1
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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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Chen H, Sahu SK, Wang S, Liu J, Yang J, Cheng L, Chiu TY, Liu H. Chromosome-level Alstonia scholaris genome unveils evolutionary insights into biosynthesis of monoterpenoid indole alkaloids. iScience 2024; 27:109599. [PMID: 38646178 PMCID: PMC11033161 DOI: 10.1016/j.isci.2024.109599] [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: 11/17/2023] [Revised: 01/25/2024] [Accepted: 03/25/2024] [Indexed: 04/23/2024] Open
Abstract
Alstonia scholaris of the Apocynaceae family is a medicinal plant with a rich source of bioactive monoterpenoid indole alkaloids (MIAs), which possess anti-cancer activity like vinca alkaloids. To gain genomic insights into MIA biosynthesis, we assembled a high-quality chromosome-level genome for A. scholaris using nanopore and Hi-C data. The 444.95 Mb genome contained 35,488 protein-coding genes. A total of 20 chromosomes were assembled with a scaffold N50 of 21.75 Mb. The genome contained a cluster of strictosidine synthases and tryptophan decarboxylases with synteny to other species and a saccharide-terpene cluster involved in the monoterpenoid biosynthesis pathway of the MIA upstream pathway. The multi-omics data of A. scholaris provide a valuable resource for understanding the evolutionary origins of MIAs and for discovering biosynthetic pathways and synthetic biology efforts for producing pharmaceutically useful alkaloids.
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Affiliation(s)
- Haixia Chen
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Sunil Kumar Sahu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Shujie Wang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Jia Liu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Jinlong Yang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Le Cheng
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Tsan-Yu Chiu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
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Tartaglia M. Extraction of Proteins from Green Tissues of Plants and Phyllosphere. Methods Mol Biol 2024; 2820:41-47. [PMID: 38941013 DOI: 10.1007/978-1-0716-3910-8_5] [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: 06/29/2024]
Abstract
The proteomic approach plays a key role to characterize a biological system at any given time. In recent years, advances in proteomics have led to an increasing application in all biological fields, including plant matrices and associated microbiome studies. However, extracting adequate protein samples remains the most critical step for any plant proteomics study. The protein extraction protocols proposed for the phyllosphere involve an initial leaf washing step; however, this is an approach only applicable if interest is restricted to epiphytes. A metaproteomic approach is required to obtain an overall picture and consequently an extraction that considers proteins derived from the plant, epiphytic and endophytic microorganisms. The most commonly used extractions for plant tissue involve the use of phenol or TCA-acetone. However, for efficient protein recovery is essential to remove interfering components abundant in plant tissues, such as polysaccharides, lipids, and phenolic compounds. A well-proven protocol on the basis of a combination of TCA-acetone and phenol extraction is presented here, obtaining some cleaned protein pellets, suitable for electrophoresis and subsequent proteomics studies. Important points for the success of this protocol are (i) a proper sampling and sample preparation, (ii) maintaining samples at a low temperature during extraction and using protease inhibitors, (iii) an initial step in TCA-acetone to remove part of the interfering substances, and (iv) careful recovery of the phenolic phase. Furthermore, the protocol is timesaving and can be completed in one working day.
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Affiliation(s)
- Maria Tartaglia
- University of Sannio, Department of Science and Technology, Benevento, Italy.
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Niu L, Li C, Wang W, Zhang J, Scali M, Li W, Liu H, Tai F, Hu X, Wu X. Cadmium tolerance and hyperaccumulation in plants - A proteomic perspective of phytoremediation. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 256:114882. [PMID: 37037105 DOI: 10.1016/j.ecoenv.2023.114882] [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: 11/21/2022] [Revised: 02/27/2023] [Accepted: 04/04/2023] [Indexed: 06/19/2023]
Abstract
Cadmium (Cd) is a major environmental pollutant and poses a risk of transfer into the food chain through contaminated plants. Mechanisms underlying Cd tolerance and hyperaccumulation in plants are not fully understood. Proteomics-based approaches facilitate an in-depth understanding of plant responses to Cd stress at the systemic level by identifying Cd-inducible differentially abundant proteins (DAPs). In this review, we summarize studies related to proteomic changes associated with Cd-tolerance mechanisms in Cd-tolerant crops and Cd-hyperaccumulating plants, especially the similarities and differences across plant species. The enhanced DAPs identified through proteomic studies can be potential targets for developing Cd-hyperaccumulators to remediate Cd-contaminated environments and Cd-tolerant crops with low Cd content in the edible organs. This is of great significance for ensuring the food security of an exponentially growing global population. Finally, we discuss the methodological drawbacks in current proteomic studies and propose that better protocols and advanced techniques should be utilized to further strengthen the reliability and applicability of future Cd-stress-related studies in plants. This review provides insights into the improvement of phytoremediation efficiency and an in-depth study of the molecular mechanisms of Cd enrichment in plants.
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Affiliation(s)
- Liangjie Niu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Chunyang Li
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China.
| | - Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Monica Scali
- Department of Life Sciences, University of Siena, Siena, Italy
| | - Weiqiang Li
- Jilin Da'an Agro-ecosystem National Observation Research Station, Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Hui Liu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Fuju Tai
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xiuli Hu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Xiaolin Wu
- National Key Laboratory of Wheat and Maize Crop Science, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
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Noone J, Wallace RG, Rochfort KD. Immunoprecipitation: Variations, Considerations, and Applications. Methods Mol Biol 2023; 2699:271-303. [PMID: 37647004 DOI: 10.1007/978-1-0716-3362-5_15] [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: 09/01/2023]
Abstract
Immunoprecipitation (IP) refers to methods of affinity chromatography that enrich and/or purify a specific protein from a complex mixture using a specific antibody immobilized on a solid support. Several operations and processes that are dependent on the isolation, concentration, and modification of proteins have seen improvement in their selectivity and separation based on the integration of IP-specific reactions into their workflows. This relatively simple principle has contributed significantly to our understanding of proteins and their behaviors and has become increasingly fundamental to most protein characterization studies today. In this chapter, we review the basic principles of IP and the several factors that influence each stage, and subsequently the success, of an IP experiment. Moreover, variations in application of the IP principle are discussed, and the adaptability of the techniques based on such is highlighted in the provision of two IP workflows to purify a particular protein from an entire cellular proteosome. These workflows cover the preparation and fractionation of crude cellular lysate into individual subcellular fractions, through to both "batch" and "column"-based extractions of the target protein of interest. Protocols for determining the validity of the workflows, and the presence/abundance of the protein of interest, are also briefly described.
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Affiliation(s)
- John Noone
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
- AdventHealth, Translational Research Institute, Orlando, Florida, United States of America
| | - Robert G Wallace
- School of Biotechnology, Dublin City University, Glasnevin, Dublin, Ireland
| | - Keith D Rochfort
- School of Nursing, Psychotherapy, and Community Health, Dublin City University, Glasnevin, Dublin, Ireland.
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6
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Protein extraction from microalgae residue and nutritional assessment. Bioprocess Biosyst Eng 2022; 45:1879-1888. [DOI: 10.1007/s00449-022-02794-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 09/27/2022] [Indexed: 11/02/2022]
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7
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He M, Wang J, Herold S, Xi L, Schulze WX. A Rapid and Universal Workflow for Label-Free-Quantitation-Based Proteomic and Phosphoproteomic Studies in Cereals. Curr Protoc 2022; 2:e425. [PMID: 35674286 DOI: 10.1002/cpz1.425] [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: 06/15/2023]
Abstract
Proteomics and phosphoproteomics are robust tools to analyze dynamics of post-transcriptional processes during growth and development. A variety of experimental methods and workflows have been published, but most of them were developed for model plants and have not been adapted to high-throughput platforms. Here, we describe an experimental workflow for proteome and phosphoproteome studies tailored to cereal crop tissues. The workflow consists of two parallel parts that are suitable for analyzing protein/phosphoprotein from total proteins and the microsomal membrane fraction. We present phosphoproteomic data regarding quantification coverage and analytical reproducibility for example preparations from maize root and shoot, wheat leaf, and a microsomal protein preparation from maize leaf. To enable users to adjust for tissue specific requirements, we provide two different methods of protein clean-up: traditional ethanol precipitation (PC) and a recently developed technology termed single-pot, solid-phase-enhanced sample preparation (SP3). Both the PC and SP3 methods are effective in the removal of unwanted substances in total protein crude extracts. In addition, two different methods of phosphopeptide enrichment are presented: a TiO2 -based method and Fe(III)-NTA cartridges on a robotized platform. Although the overall number of phosphopeptides is stable across protein clean-up and phosphopeptide enrichment methods, there are differences in the preferred phosphopeptides in each enrichment method. The preferred protocol depends on laboratory capabilities and research objective. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Total protein crude extraction Basic Protocol 2: Total protein clean-up with ethanol precipitation Alternate Protocol 1: Total protein clean-up with SP3 method Basic Protocol 3: Microsomal fraction protein extraction Basic Protocol 4: Protein concentration determination by Bradford assay Basic Protocol 5: In-solution digestion with trypsin Basic Protocol 6: Phosphopeptide enrichment with TiO2 Alternate Protocol 2: Phosphopeptide enrichment with Fe(III)-NTA cartridges Basic Protocol 7: Peptide desalting with C18 material Basic Protocol 8: LC-MS/MS analysis of (phospho)peptides and spectrum matching.
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Affiliation(s)
- Mingjie He
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Jiahui Wang
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Sandra Herold
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Lin Xi
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Waltraud X Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
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8
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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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Balotf S, Wilson R, Tegg RS, Nichols DS, Wilson CR. Shotgun Proteomics as a Powerful Tool for the Study of the Proteomes of Plants, Their Pathogens, and Plant-Pathogen Interactions. Proteomes 2022; 10:5. [PMID: 35225985 PMCID: PMC8883913 DOI: 10.3390/proteomes10010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/31/2022] Open
Abstract
The interaction between plants and pathogenic microorganisms is a multifaceted process mediated by both plant- and pathogen-derived molecules, including proteins, metabolites, and lipids. Large-scale proteome analysis can quantify the dynamics of proteins, biological pathways, and posttranslational modifications (PTMs) involved in the plant-pathogen interaction. Mass spectrometry (MS)-based proteomics has become the preferred method for characterizing proteins at the proteome and sub-proteome (e.g., the phosphoproteome) levels. MS-based proteomics can reveal changes in the quantitative state of a proteome and provide a foundation for understanding the mechanisms involved in plant-pathogen interactions. This review is intended as a primer for biologists that may be unfamiliar with the diverse range of methodology for MS-based shotgun proteomics, with a focus on techniques that have been used to investigate plant-pathogen interactions. We provide a summary of the essential steps required for shotgun proteomic studies of plants, pathogens and plant-pathogen interactions, including methods for protein digestion, identification, separation, and quantification. Finally, we discuss how protein PTMs may directly participate in the interaction between a pathogen and its host plant.
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Affiliation(s)
- Sadegh Balotf
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Robert S. Tegg
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
| | - David S. Nichols
- Central Science Laboratory, University of Tasmania, Hobart, TAS 7001, Australia;
| | - Calum R. Wilson
- New Town Research Laboratories, Tasmanian Institute of Agriculture, University of Tasmania, New Town, TAS 7008, Australia; (S.B.); (R.S.T.)
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10
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Bojórquez-Velázquez E, Elizalde-Contreras JM, Zamora-Briseño JA, Ruiz-May E. Efficient Protein Extraction Protocols for NanoLC-MS/MS Proteomics Analysis of Plant Tissues with High Proteolytic Activity: A Case Study with Pineapple Pulp. Methods Mol Biol 2022; 2512:281-290. [PMID: 35818012 DOI: 10.1007/978-1-0716-2429-6_17] [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: 06/15/2023]
Abstract
Proteomics is an essential tool to uncover the regulatory processes of fruit biology. In fruits with high proteolytic activity, the inhibition of endogenous proteases is key for successful protein extraction. In this chapter, we describe an efficient protocol for total protein extraction to deal with this inconvenience using pineapple pulp as an example. We corroborated the efficacy of our protein extraction protocols by carrying out nano LC-MS/MS analyses using a highly sensitive hybrid mass spectrometer. In doing so, we were able to identify over 3000 proteins in pineapple pulp. Our contribution paves the way for massive comparative proteomics scrutiny in pineapple fruits, as well as others plant tissues with high protease activity such as papaya, fig, and kiwi fruits.
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Affiliation(s)
- Esaú Bojórquez-Velázquez
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, Mexico
| | - José M Elizalde-Contreras
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, Mexico
| | - Jesús Alejandro Zamora-Briseño
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, Mexico.
| | - Eliel Ruiz-May
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico BioMimic®, Instituto de Ecología A.C. (INECOL), Xalapa, Veracruz, Mexico.
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11
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Arae T, Nakakoji M, Noguchi M, Kamon E, Sano R, Demura T, Ohtani M. Plant secondary cell wall proteome analysis with an inducible system for xylem vessel cell differentiation. Dev Growth Differ 2021; 64:5-15. [PMID: 34918343 DOI: 10.1111/dgd.12767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 11/29/2021] [Accepted: 12/08/2021] [Indexed: 11/29/2022]
Abstract
Plant cell walls are typically composed of polysaccharide polymers and cell wall proteins (CWPs). CWPs account for approximately 10% of the plant cell wall structure and perform a wide range of functions. Previous studies have identified approximately 1000 CWPs in the model plant Arabidopsis thaliana; however, the analyses mainly targeted primary cell walls, which are generated at cell division. In contrast, little is known about CWPs in secondary cell walls (SCWs), which are rigid and contain the phenolic polymer lignin. Here, we performed a cell wall proteome analysis to obtain novel insights into CWPs in SCWs. To this end, we tested multiple methods for cell wall extraction with cultured Arabidopsis cells carrying the VND7-VP16-GR system, with which cells can be transdifferentiated into xylem-vessel-like cells with lignified SCWs by dexamethasone treatment. We then subjected the protein samples to in-gel trypsin digestion followed by LC-MS/MS analysis. The different extraction methods resulted in the detection of different cell wall fraction proteins (CWFPs). In particular, centrifugation conditions had a strong impact on the extracted CWFP species, resulting in the increased number of identified CWFPs. We successfully identified 896 proteins as CWFPs in total, including proteases, expansins, purple phosphatase, well-known lignin-related enzymes (laccase and peroxidase), and 683 of 896 proteins were newly identified CWFPs. These results demonstrate the usefulness of our CWP analysis method. Further analyses of SCW-related CWPs could be expected to produce information useful for understanding the roles of CWPs in plant cell functions.
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Affiliation(s)
- Toshihiro Arae
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Mai Nakakoji
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Masahiro Noguchi
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Eri Kamon
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan.,RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
| | - Misato Ohtani
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.,Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan.,RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
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12
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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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13
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Venegas-Molina J, Molina-Hidalgo FJ, Clicque E, Goossens A. Why and How to Dig into Plant Metabolite-Protein Interactions. TRENDS IN PLANT SCIENCE 2021; 26:472-483. [PMID: 33478816 DOI: 10.1016/j.tplants.2020.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Interaction between metabolites and proteins drives cellular regulatory processes within and between organisms. Recent reports highlight that numerous plant metabolites embrace multiple biological activities, beyond a sole role as substrates, products, or cofactors of enzymes, or as defense or growth-regulatory compounds. Though several technologies have been developed to identify and characterize metabolite-protein interactions, the systematic implementation of such methods in the plant field remains limited. Here, we discuss the plant metabolic space, with a specific focus on specialized metabolites and their roles, and review the technologies to study their interaction with proteins. We approach it both from a plant's perspective, to increase our understanding of plant metabolite-dependent regulatory networks, and from a human perspective, to empower agrochemical and drug discoveries.
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Affiliation(s)
- Jhon Venegas-Molina
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Francisco J Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elke Clicque
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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14
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Mikulášek K, Konečná H, Potěšil D, Holánková R, Havliš J, Zdráhal Z. SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS. FRONTIERS IN PLANT SCIENCE 2021; 12:635550. [PMID: 33777071 PMCID: PMC7988192 DOI: 10.3389/fpls.2021.635550] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.
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Affiliation(s)
- Kamil Mikulášek
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Hana Konečná
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - David Potěšil
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Renata Holánková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Havliš
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
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15
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Kaushal P, Lee C. N-terminomics - its past and recent advancements. J Proteomics 2020; 233:104089. [PMID: 33359939 DOI: 10.1016/j.jprot.2020.104089] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 07/22/2020] [Accepted: 12/20/2020] [Indexed: 02/06/2023]
Abstract
N-terminomics is a rapidly evolving branch of proteomics that encompasses the study of protein N-terminal sequence. A proteome-wide collection of such sequences has been widely used to understand the proteolytic cascades and in annotating the genome. Over the last two decades, various N-terminomic strategies have been developed for achieving high sensitivity, greater depth of coverage, and high-throughputness. We, in this review, cover how the field of N-terminomics has evolved to date, including discussion on various sample preparation and N-terminal peptide enrichment strategies. We also compare different N-terminomic methods and highlight their relative benefits and shortcomings in their implementation. In addition, an overview of the currently available bioinformatics tools and data analysis pipelines for the annotation of N-terminomic datasets is also included. SIGNIFICANCE: It has been recognized that proteins undergo several post-translational modifications (PTM), and a number of perturbed biological pathways are directly associated with modifications at the terminal sites of a protein. In this regard, N-terminomics can be applied to generate a proteome-wide landscape of mature N-terminal sequences, annotate their source of generation, and recognize their significance in the biological pathways. Besides, a system-wide study can be used to study complicated proteolytic machinery and protease cleavage patterns for potential therapeutic targets. Moreover, due to unprecedented improvements in the analytical methods and mass spectrometry instrumentation in recent times, the N-terminomic methodologies now offers an unparalleled ability to study proteoforms and their implications in clinical conditions. Such approaches can further be applied for the detection of low abundant proteoforms, annotation of non-canonical protein coding sites, identification of candidate disease biomarkers, and, last but not least, the discovery of novel drug targets.
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Affiliation(s)
- Prashant Kaushal
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea; Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea; KHU-KIST Department of Converging Science and Technology, Kyung Hee University, 26 Kyunghee-daero, Dongdaemun-gu, Seoul 02447, Republic of Korea.
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16
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Yilmaz-Turan S, Jiménez-Quero A, Moriana R, Arte E, Katina K, Vilaplana F. Cascade extraction of proteins and feruloylated arabinoxylans from wheat bran. Food Chem 2020; 333:127491. [PMID: 32659672 DOI: 10.1016/j.foodchem.2020.127491] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/28/2020] [Accepted: 07/02/2020] [Indexed: 12/18/2022]
Abstract
A cascade process for the sequential recovery of proteins and feruloylated arabinoxylan from wheat bran is proposed, involving a protein isolation step, enzymatic destarching and subcritical water extraction. The protein isolation step combining lactic acid fermentation and cold alkaline extraction reduced the recalcitrance of wheat bran, thus improving the total yields of the subsequent subcritical water extraction. The time evolution of subcritical water extraction of feruloylated arabinoxylan was compared at two temperatures (160 °C and 180 °C). Longer residence times enhanced the purity of target feruloylated arabinoxylans, whereas higher temperatures resulted in faster extraction at the expense of significant molar mass reduction. The radical scavenging activity of the extracted feruloylated arabinoxylans was preserved after the initial protein isolation step. This study opens new possibilities for the cascade valorization of wheat bran into enriched protein and non-starch polysaccharide fractions, which show potential to be used as functional food ingredients.
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Affiliation(s)
- Secil Yilmaz-Turan
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Amparo Jiménez-Quero
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Rosana Moriana
- Division of Polymeric Materials, Department of Fibre and Polymer Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Molecular Sciences, SLU-Swedish University of Agricultural Sciences, Almas Allé 5, Uppsala, Sweden
| | - Elisa Arte
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI-00014, Finland
| | - Kati Katina
- Department of Food and Nutrition, University of Helsinki, P.O. Box 66, FI-00014, Finland
| | - Francisco Vilaplana
- Division of Glycoscience, Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.
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17
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Li Y, Fang F, Sun M, Zhao Q, Hu Y, Sui Z, Liang Z, Zhang L, Zhang Y. Ionic liquid-assisted protein extraction method for plant phosphoproteome analysis. Talanta 2020; 213:120848. [PMID: 32200934 DOI: 10.1016/j.talanta.2020.120848] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/11/2020] [Accepted: 02/13/2020] [Indexed: 11/21/2022]
Abstract
Protein phosphorylation is one of the most important post-translational modifications (PTM) and plays critical roles in maintaining many biological processes of plant species, such as being a significant signal related to resistance to tobacco mosaic virus (TMV) infection in tobacco. Compared to other organisms, in-depth profiling of plant phosphoproteome remains challenging due to the harsh extraction environment of plant proteins and low abundance of plant phosphorylation, generally requiring large amount of plant materials. Herein, we developed an integrated strategy for efficient sample preparation of amounts of plant tissues, by integrating ionic liquid (IL)-assisted protein extraction, in-solution digestion, precipitation-assisted IL removal, as well as immobilized metal ion affinity chromatography (IMAC) enrichment of phosphopeptides together. In this strategy, to improve the efficiency of protein extraction and enzymatic digestion, IL of 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) was used as the solubilizer due to its excellent solubilizing ability and enzyme compatibility demonstrated in our previous work. Briefly, the extraction capability of C12Im-Cl for protein amount from tobacco leaves was improved 1.9-fold compared to the commonly used urea-assisted method. Notably, to avoid its interference with subsequent LC-MS analysis, the IL was easily removed from the peptide solution by our proposed ion substitution-mediated C12Im + precipitation strategy with high efficiency. By handling 10 mg of starting protein materials of tobacco leaves, 14,441 unique phosphopeptides, assigned to 5153 unique phosphoproteins were confidently identified. To the best of our knowledge, this was the most comprehensive phosphorylation dataset for tobacco so far. All the results demonstrated our strategy was of great potential to promote the large-scale analysis of plant phosphoproteome.
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Affiliation(s)
- Yang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Fei Fang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; Department of Pharmacology and Chemical Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Mingwei Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China; Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, Guangdong, 510005, China
| | - Qun Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Yechen Hu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China.
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R. & A. Center, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, 116023, China
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18
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Niu L, Ding H, Zhang J, Wang W. Proteomic Analysis of Starch Biosynthesis in Maize Seeds. STARCH-STARKE 2019. [DOI: 10.1002/star.201800294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Huiying Ding
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Jinghua Zhang
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
| | - Wei Wang
- State Key Laboratory of Wheat & Maize Crop ScienceCollege of Life SciencesHenan Agricultural UniversityZhengzhouP. R. China
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19
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San Segundo-Acosta P, Oeo-Santos C, Benedé S, de Los Ríos V, Navas A, Ruiz-Leon B, Moreno C, Pastor-Vargas C, Jurado A, Villalba M, Barderas R. Delineation of the Olive Pollen Proteome and Its Allergenome Unmasks Cyclophilin as a Relevant Cross-Reactive Allergen. J Proteome Res 2019; 18:3052-3066. [PMID: 31192604 DOI: 10.1021/acs.jproteome.9b00167] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Olive pollen is a major allergenic source worldwide due to its extensive cultivation. We have combined available genomics data with a comprehensive proteomics approach to get the annotated olive tree (Olea europaea L.) pollen proteome and define its complex allergenome. A total of 1907 proteins were identified by LC-MS/MS using predicted protein sequences from its genome. Most proteins (60%) were predicted to possess catalytic activity and be involved in metabolic processes. In total, 203 proteins belonging to 47 allergen families were found in olive pollen. A peptidyl-prolyl cis-trans isomerase, cyclophilin, produced in Escherichia coli, was found as a new olive pollen allergen (Ole e 15). Most Ole e 15-sensitized patients were children (63%) and showed strong IgE recognition to the allergen. Ole e 15 shared high sequence identity with other plant, animal, and fungal cyclophilins and presented high IgE cross-reactivity with pollen, plant food, and animal extracts.
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Affiliation(s)
- Pablo San Segundo-Acosta
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain
| | - Carmen Oeo-Santos
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain
| | - Sara Benedé
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain
| | | | - Ana Navas
- Hospital Universitario Reina Sofía de Córdoba , E-14004 Córdoba , Spain
| | - Berta Ruiz-Leon
- Hospital Universitario Reina Sofía de Córdoba , E-14004 Córdoba , Spain
| | - Carmen Moreno
- Hospital Universitario Reina Sofía de Córdoba , E-14004 Córdoba , Spain
| | - Carlos Pastor-Vargas
- Department of Immunology , Instituto de Investigación Sanitaria Hospital Universitario Fundación Jiménez Díaz (IIS-FJD, UAM) , E-28040 Madrid , Spain
| | - Aurora Jurado
- Hospital Universitario Reina Sofía de Córdoba , E-14004 Córdoba , Spain
| | - Mayte Villalba
- Departamento de Bioquímica y Biología Molecular, Facultad de Ciencias Químicas , Universidad Complutense de Madrid , E-28040 Madrid , Spain
| | - Rodrigo Barderas
- Chronic Disease Programme (UFIEC) , Instituto de Salud Carlos III , Majadahonda, E-28220 Madrid , Spain
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20
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Al-Mohanna T, Ahsan N, Bokros NT, Dimlioglu G, Reddy KR, Shankle M, Popescu GV, Popescu SC. Proteomics and Proteogenomics Analysis of Sweetpotato (Ipomoea batatas) Leaf and Root. J Proteome Res 2019; 18:2719-2734. [DOI: 10.1021/acs.jproteome.8b00943] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Thualfeqar Al-Mohanna
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Nagib Ahsan
- COBRE Center for Cancer Research Development, Proteomics Core Facility, Rhode Island, USA Hospital, Providence, Rhode Island 02903, United States
- Division of Biology and Medicine, Brown University, Providence, Rhode Island 02903, United States
| | - Norbert T. Bokros
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Gizem Dimlioglu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Kambham R. Reddy
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, Mississippi 39759, United States
| | - Mark Shankle
- Pontotoc Experimental Station, Mississippi State University, Pontotoc, Mississippi 38863, United States
| | - George V. Popescu
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, Mississippi 39759, United States
- The National Institute for Laser, Plasma and Radiation Physics, Bucharest RO-077125, Romania
| | - Sorina C. Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, Mississippi 39759, United States
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21
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Rodziewicz P, Chmielewska K, Sawikowska A, Marczak Ł, Łuczak M, Bednarek P, Mikołajczak K, Ogrodowicz P, Kuczyńska A, Krajewski P, Stobiecki M. Identification of drought responsive proteins and related proteomic QTLs in barley. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2823-2837. [PMID: 30816960 PMCID: PMC6506773 DOI: 10.1093/jxb/erz075] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Accepted: 02/11/2019] [Indexed: 05/08/2023]
Abstract
Drought is a major abiotic stress that negatively influences crop yield. Breeding strategies for improved drought resistance require an improved knowledge of plant drought responses. We therefore applied drought to barley recombinant inbred lines and their parental genotypes shortly before tillering. A large-scale proteomic analysis of leaf and root tissue revealed proteins that respond to drought in a genotype-specific manner. Of these, Rubisco activase in chloroplast, luminal binding protein in endoplasmic reticulum, phosphoglycerate mutase, glutathione S-transferase, heat shock proteins and enzymes involved in phenylpropanoid biosynthesis showed strong genotype×environment interactions. These data were subjected to genetic linkage analysis and the identification of proteomic QTLs that have potential value in marker-assisted breeding programs.
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Affiliation(s)
- Paweł Rodziewicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznań, Poland
| | - Klaudia Chmielewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznań, Poland
| | - Aneta Sawikowska
- Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, Poznań, Poland
| | - Łukasz Marczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznań, Poland
| | - Magdalena Łuczak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznań, Poland
| | - Paweł Bednarek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznań, Poland
| | - Krzysztof Mikołajczak
- Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Piotr Ogrodowicz
- Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Anetta Kuczyńska
- Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
| | - Paweł Krajewski
- Institute of Plant Genetics Polish Academy of Sciences, Strzeszyńska 34, 60–479 Poznań, Poland
- Correspondence: or
| | - Maciej Stobiecki
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznań, Poland
- Correspondence: or
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22
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Optimisation of protein extraction for in-depth profiling of the cereal grain proteome. J Proteomics 2019; 197:23-33. [DOI: 10.1016/j.jprot.2019.02.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 02/01/2019] [Accepted: 02/11/2019] [Indexed: 12/20/2022]
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23
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Freitas AC, Gomes AM. Analytical approaches for proteomics and lipidomics of arsenic in algae. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/bs.coac.2019.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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24
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Niu L, Zhang H, Wu Z, Wang Y, Liu H, Wu X, Wang W. Modified TCA/acetone precipitation of plant proteins for proteomic analysis. PLoS One 2018; 13:e0202238. [PMID: 30557402 PMCID: PMC6296544 DOI: 10.1371/journal.pone.0202238] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/29/2018] [Indexed: 01/01/2023] Open
Abstract
Protein extracts obtained from cells or tissues often require removal of interfering substances for the preparation of high-quality protein samples in proteomic analysis. A number of protein extraction methods have been applied to various biological samples. TCA/acetone precipitation and phenol extraction, a common method of protein extraction, is thought to minimize protein degradation and activity of proteases as well as reduce contaminants like salts and polyphenols. However, the TCA/acetone precipitation method relies on the complete pulverization and repeated rinsing of tissue powder to remove the interfering substances, which is laborious and time-consuming. In addition, by prolonged incubation in TCA/acetone, the precipitated proteins are more difficult to re-dissolve. We have described a modified method of TCA/acetone precipitation of plant proteins for proteomic analysis. Proteins of cells or tissues were extracted using SDS-containing buffer, precipitated with equal volume of 20% TCA/acetone, and washed with acetone. Compared to classical TCA/acetone precipitation and simple acetone precipitation, this protocol generates comparable yields, spot numbers, and proteome profiling, but takes less time (ca. 45 min), thus avoiding excess protein modification and degradation after extended-period incubation in TCA/acetone or acetone. The modified TCA/acetone precipitation method is simple, fast, and suitable for proteomic analysis of various plant tissues in proteomic analysis.
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Affiliation(s)
- Liangjie Niu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hang Zhang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Zhaokun Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yibo Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Hui Liu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- * E-mail: (WW); (HL)
| | - Xiaolin Wu
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
| | - Wei Wang
- State Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Life Sciences, Henan Agricultural University, Zhengzhou, China
- * E-mail: (WW); (HL)
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25
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Aguilar-Hernández V, Loyola-Vargas VM. Advanced Proteomic Approaches to Elucidate Somatic Embryogenesis. FRONTIERS IN PLANT SCIENCE 2018; 9:1658. [PMID: 30524454 PMCID: PMC6262180 DOI: 10.3389/fpls.2018.01658] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 10/25/2018] [Indexed: 05/06/2023]
Abstract
Somatic embryogenesis (SE) is a cell differentiation process by which a somatic cell changes its genetic program and develops into an embryonic cell. Investigating this process with various explant sources in vitro has allowed us to trace somatic embryo development from germination to plantlets and has led to the generation of new technologies, including genetic transformation, endangered species conservation, and synthetic seed production. A transcriptome data comparison from different stages of the developing somatic embryo has revealed a complex network controlling the somatic cell's fate, suggesting that an interconnected network acts at the protein level. Here, we discuss the current progress on SE using proteomic-based data, focusing on changing patterns of proteins during the establishment of the somatic embryo. Despite the advanced proteomic approaches available so far, deciphering how the somatic embryo is induced is still in its infancy. The new proteomics techniques that lead to the quantification of proteins with different abundances during the induction of SE are opening this area of study for the first time. These quantitative differences can elucidate the different pathways involved in SE induction. We envisage that the application of these proteomic technologies can be pivotal to identifying proteins critical to the process of SE, demonstrating the cellular localization, posttranslational modifications, and turnover protein events required to switch from a somatic cell to a somatic embryo cell and providing new insights into the molecular mechanisms underlying SE. This work will help to develop biotechnological strategies for mass production of quality crop material.
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Affiliation(s)
- Victor Aguilar-Hernández
- Catedrático CONACYT, Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
- *Correspondence: Victor Aguilar-Hernández, orcid.org/0000-0001-8239-4047
| | - Víctor M. Loyola-Vargas
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán, Mérida, Mexico
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