to investigate the current status of the field, discuss recent research challenges, and encourage the application of proteomics techniques to further research.
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Affiliation(s)
- Yahui Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- National Institute of Metrology, Beijing, China
| | - Song Lu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Kefu Liu
- School of Life Science, Beijing Institute of Technology, Beijing, China
| | - Sheng Wang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lanping Guo
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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35
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Wang H, Wang M, Xia Z. Overexpression of a maize SUMO conjugating enzyme gene (ZmSCE1e) increases Sumoylation levels and enhances salt and drought tolerance in transgenic tobacco. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:113-121. [PMID: 30824044 DOI: 10.1016/j.plantsci.2019.01.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 05/16/2023]
Abstract
As an essential regulatory process of post-translational modifications, Sumoylation has been shown to play a central role in stress responses in higher plants. However, the mechanisms underlying the involvement of the Sumoylation in stress responses in crops are largely unknown. In this study, a putative SUMO conjugating enzyme ortholog from Zea mays (ZmSCE1e) was isolated. Sequence alignments and phylogenetic analysis showed that ZmSCE1e possesses a central active domain similar to known SCE1 proteins, but is the cereal-specific isoform.The transcript levels of ZmSCE1e were markedly up-regulated by salt or drought stress. Over-expression of ZmSCE1e in tobacco plants increased levels of SUMO conjugates and enhanced their tolerances to salt and drought stresses. ZmSCE1e-transgenic plants showed higher activities of key antioxidant enzymes but lower hydrogen peroxide (H2O2) and malondialdehyde (MDA) accumulations under salt or drought stress. Furthermore, expression of several stress defense genes was significantly elevated as revealed by qPCR in the ZmSCE1e-transgenic lines. Together, these data have demonstrated that ZmSCE1e improved salt and drought tolerance likely by modulating Sumoylation levels, antioxidant capability, and stress defense gene expression in transgenic plants. This study may facilitate our understanding of the biological roles of SCE-mediated Sumoylation under stress conditions in higher plants and accelerate genetic improvement of crop plants tolerant to environmental stresses.
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Affiliation(s)
- Huanyan Wang
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, PR China
| | - Meiping Wang
- Library of Henan Agricultural University, Zhengzhou 450002, PR China
| | - Zongliang Xia
- College of Life Science, Henan Agricultural University, Zhengzhou 450002, PR China.
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36
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The Proteomic Analysis of Maize Endosperm Protein Enriched by Phos-tag tm Reveals the Phosphorylation of Brittle-2 Subunit of ADP-Glc Pyrophosphorylase in Starch Biosynthesis Process. Int J Mol Sci 2019; 20:ijms20040986. [PMID: 30813492 PMCID: PMC6412418 DOI: 10.3390/ijms20040986] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/14/2019] [Accepted: 02/18/2019] [Indexed: 11/17/2022] Open
Abstract
AGPase catalyzes a key rate-limiting step that converts ATP and Glc-1-p into ADP-glucose and diphosphate in maize starch biosynthesis. Previous studies suggest that AGPase is modulated by redox, thermal and allosteric regulation. However, the phosphorylation of AGPase is unclear in the kernel starch biosynthesis process. Phos-tagTM technology is a novel method using phos-tagTM agarose beads for separation, purification, and detection of phosphorylated proteins. Here we identified phos-tagTM agarose binding proteins from maize endosperm. Results showed a total of 1733 proteins identified from 10,678 distinct peptides. Interestingly, a total of 21 unique peptides for AGPase sub-unit Brittle-2 (Bt2) were identified. Bt2 was demonstrated by immunoblot when enriched maize endosperm protein with phos-tagTM agarose was in different pollination stages. In contrast, Bt2 would lose binding to phos-tagTM when samples were treated with alkaline phosphatase (ALP). Furthermore, Bt2 could be detected by Pro-Q diamond staining specifically for phosphorylated protein. We further identified the phosphorylation sites of Bt2 at Ser10, Thr451, and Thr462 by iTRAQ. In addition, dephosphorylation of Bt2 decreased the activity of AGPase in the native gel assay through ALP treatment. Taking together, these results strongly suggest that the phosphorylation of AGPase may be a new model to regulate AGPase activity in the starch biosynthesis process.
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Ma S, Tang N, Li X, Xie Y, Xiang D, Fu J, Shen J, Yang J, Tu H, Li X, Hu H, Xiong L. Reversible Histone H2B Monoubiquitination Fine-Tunes Abscisic Acid Signaling and Drought Response in Rice. MOLECULAR PLANT 2019; 12:263-277. [PMID: 30578854 DOI: 10.1016/j.molp.2018.12.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 11/09/2018] [Accepted: 12/09/2018] [Indexed: 05/23/2023]
Abstract
Histone H2B monoubiquitination (H2Bub1) plays important roles in several physiological and developmental processes, but its roles in the regulation of plant stress responses remain elusive. Here, we report that H2Bub1 is crucially involved in abscisic acid (ABA) signaling and drought response in rice. We found that rice HISTONE MONOUBIQUITINATION2 (OsHUB2), an E3 ligase for H2Bub1, interacted with OsbZIP46, a key transcription factor regulating ABA signaling and drought response in rice. Genetic analyses suggest that OsHUB2, upregulated by drought and ABA, positively modulates ABA sensitivity and drought resistance. The H2Bub1 levels were increased in the target genes of OsbZIP46 under the drought stress and ABA treatments, which were positively correlated with their increased expression levels. Interestingly, MODD, a reported suppressor of ABA signaling and drought resistance by mediating OsbZIP46 deactivation and degradation, could reduce the H2Bub1 levels in the target genes of OsbZIP46 by recruiting a putative deubiquitinase OsOTLD1. Suppression of OsOTLD1 in vivo resulted in increased H2Bub1 levels and expression of OsbZIP46 target genes. Collectively, these findings established an elaborate mechanism of histone monoubiquitination in the fine-turning of ABA signaling and drought response by balancing H2Bub1 deposition and removal.
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Affiliation(s)
- Siqi Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Ning Tang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; BPMP, CNRS, INRA, Montpellier SupAgro, Université de Montpellier, 34060 Montpellier, France.
| | - Xu Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Yongjun Xie
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Denghao Xiang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jie Fu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jianqiang Shen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Haifu Tu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Xianghua Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Honghong Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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Vu LD, Zhu T, Verstraeten I, van de Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4609-4624. [PMID: 29939309 PMCID: PMC6117581 DOI: 10.1093/jxb/ery204] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 05/16/2018] [Indexed: 05/20/2023]
Abstract
Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity.
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Affiliation(s)
- Lam Dai Vu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Tingting Zhu
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Inge Verstraeten
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Brigitte van de Cotte
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Kris Gevaert
- Department of Biochemistry, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Shokri-Gharelo R, Noparvar PM. Molecular response of canola to salt stress: insights on tolerance mechanisms. PeerJ 2018; 6:e4822. [PMID: 29844974 PMCID: PMC5969047 DOI: 10.7717/peerj.4822] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 01/16/2023] Open
Abstract
Canola (Brassica napus L.) is widely cultivated around the world for the production of edible oils and biodiesel fuel. Despite many canola varieties being described as ‘salt-tolerant’, plant yield and growth decline drastically with increasing salinity. Although many studies have resulted in better understanding of the many important salt-response mechanisms that control salt signaling in plants, detoxification of ions, and synthesis of protective metabolites, the engineering of salt-tolerant crops has only progressed slowly. Genetic engineering has been considered as an efficient method for improving the salt tolerance of canola but there are many unknown or little-known aspects regarding canola response to salinity stress at the cellular and molecular level. In order to develop highly salt-tolerant canola, it is essential to improve knowledge of the salt-tolerance mechanisms, especially the key components of the plant salt-response network. In this review, we focus on studies of the molecular response of canola to salinity to unravel the different pieces of the salt response puzzle. The paper includes a comprehensive review of the latest studies, particularly of proteomic and transcriptomic analysis, including the most recently identified canola tolerance components under salt stress, and suggests what researchers should focus on in future studies.
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Affiliation(s)
- Reza Shokri-Gharelo
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran
| | - Pouya Motie Noparvar
- Department of Plant Breeding and Biotechnology, University of Tabriz, Tabriz, Iran.,Young Researchers and Elite Club, Islamic Azad University, Tabriz, Iran
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40
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Kosová K, Vítámvás P, Urban MO, Prášil IT, Renaut J. Plant Abiotic Stress Proteomics: The Major Factors Determining Alterations in Cellular Proteome. FRONTIERS IN PLANT SCIENCE 2018; 9:122. [PMID: 29472941 PMCID: PMC5810178 DOI: 10.3389/fpls.2018.00122] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 01/23/2018] [Indexed: 05/19/2023]
Abstract
HIGHLIGHTS: Major environmental and genetic factors determining stress-related protein abundance are discussed.Major aspects of protein biological function including protein isoforms and PTMs, cellular localization and protein interactions are discussed.Functional diversity of protein isoforms and PTMs is discussed. Abiotic stresses reveal profound impacts on plant proteomes including alterations in protein relative abundance, cellular localization, post-transcriptional and post-translational modifications (PTMs), protein interactions with other protein partners, and, finally, protein biological functions. The main aim of the present review is to discuss the major factors determining stress-related protein accumulation and their final biological functions. A dynamics of stress response including stress acclimation to altered ambient conditions and recovery after the stress treatment is discussed. The results of proteomic studies aimed at a comparison of stress response in plant genotypes differing in stress adaptability reveal constitutively enhanced levels of several stress-related proteins (protective proteins, chaperones, ROS scavenging- and detoxification-related enzymes) in the tolerant genotypes with respect to the susceptible ones. Tolerant genotypes can efficiently adjust energy metabolism to enhanced needs during stress acclimation. Stress tolerance vs. stress susceptibility are relative terms which can reflect different stress-coping strategies depending on the given stress treatment. The role of differential protein isoforms and PTMs with respect to their biological functions in different physiological constraints (cellular compartments and interacting partners) is discussed. The importance of protein functional studies following high-throughput proteome analyses is presented in a broader context of plant biology. In summary, the manuscript tries to provide an overview of the major factors which have to be considered when interpreting data from proteomic studies on stress-treated plants.
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Affiliation(s)
- Klára Kosová
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Pavel Vítámvás
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Milan O. Urban
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
- Department of Experimental Plant Biology, Faculty of Science, Charles University in Prague, Prague, Czechia
| | - Ilja T. Prášil
- Division of Crop Genetics and Breeding, Laboratory of Plant Stress Biology and Biotechnology, Crop Research Institute, Prague, Czechia
| | - Jenny Renaut
- Environmental Research and Technology Platform, Environmental Research and Innovation, Luxembourg Institute of Science and Technology (LIST), Esch-sur-Alzette, Luxembourg
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Zhang Z, Hu M, Feng X, Gong A, Cheng L, Yuan H. Proteomes and Phosphoproteomes of Anther and Pollen: Availability and Progress. Proteomics 2018; 17. [PMID: 28665021 DOI: 10.1002/pmic.201600458] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 06/02/2017] [Indexed: 12/24/2022]
Abstract
In flowering plants, anther development plays crucial role in sexual reproduction. Within the anther, microspore mother cells meiosis produces microspores, which further develop into pollen grains that play decisive role in plant reproduction. Previous studies on anther biology mainly focused on single gene functions relying on genetic and molecular methods. Recently, anther development has been expanded from multiple OMICS approaches like transcriptomics, proteomics/phosphoproteomics, and metabolomics. The development of proteomics techniques allowing increased proteome coverage and quantitative measurements of proteins which can characterize proteomes and their modulation during normal development, biotic and abiotic stresses in anther development. In this review, we summarize the achievements of proteomics and phosphoproteomics with anther and pollen organs from model plant and crop species (i.e. Arabidopsis, rice, tobacco). The increased proteomic information facilitated translation of information from the models to crops and thus aid in agricultural improvement.
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Affiliation(s)
- Zaibao Zhang
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Menghui Hu
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Xiaobing Feng
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Andong Gong
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Lin Cheng
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
| | - Hongyu Yuan
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang, Henan, P. R. China.,College of Life Science, Xinyang Normal College, Xinyang, Henan, P. R. China
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42
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Tan BC, Lim YS, Lau SE. Proteomics in commercial crops: An overview. J Proteomics 2017; 169:176-188. [PMID: 28546092 DOI: 10.1016/j.jprot.2017.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 04/21/2017] [Accepted: 05/19/2017] [Indexed: 02/06/2023]
Abstract
Proteomics is a rapidly growing area of biological research that is positively affecting plant science. Recent advances in proteomic technology, such as mass spectrometry, can now identify a broad range of proteins and monitor their modulation during plant growth and development, as well as during responses to abiotic and biotic stresses. In this review, we highlight recent proteomic studies of commercial crops and discuss the advances in understanding of the proteomes of these crops. We anticipate that proteomic-based research will continue to expand and contribute to crop improvement. SIGNIFICANCE Plant proteomics study is a rapidly growing area of biological research that is positively impacting plant science. With the recent advances in new technologies, proteomics not only allows us to comprehensively analyses crop proteins, but also help us to understand the functions of the genes. In this review, we highlighted recent proteomic studies in commercial crops and updated the advances in our understanding of the proteomes of these crops. We believe that proteomic-based research will continue to grow and contribute to the improvement of crops.
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Affiliation(s)
- Boon Chin Tan
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia.
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science, University of Nottingham Malaysia Campus, Jalan Broga, 43500 Semenyih, Selangor, Malaysia
| | - Su-Ee Lau
- Centre for Research in Biotechnology for Agriculture, University of Malaya, Lembah Pantai, 50603 Kuala Lumpur, Malaysia
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43
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Vu LD, Verstraeten I, Stes E, Van Bel M, Coppens F, Gevaert K, De Smet I. Proteome Profiling of Wheat Shoots from Different Cultivars. FRONTIERS IN PLANT SCIENCE 2017; 8:332. [PMID: 28348574 PMCID: PMC5346552 DOI: 10.3389/fpls.2017.00332] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/24/2017] [Indexed: 05/20/2023]
Abstract
Wheat is a cereal grain and one of the world's major food crops. Recent advances in wheat genome sequencing are by now facilitating its genomic and proteomic analyses. However, little is known about possible differences in total protein levels of hexaploid versus tetraploid wheat cultivars, and also knowledge of phosphorylated wheat proteins is still limited. Here, we performed a detailed analysis of the proteome of seedling leaves from two hexaploid wheat cultivars (Triticum aestivum L. Pavon 76 and USU-Apogee) and one tetraploid wheat (T. turgidum ssp. durum cv. Senatore Cappelli). Our shotgun proteomics data revealed that, whereas we observed some significant differences, overall a high similarity between hexaploid and tetraploid varieties with respect to protein abundance was observed. In addition, already at the seedling stage, a small set of proteins was differential between the small (USU-Apogee) and larger hexaploid wheat cultivars (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first searchable repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.
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Affiliation(s)
- Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Center for Plant Systems Biology, VIBGhent, Belgium
- Medical Biotechnology Center, VIBGhent, Belgium
- Department of Biochemistry, Ghent UniversityGhent, Belgium
| | - Inge Verstraeten
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Center for Plant Systems Biology, VIBGhent, Belgium
| | - Elisabeth Stes
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Center for Plant Systems Biology, VIBGhent, Belgium
- Medical Biotechnology Center, VIBGhent, Belgium
- Department of Biochemistry, Ghent UniversityGhent, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Center for Plant Systems Biology, VIBGhent, Belgium
| | - Frederik Coppens
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Center for Plant Systems Biology, VIBGhent, Belgium
| | - Kris Gevaert
- Medical Biotechnology Center, VIBGhent, Belgium
- Department of Biochemistry, Ghent UniversityGhent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent UniversityGhent, Belgium
- Center for Plant Systems Biology, VIBGhent, Belgium
- *Correspondence: Ive De Smet,
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44
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Vu LD, Stes E, Van Bel M, Nelissen H, Maddelein D, Inzé D, Coppens F, Martens L, Gevaert K, De Smet I. Up-to-Date Workflow for Plant (Phospho)proteomics Identifies Differential Drought-Responsive Phosphorylation Events in Maize Leaves. J Proteome Res 2016; 15:4304-4317. [DOI: 10.1021/acs.jproteome.6b00348] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lam Dai Vu
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Elisabeth Stes
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Michiel Van Bel
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Hilde Nelissen
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Davy Maddelein
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Dirk Inzé
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Frederik Coppens
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Lennart Martens
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Kris Gevaert
- Medical
Biotechnology Center, VIB, 9000 Ghent, Belgium
- Department
of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Ive De Smet
- Department
of Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department
of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
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Barkla BJ. Identification of Abiotic Stress Protein Biomarkers by Proteomic Screening of Crop Cultivar Diversity. Proteomes 2016; 4:proteomes4030026. [PMID: 28248236 PMCID: PMC5217352 DOI: 10.3390/proteomes4030026] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/01/2016] [Accepted: 09/03/2016] [Indexed: 12/11/2022] Open
Abstract
Modern day agriculture practice is narrowing the genetic diversity in our food supply. This may compromise the ability to obtain high yield under extreme climactic conditions, threatening food security for a rapidly growing world population. To identify genetic diversity, tolerance mechanisms of cultivars, landraces and wild relatives of major crops can be identified and ultimately exploited for yield improvement. Quantitative proteomics allows for the identification of proteins that may contribute to tolerance mechanisms by directly comparing protein abundance under stress conditions between genotypes differing in their stress responses. In this review, a summary is provided of the data accumulated from quantitative proteomic comparisons of crop genotypes/cultivars which present different stress tolerance responses when exposed to various abiotic stress conditions, including drought, salinity, high/low temperature, nutrient deficiency and UV-B irradiation. This field of research aims to identify molecular features that can be developed as biomarkers for crop improvement, however without accurate phenotyping, careful experimental design, statistical robustness and appropriate biomarker validation and verification it will be challenging to deliver what is promised.
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Affiliation(s)
- Bronwyn J Barkla
- Southern Cross Plant Sciences, Southern Cross University, Lismore 2481, NSW, Australia.
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46
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Wu X, Wang W. Increasing Confidence of Proteomics Data Regarding the Identification of Stress-Responsive Proteins in Crop Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:702. [PMID: 27252718 PMCID: PMC4877514 DOI: 10.3389/fpls.2016.00702] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 05/06/2016] [Indexed: 05/28/2023]
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