1
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Duchovni L, Shmunis G, Lobel L. Posttranslational modifications: an emerging functional layer of diet-host-microbe interactions. mBio 2024:e0238724. [PMID: 39254316 DOI: 10.1128/mbio.02387-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/11/2024] Open
Abstract
The microbiome plays a vital role in human health, with changes in its composition impacting various aspects of the body. Posttranslational modification (PTM) regulates protein activity by attaching chemical groups to amino acids in an enzymatic or non-enzymatic manner. PTMs offer fast and dynamic regulation of protein expression and can be influenced by specific dietary components that induce PTM events in gut microbiomes and their hosts. PTMs on microbiome proteins have been found to contribute to host-microbe interactions. For example, in Escherichia coli, S-sulfhydration of tryptophanase regulates uremic toxin production and chronic kidney disease in mice. On a broader microbial scale, the microbiomes of patients with inflammatory bowel disease exhibit distinct PTM patterns in their metaproteomes. Moreover, pathogens and commensals can alter host PTM profiles through protein secretion and diet-regulated metabolic shifts. The emerging field of metaPTMomics focuses on understanding PTM profiles in the microbiota, their association with lifestyle factors like diet, and their functional effects on host-microbe interactions.
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Affiliation(s)
- Lirit Duchovni
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Genrieta Shmunis
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
| | - Lior Lobel
- The Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
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2
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Dang J, Shu J, Wang R, Yu H, Chen Z, Yan W, Zhao B, Ding L, Wang Y, Hu H, Li Z. The glycopatterns of Pseudomonas aeruginosa as a potential biomarker for its carbapenem resistance. Microbiol Spectr 2023; 11:e0200123. [PMID: 37861315 PMCID: PMC10714932 DOI: 10.1128/spectrum.02001-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/08/2023] [Indexed: 10/21/2023] Open
Abstract
IMPORTANCE Bacterial surface glycans are an attractive therapeutic target in response to antibiotics; however, current knowledge of the corresponding mechanisms is rather limited. Antimicrobial susceptibility testing, genome sequencing, and MALDI-TOF MS, commonly used in recent years to analyze bacterial resistance, are unable to rapidly and efficiently establish associations between glycans and resistance. The discovery of new antimicrobial strategies still requires the introduction of promising analytical methods. In this study, we applied lectin microarray technology and a machine-learning model to screen for important glycan structures associated with carbapenem-resistant P. aeruginosa. This work highlights that specific glycopatterns can be important biomarkers associated with bacterial antibiotic resistance, which promises to provide a rapid entry point for exploring new resistance mechanisms in pathogens.
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Affiliation(s)
- Jing Dang
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Jian Shu
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Ruiying Wang
- Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Hanjie Yu
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhuo Chen
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Wenbo Yan
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Bingxiang Zhao
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Li Ding
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Yuzi Wang
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Huizheng Hu
- Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Zheng Li
- Laboratory of Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
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3
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Mahameed M, Wang P, Xue S, Fussenegger M. Engineering receptors in the secretory pathway for orthogonal signalling control. Nat Commun 2022; 13:7350. [PMID: 36446786 PMCID: PMC9708828 DOI: 10.1038/s41467-022-35161-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 11/21/2022] [Indexed: 12/02/2022] Open
Abstract
Synthetic receptors targeted to the secretory pathway often fail to exhibit the expected activity due to post-translational modifications (PTMs) and/or improper folding. Here, we engineered synthetic receptors that reside in the cytoplasm, inside the endoplasmic reticulum (ER), or on the plasma membrane through orientation adjustment of the receptor parts and by elimination of dysfunctional PTMs sites. The cytoplasmic receptors consist of split-TEVp domains that reconstitute an active protease through chemically-induced dimerization (CID) that is triggered by rapamycin, abscisic acid, or gibberellin. Inside the ER, however, some of these receptors were non-functional, but their activity was restored by mutagenesis of cysteine and asparagine, residues that are typically associated with PTMs. Finally, we engineered orthogonal chemically activated cell-surface receptors (OCARs) consisting of the Notch1 transmembrane domain fused to cytoplasmic tTA and extracellular CID domains. Mutagenesis of cysteine residues in CID domains afforded functional OCARs which enabled fine-tuning of orthogonal signalling in mammalian cells.
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Affiliation(s)
- Mohamed Mahameed
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Pengli Wang
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Shuai Xue
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland
| | - Martin Fussenegger
- Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, CH-4058, Basel, Switzerland.
- Faculty of Life Science, University of Basel, Mattenstrasse 26, CH-4058, Basel, Switzerland.
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4
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Integrated mass spectrometry-based multi-omics for elucidating mechanisms of bacterial virulence. Biochem Soc Trans 2021; 49:1905-1926. [PMID: 34374408 DOI: 10.1042/bst20191088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/19/2021] [Accepted: 07/21/2021] [Indexed: 11/17/2022]
Abstract
Despite being considered the simplest form of life, bacteria remain enigmatic, particularly in light of pathogenesis and evolving antimicrobial resistance. After three decades of genomics, we remain some way from understanding these organisms, and a substantial proportion of genes remain functionally unknown. Methodological advances, principally mass spectrometry (MS), are paving the way for parallel analysis of the proteome, metabolome and lipidome. Each provides a global, complementary assay, in addition to genomics, and the ability to better comprehend how pathogens respond to changes in their internal (e.g. mutation) and external environments consistent with infection-like conditions. Such responses include accessing necessary nutrients for survival in a hostile environment where co-colonizing bacteria and normal flora are acclimated to the prevailing conditions. Multi-omics can be harnessed across temporal and spatial (sub-cellular) dimensions to understand adaptation at the molecular level. Gene deletion libraries, in conjunction with large-scale approaches and evolving bioinformatics integration, will greatly facilitate next-generation vaccines and antimicrobial interventions by highlighting novel targets and pathogen-specific pathways. MS is also central in phenotypic characterization of surface biomolecules such as lipid A, as well as aiding in the determination of protein interactions and complexes. There is increasing evidence that bacteria are capable of widespread post-translational modification, including phosphorylation, glycosylation and acetylation; with each contributing to virulence. This review focuses on the bacterial genotype to phenotype transition and surveys the recent literature showing how the genome can be validated at the proteome, metabolome and lipidome levels to provide an integrated view of organism response to host conditions.
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5
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Yoshida S, Inaba H, Nomura R, Murakami M, Yasuda H, Nakano K, Matsumoto-Nakano M. Efficacy of FimA antibody and clindamycin in silkworm larvae stimulated with Porphyromonas gulae. J Oral Microbiol 2021; 13:1914499. [PMID: 33968314 PMCID: PMC8079003 DOI: 10.1080/20002297.2021.1914499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Objective: Porphyromonas gulae, a major periodontal pathogen in animals, possesses fimbriae that have been classified into three genotypes (A, B, C) based on the diversity of fimA genes encoding fimbrillin protein (FimA). P. gulae strains with type C fimbriae were previously shown to be more virulent than other types. In this study, we further examined the host toxicity mediated by P. gulae fimbriae by constructing recombinant FimA (rFimA) expression vectors for each genotype and raised antibodies to the purified proteins. Methods and Results: All larvae died within 204 h following infection with P. gulae type C at the low-dose infection, whereas type A and B did not. Among fimA types, the survival rates of the larvae injected with rFimA type C were remarkably decreased, while the survival rates of the larvae injected with rFimA type A and type B were greater than 50%. Clindamycin treatment inhibited the growth of type C strains in a dose-dependent manner, resulting in an increased rate of silkworm survival. Finally, type C rFimA-specific antiserum prolonged the survival of silkworm larvae stimulated by infection with P. gulae type C strain or injection of rFimA type C protein. Conclusion: These results suggested that type C fimbriae have high potential for enhancement of bacterial pathogenesis, and that both clindamycin and anti-type C rFimA-specific antibodies are potent inhibitors of type C fimbriae-induced toxicity. This is the first report to establish a silkworm infection model using P. gulae for toxicity assessment.
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Affiliation(s)
- Sho Yoshida
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Hiroaki Inaba
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Ryota Nomura
- Department of Pediatric Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Masaru Murakami
- Departments of Pharmacology, Veterinary Public Health II and Molecular Biology, School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | | | - Kazuhiko Nakano
- Department of Pediatric Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Michiyo Matsumoto-Nakano
- Department of Pediatric Dentistry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
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6
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Sterlin D, Fadlallah J, Adams O, Fieschi C, Parizot C, Dorgham K, Rajkumar A, Autaa G, El-Kafsi H, Charuel JL, Juste C, Jönsson F, Candela T, Wardemann H, Aubry A, Capito C, Brisson H, Tresallet C, Cummings RD, Larsen M, Yssel H, von Gunten S, Gorochov G. Human IgA binds a diverse array of commensal bacteria. J Exp Med 2020; 217:133553. [PMID: 31891367 PMCID: PMC7062531 DOI: 10.1084/jem.20181635] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 05/10/2019] [Accepted: 11/22/2019] [Indexed: 11/23/2022] Open
Abstract
In humans, several grams of IgA are secreted every day in the intestinal lumen. While only one IgA isotype exists in mice, humans secrete IgA1 and IgA2, whose respective relations with the microbiota remain elusive. We compared the binding patterns of both polyclonal IgA subclasses to commensals and glycan arrays and determined the reactivity profile of native human monoclonal IgA antibodies. While most commensals are dually targeted by IgA1 and IgA2 in the small intestine, IgA1+IgA2+ and IgA1−IgA2+ bacteria coexist in the colon lumen, where Bacteroidetes is preferentially targeted by IgA2. We also observed that galactose-α terminated glycans are almost exclusively recognized by IgA2. Although bearing signs of affinity maturation, gut-derived IgA monoclonal antibodies are cross-reactive in the sense that they bind to multiple bacterial targets. Private anticarbohydrate-binding patterns, observed at clonal level as well, could explain these apparently opposing features of IgA, being at the same time cross-reactive and selective in its interactions with the microbiota.
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Affiliation(s)
- Delphine Sterlin
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jehane Fadlallah
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Olivia Adams
- Institute of Pharmacology, University of Bern, Bern, Switzerland
| | - Claire Fieschi
- Université Paris Diderot Paris 7, Department of Clinical Immunology, Hôpital Saint-Louis, Assistance Publique Hôpitaux de Paris, EA 3518, Paris, France
| | - Christophe Parizot
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Karim Dorgham
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Asok Rajkumar
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Gaëlle Autaa
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Hela El-Kafsi
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Jean-Luc Charuel
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Catherine Juste
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Friederike Jönsson
- Unit of Antibodies in Therapy and Pathology, Institut Pasteur, UMR1222 Institut national de la santé et de la recherche médicale, Paris, France
| | - Thomas Candela
- EA 4043, Unité Bactéries Pathogènes et Santé, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Hedda Wardemann
- Division of B Cell Immunology, German Cancer Research Center, Heidelberg, Germany
| | - Alexandra Aubry
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Carmen Capito
- EA 4043, Unité Bactéries Pathogènes et Santé, Université Paris-Sud, Université Paris-Saclay, Châtenay-Malabry, France
| | - Hélène Brisson
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Christophe Tresallet
- Sorbonne Université, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Martin Larsen
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Hans Yssel
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | | | - Guy Gorochov
- Sorbonne Université, Institut national de la santé et de la recherche médicale, Centre d'Immunologie et des Maladies Infectieuses, Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
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7
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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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8
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Kuiper EG, Dey D, LaMore PA, Owings JP, Prezioso SM, Goldberg JB, Conn GL. Substrate recognition by the Pseudomonas aeruginosa EF-Tu-modifying methyltransferase EftM. J Biol Chem 2019; 294:20109-20121. [PMID: 31753919 DOI: 10.1074/jbc.ra119.011213] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/20/2019] [Indexed: 01/09/2023] Open
Abstract
The opportunistic bacterial pathogen Pseudomonas aeruginosa is a leading cause of serious infections in individuals with cystic fibrosis, compromised immune systems, or severe burns. P. aeruginosa adhesion to host epithelial cells is enhanced by surface-exposed translation elongation factor EF-Tu carrying a Lys-5 trimethylation, incorporated by the methyltransferase EftM. Thus, the EF-Tu modification by EftM may represent a target to prevent P. aeruginosa infections in vulnerable individuals. Here, we extend our understanding of EftM activity by defining the molecular mechanism by which it recognizes EF-Tu. Acting on the observation that EftM can bind to EF-Tu lacking its N-terminal peptide (encompassing the Lys-5 target site), we generated an EftM homology model and used it in protein/protein docking studies to predict EftM/EF-Tu interactions. Using site-directed mutagenesis of residues in both proteins, coupled with binding and methyltransferase activity assays, we experimentally validated the predicted protein/protein interface. We also show that EftM cannot methylate the isolated N-terminal EF-Tu peptide and that binding-induced conformational changes in EftM are likely needed to enable placement of the first 5-6 amino acids of EF-Tu into a conserved peptide-binding channel in EftM. In this channel, a group of residues that are highly conserved in EftM proteins position the N-terminal sequence to facilitate Lys-5 modification. Our findings reveal that EftM employs molecular strategies for substrate recognition common among both class I (Rossmann fold) and class II (SET domain) methyltransferases and pave the way for studies seeking a deeper understanding of EftM's mechanism of action on EF-Tu.
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Affiliation(s)
- Emily G Kuiper
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322.,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Paige A LaMore
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322
| | - Joshua P Owings
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322
| | - Samantha M Prezioso
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322.,Graduate Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322
| | - Joanna B Goldberg
- Department of Pediatrics, Division of Pulmonology, Allergy/Immunology, Cystic Fibrosis and Sleep, and Emory Children's Center for Cystic Fibrosis Research, Emory University and Children's Healthcare of Atlanta, Atlanta, Georgia 30322.,Graduate Program in Microbiology and Molecular Genetics (MMG), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322.,Emory Antibiotic Resistance Center (ARC), Emory University School of Medicine, Atlanta, Georgia 30322
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia 30322 .,Graduate Program in Biochemistry, Cell and Developmental Biology (BCDB), Graduate Division of Biological and Biomedical Sciences (GDBBS), Emory University, Atlanta, Georgia 30322.,Emory Antibiotic Resistance Center (ARC), Emory University School of Medicine, Atlanta, Georgia 30322
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9
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Christensen DG, Baumgartner JT, Xie X, Jew KM, Basisty N, Schilling B, Kuhn ML, Wolfe AJ. Mechanisms, Detection, and Relevance of Protein Acetylation in Prokaryotes. mBio 2019; 10:e02708-18. [PMID: 30967470 PMCID: PMC6456759 DOI: 10.1128/mbio.02708-18] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Posttranslational modification of a protein, either alone or in combination with other modifications, can control properties of that protein, such as enzymatic activity, localization, stability, or interactions with other molecules. N-ε-Lysine acetylation is one such modification that has gained attention in recent years, with a prevalence and significance that rival those of phosphorylation. This review will discuss the current state of the field in bacteria and some of the work in archaea, focusing on both mechanisms of N-ε-lysine acetylation and methods to identify, quantify, and characterize specific acetyllysines. Bacterial N-ε-lysine acetylation depends on both enzymatic and nonenzymatic mechanisms of acetylation, and recent work has shed light into the regulation of both mechanisms. Technological advances in mass spectrometry have allowed researchers to gain insight with greater biological context by both (i) analyzing samples either with stable isotope labeling workflows or using label-free protocols and (ii) determining the true extent of acetylation on a protein population through stoichiometry measurements. Identification of acetylated lysines through these methods has led to studies that probe the biological significance of acetylation. General and diverse approaches used to determine the effect of acetylation on a specific lysine will be covered.
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Affiliation(s)
- D G Christensen
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
| | - J T Baumgartner
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - X Xie
- Buck Institute for Research on Aging, Novato, California, USA
| | - K M Jew
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - N Basisty
- Buck Institute for Research on Aging, Novato, California, USA
| | - B Schilling
- Buck Institute for Research on Aging, Novato, California, USA
| | - M L Kuhn
- Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA
| | - A J Wolfe
- Department of Microbiology and Immunology, Loyola University Chicago, Health Sciences Division, Stritch School of Medicine, Maywood, Illinois, USA
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10
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Hurtado Silva M, Berry IJ, Strange N, Djordjevic SP, Padula MP. Terminomics Methodologies and the Completeness of Reductive Dimethylation: A Meta-Analysis of Publicly Available Datasets. Proteomes 2019; 7:proteomes7020011. [PMID: 30934878 PMCID: PMC6631386 DOI: 10.3390/proteomes7020011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022] Open
Abstract
Methods for analyzing the terminal sequences of proteins have been refined over the previous decade; however, few studies have evaluated the quality of the data that have been produced from those methodologies. While performing global N-terminal labelling on bacteria, we observed that the labelling was not complete and investigated whether this was a common occurrence. We assessed the completeness of labelling in a selection of existing, publicly available N-terminomics datasets and empirically determined that amine-based labelling chemistry does not achieve complete labelling and potentially has issues with labelling amine groups at sequence-specific residues. This finding led us to conduct a thorough review of the historical literature that showed that this is not an unexpected finding, with numerous publications reporting incomplete labelling. These findings have implications for the quantitation of N-terminal peptides and the biological interpretations of these data.
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Affiliation(s)
- Mariella Hurtado Silva
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Iain J Berry
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
- The ithree Institute, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Natalie Strange
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Steven P Djordjevic
- The ithree Institute, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
| | - Matthew P Padula
- Proteomics Core Facility and School of Life Sciences, Faculty of Science, University of Technology Sydney, Broadway NSW 2007, Australia.
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11
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12
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Latousakis D, Juge N. How Sweet Are Our Gut Beneficial Bacteria? A Focus on Protein Glycosylation in Lactobacillus. Int J Mol Sci 2018; 19:ijms19010136. [PMID: 29301365 PMCID: PMC5796085 DOI: 10.3390/ijms19010136] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 02/07/2023] Open
Abstract
Protein glycosylation is emerging as an important feature in bacteria. Protein glycosylation systems have been reported and studied in many pathogenic bacteria, revealing an important diversity of glycan structures and pathways within and between bacterial species. These systems play key roles in virulence and pathogenicity. More recently, a large number of bacterial proteins have been found to be glycosylated in gut commensal bacteria. We present an overview of bacterial protein glycosylation systems (O- and N-glycosylation) in bacteria, with a focus on glycoproteins from gut commensal bacteria, particularly Lactobacilli. These emerging studies underscore the importance of bacterial protein glycosylation in the interaction of the gut microbiota with the host.
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Affiliation(s)
- Dimitrios Latousakis
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK.
| | - Nathalie Juge
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK.
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Mlecnik B, Galon J, Bindea G. Comprehensive functional analysis of large lists of genes and proteins. J Proteomics 2018; 171:2-10. [DOI: 10.1016/j.jprot.2017.03.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 03/13/2017] [Accepted: 03/19/2017] [Indexed: 01/16/2023]
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Starr AE, Deeke SA, Li L, Zhang X, Daoud R, Ryan J, Ning Z, Cheng K, Nguyen LVH, Abou-Samra E, Lavallée-Adam M, Figeys D. Proteomic and Metaproteomic Approaches to Understand Host–Microbe Interactions. Anal Chem 2017; 90:86-109. [DOI: 10.1021/acs.analchem.7b04340] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Amanda E. Starr
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Shelley A. Deeke
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Leyuan Li
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Xu Zhang
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Rachid Daoud
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - James Ryan
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Zhibin Ning
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Kai Cheng
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Linh V. H. Nguyen
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Elias Abou-Samra
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Mathieu Lavallée-Adam
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada
- Molecular Architecture of Life Program, Canadian Institute for Advanced Research, Toronto, Ontario, M5G 1M1, Canada
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15
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Berry IJ, Jarocki VM, Tacchi JL, Raymond BBA, Widjaja M, Padula MP, Djordjevic SP. N-terminomics identifies widespread endoproteolysis and novel methionine excision in a genome-reduced bacterial pathogen. Sci Rep 2017; 7:11063. [PMID: 28894154 PMCID: PMC5593965 DOI: 10.1038/s41598-017-11296-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/21/2017] [Indexed: 12/12/2022] Open
Abstract
Proteolytic processing alters protein function. Here we present the first systems-wide analysis of endoproteolysis in the genome-reduced pathogen Mycoplasma hyopneumoniae. 669 N-terminal peptides from 164 proteins were identified, demonstrating that functionally diverse proteins are processed, more than half of which 75 (53%) were accessible on the cell surface. Multiple cleavage sites were characterised, but cleavage with arginine in P1 predominated. Putative functions for a subset of cleaved fragments were assigned by affinity chromatography using heparin, actin, plasminogen and fibronectin as bait. Binding affinity was correlated with the number of cleavages in a protein, indicating that novel binding motifs are exposed, and protein disorder increases, after a cleavage event. Glyceraldehyde 3-phosphate dehydrogenase was used as a model protein to demonstrate this. We define the rules governing methionine excision, show that several aminopeptidases are involved, and propose that through processing, genome-reduced organisms can expand protein function.
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Affiliation(s)
- Iain J Berry
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Veronica M Jarocki
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Jessica L Tacchi
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Benjamin B A Raymond
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Michael Widjaja
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Matthew P Padula
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
| | - Steven P Djordjevic
- The ithree institute, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia. .,Proteomics Core Facility, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia.
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16
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Barel M, Charbit A. Role of Glycosylation/Deglycolysation Processes in Francisella tularensis Pathogenesis. Front Cell Infect Microbiol 2017; 7:71. [PMID: 28377902 PMCID: PMC5359314 DOI: 10.3389/fcimb.2017.00071] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/27/2017] [Indexed: 12/15/2022] Open
Abstract
Francisella tularensis is able to invade, survive and replicate inside a variety of cell types. However, in vivo F. tularensis preferentially enters host macrophages where it rapidly escapes to the cytosol to avoid phagosomal stresses and to multiply to high numbers. We previously showed that human monocyte infection by F. tularensis LVS triggered deglycosylation of the glutamine transporter SLC1A5. However, this deglycosylation, specifically induced by Francisella infection, was not restricted to SLC1A5, suggesting that host protein deglycosylation processes in general might contribute to intracellular bacterial adaptation. Indeed, we later found that Francisella infection modulated the transcription of numerous glycosidase and glycosyltransferase genes in human macrophages and analysis of cell extracts revealed an important increase of N and O-protein glycosylation. In eukaryotic cells, glycosylation has significant effects on protein folding, conformation, distribution, stability, and activity and dysfunction of protein glycosylation may lead to development of diseases like cancer and pathogenesis of infectious diseases. Pathogenic bacteria have also evolved dedicated glycosylation machineries and have notably been shown to use these glycoconjugates as ligands to specifically interact with the host. In this review, we will focus on Francisella and summarize our current understanding of the importance of these post-translational modifications on its intracellular niche adaptation.
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Affiliation(s)
- Monique Barel
- Sorbonne Paris Cité, Bâtiment Leriche, Université Paris DescartesParis, France; Institut National de la Santé et de la Recherche Médicale, Institut Necker-Enfants Malades, INSERM U1151 -Team 11, Pathogenesis of Systemic InfectionsParis, France; Centre National de la Recherche Scientifique, UMR8253Paris, France
| | - Alain Charbit
- Sorbonne Paris Cité, Bâtiment Leriche, Université Paris DescartesParis, France; Institut National de la Santé et de la Recherche Médicale, Institut Necker-Enfants Malades, INSERM U1151 -Team 11, Pathogenesis of Systemic InfectionsParis, France; Centre National de la Recherche Scientifique, UMR8253Paris, France
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