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Gomaa AE, El Mounadi K, Parperides E, Garcia-Ruiz H. Cell Fractionation and the Identification of Host Proteins Involved in Plant-Virus Interactions. Pathogens 2024; 13:53. [PMID: 38251360 PMCID: PMC10819628 DOI: 10.3390/pathogens13010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024] Open
Abstract
Plant viruses depend on host cellular factors for their replication and movement. There are cellular proteins that change their localization and/or expression and have a proviral role or antiviral activity and interact with or target viral proteins. Identification of those proteins and their roles during infection is crucial for understanding plant-virus interactions and to design antiviral resistance in crops. Important host proteins have been identified using approaches such as tag-dependent immunoprecipitation or yeast two hybridization that require cloning individual proteins or the entire virus. However, the number of possible interactions between host and viral proteins is immense. Therefore, an alternative method is needed for proteome-wide identification of host proteins involved in host-virus interactions. Here, we present cell fractionation coupled with mass spectrometry as an option to identify protein-protein interactions between viruses and their hosts. This approach involves separating subcellular organelles using differential and/or gradient centrifugation from virus-free and virus-infected cells (1) followed by comparative analysis of the proteomic profiles obtained for each subcellular organelle via mass spectrometry (2). After biological validation, prospect host proteins with proviral or antiviral roles can be subject to fundamental studies in the context of basic biology to shed light on both virus replication and cellular processes. They can also be targeted via gene editing to develop virus-resistant crops.
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Affiliation(s)
- Amany E. Gomaa
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
- Department of Botany, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Kaoutar El Mounadi
- Department of Biology, Kutztown University of Pennsylvania, Kutztown, PA 19530, USA
| | - Eric Parperides
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
| | - Hernan Garcia-Ruiz
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska-Lincoln, Lincoln, NE 68583, USA (E.P.)
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2
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Chavez JD, Park SG, Mohr JP, Bruce JE. Applications and advancements of FT-ICR-MS for interactome studies. MASS SPECTROMETRY REVIEWS 2022; 41:248-261. [PMID: 33289940 PMCID: PMC8184889 DOI: 10.1002/mas.21675] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 05/05/2023]
Abstract
The set of all intra- and intermolecular interactions, collectively known as the interactome, is currently an unmet challenge for any analytical method, but if measured, could provide unparalleled insight on molecular function in living systems. Developments and applications of chemical cross-linking and high-performance mass spectrometry technologies are beginning to reveal details on how proteins interact in cells and how protein conformations and interactions inside cells change with phenotype or during drug treatment or other perturbations. A major contributor to these advances is Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) technology and its implementation with accurate mass measurements on cross-linked peptide-pair precursor and fragment ions to enable improved identification methods. However, these applications place increased demands on mass spectrometer performance in terms of high-resolution spectral acquisition rates for on-line MSn experiments. Moreover, FT-ICR-MS also offers unique opportunities to develop and implement parallel ICR cells for multiplexed signal acquisition and the potential to greatly advance accurate mass acquisition rates for interactome studies. This review highlights our efforts to exploit accurate mass FT-ICR-MS technologies with chemical cross-linking and developments being pursued to realize parallel MS array capabilities that will further advance visualization of the interactome.
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Affiliation(s)
- Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
| | - Sung-Gun Park
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
| | - Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98109
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3
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Adams MC, Schiltz CJ, Heck ML, Chappie JS. Crystal structure of the potato leafroll virus coat protein and implications for viral assembly. J Struct Biol 2021; 214:107811. [PMID: 34813955 DOI: 10.1016/j.jsb.2021.107811] [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: 08/03/2021] [Revised: 11/04/2021] [Accepted: 11/13/2021] [Indexed: 10/19/2022]
Abstract
Luteoviruses, poleroviruses, and enamoviruses are insect-transmitted, agricultural pathogens that infect a wide array of plants, including staple food crops. Previous cryo-electron microscopy studies of virus-like particles show that luteovirid viral capsids are built from a structural coat protein that organizes with T = 3 icosahedral symmetry. Here, we present the crystal structure of a truncated version of the coat protein monomer from potato leafroll virus at 1.80-Å resolution. In the crystal lattice, monomers pack into flat sheets that preserve the two-fold and three-fold axes of icosahedral symmetry and show minimal structural deviations when compared to the full-length subunits of the assembled virus-like particle. These observations have important implications in viral assembly and maturation and suggest that the CP N-terminus and its interactions with RNA play an important role in generating capsid curvature.
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Affiliation(s)
- Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Michelle L Heck
- Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA; Boyce Thompson Institute, Ithaca, NY 14853, USA; Robert W. Holley Center for Agriculture and Health, Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY 14853, USA
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA.
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4
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Chavez JD, Wippel HH, Tang X, Keller A, Bruce JE. In-Cell Labeling and Mass Spectrometry for Systems-Level Structural Biology. Chem Rev 2021; 122:7647-7689. [PMID: 34232610 PMCID: PMC8966414 DOI: 10.1021/acs.chemrev.1c00223] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Biological systems have evolved to utilize proteins to accomplish nearly all functional roles needed to sustain life. A majority of biological functions occur within the crowded environment inside cells and subcellular compartments where proteins exist in a densely packed complex network of protein-protein interactions. The structural biology field has experienced a renaissance with recent advances in crystallography, NMR, and CryoEM that now produce stunning models of large and complex structures previously unimaginable. Nevertheless, measurements of such structural detail within cellular environments remain elusive. This review will highlight how advances in mass spectrometry, chemical labeling, and informatics capabilities are merging to provide structural insights on proteins, complexes, and networks that exist inside cells. Because of the molecular detection specificity provided by mass spectrometry and proteomics, these approaches provide systems-level information that not only benefits from conventional structural analysis, but also is highly complementary. Although far from comprehensive in their current form, these approaches are currently providing systems structural biology information that can uniquely reveal how conformations and interactions involving many proteins change inside cells with perturbations such as disease, drug treatment, or phenotypic differences. With continued advancements and more widespread adaptation, systems structural biology based on in-cell labeling and mass spectrometry will provide an even greater wealth of structural knowledge.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, United States
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5
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Simanjuntak Y, Schamoni-Kast K, Grün A, Uetrecht C, Scaturro P. Top-Down and Bottom-Up Proteomics Methods to Study RNA Virus Biology. Viruses 2021; 13:668. [PMID: 33924391 PMCID: PMC8070632 DOI: 10.3390/v13040668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/01/2021] [Accepted: 04/10/2021] [Indexed: 02/06/2023] Open
Abstract
RNA viruses cause a wide range of human diseases that are associated with high mortality and morbidity. In the past decades, the rise of genetic-based screening methods and high-throughput sequencing approaches allowed the uncovering of unique and elusive aspects of RNA virus replication and pathogenesis at an unprecedented scale. However, viruses often hijack critical host functions or trigger pathological dysfunctions, perturbing cellular proteostasis, macromolecular complex organization or stoichiometry, and post-translational modifications. Such effects require the monitoring of proteins and proteoforms both on a global scale and at the structural level. Mass spectrometry (MS) has recently emerged as an important component of the RNA virus biology toolbox, with its potential to shed light on critical aspects of virus-host perturbations and streamline the identification of antiviral targets. Moreover, multiple novel MS tools are available to study the structure of large protein complexes, providing detailed information on the exact stoichiometry of cellular and viral protein complexes and critical mechanistic insights into their functions. Here, we review top-down and bottom-up mass spectrometry-based approaches in RNA virus biology with a special focus on the most recent developments in characterizing host responses, and their translational implications to identify novel tractable antiviral targets.
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Affiliation(s)
- Yogy Simanjuntak
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Kira Schamoni-Kast
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
| | - Alice Grün
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
| | - Charlotte Uetrecht
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
- Centre for Structural Systems Biology, 22607 Hamburg, Germany
- European XFEL GmbH, 22869 Schenefeld, Germany
| | - Pietro Scaturro
- Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (Y.S.); (K.S.-K.); (A.G.)
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6
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Tang X, Wippel HH, Chavez JD, Bruce JE. Crosslinking mass spectrometry: A link between structural biology and systems biology. Protein Sci 2021; 30:773-784. [PMID: 33594738 DOI: 10.1002/pro.4045] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/11/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
Protein structure underpins functional roles in all biological processes; therefore, improved understanding of protein structures is of fundamental importance in nearly all biological and biomedical research areas. Traditional techniques such as X-ray crystallography and more recently, cryo-EM, can reveal structural features on isolated proteins/protein complexes at atomic resolution level and have become indispensable tools for structural biology. Crosslinking mass spectrometry (XL-MS), on the other hand, is an emerging technique capable of capturing transient and dynamic information on protein interactions and assemblies in their native environment. The combination of XL-MS with traditional techniques holds potential for bridging the gap between structural biology and systems biology approaches. Such a combination will enable visualization of protein structures and interactions within the crowded macromolecular environment in living systems that can dramatically increase understanding of biological functions. In this review, we first discuss general strategies of XL-MS and then survey recent examples to show how qualitative and quantitative XL-MS studies can be integrated with available protein structural data to better understand biological function at systems level.
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Affiliation(s)
- Xiaoting Tang
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Helisa H Wippel
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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7
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Holkar SK, Balasubramaniam P, Kumar A, Kadirvel N, Shingote PR, Chhabra ML, Kumar S, Kumar P, Viswanathan R, Jain RK, Pathak AD. Present Status and Future Management Strategies for Sugarcane Yellow Leaf Virus: A Major Constraint to the Global Sugarcane Production. THE PLANT PATHOLOGY JOURNAL 2020; 36:536-557. [PMID: 33312090 PMCID: PMC7721539 DOI: 10.5423/ppj.rw.09.2020.0183] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/23/2020] [Accepted: 11/07/2020] [Indexed: 02/08/2023]
Abstract
Sugarcane yellow leaf virus (SCYLV) is a distinct member of the Polerovirus genus of the Luteoviridae family. SCYLV is the major limitation to sugarcane production worldwide and presently occurring in most of the sugarcane growing countries. SCYLV having high genetic diversity within the species and presently ten genotypes are known to occur based on the complete genome sequence information. SCYLV is present in almost all the states of India where sugarcane is grown. Virion comprises of 180 coat protein units and are 24-29 nm in diameter. The genome of SCYLV is a monopartite and comprised of single-stranded (ss) positive-sense (+) linear RNA of about 6 kb in size. Virus genome consists of six open reading frames (ORFs) that are expressed by sub-genomic RNAs. The SCYLV is phloem-limited and transmitted by sugarcane aphid Melanaphis sacchari in a circulative and non-propagative manner. The other aphid species namely, Ceratovacuna lanigera, Rhopalosiphum rufiabdominalis, and R. maidis also been reported to transmit the virus. The virus is not transmitted mechanically, therefore, its transmission by M. sacchari has been studied in different countries. SCYLV has a limited natural host range and mainly infect sugarcane (Sachharum hybrid), grain sorghum (Sorghum bicolor), and Columbus grass (Sorghum almum). Recent insights in the protein-protein interactions of Polerovirus through protein interaction reporter (PIR) technology enable us to understand viral encoded proteins during virus replication, assembly, plant defence mechanism, short and long-distance travel of the virus. This review presents the recent understandings on virus biology, diagnosis, genetic diversity, virus-vector and host-virus interactions and conventional and next generation management approaches.
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Affiliation(s)
- Somnath Kadappa Holkar
- ICAR-Indian Institute of Sugarcane Research, Biological Control Centre, Pravaranagar, Maharashtra 43 72, India
| | | | - Atul Kumar
- ICAR-Indian Institute of Sugarcane Research, Biological Control Centre, Pravaranagar, Maharashtra 43 72, India.,Amity Institute of Biotechnology, Amity University, Lucknow Campus, Lucknow 226 010, Uttar Pradesh, India
| | - Nithya Kadirvel
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore 61 007, Tamil Nadu, India
| | | | - Manohar Lal Chhabra
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, Haryana 13 001, India
| | - Shubham Kumar
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, Haryana 13 001, India
| | - Praveen Kumar
- ICAR-Sugarcane Breeding Institute, Regional Centre, Karnal, Haryana 13 001, India
| | - Rasappa Viswanathan
- Division of Crop Protection, ICAR-Sugarcane Breeding Institute, Coimbatore 61 007, Tamil Nadu, India
| | - Rakesh Kumar Jain
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, Pusa Campus, New Delhi 110 012, India
| | - Ashwini Dutt Pathak
- ICAR-Indian Institute of Sugarcane Research, Lucknow 226 002, Uttar Pradesh, India
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8
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Huang W, Reyes-Caldas P, Mann M, Seifbarghi S, Kahn A, Almeida RPP, Béven L, Heck M, Hogenhout SA, Coaker G. Bacterial Vector-Borne Plant Diseases: Unanswered Questions and Future Directions. MOLECULAR PLANT 2020; 13:1379-1393. [PMID: 32835885 PMCID: PMC7769051 DOI: 10.1016/j.molp.2020.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/18/2020] [Accepted: 08/18/2020] [Indexed: 06/01/2023]
Abstract
Vector-borne plant diseases have significant ecological and economic impacts, affecting farm profitability and forest composition throughout the world. Bacterial vector-borne pathogens have evolved sophisticated strategies to interact with their hemipteran insect vectors and plant hosts. These pathogens reside in plant vascular tissue, and their study represents an excellent opportunity to uncover novel biological mechanisms regulating intracellular pathogenesis and to contribute to the control of some of the world's most invasive emerging diseases. In this perspective, we highlight recent advances and major unanswered questions in the realm of bacterial vector-borne disease, focusing on liberibacters, phytoplasmas, spiroplasmas, and Xylella fastidiosa.
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Affiliation(s)
- Weijie Huang
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Paola Reyes-Caldas
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Marina Mann
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA
| | - Shirin Seifbarghi
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA
| | - Alexandra Kahn
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Rodrigo P P Almeida
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
| | - Laure Béven
- UMR 1332 Biologie du Fruit et Pathologie, Univ. Bordeaux, INRAE, Villenave d'Ornon 33882 France
| | - Michelle Heck
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, USA; Boyce Thompson Institute, Ithaca, NY 14853, USA; Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, USDA ARS, Ithaca, NY 14853, USA
| | - Saskia A Hogenhout
- Department of Crop Genetics, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Gitta Coaker
- Department of Plant Pathology, University of California, Davis, CA, 95616, USA.
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9
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Abstract
For the last century we have relied on model organisms to help understand fundamental biological processes. Now, with advancements in genome sequencing, assembly, and annotation, non-model organisms may be studied with the same advanced bioanalytical toolkit as model organisms. Proteomics is one such technique, which classically relies on predicted protein sequences to catalog and measure complex proteomes across tissues and biofluids. Applying proteomics to non-model organisms can advance and accelerate biomimicry studies, biomedical advancements, veterinary medicine, agricultural research, behavioral ecology, and food safety. In this postmodel organism era, we can study almost any species, meaning that many non-model organisms are, in fact, important emerging model organisms. Herein we specifically focus on eukaryotic organisms and discuss the steps to generate sequence databases, analyze proteomic data with or without a database, and interpret results as well as future research opportunities. Proteomics is more accessible than ever before and will continue to rapidly advance in the coming years, enabling critical research and discoveries in non-model organisms that were hitherto impossible.
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Affiliation(s)
- Michelle Heck
- Emerging Pests and Pathogens Research Unit, USDA Agricultural Research Service, Ithaca, NY, USA
- Plant Pathology and Plant Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Benjamin A. Neely
- Chemical Sciences Division, National Institute of Standards and Technology, Charleston, SC, USA
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10
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Hu B, Zheng X, Wang Y, Wang J, Zhang F. Computational Approaches for Elucidating Protein-Protein Interactions in Cation Channel Signaling. Curr Drug Targets 2019; 21:179-192. [PMID: 31490747 DOI: 10.2174/1389450120666190906154412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 08/10/2019] [Accepted: 08/23/2019] [Indexed: 11/22/2022]
Abstract
BACKGROUND The lipid bilayer of the plasma membrane is impermeable to ions, yet changes in the flux of ions across the cell membrane are critical regulatory events in cells. Because of their regulatory roles in a range of physiological processes, such as electrical signaling in muscles and neurons, to name a few, these proteins are one of the most important drug targets. OBJECTIVE This review mainly focused on the computational approaches for elucidating proteinprotein interactions in cation channel signaling. DISCUSSION Due to continuously advanced facilities and technologies in computer sciences, the physical contacts of macromolecules of channel structures have been virtually visualized. Indeed, techniques like protein-protein docking, homology modeling, and molecular dynamics simulation are valuable tools for predicting the protein complex and refining channels with unreleased structures. Undoubtedly, these approaches will greatly expand the cation channel signaling research, thereby speeding up structure-based drug design and discovery. CONCLUSION We introduced a series of valuable computational tools for elucidating protein-protein interactions in cation channel signaling, including molecular graphics, protein-protein docking, homology modeling, and molecular dynamics simulation.
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Affiliation(s)
- Baichun Hu
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaoming Zheng
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Ying Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China.,Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China.,School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jian Wang
- Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.,School of Pharmaceutical Engineering, Shenyang Pharmaceutical University, Shenyang, China
| | - Fengjiao Zhang
- Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang, Liaoning, 110016, China
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11
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Dülfer J, Kadek A, Kopicki JD, Krichel B, Uetrecht C. Structural mass spectrometry goes viral. Adv Virus Res 2019; 105:189-238. [PMID: 31522705 DOI: 10.1016/bs.aivir.2019.07.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Over the last 20 years, mass spectrometry (MS), with its ability to analyze small sample amounts with high speed and sensitivity, has more and more entered the field of structural virology, aiming to investigate the structure and dynamics of viral proteins as close to their native environment as possible. The use of non-perturbing labels in hydrogen-deuterium exchange MS allows for the analysis of interactions between viral proteins and host cell factors as well as their dynamic responses to the environment. Cross-linking MS, on the other hand, can analyze interactions in viral protein complexes and identify virus-host interactions in cells. Native MS allows transferring viral proteins, complexes and capsids into the gas phase and has broken boundaries to overcome size limitations, so that now even the analysis of intact virions is possible. Different MS approaches not only inform about size, stability, interactions and dynamics of virus assemblies, but also bridge the gap to other biophysical techniques, providing valuable constraints for integrative structural modeling of viral complex assemblies that are often inaccessible by single technique approaches. In this review, recent advances are highlighted, clearly showing that structural MS approaches in virology are moving towards systems biology and ever more experiments are performed on cellular level.
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Affiliation(s)
- Jasmin Dülfer
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Alan Kadek
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany
| | - Janine-Denise Kopicki
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Boris Krichel
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Charlotte Uetrecht
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany; European XFEL GmbH, Schenefeld, Germany.
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12
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Chavez JD, Mohr JP, Mathay M, Zhong X, Keller A, Bruce JE. Systems structural biology measurements by in vivo cross-linking with mass spectrometry. Nat Protoc 2019; 14:2318-2343. [PMID: 31270507 DOI: 10.1038/s41596-019-0181-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 04/18/2019] [Indexed: 12/23/2022]
Abstract
This protocol describes a workflow for utilizing large-scale cross-linking with mass spectrometry (XL-MS) to make systems-level structural biology measurements in complex biological samples, including cells, isolated organelles, and tissue samples. XL-MS is a structural biology technique that provides information on the molecular structure of proteins and protein complexes using chemical probes that report the proximity of probe-reactive amino acids within proteins, typically lysine residues. Information gained through XL-MS studies is often complementary to more traditional methods, such as X-ray crystallography, nuclear magnetic resonance, and cryo-electron microscopy. The use of MS-cleavable cross-linkers, including protein interaction reporter (PIR) technologies, enables XL-MS studies on protein structures and interactions in extremely complex biological samples, including intact living cells. PIR cross-linkers are designed to contain chemical bonds at specific locations within the cross-linker molecule that can be selectively cleaved by collision-induced dissociation or UV light. When broken, these bonds release the intact peptides that were cross-linked, as well as a reporter ion. Conservation of mass dictates that the sum of the two released peptide masses and the reporter mass equals the measured precursor mass. This relationship is used to identify cross-linked peptide pairs. Release of the individual peptides permits accurate measurement of their masses and independent amino acid sequence determination by tandem MS, allowing the use of standard proteomics search engines such as Comet for peptide sequence assignment, greatly simplifying data analysis of cross-linked peptide pairs. Search results are processed with XLinkProphet for validation and can be uploaded into XlinkDB for interaction network and structural analysis.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jared P Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Martin Mathay
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Xuefei Zhong
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
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13
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Cook KC, Cristea IM. Location is everything: protein translocations as a viral infection strategy. Curr Opin Chem Biol 2019; 48:34-43. [PMID: 30339987 PMCID: PMC6382524 DOI: 10.1016/j.cbpa.2018.09.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/16/2018] [Accepted: 09/20/2018] [Indexed: 12/13/2022]
Abstract
Protein movement between different subcellular compartments is an essential aspect of biological processes, including transcriptional and metabolic regulation, and immune and stress responses. As obligate intracellular parasites, viruses are master manipulators of cellular composition and organization. Accumulating evidences have highlighted the importance of infection-induced protein translocations between organelles. Both directional and temporal, these translocation events facilitate localization-dependent protein interactions and changes in protein functions that contribute to either host defense or virus replication. The discovery and characterization of protein movement is technically challenging, given the necessity for sensitive detection and subcellular resolution. Here, we discuss infection-induced translocations of host and viral proteins, and the value of integrating quantitative proteomics with advanced microscopy for understanding the biology of human virus infections.
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Affiliation(s)
- Katelyn C Cook
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
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14
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Kaur U, Johnson DT, Chea EE, Deredge DJ, Espino JA, Jones LM. Evolution of Structural Biology through the Lens of Mass Spectrometry. Anal Chem 2019; 91:142-155. [PMID: 30457831 PMCID: PMC6472977 DOI: 10.1021/acs.analchem.8b05014] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Danté T. Johnson
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Emily E. Chea
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Daniel J. Deredge
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Jessica A. Espino
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Lisa M. Jones
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
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15
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Kaur U, Johnson DT, Chea EE, Deredge DJ, Espino JA, Jones LM. Evolution of Structural Biology through the Lens of Mass Spectrometry. Anal Chem 2019; 91:142-155. [PMID: 30457831 DOI: 10.1021/acs.analchem.1028b05014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Affiliation(s)
- Upneet Kaur
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Danté T Johnson
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Emily E Chea
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Daniel J Deredge
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Jessica A Espino
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
| | - Lisa M Jones
- Department of Pharmaceutical Sciences , University of Maryland , Baltimore , Maryland 21201 , United States
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16
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Targeted disruption of aphid transmission: a vision for the management of crop diseases caused by Luteoviridae members. Curr Opin Virol 2018; 33:24-32. [DOI: 10.1016/j.coviro.2018.07.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
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17
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DeBlasio SL, Xu Y, Johnson RS, Rebelo AR, MacCoss MJ, Gray SM, Heck M. The Interaction Dynamics of Two Potato Leafroll Virus Movement Proteins Affects Their Localization to the Outer Membranes of Mitochondria and Plastids. Viruses 2018; 10:E585. [PMID: 30373157 PMCID: PMC6265731 DOI: 10.3390/v10110585] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
The Luteoviridae is an agriculturally important family of viruses whose replication and transport are restricted to plant phloem. Their genomes encode for four proteins that regulate viral movement. These include two structural proteins that make up the capsid and two non-structural proteins known as P3a and P17. Little is known about how these proteins interact with each other and the host to coordinate virus movement within and between cells. We used quantitative, affinity purification-mass spectrometry to show that the P3a protein of Potato leafroll virus complexes with virus and that this interaction is partially dependent on P17. Bimolecular complementation assays (BiFC) were used to validate that P3a and P17 self-interact as well as directly interact with each other. Co-localization with fluorescent-based organelle markers demonstrates that P3a directs P17 to the mitochondrial outer membrane while P17 regulates the localization of the P3a-P17 heterodimer to plastids. Residues in the C-terminus of P3a were shown to regulate P3a association with host mitochondria by using mutational analysis and also varying BiFC tag orientation. Collectively, our work reveals that the PLRV movement proteins play a game of intracellular hopscotch along host organelles to transport the virus to the cell periphery.
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Affiliation(s)
- Stacy L DeBlasio
- United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
| | - Yi Xu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle WA 98109, USA.
| | - Ana Rita Rebelo
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle WA 98109, USA.
| | - Stewart M Gray
- United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Michelle Heck
- United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
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18
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DeBlasio SL, Rebelo AR, Parks K, Gray SM, Heck MC. Disruption of Chloroplast Function Through Downregulation of Phytoene Desaturase Enhances the Systemic Accumulation of an Aphid-Borne, Phloem-Restricted Virus. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1095-1110. [PMID: 29767548 DOI: 10.1094/mpmi-03-18-0057-r] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Chloroplasts play a central role in pathogen defense in plants. However, most studies explaining the relationship between pathogens and chloroplasts have focused on pathogens that infect mesophyll cells. In contrast, the family Luteoviridae includes RNA viruses that replicate and traffic exclusively in the phloem. Recently, our lab has shown that Potato leafroll virus (PLRV), the type species in the genus Polerovirus, forms an extensive interaction network with chloroplast-localized proteins that is partially dependent on the PLRV capsid readthrough domain (RTD). In this study, we used virus-induced gene silencing to disrupt chloroplast function and assess the effects on PLRV accumulation in two host species. Silencing of phytoene desaturase (PDS), a key enzyme in carotenoid, chlorophyll, and gibberellic acid (GA) biosynthesis, resulted in a substantial increase in the systemic accumulation of PLRV. This increased accumulation was attenuated when plants were infected with a viral mutant that does not express the RTD. Application of GA partially suppressed the increase in virus accumulation in PDS-silenced plants, suggesting that GA signaling also plays a role in limiting PLRV infection. In addition, the fecundity of the aphid vector of PLRV was increased when fed on PDS-silenced plants relative to PLRV-infected plants.
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Affiliation(s)
- Stacy L DeBlasio
- 1 USDA-Agricultural Research Service, Ithaca, NY 14853, U.S.A
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A.; and
| | - Ana Rita Rebelo
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A.; and
| | - Katherine Parks
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A.; and
| | - Stewart M Gray
- 1 USDA-Agricultural Research Service, Ithaca, NY 14853, U.S.A
- 3 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A
| | - Michelle C Heck
- 1 USDA-Agricultural Research Service, Ithaca, NY 14853, U.S.A
- 2 Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, U.S.A.; and
- 3 Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853, U.S.A
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19
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Chavez JD, Bruce JE. Chemical cross-linking with mass spectrometry: a tool for systems structural biology. Curr Opin Chem Biol 2018; 48:8-18. [PMID: 30172868 DOI: 10.1016/j.cbpa.2018.08.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 08/09/2018] [Accepted: 08/10/2018] [Indexed: 01/14/2023]
Abstract
Biological processes supporting life are orchestrated by a highly dynamic array of protein structures and interactions comprising the interactome. Defining the interactome, visualizing how structures and interactions change and function to support life is essential to improved understanding of fundamental molecular processes, but represents a challenge unmet by any single analytical technique. Chemical cross-linking with mass spectrometry provides identification of proximal amino acid residues within proteins and protein complexes, yielding low resolution structural information. This approach has predominantly been employed to provide structural insight on isolated protein complexes, and has been particularly useful for molecules that are recalcitrant to conventional structural biology studies. Here we discuss recent developments in cross-linking and mass spectrometry technologies that are providing large-scale or systems-level interactome data with successful applications to isolated organelles, cell lysates, virus particles, intact bacterial and mammalian cultured cells and tissue samples.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
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20
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Xu Y, Ju HJ, DeBlasio S, Carino EJ, Johnson R, MacCoss MJ, Heck M, Miller WA, Gray SM. A Stem-Loop Structure in Potato Leafroll Virus Open Reading Frame 5 (ORF5) Is Essential for Readthrough Translation of the Coat Protein ORF Stop Codon 700 Bases Upstream. J Virol 2018; 92:e01544-17. [PMID: 29514911 PMCID: PMC5952135 DOI: 10.1128/jvi.01544-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 03/06/2018] [Indexed: 11/20/2022] Open
Abstract
Translational readthrough of the stop codon of the capsid protein (CP) open reading frame (ORF) is used by members of the Luteoviridae to produce their minor capsid protein as a readthrough protein (RTP). The elements regulating RTP expression are not well understood, but they involve long-distance interactions between RNA domains. Using high-resolution mass spectrometry, glutamine and tyrosine were identified as the primary amino acids inserted at the stop codon of Potato leafroll virus (PLRV) CP ORF. We characterized the contributions of a cytidine-rich domain immediately downstream and a branched stem-loop structure 600 to 700 nucleotides downstream of the CP stop codon. Mutations predicted to disrupt and restore the base of the distal stem-loop structure prevented and restored stop codon readthrough. Motifs in the downstream readthrough element (DRTE) are predicted to base pair to a site within 27 nucleotides (nt) of the CP ORF stop codon. Consistent with a requirement for this base pairing, the DRTE of Cereal yellow dwarf virus was not compatible with the stop codon-proximal element of PLRV in facilitating readthrough. Moreover, deletion of the complementary tract of bases from the stop codon-proximal region or the DRTE of PLRV prevented readthrough. In contrast, the distance and sequence composition between the two domains was flexible. Mutants deficient in RTP translation moved long distances in plants, but fewer infection foci developed in systemically infected leaves. Selective 2'-hydroxyl acylation and primer extension (SHAPE) probing to determine the secondary structure of the mutant DRTEs revealed that the functional mutants were more likely to have bases accessible for long-distance base pairing than the nonfunctional mutants. This study reveals a heretofore unknown combination of RNA structure and sequence that reduces stop codon efficiency, allowing translation of a key viral protein.IMPORTANCE Programmed stop codon readthrough is used by many animal and plant viruses to produce key viral proteins. Moreover, such "leaky" stop codons are used in host mRNAs or can arise from mutations that cause genetic disease. Thus, it is important to understand the mechanism(s) of stop codon readthrough. Here, we shed light on the mechanism of readthrough of the stop codon of the coat protein ORFs of viruses in the Luteoviridae by identifying the amino acids inserted at the stop codon and RNA structures that facilitate this "leakiness" of the stop codon. Members of the Luteoviridae encode a C-terminal extension to the capsid protein known as the readthrough protein (RTP). We characterized two RNA domains in Potato leafroll virus (PLRV), located 600 to 700 nucleotides apart, that are essential for efficient RTP translation. We further determined that the PLRV readthrough process involves both local structures and long-range RNA-RNA interactions. Genetic manipulation of the RNA structure altered the ability of PLRV to translate RTP and systemically infect the plant. This demonstrates that plant virus RNA contains multiple layers of information beyond the primary sequence and extends our understanding of stop codon readthrough. Strategic targets that can be exploited to disrupt the virus life cycle and reduce its ability to move within and between plant hosts were revealed.
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Affiliation(s)
- Yi Xu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, New York, USA
| | - Ho-Jong Ju
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, New York, USA
| | - Stacy DeBlasio
- Emerging Pests and Pathogens Research Unit, USDA, ARS, Ithaca, New York, USA
| | - Elizabeth J Carino
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michelle Heck
- Emerging Pests and Pathogens Research Unit, USDA, ARS, Ithaca, New York, USA
- Boyce Thompson Institute, Ithaca, New York, USA
| | - W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA
| | - Stewart M Gray
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, New York, USA
- Emerging Pests and Pathogens Research Unit, USDA, ARS, Ithaca, New York, USA
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21
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Mohr JP, Perumalla P, Chavez JD, Eng JK, Bruce JE. Mango: A General Tool for Collision Induced Dissociation-Cleavable Cross-Linked Peptide Identification. Anal Chem 2018; 90:6028-6034. [PMID: 29676898 PMCID: PMC5959040 DOI: 10.1021/acs.analchem.7b04991] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Chemical cross-linking combined with mass spectrometry provides a method to study protein structures and interactions. The introduction of cleavable bonds in a cross-linker provides an avenue to decouple released peptide masses from their precursor species, greatly simplifying the downstream search, allowing for whole proteome investigations to be performed. Typically, these experiments have been challenging to carry out, often utilizing nonstandard methods to fully identify cross-linked peptides. Mango is an open source software tool that extracts precursor masses from chimeric spectra generated using cleavable cross-linkers, greatly simplifying the downstream search. As it is designed to work with chimeric spectra, Mango can be used on traditional high-resolution tandem mass spectrometry (MS/MS) capable mass spectrometers without the need for additional modifications. When paired with a traditional proteomics search engine, Mango can be used to identify several thousand cross-linked peptide pairs searching against the entire Escherichia coli proteome. Mango provides an avenue to perform whole proteome cross-linking experiments without specialized instrumentation or access to nonstandard methods.
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Affiliation(s)
- Jared P. Mohr
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Poorna Perumalla
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Juan D. Chavez
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - Jimmy K. Eng
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
| | - James E. Bruce
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, United States
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22
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Insect Transmission of Plant Pathogens: a Systems Biology Perspective. mSystems 2018; 3:mSystems00168-17. [PMID: 29629417 PMCID: PMC5881024 DOI: 10.1128/msystems.00168-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/02/2018] [Indexed: 11/20/2022] Open
Abstract
Insect-vectored pathogens pose one of the greatest threats to plant and animal, including human, health on a global scale. Few effective control strategies have been developed to thwart the transmission of any insect-transmitted pathogen. Most have negative impacts on the environment and human health and are unsustainable. Plant pathogen transmission by insect vectors involves a combination of coevolving biological players: plant hosts, insect vectors, plant pathogens, and bacterial endosymbionts harbored by the insect. Our ability to help growers to control vector-borne disease depends on our ability to generate pathogen- and/or disease-resistant crops by traditional or synthetic approaches and to block pathogen transmission by the insect vector. Systems biology studies have led to the reexamination of existing paradigms on how pathogens interact with insect vectors, including the bacterial symbionts, and have identified vector-pathogen interactions at the molecular and cellular levels for the development of novel transmission interdiction strategies.
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23
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Chavez JD, Lee CF, Caudal A, Keller A, Tian R, Bruce JE. Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue. Cell Syst 2018; 6:136-141.e5. [PMID: 29199018 PMCID: PMC5799023 DOI: 10.1016/j.cels.2017.10.017] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/05/2017] [Accepted: 10/25/2017] [Indexed: 12/16/2022]
Abstract
While modern structural biology technologies have greatly expanded the size and type of protein complexes that can now be studied, the ability to derive large-scale structural information on proteins and complexes as they exist within tissues is practically nonexistent. Here, we demonstrate the application of crosslinking mass spectrometry to identify protein structural features and interactions in tissue samples, providing systems structural biology insight into protein complexes as they exist in the mouse heart. This includes insights into multiple conformational states of sarcomere proteins, as well as interactions among OXPHOS complexes indicative of supercomplex assembly. The extension of crosslinking mass spectrometry analysis into the realm of tissues opens the door to increasing our understanding of protein structures and interactions within the context of the greater biological system.
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Affiliation(s)
- Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Chi Fung Lee
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98105, USA
| | - Arianne Caudal
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98105, USA
| | - Andrew Keller
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Rong Tian
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98105, USA; Mitochondria and Metabolism Center, University of Washington, Seattle, WA 98105, USA
| | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA.
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24
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Alexander MM, Mohr JP, DeBlasio SL, Chavez JD, Ziegler-Graff V, Brault V, Bruce JE, Heck MC. Insights in luteovirid structural biology guided by chemical cross-linking and high resolution mass spectrometry. Virus Res 2017; 241:42-52. [PMID: 28502641 DOI: 10.1016/j.virusres.2017.05.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/09/2017] [Accepted: 05/09/2017] [Indexed: 10/19/2022]
Abstract
Interactions among plant pathogenic viruses in the family Luteoviridae and their plant hosts and insect vectors are governed by the topology of the viral capsid, which is the sole vehicle for long distance movement of the viral genome. Previous application of a mass spectrometry-compatible cross-linker to preparations of the luteovirid Potato leafroll virus (PLRV; Luteoviridae: Polerovirus) revealed a detailed network of interactions between viral structural proteins and enabled generation of the first cross-linking guided coat protein models. In this study, we extended application of chemical cross-linking technology to the related Turnip yellows virus (TuYV; Luteoviridae: Polerovirus). Remarkably, all cross-links found between sites in the viral coat protein found for TuYV were also found in PLRV. Guided by these data, we present two models for the TuYV coat protein trimer, the basic structural unit of luteovirid virions. Additional cross-links found between the TuYV coat protein and a site in the viral protease domain suggest a possible role for the luteovirid protease in regulating the structural biology of these viruses.
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Affiliation(s)
- Mariko M Alexander
- School of Integrative Plant Science, Plant Pathology and Plant Microbe Biology Section, Cornell University, Ithaca, NY, USA; Boyce Thompson Institute, Ithaca, NY, USA
| | - Jared P Mohr
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stacy L DeBlasio
- USDA-Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - Juan D Chavez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | | | - James E Bruce
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Cilia Heck
- School of Integrative Plant Science, Plant Pathology and Plant Microbe Biology Section, Cornell University, Ithaca, NY, USA; Boyce Thompson Institute, Ithaca, NY, USA; USDA-Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA.
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25
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Abstract
Viral replication in eukaryotes is a process inherently organized in both space and time. Viral components target subcellular organelles to access host machineries required for replication and spread. Diverse viruses are known to alter organelle shape, composition, function, and dynamics as part of their replication cycles. Here, we highlight recent advances in microscopy and proteomic methods that have helped and will continue to help define mechanisms used by viruses to exploit host proteome organization.
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26
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DeBlasio SL, Bereman MS, Mahoney J, Thannhauser TW, Gray SM, MacCoss MJ, Cilia Heck M. Evaluation of a Bead-Free Coimmunoprecipitation Technique for Identification of Virus-Host Protein Interactions Using High-Resolution Mass Spectrometry. J Biomol Tech 2017; 28:111-121. [PMID: 28785175 DOI: 10.7171/jbt.17-2803-002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Protein interactions between virus and host are essential for viral propagation and movement, as viruses lack most of the proteins required to thrive on their own. Precision methods aimed at disrupting virus-host interactions represent new approaches to disease management but require in-depth knowledge of the identity and binding specificity of host proteins within these interaction networks. Protein coimmunoprecipitation (co-IP) coupled with mass spectrometry (MS) provides a high-throughput way to characterize virus-host interactomes in a single experiment. Common co-IP methods use antibodies immobilized on agarose or magnetic beads to isolate virus-host complexes in solutions of host tissue homogenate. Although these workflows are well established, they can be fairly laborious and expensive. Therefore, we evaluated the feasibility of using antibody-coated microtiter plates coupled with MS analysis as an easy, less expensive way to identify host proteins that interact with Potato leafroll virus (PLRV), an insect-borne RNA virus that infects potatoes. With the use of the bead-free platform, we were able to detect 36 plant and 1 nonstructural viral protein significantly coimmunoprecipitating with PLRV. Two of these proteins, a 14-3-3 signal transduction protein and malate dehydrogenase 2 (mMDH2), were detected as having a weakened or lost association with a structural mutant of the virus, demonstrating that the bead-free method is sensitive enough to detect quantitative differences that can be used to pin-point domains of interaction. Collectively, our analysis shows that the bead-free platform is a low-cost alternative that can be used by core facilities and other investigators to identify plant and viral proteins interacting with virions and/or the viral structural proteins.
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Affiliation(s)
- Stacy L DeBlasio
- U.S. Department of Agriculture, Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, USA.,Boyce Thompson Institute, Ithaca, New York 14853, USA
| | - Michael S Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh-Durham North Carolina 27695, USA
| | | | - Theodore W Thannhauser
- U.S. Department of Agriculture, Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, USA
| | - Stewart M Gray
- U.S. Department of Agriculture, Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, USA.,Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA; and
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington 98109, USA
| | - Michelle Cilia Heck
- U.S. Department of Agriculture, Agricultural Research Service, Emerging Pests and Pathogens Research Unit, Ithaca, New York 14853, USA.,Boyce Thompson Institute, Ithaca, New York 14853, USA.,Plant Pathology and Plant-Microbe Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853, USA; and
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27
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Jean Beltran PM, Federspiel JD, Sheng X, Cristea IM. Proteomics and integrative omic approaches for understanding host-pathogen interactions and infectious diseases. Mol Syst Biol 2017; 13:922. [PMID: 28348067 PMCID: PMC5371729 DOI: 10.15252/msb.20167062] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Organisms are constantly exposed to microbial pathogens in their environments. When a pathogen meets its host, a series of intricate intracellular interactions shape the outcome of the infection. The understanding of these host–pathogen interactions is crucial for the development of treatments and preventive measures against infectious diseases. Over the past decade, proteomic approaches have become prime contributors to the discovery and understanding of host–pathogen interactions that represent anti‐ and pro‐pathogenic cellular responses. Here, we review these proteomic methods and their application to studying viral and bacterial intracellular pathogens. We examine approaches for defining spatial and temporal host–pathogen protein interactions upon infection of a host cell. Further expanding the understanding of proteome organization during an infection, we discuss methods that characterize the regulation of host and pathogen proteomes through alterations in protein abundance, localization, and post‐translational modifications. Finally, we highlight bioinformatic tools available for analyzing such proteomic datasets, as well as novel strategies for integrating proteomics with other omic tools, such as genomics, transcriptomics, and metabolomics, to obtain a systems‐level understanding of infectious diseases.
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Affiliation(s)
- Pierre M Jean Beltran
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ, USA
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Greco TM, Cristea IM. Proteomics Tracing the Footsteps of Infectious Disease. Mol Cell Proteomics 2017; 16:S5-S14. [PMID: 28163258 DOI: 10.1074/mcp.o116.066001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/25/2017] [Indexed: 01/20/2023] Open
Abstract
Every year, a major cause of human disease and death worldwide is infection with the various pathogens-viruses, bacteria, fungi, and protozoa-that are intrinsic to our ecosystem. In efforts to control the prevalence of infectious disease and develop improved therapies, the scientific community has focused on building a molecular picture of pathogen infection and spread. These studies have been aimed at defining the cellular mechanisms that allow pathogen entry into hosts cells, their replication and transmission, as well as the core mechanisms of host defense against pathogens. The past two decades have demonstrated the valuable implementation of proteomic methods in all these areas of infectious disease research. Here, we provide a perspective on the contributions of mass spectrometry and other proteomics approaches to understanding the molecular details of pathogen infection. Specifically, we highlight methods used for defining the composition of viral and bacterial pathogens and the dynamic interaction with their hosts in space and time. We discuss the promise of MS-based proteomics in supporting the development of diagnostics and therapies, and the growing need for multiomics strategies for gaining a systems view of pathogen infection.
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Affiliation(s)
- Todd M Greco
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544
| | - Ileana M Cristea
- From the ‡Department of Molecular Biology, Princeton University, Princeton, New Jersey, 08544
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Lee CM, Adamchek C, Feke A, Nusinow DA, Gendron JM. Mapping Protein-Protein Interactions Using Affinity Purification and Mass Spectrometry. Methods Mol Biol 2017; 1610:231-249. [PMID: 28439867 DOI: 10.1007/978-1-4939-7003-2_15] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The mapping of protein-protein interaction (PPI) networks and their dynamics are crucial steps to deciphering the function of a protein and its role in cellular pathways, making it critical to have comprehensive knowledge of a protein's interactome. Advances in affinity purification and mass spectrometry technology (AP-MS) have provided a powerful and unbiased method to capture higher-order protein complexes and decipher dynamic PPIs. However, the unbiased calling of nonspecific interactions and the ability to detect transient interactions remains challenging when using AP-MS, thereby hampering the detection of biologically meaningful complexes. Additionally, there are plant-specific challenges with AP-MS, such as a lack of protein-specific antibodies, which must be overcome to successfully identify PPIs. Here we discuss and describe a protocol designed to bypass the traditional challenges of AP-MS and provide a roadmap to identify bona fide PPIs in plants.
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Affiliation(s)
- Chin-Mei Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Christopher Adamchek
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | - Ann Feke
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA
| | | | - Joshua M Gendron
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT, 06511, USA.
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30
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Rodrigo G, Daròs JA, Elena SF. Virus-host interactome: Putting the accent on how it changes. J Proteomics 2016; 156:1-4. [PMID: 28007618 DOI: 10.1016/j.jprot.2016.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/26/2016] [Accepted: 12/16/2016] [Indexed: 12/27/2022]
Abstract
Viral infections are extremely complex processes that could only be well understood by precisely characterizing the interaction networks between the virus and the host components. In recent years, much effort has gone in this direction with the aim of unveiling the molecular basis of viral pathology. These networks are mostly formed by viral and host proteins, and are expected to be dynamic both with time and space (i.e., with the progression of infection, as well as with the virus and host genotypes; what we call plastodynamic). This largely overlooked spatio-temporal evolution urgently calls for a change both in the conceptual paradigms and experimental techniques used so far to characterize virus-host interactions. More generally, molecular plasticity and temporal dynamics are unavoidable components of the mechanisms that underlie any complex disease; components whose understanding will eventually enhance our ability to modulate those networks with the aim of improving disease treatments.
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Affiliation(s)
- Guillermo Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, 46022, Valencia, Spain; Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas - Universitat de València, 46980 Paterna, Spain.
| | - José-Antonio Daròs
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, 46022, Valencia, Spain.
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas - Universidad Politécnica de Valencia, 46022, Valencia, Spain; Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas - Universitat de València, 46980 Paterna, Spain; Santa Fe Institute, Santa Fe, NM 87501, USA.
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Chakrabarty JK, Naik AG, Fessler MB, Munske GR, Chowdhury SM. Differential Tandem Mass Spectrometry-Based Cross-Linker: A New Approach for High Confidence in Identifying Protein Cross-Linking. Anal Chem 2016; 88:10215-10222. [PMID: 27649375 DOI: 10.1021/acs.analchem.6b02886] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chemical cross-linking and mass spectrometry are now widely used to analyze large-scale protein-protein interactions. The major challenge in cross-linking approaches is the complexity of the mass spectrometric data. New approaches are required that can identify cross-linked peptides with high-confidence and establish a user-friendly analysis protocol for the biomedical scientific community. Here, we introduce a novel cross-linker that can be selectively cleaved in the gas phase using two differential tandem mass-spectrometric fragmentation methods, such as collision-induced or electron transfer dissociation (CID and ETD). This technique produces two signature mass spectra of the same cross-linked peptide, thereby producing high confidence in identifying the sites of interaction. Further tandem mass spectrometry can also give additional confidence on the peptide sequences. We demonstrate a proof-of-concept for this method using standard peptides and proteins. Peptides and proteins were cross-linked and their fragmentation characteristics were analyzed using CID and ETD tandem mass spectrometry. Two sequential cleavages unambiguously identified cross-linked peptides. In addition, the labeling efficiency of the new cross-linker was evaluated in macrophage immune cells after stimulation with the microbial ligand lipopolysaccharide and subsequent pulldown experiments with biotin-avidin affinity chromatography. We believe this strategy will help advance insights into the structural biology and systems biology of cell signaling.
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Affiliation(s)
| | | | - Michael B Fessler
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, NIH , Research Triangle Park, North Carolina 27709, United States
| | - Gerhard R Munske
- Laboratory of Bioanalysis, Washington State University , Pullman, Washington 98195, United States
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Ashford P, Hernandez A, Greco TM, Buch A, Sodeik B, Cristea IM, Grünewald K, Shepherd A, Topf M. HVint: A Strategy for Identifying Novel Protein-Protein Interactions in Herpes Simplex Virus Type 1. Mol Cell Proteomics 2016; 15:2939-53. [PMID: 27384951 PMCID: PMC5013309 DOI: 10.1074/mcp.m116.058552] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Indexed: 11/12/2022] Open
Abstract
Human herpesviruses are widespread human pathogens with a remarkable impact on worldwide public health. Despite intense decades of research, the molecular details in many aspects of their function remain to be fully characterized. To unravel the details of how these viruses operate, a thorough understanding of the relationships between the involved components is key. Here, we present HVint, a novel protein-protein intraviral interaction resource for herpes simplex virus type 1 (HSV-1) integrating data from five external sources. To assess each interaction, we used a scoring scheme that takes into consideration aspects such as the type of detection method and the number of lines of evidence. The coverage of the initial interactome was further increased using evolutionary information, by importing interactions reported for other human herpesviruses. These latter interactions constitute, therefore, computational predictions for potential novel interactions in HSV-1. An independent experimental analysis was performed to confirm a subset of our predicted interactions. This subset covers proteins that contribute to nuclear egress and primary envelopment events, including VP26, pUL31, pUL40, and the recently characterized pUL32 and pUL21. Our findings support a coordinated crosstalk between VP26 and proteins such as pUL31, pUS9, and the CSVC complex, contributing to the development of a model describing the nuclear egress and primary envelopment pathways of newly synthesized HSV-1 capsids. The results are also consistent with recent findings on the involvement of pUL32 in capsid maturation and early tegumentation events. Further, they open the door to new hypotheses on virus-specific regulators of pUS9-dependent transport. To make this repository of interactions readily accessible for the scientific community, we also developed a user-friendly and interactive web interface. Our approach demonstrates the power of computational predictions to assist in the design of targeted experiments for the discovery of novel protein-protein interactions.
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Affiliation(s)
- Paul Ashford
- From the: ‡Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK
| | - Anna Hernandez
- From the: ‡Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK; §Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Todd Michael Greco
- ¶Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544
| | - Anna Buch
- ‖Institute of Virology, Hannover Medical School, OE 4310, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany
| | - Beate Sodeik
- ‖Institute of Virology, Hannover Medical School, OE 4310, Carl-Neuberg-Str. 1, D-30623, Hannover, Germany
| | - Ileana Mihaela Cristea
- ¶Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, New Jersey 08544;
| | - Kay Grünewald
- §Oxford Particle Imaging Centre, Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Adrian Shepherd
- From the: ‡Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK
| | - Maya Topf
- From the: ‡Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, WC1E 7HX, UK;
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