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Janhvi S, Saini S, Singh V, Sharma T, Rao A. ProGlycProt V3.0: updated insights into prokaryotic glycoproteins and their glycosyltransferases. Glycobiology 2024; 34:cwad103. [PMID: 38153163 DOI: 10.1093/glycob/cwad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/15/2023] [Accepted: 12/18/2023] [Indexed: 12/29/2023] Open
Abstract
ProGlycProt is a comprehensive database of experimentally validated information about protein glycosylation in prokaryotes, including the glycoproteins, glycosyltransferases, and their accessory enzymes. The first release of ProGlycProt featured experimentally validated information on glycoproteins only. For the second release in 2019, the size and scope of the database were expanded twofold, and experimental data on cognate glycosyltransferases and their accessory proteins was incorporated. The growing research and technology interest in microbial glycoproteins and their enzymes is evident from the steady rise in academic publications and patents in this area. Accordingly, the third update comprises a new section on patents related to glycosylation methods, novel glycosyltransferases, and technologies developed therefrom. The structure gallery is reorganized, wherein the number and quality of the models are upgraded with the help of AlphaFold2. Over the years, the influx of experimental proteomics data into public repositories like PRIDE has surged. Harnessing this legacy data for in-silico glycoprotein identification is a smart approach. Version 3.0 adds 45 N-glycoprotein entries annotated from MS datasets available on PRIDE and reviewed by independent research groups. With a 67% rise in entries corresponding to 119 genera of prokaryotes, the ProGlycProt continues to be the exclusive database of experimentally validated comprehensive information about protein glycosylation in prokaryotes.
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Affiliation(s)
- Shreya Janhvi
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Shikha Saini
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Vaidhvi Singh
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Tarun Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
- Academy of Scientific and Innovation Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, Uttar Pradesh 201002, India
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Glycan-mediated molecular interactions in bacterial pathogenesis. Trends Microbiol 2022; 30:254-267. [PMID: 34274195 PMCID: PMC8758796 DOI: 10.1016/j.tim.2021.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023]
Abstract
Glycans are expressed on the surface of nearly all host and bacterial cells. Not surprisingly, glycan-mediated molecular interactions play a vital role in bacterial pathogenesis and host responses against pathogens. Glycan-mediated host-pathogen interactions can benefit the pathogen, host, or both. Here, we discuss (i) bacterial glycans that play a critical role in bacterial colonization and/or immune evasion, (ii) host glycans that are utilized by bacteria for pathogenesis, and (iii) bacterial and host glycans involved in immune responses against pathogens. We further discuss (iv) opportunities and challenges for transforming these research findings into more effective antibacterial strategies, and (v) technological advances in glycoscience that have helped to accelerate progress in research. These studies collectively offer valuable insights into new perspectives on antibacterial strategies that may effectively tackle the drug-resistant pathogens that are rapidly spreading globally.
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Sharma Y, Ahlawat S, Rao A. Biochemical characterization of an inverting S/O-HexNAc-transferase and evidence of S-linked glycosylation in Actinobacteria. Glycobiology 2021; 32:148-161. [PMID: 34420053 DOI: 10.1093/glycob/cwab089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 07/31/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Antimicrobial peptides harboring S- and or O-linked glycans are known as glycocins. Glycocins were first discovered and best characterized in Firmicutes. S-glycosylation is an enzymatic process catalyzed by S-glycosyltransferases of the GT2 family. Using a heterologous expression system, here we describe an inverting S/O-HexNAc-transferase (SvGT), encoded by ORF AQF52_3101 of S. venezuelae ATCC 15439, along with its acceptor substrate (SvC), encoded by ORF AQF52_3099. Using in vitro and in vivo assays, we define the distinct donor specificity, acceptor specificity, regioselectivity, chemoselectivity, and Y(G/A/K/Q/E ≠ ΔG)(C/S/T ≠ Y/N)(G/A ≠ P/Q)G as the minimum acceptor sequon of SvGT. Although UDP-GlcNAc served as the donor in the cellular milieu, SvGT could also utilize UDP-Glc and UDP-GalNAc as donors in vitro. Using mass spectrometry and western blotting, we provide evidence that an anti-O-GlcNAc antibody (CTD110.6) cross-reacts with S-GlcNAc and may be used to detect S-GlcNAcylated glycoconjugates directly. With an understanding of enzyme specificities, we finally employed SvGT to generate two proof-of-concept neoglycocins against L. monocytogenes. In conclusion, this study provides the first experimental evidence for S-glycosylation in Actinobacteria and the application of its S/O-HexNAc-transferase in glycocin engineering.
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Affiliation(s)
- Yogita Sharma
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Shimona Ahlawat
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India.,Academy of Scientific and Innovation Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad, 201002, India
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Comprehensive glycoproteomics shines new light on the complexity and extent of glycosylation in archaea. PLoS Biol 2021; 19:e3001277. [PMID: 34138841 PMCID: PMC8241124 DOI: 10.1371/journal.pbio.3001277] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/29/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
Glycosylation is one of the most complex posttranslational protein modifications. Its importance has been established not only for eukaryotes but also for a variety of prokaryotic cellular processes, such as biofilm formation, motility, and mating. However, comprehensive glycoproteomic analyses are largely missing in prokaryotes. Here, we extend the phenotypic characterization of N-glycosylation pathway mutants in Haloferax volcanii and provide a detailed glycoproteome for this model archaeon through the mass spectrometric analysis of intact glycopeptides. Using in-depth glycoproteomic datasets generated for the wild-type (WT) and mutant strains as well as a reanalysis of datasets within the Archaeal Proteome Project (ArcPP), we identify the largest archaeal glycoproteome described so far. We further show that different N-glycosylation pathways can modify the same glycosites under the same culture conditions. The extent and complexity of the Hfx. volcanii N-glycoproteome revealed here provide new insights into the roles of N-glycosylation in archaeal cell biology. A comprehensive glycoproteomic analysis of Haloferax volcanii reveals the extent and complexity of glycosylation in archaea and provides new insights into the roles of this post-translational modification in various cellular processes, including cell shape determination.
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Scherbinina SI, Toukach PV. Three-Dimensional Structures of Carbohydrates and Where to Find Them. Int J Mol Sci 2020; 21:E7702. [PMID: 33081008 PMCID: PMC7593929 DOI: 10.3390/ijms21207702] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/15/2020] [Accepted: 10/16/2020] [Indexed: 02/06/2023] Open
Abstract
Analysis and systematization of accumulated data on carbohydrate structural diversity is a subject of great interest for structural glycobiology. Despite being a challenging task, development of computational methods for efficient treatment and management of spatial (3D) structural features of carbohydrates breaks new ground in modern glycoscience. This review is dedicated to approaches of chemo- and glyco-informatics towards 3D structural data generation, deposition and processing in regard to carbohydrates and their derivatives. Databases, molecular modeling and experimental data validation services, and structure visualization facilities developed for last five years are reviewed.
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Affiliation(s)
- Sofya I. Scherbinina
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
- Higher Chemical College, D. Mendeleev University of Chemical Technology of Russia, Miusskaya Square 9, 125047 Moscow, Russia
| | - Philip V. Toukach
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninsky prospect 47, 119991 Moscow, Russia
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Choudhary P, Badmalia MD, Rao A. Shape-function insights into bifunctional O-GlcNActransferase of Listeria monocytogenes EGD-e. Glycobiology 2020; 31:275-287. [PMID: 32776104 DOI: 10.1093/glycob/cwaa076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 08/04/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022] Open
Abstract
O-GlcNAcylation is an important post-translational modification of proteins. O-GlcNAcylated proteins have crucial roles in several cellular contexts both in eukaryotes and bacteria. O-GlcNActransferase (OGT) is the enzyme instrumental in O-GlcNAcylation of proteins. OGT is conserved across eukaryotes. The first bacterial OGT discovered is GmaR in Listeria monocytogenes. GmaR is a GT-2 family bifunctional protein that catalyzes glycosylation of the flagellin protein FlaA and controls transcription of flagellar motility genes in a temperature-dependent manner. Here, we provide methods for heterologous expression and purification of recombinant GmaR and FlaA, in vivo/in vitro glycosylation assays, analysis of the molecular form of recombinant GmaR and detailed enzyme kinetics. We study the structure and functional dynamics of GmaR. Using solution small-angle X-ray scattering and molecular modeling, we show that GmaR adopts an extended shape with two distinctly spaced structural units in the presence of cofactor Mg2+ and with donor UDP-GlcNAc and cofactor combined. Comparisons of restored structures revealed that in-solution binding of Mg2+ ions brings about shape rearrangements and induces structural-rigidity in hyper-variable regions at the N-terminus of GmaR protein. Taking function and shape data together, we describe that Mg2+ binding enables GmaR to adopt a shape that can bind the substrate. The manuscript provides the first 3D solution structure of a bacterial OGT of GT-2 family and detailed biochemical characterization of GmaR to facilitate its future applications.
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Affiliation(s)
| | - Maulik D Badmalia
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India
| | | | - Alka Rao
- CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh 160036, India.,Academy of Scientific and Innovation Research (AcSIR), Sector 19, Kamla Nehru Nagar, Ghaziabad 201002, India
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Copoiu L, Malhotra S. The current structural glycome landscape and emerging technologies. Curr Opin Struct Biol 2020; 62:132-139. [PMID: 32006784 DOI: 10.1016/j.sbi.2019.12.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 11/19/2022]
Abstract
Carbohydrates represent one of the building blocks of life, along with nucleic acids, proteins and lipids. Although glycans are involved in a wide range of processes from embryogenesis to protein trafficking and pathogen infection, we are still a long way from deciphering the glycocode. In this review, we aim to present a few of the challenges that researchers working in the area of glycobiology can encounter and what strategies can be utilised to overcome them. Our goal is to paint a comprehensive picture of the current saccharide landscape available in the Protein Data Bank (PDB). We also review recently updated repositories relevant to the topic proposed, the impact of software development on strategies to structurally solve carbohydrate moieties, and state-of-the-art molecular and cellular biology methods that can shed some light on the function and structure of glycans.
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Affiliation(s)
- Liviu Copoiu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, United Kingdom
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, Malet Street, London WC1E 7HX, United Kingdom.
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Cao WQ, Liu MQ, Kong SY, Wu MX, Huang ZZ, Yang PY. Novel methods in glycomics: a 2019 update. Expert Rev Proteomics 2020; 17:11-25. [PMID: 31914820 DOI: 10.1080/14789450.2020.1708199] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Introduction: Glycomics, which aims to define the glycome of a biological system to better assess the biological attributes of the glycans, has attracted increasing interest. However, the complexity and diversity of glycans present challenging barriers to glycome definition. Technological advances are major drivers in glycomics.Areas covered: This review summarizes the main methods and emphasizes the most recent advances in mass spectrometry-based methods regarding glycomics following the general workflow in glycomic analysis.Expert opinion: Recent mass spectrometry-based technological advances have significantly lowered the barriers in glycomics. The field of glycomics is moving toward both generic and precise analysis.
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Affiliation(s)
- Wei-Qian Cao
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
| | - Ming-Qi Liu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Si-Yuan Kong
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Meng-Xi Wu
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
| | - Zheng-Ze Huang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Peng-Yuan Yang
- Shanghai Fifth People's Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China.,NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China.,Department of Chemistry, Fudan University, Shanghai, China
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Copoiu L, Torres PHM, Ascher DB, Blundell TL, Malhotra S. ProCarbDB: a database of carbohydrate-binding proteins. Nucleic Acids Res 2020; 48:D368-D375. [PMID: 31598690 PMCID: PMC6943041 DOI: 10.1093/nar/gkz860] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/12/2019] [Accepted: 10/05/2019] [Indexed: 02/02/2023] Open
Abstract
Carbohydrate-binding proteins play crucial roles across all organisms and viruses. The complexity of carbohydrate structures, together with inconsistencies in how their 3D structures are reported, has led to difficulties in characterizing the protein-carbohydrate interfaces. In order to better understand protein-carbohydrate interactions, we have developed an open-access database, ProCarbDB, which, unlike the Protein Data Bank (PDB), clearly distinguishes between the complete carbohydrate ligands and their monomeric units. ProCarbDB is a comprehensive database containing over 5200 3D X-ray crystal structures of protein-carbohydrate complexes. In ProCarbDB, the complete carbohydrate ligands are annotated and all their interactions are displayed. Users can also select any protein residue in the proximity of the ligand to inspect its interactions with the carbohydrate ligand and with other neighbouring protein residues. Where available, additional curated information on the binding affinity of the complex and the effects of mutations on the binding have also been provided in the database. We believe that ProCarbDB will be an invaluable resource for understanding protein-carbohydrate interfaces. The ProCarbDB web server is freely available at http://www.procarbdb.science/procarb.
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Affiliation(s)
- Liviu Copoiu
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Pedro H M Torres
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - David B Ascher
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK,Department of Biochemistry, University of Melbourne, Flemington Road, Parkville, Australia
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK,To whom correspondence should be addressed. Tel: +44 1223 333628;
| | - Sony Malhotra
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1GA, UK,Correspondence may also be addressed to Sony Malhotra.
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