1
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Nourbakhsh F, Lotfalizadeh M, Badpeyma M, Shakeri A, Soheili V. From plants to antimicrobials: Natural products against bacterial membranes. Phytother Res 2021; 36:33-52. [PMID: 34532918 DOI: 10.1002/ptr.7275] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 07/16/2021] [Accepted: 08/25/2021] [Indexed: 12/24/2022]
Abstract
Bacterial membrane barrier provides a cytoplasmic environment for organelles of bacteria. The membrane is composed of lipid compounds containing phosphatide protein and a minimal amount of sugars, and is responsible for intercellular transfers of chemicals. Several antimicrobials have been found that affect bacterial cytoplasmic membranes. These compounds generally disrupt the organization of the membrane or perforate it. By destroying the membrane, the drugs can permeate and replace the effective macromolecules necessary for cell life. Furthermore, they can disrupt electrical gradients of the cells through impairment of the membrane integrity. In recent years, considering the spread of microbial resistance and the side effects of antibiotics, natural antimicrobial compounds have been studied by researchers extensively. These molecules are the best alternative for controlling bacterial infections and reducing drug resistance due to the lack of severe side effects, low cost of production, and biocompatibility. Better understanding of the natural compounds' mechanisms against bacteria provides improved strategies for antimicrobial therapies. In this review, natural products with antibacterial activities focusing on membrane damaging mechanisms were described. However, further high-quality research studies are needed to confirm the clinical efficacy of these natural products.
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Affiliation(s)
- Fahimeh Nourbakhsh
- Medical Toxicology Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Marzieh Lotfalizadeh
- Department of Obstetrics and Gynecology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohaddeseh Badpeyma
- Student Research Committee, Department of Clinical Nutrition, Nutrition Research Center, School of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abolfazl Shakeri
- Department of Pharmacognosy, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Soheili
- Department of Pharmaceutical Control, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
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2
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Guo Z, Tang Y, Tang W, Chen Y. Heptose-containing bacterial natural products: structures, bioactivities, and biosyntheses. Nat Prod Rep 2021; 38:1887-1909. [PMID: 33704304 DOI: 10.1039/d0np00075b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Covering: up to 2020Glycosylated natural products hold great potential as drugs for the treatment of human and animal diseases. Heptoses, known as seven-carbon-chain-containing sugars, are a group of saccharides that are rarely observed in natural products. Based on the structures of the heptoses, the heptose-containing natural products can be divided into four groups, characterized by heptofuranose, highly-reduced heptopyranose, d-heptopyranose, and l-heptopyranose. Many of them possess remarkable biological properties, including antibacterial, antifungal, antitumor, and pain relief activities, thereby attracting great interest in biosynthesis and chemical synthesis studies to understand their construction mechanisms and structure-activity relationships. In this review, we summarize the structural properties, biological activities, and recent progress in the biosynthesis of bacterial natural products featuring seven-carbon-chain-containing sugars. The biosynthetic origins of the heptose moieties are emphasized.
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Affiliation(s)
- Zhengyan Guo
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yue Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Wei Tang
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, 100101 Beijing, China. and University of Chinese Academy of Sciences, 100049 Beijing, China
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3
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Jakubovics NS, Goodman SD, Mashburn-Warren L, Stafford GP, Cieplik F. The dental plaque biofilm matrix. Periodontol 2000 2021; 86:32-56. [PMID: 33690911 PMCID: PMC9413593 DOI: 10.1111/prd.12361] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Steven D Goodman
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Lauren Mashburn-Warren
- Center for Microbial Pathogenesis, The Abigail Wexner Research Institute at Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Graham P Stafford
- Integrated Biosciences, School of Clinical Dentistry, University of Sheffield, Sheffield, UK
| | - Fabian Cieplik
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, Regensburg, Germany
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4
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McDonald ND, Boyd EF. Structural and Biosynthetic Diversity of Nonulosonic Acids (NulOs) That Decorate Surface Structures in Bacteria. Trends Microbiol 2021; 29:142-157. [PMID: 32950378 PMCID: PMC7855311 DOI: 10.1016/j.tim.2020.08.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 08/14/2020] [Accepted: 08/19/2020] [Indexed: 12/12/2022]
Abstract
Nonulosonic acids (NulOs) are a diverse family of 9-carbon α-keto acid sugars that are involved in a wide range of functions across all branches of life. The family of NulOs includes the sialic acids as well as the prokaryote-specific NulOs. Select bacteria biosynthesize the sialic acid N-acetylneuraminic acid (Neu5Ac), and the ability to produce this sugar and its subsequent incorporation into cell-surface structures is implicated in a variety of bacteria-host interactions. Furthermore, scavenging of sialic acid from the environment for energy has been characterized across a diverse group of bacteria, mainly human commensals and pathogens. In addition to sialic acid, bacteria have the ability to biosynthesize prokaryote-specific NulOs, of which there are several known isomers characterized. These prokaryotic NulOs are similar in structure to Neu5Ac but little is known regarding their role in bacterial physiology. Here, we discuss the diversity in structure, the biosynthesis pathways, and the functions of bacteria-specific NulOs. These carbohydrates are phylogenetically widespread among bacteria, with numerous structurally unique modifications recognized. Despite the diversity in structure, the NulOs are involved in similar functions such as motility, biofilm formation, host colonization, and immune evasion.
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Affiliation(s)
- Nathan D McDonald
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - E Fidelma Boyd
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA.
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5
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Malamud M, Cavallero GJ, Casabuono AC, Lepenies B, Serradell MDLÁ, Couto AS. Immunostimulation by Lactobacillus kefiri S-layer proteins with distinct glycosylation patterns requires different lectin partners. J Biol Chem 2020; 295:14430-14444. [PMID: 32817316 DOI: 10.1074/jbc.ra120.013934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 08/12/2020] [Indexed: 12/12/2022] Open
Abstract
S-layer (glyco)-proteins (SLPs) form a nanostructured envelope that covers the surface of different prokaryotes and show immunomodulatory activity. Previously, we have demonstrated that the S-layer glycoprotein from probiotic Lactobacillus kefiri CIDCA 8348 (SLP-8348) is recognized by Mincle (macrophage inducible C-type lectin receptor), and its adjuvanticity depends on the integrity of its glycans. However, the glycan's structure has not been described so far. Herein, we analyze the glycosylation pattern of three SLPs, SLP-8348, SLP-8321, and SLP-5818, and explore how these patterns impact their recognition by C-type lectin receptors and the immunomodulatory effect of the L. kefiri SLPs on antigen-presenting cells. High-performance anion-exchange chromatography-pulse amperometric detector performed after β-elimination showed glucose as the major component in the O-glycans of the three SLPs; however, some differences in the length of hexose chains were observed. No N-glycosylation signals were detected in SLP-8348 and SLP-8321, but SLP-5818 was observed to have two sites carrying complex N-glycans based on a site-specific analysis and a glycomic workflow of the permethylated glycans. SLP-8348 was previously shown to enhance LPS-induced activation on both RAW264.7 macrophages and murine bone marrow-derived dendritic cells; we now show that SLP-8321 and SLP-5818 have a similar effect regardless of the differences in their glycosylation patterns. Studies performed with bone marrow-derived dendritic cells from C-type lectin receptor-deficient mice revealed that the immunostimulatory activity of SLP-8321 depends on its recognition by Mincle, whereas SLP-5818's effects are dependent on SignR3 (murine ortholog of human DC-SIGN). These findings encourage further investigation of both the potential application of these SLPs as new adjuvants and the protein glycosylation mechanisms in these bacteria.
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Affiliation(s)
- Mariano Malamud
- Cátedra de Microbiología, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina.,University of Veterinary Medicine Hannover, Immunology Unit & Research Center for Emerging Infections and Zoonoses, Hannover, Germany
| | - Gustavo J Cavallero
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica-Consejo Nacional de Investigaciones Científicas y Técnicas, Centro de Investigación en Hidratos de Carbono, Buenos Aires, Argentina
| | - Adriana C Casabuono
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica-Consejo Nacional de Investigaciones Científicas y Técnicas, Centro de Investigación en Hidratos de Carbono, Buenos Aires, Argentina
| | - Bernd Lepenies
- University of Veterinary Medicine Hannover, Immunology Unit & Research Center for Emerging Infections and Zoonoses, Hannover, Germany
| | - María de Los Ángeles Serradell
- Cátedra de Microbiología, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
| | - Alicia S Couto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica-Consejo Nacional de Investigaciones Científicas y Técnicas, Centro de Investigación en Hidratos de Carbono, Buenos Aires, Argentina
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6
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Freudenberger Catanzaro KC, Inzana TJ. The Francisella tularensis Polysaccharides: What Is the Real Capsule? Microbiol Mol Biol Rev 2020; 84:e00065-19. [PMID: 32051235 PMCID: PMC7018499 DOI: 10.1128/mmbr.00065-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Francisella tularensis is a tier 1 select agent responsible for tularemia in humans and a wide variety of animal species. Extensive research into understanding the virulence factors of the bacterium has been ongoing to develop an efficacious vaccine. At least two such virulence factors are described as capsules of F. tularensis: the O-antigen capsule and the capsule-like complex (CLC). These two separate entities aid in avoiding host immune defenses but have not been clearly differentiated. These components are distinct and differ in composition and genetic basis. The O-antigen capsule consists of a polysaccharide nearly identical to the lipopolysaccharide (LPS) O antigen, whereas the CLC is a heterogeneous complex of glycoproteins, proteins, and possibly outer membrane vesicles and tubes (OMV/Ts). In this review, the current understanding of these two capsules is summarized, and the historical references to "capsules" of F. tularensis are clarified. A significant amount of research has been invested into the composition of each capsule and the genes involved in synthesis of the polysaccharide portion of each capsule. Areas of future research include further exploration into the molecular regulation and pathways responsible for expression of each capsule and further elucidating the role that each capsule plays in virulence.
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Affiliation(s)
- Kelly C Freudenberger Catanzaro
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
| | - Thomas J Inzana
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, Virginia, USA
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
- College of Veterinary Medicine, Long Island University, Brookville, New York, USA
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7
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Damiati S, Schuster B. Electrochemical Biosensors Based on S-Layer Proteins. SENSORS (BASEL, SWITZERLAND) 2020; 20:E1721. [PMID: 32204503 PMCID: PMC7147708 DOI: 10.3390/s20061721] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 03/05/2020] [Accepted: 03/17/2020] [Indexed: 01/29/2023]
Abstract
Designing and development of electrochemical biosensors enable molecule sensing and quantification of biochemical compositions with multitudinous benefits such as monitoring, detection, and feedback for medical and biotechnological applications. Integrating bioinspired materials and electrochemical techniques promote specific, rapid, sensitive, and inexpensive biosensing platforms for (e.g., point-of-care testing). The selection of biomaterials to decorate a biosensor surface is a critical issue as it strongly affects selectivity and sensitivity. In this context, smart biomaterials with the intrinsic self-assemble capability like bacterial surface (S-) layer proteins are of paramount importance. Indeed, by forming a crystalline two-dimensional protein lattice on many sensors surfaces and interfaces, the S-layer lattice constitutes an immobilization matrix for small biomolecules and lipid membranes and a patterning structure with unsurpassed spatial distribution for sensing elements and bioreceptors. This review aims to highlight on exploiting S-layer proteins in biosensor technology for various applications ranging from detection of metal ions over small organic compounds to cells. Furthermore, enzymes immobilized on the S-layer proteins allow specific detection of several vital biomolecules. The special features of the S-layer protein lattice as part of the sensor architecture enhances surface functionalization and thus may feature an innovative class of electrochemical biosensors.
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Affiliation(s)
- Samar Damiati
- Department of Biochemistry, Faculty of Science, King Abdulaziz University (KAU), Jeddah 21589, Saudi Arabia;
- Institute for Synthetic Bioarchitectures, Department of NanoBiotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
- Current address: Division of Nanobiotechnology, Department of Protein Science, Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 171 21 Solna, Stockholm, Sweden
| | - Bernhard Schuster
- Institute for Synthetic Bioarchitectures, Department of NanoBiotechnology, BOKU - University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria
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8
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Blackler RJ, López-Guzmán A, Hager FF, Janesch B, Martinz G, Gagnon SML, Haji-Ghassemi O, Kosma P, Messner P, Schäffer C, Evans SV. Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei. Nat Commun 2018; 9:3120. [PMID: 30087354 PMCID: PMC6081394 DOI: 10.1038/s41467-018-05471-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 06/19/2018] [Indexed: 12/20/2022] Open
Abstract
Self-assembling protein surface (S-) layers are common cell envelope structures of prokaryotes and have critical roles from structural maintenance to virulence. S-layers of Gram-positive bacteria are often attached through the interaction of S-layer homology (SLH) domain trimers with peptidoglycan-linked secondary cell wall polymers (SCWPs). Here we present an in-depth characterization of this interaction, with co-crystal structures of the three consecutive SLH domains from the Paenibacillus alvei S-layer protein SpaA with defined SCWP ligands. The most highly conserved SLH domain residue SLH-Gly29 is shown to enable a peptide backbone flip essential for SCWP binding in both biophysical and cellular experiments. Furthermore, we find that a significant domain movement mediates binding by two different sites in the SLH domain trimer, which may allow anchoring readjustment to relieve S-layer strain caused by cell growth and division. Gram-positive bacterial envelopes comprise proteinaceous surface layers (S-layers) important for survival and virulence that are often anchored to the cell wall through secondary cell wall polymers. Here the authors use a structural and biophysical approach to define the molecular mechanism of this important interaction.
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Affiliation(s)
- Ryan J Blackler
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.,Zymeworks Inc., Vancouver, BC, V6H 3V9, Canada
| | - Arturo López-Guzmán
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, 1190, Vienna, Austria
| | - Fiona F Hager
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, 1190, Vienna, Austria
| | - Bettina Janesch
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, 1190, Vienna, Austria
| | - Gudrun Martinz
- Department of Chemistry, Universität für Bodenkultur Wien, 1190, Vienna, Austria
| | - Susannah M L Gagnon
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Omid Haji-Ghassemi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Paul Kosma
- Department of Chemistry, Universität für Bodenkultur Wien, 1190, Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, 1190, Vienna, Austria
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, 1190, Vienna, Austria.
| | - Stephen V Evans
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.
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9
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do Carmo FLR, Rabah H, De Oliveira Carvalho RD, Gaucher F, Cordeiro BF, da Silva SH, Le Loir Y, Azevedo V, Jan G. Extractable Bacterial Surface Proteins in Probiotic-Host Interaction. Front Microbiol 2018; 9:645. [PMID: 29670603 PMCID: PMC5893755 DOI: 10.3389/fmicb.2018.00645] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/19/2018] [Indexed: 01/09/2023] Open
Abstract
Some Gram-positive bacteria, including probiotic ones, are covered with an external proteinaceous layer called a surface-layer. Described as a paracrystalline layer and formed by the self-assembly of a surface-layer-protein (Slp), this optional structure is peculiar. The surface layer per se is conserved and encountered in many prokaryotes. However, the sequence of the corresponding Slp protein is highly variable among bacterial species, or even among strains of the same species. Other proteins, including surface layer associated proteins (SLAPs), and other non-covalently surface-bound proteins may also be extracted with this surface structure. They can be involved a various functions. In probiotic Gram-positives, they were shown by different authors and experimental approaches to play a role in key interactions with the host. Depending on the species, and sometime on the strain, they can be involved in stress tolerance, in survival within the host digestive tract, in adhesion to host cells or mucus, or in the modulation of intestinal inflammation. Future trends include the valorization of their properties in the formation of nanoparticles, coating and encapsulation, and in the development of new vaccines.
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Affiliation(s)
- Fillipe L R do Carmo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil.,STLO, Agrocampus Ouest, INRA, Rennes, France
| | - Houem Rabah
- STLO, Agrocampus Ouest, INRA, Rennes, France.,Pôle Agronomique Ouest, Rennes, France
| | | | - Floriane Gaucher
- STLO, Agrocampus Ouest, INRA, Rennes, France.,Bioprox, Levallois-Perret, France
| | - Barbara F Cordeiro
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Sara H da Silva
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Vasco Azevedo
- Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Gwénaël Jan
- STLO, Agrocampus Ouest, INRA, Rennes, France
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10
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De Maayer P, Cowan DA. Comparative genomic analysis of the flagellin glycosylation island of the Gram-positive thermophile Geobacillus. BMC Genomics 2016; 17:913. [PMID: 27842516 PMCID: PMC5109656 DOI: 10.1186/s12864-016-3273-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/05/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Protein glycosylation involves the post-translational attachment of sugar chains to target proteins and has been observed in all three domains of life. Post-translational glycosylation of flagellin, the main structural protein of the flagellum, is a common characteristic among many Gram-negative bacteria and Archaea. Several distinct functions have been ascribed to flagellin glycosylation, including stabilisation and maintenance of the flagellar filament, motility, surface recognition, adhesion, and virulence. However, little is known about this trait among Gram-positive bacteria. RESULTS Using comparative genomic approaches the flagellin glycosylation loci of multiple strains of the Gram-positive thermophilic genus Geobacillus were identified and characterized. Eighteen of thirty-six compared strains of the genus carry these loci, which show evidence of horizontal acquisition. The Geobacillus flagellin glycosylation islands (FGIs) can be clustered into five distinct types, which are predicted to encode highly variable glycans decorated with distinct and heavily modified sugars. CONCLUSIONS Our comparative genomic analyses showed that, while not universal, flagellin glycosylation islands are relatively common among members of the genus Geobacillus and that the encoded flagellin glycans are highly variable. This suggests that flagellin glycosylation plays an important role in the lifestyles of members of this thermophilic genus.
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Affiliation(s)
- Pieter De Maayer
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, Wits, 2050, Johannesburg, South Africa.
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Genomics Research Institute, University of Pretoria, Pretoria, 0002, South Africa
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11
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van Teeseling MCF, Maresch D, Rath CB, Figl R, Altmann F, Jetten MSM, Messner P, Schäffer C, van Niftrik L. The S-Layer Protein of the Anammox Bacterium Kuenenia stuttgartiensis Is Heavily O-Glycosylated. Front Microbiol 2016; 7:1721. [PMID: 27847504 PMCID: PMC5088730 DOI: 10.3389/fmicb.2016.01721] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 10/13/2016] [Indexed: 01/11/2023] Open
Abstract
Anaerobic ammonium oxidation (anammox) bacteria are a distinct group of Planctomycetes that are characterized by their unique ability to perform anammox with nitrite to dinitrogen gas in a specialized organelle. The cell of anammox bacteria comprises three membrane-bound compartments and is surrounded by a two-dimensional crystalline S-layer representing the direct interaction zone of anammox bacteria with the environment. Previous results from studies with the model anammox organism Kuenenia stuttgartiensis suggested that the protein monomers building the S-layer lattice are glycosylated. In the present study, we focussed on the characterization of the S-layer protein glycosylation in order to increase our knowledge on the cell surface characteristics of anammox bacteria. Mass spectrometry (MS) analysis showed an O-glycan attached to 13 sites distributed over the entire 1591-amino acid S-layer protein. This glycan is composed of six monosaccharide residues, of which five are N-acetylhexosamine (HexNAc) residues. Four of these HexNAc residues have been identified as GalNAc. The sixth monosaccharide in the glycan is a putative dimethylated deoxyhexose. Two of the HexNAc residues were also found to contain a methyl group, thereby leading to an extensive degree of methylation of the glycan. This study presents the first characterization of a glycoprotein in a planctomycete and shows that the S-layer protein Kustd1514 of K. stuttgartiensis is heavily glycosylated with an O-linked oligosaccharide which is additionally modified by methylation. S-layer glycosylation clearly contributes to the diversification of the K. stuttgartiensis cell surface and can be expected to influence the interaction of the bacterium with other cells or abiotic surfaces.
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Affiliation(s)
- Muriel C. F. van Teeseling
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud UniversityNijmegen, Netherlands
| | - Daniel Maresch
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesVienna, Austria
| | - Cornelia B. Rath
- NanoGlycobiology Unit, Department of NanoBiotechnology, University of Natural Resources and Life SciencesVienna, Austria
| | - Rudolf Figl
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesVienna, Austria
| | - Friedrich Altmann
- Division of Biochemistry, Department of Chemistry, University of Natural Resources and Life SciencesVienna, Austria
| | - Mike S. M. Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud UniversityNijmegen, Netherlands
| | - Paul Messner
- NanoGlycobiology Unit, Department of NanoBiotechnology, University of Natural Resources and Life SciencesVienna, Austria
| | - Christina Schäffer
- NanoGlycobiology Unit, Department of NanoBiotechnology, University of Natural Resources and Life SciencesVienna, Austria
| | - Laura van Niftrik
- Department of Microbiology, Institute for Water and Wetland Research, Faculty of Science, Radboud UniversityNijmegen, Netherlands
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12
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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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Lombard J. The multiple evolutionary origins of the eukaryotic N-glycosylation pathway. Biol Direct 2016; 11:36. [PMID: 27492357 PMCID: PMC4973528 DOI: 10.1186/s13062-016-0137-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/26/2016] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND The N-glycosylation is an essential protein modification taking place in the membranes of the endoplasmic reticulum (ER) in eukaryotes and the plasma membranes in archaea. It shares mechanistic similarities based on the use of polyisoprenol lipid carriers with other glycosylation pathways involved in the synthesis of bacterial cell wall components (e.g. peptidoglycan and teichoic acids). Here, a phylogenomic analysis was carried out to examine the validity of rival hypotheses suggesting alternative archaeal or bacterial origins to the eukaryotic N-glycosylation pathway. RESULTS The comparison of several polyisoprenol-based glycosylation pathways from the three domains of life shows that most of the implicated proteins belong to a limited number of superfamilies. The N-glycosylation pathway enzymes are ancestral to the eukaryotes, but their origins are mixed: Alg7, Dpm and maybe also one gene of the glycosyltransferase 1 (GT1) superfamily and Stt3 have proteoarchaeal (TACK superphylum) origins; alg2/alg11 may have resulted from the duplication of the original GT1 gene; the lumen glycosyltransferases were probably co-opted and multiplied through several gene duplications during eukaryogenesis; Alg13/Alg14 are more similar to their bacterial homologues; and Alg1, Alg5 and a putative flippase have unknown origins. CONCLUSIONS The origin of the eukaryotic N-glycosylation pathway is not unique and less straightforward than previously thought: some basic components likely have proteoarchaeal origins, but the pathway was extensively developed before the eukaryotic diversification through multiple gene duplications, protein co-options, neofunctionalizations and even possible horizontal gene transfers from bacteria. These results may have important implications for our understanding of the ER evolution and eukaryogenesis. REVIEWERS This article was reviewed by Pr. Patrick Forterre and Dr. Sergei Mekhedov (nominated by Editorial Board member Michael Galperin).
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Affiliation(s)
- Jonathan Lombard
- National Evolutionary Synthesis Center, 2024 W. Main Street Suite A200, Durham, NC, 27705, USA.
- Biosciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter, EX4 4QD, UK.
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Zhu C, Guo G, Ma Q, Zhang F, Ma F, Liu J, Xiao D, Yang X, Sun M. Diversity in S-layers. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 123:1-15. [PMID: 27498171 DOI: 10.1016/j.pbiomolbio.2016.08.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/16/2016] [Accepted: 08/02/2016] [Indexed: 01/29/2023]
Abstract
Surface layers, referred simply as S-layers, are the two-dimensional crystalline arrays of protein or glycoprotein subunits on cell surface. They are one of the most common outermost envelope components observed in prokaryotic organisms (Archaea and Bacteria). Over the past decades, S-layers have become an issue of increasing interest due to their ubiquitousness, special features and functions. Substantial work in this field provides evidences of an enormous diversity in S-layers. This paper reviews and illustrates the diversity from several different aspects, involving the S-layer-carrying strains, the structure of S-layers, the S-layer proteins and genes, as well as the functions of S-layers.
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Affiliation(s)
- Chaohua Zhu
- College of Environment and Plant protection, Hainan University/Key Laboratory of Protection and Development Utilization of Tropical Crop Germplasm Resources (Hainan University), Ministry of Education, Haikou, 570228, Hainan, PR China
| | - Gang Guo
- Haikou Experimental Station/Hainan Key Laboratory of Banana Genetic Improvement, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, Hainan, PR China; State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Qiqi Ma
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China
| | - Fengjuan Zhang
- Haikou Experimental Station/Hainan Key Laboratory of Banana Genetic Improvement, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, Hainan, PR China
| | - Funing Ma
- Haikou Experimental Station/Hainan Key Laboratory of Banana Genetic Improvement, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, Hainan, PR China
| | - Jianping Liu
- Division of Functional Genomics, Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, Stockholm 17177, Sweden
| | - Dao Xiao
- Haikou Experimental Station/Hainan Key Laboratory of Banana Genetic Improvement, Chinese Academy of Tropical Agricultural Sciences, Haikou, 570102, Hainan, PR China
| | - Xiaolin Yang
- College of Environment and Plant protection, Hainan University/Key Laboratory of Protection and Development Utilization of Tropical Crop Germplasm Resources (Hainan University), Ministry of Education, Haikou, 570228, Hainan, PR China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, PR China.
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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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16
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Production and cell surface display of recombinant anthrax protective antigen on the surface layer of attenuated Bacillus anthracis. World J Microbiol Biotechnol 2014; 31:345-52. [PMID: 25504373 DOI: 10.1007/s11274-014-1786-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 12/05/2014] [Indexed: 10/24/2022]
Abstract
To investigate the surface display of the anthrax protective antigen (PA) on attenuated Bacillus anthracis, a recombinant B. anthracis strain, named AP429 was constructed by integrating into the chromosome a translational fusion harboring the DNA fragments encoding the cell wall-targeting domain of the S-layer protein EA1 and the anthrax PA. Crerecombinase action at the loxP sites excised the antibiotic marker. Western blot analysis, fluorescence-activated cell sorting and immunofluorescence analysis confirmed that PA was successfully expressed on the S-layer of the recombinant antibiotic marker-free strain. Notwithstanding extensive proteolytic degradation of the hybrid protein SLHs-PA, quantitative ELISA revealed that approximately 8.1 × 10(6) molecules of SLHs-PA were gained from each Bacillus cell. Moreover, electron microscopy assay indicated that the typical S-layer structures could be clearly observed from the recombinant strain micrographs.
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Sleytr UB, Schuster B, Egelseer E, Pum D. S-layers: principles and applications. FEMS Microbiol Rev 2014; 38:823-64. [PMID: 24483139 PMCID: PMC4232325 DOI: 10.1111/1574-6976.12063] [Citation(s) in RCA: 232] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2013] [Revised: 01/10/2014] [Accepted: 01/13/2014] [Indexed: 01/12/2023] Open
Abstract
Monomolecular arrays of protein or glycoprotein subunits forming surface layers (S-layers) are one of the most commonly observed prokaryotic cell envelope components. S-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. The isoporous lattices completely covering the cell surface provide organisms with various selection advantages including functioning as protective coats, molecular sieves and ion traps, as structures involved in surface recognition and cell adhesion, and as antifouling layers. S-layers are also identified to contribute to virulence when present as a structural component of pathogens. In Archaea, most of which possess S-layers as exclusive wall component, they are involved in determining cell shape and cell division. Studies on structure, chemistry, genetics, assembly, function, and evolutionary relationship of S-layers revealed considerable application potential in (nano)biotechnology, biomimetics, biomedicine, and synthetic biology.
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Affiliation(s)
- Uwe B. Sleytr
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bernhard Schuster
- Institute of Synthetic BiologyDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Eva‐Maria Egelseer
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
| | - Dietmar Pum
- Institute of BiophysicsDepartment of NanobiotechnologyUniversity of Natural Resources and Life SciencesViennaAustria
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Habibi N, Karimi B. Fabrication and characterization of zinc oxide nanoparticle coated magnetic iron oxide: Effect of S-layers adsorption on surface of oxide. J IND ENG CHEM 2014. [DOI: 10.1016/j.jiec.2013.11.039] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Schuster B, Sleytr UB. Biomimetic interfaces based on S-layer proteins, lipid membranes and functional biomolecules. J R Soc Interface 2014; 11:20140232. [PMID: 24812051 PMCID: PMC4032536 DOI: 10.1098/rsif.2014.0232] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 04/15/2014] [Indexed: 12/20/2022] Open
Abstract
Designing and utilization of biomimetic membrane systems generated by bottom-up processes is a rapidly growing scientific and engineering field. Elucidation of the supramolecular construction principle of archaeal cell envelopes composed of S-layer stabilized lipid membranes led to new strategies for generating highly stable functional lipid membranes at meso- and macroscopic scale. In this review, we provide a state-of-the-art survey of how S-layer proteins, lipids and polymers may be used as basic building blocks for the assembly of S-layer-supported lipid membranes. These biomimetic membrane systems are distinguished by a nanopatterned fluidity, enhanced stability and longevity and, thus, provide a dedicated reconstitution matrix for membrane-active peptides and transmembrane proteins. Exciting areas in the (lab-on-a-) biochip technology are combining composite S-layer membrane systems involving specific membrane functions with the silicon world. Thus, it might become possible to create artificial noses or tongues, where many receptor proteins have to be exposed and read out simultaneously. Moreover, S-layer-coated liposomes and emulsomes copying virus envelopes constitute promising nanoformulations for the production of novel targeting, delivery, encapsulation and imaging systems.
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Affiliation(s)
- Bernhard Schuster
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Institute for Synthetic Bioarchitectures, Muthgasse 11, 1190 Vienna, Austria
| | - Uwe B. Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Institute for Biophysics, Muthgasse 11, 1190 Vienna, Austria
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20
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Abstract
Prokaryotic glycosylation fulfills an important role in maintaining and protecting the structural integrity and function of the bacterial cell wall, as well as serving as a flexible adaption mechanism to evade environmental and host-induced pressure. The scope of bacterial and archaeal protein glycosylation has considerably expanded over the past decade(s), with numerous examples covering the glycosylation of flagella, pili, glycosylated enzymes, as well as surface-layer proteins. This article addresses structure, analysis, function, genetic basis, biosynthesis, and biomedical and biotechnological applications of cell-envelope glycoconjugates, S-layer glycoprotein glycans, and "nonclassical" secondary-cell wall polysaccharides. The latter group of polymers mediates the important attachment and regular orientation of the S-layer to the cell wall. The structures of these glycopolymers reveal an enormous diversity, resembling the structural variability of bacterial lipopolysaccharides and capsular polysaccharides. While most examples are presented for Gram-positive bacteria, the S-layer glycan of the Gram-negative pathogen Tannerella forsythia is also discussed. In addition, archaeal S-layer glycoproteins are briefly summarized.
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Affiliation(s)
- Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology Unit, University of Natural Resources and Life Sciences, Vienna, Austria
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21
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Profile of secreted hydrolases, associated proteins, and SlpA in Thermoanaerobacterium saccharolyticum during the degradation of hemicellulose. Appl Environ Microbiol 2014; 80:5001-11. [PMID: 24907337 DOI: 10.1128/aem.00998-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Thermoanaerobacterium saccharolyticum, a Gram-positive thermophilic anaerobic bacterium, grows robustly on insoluble hemicellulose, which requires a specialized suite of secreted and transmembrane proteins. We report here the characterization of proteins secreted by this organism. Cultures were grown on hemicellulose, glucose, xylose, starch, and xylan in pH-controlled bioreactors, and samples were analyzed via spotted microarrays and liquid chromatography-mass spectrometry. Key hydrolases and transporters employed by T. saccharolyticum for growth on hemicellulose were, for the most part, hitherto uncharacterized and existed in two clusters (Tsac_1445 through Tsac_1464 for xylan/xylose and Tsac_1344 through Tsac_1349 for starch). A phosphotransferase system subunit, Tsac_0032, also appeared to be exclusive to growth on glucose. Previously identified hydrolases that showed strong conditional expression changes included XynA (Tsac_1459), XynC (Tsac_0897), and a pullulanase, Apu (Tsac_1342). An omnipresent transcript and protein making up a large percentage of the overall secretome, Tsac_0361, was tentatively identified as the primary S-layer component in T. saccharolyticum, and deletion of the Tsac_0361 gene resulted in gross morphological changes to the cells. The view of hemicellulose degradation revealed here will be enabling for metabolic engineering efforts in biofuel-producing organisms that degrade cellulose well but lack the ability to catabolize C5 sugars.
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22
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Abstract
The outer surface of many archaea and bacteria is coated with a proteinaceous surface layer (known as an S-layer), which is formed by the self-assembly of monomeric proteins into a regularly spaced, two-dimensional array. Bacteria possess dedicated pathways for the secretion and anchoring of the S-layer to the cell wall, and some Gram-positive species have large S-layer-associated gene families. S-layers have important roles in growth and survival, and their many functions include the maintenance of cell integrity, enzyme display and, in pathogens and commensals, interaction with the host and its immune system. In this Review, we discuss our current knowledge of S-layer and related proteins, including their structures, mechanisms of secretion and anchoring and their diverse functions.
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23
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Close DW, Ferrara F, Dichosa AEK, Kumar S, Daughton AR, Daligault HE, Reitenga KG, Velappan N, Sanchez TC, Iyer S, Kiss C, Han CS, Bradbury ARM. Using phage display selected antibodies to dissect microbiomes for complete de novo genome sequencing of low abundance microbes. BMC Microbiol 2013; 13:270. [PMID: 24279426 PMCID: PMC3907030 DOI: 10.1186/1471-2180-13-270] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 11/21/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Single cell genomics has revolutionized microbial sequencing, but complete coverage of genomes in complex microbiomes is imperfect due to enormous variation in organismal abundance and amplification bias. Empirical methods that complement rapidly improving bioinformatic tools will improve characterization of microbiomes and facilitate better genome coverage for low abundance microbes. METHODS We describe a new approach to sequencing individual species from microbiomes that combines antibody phage display against intact bacteria with fluorescence activated cell sorting (FACS). Single chain (scFv) antibodies are selected using phage display against a bacteria or microbial community, resulting in species-specific antibodies that can be used in FACS for relative quantification of an organism in a community, as well as enrichment or depletion prior to genome sequencing. RESULTS We selected antibodies against Lactobacillus acidophilus and demonstrate a FACS-based approach for identification and enrichment of the organism from both laboratory-cultured and commercially derived bacterial mixtures. The ability to selectively enrich for L. acidophilus when it is present at a very low abundance (<0.2%) leads to complete (>99.8%) de novo genome coverage whereas the standard single-cell sequencing approach is incomplete (<68%). We show that specific antibodies can be selected against L. acidophilus when the monoculture is used as antigen as well as when a community of 10 closely related species is used demonstrating that in principal antibodies can be generated against individual organisms within microbial communities. CONCLUSIONS The approach presented here demonstrates that phage-selected antibodies against bacteria enable identification, enrichment of rare species, and depletion of abundant organisms making it tractable to virtually any microbe or microbial community. Combining antibody specificity with FACS provides a new approach for characterizing and manipulating microbial communities prior to genome sequencing.
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Affiliation(s)
- Devin W Close
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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24
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Anzengruber J, Pabst M, Neumann L, Sekot G, Heinl S, Grabherr R, Altmann F, Messner P, Schäffer C. Protein O-glucosylation in Lactobacillus buchneri. Glycoconj J 2013; 31:117-31. [PMID: 24162649 DOI: 10.1007/s10719-013-9505-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 02/02/2023]
Abstract
Based on the previous demonstration of surface (S-) layer protein glycosylation in Lactobacillus buchneri 41021/251 and because of general advantages of lactic acid bacteria for applied research, protein glycosylation in this bacterial species was investigated in detail. The cell surface of L. buchneri CD034 is completely covered with an oblique 2D crystalline array (lattice parameters, a = 5.9 nm; b = 6.2 nm; γ ~ 77°) formed by self-assembly of the S-layer protein SlpB. Biochemical and mass spectrometric analyses revealed that SlpB is the most abundant protein and that it is O-glycosylated at four serine residues within the sequence S(152)-A-S(154)-S(155)-A-S(157) with, on average, seven Glc(α1-6) residues, each. Subcellular fractionation of strain CD034 indicated a sequential order of SlpB export and glucosylation as evidenced by lack of glucosylation of cytosolic SlpB. Protein glycosylation analysis was extended to strain L. buchneri NRRL B-30929 where an analogous glucosylation scenario could be detected, with the S-layer glycoprotein SlpN containing an O-glycosylation motif identical to that of SlpB. This corroborates previous data on S-layer protein glucosylation of strain 41021/251 and let us propose a species-wide S-layer protein O-glucosylation in L. buchneri targeted at the sequence motif S-A-S-S-A-S. Search of the L. buchneri genomes for the said glucosylation motif revealed one further ORF, encoding the putative glycosyl-hydrolase LbGH25B and LbGH25N in L. buchneri CD034 and NRRL B-30929, respectively, for which we have indications of a glycosylation comparable to that of the S-layer proteins. These findings demonstrate the presence of a distinct protein O-glucosylation system in Gram-positive and beneficial microbes.
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Affiliation(s)
- Julia Anzengruber
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria,
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25
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Settem RP, Honma K, Stafford GP, Sharma A. Protein-linked glycans in periodontal bacteria: prevalence and role at the immune interface. Front Microbiol 2013; 4:310. [PMID: 24146665 PMCID: PMC3797959 DOI: 10.3389/fmicb.2013.00310] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Accepted: 09/27/2013] [Indexed: 12/20/2022] Open
Abstract
Protein modification with complex glycans is increasingly being recognized in many pathogenic and non-pathogenic bacteria, and is now thought to be central to the successful life-style of those species in their respective hosts. This review aims to convey current knowledge on the extent of protein glycosylation in periodontal pathogenic bacteria and its role in the modulation of the host immune responses. The available data show that surface glycans of periodontal bacteria orchestrate dendritic cell cytokine responses to drive T cell immunity in ways that facilitate bacterial persistence in the host and induce periodontal inflammation. In addition, surface glycans may help certain periodontal bacteria protect against serum complement attack or help them escape immune detection through glycomimicry. In this review we will focus mainly on the generalized surface-layer protein glycosylation system of the periodontal pathogen Tannerella forsythia in shaping innate and adaptive host immunity in the context of periodontal disease. In addition, we will also review the current state of knowledge of surface protein glycosylation and its potential for immune modulation in other periodontal pathogens.
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Affiliation(s)
- Rajendra P Settem
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, State University of New York Buffalo, NY, USA
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26
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Khmelenina VN, Suzina NE, Trotsenko YA. Surface layers of methanotrophic bacteria. Microbiology (Reading) 2013. [DOI: 10.1134/s0026261713050068] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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27
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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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28
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Lin CI, McCarty RM, Liu HW. The biosynthesis of nitrogen-, sulfur-, and high-carbon chain-containing sugars. Chem Soc Rev 2013; 42:4377-407. [PMID: 23348524 PMCID: PMC3641179 DOI: 10.1039/c2cs35438a] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Carbohydrates serve many structural and functional roles in biology. While the majority of monosaccharides are characterized by the chemical composition (CH2O)n, modifications including deoxygenation, C-alkylation, amination, O- and N-methylation, which are characteristic of many sugar appendages of secondary metabolites, are not uncommon. Interestingly, some sugar molecules are formed via modifications including amine oxidation, sulfur incorporation, and "high-carbon" chain attachment. Most of these unusual sugars have been identified over the past several decades as components of microbially produced natural products, although a few high-carbon sugars are also found in the lipooligosaccharides of the outer cell walls of Gram-negative bacteria. Despite their broad distribution in nature, these sugars are considered "rare" due to their relative scarcity. The biosynthetic steps that underlie their formation continue to perplex researchers to this day and many questions regarding key transformations remain unanswered. This review will focus on our current understanding of the biosynthesis of unusual sugars bearing oxidized amine substituents, thio-functional groups, and high-carbon chains.
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Affiliation(s)
| | | | - Hung-wen Liu
- Division of Medicinal Chemistry, College of Pharmacy, and Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712
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Hynönen U, Palva A. Lactobacillus surface layer proteins: structure, function and applications. Appl Microbiol Biotechnol 2013; 97:5225-43. [PMID: 23677442 PMCID: PMC3666127 DOI: 10.1007/s00253-013-4962-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 12/26/2022]
Abstract
Bacterial surface (S) layers are the outermost proteinaceous cell envelope structures found on members of nearly all taxonomic groups of bacteria and Archaea. They are composed of numerous identical subunits forming a symmetric, porous, lattice-like layer that completely covers the cell surface. The subunits are held together and attached to cell wall carbohydrates by non-covalent interactions, and they spontaneously reassemble in vitro by an entropy-driven process. Due to the low amino acid sequence similarity among S-layer proteins in general, verification of the presence of an S-layer on the bacterial cell surface usually requires electron microscopy. In lactobacilli, S-layer proteins have been detected on many but not all species. Lactobacillus S-layer proteins differ from those of other bacteria in their smaller size and high predicted pI. The positive charge in Lactobacillus S-layer proteins is concentrated in the more conserved cell wall binding domain, which can be either N- or C-terminal depending on the species. The more variable domain is responsible for the self-assembly of the monomers to a periodic structure. The biological functions of Lactobacillus S-layer proteins are poorly understood, but in some species S-layer proteins mediate bacterial adherence to host cells or extracellular matrix proteins or have protective or enzymatic functions. Lactobacillus S-layer proteins show potential for use as antigen carriers in live oral vaccine design because of their adhesive and immunomodulatory properties and the general non-pathogenicity of the species.
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Affiliation(s)
- Ulla Hynönen
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
| | - Airi Palva
- Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, 00014 Helsinki, Finland
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Ruiz N. A bird's eye view of the bacterial landscape. Methods Mol Biol 2013; 966:1-14. [PMID: 23299725 DOI: 10.1007/978-1-62703-245-2_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Bacteria interact with the environment through their cell surface. Activities as diverse as attaching to a catheter, crawling on a surface, swimming through a pond, or being preyed on by a bacteriophage depend on the composition and structure of the cell surface. The cell surface must also protect bacteria from harmful chemicals present in the environment while allowing the intake of nutrients and excretion of toxic molecules. Bacteria have evolved four main types of bacterial cell surfaces to accomplish these functions: those of the typical gram-negative and gram-positive bacteria, and those of the Actinobacteria and Mollicutes. So few types seems remarkable since bacteria are very diverse and abundant, and they can live in many different environments. However, each species has tweaked these stereotypical bacterial surfaces to best fit its needs. The result is an amazing diversity of the bacterial landscape, most of which remains unexplored. Here I give an overview of the main features of the bacterial cell surface and highlight how advances in methodology have moved forward this field of study.
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Affiliation(s)
- Natividad Ruiz
- Department of Microbiology, The Ohio State University, Columbus, OH, USA.
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Posch G, Sekot G, Friedrich V, Megson ZA, Koerdt A, Messner P, Schäffer C. Glycobiology Aspects of the Periodontal Pathogen Tannerella forsythia. Biomolecules 2012; 2:467-82. [PMID: 24970146 PMCID: PMC4030854 DOI: 10.3390/biom2040467] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2012] [Revised: 09/27/2012] [Accepted: 09/29/2012] [Indexed: 12/22/2022] Open
Abstract
Glycobiology is important for the periodontal pathogen Tannerella forsythia, affecting the bacterium's cellular integrity, its life-style, and virulence potential. The bacterium possesses a unique Gram-negative cell envelope with a glycosylated surface (S-) layer as outermost decoration that is proposed to be anchored via a rough lipopolysaccharide. The S-layer glycan has the structure 4‑MeO-b-ManpNAcCONH2-(1→3)-[Pse5Am7Gc-(2→4)-]-b-ManpNAcA-(1→4)-[4-MeO-a-Galp-(1→2)-]-a-Fucp-(1→4)-[-a-Xylp-(1→3)-]-b-GlcpA-(1→3)-[-b-Digp-(1→2)-]-a-Galp and is linked to distinct serine and threonine residues within the D(S/T)(A/I/L/M/T/V) amino acid motif. Also several other Tannerella proteins are modified with the S‑layer oligosaccharide, indicating the presence of a general O‑glycosylation system. Protein O‑glycosylation impacts the life-style of T. forsythia since truncated S-layer glycans present in a defined mutant favor biofilm formation. While the S‑layer has also been shown to be a virulence factor and to delay the bacterium's recognition by the innate immune system of the host, the contribution of glycosylation to modulating host immunity is currently unraveling. Recently, it was shown that Tannerella surface glycosylation has a role in restraining the Th17-mediated neutrophil infiltration in the gingival tissues. Related to its asaccharolytic physiology, T. forsythia expresses a robust enzymatic repertoire, including several glycosidases, such as sialidases, which are linked to specific growth requirements and are involved in triggering host tissue destruction. This review compiles the current knowledge on the glycobiology of T. forsythia.
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Affiliation(s)
- Gerald Posch
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
| | - Gerhard Sekot
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
| | - Valentin Friedrich
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
| | - Zoë A Megson
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
| | - Andrea Koerdt
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
| | - Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology Unit, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
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Tomás JM. The main Aeromonas pathogenic factors. ISRN MICROBIOLOGY 2012; 2012:256261. [PMID: 23724321 PMCID: PMC3658858 DOI: 10.5402/2012/256261] [Citation(s) in RCA: 184] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 07/19/2012] [Indexed: 12/27/2022]
Abstract
The members of the Aeromonas genus are ubiquitous, water-borne bacteria. They have been isolated from marine waters, rivers, lakes, swamps, sediments, chlorine water, water distribution systems, drinking water and residual waters; different types of food, such as meat, fish, seafood, vegetables, and processed foods. Aeromonas strains are predominantly pathogenic to poikilothermic animals, and the mesophilic strains are emerging as important pathogens in humans, causing a variety of extraintestinal and systemic infections as well as gastrointestinal infections. The most commonly described disease caused by Aeromonas is the gastroenteritis; however, no adequate animal model is available to reproduce this illness caused by Aeromonas. The main pathogenic factors associated with Aeromonas are: surface polysaccharides (capsule, lipopolysaccharide, and glucan), S-layers, iron-binding systems, exotoxins and extracellular enzymes, secretion systems, fimbriae and other nonfilamentous adhesins, motility and flagella.
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Affiliation(s)
- J M Tomás
- Departamento Microbiología, Universidad de Barcelona, Diagonal 643, 08071 Barcelona, Spain
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Yamashita H, Taoka A, Uchihashi T, Asano T, Ando T, Fukumori Y. Single-Molecule Imaging on Living Bacterial Cell Surface by High-Speed AFM. J Mol Biol 2012; 422:300-9. [DOI: 10.1016/j.jmb.2012.05.018] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Accepted: 05/14/2012] [Indexed: 11/27/2022]
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Vinogradov E, Deschatelets L, Lamoureux M, Patel GB, Tremblay TL, Robotham A, Goneau MF, Cummings-Lorbetskie C, Watson DC, Brisson JR, Kelly JF, Gilbert M. Cell surface glycoproteins from Thermoplasma acidophilum are modified with an N-linked glycan containing 6-C-sulfofucose. Glycobiology 2012; 22:1256-67. [PMID: 22692048 DOI: 10.1093/glycob/cws094] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Thermoplasma acidophilum is a thermoacidophilic archaeon that grows optimally at pH 2 and 59°C. This extremophile is remarkable by the absence of a cell wall or an S-layer. Treating the cells with Triton X-100 at pH 3 allowed the extraction of all of the cell surface glycoproteins while keeping cells intact. The extracted glycoproteins were partially purified by cation-exchange chromatography, and we identified five glycoproteins by N-terminal sequencing and mass spectrometry of in-gel tryptic digests. These glycoproteins are positive for periodic acid-Schiff staining, have a high content of Asn including a large number in the Asn-X-Ser/Thr sequon and have apparent masses that are 34-48% larger than the masses deduced from their amino acid sequences. The pooled glycoproteins were digested with proteinase K and the purified glycopeptides were analyzed by NMR. Structural determination showed that the carbohydrate part was represented by two structures in nearly equal amounts, differing by the presence of one terminal mannose residue. The larger glycan chain consists of eight residues: six hexoses, one heptose and one sugar with an unusual residue mass of 226 Da which was identified as 6-deoxy-6-C-sulfo-D-galactose (6-C-sulfo-D-fucose). Mass spectrometry analyses of the peptides obtained by trypsin and chymotrypsin digestion confirmed the principal structures to be those determined by NMR and identified 14 glycopeptides derived from the main glycoprotein, Ta0280, all containing the Asn-X-Ser/Thr sequons. Thermoplasma acidophilum appears to have a "general" protein N-glycosylation system that targets a number of cell surface proteins.
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Affiliation(s)
- Evgeny Vinogradov
- Human Health Therapeutics, National Research Council Canada, Ottawa, Ontario, Canada K1A 0R6
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Acosta F, de Pedro MA, Berenguer J. Homogeneous incorporation of secondary cell wall polysaccharides to the cell wall of Thermus thermophilus HB27. Extremophiles 2012; 16:485-95. [PMID: 22527042 DOI: 10.1007/s00792-012-0448-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 04/02/2012] [Indexed: 11/27/2022]
Abstract
Regular surface protein layers (S-layers) from most Gram-positive bacteria and from the ancestral bacterium Thermus thermophilus attach to pyruvylated polysaccharides (SCWP) covalently bound to the peptidoglycan through their SLH domain. However, it is not known whether the synthesis of SCWP and S-layer is coordinated enough as to follow a similar pattern of incorporation to the cell wall during growth. In this work we analyse the localization of newly synthesized SCWP on the cell wall of T. thermophilus by immunoelectron microscopy. For this, we obtained mutants with a reduced amount of pyruvylated SCWP through mutation of the csaB gene encoding the SCWP-pyruvylating activity, and its upstream gene csaA, a putative sugar transporter. We hypothesized that CsaA would be required for the synthesis of the SCWP. However, we found that csaA mutants showed only a minor decrease in the amount of SCWP immunodetected on the cell walls in comparison with csaB mutants, revealing its irrelevance in the process. Complementation experiments of csaB mutants with CsaB expressed from inducible promoters revealed that newly synthesized SCWP was homogeneously distributed along the cell wall. Fusions with thermostable fluorescent protein revealed that CsaB was distributed also in homogeneous pattern associated with the membrane. These data support that synthesis of SCWP takes place in disperse and homogeneous form all over the cell surface, in contrast to the zonal incorporation at the cell centre recently demonstrated for SlpA.
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Affiliation(s)
- Federico Acosta
- Departamento de Biología Molecular, Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Campus de la UAM, 28049, Madrid, Spain
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2007-2008. MASS SPECTROMETRY REVIEWS 2012; 31:183-311. [PMID: 21850673 DOI: 10.1002/mas.20333] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 01/04/2011] [Accepted: 01/04/2011] [Indexed: 05/31/2023]
Abstract
This review is the fifth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2008. The first section of the review covers fundamental studies, fragmentation of carbohydrate ions, use of derivatives and new software developments for analysis of carbohydrate spectra. Among newer areas of method development are glycan arrays, MALDI imaging and the use of ion mobility spectrometry. The second section of the review discusses applications of MALDI MS to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, biopharmaceuticals, glycated proteins, glycolipids, glycosides and various other natural products. There is a short section on the use of MALDI mass spectrometry for the study of enzymes involved in glycan processing and a section on the use of MALDI MS to monitor products of the chemical synthesis of carbohydrates with emphasis on carbohydrate-protein complexes and glycodendrimers. Corresponding analyses by electrospray ionization now appear to outnumber those performed by MALDI and the amount of literature makes a comprehensive review on this technique impractical. However, most of the work relating to sample preparation and glycan synthesis is equally relevant to electrospray and, consequently, those proposing analyses by electrospray should also find material in this review of interest.
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Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
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Cui YB, Zhou Y, Liu WN, Chen QW, Ma GF, Shi WH, Wang YG, Yang L. Cloning of the surface layer gene sllB from Bacillus sphaericus ATCC 14577 and its heterologous expression and purification. Int J Mol Med 2012; 29:677-82. [PMID: 22266829 PMCID: PMC3573754 DOI: 10.3892/ijmm.2012.890] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Accepted: 12/13/2011] [Indexed: 01/31/2023] Open
Abstract
A cDNA fragment encoding the S-layer protein SllB cloned from Bacillus sphaericus ATCC 14577 was expressed on the surface of E. coli BL21 (DE3) cells and confirmed by the square lattice structure at the nanoscale level. The amplified gene fragment designed with PCR primers from a specified reference sequence (GenBank accession no. AJ849550) showed a high degree of sequence identity with the known sequences for S-layer protein. The best alignment scores were seen in B. sphaericus strains JG-A12 and NCTC9602, which code for a pre-form protein with a predicted cleavage site located between the two alanine residues 31 and 32. After this signal peptide sequence was removed, the mature protein had a molecular mass of 116.2613 kDa and a theoretical pI of 5.40. Further bioinformatic analysis revealed three S-layer homology (SLH) domains in the N-terminus of the mature protein, positioned at the 1–61, 63–128 and 137–197 residues. The mature S-layer protein was composed of alpha helices (24.86%), extended strands (27.01%), and rich random coils (48.13%). Bioinformatics-driven characterization of SllB may provide scientific evidence for further application of this gene in the fields of nanobiotechnology and biomimetics in the future.
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Affiliation(s)
- Yu-Bao Cui
- Department of Laboratory Medicine, Yancheng Health Vocational and Technical College, Yancheng 224006, Jiangsu Province, PR China.
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Localized synthesis of the outer envelope from Thermus thermophilus. Extremophiles 2012; 16:267-75. [DOI: 10.1007/s00792-011-0427-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 12/13/2011] [Indexed: 10/14/2022]
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Holkenbrink A, Koester DC, Kaschel J, Werz DB. Total Synthesis of α-Linked Rha-Rha-Gal Undecaprenyl Diphosphate Found in Geobacillus stearothermophilus. European J Org Chem 2011. [DOI: 10.1002/ejoc.201101021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Posch G, Pabst M, Brecker L, Altmann F, Messner P, Schäffer C. Characterization and scope of S-layer protein O-glycosylation in Tannerella forsythia. J Biol Chem 2011; 286:38714-38724. [PMID: 21911490 DOI: 10.1074/jbc.m111.284893] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cell surface glycosylation is an important element in defining the life of pathogenic bacteria. Tannerella forsythia is a Gram-negative, anaerobic periodontal pathogen inhabiting the subgingival plaque biofilms. It is completely covered by a two-dimensional crystalline surface layer (S-layer) composed of two glycoproteins. Although the S-layer has previously been shown to delay the bacterium's recognition by the innate immune system, we characterize here the S-layer protein O-glycosylation as a potential virulence factor. The T. forsythia S-layer glycan was elucidated by a combination of electrospray ionization-tandem mass spectrometry and nuclear magnetic resonance spectroscopy as an oligosaccharide with the structure 4-Me-β-ManpNAcCONH(2)-(1→3)-[Pse5Am7Gc-(2→4)-]-β-ManpNAcA-(1→4)-[4-Me-α-Galp-(1→2)-]-α-Fucp-(1→4)-[-α-Xylp-(1→3)-]-β-GlcpA-(1→3)-[-β-Digp-(1→2)-]-α-Galp, which is O-glycosidically linked to distinct serine and threonine residues within the three-amino acid motif (D)(S/T)(A/I/L/M/T/V) on either S-layer protein. This S-layer glycan obviously impacts the life style of T. forsythia because increased biofilm formation of an UDP-N-acetylmannosaminuronic acid dehydrogenase mutant can be correlated with the presence of truncated S-layer glycans. We found that several other proteins of T. forsythia are modified with that specific oligosaccharide. Proteomics identified two of them as being among previously classified antigenic outer membrane proteins that are up-regulated under biofilm conditions, in addition to two predicted antigenic lipoproteins. Theoretical analysis of the S-layer O-glycosylation of T. forsythia indicates the involvement of a 6.8-kb gene locus that is conserved among different bacteria from the Bacteroidetes phylum. Together, these findings reveal the presence of a protein O-glycosylation system in T. forsythia that is essential for creating a rich glycoproteome pinpointing a possible relevance for the virulence of this bacterium.
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Affiliation(s)
- Gerald Posch
- Department of NanoBiotechnology, NanoGlycobiology, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
| | - Martin Pabst
- Department of Chemistry, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria
| | - Lothar Brecker
- Institute for Organic Chemistry, Universität Wien, Währingerstrasse 38, A-1090 Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 18, A-1190 Vienna, Austria
| | - Paul Messner
- Department of NanoBiotechnology, NanoGlycobiology, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria
| | - Christina Schäffer
- Department of NanoBiotechnology, NanoGlycobiology, Vienna Institute of BioTechnology, Universität für Bodenkultur Wien, Muthgasse 11, A-1190 Vienna, Austria.
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Bandara AB, Champion AE, Wang X, Berg G, Apicella MA, McLendon M, Azadi P, Snyder DS, Inzana TJ. Isolation and mutagenesis of a capsule-like complex (CLC) from Francisella tularensis, and contribution of the CLC to F. tularensis virulence in mice. PLoS One 2011; 6:e19003. [PMID: 21544194 PMCID: PMC3081320 DOI: 10.1371/journal.pone.0019003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Accepted: 03/24/2011] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Francisella tularensis is a category-A select agent and is responsible for tularemia in humans and animals. The surface components of F. tularensis that contribute to virulence are not well characterized. An electron-dense capsule has been postulated to be present around F. tularensis based primarily on electron microscopy, but this specific antigen has not been isolated or characterized. METHODS AND FINDINGS A capsule-like complex (CLC) was effectively extracted from the cell surface of an F. tularensis live vaccine strain (LVS) lacking O-antigen with 0.5% phenol after 10 passages in defined medium broth and growth on defined medium agar for 5 days at 32°C in 7% CO₂. The large molecular size CLC was extracted by enzyme digestion, ethanol precipitation, and ultracentrifugation, and consisted of glucose, galactose, mannose, and Proteinase K-resistant protein. Quantitative reverse transcriptase PCR showed that expression of genes in a putative polysaccharide locus in the LVS genome (FTL_1432 through FTL_1421) was upregulated when CLC expression was enhanced. Open reading frames FTL_1423 and FLT_1422, which have homology to genes encoding for glycosyl transferases, were deleted by allelic exchange, and the resulting mutant after passage in broth (LVSΔ1423/1422_P10) lacked most or all of the CLC, as determined by electron microscopy, and CLC isolation and analysis. Complementation of LVSΔ1423/1422 and subsequent passage in broth restored CLC expression. LVSΔ1423/1422_P10 was attenuated in BALB/c mice inoculated intranasally (IN) and intraperitoneally with greater than 80 times and 270 times the LVS LD₅₀, respectively. Following immunization, mice challenged IN with over 700 times the LD₅₀ of LVS remained healthy and asymptomatic. CONCLUSIONS Our results indicated that the CLC may be a glycoprotein, FTL_1422 and -FTL_1423 were involved in CLC biosynthesis, the CLC contributed to the virulence of F. tularensis LVS, and a CLC-deficient mutant of LVS can protect mice against challenge with the parent strain.
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Affiliation(s)
- Aloka B. Bandara
- Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Anna E. Champion
- Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Xiaoshan Wang
- Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Gretchen Berg
- Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
| | - Michael A. Apicella
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
| | - Molly McLendon
- Department of Microbiology, University of Iowa, Iowa City, Iowa, United States of America
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - D. Scott Snyder
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, United States of America
| | - Thomas J. Inzana
- Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America
- * E-mail:
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Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotes. Int J Microbiol 2011; 2010:148178. [PMID: 21490701 PMCID: PMC3068309 DOI: 10.1155/2010/148178] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/08/2010] [Indexed: 01/17/2023] Open
Abstract
Recent years have witnessed a rapid growth in the number and diversity of prokaryotic proteins shown to carry N- and/or O-glycans, with protein glycosylation now considered as fundamental to the biology of these organisms as it is in eukaryotic systems. This article overviews the major glycosylation pathways that are known to exist in eukarya, bacteria and archaea. These are (i) oligosaccharyltransferase (OST)-mediated N-glycosylation which is abundant in eukarya and archaea, but is restricted to a limited range of bacteria; (ii) stepwise cytoplasmic N-glycosylation that has so far only been confirmed in the bacterial domain; (iii) OST-mediated O-glycosylation which appears to be characteristic of bacteria; and (iv) stepwise O-glycosylation which is common in eukarya and bacteria. A key aim of the review is to integrate information from the three domains of life in order to highlight commonalities in glycosylation processes. We show how the OST-mediated N- and O-glycosylation pathways share cytoplasmic assembly of lipid-linked oligosaccharides, flipping across the ER/periplasmic/cytoplasmic membranes, and transferring “en bloc” to the protein acceptor. Moreover these hallmarks are mirrored in lipopolysaccharide biosynthesis. Like in eukaryotes, stepwise O-glycosylation occurs on diverse bacterial proteins including flagellins, adhesins, autotransporters and lipoproteins, with O-glycosylation chain extension often coupled with secretory mechanisms.
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Sleytr UB, Schuster B, Egelseer EM, Pum D, Horejs CM, Tscheliessnig R, Ilk N. Nanobiotechnology with S-layer proteins as building blocks. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:277-352. [PMID: 21999999 DOI: 10.1016/b978-0-12-415906-8.00003-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
One of the key challenges in nanobiotechnology is the utilization of self- assembly systems, wherein molecules spontaneously associate into reproducible aggregates and supramolecular structures. In this contribution, we describe the basic principles of crystalline bacterial surface layers (S-layers) and their use as patterning elements. The broad application potential of S-layers in nanobiotechnology is based on the specific intrinsic features of the monomolecular arrays composed of identical protein or glycoprotein subunits. Most important, physicochemical properties and functional groups on the protein lattice are arranged in well-defined positions and orientations. Many applications of S-layers depend on the capability of isolated subunits to recrystallize into monomolecular arrays in suspension or on suitable surfaces (e.g., polymers, metals, silicon wafers) or interfaces (e.g., lipid films, liposomes, emulsomes). S-layers also represent a unique structural basis and patterning element for generating more complex supramolecular structures involving all major classes of biological molecules (e.g., proteins, lipids, glycans, nucleic acids, or combinations of these). Thus, S-layers fulfill key requirements as building blocks for the production of new supramolecular materials and nanoscale devices as required in molecular nanotechnology, nanobiotechnology, biomimetics, and synthetic biology.
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Affiliation(s)
- Uwe B Sleytr
- Department of NanoBiotechnology, University of Natural Resources and Life Sciences, Vienna, Austria
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The Structure of Bacterial S-Layer Proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2011; 103:73-130. [DOI: 10.1016/b978-0-12-415906-8.00004-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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The s-layer glycome-adding to the sugar coat of bacteria. Int J Microbiol 2010; 2011. [PMID: 20871840 PMCID: PMC2943079 DOI: 10.1155/2011/127870] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Accepted: 06/29/2010] [Indexed: 11/29/2022] Open
Abstract
The amazing repertoire of glycoconjugates present on bacterial cell surfaces includes lipopolysaccharides, capsular polysaccharides, lipooligosaccharides, exopolysaccharides, and glycoproteins. While the former are constituents of Gram-negative cells, we review here the cell surface S-layer glycoproteins of Gram-positive bacteria. S-layer glycoproteins have the unique feature of self-assembling into 2D lattices providing a display matrix for glycans with periodicity at the nanometer scale. Typically, bacterial S-layer glycans are O-glycosidically linked to serine, threonine, or tyrosine residues, and they rely on a much wider variety of constituents, glycosidic linkage types, and structures than their eukaryotic counterparts. As the S-layer glycome of several bacteria is unravelling, a picture of how S-layer glycoproteins are biosynthesized is evolving. X-ray crystallography experiments allowed first insights into the catalysis mechanism of selected enzymes. In the future, it will be exciting to fully exploit the S-layer glycome for glycoengineering purposes and to link it to the bacterial interactome.
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47
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Koopmans RJ, Aggeli A. Nanobiotechnology—quo vadis? Curr Opin Microbiol 2010; 13:327-34. [DOI: 10.1016/j.mib.2010.01.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Accepted: 01/18/2010] [Indexed: 01/12/2023]
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Zarschler K, Janesch B, Pabst M, Altmann F, Messner P, Schäffer C. Protein tyrosine O-glycosylation--a rather unexplored prokaryotic glycosylation system. Glycobiology 2010; 20:787-98. [PMID: 20200052 DOI: 10.1093/glycob/cwq035] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Glycosylation is a frequent and heterogeneous posttranslational protein modification occurring in all domains of life. While protein N-glycosylation at asparagine and O-glycosylation at serine, threonine or hydroxyproline residues have been studied in great detail, only few data are available on O-glycosidic attachment of glycans to the amino acid tyrosine. In this study, we describe the identification and characterization of a bacterial protein tyrosine O-glycosylation system. In the Gram-positive, mesophilic bacterium Paenibacillus alvei CCM 2051(T), a polysaccharide consisting of [-->3)-beta-d-Galp-(1[alpha-d-Glcp-(1-->6)] -->4)-beta-d-ManpNAc-(1-->] repeating units is O-glycosidically linked via an adaptor with the structure -[GroA-2-->OPO(2)-->4-beta-d-ManpNAc-(1-->4)] -->3)-alpha-l-Rhap-(1-->3)-alpha-l-Rhap-(1-->3)-alpha-l-Rhap-(1-->3)-beta-d-Galp-(1--> to specific tyrosine residues of the S-layer protein SpaA. A +AH4-24.3-kb S-layer glycosylation (slg) gene cluster encodes the information necessary for the biosynthesis of this glycan chain within 18 open reading frames (ORF). The corresponding translation products are involved in the biosynthesis of nucleotide-activated monosaccharides, assembly and export as well as in the transfer of the completed polysaccharide chain to the S-layer target protein. All ORFs of the cluster, except those encoding the nucleotide sugar biosynthesis enzymes and the ATP binding cassette (ABC) transporter integral transmembrane proteins, were disrupted by the insertion of the mobile group II intron Ll.LtrB, and S-layer glycoproteins produced in mutant backgrounds were analyzed by mass spectrometry. There is evidence that the glycan chain is synthesized in a process comparable to the ABC-transporter-dependent pathway of the lipopolysaccharide O-polysaccharide biosynthesis. Furthermore, with the protein WsfB, we have identified an O-oligosaccharyl:protein transferase required for the formation of the covalent beta-d-Gal-->Tyr linkage between the glycan chain and the S-layer protein.
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Affiliation(s)
- Kristof Zarschler
- Department of NanoBiotechnology, ViennaInstitute of BioTechnology, Universität für Bodenkultur Wien, A-1190 Vienna,Austria
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Steiner K, Hagelueken G, Messner P, Schäffer C, Naismith JH. Structural basis of substrate binding in WsaF, a rhamnosyltransferase from Geobacillus stearothermophilus. J Mol Biol 2010; 397:436-47. [PMID: 20097205 PMCID: PMC3898925 DOI: 10.1016/j.jmb.2010.01.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/13/2010] [Accepted: 01/15/2010] [Indexed: 11/27/2022]
Abstract
Carbohydrate polymers are medically and industrially important. The S-layer of many Gram-positive organisms comprises protein and carbohydrate polymers and forms an almost paracrystalline array on the cell surface. Not only is this array important for the bacteria but it has potential application in the manufacture of commercially important polysaccharides and glycoconjugates as well. The S-layer glycoprotein glycan from Geobacillus stearothermophilus NRS 2004/3a is mainly composed of repeating units of three rhamnose sugars linked by α-1,3-, α-1,2-, and β-1,2-linkages. The formation of the β-1,2-linkage is catalysed by the enzyme WsaF. The rational use of this system is hampered by the fact that WsaF and other enzymes in the pathway share very little homology to other enzymes. We report the structural and biochemical characterisation of WsaF, the first such rhamnosyltransferase to be characterised. Structural work was aided by the surface entropy reduction method. The enzyme has two domains, the N-terminal domain, which binds the acceptor (the growing rhamnan chain), and the C-terminal domain, which binds the substrate (dTDP-β-l-rhamnose). The structure of WsaF bound to dTDP and dTDP-β-l-rhamnose coupled to biochemical analysis identifies the residues that underlie catalysis and substrate recognition. We have constructed and tested by site-directed mutagenesis a model for acceptor recognition.
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Affiliation(s)
- Kerstin Steiner
- Centre for Biomolecular Sciences, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, UK
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Feldman MF. Industrial exploitation by genetic engineering of bacterial glycosylation systems. MICROBIAL GLYCOBIOLOGY 2010:903-914. [DOI: 10.1016/b978-0-12-374546-0.00046-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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