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Ghanbarzadeh Z, Mohagheghzadeh A, Hemmati S. The Roadmap of Plant Antimicrobial Peptides Under Environmental Stress: From Farm to Bedside. Probiotics Antimicrob Proteins 2024:10.1007/s12602-024-10354-9. [PMID: 39225894 DOI: 10.1007/s12602-024-10354-9] [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] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Antimicrobial peptides (AMPs) are the most favorable alternatives in overcoming multidrug resistance, alone or synergistically with conventional antibiotics. Plant-derived AMPs, as cysteine-rich peptides, widely compensate the pharmacokinetic drawbacks of peptide therapeutics. Compared to the putative genes encrypted in the genome, AMPs that are produced under stress are active forms with the ability to combat resistant microbial species. Within this study, plant-derived AMPs, namely, defensins, nodule-specific cysteine-rich peptides, snakins, lipid transfer proteins, hevein-like proteins, α-hairpinins, and aracins, expressed under biotic and abiotic stresses, are classified. We could observe that while α-hairpinins and snakins display a helix-turn-helix structure, conserved motif patterns such as β1αβ2β3 and β1β2β3 exist in plant defensins and hevein-like proteins, respectively. According to the co-expression data, several plant AMPs are expressed together to trigger synergistic effects with membrane disruption mechanisms such as toroidal pore, barrel-stave, and carpet models. The application of AMPs as an eco-friendly strategy in maintaining agricultural productivity through the development of transgenes and bio-pesticides is discussed. These AMPs can be consumed in packaging material, wound-dressing products, coating catheters, implants, and allergology. AMPs with cell-penetrating properties are verified for the clearance of intracellular pathogens. Finally, the dominant pharmacological activities of bioactive peptides derived from the gastrointestinal digestion of plant AMPs, namely, inhibitors of renin and angiotensin-converting enzymes, dipeptidyl peptidase IV and α-glucosidase inhibitors, antioxidants, anti-inflammatory, immunomodulating, and hypolipidemic peptides, are analyzed. Conclusively, as phytopathogens and human pathogens can be affected by plant-derived AMPs, they provide a bright perspective in agriculture, breeding, food, cosmetics, and pharmaceutical industries, translated as farm to bedside.
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Affiliation(s)
- Zohreh Ghanbarzadeh
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abdolali Mohagheghzadeh
- Department of Phytopharmaceuticals, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran.
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, 56000, Kuala Lumpur, Malaysia.
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Gao Z, Tu Y, Liao C, Guo P, Tian Y, Zhou Y, Xie Q, Chen G, Hu Z. Overexpression of SlALC Increases Drought and Salt Tolerance and Affects Fruit Dehiscence in Tomatoes. Int J Mol Sci 2024; 25:9433. [PMID: 39273380 PMCID: PMC11395450 DOI: 10.3390/ijms25179433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 08/08/2024] [Accepted: 08/28/2024] [Indexed: 09/15/2024] Open
Abstract
The bHLH transcription factors are important plant regulators against abiotic stress and involved in plant growth and development. In this study, SlALC, a gene coding for a prototypical DNA-binding protein in the bHLH family, was isolated, and SlALC-overexpression tomato (SlALC-OE) plants were generated by Agrobacterium-mediated genetic transformation. SlALC transgenic lines manifested higher osmotic stress tolerance than the wild-type plants, estimated by higher relative water content and lower water loss rate, higher chlorophyll, reducing sugar, starch, proline, soluble protein contents, antioxidant enzyme activities, and lower MDA and reactive oxygen species contents in the leaves. In SlALC-OE lines, there were more significant alterations in the expression of genes associated with stress. Furthermore, SlALC-OE fruits were more vulnerable to dehiscence, with higher water content, reduced lignin content, SOD/POD/PAL enzyme activity, and lower phenolic compound concentrations, all of which corresponded to decreased expression of lignin biosynthetic genes. Moreover, the dual luciferase reporter test revealed that SlTAGL1 inhibits SlALC expression. This study revealed that SlALC may play a role in controlling plant tolerance to drought and salt stress, as well as fruit lignification, which influences fruit dehiscence. The findings of this study have established a foundation for tomato tolerance breeding and fruit quality improvement.
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Affiliation(s)
- Zihan Gao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Yuqing Tu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Changguang Liao
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Pengyu Guo
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Yanling Tian
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Ying Zhou
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Qiaoli Xie
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Guoping Chen
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
| | - Zongli Hu
- Laboratory of Molecular Biology of Tomato, Bioengineering College, Chongqing University, Chongqing 400030, China
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Niekerk LA, Gokul A, Basson G, Badiwe M, Nkomo M, Klein A, Keyster M. Heavy metal stress and mitogen activated kinase transcription factors in plants: Exploring heavy metal-ROS influences on plant signalling pathways. PLANT, CELL & ENVIRONMENT 2024; 47:2793-2810. [PMID: 38650576 DOI: 10.1111/pce.14926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/09/2024] [Accepted: 04/12/2024] [Indexed: 04/25/2024]
Abstract
Due to their stationary nature, plants are exposed to a diverse range of biotic and abiotic stresses, of which heavy metal (HM) stress poses one of the most detrimental abiotic stresses, targeting diverse plant processes. HMs instigate the overproduction of reactive oxygen species (ROS), and to mitigate the adverse effects of ROS, plants induce multiple defence mechanisms. Besides the negative implications of overproduction of ROS, these molecules play a multitude of signalling roles in plants, acting as a central player in the complex signalling network of cells. One of the ROS-associated signalling mechanisms is the mitogen-activated protein kinase (MAPK) cascade, a signalling pathway which transduces extracellular stimuli into intracellular responses. Plant MAPKs have been implicated in signalling involved in stress response, phytohormone regulation, and cell cycle cues. However, the influence of various HMs on MAPK activation has not been well documented. In this review, we address and summarise several aspects related to various HM-induced ROS signalling. Additionally, we touch on how these signals activate the MAPK cascade and the downstream transcription factors that influence plant responses to HMs. Moreover, we propose a workflow that could characterise genes associated with MAPKs and their roles during plant HM stress responses.
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Affiliation(s)
- Lee-Ann Niekerk
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Arun Gokul
- Department of Plant Sciences, Qwaqwa Campus, University of the Free State, Phuthaditjhaba, South Africa
| | - Gerhard Basson
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Mihlali Badiwe
- Plant Pathology Department, AgriScience Faculty, Stellenbosch University, Stellenbosch, South Africa
| | - Mbukeni Nkomo
- Plant Biotechnology Laboratory, Department of Agriculture, University of Zululand, Main Road, KwaDlangezwa, South Africa
| | - Ashwil Klein
- Plant Omics Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Marshall Keyster
- Environmental Biotechnology Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
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4
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Ontoy JC, Ham JH. Mapping and Omics Integration: Towards Precise Rice Disease Resistance Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:1205. [PMID: 38732420 PMCID: PMC11085595 DOI: 10.3390/plants13091205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
Rice (Oryza sativa), as a staple crop feeding a significant portion of the global population, particularly in Asian countries, faces constant threats from various diseases jeopardizing global food security. A precise understanding of disease resistance mechanisms is crucial for developing resilient rice varieties. Traditional genetic mapping methods, such as QTL mapping, provide valuable insights into the genetic basis of diseases. However, the complex nature of rice diseases demands a holistic approach to gain an accurate knowledge of it. Omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, enable a comprehensive analysis of biological molecules, uncovering intricate molecular interactions within the rice plant. The integration of various mapping techniques using multi-omics data has revolutionized our understanding of rice disease resistance. By overlaying genetic maps with high-throughput omics datasets, researchers can pinpoint specific genes, proteins, or metabolites associated with disease resistance. This integration enhances the precision of disease-related biomarkers with a better understanding of their functional roles in disease resistance. The improvement of rice breeding for disease resistance through this integration represents a significant stride in agricultural science because a better understanding of the molecular intricacies and interactions underlying disease resistance architecture leads to a more precise and efficient development of resilient and productive rice varieties. In this review, we explore how the integration of mapping and omics data can result in a transformative impact on rice breeding for enhancing disease resistance.
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Affiliation(s)
- John Christian Ontoy
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA;
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Jong Hyun Ham
- Department of Plant Pathology and Crop Physiology, LSU AgCenter, Baton Rouge, LA 70803, USA;
- Department of Plant Pathology and Crop Physiology, College of Agriculture, Louisiana State University, Baton Rouge, LA 70803, USA
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Perveen S, Padula MP, Safdar N, Abbas S. Functional annotation of proteins in Catharanthus roseus shoot cultures under biogenic zinc nanotreatment. PLANT MOLECULAR BIOLOGY 2024; 114:26. [PMID: 38459275 DOI: 10.1007/s11103-024-01432-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 02/21/2024] [Indexed: 03/10/2024]
Abstract
Nano-interactions are well known for their positive as well as negative impacts on the morphological and physiological systems of plants. Keeping in mind, the conformational changes in plant proteins as one of the key mechanisms for stress adaptation responses, the current project was designed to explore the effect of glutathione-capped and uncapped zinc nano-entities on Catharanthus roseus shoot cultures. Zinc nanotreatment (0.05 μg/mL) significantly induced ester production in C. roseus shoots as detected by Gas Chromatography-Mass spectrometry. These nanotreated shoots were further subjected to peptide-centric nano-LC-MS/MS analysis. Mass spectrometry followed by a Heat map revealed a significant effect of zinc nanoparticles on 59 distinct classes of proteins as compared to control. Proteins involved in regulating stress scavenging, transport, and secondary metabolite biosynthesis were robustly altered under capped zinc nanotreatment. UniProt database identified majority of the localization of the abundantly altered protein in cell membranes and chloroplasts. STRING and Cytoscape analysis assessed inter and intra coordination of triosephosphate isomerase with other identified proteins and highlighted its role in the regulation of protein abundance under applied stress. This study highlights the understanding of complex underlying mechanisms and regulatory networks involved in proteomic alterations and interactions within the plant system to cope with the nano-effect.
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Affiliation(s)
- Shaghufta Perveen
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | - Matthew P Padula
- School of Life Sciences, University of Technology Sydney (UTS), Sydney, NSW, Australia
| | - Naila Safdar
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University, Rawalpindi, Pakistan.
| | - Sidra Abbas
- Microbiology and Biotechnology Research Lab, Fatima Jinnah Women University, Rawalpindi, Pakistan
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Raza A, Salehi H, Bashir S, Tabassum J, Jamla M, Charagh S, Barmukh R, Mir RA, Bhat BA, Javed MA, Guan DX, Mir RR, Siddique KHM, Varshney RK. Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity. PLANT CELL REPORTS 2024; 43:80. [PMID: 38411713 PMCID: PMC10899315 DOI: 10.1007/s00299-024-03153-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/05/2024] [Indexed: 02/28/2024]
Abstract
The escalating challenges posed by metal(loid) toxicity in agricultural ecosystems, exacerbated by rapid climate change and anthropogenic pressures, demand urgent attention. Soil contamination is a critical issue because it significantly impacts crop productivity. The widespread threat of metal(loid) toxicity can jeopardize global food security due to contaminated food supplies and pose environmental risks, contributing to soil and water pollution and thus impacting the whole ecosystem. In this context, plants have evolved complex mechanisms to combat metal(loid) stress. Amid the array of innovative approaches, omics, notably transcriptomics, proteomics, and metabolomics, have emerged as transformative tools, shedding light on the genes, proteins, and key metabolites involved in metal(loid) stress responses and tolerance mechanisms. These identified candidates hold promise for developing high-yielding crops with desirable agronomic traits. Computational biology tools like bioinformatics, biological databases, and analytical pipelines support these omics approaches by harnessing diverse information and facilitating the mapping of genotype-to-phenotype relationships under stress conditions. This review explores: (1) the multifaceted strategies that plants use to adapt to metal(loid) toxicity in their environment; (2) the latest findings in metal(loid)-mediated transcriptomics, proteomics, and metabolomics studies across various plant species; (3) the integration of omics data with artificial intelligence and high-throughput phenotyping; (4) the latest bioinformatics databases, tools and pipelines for single and/or multi-omics data integration; (5) the latest insights into stress adaptations and tolerance mechanisms for future outlooks; and (6) the capacity of omics advances for creating sustainable and resilient crop plants that can thrive in metal(loid)-contaminated environments.
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Affiliation(s)
- Ali Raza
- Guangdong Key Laboratory of Plant Epigenetics, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Hajar Salehi
- Department for Sustainable Food Process, Università Cattolica del Sacro Cuore, Via Emilia Parmense 84, 29122, Piacenza, Italy
| | - Shanza Bashir
- Institute of Environmental Sciences and Engineering, School of Civil and Environmental Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Javaria Tabassum
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Monica Jamla
- Department of Biotechnology, Modern College of Arts, Science and Commerce, Savitribai Phule Pune University, Ganeshkhind, Pune, 411016, India
| | - Sidra Charagh
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Hangzhou, China
| | - Rutwik Barmukh
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia
| | - Rakeeb Ahmad Mir
- Department of Biotechnology, School of Life Sciences, Central University of Kashmir, Ganderbal, India
| | - Basharat Ahmad Bhat
- Department of Bio-Resources, Amar Singh College Campus, Cluster University Srinagar, Srinagar, JK, India
| | - Muhammad Arshad Javed
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab, Lahore, Pakistan
| | - Dong-Xing Guan
- Zhejiang Provincial Key Laboratory of Agricultural Resources and Environment, Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST), Srinagar, Kashmir, India
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia.
| | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, WA, 6150, Australia.
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Quintana-Escobar AO, Loyola-Vargas VM. Proteomic Analysis of In Vitro Plant Tissues (Coffea canephora): A Case of Study. Methods Mol Biol 2024; 2827:351-362. [PMID: 38985281 DOI: 10.1007/978-1-0716-3954-2_23] [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: 07/11/2024]
Abstract
Since the term proteomics was coined by Marc Wilkins in 1994, there has been an explosion in the number of articles reporting the use of the proteomics technique. As the layers of biological organization and their regulation increase, the complexity of living beings increases. Thus, we go from the genome to tissues, cells, cellular compartments, and phenotypes and the complexity of the tools used to study this complexity also increases. Unlike the genome study, in the case of the proteome, we have a more complex panorama. We have a spatial and temporal proteome. Proteomics helps to answer complex biological questions since proteins' function depends on their molecular structure, subcellular localization, and posttranslational modifications. In this protocol, we describe a methodology to extract proteins using different methods, separating proteins by electrophoresis in double-dimensional gels and analyzing the gels using specialized software that allows obtaining information on the number and abundance of the proteins from the gels.
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Affiliation(s)
- Ana O Quintana-Escobar
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Mérida, Mexico
| | - Víctor M Loyola-Vargas
- Unidad de Biología Integrativa, Centro de Investigación Científica de Yucatán, Mérida, Mexico.
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Sougrakpam Y, Babuta P, Deswal R. Nitric oxide (NO) modulates low temperature-stress signaling via S-nitrosation, a NO PTM, inducing ethylene biosynthesis inhibition leading to enhanced post-harvest shelf-life of agricultural produce. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:2051-2065. [PMID: 38222283 PMCID: PMC10784255 DOI: 10.1007/s12298-023-01371-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 01/16/2024]
Abstract
Low temperature (cold) stress is one of the major abiotic stress conditions affecting crop productivity worldwide. Nitric oxide (NO) is a dynamic signaling molecule that interacts with various stress regulators and provides abiotic stress tolerance. Stress enhanced NO contributes to S-nitrosothiol accumulation which causes oxidation of the -SH group in proteins leading to S-nitrosation, a post-translational modification. Cold stress induced in vivo S-nitrosation of > 240 proteins majorly belonging to stress/signaling/redox (myrosinase, SOD, GST, CS, DHAR), photosynthesis (RuBisCO, PRK), metabolism (FBA, GAPDH, TPI, SBPase), and cell wall modification (Beta-xylosidases, alpha-l-arabinogalactan) in different crop plants indicated role of NO in these important cellular and metabolic pathways. NO mediated regulation of a transcription factor CBF (C-repeat Binding Factor, a transcription factor) at transcriptional and post-translational level was shown in Solanum lycopersicum seedlings. NO donor priming enhances seed germination, breaks dormancy and provides tolerance to stress in crops. Its role in averting stress, promoting seed germination, and delaying senescence paved the way for use of NO and NO releasing compounds to prevent crop loss and increase the shelf-life of fruits and vegetables. An alternative to energy consuming and expensive cold storage led to development of a storage device called "shelf-life enhancer" that delays senescence and increases shelf-life at ambient temperature (25-27 °C) using NO donor. The present review summarizes NO research in plants and exploration of NO for its translational potential to improve agricultural yield and post-harvest crop loss. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01371-z.
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Affiliation(s)
- Yaiphabi Sougrakpam
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
| | - Priyanka Babuta
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
| | - Renu Deswal
- Molecular Physiology and Proteomics Laboratory, Department of Botany, University of Delhi, New Delhi, Delhi 110007 India
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Franzoni G, Spadafora ND, Sirangelo TM, Ferrante A, Rogers HJ. Biochemical and molecular changes in peach fruit exposed to cold stress conditions. MOLECULAR HORTICULTURE 2023; 3:24. [PMID: 37953307 PMCID: PMC10641970 DOI: 10.1186/s43897-023-00073-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/26/2023] [Indexed: 11/14/2023]
Abstract
Storage or transportation temperature is very important for preserving the quality of fruit. However, low temperature in sensitive fruit such as peach can induce loss of quality. Fruit exposed to a specific range of temperatures and for a longer period can show chilling injury (CI) symptoms. The susceptibility to CI at low temperature varies among cultivars and genetic backgrounds. Along with agronomic management, appropriate postharvest management can limit quality losses. The importance of correct temperature management during postharvest handling has been widely demonstrated. Nowadays, due to long-distance markets and complex logistics that require multiple actors, the management of storage/transportation conditions is crucial for the quality of products reaching the consumer.Peach fruit exposed to low temperatures activate a suite of physiological, metabolomic, and molecular changes that attempt to counteract the negative effects of chilling stress. In this review an overview of the factors involved, and plant responses is presented and critically discussed. Physiological disorders associated with CI generally only appear after the storage/transportation, hence early detection methods are needed to monitor quality and detect internal changes which will lead to CI development. CI detection tools are assessed: they need to be easy to use, and preferably non-destructive to avoid loss of products.
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Affiliation(s)
- Giulia Franzoni
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Natasha Damiana Spadafora
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara, 44121, Ferrara, Italy.
| | - Tiziana Maria Sirangelo
- ENEA-Italian National Agency for New Technologies, Energy and Sustainable Economic Development-Division Biotechnologies and Agroindustry, 00123, Rome, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133, Milan, Italy
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
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Rodríguez-Vázquez R, Mesa-Marín J. Plant responses to plant growth promoting bacteria: Insights from proteomics. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154031. [PMID: 37321049 DOI: 10.1016/j.jplph.2023.154031] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/17/2023]
Affiliation(s)
| | - Jennifer Mesa-Marín
- Department of Plant Biology and Ecology, Faculty of Biology, University of Seville, Seville, Spain.
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Huo Y, Yang H, Ding W, Huang T, Yuan Z, Zhu Z. Combined Transcriptome and Proteome Analysis Provides Insights into Petaloidy in Pomegranate. PLANTS (BASEL, SWITZERLAND) 2023; 12:2402. [PMID: 37446962 DOI: 10.3390/plants12132402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/20/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
Petaloidy leads to a plump floral pattern and increases the landscape value of ornamental pomegranates; however, research on the mechanism of petaloidy in ornamental pomegranates is limited. In this study, we aimed to screen candidate genes related to petaloidy. We performed transcriptomic and proteomic sequencing of the stamens and petals of single-petal and double-petal flowers of ornamental pomegranates. Briefly, 24,567 genes and 5865 proteins were identified, of which 5721 genes were quantified at both transcriptional and translational levels. In the petal and stamen comparison groups, the association between differentially abundant proteins (DAPs) and differentially expressed genes (DEGs) was higher than that between all genes and all proteins, indicating that petaloidy impacts the correlation between genes and proteins. The enrichment results of transcriptome, proteome, and correlation analyses showed that cell wall metabolism, jasmonic acid signal transduction, redox balance, and transmembrane transport affected petaloidy. Nine hormone-related DEGs/DAPs were selected, among which ARF, ILR1, LAX2, and JAR1 may promote petal doubling. Sixteen transcription factor DEGs/DAPs were selected, among which EREBP, LOB, MEF2, MYB, C3H, and trihelix may promote petal doubling. Our results provide transcriptomic and proteomic data on the formation mechanism of petaloidy and a theoretical basis for breeding new ornamental pomegranate varieties.
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Affiliation(s)
- Yan Huo
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China
- Jinpu Research Institute, Nanjing Forestry University, Nanjing 210037, China
- Research Center for Digital Innovation Design, Nanjing Forestry University, Nanjing 210037, China
| | - Han Yang
- College of Traditional Chinese Medicine, Weifang Medical University, Weifang 261053, China
| | - Wenjie Ding
- College of Landscape Engineering, Suzhou Polytechnic Institute of Agriculture, Suzhou 215008, China
| | - Tao Huang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China
- Jinpu Research Institute, Nanjing Forestry University, Nanjing 210037, China
- Research Center for Digital Innovation Design, Nanjing Forestry University, Nanjing 210037, China
| | - Zhaohe Yuan
- Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China
- College of Forestry, Nanjing Forestry University, Nanjing 210037, China
| | - Zunling Zhu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China
- Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China
- Jinpu Research Institute, Nanjing Forestry University, Nanjing 210037, China
- Research Center for Digital Innovation Design, Nanjing Forestry University, Nanjing 210037, China
- College of Art and Design, Nanjing Forestry University, Nanjing 210037, China
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Mahlare MJS, Husselmann L, Lewu MN, Bester C, Lewu FB, Caleb OJ. Analysis of the Differentially Expressed Proteins and Metabolic Pathways of Honeybush ( Cyclopia subternata) in Response to Water Deficit Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112181. [PMID: 37299160 DOI: 10.3390/plants12112181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/10/2023] [Accepted: 05/13/2023] [Indexed: 06/12/2023]
Abstract
Honeybush (Cyclopia spp.) is a rich source of antioxidant properties and phenolic compounds. Water availability plays a crucial role in plant metabolic processes, and it contributes to overall quality. Thus, this study aimed to investigate changes in molecular functions, cellular components, and biological processes of Cyclopia subternata exposed to different water stress conditions, which include well-watered (as Control, T1), semi-water stressed (T2), and water-deprived (T3) potted plants. Samples were also collected from a well-watered commercial farm first cultivated in 2013 (T13) and then cultivated in 2017 (T17) and 2019 (T19). Differentially expressed proteins extracted from C. subternata leaves were identified using LC-MS/MS spectrometry. A total of 11 differentially expressed proteins (DEPs) were identified using Fisher's exact test (p < 0.00100). Only α-glucan phosphorylase was found to be statistically common between T17 and T19 (p < 0.00100). Notably, α-glucan phosphorylase was upregulated in the older vegetation (T17) and downregulated in T19 by 1.41-fold. This result suggests that α-glucan phosphorylase was needed in T17 to support the metabolic pathway. In T19, five DEPs were upregulated, while the other six were downregulated. Based on gene ontology, the DEPs in the stressed plant were associated with cellular and metabolic processes, response to stimulus, binding, catalytic activity, and cellular anatomical entity. Differentially expressed proteins were clustered based on the Kyoto Encyclopedia of Genes and Genomes (KEGG), and sequences were linked to metabolic pathways via enzyme code and KEGG ortholog. Most proteins were involved in photosynthesis, phenylpropanoid biosynthesis, thiamine, and purine metabolism. This study revealed the presence of trans-cinnamate 4-monooxygenase, an intermediate for the biosynthesis of a large number of substances, such as phenylpropanoids and flavonoids.
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Affiliation(s)
- Mary-Jane S Mahlare
- Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
- Department of Agriculture, Faculty of Applied Sciences, Cape Peninsula University of Technology, Wellington Campus, Private Bag X8, Wellington 7654, South Africa
| | - Lizex Husselmann
- Department of Biotechnology, University of the Western Cape, Bellville 7535, South Africa
| | - Muinat N Lewu
- Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Cecilia Bester
- Agricultural Research Council (ARC) Infruitec-Nietvoorbij, Stellenbosch 7599, South Africa
| | - Francis B Lewu
- Department of Agriculture, Faculty of Applied Sciences, Cape Peninsula University of Technology, Wellington Campus, Private Bag X8, Wellington 7654, South Africa
| | - Oluwafemi James Caleb
- Africa Institute for Postharvest Technology, Faculty of AgriSciences, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Department of Horticultural Science, Faculty of AgriSciences, Stellenbosch University, Matieland 7602, South Africa
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13
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Li W, Keller AA. Optimization of Targeted Plant Proteomics Using Liquid Chromatography with Tandem Mass Spectrometry (LC-MS/MS). ACS AGRICULTURAL SCIENCE & TECHNOLOGY 2023; 3:421-431. [PMID: 37206883 PMCID: PMC10189723 DOI: 10.1021/acsagscitech.3c00017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/05/2023] [Accepted: 04/06/2023] [Indexed: 05/21/2023]
Abstract
This study was conducted to optimize a targeted plant proteomics approach from signature peptide selection and liquid chromatography with tandem mass spectrometry (LC-MS/MS) analytical method development and optimization to sample preparation method optimization. Three typical protein extraction and precipitation methods, including trichloroacetic acid (TCA)/acetone method, phenol method, and TCA/acetone/phenol method, and two digestion methods, including trypsin digestion and LysC/trypsin digestion, were evaluated for selected proteins related to the impact of engineered nanomaterials (ENMs) on wheat (Triticum aestivum) plant growth. In addition, we compared two plant tissue homogenization methods: grinding freeze-dried tissue and fresh tissue into a fine powder using a mortar and pestle aided with liquid nitrogen. Wheat plants were grown under a 16 h photoperiod (light intensity 150 μmol·m-2·s-1) for 4 weeks at 22 °C with a relative humidity of 60% and were watered daily to maintain a 70-90% water content in the soil. Processed samples were analyzed with an optimized LC-MS/MS method. The concentration of selected signature peptides for the wheat proteins of interest indicated that the phenol extraction method using fresh plant tissue, coupled with trypsin digestion, was the best sample preparation method for the targeted proteomics study. Overall, the optimized approach yielded the highest total peptide concentration (68,831 ng/g, 2.4 times the lowest concentration) as well as higher signature peptide concentrations for most peptides (19 out of 28). In addition, three of the signature peptides could only be detected using the optimized approach. This study provides a workflow for optimizing targeted proteomics studies.
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14
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Lu S, Zou T, Qin P, Zhang X, Wang G, Qin Y, Wang Q. Effect of organophosphate esters on microbial community and proteomics in constructed wetlands and its removal mechanism. CHEMOSPHERE 2023; 319:137803. [PMID: 36640982 DOI: 10.1016/j.chemosphere.2023.137803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/27/2022] [Accepted: 01/08/2023] [Indexed: 06/17/2023]
Abstract
Organophosphorus esters (OPEs) may cause potential risks to human health and ecological environment safety when they enter water. In this study, A lab-scale vertical flow constructed wetlands (VFCWs) exposed to dichlorvos (DDVP) was carried out to reveal removal effect and mechanism of DDVP in VFCWs. The findings indicated CWs can remove DDVP with 94%-95% average removal efficiency in long-term operation. Besides, soluble phosphate (SRP) and total phosphorus (TP) were removed by VFCWs with 48.60%-64.10% average removal efficiency, and the addition of DDVP enhanced the effect of CWs on nitrogen removal. High-throughput sequencing demonstrated that Massiilia (2.67%-18.06%), Denitratisoma (2.07%-3.80%) and SM1A02 (2.85%-4.67%) played an important role in the removal process of DDVP in VFCWs. Proteomics of plant root showed that A0A3B6ARQ4 (increased 29.53 times) and LOC_Os11g38050.1 protein (decreased 0.001 times) responsed more sensitive to OPEs which suggested DDVP enhancesenhancing plants energy production and hydrolyase synthesis, thereby promoting it hydrolysis. Therefore, the use of VFCWs to treat organic phosphate wastewater has future prospects.
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Affiliation(s)
- Shaoyong Lu
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria and Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Tao Zou
- College of Ecological Environment, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Pan Qin
- State Environmental Protection Scientific Observation and Research Station for Lake Dongtinghu (SEPSORSLD), National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Key Laboratory of Environmental Criteria and Risk Assessment, Research Centre of Lake Environment, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Xuan Zhang
- College of Ecological Environment, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Guoqiang Wang
- College of Water Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yuchun Qin
- College of Ecological Environment, Hainan Tropical Ocean University, Sanya, 572022, China
| | - Quan Wang
- College of Chemistry, Biology and Environment, Yuxi Normal University, Yuxi, 653100, China.
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15
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Sheng P, Xu M, Zheng Z, Liu X, Ma W, Ding T, Zhang C, Chen M, Zhang M, Cheng B, Zhang X. Peptidome and Transcriptome Analysis of Plant Peptides Involved in Bipolaris maydis Infection of Maize. PLANTS (BASEL, SWITZERLAND) 2023; 12:1307. [PMID: 36986996 PMCID: PMC10056677 DOI: 10.3390/plants12061307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 06/19/2023]
Abstract
Southern corn leaf blight (SCLB) caused by Bipolaris maydis threatens maize growth and yield worldwide. In this study, TMT-labeled comparative peptidomic analysis was established between infected and uninfected maize leaf samples using liquid-chromatography-coupled tandem mass spectrometry. The results were further compared and integrated with transcriptome data under the same experimental conditions. Plant peptidomic analysis identified 455 and 502 differentially expressed peptides (DEPs) in infected maize leaves on day 1 and day 5, respectively. A total of 262 common DEPs were identified in both cases. Bioinformatic analysis indicated that the precursor proteins of DEPs are associated with many pathways generated by SCLB-induced pathological changes. The expression profiles of plant peptides and genes in maize plants were considerably altered after B. maydis infection. These findings provide new insights into the molecular mechanisms of SCLB pathogenesis and offer a basis for the development of maize genotypes with SCLB resistance.
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Affiliation(s)
- Pijie Sheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Minyan Xu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Zhenzhen Zheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xiaojing Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Wanlu Ma
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Ting Ding
- School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Chenchen Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Meng Chen
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Mengting Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Beijiu Cheng
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Xin Zhang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
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Serag A, Salem MA, Gong S, Wu JL, Farag MA. Decoding Metabolic Reprogramming in Plants under Pathogen Attacks, a Comprehensive Review of Emerging Metabolomics Technologies to Maximize Their Applications. Metabolites 2023; 13:424. [PMID: 36984864 PMCID: PMC10055942 DOI: 10.3390/metabo13030424] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/01/2023] [Accepted: 03/09/2023] [Indexed: 03/15/2023] Open
Abstract
In their environment, plants interact with a multitude of living organisms and have to cope with a large variety of aggressions of biotic or abiotic origin. What has been known for several decades is that the extraordinary variety of chemical compounds the plants are capable of synthesizing may be estimated in the range of hundreds of thousands, but only a fraction has been fully characterized to be implicated in defense responses. Despite the vast importance of these metabolites for plants and also for human health, our knowledge about their biosynthetic pathways and functions is still fragmentary. Recent progress has been made particularly for the phenylpropanoids and oxylipids metabolism, which is more emphasized in this review. With an increasing interest in monitoring plant metabolic reprogramming, the development of advanced analysis methods should now follow. This review capitalizes on the advanced technologies used in metabolome mapping in planta, including different metabolomics approaches, imaging, flux analysis, and interpretation using bioinformatics tools. Advantages and limitations with regards to the application of each technique towards monitoring which metabolite class or type are highlighted, with special emphasis on the necessary future developments to better mirror such intricate metabolic interactions in planta.
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Affiliation(s)
- Ahmed Serag
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Al-Azhar University, Cairo 11751, Egypt
| | - Mohamed A. Salem
- Department of Pharmacognosy and Natural Products, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom 32511, Menoufia, Egypt
| | - Shilin Gong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Lin Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, China
| | - Mohamed A. Farag
- Pharmacognosy Department, College of Pharmacy, Cairo University, Kasr el Aini St., Cairo 11562, Egypt
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Manan A, Roytrakul S, Charoenlappanit S, Poolpak T, Ounjai P, Kruatrachue M, Yang KM, Pokethitiyook P. Glyphosate metabolism in Tetrahymena thermophila: A shotgun proteomic analysis approach. ENVIRONMENTAL TOXICOLOGY 2023; 38:867-882. [PMID: 36602419 DOI: 10.1002/tox.23735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/11/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
Glyphosate is one of the most widely used herbicides in the world. However, because of its overuse and resistance to degradation, high levels of glyphosate residues in the environment are reported. Therefore, this study aimed to investigate the effects of glyphosate on proteomic aspects of Tetrahymena thermophila and their uses as bioindicators of freshwater ecosystem. First, an acute toxicity test was performed to determine the median inhibition concentration (IC50 ). The toxicity test results showed that glyphosate inhibited the growth (proliferation) of T. thermophila. The 96 h-IC50 value of glyphosate was 171 mg L-1 . No visible changes in aggregation behavior and cell morphology were observed under glyphosate exposure. In addition, the effects of low and high dose glyphosate concentrations (77.5 mg L-1 , 171 mg L-1 ) on the proteomic changes of T. thermophila was investigated using a label-free shotgun proteomic approach. A total of 3191 proteins were identified, 2791 proteins were expressed in the control, 2651 proteins were expressed in 77.5 mg L-1 glyphosates, and 3012 proteins were expressed in 171 mg L-1 glyphosates. Under glyphosate exposure at both low and high dose glyphosate, 400 unique proteins were upregulated. The majority of these proteins was classified as proteins associated with oxidative stress response and intracellular transport indicating the shifts in the internal metabolism. Proteomics revealed that the glyphosate metabolism by T. thermophila is a multi-step process involving several enzymes, which can be divided into four phases, including modification (phase I), conjugation (phase II), transport (phase III), and degradation (phase IV). The accumulation of various biochemical reactions contributes to overall glyphosate resistance. With the proteomics approach, we have found that T. thermophila was equipped with glyphosate detoxification and degradation mechanisms.
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Affiliation(s)
- Abdul Manan
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
- Department of Aquaculture, Faculty of Fisheries and Marine, Universitas Airlangga, Surabaya, Indonesia
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sawanya Charoenlappanit
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Toemthip Poolpak
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Puey Ounjai
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Maleeya Kruatrachue
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Kwang Mo Yang
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
| | - Prayad Pokethitiyook
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, MHESI, Bangkok, Thailand
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18
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Fortini EA, Batista DS, Felipe SHS, Silva TD, Correia LNF, Farias LM, Faria DV, Pinto VB, Santa-Catarina C, Silveira V, De-la-Peña C, Castillo-Castro E, Otoni WC. Physiological, epigenetic, and proteomic responses in Pfaffia glomerata growth in vitro under salt stress and 5-azacytidine. PROTOPLASMA 2023; 260:467-482. [PMID: 35788779 DOI: 10.1007/s00709-022-01789-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Plants adjust their complex molecular, biochemical, and metabolic processes to overcome salt stress. Here, we investigated the proteomic and epigenetic alterations involved in the morphophysiological responses of Pfaffia glomerata, a medicinal plant, to salt stress and the demethylating agent 5-azacytidine (5-azaC). Moreover, we investigated how these changes affected the biosynthesis of 20-hydroxyecdysone (20-E), a pharmacologically important specialized metabolite. Plants were cultivated in vitro for 40 days in Murashige and Skoog medium supplemented with NaCl (50 mM), 5-azaC (25 μM), and NaCl + 5-azaC. Compared with the control (medium only), the treatments reduced growth, photosynthetic rates, and photosynthetic pigment content, with increase in sucrose, total amino acids, and proline contents, but a reduction in starch and protein. Comparative proteomic analysis revealed 282 common differentially accumulated proteins involved in 87 metabolic pathways, most of them related to amino acid and carbohydrate metabolism, and specialized metabolism. 5-azaC and NaCl + 5-azaC lowered global DNA methylation levels and 20-E content, suggesting that 20-E biosynthesis may be regulated by epigenetic mechanisms. Moreover, downregulation of a key protein in jasmonate biosynthesis indicates the fundamental role of this hormone in the 20-E biosynthesis. Taken together, our results highlight possible regulatory proteins and epigenetic changes related to salt stress tolerance and 20-E biosynthesis in P. glomerata, paving the way for future studies of the mechanisms involved in this regulation.
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Affiliation(s)
- Evandro Alexandre Fortini
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Diego Silva Batista
- Departamento de Agricultura, Universidade Federal da Paraíba, Campus III, Bananeiras, PB, 58220-000, Brazil
| | - Sérgio Heitor Sousa Felipe
- PPG em Agroecologia, Universidade Estadual do Maranhão, Av. Lourenço Vieira da Silva, s/nº, Cidade Universitária Paulo VI, São Luís, MA, Brazil
| | - Tatiane Dulcineia Silva
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Ludmila Nayara Freitas Correia
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Letícia Monteiro Farias
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil
| | - Daniele Vidal Faria
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil
| | - Vitor Batista Pinto
- Laboratório de Biotecnologia (LBT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Claudete Santa-Catarina
- Laboratório de Biologia Celular e Tecidual (LBCT), CBB-UENF, Campos dos Goytacazes, RJ, Brazil
| | - Vanildo Silveira
- Laboratório de Biotecnologia (LBT), Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego 2000, Campos dos Goytacazes, RJ, 28013-602, Brazil
| | - Clelia De-la-Peña
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C. (CICY), 97205, Mérida, Yucatán, Mexico
| | - Eduardo Castillo-Castro
- Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, A. C. (CICY), 97205, Mérida, Yucatán, Mexico
| | - Wagner Campos Otoni
- Laboratório de Cultura de Tecidos Vegetais (LCTII), Departamento de Biologia Vegetal/BIOAGRO, Universidade Federal de Viçosa, Campus Universitário, Avenida Peter Henry Rolfs s/n, Viçosa, MG, 36570-900, Brazil.
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19
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Wei L, Wang D, Gupta R, Kim ST, Wang Y. A Proteomics Insight into Advancements in the Rice-Microbe Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12051079. [PMID: 36903938 PMCID: PMC10005616 DOI: 10.3390/plants12051079] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 05/23/2023]
Abstract
Rice is one of the most-consumed foods worldwide. However, the productivity and quality of rice grains are severely constrained by pathogenic microbes. Over the last few decades, proteomics tools have been applied to investigate the protein level changes during rice-microbe interactions, leading to the identification of several proteins involved in disease resistance. Plants have developed a multi-layered immune system to suppress the invasion and infection of pathogens. Therefore, targeting the proteins and pathways associated with the host's innate immune response is an efficient strategy for developing stress-resistant crops. In this review, we discuss the progress made thus far with respect to rice-microbe interactions from side views of the proteome. Genetic evidence associated with pathogen-resistance-related proteins is also presented, and challenges and future perspectives are highlighted in order to understand the complexity of rice-microbe interactions and to develop disease-resistant crops in the future.
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Affiliation(s)
- Lirong Wei
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Dacheng Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
| | - Ravi Gupta
- College of General Education, Kookmin University, Seoul 02707, Republic of Korea
| | - Sun Tae Kim
- Department of Plant Bioscience, Pusan National University, Miryang 50463, Republic of Korea
| | - Yiming Wang
- Key Laboratory of Integrated Management of Crop Disease and Pests, Ministry of Education, Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China
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20
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Tola AJ, Missihoun TD. Ammonium sulfate-based prefractionation improved proteome coverage and detection of carbonylated proteins in Arabidopsis thaliana leaf extract. PLANTA 2023; 257:62. [PMID: 36808312 DOI: 10.1007/s00425-023-04083-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/29/2023] [Indexed: 06/18/2023]
Abstract
Ammonium sulfate is well known to salt out proteins at high concentrations. The study revealed that it can serve to increase by 60% the total number of identified carbonylated proteins by LC-MS/MS. Protein carbonylation is a significant post-translational modification associated with reactive oxygen species signaling in animal and plant cells. However, the detection of carbonylated proteins involved in signaling is still challenging, as they only represent a small subset of the proteome in the absence of stress. In this study, we investigated the hypothesis that a prefractionation step with ammonium sulphate will improve the detection of the carbonylated proteins in a plant extract. For this, we extracted total protein from the Arabidopsis thaliana leaves and subjected the extract to stepwise precipitation with ammonium sulfate to 40%, 60%, and 80% saturation. The protein fractions were then analyzed by liquid chromatography-tandem mass spectrometry for protein identification. We found that all the proteins identified in the non-fractionated samples were also found in the prefractionated samples, indicating no loss was incurred during the prefractionation. About 45% more proteins were identified in the fractionated samples compared to the non-fractionated total crude extract. When the prefractionation steps were combined with the enrichment of carbonylated proteins labeled with a fluorescent hydrazide probe, several carbonylated proteins, which were unseen in the non-fractionated samples, became visible in the prefractionated samples. Consistently, the prefractionation method allowed to identify 63% more carbonylated proteins by mass spectrometry compared to the number of carbonylated proteins identified from the total crude extract without prefractionation. These results indicated that the ammonium sulfate-based proteome prefractionation can be used to improve proteome coverage and identification of carbonylated proteins from a complex proteome sample.
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Affiliation(s)
- Adesola Julius Tola
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada
| | - Tagnon D Missihoun
- Groupe de Recherche en Biologie Végétale (GRBV), Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351 boul. des Forges, Trois-Rivières, QC, G9A 5H7, Canada.
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21
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Proteomic Analysis Reveals a Critical Role of the Glycosyl Hydrolase 17 Protein in Panax ginseng Leaves under Salt Stress. Int J Mol Sci 2023; 24:ijms24043693. [PMID: 36835103 PMCID: PMC9965409 DOI: 10.3390/ijms24043693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 02/01/2023] [Accepted: 02/10/2023] [Indexed: 02/16/2023] Open
Abstract
Ginseng, an important crop in East Asia, exhibits multiple medicinal and nutritional benefits because of the presence of ginsenosides. On the other hand, the ginseng yield is severely affected by abiotic stressors, particularly salinity, which reduces yield and quality. Therefore, efforts are needed to improve the ginseng yield during salinity stress, but salinity stress-induced changes in ginseng are poorly understood, particularly at the proteome-wide level. In this study, we report the comparative proteome profiles of ginseng leaves at four different time points (mock, 24, 72, and 96 h) using a label-free quantitative proteome approach. Of the 2484 proteins identified, 468 were salt-responsive. In particular, glycosyl hydrolase 17 (PgGH17), catalase-peroxidase 2, voltage-gated potassium channel subunit beta-2, fructose-1,6-bisphosphatase class 1, and chlorophyll a-b binding protein accumulated in ginseng leaves in response to salt stress. The heterologous expression of PgGH17 in Arabidopsis thaliana improved the salt tolerance of transgenic lines without compromising plant growth. Overall, this study uncovers the salt-induced changes in ginseng leaves at the proteome level and highlights the critical role of PgGH17 in salt stress tolerance in ginseng.
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Pierre E, Marcelo P, Croutte A, Dauvé M, Bouton S, Rippa S, Pageau K. Impact of Rhamnolipids (RLs), Natural Defense Elicitors, on Shoot and Root Proteomes of Brassica napus by a Tandem Mass Tags (TMTs) Labeling Approach. Int J Mol Sci 2023; 24:ijms24032390. [PMID: 36768708 PMCID: PMC9916879 DOI: 10.3390/ijms24032390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/19/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023] Open
Abstract
The rapeseed crop is susceptible to many pathogens such as parasitic plants or fungi attacking aerial or root parts. Conventional plant protection products, used intensively in agriculture, have a negative impact on the environment as well as on human health. There is therefore a growing demand for the development of more planet-friendly alternative protection methods such as biocontrol compounds. Natural rhamnolipids (RLs) can be used as elicitors of plant defense mechanisms. These glycolipids, from bacteria secretome, are biodegradable, non-toxic and are known for their stimulating and protective effects, in particular on rapeseed against filamentous fungi. Characterizing the organ responsiveness to defense-stimulating compounds such as RLs is missing. This analysis is crucial in the frame of optimizing the effectiveness of RLs against various diseases. A Tandem Mass Tags (TMT) labeling of the proteins extracted from the shoots and roots of rapeseed has been performed and showed a differential pattern of protein abundance between them. Quantitative proteomic analysis highlighted the differential accumulation of parietal and cytoplasmic defense or stress proteins in response to RL treatments with a clear effect of the type of application (foliar spraying or root absorption). These results must be considered for further use of RLs to fight specific rapeseed pathogens.
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Affiliation(s)
- Elise Pierre
- Unité Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UMRt 1158, Université de Picardie Jules Verne, 80039 Amiens, France
- Plateforme d’Ingénierie Cellulaire & Analyses des Protéines ICAP, FR CNRS 3085 ICP, Université de Picardie Jules Verne, 80039 Amiens, France
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Alliance Sorbonne Universités, Université de Technologie de Compiègne, 60203 Compiègne, France
| | - Paulo Marcelo
- Plateforme d’Ingénierie Cellulaire & Analyses des Protéines ICAP, FR CNRS 3085 ICP, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Antoine Croutte
- Plateforme d’Ingénierie Cellulaire & Analyses des Protéines ICAP, FR CNRS 3085 ICP, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Morgane Dauvé
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Alliance Sorbonne Universités, Université de Technologie de Compiègne, 60203 Compiègne, France
| | - Sophie Bouton
- Unité Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UMRt 1158, Université de Picardie Jules Verne, 80039 Amiens, France
| | - Sonia Rippa
- Unité de Génie Enzymatique et Cellulaire, UMR CNRS 7025, Alliance Sorbonne Universités, Université de Technologie de Compiègne, 60203 Compiègne, France
- Correspondence: (S.R.); (K.P.)
| | - Karine Pageau
- Unité Transfrontalière BioEcoAgro, BIOlogie des Plantes et Innovation (BIOPI), UMRt 1158, Université de Picardie Jules Verne, 80039 Amiens, France
- Correspondence: (S.R.); (K.P.)
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Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Abid G, Muhovski Y. Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley ( Hordeum vulgare L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:526. [PMID: 36771612 PMCID: PMC9921465 DOI: 10.3390/plants12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Olive Tree Institute, Cité Mahragène, P.O. Box 208, Tunis 1082, Tunisia
| | - Hatem Cheikh M’Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), Carthage University, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79403-6603, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Jouhaina Riahi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
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Srivastava A, Kumar A, Biswas S, Kumar R, Srivastava V, Rajaram H, Mishra Y. Gamma (γ)-radiation stress response of the cyanobacterium Anabaena sp. PCC7120: Regulatory role of LexA and photophysiological changes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 326:111529. [PMID: 36332765 DOI: 10.1016/j.plantsci.2022.111529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 06/16/2023]
Abstract
High radioresistance of the cyanobacterium, Anabaena sp. PCC7120 has been attributed to efficient DNA repair, protein recycling, and oxidative stress management. However, the regulatory network involved in these batteries of responses remains unexplored. In the present study, the role of a global regulator, LexA in modulating gamma (γ)-radiation stress response of Anabaena was investigated. Comparison of the cytosolic proteome profiles upon γ-radiation in recombinant Anabaena strains, AnpAM (vector-control) and AnlexA+ (LexA-overexpressing), revealed 41 differentially accumulated proteins, corresponding to 29 distinct proteins. LexA was found to be involved in the regulation of 27 of the corresponding genes based on the presence of AnLexA-Box, EMSA, and/or qRT-PCR studies. The majority of the regulated genes were found to be involved in C-assimilation either through photosynthesis or C-catabolism and oxidative stress alleviation. Photosynthesis, measured in terms of PSII photophysiological parameters and thylakoid membrane proteome was found to be affected by γ-radiation in both AnpAM and AnlexA+ cells, with LexA affecting them even under control growth conditions. Thus, LexA functioned as one of the transcriptional regulators involved in modulating γ-radiation stress response in Anabaena. This study could pave the way for a deeper understanding of the regulation of γ-radiation-responsive genes in cyanobacteria at large.
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Affiliation(s)
- Akanksha Srivastava
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Arvind Kumar
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India
| | - Subhankar Biswas
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Rajender Kumar
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Vaibhav Srivastava
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm 10691, Sweden
| | - Hema Rajaram
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
| | - Yogesh Mishra
- Department of Botany, Centre of Advanced Study in Botany, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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Shoko R, Magogo B, Pullen J, Mudziwapasi R, Ndlovu J. Construction and analysis of protein-protein interaction networks based on nuclear proteomics data of the desiccation-tolerant Xerophyta schlechteri leaves subjected to dehydration stress. Commun Integr Biol 2023; 16:2193000. [PMID: 36969388 PMCID: PMC10038031 DOI: 10.1080/19420889.2023.2193000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
In order to understand the mechanism of desiccation tolerance in Xerophyta schlechteri, we carried out an in silico study to identify hub proteins and functional modules in the nuclear proteome of the leaves. Protein-protein interaction networks were constructed and analyzed from proteome data obtained from Abdalla and Rafudeen. We constructed networks in Cytoscape using the GeneMania software and analyzed them using a Network Analyzer. Functional enrichment analysis of key proteins in the respective networks was done using GeneMania network enrichment analysis, and GO (Gene Ontology) terms were summarized using REViGO. Also, community analysis of differentially expressed proteins was conducted using the Cytoscape Apps, GeneMania and ClusterMaker. Functional modules associated with the communities were identified using an online tool, ShinyGO. We identified HSP 70-2 as the super-hub protein among the up-regulated proteins. On the other hand, 40S ribosomal protein S2-3 (a protein added by GeneMANIA) was identified as a super-hub protein associated with the down-regulated proteins. For up-regulated proteins, the enriched biological process terms were those associated with chromatin organization and negative regulation of transcription. In the down-regulated protein-set, terms associated with protein synthesis were significantly enriched. Community analysis identified three functional modules that can be categorized as chromatin organization, anti-oxidant activity and metabolic processes.
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Affiliation(s)
- Ryman Shoko
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
- CONTACT Ryman Shoko Department of Biology, Chinhoyi University of Technology, Private Bag 7724, Chinhoyi, Zimbabwe
| | - Babra Magogo
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
| | - Jessica Pullen
- Department of Animal Science and Rangeland Management, Lupane State University, Lupane, Zimbabwe
| | - Reagan Mudziwapasi
- Department of Research and Innovation, Midlands State University, Gweru, Zimbabwe
| | - Joice Ndlovu
- Department of Biology, Chinhoyi University of Technology, Chinhoyi, Zimbabwe
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26
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Boyaci Gunduz CP, Agirman B, Erten H. Identification of yeasts in fermented foods and beverages using MALDI-TOF MS. FEMS Yeast Res 2022; 22:6823700. [PMID: 36367538 DOI: 10.1093/femsyr/foac056] [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: 08/26/2022] [Revised: 10/21/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022] Open
Abstract
Yeasts are an important group of microorganisms and contribute to the fermentation of a broad range of foods and beverages spontaneously or as a starter culture. Rapid and reliable microbial species identification is essential to evaluate biodiversity in fermented foods and beverages. Nowadays, high-throughput omics technologies and bioinformatics tools produce large-scale molecular-level data in many fields. These omics technologies generate data at different expression levels and are used to identify microorganisms. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful analytical technique in proteomic technology. It is a tool used to analyze the peptides or proteins of microorganisms for identification. MALDI-TOF MS has been used for the taxonomic identification of microorganisms as a fast, high-throughput, and cost-effective method. This review briefly discussed the application of MALDI-TOF MS in identifying yeasts in fermented foods and beverages.
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Affiliation(s)
- Cennet Pelin Boyaci Gunduz
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey.,Department of Food Engineering, Faculty of Engineering, Adana Alparslan Turkes Science and Technology University, Adana 01250, Turkey
| | - Bilal Agirman
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey
| | - Huseyin Erten
- Department of Food Engineering, Faculty of Engineering, Cukurova University, TR-01330 Adana, Turkey
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27
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Bawa G, Liu Z, Zhou Y, Fan S, Ma Q, Tissue DT, Sun X. Cotton proteomics: Dissecting the stress response mechanisms in cotton. FRONTIERS IN PLANT SCIENCE 2022; 13:1035801. [PMID: 36466262 PMCID: PMC9714328 DOI: 10.3389/fpls.2022.1035801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
The natural environment of plants comprises a complex set of biotic and abiotic stresses, and plant responses to these stresses are complex as well. Plant proteomics approaches have significantly revealed dynamic changes in plant proteome responses to stress and developmental processes. Thus, we reviewed the recent advances in cotton proteomics research under changing environmental conditions, considering the progress and challenging factors. Finally, we highlight how single-cell proteomics is revolutionizing plant research at the proteomics level. We envision that future cotton proteomics research at the single-cell level will provide a more complete understanding of cotton's response to stresses.
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Affiliation(s)
- George Bawa
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Zhixin Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Yaping Zhou
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
| | - Shuli Fan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - Qifeng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), Anyang, China
| | - David T. Tissue
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW, Australia
| | - Xuwu Sun
- State Key Laboratory of Cotton Biology, Key Laboratory of Plant Stress Biology, School of Life Sciences, Henan University, Kaifeng, China
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28
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Álvarez C, Brenes-Álvarez M, Molina-Heredia FP, Mariscal V. Quantitative Proteomics at Early Stages of the Symbiotic Interaction Between Oryza sativa and Nostoc punctiforme Reveals Novel Proteins Involved in the Symbiotic Crosstalk. PLANT & CELL PHYSIOLOGY 2022; 63:1433-1445. [PMID: 35373828 PMCID: PMC9620832 DOI: 10.1093/pcp/pcac043] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/22/2022] [Accepted: 04/09/2022] [Indexed: 06/14/2023]
Abstract
Symbiosis between cyanobacteria and plants is considered pivotal for biological nitrogen deposition in terrestrial ecosystems. Despite extensive knowledge of the ecology of plant-cyanobacterium symbioses, little is known about the molecular mechanisms involved in recognition between partners. Here, we conducted a quantitative sequential window acquisition of all theoretical fragment ion spectra mass spectrometry pipeline to analyze protein changes in Oryza sativa and Nostoc punctiforme during early events of symbiosis. We found differentially expressed proteins in both organisms linked to several biological functions, including signal transduction, adhesion, defense-related proteins and cell wall modification. In N. punctiforme we found increased expression of 62 proteins that have been previously described in other Nostoc-plant symbioses, reinforcing the robustness of our study. Our findings reveal new proteins activated in the early stages of the Nostoc-Oryza symbiosis that might be important for the recognition between the plant and the host. Oryza mutants in genes in the common symbiosis signaling pathway (CSSP) show reduced colonization efficiency, providing first insights on the involvement of the CSSP for the accommodation of N. punctiforme inside the plant cells. This information may have long-term implications for a greater understanding of the symbiotic interaction between Nostoc and land plants.
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Affiliation(s)
- Consolación Álvarez
- *Corresponding authors: Vicente Mariscal, E-mail, ; Consolación Álvarez, E-mail,
| | - Manuel Brenes-Álvarez
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Américo Vespucio 49, Seville 41092, Spain
| | - Fernando P Molina-Heredia
- Instituto de Bioquímica Vegetal y Fotosíntesis, Consejo Superior de Investigaciones Científicas and Universidad de Sevilla, cicCartuja, Américo Vespucio 49, Seville 41092, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Biología, Universidad de Sevilla, Avda. Reina Mercedes s/n, Seville 41012, Spain
| | - Vicente Mariscal
- *Corresponding authors: Vicente Mariscal, E-mail, ; Consolación Álvarez, E-mail,
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Park SY, Jung WJ, Bang G, Hwang H, Kim JY. Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat ( Triticum aestivum). PLANTS (BASEL, SWITZERLAND) 2022; 11:2807. [PMID: 36365261 PMCID: PMC9657071 DOI: 10.3390/plants11212807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresses that frequently occurs due to irregular climate conditions, causing serious damage to wheat and its quality. In this study, transcriptomic analysis with RNA-seq and proteomic analysis with LC-MS/MS were performed in PHS-treated spikes from two wheat cultivars presenting PHS sensitivity and tolerance, respectively. A total of 13,154 differentially expressed genes (DEGs) and 706 differentially expressed proteins (DEPs) were identified in four comparison groups between the susceptible/tolerant cultivars. Gene function and correlation analysis were performed to determine the co-profiled genes and proteins affected by PHS treatment. In the functional annotation of each comparative group, similar functions were confirmed in each cultivar under PHS treatment; however, in Keumgang PHS+7 (K7) vs. Woori PHS+7 (W7), functional annotations presented clear differences in the "spliceosome" and "proteasome" pathways. In addition, our results indicate that alternative splicing and ubiquitin-proteasome support the regulation of germination and seed dormancy. This study provides an advanced understanding of the functions involved in transcription and translation related to PHS mechanisms, thus enabling specific proposals for the further analysis of germination and seed dormancy mechanisms and pathways in wheat.
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Affiliation(s)
- Sang Yong Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Jae Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
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30
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Zhang K, Cao H, Ma Y, Si H, Zang J, Bai H, Yu L, Pang X, Zhou F, Xing J, Dong J. Global analysis of lysine 2-hydroxyisobutyrylation during Fusarium graminearum infection in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:1000039. [PMID: 36186065 PMCID: PMC9521605 DOI: 10.3389/fpls.2022.1000039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Proteins post-translational modification (PTMs) is necessary in the whole life process of organisms. Among them, lysine 2-hydroxyisobutyrylation (Khib) plays an important role in protein synthesis, transcriptional regulation, and cell metabolism. Khib is a newly identified PTM in several plant species. However, the function of Khib in maize was unclear. In this study, western blotting results showed that Khib modification level increased significantly after Fusarium graminearum infection, and 2,066 Khib modified sites on 728 proteins were identified in maize, among which 24 Khib sites occurred on core histones. Subcellular localization results showed that these Khib modified proteins were localized in cytoplasm, chloroplast, and nucleus. Then, comparative proteomic analysis of the defense response to F. graminearum infection showed that Khib modification participated in plant resistance to pathogen infection by regulating glycolysis, TCA cycle, protein synthesis, peroxisome, and secondary metabolic processes, such as benzoxazinoid biosynthesis, phenylpropanoid biosynthesis, jasmonic acid synthesis, and tyrosine and tryptophan biosynthesis. In addition, we also demonstrated that lysine 2-hydroxyisobutyrylation sites on histones were involved in the gene expression of pathogenesis-related proteins. Our results provide a new perspective for the study of plant disease resistance, and had directive significance of maize disease resistance for molecular breeding.
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Affiliation(s)
- Kang Zhang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hongzhe Cao
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Yuxin Ma
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Helong Si
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jinping Zang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Hua Bai
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Lu Yu
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Xi Pang
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Fan Zhou
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jihong Xing
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
| | - Jingao Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, Hebei, China
- Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, Hebei, China
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31
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Sharma S, Shree B, Sharma A, Irfan M, Kumar P. Nanoparticle-based toxicity in perishable vegetable crops: Molecular insights, impact on human health and mitigation strategies for sustainable cultivation. ENVIRONMENTAL RESEARCH 2022; 212:113168. [PMID: 35346658 DOI: 10.1016/j.envres.2022.113168] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 02/08/2022] [Accepted: 03/16/2022] [Indexed: 05/27/2023]
Abstract
With the advancement of nanotechnology, the use of nanoparticles (NPs) and nanomaterials (NMs) in agriculture including perishable vegetable crops cultivation has been increased significantly. NPs/NMs positively affect plant growth and development, seed germination, plant stress management, and postharvest handling of fruits and vegetables. However, these NPs sometimes cause toxicity in plants by oxidative stress and excess reactive oxygen species production that affect cellular biomolecules resulting in imbalanced biological and metabolic processes in plants. Therefore, information about the mechanism underlying interactions of NPs with plants is important for the understanding of various physiological and biochemical responses of plants, evaluating phytotoxicity, and developing mitigation strategies for vegetable crops cultivation. To address this, recent morpho-physiological, biochemical and molecular insights of nanotoxicity in the vegetable crops have been discussed in this review. Further, factors affecting the nanotoxicity in vegetables and mitigation strategies for sustainable cultivation have been reviewed. Moreover, the bioaccumulation and biomagnification of NPs and associated phytotoxicity can cause serious effects on human health which has also been summarized. The review also highlights the use of advanced omics approaches and interdisciplinary tools for understanding the nanotoxicity and their possible use for mitigating phytotoxicity.
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Affiliation(s)
- Shweta Sharma
- MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Solan, 173229, HP, India
| | - Bharti Shree
- Department of Agricultural Biotechnology, CSK HPKV, Palampur, 176062, HP, India
| | - Ajit Sharma
- Dr YS Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, HP, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
| | - Pankaj Kumar
- Dr YS Parmar University of Horticulture and Forestry, Nauni, Solan, 173230, HP, India.
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Elicitation of Roots and AC-DC with PEP-13 Peptide Shows Differential Defense Responses in Multi-Omics. Cells 2022; 11:cells11162605. [PMID: 36010682 PMCID: PMC9406913 DOI: 10.3390/cells11162605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/08/2022] [Accepted: 08/20/2022] [Indexed: 12/03/2022] Open
Abstract
The root extracellular trap (RET) has emerged as a specialized compartment consisting of root AC-DC and mucilage. However, the RET’s contribution to plant defense is still poorly understood. While the roles of polysaccharides and glycoproteins secreted by root AC-DC have started to be elucidated, how the low-molecular-weight exudates of the RET contribute to root defense is poorly known. In order to better understand the RET and its defense response, the transcriptomes, proteomes and metabolomes of roots, root AC-DC and mucilage of soybean (Glycine max (L.) Merr, var. Castetis) upon elicitation with the peptide PEP-13 were investigated. This peptide is derived from the pathogenic oomycete Phytophthora sojae. In this study, the root and the RET responses to elicitation were dissected and sequenced using transcriptional, proteomic and metabolomic approaches. The major finding is increased synthesis and secretion of specialized metabolites upon induced defense activation following PEP-13 peptide elicitation. This study provides novel findings related to the pivotal role of the root extracellular trap in root defense.
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Yan S, Bhawal R, Yin Z, Thannhauser TW, Zhang S. Recent advances in proteomics and metabolomics in plants. MOLECULAR HORTICULTURE 2022; 2:17. [PMID: 37789425 PMCID: PMC10514990 DOI: 10.1186/s43897-022-00038-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/20/2022] [Indexed: 10/05/2023]
Abstract
Over the past decade, systems biology and plant-omics have increasingly become the main stream in plant biology research. New developments in mass spectrometry and bioinformatics tools, and methodological schema to integrate multi-omics data have leveraged recent advances in proteomics and metabolomics. These progresses are driving a rapid evolution in the field of plant research, greatly facilitating our understanding of the mechanistic aspects of plant metabolisms and the interactions of plants with their external environment. Here, we review the recent progresses in MS-based proteomics and metabolomics tools and workflows with a special focus on their applications to plant biology research using several case studies related to mechanistic understanding of stress response, gene/protein function characterization, metabolic and signaling pathways exploration, and natural product discovery. We also present a projection concerning future perspectives in MS-based proteomics and metabolomics development including their applications to and challenges for system biology. This review is intended to provide readers with an overview of how advanced MS technology, and integrated application of proteomics and metabolomics can be used to advance plant system biology research.
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Affiliation(s)
- Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Ruchika Bhawal
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA
| | - Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | | | - Sheng Zhang
- Proteomics and Metabolomics Facility, Institute of Biotechnology, Cornell University, 139 Biotechnology Building, 526 Campus Road, Ithaca, NY, 14853, USA.
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Wheat Proteomics for Abiotic Stress Tolerance and Root System Architecture: Current Status and Future Prospects. Proteomes 2022; 10:proteomes10020017. [PMID: 35645375 PMCID: PMC9150004 DOI: 10.3390/proteomes10020017] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/03/2022] [Accepted: 05/11/2022] [Indexed: 02/06/2023] Open
Abstract
Wheat is an important staple cereal for global food security. However, climate change is hampering wheat production due to abiotic stresses, such as heat, salinity, and drought. Besides shoot architectural traits, improving root system architecture (RSA) traits have the potential to improve yields under normal and stressed environments. RSA growth and development and other stress responses involve the expression of proteins encoded by the trait controlling gene/genes. Hence, mining the key proteins associated with abiotic stress responses and RSA is important for improving sustainable yields in wheat. Proteomic studies in wheat started in the early 21st century using the two-dimensional (2-DE) gel technique and have extensively improved over time with advancements in mass spectrometry. The availability of the wheat reference genome has allowed the exploration of proteomics to identify differentially expressed or abundant proteins (DEPs or DAPs) for abiotic stress tolerance and RSA improvement. Proteomics contributed significantly to identifying key proteins imparting abiotic stress tolerance, primarily related to photosynthesis, protein synthesis, carbon metabolism, redox homeostasis, defense response, energy metabolism and signal transduction. However, the use of proteomics to improve RSA traits in wheat is in its infancy. Proteins related to cell wall biogenesis, carbohydrate metabolism, brassinosteroid biosynthesis, and transportation are involved in the growth and development of several RSA traits. This review covers advances in quantification techniques of proteomics, progress in identifying DEPs and/or DAPs for heat, salinity, and drought stresses, and RSA traits, and the limitations and future directions for harnessing proteomics in wheat improvement.
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Jha UC, Sharma KD, Nayyar H, Parida SK, Siddique KHM. Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes. Int J Mol Sci 2022; 23:ijms23042217. [PMID: 35216334 PMCID: PMC8880496 DOI: 10.3390/ijms23042217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.
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Affiliation(s)
- Uday C. Jha
- Indian Institute of Pulses Research, Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Kamal Dev Sharma
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur 176062, India;
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 0172, India;
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi 110001, India;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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Tortosa M, Velasco P, Rodríguez VM, Cartea ME. Changes in Brassica oleracea Leaves Infected With Xanthomonas campestris pv. campestris by Proteomics Analysis. FRONTIERS IN PLANT SCIENCE 2022; 12:781984. [PMID: 35211128 PMCID: PMC8860909 DOI: 10.3389/fpls.2021.781984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
Abstract
Understanding plant's response mechanisms against pathogenesis is fundamental for the development of resistant crop varieties and more productive agriculture. In this regard, "omic" approaches are heralded as valuable technologies. In this work, combining isobaric tags for relative and absolute quantification (iTRAQ) technology with mass spectrometry, the proteomes from leaves of Brassica oleracea plants infected with Xanthomonas campestris pv. campestris (Xcc), and control plants at two different post-infection times were compared. Stronger proteomic changes were obtained at 12 days post-infection in comparison with 3 days. The responses observed involved different cell processes, from primary metabolism, such as photosynthesis or photorespiration, to other complex processes such as redox homeostasis, hormone signaling, or defense mechanisms. Most of the proteins decreased in the earlier response were involved in energetic metabolism, whereas later response was characterized by a recovery of primary metabolism. Furthermore, our results indicated that proteolysis machinery and reactive oxygen species (ROS) homeostasis could be key processes during this plant-pathogen interaction. Current data provide new insights into molecular mechanisms that may be involved in defense responses of B. oleracea to Xcc.
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Affiliation(s)
| | | | | | - María Elena Cartea
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia, Spanish Council for Scientific Research (CSIC), Pontevedra, Spain
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Mohd Afandi NS, Habib MAH, Ismail MN. Recent insights on gene expression studies on Hevea Brasiliensis fatal leaf fall diseases. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:471-484. [PMID: 35400887 PMCID: PMC8943083 DOI: 10.1007/s12298-022-01145-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Hevea brasiliensis is one of the most important agricultural commodities globally, heavily cultivated in Southeast Asia. Fatal leaf fall diseases cause aggressive leaf defoliation, linked to lower latex yield and death of crops before maturity. Due to the significant consequences of the disease to H. brasiliensis, the recent gene expression studies from four fall leaf diseases of H. brasiliensis were gathered; South American leaf blight, powdery mildew, Corynespora cassiicola and Phytophthora leaf fall disease. The differential analysis observed the pattern of commonly expressed genes upon fungi triggers using RT-PCR, DDRT-PCR, Real-time qRT-PCR and RNA-Seq. We have observed that RNA-Seq is the best tool to seek novel genes. Among the identified genes with defence-against fungi were pathogenesis-related genes such as β-1,3-glucanase and chitinase, the reactive oxygen species, and the phytoalexin biosynthesis. This manuscript also provided functional elaboration on the responsive genes and predicted possible biosynthetic pathways to identify and characterise novel genes in the future. At the end of the manuscript, the PCR methods and proteomic approaches were presented for future molecular and biochemical studies in the related diseases to H. brasiliensis.
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Affiliation(s)
- Nur Syafiqah Mohd Afandi
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Mohd Afiq Hazlami Habib
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
| | - Mohd Nazri Ismail
- Analytical Biochemistry Research Centre, Universiti Sains Malaysia, 11900 Bayan Lepas, Penang, Malaysia
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800 USM Penang, Malaysia
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Pu Y, Brandizzi F. Protein Preparation for Proteomic Analysis of the Unfolded Protein Response in Arabidopsis thaliana. Methods Mol Biol 2022; 2378:279-289. [PMID: 34985707 PMCID: PMC8935445 DOI: 10.1007/978-1-0716-1732-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Excessive accumulation of unfolded or misfolded proteins in the endoplasmic reticulum (ER) leads to a potentially cytotoxic condition known as the ER stress. Upon ER stress, cells initiate a homeostatic response called unfolded protein response (UPR) to assist proper folding the unfolded or misfolded proteins. Proteomics have been broadly used in plants with Liquid Chromatography coupled to tandem MS (LC-MS/MS) technologies. LC-MS/MS techniques have also been a great tool for studies of posttranslational modifications (PTMs). Here we describe our protocol of a fast method for large amount of seedling treatment and collection for UPR study in Arabidopsis thaliana and the preparation of total proteins for proteomic analysis.
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Affiliation(s)
- Yunting Pu
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI, USA
| | - Federica Brandizzi
- MSU-DOE Plant Research Lab and Plant Biology Department, Michigan State University, East Lansing, MI, USA.
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Ali S, Gill RA, Shafique MS, Ahmar S, Kamran M, Zhang N, Riaz M, Nawaz M, Fang R, Ali B, Zhou W. Role of phytomelatonin responsive to metal stresses: An omics perspective and future scenario. FRONTIERS IN PLANT SCIENCE 2022; 13:936747. [PMID: 36147242 PMCID: PMC9486320 DOI: 10.3389/fpls.2022.936747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/08/2022] [Indexed: 05/03/2023]
Abstract
A pervasive melatonin (N-acetyl-5-methoxytryptamine) reveals a crucial role in stress tolerance and plant development. Melatonin (MT) is a unique molecule with multiple phenotypic expressions and numerous actions within the plants. It has been extensively studied in crop plants under different abiotic stresses such as drought, salinity, heat, cold, and heavy metals. Mainly, MT role is appraised as an antioxidant molecule that deals with oxidative stress by scavenging reactive oxygen species (ROS) and modulating stress related genes. It improves the contents of different antioxidant enzyme activities and thus, regulates the redox hemostasis in crop plants. In this comprehensive review, regulatory effects of melatonin in plants as melatonin biosynthesis, signaling pathway, modulation of stress related genes and physiological role of melatonin under different heavy metal stress have been reviewed in detail. Further, this review has discussed how MT regulates different genes/enzymes to mediate defense responses and overviewed the context of transcriptomics and phenomics followed by the metabolomics pathways in crop plants.
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Affiliation(s)
- Skhawat Ali
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Wuhan, China
| | | | - Sunny Ahmar
- Faculty of Natural Sciences, Institute of Biology, Biotechnology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Muhammad Kamran
- School of Agriculture, Food and Wine, The University of Adelaide, Urrbrae, SA, Australia
| | - Na Zhang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Muhammad Riaz
- College of Natural Resources and Environment, South China Agricultural University, Guangzhou, Guangdong, China
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Rouyi Fang
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
| | - Basharat Ali
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
- Basharat Ali,
| | - Weijun Zhou
- Institute of Crop Science and Zhejiang Key Laboratory of Crop Germplasm, Zhejiang University, Hangzhou, China
- *Correspondence: Weijun Zhou,
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Ma TL, Li WJ, Hong YS, Zhou YM, Tian L, Zhang XG, Liu FL, Liu P. TMT based proteomic profiling of Sophora alopecuroides leaves reveal flavonoid biosynthesis processes in response to salt stress. J Proteomics 2021; 253:104457. [PMID: 34933133 DOI: 10.1016/j.jprot.2021.104457] [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: 08/01/2021] [Revised: 11/26/2021] [Accepted: 12/09/2021] [Indexed: 10/19/2022]
Abstract
Salt stress is the major abiotic stress worldwide, adversely affecting crop yield and quality. Utilizing salt tolerance genes for the genetic breeding of crops is one of the most effective measures to withstand salinization. Sophora alopecuroides is a well-known saline-alkaline and drought-tolerant medicinal plant. Understanding the underlying molecular mechanism for Sophora alopecuroides salt tolerance is crucial to identifying the salt-tolerant genes. In this study, we performed tandem mass tag (TMT) based proteomic profiling of S. alopecuroides leaves under 150 mM NaCl induced salt stress condition for 3 d and 7 d. Data are available on ProteomeXchange (PXD027627). Furthermore, the proteomic findings were validated through parallel reaction monitoring (PRM). We observed that the expression levels of several transporter proteins related to the secondary messenger signaling pathway were altered under salt stress conditions induced for 3 d. However, the expression of the certain transferase, oxidoreductase, dehydrogenase, which are involved in the biosynthesis of flavonoids, alkaloids, phenylpropanoids, and amino acid metabolism, were mainly alerted after 7 d post-salt-stress induction. Several potential genes that might be involved in salt stress conditions were identified; however, it demands further investigation. Although salt stress affects the level of secondary metabolites, their correlation needs to be investigated further. SIGNIFICANCE: Salinization is the most severe abiotic adversity, which has had a significant negative effect on world food security over the time. Excavating salt-tolerant genes from halophytes or medicinal plants is one of the important measures to cope with salt stress. S. alopecuroides is a well-known medicinal plant with anti-tumor, anti-inflammatory, and antibacterial effects, anti-saline properties, and resistance to drought stress. Currently, only a few studies have explored the S. alopecuroides' gene function, and regulation and these studies are mostly related to the unpublished genome sequence information of S. alopecuroides. Recently, transcriptomics and metabolomics studies have been carried on the abiotic stress in S. alopecuroides roots. Multiple studies have shown that altered gene expression at the transcript level and altered metabolite levels do not correspond to the altered protein levels. In this study, TMT and PRM based proteomic analyses of S. alopecuroides leaves under salt stress condition induced using 150 mM NaCl for 3 d and 7 d was performed. These analyses elucidated the activation of different mechanisms in response to salt stress. A total of 434 differentially abundant proteins (DAPs) in salt stress conditions were identified and analyzed. For the first time, this study utilized proteomics technology to dig out plentiful underlying salt-tolerant genes from the medicinal plant, S. alopecuroides. We believe that this study will be of great significance to crop genetics and breeding.
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Affiliation(s)
- Tian-Li Ma
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China.
| | - Wen-Juan Li
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China
| | - Yuan-Shu Hong
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China
| | - Yu-Mei Zhou
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China
| | - Lei Tian
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China
| | - Xiao-Gang Zhang
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China
| | - Feng-Lou Liu
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China
| | - Ping Liu
- School of Agriculture, Ningxia University, Yinchuan, Ningxia 750021, China; Key Laboratory of Modern Molecular Breeding for Dominant and Special Crops in Ningxia, Yinchuan, Ningxia 750021, China.
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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: 10] [Impact Index Per Article: 3.3] [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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Differences in the Abundance of Auxin Homeostasis Proteins Suggest Their Central Roles for In Vitro Tissue Differentiation in Coffea arabica. PLANTS 2021; 10:plants10122607. [PMID: 34961078 PMCID: PMC8708889 DOI: 10.3390/plants10122607] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 02/04/2023]
Abstract
Coffea arabica is one of the most important crops worldwide. In vitro culture is an alternative for achieving Coffea regeneration, propagation, conservation, genetic improvement, and genome editing. The aim of this work was to identify proteins involved in auxin homeostasis by isobaric tandem mass tag (TMT) and the synchronous precursor selection (SPS)-based MS3 technology on the Orbitrap Fusion™ Tribrid mass spectrometer™ in three types of biological materials corresponding to C. arabica: plantlet leaves, calli, and suspension cultures. Proteins included in the β-oxidation of indole butyric acid and in the signaling, transport, and conjugation of indole-3-acetic acid were identified, such as the indole butyric response (IBR), the auxin binding protein (ABP), the ATP-binding cassette transporters (ABC), the Gretchen-Hagen 3 proteins (GH3), and the indole-3-acetic-leucine-resistant proteins (ILR). A more significant accumulation of proteins involved in auxin homeostasis was found in the suspension cultures vs. the plantlet, followed by callus vs. plantlet and suspension culture vs. callus, suggesting important roles of these proteins in the cell differentiation process.
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Abreha KB, Alexandersson E, Resjö S, Lankinen Å, Sueldo D, Kaschani F, Kaiser M, van der Hoorn RAL, Levander F, Andreasson E. Leaf Apoplast of Field-Grown Potato Analyzed by Quantitative Proteomics and Activity-Based Protein Profiling. Int J Mol Sci 2021; 22:12033. [PMID: 34769464 PMCID: PMC8584485 DOI: 10.3390/ijms222112033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/01/2021] [Accepted: 11/02/2021] [Indexed: 01/11/2023] Open
Abstract
Multiple biotic and abiotic stresses challenge plants growing in agricultural fields. Most molecular studies have aimed to understand plant responses to challenges under controlled conditions. However, studies on field-grown plants are scarce, limiting application of the findings in agricultural conditions. In this study, we investigated the composition of apoplastic proteomes of potato cultivar Bintje grown under field conditions, i.e., two field sites in June-August across two years and fungicide treated and untreated, using quantitative proteomics, as well as its activity using activity-based protein profiling (ABPP). Samples were clustered and some proteins showed significant intensity and activity differences, based on their field site and sampling time (June-August), indicating differential regulation of certain proteins in response to environmental or developmental factors. Peroxidases, class II chitinases, pectinesterases, and osmotins were among the proteins more abundant later in the growing season (July-August) as compared to early in the season (June). We did not detect significant differences between fungicide Shirlan treated and untreated field samples in two growing seasons. Using ABPP, we showed differential activity of serine hydrolases and β-glycosidases under greenhouse and field conditions and across a growing season. Furthermore, the activity of serine hydrolases and β-glycosidases, including proteins related to biotic stress tolerance, decreased as the season progressed. The generated proteomics data would facilitate further studies aiming at understanding mechanisms of molecular plant physiology in agricultural fields and help applying effective strategies to mitigate biotic and abiotic stresses.
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Affiliation(s)
- Kibrom B. Abreha
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Erik Alexandersson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Svante Resjö
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Åsa Lankinen
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
| | - Daniela Sueldo
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Farnusch Kaschani
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Markus Kaiser
- Chemische Biologie, Zentrum für Medizinische Biotechnologie, Fakultät für Biologie, Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany; (F.K.); (M.K.)
| | - Renier A. L. van der Hoorn
- Plant Chemetics Laboratory, Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK; (D.S.); (R.A.L.v.d.H.)
| | - Fredrik Levander
- Department of Immunotechnology, Lund University, SE-221 00 Lund, Sweden;
- National Bioinformatics Infrastructure Sweden (NBIS), Science for Life Laboratory, Lund University, SE-221 00 Lund, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-234 22 Lomma, Sweden; (E.A.); (S.R.); (Å.L.); (E.A.)
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Tsugawa H, Rai A, Saito K, Nakabayashi R. Metabolomics and complementary techniques to investigate the plant phytochemical cosmos. Nat Prod Rep 2021; 38:1729-1759. [PMID: 34668509 DOI: 10.1039/d1np00014d] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Plants and their associated microbial communities are known to produce millions of metabolites, a majority of which are still not characterized and are speculated to possess novel bioactive properties. In addition to their role in plant physiology, these metabolites are also relevant as existing and next-generation medicine candidates. Elucidation of the plant metabolite diversity is thus valuable for the successful exploitation of natural resources for humankind. Herein, we present a comprehensive review on recent metabolomics approaches to illuminate molecular networks in plants, including chemical isolation and enzymatic production as well as the modern metabolomics approaches such as stable isotope labeling, ultrahigh-resolution mass spectrometry, metabolome imaging (spatial metabolomics), single-cell analysis, cheminformatics, and computational mass spectrometry. Mass spectrometry-based strategies to characterize plant metabolomes through metabolite identification and annotation are described in detail. We also highlight the use of phytochemical genomics to mine genes associated with specialized metabolites' biosynthesis. Understanding the metabolic diversity through biotechnological advances is fundamental to elucidate the functions of the plant-derived specialized metabolome.
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Affiliation(s)
- Hiroshi Tsugawa
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.,Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei, Tokyo 184-8588, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Amit Rai
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Kazuki Saito
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. .,Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
| | - Ryo Nakabayashi
- RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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Iqbal Z, Iqbal MS, Khan MIR, Ansari MI. Toward Integrated Multi-Omics Intervention: Rice Trait Improvement and Stress Management. FRONTIERS IN PLANT SCIENCE 2021; 12:741419. [PMID: 34721467 PMCID: PMC8554098 DOI: 10.3389/fpls.2021.741419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 05/04/2023]
Abstract
Rice (Oryza sativa) is an imperative staple crop for nearly half of the world's population. Challenging environmental conditions encompassing abiotic and biotic stresses negatively impact the quality and yield of rice. To assure food supply for the unprecedented ever-growing world population, the improvement of rice as a crop is of utmost importance. In this era, "omics" techniques have been comprehensively utilized to decipher the regulatory mechanisms and cellular intricacies in rice. Advancements in omics technologies have provided a strong platform for the reliable exploration of genetic resources involved in rice trait development. Omics disciplines like genomics, transcriptomics, proteomics, and metabolomics have significantly contributed toward the achievement of desired improvements in rice under optimal and stressful environments. The present review recapitulates the basic and applied multi-omics technologies in providing new orchestration toward the improvement of rice desirable traits. The article also provides a catalog of current scenario of omics applications in comprehending this imperative crop in relation to yield enhancement and various environmental stresses. Further, the appropriate databases in the field of data science to analyze big data, and retrieve relevant information vis-à-vis rice trait improvement and stress management are described.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
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Voke E, Pinals RL, Goh NS, Landry MP. In Planta Nanosensors: Understanding Biocorona Formation for Functional Design. ACS Sens 2021; 6:2802-2814. [PMID: 34279907 PMCID: PMC10461777 DOI: 10.1021/acssensors.1c01159] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Climate change and population growth are straining agricultural output. To counter these changes and meet the growing demand for food and energy, the monitoring and engineering of crops are becoming increasingly necessary. Nanoparticle-based sensors have emerged in recent years as new tools to advance agricultural practices. As these nanoparticle-based sensors enter and travel through the complex biofluids within plants, biomolecules including proteins, metabolites, lipids, and carbohydrates adsorb onto the nanoparticle surfaces, forming a coating known as the "bio-corona". Understanding these nanoparticle-biomolecule interactions that govern nanosensor function in plants will be essential to successfully develop and translate nanoparticle-based sensors into broader agricultural practice.
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Affiliation(s)
- Elizabeth Voke
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Rebecca L Pinals
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Natalie S Goh
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Innovative Genomics Institute (IGI), Berkeley, California 94720, United States
- California Institute for Quantitative Biosciences, QB3, University of California, Berkeley, California 94720, United States
- Chan-Zuckerberg Biohub, San Francisco, California 94158, United States
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47
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Balasubramanian VK, Purvine SO, Liang Y, Kelly RT, Pasa-Tolic L, Chrisler WB, Blumwald E, Stewart CN, Zhu Y, Ahkami AH. Cell-Type-Specific Proteomics Analysis of a Small Number of Plant Cells by Integrating Laser Capture Microdissection with a Nanodroplet Sample Processing Platform. Curr Protoc 2021; 1:e153. [PMID: 34043287 DOI: 10.1002/cpz1.153] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Plant organs and tissues contain multiple cell types, which are well organized in 3-dimensional structure to efficiently perform physiological functions such as homeostasis and response to environmental perturbation and pathogen infection. It is critically important to perform molecular measurements at the cell-type-specific level to discover mechanisms and unique features of cell populations that govern differentiation and respond to external perturbations. Although mass spectrometry-based proteomics has been demonstrated as an enabling discovery tool for studying plant physiology, conventional approaches require millions of cells to generate robust biological conclusions. Such requirements mask the cell-to-cell heterogeneities and limit the comprehensive profiling of plant proteins at spatially resolved and cell-type-specific resolutions. This article describes a recently developed proteomics workflow for studying a small number of plant cells by integrating laser capture microdissection, microfluidic nanodroplet-based sample preparation, and ultrasensitive liquid chromatography-mass spectrometry. Using poplar as a model tree species, we provide detailed protocols, including plant leaf and root tissue harvest, sample preparation, cryosectioning, laser microdissection, protein digestion, mass spectrometry measurement, and data analysis. We show that the workflow enables the precise identification and quantification of thousands of proteins from hundreds of isolated plant root and leaf cells. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Plant tissue fixation and embedding Support Protocol 1: Preparation of 2.5% CMC solution Support Protocol 2: Slow freezing of CMC blocks to avoid crack development in the block Basic Protocol 2: Preparation of cryosections Alternate Protocol: Using a vacuum manifold to dehydrate the cryosection slides (primarily for root tissues) Basic Protocol 3: Laser capture microdissection of specific types of plant cells Basic Protocol 4: Nanodroplet-based sample preparation for ultrasensitive proteomic analysis Support Protocol 3: Fabrication of nanowell chips Basic Protocol 5: Liquid chromatography and mass spectrometry.
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Affiliation(s)
- Vimal K Balasubramanian
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Samuel O Purvine
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Yiran Liang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ryan T Kelly
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - William B Chrisler
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Eduardo Blumwald
- Department of Plant Sciences, University of California, Davis, California
| | - C Neal Stewart
- Department of Plant Sciences, Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, Tennessee
| | - Ying Zhu
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
| | - Amir H Ahkami
- Environmental Molecular Sciences Laboratory (EMSL), Pacific Northwest National Laboratory (PNNL), Richland, Washington
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Jocković M, Jocić S, Cvejić S, Marjanović-Jeromela A, Jocković J, Radanović A, Miladinović D. Genetic Improvement in Sunflower Breeding—Integrated Omics Approach. PLANTS 2021; 10:plants10061150. [PMID: 34200113 PMCID: PMC8228292 DOI: 10.3390/plants10061150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/31/2021] [Accepted: 06/01/2021] [Indexed: 01/23/2023]
Abstract
Foresight in climate change and the challenges ahead requires a systematic approach to sunflower breeding that will encompass all available technologies. There is a great scarcity of desirable genetic variation, which is in fact undiscovered because it has not been sufficiently researched as detection and designing favorable genetic variation largely depends on thorough genome sequencing through broad and deep resequencing. Basic exploration of genomes is insufficient to find insight about important physiological and molecular mechanisms unique to crops. That is why integrating information from genomics, epigenomics, transcriptomics, proteomics, metabolomics and phenomics enables a comprehensive understanding of the molecular mechanisms in the background of architecture of many important quantitative traits. Omics technologies offer novel possibilities for deciphering the complex pathways and molecular profiling through the level of systems biology and can provide important answers that can be utilized for more efficient breeding of sunflower. In this review, we present omics profiling approaches in order to address their possibilities and usefulness as a potential breeding tools in sunflower genetic improvement.
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Affiliation(s)
- Milan Jocković
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
- Correspondence:
| | - Siniša Jocić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Sandra Cvejić
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Ana Marjanović-Jeromela
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Jelena Jocković
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Dositeja Obradovića 3, 21000 Novi Sad, Serbia;
| | - Aleksandra Radanović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia; (S.J.); (S.C.); (A.M.-J.); (A.R.); (D.M.)
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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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50
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Jorrin Novo JV. Proteomics and plant biology: contributions to date and a look towards the next decade. Expert Rev Proteomics 2021; 18:93-103. [PMID: 33770454 DOI: 10.1080/14789450.2021.1910028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
INTRODUCTION This review presents the view of the author, that is opinionable and even speculative, on the field of proteomics, its application to plant biology knowledge, and translation to biotechnology. Written in a more academic than scientific style, it is based on past original and review articles by the author´s group, and those published by leading scientists in the last two years. AREAS COVERED Starting with a general definition and references to historical milestones, it covers sections devoted to the different platforms employed, the plant biology discourse in the protein language, challenges and future prospects, ending with the author opinion. EXPERT OPINION In 25 years, five proteomics platform generations have appeared. We are now moving from proteomics to Systems Biology. While feasible with model organisms, proteomics of orphan species remains challenging. Proteomics, even in its simplest approach, sheds light on plant biological processes, central dogma, and molecular bases of phenotypes of interest, and it can be translated to areas such as food traceability and allergen detection. Proteomics should be validated and optimized to each experimental system, objectives, and hypothesis. It has limitations, artifacts, and biases. We should not blindly accept proteomics data and just create a list of proteins, networks, and avoid speculative biological interpretations. From the hundred to thousand proteins identified and quantified, it is important to obtain a focus and validate some of them, otherwise it is merely. We are starting to have the protein pieces, so let, from now, build the proteomics and biological puzzle.
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Affiliation(s)
- J V Jorrin Novo
- Dpt. Biochemistry and Molecular Biology, Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, ETSIAM, University of Cordoba, Cordoba , Spain
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