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Melo RM, de Souza JMF, Williams TCR, Fontes W, de Sousa MV, Ricart CAO, do Vale LHF. Revealing Corynebacterium glutamicum proteoforms through top-down proteomics. Sci Rep 2023; 13:2602. [PMID: 36788287 PMCID: PMC9929327 DOI: 10.1038/s41598-023-29857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/11/2023] [Indexed: 02/16/2023] Open
Abstract
Corynebacterium glutamicum is a bacterium widely employed in the industrial production of amino acids as well as a broad range of other biotechnological products. The present study describes the characterization of C. glutamicum proteoforms, and their post-translational modifications (PTMs) employing top-down proteomics. Despite previous evidence of PTMs having roles in the regulation of C. glutamicum metabolism, this is the first top-down proteome analysis of this organism. We identified 1125 proteoforms from 273 proteins, with 60% of proteins presenting at least one mass shift, suggesting the presence of PTMs, including several acetylated, oxidized and formylated proteoforms. Furthermore, proteins relevant to amino acid production, protein secretion, and oxidative stress were identified with mass shifts suggesting the presence of uncharacterized PTMs and proteoforms that may affect biotechnologically relevant processes in this industrial workhorse. For instance, the membrane proteins mepB and SecG were identified as a cleaved and a formylated proteoform, respectively. While in the central metabolism, OdhI was identified as two proteoforms with potential biological relevance: a cleaved proteoform and a proteoform with PTMs corresponding to a 70 Da mass shift.
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Affiliation(s)
- Reynaldo Magalhães Melo
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Jaques Miranda Ferreira de Souza
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | | | - Wagner Fontes
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Marcelo Valle de Sousa
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Carlos André Ornelas Ricart
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil
| | - Luis Henrique Ferreira do Vale
- Laboratory of Protein Chemistry and Biochemistry, Department of Cell Biology, Institute of Biology, University of Brasilia, Brasilia, Brazil.
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2
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Dupré M, Duchateau M, Malosse C, Borges-Lima D, Calvaresi V, Podglajen I, Clermont D, Rey M, Chamot-Rooke J. Optimization of a Top-Down Proteomics Platform for Closely Related Pathogenic Bacterial Discrimination. J Proteome Res 2020; 20:202-211. [PMID: 32929970 DOI: 10.1021/acs.jproteome.0c00351] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The current technique used for microbial identification in hospitals is matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). However, it suffers from important limitations, in particular, for closely related species or when the database used for the identification lacks the appropriate reference. In this work, we set up a liquid chromatography (LC)-MS/MS top-down proteomics platform, which aims at discriminating closely related pathogenic bacteria through the identification of specific proteoforms. Using Escherichia coli as a model, all steps of the workflow were optimized: protein extraction, on-line LC separation, MS method, and data analysis. Using optimized parameters, about 220 proteins, corresponding to more than 500 proteoforms, could be identified in a single run. We then used this platform for the discrimination of enterobacterial pathogens undistinguishable by MALDI-TOF, although leading to very different clinical outcomes. For each pathogen, we identified specific proteoforms that could potentially be used as biomarkers. We also improved the characterization of poorly described bacterial strains. Our results highlight the advantage of addressing proteoforms rather than peptides for accurate bacterial characterization and qualify top-down proteomics as a promising tool in clinical microbiology. Data are available via ProteomeXchange with the identifier PXD019247.
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Affiliation(s)
- Mathieu Dupré
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Magalie Duchateau
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Christian Malosse
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Diogo Borges-Lima
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Valeria Calvaresi
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Isabelle Podglajen
- Microbiology Department, Georges Pompidou European Hospital, Assistance Publique-Hôpitaux de Paris, Paris 75015, France
| | - Dominique Clermont
- Collection of the Institut Pasteur (CIP), Institut Pasteur, Paris 75015, France
| | - Martial Rey
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
| | - Julia Chamot-Rooke
- Mass Spectrometry for Biology Unit, CNRS USR2000, Institut Pasteur, Paris 75015, France
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3
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Forrest S, Welch M. Arming the troops: Post-translational modification of extracellular bacterial proteins. Sci Prog 2020; 103:36850420964317. [PMID: 33148128 PMCID: PMC10450907 DOI: 10.1177/0036850420964317] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein secretion is almost universally employed by bacteria. Some proteins are retained on the cell surface, whereas others are released into the extracellular milieu, often playing a key role in virulence. In this review, we discuss the diverse types and potential functions of post-translational modifications (PTMs) occurring to extracellular bacterial proteins.
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Affiliation(s)
- Suzanne Forrest
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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4
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Abstract
Mass spectrometry (MS) proteomics allows systematic identification, characterization, and relative quantification of the full suite of proteins in a biological sample, and is a powerful analytical approach for investigation of many aspects of the biology of Neisseria meningitidis. Here, we describe methods for robust and efficient sample preparation of the proteome of N. meningitidis suitable for diverse MS proteomics workflows.
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Affiliation(s)
- Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia.
- Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, QLD, Australia.
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5
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Mirgorodskaya E, Karlsson NG, Sihlbom C, Larson G, Nilsson CL. Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1065-1074. [PMID: 29644549 PMCID: PMC6003999 DOI: 10.1007/s13361-018-1912-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/06/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
The structural study of glycans and glycoconjugates is essential to assign their roles in homeostasis, health, and disease. Once dominated by nuclear magnetic resonance spectroscopy, mass spectrometric methods have become the preferred toolbox for the determination of glycan structures at high sensitivity. The patterns of such structures in different cellular states now allow us to interpret the sugar codes in health and disease, based on structure-function relationships. Dr. Catherine E. Costello was the 2017 recipient of the American Society for Mass Spectrometry's Distinguished Contribution Award. In this Perspective article, we describe her seminal work in a historical and geographical context and review the impact of her research accomplishments in the field.8 ᅟ Graphical abstract.
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Affiliation(s)
- Ekaterina Mirgorodskaya
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Box 413, SE-405 30, Gothenburg, Sweden
| | - Niclas G Karlsson
- Department of Medical Biochemistry, University of Gothenburg, Sahlgrenska Academy, Box 440, SE-405 30, Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, University of Gothenburg, Sahlgrenska Academy, Box 413, SE-405 30, Gothenburg, Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, University of Gothenburg, Sahlgrenska Academy, Institute of Biomedicine, SE-413 45, Gothenburg, Sweden
| | - Carol L Nilsson
- Department of Experimental Medical Science, Lund University, SE-223 62, Lund, Sweden.
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6
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Kachuk C, Doucette AA. The benefits (and misfortunes) of SDS in top-down proteomics. J Proteomics 2018; 175:75-86. [DOI: 10.1016/j.jprot.2017.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/19/2017] [Accepted: 03/03/2017] [Indexed: 12/18/2022]
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7
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Calvete JJ, Petras D, Calderón-Celis F, Lomonte B, Encinar JR, Sanz-Medel A. Protein-species quantitative venomics: looking through a crystal ball. J Venom Anim Toxins Incl Trop Dis 2017; 23:27. [PMID: 28465678 PMCID: PMC5408492 DOI: 10.1186/s40409-017-0116-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/19/2017] [Indexed: 12/16/2022] Open
Abstract
In this paper we discuss recent significant developments in the field of venom research, specifically the emergence of top-down proteomic applications that allow achieving compositional resolution at the level of the protein species present in the venom, and the absolute quantification of the venom proteins (the term “protein species” is used here to refer to all the different molecular forms in which a protein can be found. Please consult the special issue of Jornal of Proteomics “Towards deciphering proteomes via the proteoform, protein speciation, moonlighting and protein code concepts” published in 2016, vol. 134, pages 1-202). Challenges remain to be solved in order to achieve a compact and automated platform with which to routinely carry out comprehensive quantitative analysis of all toxins present in a venom. This short essay reflects the authors’ view of the immediate future in this direction for the proteomic analysis of venoms, particularly of snakes.
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Affiliation(s)
- Juan J Calvete
- Structural and Functional Venomics Laboratory, Instituto de Biomedicina de Valencia, C.S.I.C, Jaime Roig 11, 46010 Valencia, Spain
| | - Daniel Petras
- Skaggs School of Pharmacy & Pharmaceutical Sciences, University of California-San Diego, La Jolla, CA USA
| | | | - Bruno Lomonte
- Instituto Clodomiro Picado, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Jorge Ruiz Encinar
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
| | - Alfredo Sanz-Medel
- Department of Physical and Analytical Chemistry, University of Oviedo, Oviedo, Spain
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8
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Banazadeh A, Veillon L, Wooding KM, Zabet-Moghaddam M, Mechref Y. Recent advances in mass spectrometric analysis of glycoproteins. Electrophoresis 2016; 38:162-189. [PMID: 27757981 DOI: 10.1002/elps.201600357] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 09/23/2016] [Accepted: 09/24/2016] [Indexed: 12/13/2022]
Abstract
Glycosylation is one of the most common posttranslational modifications of proteins that plays essential roles in various biological processes, including protein folding, host-pathogen interaction, immune response, and inflammation and aberrant protein glycosylation is a well-known event in various disease states including cancer. As a result, it is critical to develop rapid and sensitive methods for the analysis of abnormal glycoproteins associated with diseases. Mass spectrometry (MS) in conjunction with different separation methods, such as capillary electrophoresis (CE), ion mobility (IM), and high performance liquid chromatography (HPLC) has become a popular tool for glycoprotein analysis, providing highly informative fragments for structural identification of glycoproteins. This review provides an overview of the developments and accomplishments in the field of glycomics and glycoproteomics reported between 2014 and 2016.
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Affiliation(s)
- Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Lucas Veillon
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Kerry M Wooding
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | | | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA.,Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX, USA
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9
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Ruhaak LR, van der Burgt YE, Cobbaert CM. Prospective applications of ultrahigh resolution proteomics in clinical mass spectrometry. Expert Rev Proteomics 2016; 13:1063-1071. [DOI: 10.1080/14789450.2016.1253477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Yuri E.M. van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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10
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Vorontsov EA, Rensen E, Prangishvili D, Krupovic M, Chamot-Rooke J. Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics. Mol Cell Proteomics 2016; 15:3388-3404. [PMID: 27555370 PMCID: PMC5098037 DOI: 10.1074/mcp.m116.058073] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 07/06/2016] [Indexed: 12/18/2022] Open
Abstract
Protein post-translational methylation has been reported to occur in archaea, including members of the genus Sulfolobus, but has never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modification are the chromatin proteins that have been described to be methylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of this modification and its dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus LAL14/1, we performed a global and deep proteomic analysis using a combination of high-throughput bottom-up and top-down approaches on a single high-resolution mass spectrometer. 1,931 methylation sites on 751 proteins were found by the bottom-up analysis, with methylation sites on 526 proteins monitored throughout three cell culture growth stages: early-exponential, mid-exponential, and stationary. The top-down analysis revealed 3,978 proteoforms arising from 681 proteins, including 292 methylated proteoforms, 85 of which were comprehensively characterized. Methylated proteoforms of the five chromatin proteins (Alba1, Alba2, Cren7, Sul7d1, Sul7d2) were fully characterized by a combination of bottom-up and top-down data. The top-down analysis also revealed an increase of methylation during cell growth for two chromatin proteins, which had not been evidenced by bottom-up. These results shed new light on the ubiquitous lysine methylation throughout the S. islandicus proteome. Furthermore, we found that S. islandicus proteins are frequently acetylated at the N terminus, following the removal of the N-terminal methionine. This study highlights the great value of combining bottom-up and top-down proteomics for obtaining an unprecedented level of accuracy in detecting differentially modified intact proteoforms. The data have been deposited to the ProteomeXchange with identifiers PXD003074 and PXD004179.
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Affiliation(s)
- Egor A Vorontsov
- From the ‡Structural Mass Spectrometry and Proteomics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 75015 Paris, France
| | - Elena Rensen
- §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - David Prangishvili
- §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France
| | - Mart Krupovic
- §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France; julia.chamot-rooke@pasteur
| | - Julia Chamot-Rooke
- From the ‡Structural Mass Spectrometry and Proteomics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 75015 Paris, France; julia.chamot-rooke@pasteur
- ¶UMR3528 CNRS, Paris, France
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11
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Nivaskumar M, Santos-Moreno J, Malosse C, Nadeau N, Chamot-Rooke J, Tran Van Nhieu G, Francetic O. Pseudopilin residue E5 is essential for recruitment by the type 2 secretion system assembly platform. Mol Microbiol 2016; 101:924-41. [DOI: 10.1111/mmi.13432] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Mangayarkarasi Nivaskumar
- Department of Microbiology, Laboratory of Macromolecular Systems and Signalling; Institut Pasteur, CNRS ERL3526; 25 rue du Dr Roux 75724 Paris, Cedex 15 France
- Université Paris Diderot (Paris 7) Sorbonne Paris Cité
| | - Javier Santos-Moreno
- Université Paris Diderot (Paris 7) Sorbonne Paris Cité
- Laboratory of Intercellular Communication and Microbial Infections; CIRB, Collège de France; Paris France
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1050; France
- Centre National de la Recherche Scientifique (CNRS), UMR7241; France
- MEMOLIFE Laboratory of Excellence and Paris Science Lettre; France
| | - Christian Malosse
- Structural Mass spectrometry and Proteomics unit; CNRS UMR3528, Institut Pasteur; Paris France
| | - Nathalie Nadeau
- Department of Microbiology, Laboratory of Macromolecular Systems and Signalling; Institut Pasteur, CNRS ERL3526; 25 rue du Dr Roux 75724 Paris, Cedex 15 France
| | - Julia Chamot-Rooke
- Structural Mass spectrometry and Proteomics unit; CNRS UMR3528, Institut Pasteur; Paris France
| | - Guy Tran Van Nhieu
- Laboratory of Intercellular Communication and Microbial Infections; CIRB, Collège de France; Paris France
- Institut National de la Santé et de la Recherche Médicale (Inserm) U1050; France
- Centre National de la Recherche Scientifique (CNRS), UMR7241; France
- MEMOLIFE Laboratory of Excellence and Paris Science Lettre; France
| | - Olivera Francetic
- Department of Microbiology, Laboratory of Macromolecular Systems and Signalling; Institut Pasteur, CNRS ERL3526; 25 rue du Dr Roux 75724 Paris, Cedex 15 France
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12
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Önder Ö, Sidoli S, Carroll M, Garcia BA. Progress in epigenetic histone modification analysis by mass spectrometry for clinical investigations. Expert Rev Proteomics 2016; 12:499-517. [PMID: 26400466 DOI: 10.1586/14789450.2015.1084231] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Chromatin biology and epigenetics are scientific fields that are rapid expanding due to their fundamental role in understanding cell development, heritable characters and progression of diseases. Histone post-translational modifications (PTMs) are major regulators of the epigenetic machinery due to their ability to modulate gene expression, DNA repair and chromosome condensation. Large-scale strategies based on mass spectrometry have been impressively improved in the last decade, so that global changes of histone PTM abundances are quantifiable with nearly routine proteomics analyses and it is now possible to determine combinatorial patterns of modifications. Presented here is an overview of the most utilized and newly developed proteomics strategies for histone PTM characterization and a number of case studies where epigenetic mechanisms have been comprehensively characterized. Moreover, a number of current epigenetic therapies are illustrated, with an emphasis on cancer.
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Affiliation(s)
- Özlem Önder
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA.,b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Simone Sidoli
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Martin Carroll
- a 1 Division of Hematology and Oncology, Philadelphia, 19104, USA
| | - Benjamin A Garcia
- b 2 Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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13
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Eichberg S, Sanz L, Calvete JJ, Pla D. Constructing comprehensive venom proteome reference maps for integrative venomics. Expert Rev Proteomics 2016; 12:557-73. [PMID: 26400467 DOI: 10.1586/14789450.2015.1073590] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Understanding the molecular basis of complex adaptive traits, such as snake venom, demands qualitative and quantitative comparisons of the temporal and spatial patterns of venom variation. Here, we assessed the proof-of-concept that locus-resolved reference venom proteome maps can be achieved through efficient pre-MS venom proteome decomplexation, peptide-centric MS/MS analysis and species-specific database searching. METHODS Venom proteome components were fractionated and quantified by RP-HPLC, SDS-PAGE and 2DE prior to LC-MS/MS matching against a species-specific transcriptomic dataset. RESULTS Combination of RP-HPLC/SDS-PAGE and 2DE followed by LC-MS/MS showed the existence of ∼178-180 venom protein species generated from ∼48 unique transcripts. CONCLUSIONS Our results underscore that if sufficient pre-MS and MS efforts are applied, comprehensive venom maps can be achieved. And - equally important - dissociating the venom decomplexing steps from the protein identification process represents the key to achieving a quantitative and locus-resolved insight of the venom proteome.
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Affiliation(s)
- Susann Eichberg
- a 1 Beuth Hochschule für Technik Berlin, Luxemburger Straße 10, 13353 Berlin, Germany
| | - Libia Sanz
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Juan J Calvete
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
| | - Davinia Pla
- b 2 Laboratorio de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, Valencia, Spain
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14
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Serra A, Gallart-Palau X, See-Toh RSE, Hemu X, Tam JP, Sze SK. Commercial processed soy-based food product contains glycated and glycoxidated lunasin proteoforms. Sci Rep 2016; 6:26106. [PMID: 27189269 PMCID: PMC4870627 DOI: 10.1038/srep26106] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 04/26/2016] [Indexed: 02/07/2023] Open
Abstract
Nutraceuticals have been proposed to exert positive effects on human health and confer protection against many chronic diseases. A major bioactive component of soy-based foods is lunasin peptide, which has potential to exert a major impact on the health of human consumers worldwide, but the biochemical features of dietary lunasin still remain poorly characterized. In this study, lunasin was purified from a soy-based food product via strong anion exchange solid phase extraction and then subjected to top-down mass spectrometry analysis that revealed in detail the molecular diversity of lunasin in processed soybean foods. We detected multiple glycated proteoforms together with potentially toxic advanced glycation end products (AGEs) derived from lunasin. In both cases, modification sites were Lys24 and Lys29 located at the helical region that shows structural homology with a conserved region of chromatin-binding proteins. The identified post-translational modifications may have an important repercussion on lunasin epigenetic regulatory capacity. Taking together, our results demonstrate the importance of proper chemical characterization of commercial processed food products to assess their impact on consumer's health and risk of chronic diseases.
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Affiliation(s)
- Aida Serra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Rachel Su-En See-Toh
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Xinya Hemu
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [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: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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16
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Vinella D, Fischer F, Vorontsov E, Gallaud J, Malosse C, Michel V, Cavazza C, Robbe-Saule M, Richaud P, Chamot-Rooke J, Brochier-Armanet C, De Reuse H. Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization. PLoS Pathog 2015; 11:e1005312. [PMID: 26641249 PMCID: PMC4671568 DOI: 10.1371/journal.ppat.1005312] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. Virulence of the human gastric pathogen Helicobacter pylori is dependent on nickel, cofactor of two enzymes essential for in vivo colonization, urease and [NiFe] hydrogenase. We found that two small paralogous nickel-binding proteins with high content in Histidine (Hpn and Hpn-2) play a central role in maintaining non-toxic intracellular nickel content and in controlling its intracellular trafficking. Measurements of metal resistance, intracellular nickel contents, urease activities and interactomic analysis were performed. We observed that Hpn acts as a nickel-sequestration protein, while Hpn-2 is not. In vivo, Hpn and Hpn-2 form homo-multimers, interact with each other, Hpn interacts with the UreA urease subunit while Hpn and Hpn-2 interact with the HypAB hydrogenase maturation proteins. In addition, Hpn-2 is directly or indirectly restricting urease activity while Hpn is required for full urease activation. Based on these data, we present a model where Hpn and Hpn-2 participate in a common pathway of controlled nickel transfer to urease. Using bioinformatics and top-down proteomics to identify the predicted proteins, we established that Hpn-2 is only expressed by H. pylori and its closely related species Helicobacter acinonychis. Hpn was detected in every gastric Helicobacter species tested and is absent from the enterohepatic Helicobacter species. Our phylogenomic analysis revealed that Hpn acquisition was concomitant with the specialization of Helicobacter to colonization of the gastric environment and the duplication at the origin of hpn-2 occurred in the common ancestor of H. pylori and H. acinonychis. Finally, Hpn and Hpn-2 were found to be required for colonization of the mouse model by H. pylori. Our data show that during evolution of the Helicobacter genus, acquisition of Hpn and Hpn-2 by gastric Helicobacter species constituted a decisive evolutionary event to allow Helicobacter to colonize the hostile gastric environment, in which no other bacteria persistently thrives. This acquisition was key for the emergence of one of the most successful bacterial pathogens, H. pylori. Helicobacter pylori is a bacterium that persistently colonizes the stomach of half of the human population. Infection by H. pylori is associated with gastritis, peptic ulcer disease and adenocarcinoma. To resist gastric acidity and proliferate in the stomach, H. pylori relies on urease, an enzyme that contains a nickel-metallocenter at its active site. Thus, nickel is a virulence determinant for H. pylori. Our aim is to characterize how H. pylori controls the intracellular nickel concentration to avoid toxicity, which protein partners are involved, and how they impact urease activity and virulence. We characterized two H. pylori proteins, Hpn and Hpn-2 that are rich in Histidine residues. We demonstrated that Hpn is involved in nickel sequestration, that the two proteins interact with each other and that their combined activities participate in a nickel transfer pathway to urease. Hpn is only expressed in gastric Helicobacter species able to colonize the stomach and Hpn-2 is restricted to the H. pylori and its close relative H. acinonychis. We found that both proteins are essential for colonization of a mouse model by H. pylori. We conclude that during evolution, the acquisition of Hpn and Hpn-2 by gastric Helicobacter species was decisive for their capacity to colonize the stomach.
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Affiliation(s)
- Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | - Frédéric Fischer
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | - Egor Vorontsov
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, Paris, France
| | - Julien Gallaud
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Christian Malosse
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, Paris, France
| | - Valérie Michel
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | | | - Marie Robbe-Saule
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | - Pierre Richaud
- CEA, DSV, IBEB, SBVME and CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France and Aix Marseille Université, BVME UMR7265, Marseille, France
| | - Julia Chamot-Rooke
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, Paris, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Hilde De Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
- * E-mail:
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17
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Gault J, Ferber M, Machata S, Imhaus AF, Malosse C, Charles-Orszag A, Millien C, Bouvier G, Bardiaux B, Péhau-Arnaudet G, Klinge K, Podglajen I, Ploy MC, Seifert HS, Nilges M, Chamot-Rooke J, Duménil G. Neisseria meningitidis Type IV Pili Composed of Sequence Invariable Pilins Are Masked by Multisite Glycosylation. PLoS Pathog 2015; 11:e1005162. [PMID: 26367394 PMCID: PMC4569582 DOI: 10.1371/journal.ppat.1005162] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 08/20/2015] [Indexed: 12/27/2022] Open
Abstract
The ability of pathogens to cause disease depends on their aptitude to escape the immune system. Type IV pili are extracellular filamentous virulence factors composed of pilin monomers and frequently expressed by bacterial pathogens. As such they are major targets for the host immune system. In the human pathogen Neisseria meningitidis, strains expressing class I pilins contain a genetic recombination system that promotes variation of the pilin sequence and is thought to aid immune escape. However, numerous hypervirulent clinical isolates express class II pilins that lack this property. This raises the question of how they evade immunity targeting type IV pili. As glycosylation is a possible source of antigenic variation it was investigated using top-down mass spectrometry to provide the highest molecular precision on the modified proteins. Unlike class I pilins that carry a single glycan, we found that class II pilins display up to 5 glycosylation sites per monomer on the pilus surface. Swapping of pilin class and genetic background shows that the pilin primary structure determines multisite glycosylation while the genetic background determines the nature of the glycans. Absence of glycosylation in class II pilins affects pilus biogenesis or enhances pilus-dependent aggregation in a strain specific fashion highlighting the extensive functional impact of multisite glycosylation. Finally, molecular modeling shows that glycans cover the surface of class II pilins and strongly decrease antibody access to the polypeptide chain. This strongly supports a model where strains expressing class II pilins evade the immune system by changing their sugar structure rather than pilin primary structure. Overall these results show that sequence invariable class II pilins are cloaked in glycans with extensive functional and immunological consequences. During infection pathogens and their host engage in a series of measures and counter-measures to promote their own survival: pathogens express virulence factors, the immune system targets these surface structures and pathogens modify them to evade detection. Like numerous bacterial pathogens, Neisseria meningitidis express type IV pili, long filamentous adhesive structures composed of pilins. Intriguingly the amino acid sequences of pilins from most hypervirulent strains do not vary, raising the question of how they evade the immune system. This study shows that the pilus structure is completely coated with sugars thus limiting access of antibodies to the pilin polypeptide chain. We propose that multisite glycosylation and thus variation in the type of sugar mediates immune evasion in these strains.
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MESH Headings
- Amino Acid Sequence
- Bacterial Adhesion
- Cell Line
- Cells, Cultured
- Conserved Sequence
- Endothelium, Vascular/cytology
- Endothelium, Vascular/immunology
- Endothelium, Vascular/microbiology
- Endothelium, Vascular/pathology
- Fimbriae Proteins/chemistry
- Fimbriae Proteins/genetics
- Fimbriae Proteins/metabolism
- Fimbriae, Bacterial/immunology
- Fimbriae, Bacterial/metabolism
- Fimbriae, Bacterial/ultrastructure
- Gene Deletion
- Glycosylation
- Host-Pathogen Interactions
- Human Umbilical Vein Endothelial Cells/cytology
- Human Umbilical Vein Endothelial Cells/immunology
- Human Umbilical Vein Endothelial Cells/microbiology
- Human Umbilical Vein Endothelial Cells/pathology
- Humans
- Immune Evasion
- Meningococcal Infections/immunology
- Meningococcal Infections/metabolism
- Meningococcal Infections/microbiology
- Meningococcal Infections/pathology
- Microscopy, Electron, Transmission
- Models, Molecular
- Neisseria meningitidis/immunology
- Neisseria meningitidis/metabolism
- Neisseria meningitidis/ultrastructure
- Protein Processing, Post-Translational
- Sequence Homology, Amino Acid
- Species Specificity
- Surface Properties
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Affiliation(s)
- Joseph Gault
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Mathias Ferber
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Silke Machata
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Anne-Flore Imhaus
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Christian Malosse
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Arthur Charles-Orszag
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Corinne Millien
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
| | - Guillaume Bouvier
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | | | - Kelly Klinge
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Isabelle Podglajen
- Service de Microbiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges-Pompidou, Paris, France
| | - Marie Cécile Ploy
- INSERM UMR1092, Faculté de Médecine, Université de Limoges, Limoges, France
| | - H. Steven Seifert
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Michael Nilges
- Institut Pasteur, Unité de Bioinformatique Structurale, CNRS UMR 3528, Département de Biologie Structurale et Chimie, Paris, France
| | - Julia Chamot-Rooke
- Structural Mass Spectrometry and Proteomics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France
| | - Guillaume Duménil
- INSERM, U970, Paris Cardiovascular Research Center, Paris, France
- Université Paris Descartes, Faculté de Médecine Paris Descartes, Paris, France
- * E-mail:
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18
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Application of “Omics” Technologies for Diagnosis and Pathogenesis of Neurological Infections. Curr Neurol Neurosci Rep 2015. [DOI: 10.1007/s11910-015-0580-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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19
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Tan FY, Tang CM, Exley RM. Sugar coating: bacterial protein glycosylation and host–microbe interactions. Trends Biochem Sci 2015; 40:342-50. [DOI: 10.1016/j.tibs.2015.03.016] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 03/11/2015] [Accepted: 03/31/2015] [Indexed: 01/29/2023]
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20
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Petras D, Heiss P, Süssmuth RD, Calvete JJ. Venom Proteomics of Indonesian King Cobra, Ophiophagus hannah: Integrating Top-Down and Bottom-Up Approaches. J Proteome Res 2015; 14:2539-56. [DOI: 10.1021/acs.jproteome.5b00305] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Daniel Petras
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Paul Heiss
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Roderich D. Süssmuth
- Institut
für Chemie, Technische Universität Berlin, Müller-Breslau-Straße
10, 10623 Berlin, Germany
| | - Juan J. Calvete
- Laboratorio
de Venómica Estructural y Funcional, Instituto de Biomedicina de Valencia, CSIC, 46010 Valencia, Spain
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21
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Feng S, Zhou L, Huang C, Xie K, Nice EC. Interactomics: toward protein function and regulation. Expert Rev Proteomics 2015; 12:37-60. [DOI: 10.1586/14789450.2015.1000870] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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22
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Shining a spotlight on intact proteins. Proteomics 2014; 14:1125-7. [DOI: 10.1002/pmic.201470073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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