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Dautin N. Folding Control in the Path of Type 5 Secretion. Toxins (Basel) 2021; 13:341. [PMID: 34064645 PMCID: PMC8151025 DOI: 10.3390/toxins13050341] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 12/17/2022] Open
Abstract
The type 5 secretion system (T5SS) is one of the more widespread secretion systems in Gram-negative bacteria. Proteins secreted by the T5SS are functionally diverse (toxins, adhesins, enzymes) and include numerous virulence factors. Mechanistically, the T5SS has long been considered the simplest of secretion systems, due to the paucity of proteins required for its functioning. Still, despite more than two decades of study, the exact process by which T5SS substrates attain their final destination and correct conformation is not totally deciphered. Moreover, the recent addition of new sub-families to the T5SS raises additional questions about this secretion mechanism. Central to the understanding of type 5 secretion is the question of protein folding, which needs to be carefully controlled in each of the bacterial cell compartments these proteins cross. Here, the biogenesis of proteins secreted by the Type 5 secretion system is discussed, with a focus on the various factors preventing or promoting protein folding during biogenesis.
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Affiliation(s)
- Nathalie Dautin
- Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Université de Paris, LBPC-PM, CNRS, UMR7099, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild pour le Développement de la Recherche Scientifique, 75005 Paris, France
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2
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Kightlinger W, Warfel KF, DeLisa MP, Jewett MC. Synthetic Glycobiology: Parts, Systems, and Applications. ACS Synth Biol 2020; 9:1534-1562. [PMID: 32526139 PMCID: PMC7372563 DOI: 10.1021/acssynbio.0c00210] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 12/11/2022]
Abstract
Protein glycosylation, the attachment of sugars to amino acid side chains, can endow proteins with a wide variety of properties of great interest to the engineering biology community. However, natural glycosylation systems are limited in the diversity of glycoproteins they can synthesize, the scale at which they can be harnessed for biotechnology, and the homogeneity of glycoprotein structures they can produce. Here we provide an overview of the emerging field of synthetic glycobiology, the application of synthetic biology tools and design principles to better understand and engineer glycosylation. Specifically, we focus on how the biosynthetic and analytical tools of synthetic biology have been used to redesign glycosylation systems to obtain defined glycosylation structures on proteins for diverse applications in medicine, materials, and diagnostics. We review the key biological parts available to synthetic biologists interested in engineering glycoproteins to solve compelling problems in glycoscience, describe recent efforts to construct synthetic glycoprotein synthesis systems, and outline exemplary applications as well as new opportunities in this emerging space.
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Affiliation(s)
- Weston Kightlinger
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Katherine F. Warfel
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
| | - Matthew P. DeLisa
- Department
of Microbiology, Cornell University, 123 Wing Drive, Ithaca, New York 14853, United States
- Robert
Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, New York 14853, United States
- Nancy
E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Weill Hall, Ithaca, New York 14853, United States
| | - Michael C. Jewett
- Department
of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Tech E136, Evanston, Illinois 60208, United States
- Center
for Synthetic Biology, Northwestern University, 2145 Sheridan Road, Tech B486, Evanston, Illinois 60208, United States
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3
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Abstract
Extracellular polysaccharides and glycoproteins of pathogenic bacteria assist in adherence, autoaggregation, biofilm formation, and host immune system evasion. As a result, considerable research in the field of glycobiology is dedicated to study the composition and function of glycans associated with virulence, as well as the enzymes involved in their biosynthesis with the aim to identify novel antibiotic targets. Especially, insights into the enzyme mechanism, substrate binding, and transition-state structures are valuable as a starting point for rational inhibitor design. An intriguing aspect of enzymes that generate or process polysaccharides and glycoproteins is the level of processivity. The existence of enzymatic processivity reflects the need for regulation of the final glycan/glycoprotein length and structure, depending on the role they perform. In this Review, we describe the currently reported examples of various processive enzymes involved in polymerization and transfer of sugar moieties, predominantly in bacterial pathogens, with a focus on the biochemical methods, to showcase the importance of studying processivity for understanding the mechanism.
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Affiliation(s)
- Liubov Yakovlieva
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Marthe T. C. Walvoort
- Stratingh Institute for Chemistry, University of Groningen, 9747 AG Groningen, The Netherlands
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4
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Volkwein W, Krafczyk R, Jagtap PKA, Parr M, Mankina E, Macošek J, Guo Z, Fürst MJLJ, Pfab M, Frishman D, Hennig J, Jung K, Lassak J. Switching the Post-translational Modification of Translation Elongation Factor EF-P. Front Microbiol 2019; 10:1148. [PMID: 31178848 PMCID: PMC6544042 DOI: 10.3389/fmicb.2019.01148] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/06/2019] [Indexed: 12/31/2022] Open
Abstract
Tripeptides with two consecutive prolines are the shortest and most frequent sequences causing ribosome stalling. The bacterial translation elongation factor P (EF-P) relieves this arrest, allowing protein biosynthesis to continue. A seven amino acids long loop between beta-strands β3/β4 is crucial for EF-P function and modified at its tip by lysylation of lysine or rhamnosylation of arginine. Phylogenetic analyses unveiled an invariant proline in the -2 position of the modification site in EF-Ps that utilize lysine modifications such as Escherichia coli. Bacteria with the arginine modification like Pseudomonas putida on the contrary have selected against it. Focusing on the EF-Ps from these two model organisms we demonstrate the importance of the β3/β4 loop composition for functionalization by chemically distinct modifications. Ultimately, we show that only two amino acid changes in E. coli EF-P are needed for switching the modification strategy from lysylation to rhamnosylation.
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Affiliation(s)
- Wolfram Volkwein
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Ralph Krafczyk
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | | | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Elena Mankina
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany
| | - Jakub Macošek
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Heidelberg, Germany
| | - Zhenghuan Guo
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Maximilian Josef Ludwig Johannes Fürst
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany.,Molecular Enzymology Group, University of Groningen, Groningen, Netherlands
| | - Miriam Pfab
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Freising, Germany.,St. Petersburg State Polytechnic University, Saint Petersburg, Russia
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jürgen Lassak
- Center for Integrated Protein Science Munich, Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, Munich, Germany
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Vo JL, Martínez Ortiz GC, Subedi P, Keerthikumar S, Mathivanan S, Paxman JJ, Heras B. Autotransporter Adhesins in Escherichia coli Pathogenesis. Proteomics 2017; 17. [PMID: 28665015 DOI: 10.1002/pmic.201600431] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 06/21/2017] [Indexed: 12/14/2022]
Abstract
Most bacteria produce adhesion molecules to facilitate the interaction with host cells and establish successful infections. An important group of bacterial adhesins belong to the autotransporter (AT) superfamily, the largest group of secreted and outer membrane proteins in Gram-negative bacteria. AT adhesins possess diverse functions that facilitate bacterial colonisation, survival and persistence, and as such are often associated with increased bacterial fitness and pathogenic potential. In this review, we will describe AIDA-I type AT adhesins, which comprise the biggest and most diverse group in the AT family. We will focus on Escherichia coli proteins and define general aspects of their biogenesis, distribution, structural properties and key roles in infection.
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Affiliation(s)
- Julieanne L Vo
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Gabriela Constanza Martínez Ortiz
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Pramod Subedi
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Shivakumar Keerthikumar
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Suresh Mathivanan
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Jason J Paxman
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
| | - Begoña Heras
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia
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A novel mass spectrometric strategy "BEMAP" reveals Extensive O-linked protein glycosylation in Enterotoxigenic Escherichia coli. Sci Rep 2016; 6:32016. [PMID: 27562176 PMCID: PMC5000012 DOI: 10.1038/srep32016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 08/01/2016] [Indexed: 11/24/2022] Open
Abstract
The attachment of sugars to proteins via side-chain oxygen atoms (O-linked glycosylation) is seen in all three domains of life. However, a lack of widely-applicable analytical tools has restricted the study of this process, particularly in bacteria. In E. coli, only four O-linked glycoproteins have previously been characterized. Here we present a glycoproteomics technique, termed BEMAP, which is based on the beta-elimination of O-linked glycans followed by Michael-addition of a phosphonic acid derivative, and subsequent titanium dioxide enrichment. This strategy allows site-specific mass-spectrometric identification of proteins with O-linked glycan modifications in a complex biological sample. Using BEMAP we identified cell surface-associated and membrane vesicle glycoproteins from Enterotoxigenic E. coli (ETEC) and non-pathogenic E. coli K-12. We identified 618 glycosylated Serine and Threonine residues mapping to 140 proteins in ETEC, including several known virulence factors, and 34 in E. coli K-12. The two strains had 32 glycoproteins in common. Remarkably, the majority of the ETEC glycoproteins were conserved in both strains but nevertheless were only glycosylated in the pathogen. Therefore, bacterial O-linked glycosylation is much more extensive than previously thought, and is especially important to the pathogen.
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8
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Schäffer C, Messner P. Emerging facets of prokaryotic glycosylation. FEMS Microbiol Rev 2016; 41:49-91. [PMID: 27566466 DOI: 10.1093/femsre/fuw036] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 02/17/2016] [Accepted: 08/01/2016] [Indexed: 12/16/2022] Open
Abstract
Glycosylation of proteins is one of the most prevalent post-translational modifications occurring in nature, with a wide repertoire of biological implications. Pathways for the main types of this modification, the N- and O-glycosylation, can be found in all three domains of life-the Eukarya, Bacteria and Archaea-thereby following common principles, which are valid also for lipopolysaccharides, lipooligosaccharides and glycopolymers. Thus, studies on any glycoconjugate can unravel novel facets of the still incompletely understood fundamentals of protein N- and O-glycosylation. While it is estimated that more than two-thirds of all eukaryotic proteins would be glycosylated, no such estimate is available for prokaryotic glycoproteins, whose understanding is lagging behind, mainly due to the enormous variability of their glycan structures and variations in the underlying glycosylation processes. Combining glycan structural information with bioinformatic, genetic, biochemical and enzymatic data has opened up an avenue for in-depth analyses of glycosylation processes as a basis for glycoengineering endeavours. Here, the common themes of glycosylation are conceptualised for the major classes of prokaryotic (i.e. bacterial and archaeal) glycoconjugates, with a special focus on glycosylated cell-surface proteins. We describe the current knowledge of biosynthesis and importance of these glycoconjugates in selected pathogenic and beneficial microbes.
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Affiliation(s)
- Christina Schäffer
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, Institute of Biologically Inspired Materials, NanoGlycobiology unit, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
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9
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Sugar and Spice Make Bacteria Not Nice: Protein Glycosylation and Its Influence in Pathogenesis. J Mol Biol 2016; 428:3206-3220. [DOI: 10.1016/j.jmb.2016.04.013] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/04/2016] [Accepted: 04/08/2016] [Indexed: 01/08/2023]
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10
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Unconventional N-Linked Glycosylation Promotes Trimeric Autotransporter Function in Kingella kingae and Aggregatibacter aphrophilus. mBio 2015; 6:mBio.01206-15. [PMID: 26307167 PMCID: PMC4550697 DOI: 10.1128/mbio.01206-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Glycosylation is a widespread mechanism employed by both eukaryotes and bacteria to increase the functional diversity of their proteomes. The nontypeable Haemophilus influenzae glycosyltransferase HMW1C mediates unconventional N-linked glycosylation of the adhesive protein HMW1, which is encoded in a two-partner secretion system gene cluster that also encodes HMW1C. In this system, HMW1 is modified in the cytoplasm by sequential transfer of hexose residues. In the present study, we examined Kingella kingae and Aggregatibacter aphrophilus homologues of HMW1C that are not encoded near a gene encoding an obvious acceptor protein. We found both homologues to be functional glycosyltransferases and identified their substrates as the K. kingae Knh and the A. aphrophilus EmaA trimeric autotransporter proteins. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis revealed multiple sites of N-linked glycosylation on Knh and EmaA. Without glycosylation, Knh and EmaA failed to facilitate wild-type levels of bacterial autoaggregation or adherence to human epithelial cells, establishing that glycosylation is essential for proper protein function. IMPORTANCE This work emphasizes the importance of glycosylation for proper function of bacterial proteins. Here we show that the Kingella kingae Knh and the Aggregatibacter aphrophilus EmaA trimeric autotransporter proteins are N-glycosylated by novel homologues of the Haemophilus influenzae HMW1C glycosyltransferase, highlighting the first examples of trimeric autotransporters that are modified by HMW1C-like enzymes. In the absence of glycosylation, Knh and EmaA lack adhesive activity. This work has relevance to our understanding of bacterial pathogenicity and expression of potential vaccine antigens.
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11
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The sweet tooth of bacteria: common themes in bacterial glycoconjugates. Microbiol Mol Biol Rev 2015; 78:372-417. [PMID: 25184559 DOI: 10.1128/mmbr.00007-14] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Humans have been increasingly recognized as being superorganisms, living in close contact with a microbiota on all their mucosal surfaces. However, most studies on the human microbiota have focused on gaining comprehensive insights into the composition of the microbiota under different health conditions (e.g., enterotypes), while there is also a need for detailed knowledge of the different molecules that mediate interactions with the host. Glycoconjugates are an interesting class of molecules for detailed studies, as they form a strain-specific barcode on the surface of bacteria, mediating specific interactions with the host. Strikingly, most glycoconjugates are synthesized by similar biosynthesis mechanisms. Bacteria can produce their major glycoconjugates by using a sequential or an en bloc mechanism, with both mechanistic options coexisting in many species for different macromolecules. In this review, these common themes are conceptualized and illustrated for all major classes of known bacterial glycoconjugates, with a special focus on the rather recently emergent field of glycosylated proteins. We describe the biosynthesis and importance of glycoconjugates in both pathogenic and beneficial bacteria and in both Gram-positive and -negative organisms. The focus lies on microorganisms important for human physiology. In addition, the potential for a better knowledge of bacterial glycoconjugates in the emerging field of glycoengineering and other perspectives is discussed.
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12
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High-throughput microfluidic method to study biofilm formation and host-pathogen interactions in pathogenic Escherichia coli. Appl Environ Microbiol 2015; 81:2827-40. [PMID: 25681176 DOI: 10.1128/aem.04208-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Biofilm formation and host-pathogen interactions are frequently studied using multiwell plates; however, these closed systems lack shear force, which is present at several sites in the host, such as the intestinal and urinary tracts. Recently, microfluidic systems that incorporate shear force and very small volumes have been developed to provide cell biology models that resemble in vivo conditions. Therefore, the objective of this study was to determine if the BioFlux 200 microfluidic system could be used to study host-pathogen interactions and biofilm formation by pathogenic Escherichia coli. Strains of various pathotypes were selected to establish the growth conditions for the formation of biofilms in the BioFlux 200 system on abiotic (glass) or biotic (eukaryotic-cell) surfaces. Biofilm formation on glass was observed for the majority of strains when they were grown in M9 medium at 30 °C but not in RPMI medium at 37 °C. In contrast, HRT-18 cell monolayers enhanced binding and, in most cases, biofilm formation by pathogenic E. coli in RPMI medium at 37 °C. As a proof of principle, the biofilm-forming ability of a diffusely adherent E. coli mutant strain lacking AIDA-I, a known mediator of attachment, was assessed in our models. In contrast to the parental strain, which formed a strong biofilm, the mutant formed a thin biofilm on glass or isolated clusters on HRT-18 monolayers. In conclusion, we describe a microfluidic method for high-throughput screening that could be used to identify novel factors involved in E. coli biofilm formation and host-pathogen interactions under shear force.
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13
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Liang DM, Liu JH, Wu H, Wang BB, Zhu HJ, Qiao JJ. Glycosyltransferases: mechanisms and applications in natural product development. Chem Soc Rev 2015; 44:8350-74. [DOI: 10.1039/c5cs00600g] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Glycosylation reactions mainly catalyzed by glycosyltransferases (Gts) occur almost everywhere in the biosphere, and always play crucial roles in vital processes.
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Affiliation(s)
- Dong-Mei Liang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jia-Heng Liu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hao Wu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Bin-Bin Wang
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Hong-Ji Zhu
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
| | - Jian-Jun Qiao
- Department of Pharmaceutical Engineering
- School of Chemical Engineering and Technology
- Tianjin University
- Tianjin 300072
- China
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14
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Lu Q, Yao Q, Xu Y, Li L, Li S, Liu Y, Gao W, Niu M, Sharon M, Ben-Nissan G, Zamyatina A, Liu X, Chen S, Shao F. An Iron-Containing Dodecameric Heptosyltransferase Family Modifies Bacterial Autotransporters in Pathogenesis. Cell Host Microbe 2014; 16:351-63. [DOI: 10.1016/j.chom.2014.08.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 07/06/2014] [Accepted: 08/01/2014] [Indexed: 01/11/2023]
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15
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van Ulsen P, Rahman SU, Jong WS, Daleke-Schermerhorn MH, Luirink J. Type V secretion: From biogenesis to biotechnology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2014; 1843:1592-611. [DOI: 10.1016/j.bbamcr.2013.11.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Revised: 11/01/2013] [Accepted: 11/13/2013] [Indexed: 12/13/2022]
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16
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Sánchez-Rodríguez A, Tytgat HLP, Winderickx J, Vanderleyden J, Lebeer S, Marchal K. A network-based approach to identify substrate classes of bacterial glycosyltransferases. BMC Genomics 2014; 15:349. [PMID: 24885406 PMCID: PMC4039749 DOI: 10.1186/1471-2164-15-349] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/16/2014] [Indexed: 01/03/2023] Open
Abstract
Background Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity. Results In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred. Conclusions We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-349) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Sarah Lebeer
- Department of Microbial and Molecular Systems, KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, Leuven B-3001, Belgium.
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Naegeli A, Neupert C, Fan YY, Lin CW, Poljak K, Papini AM, Schwarz F, Aebi M. Molecular analysis of an alternative N-glycosylation machinery by functional transfer from Actinobacillus pleuropneumoniae to Escherichia coli. J Biol Chem 2013; 289:2170-9. [PMID: 24275653 DOI: 10.1074/jbc.m113.524462] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
N-Linked protein glycosylation is a frequent post-translational modification that can be found in all three domains of life. In a canonical, highly conserved pathway, an oligosaccharide is transferred by a membrane-bound oligosaccharyltransferase from a lipid donor to asparagines in the sequon NX(S/T) of secreted polypeptides. The δ-proteobacterium Actinobacillus pleuropneumoniae encodes an unusual pathway for N-linked protein glycosylation. This pathway takes place in the cytoplasm and is mediated by a soluble N-glycosyltransferase (NGT) that uses nucleotide-activated monosaccharides to glycosylate asparagine residues. To characterize the process of cytoplasmic N-glycosylation in more detail, we studied the glycosylation in A. pleuropneumoniae and functionally transferred the glycosylation system to Escherichia coli. N-Linked glucose specific human sera were used for the analysis of the glycosylation process. We identified autotransporter adhesins as the preferred protein substrate of NGT in vivo, and in depth analysis of the modified sites in E. coli revealed a surprisingly relaxed peptide substrate specificity. Although NX(S/T) is the preferred acceptor sequon, we detected glycosylation of alternative sequons, including modification of glutamine and serine residues. We also demonstrate the use of NGT to glycosylate heterologous proteins. Therefore, our study could provide the basis for a novel route for the engineering of N-glycoproteins in bacteria.
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Affiliation(s)
- Andreas Naegeli
- From the Institute of Microbiology, Swiss Federal Institute of Technology, ETH Zurich, CH-8093 Zurich, Switzerland and
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Côté JP, Charbonneau MÈ, Mourez M. Glycosylation of the Escherichia coli TibA self-associating autotransporter influences the conformation and the functionality of the protein. PLoS One 2013; 8:e80739. [PMID: 24278316 PMCID: PMC3835316 DOI: 10.1371/journal.pone.0080739] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/06/2013] [Indexed: 12/22/2022] Open
Abstract
The self-associating autotransporters (SAATs) are multifunctional secreted proteins of Escherichia coli, comprising the AIDA-I, TibA and Ag43 proteins. One of their characteristics is that they can be glycosylated. Glycosylation of AIDA-I and Ag43 have been investigated, but not that of TibA. It is still not clear whether glycosylation of the SAATs affect their structure or their functionality. Therefore, we have looked at the effects of glycosylation on the TibA adhesin/invasin. TibA is glycosylated by TibC, a specific glycosyltransferase, and the two genes are encoded in an operon. In this study, we have found that the glycosylation of TibA is not limited to the extracellular functional domain, as previously observed with AIDA-I and Ag43. We have determined that unglycosylated TibA is not able to promote the adhesion of bacteria on cultured epithelial cell, even though it is still able to promote invasion, biofilm formation and autoaggregation of bacteria. We have purified the glycosylated and unglycosylated forms of TibA, and determined that TibA is less stable when not glycosylated. We finally observed that glycosylation affects the oligomerisation of TibA and that unglycosylated TibA is locked in a conformation that is not suited for adhesion. Our results suggest that the effect of glycosylation on the functionality of TibA is indirect.
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Affiliation(s)
- Jean-Philippe Côté
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
- * E-mail:
| | - Marie-Ève Charbonneau
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Michael Mourez
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
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Zhou XY, Gao JL, Hunter N, Potempa J, Nguyen KA. Sequence-independent processing site of the C-terminal domain (CTD) influences maturation of the RgpB protease from Porphyromonas gingivalis. Mol Microbiol 2013; 89:903-17. [PMID: 23869473 DOI: 10.1111/mmi.12319] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2013] [Indexed: 11/29/2022]
Abstract
The Gram-negative periodontal pathogen Porphyromonas gingivalis produces a family of outer membrane-anchored proteases, the gingipains, shown to play an essential role in virulence of the organism. The C-terminal domain (CTD) of gingipains and other secreted proteins is known to be the targeting signal for maturation and translocation of the protein through the outer membrane. The CTD is subsequently cleaved during the secretion process. Multiple alignment of various CTDs failed to define a consensus sequence at the putative CTD processing site. Using mutagenesis, we were able to show that cleavage at the site is not dependent on a specific residue and that recognition of the site is independent of local sequence. Interestingly, length of the junction between the CTD and adjacent Ig-like subdomain has a critical influence on post-translational glycan modification of the protein, whereby insertion of additional residues immediately N-terminal to the cleavage site results in failure of glycan modification and release of soluble protease into the culture medium. Various hypotheses are presented to explain these phenomena. Knowledge of the role CTDs play in maturation of gingipains has broader application for understanding maturation of CTD homologues expressed by bacteria of the Bacteriodetes phylum.
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Affiliation(s)
- Xiao-Yan Zhou
- Institute of Dental Research, Westmead Centre for Oral Health and Westmead Millennium Institute, Sydney, NSW, Australia
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20
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Rolain T, Bernard E, Beaussart A, Degand H, Courtin P, Egge-Jacobsen W, Bron PA, Morsomme P, Kleerebezem M, Chapot-Chartier MP, Dufrêne YF, Hols P. O-glycosylation as a novel control mechanism of peptidoglycan hydrolase activity. J Biol Chem 2013; 288:22233-47. [PMID: 23760506 DOI: 10.1074/jbc.m113.470716] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Acm2, the major autolysin of Lactobacillus plantarum, is a tripartite protein. Its catalytic domain is surrounded by an O-glycosylated N-terminal region rich in Ala, Ser, and Thr (AST domain), which is of low complexity and unknown function, and a C-terminal region composed of five SH3b peptidoglycan (PG) binding domains. Here, we investigate the contribution of these two accessory domains and of O-glycosylation to Acm2 functionality. We demonstrate that Acm2 is an N-acetylglucosaminidase and identify the pattern of O-glycosylation (21 mono-N-acetylglucosamines) of its AST domain. The O-glycosylation process is species-specific as Acm2 purified from Lactococcus lactis is not glycosylated. We therefore explored the functional role of O-glycosylation by purifying different truncated versions of Acm2 that were either glycosylated or non-glycosylated. We show that SH3b domains are able to bind PG and are responsible for Acm2 targeting to the septum of dividing cells, whereas the AST domain and its O-glycosylation are not involved in this process. Notably, our data reveal that the lack of O-glycosylation of the AST domain significantly increases Acm2 enzymatic activity, whereas removal of SH3b PG binding domains dramatically reduces this activity. Based on this antagonistic role, we propose a model in which access of the Acm2 catalytic domain to its substrate may be hindered by the AST domain where O-glycosylation changes its conformation and/or mediates interdomain interactions. To the best of our knowledge, this is the first time that O-glycosylation is shown to control the activity of a bacterial enzyme.
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Affiliation(s)
- Thomas Rolain
- Institut des Sciences de la Vie, Université catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium
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21
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Iwashkiw JA, Vozza NF, Kinsella RL, Feldman MF. Pour some sugar on it: the expanding world of bacterial proteinO-linked glycosylation. Mol Microbiol 2013; 89:14-28. [DOI: 10.1111/mmi.12265] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2013] [Indexed: 11/26/2022]
Affiliation(s)
- Jeremy A. Iwashkiw
- Alberta Glycomics Centre; Department of Biological Sciences; University of Alberta; CW405 Biological Sciences Building; Edmonton; Alberta; Canada; T6G 2E9
| | - Nicolas F. Vozza
- Alberta Glycomics Centre; Department of Biological Sciences; University of Alberta; CW405 Biological Sciences Building; Edmonton; Alberta; Canada; T6G 2E9
| | - Rachel L. Kinsella
- Alberta Glycomics Centre; Department of Biological Sciences; University of Alberta; CW405 Biological Sciences Building; Edmonton; Alberta; Canada; T6G 2E9
| | - Mario F. Feldman
- Alberta Glycomics Centre; Department of Biological Sciences; University of Alberta; CW405 Biological Sciences Building; Edmonton; Alberta; Canada; T6G 2E9
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22
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Schulz BL, Jen FEC, Power PM, Jones CE, Fox KL, Ku SC, Blanchfield JT, Jennings MP. Identification of bacterial protein O-oligosaccharyltransferases and their glycoprotein substrates. PLoS One 2013; 8:e62768. [PMID: 23658772 PMCID: PMC3643930 DOI: 10.1371/journal.pone.0062768] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 03/25/2013] [Indexed: 12/16/2022] Open
Abstract
O-glycosylation of proteins in Neisseria meningitidis is catalyzed by PglL, which belongs to a protein family including WaaL O-antigen ligases. We developed two hidden Markov models that identify 31 novel candidate PglL homologs in diverse bacterial species, and describe several conserved sequence and structural features. Most of these genes are adjacent to possible novel target proteins for glycosylation. We show that in the general glycosylation system of N. meningitidis, efficient glycosylation of additional protein substrates requires local structural similarity to the pilin acceptor site. For some Neisserial PglL substrates identified by sensitive analytical approaches, only a small fraction of the total protein pool is modified in the native organism, whereas others are completely glycosylated. Our results show that bacterial protein O-glycosylation is common, and that substrate selection in the general Neisserial system is dominated by recognition of structural homology.
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Affiliation(s)
- Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Freda E. C. Jen
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Peter M. Power
- Department of Paediatrics, University of Oxford, Oxford, Oxfordshire, United Kingdom
| | - Christopher E. Jones
- School of Science and Health, The University of Western Sydney, Penrith, New South Wales, Australia
| | - Kate L. Fox
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Shan C. Ku
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Joanne T. Blanchfield
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Michael P. Jennings
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- * E-mail:
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23
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Otzen D. N for AsN - O for strOcture? A strand-loop-strand motif for prokaryotic O-glycosylation. Mol Microbiol 2012; 83:879-83. [PMID: 22221153 DOI: 10.1111/j.1365-2958.2012.07972.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
So far, it has not been possible to identify a general sequence motif for O-glycosylation in bacteria. In this issue, Charbonneau et al. (2012) demonstrate why O-glycosylation is mediated by a 13-residue strand-loop-strand motif which is part of a 19-residue imperfect repeat in the passenger domain of bacterial autotransporters. This motif provides a convenient 'glycosylation cassette' and raises intriguing questions about the structural regulation of the glycosylation pathway.
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Affiliation(s)
- Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Center for insoluble Protein Structures, Department of Molecular Biology and Genetics, University of Aarhus, Gustav Wieds Vej 10C, Aarhus C, Denmark.
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