1
|
Sanchez-Gallardo R, Bottacini F, Friess L, Esteban-Torres M, Somers C, Moore RL, McAuliffe FM, Cotter PD, van Sinderen D. Unveiling metabolic pathways of selected plant-derived glycans by Bifidobacterium pseudocatenulatum. Front Microbiol 2024; 15:1414471. [PMID: 39081887 PMCID: PMC11286577 DOI: 10.3389/fmicb.2024.1414471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 08/02/2024] Open
Abstract
Bifidobacteria are commonly encountered members of the human gut microbiota that possess the enzymatic machinery necessary for the metabolism of certain plant-derived, complex carbohydrates. In the current study we describe differential growth profiles elicited by a panel of 21 newly isolated Bifidobacterium pseudocatenulatum strains on various plant-derived glycans. Using a combination of gene-trait matching and comparative genome analysis, we identified two distinct xylanases responsible for the degradation of xylan. Furthermore, three distinct extracellular α-amylases were shown to be involved in starch degradation by certain strains of B. pseudocatenulatum. Biochemical characterization showed that all three α-amylases can cleave the related substrates amylose, amylopectin, maltodextrin, glycogen and starch. The genes encoding these enzymes are variably found in the species B. pseudocatenulatum, therefore constituting a strain-specific adaptation to the gut environment as these glycans constitute common plant-derived carbohydrates present in the human diet. Overall, our study provides insights into the metabolism of these common dietary carbohydrates by a human-derived bifidobacterial species.
Collapse
Affiliation(s)
- Rocio Sanchez-Gallardo
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Lisa Friess
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Maria Esteban-Torres
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Clarissa Somers
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Rebecca L. Moore
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Fionnuala M. McAuliffe
- UCD Perinatal Research Centre, School of Medicine, National Maternity Hospital, University College Dublin, Dublin, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Teagasc Food Research Centre Moorepark, Cork, Ireland
| | - Douwe van Sinderen
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| |
Collapse
|
2
|
Pijning T, te Poele EM, de Leeuw TC, Guskov A, Dijkhuizen L. Crystal Structure of 4,6-α-Glucanotransferase GtfC-ΔC from Thermophilic Geobacillus 12AMOR1: Starch Transglycosylation in Non-Permuted GH70 Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15283-15295. [PMID: 36442227 PMCID: PMC9732880 DOI: 10.1021/acs.jafc.2c06394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/14/2022] [Accepted: 11/16/2022] [Indexed: 06/16/2023]
Abstract
GtfC-type 4,6-α-glucanotransferase (α-GT) enzymes from Glycoside Hydrolase Family 70 (GH70) are of interest for the modification of starch into low-glycemic index food ingredients. Compared to the related GH70 GtfB-type α-GTs, found exclusively in lactic acid bacteria (LAB), GtfCs occur in non-LAB, share low sequence identity, lack circular permutation of the catalytic domain, and feature a single-segment auxiliary domain IV and auxiliary C-terminal domains. Despite these differences, the first crystal structure of a GtfC, GbGtfC-ΔC from Geobacillus 12AMOR1, and the first one representing a non-permuted GH70 enzyme, reveals high structural similarity in the core domains with most GtfBs, featuring a similar tunneled active site. We propose that GtfC (and related GtfD) enzymes evolved from starch-degrading α-amylases from GH13 by acquiring α-1,6 transglycosylation capabilities, before the events that resulted in circular permutation of the catalytic domain observed in other GH70 enzymes (glucansucrases, GtfB-type α-GTs). AlphaFold modeling and sequence alignments suggest that the GbGtfC structure represents the GtfC subfamily, although it has a so far unique alternating α-1,4/α-1,6 product specificity, likely determined by residues near acceptor binding subsites +1/+2.
Collapse
Affiliation(s)
- Tjaard Pijning
- Biomolecular
X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Evelien M. te Poele
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- CarbExplore
Research B.V., Zernikelaan
8, 9747 AA Groningen, The Netherlands
| | - Tijn C. de Leeuw
- CarbExplore
Research B.V., Zernikelaan
8, 9747 AA Groningen, The Netherlands
| | - Albert Guskov
- Biomolecular
X-ray Crystallography, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Lubbert Dijkhuizen
- Microbial
Physiology, Groningen Biomolecular Sciences and Biotechnology Institute
(GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
- CarbExplore
Research B.V., Zernikelaan
8, 9747 AA Groningen, The Netherlands
| |
Collapse
|
3
|
Soussan D, Salze M, Ledormand P, Sauvageot N, Boukerb A, Lesouhaitier O, Fichant G, Rincé A, Quentin Y, Muller C. The NagY regulator: A member of the BglG/SacY antiterminator family conserved in Enterococcus faecalis and involved in virulence. Front Microbiol 2022; 13:1070116. [PMID: 36875533 PMCID: PMC9981650 DOI: 10.3389/fmicb.2022.1070116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/21/2022] [Indexed: 02/19/2023] Open
Abstract
Enterococcus faecalis is a commensal bacterium of the gastrointestinal tract but also a major nosocomial pathogen. This bacterium uses regulators like BglG/SacY family of transcriptional antiterminators to adapt its metabolism during host colonization. In this report, we investigated the role of the BglG/SacY family antiterminator NagY in the regulation of the nagY-nagE operon in presence of N-acetylglucosamine, with nagE encoding a transporter of this carbohydrate, as well as the expression of the virulence factor HylA. We showed that this last protein is involved in biofilm formation and glycosaminoglycans degradation that are important features in bacterial infection, confirmed in the Galleria mellonella model. In order to elucidate the evolution of these actors, we performed phylogenomic analyses on E. faecalis and Enterococcaceae genomes, identified orthologous sequences of NagY, NagE, and HylA, and we report their taxonomic distribution. The study of the conservation of the upstream region of nagY and hylA genes showed that the molecular mechanism of NagY regulation involves ribonucleic antiterminator sequence overlapping a rho-independent terminator, suggesting a regulation conforming to the canonical model of BglG/SacY family antiterminators. In the perspective of opportunism understanding, we offer new insights into the mechanism of host sensing thanks to the NagY antiterminator and its targets expression.
Collapse
Affiliation(s)
- Diane Soussan
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Marine Salze
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Pierre Ledormand
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Nicolas Sauvageot
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Amine Boukerb
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France.,Plateforme de Génomique, CBSA EA4312, Normandie Université, UNIROUEN, Évreux, France
| | - Olivier Lesouhaitier
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Alain Rincé
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| | - Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, Université Paul Sabatier, Toulouse, France
| | - Cécile Muller
- Unité de Recherche Communication Bactérienne et Stratégies Anti-infectieuses, CBSA UR4312, Normandie Université, UNICAEN, Caen, France.,Fédération de Recherche SeSAD, Normandie Université, UNICAEN, Caen, France
| |
Collapse
|
4
|
Huang R, Feng H, Xu Z, Zhang N, Liu Y, Shao J, Shen Q, Zhang R. Identification of Adhesins in Plant Beneficial Rhizobacteria Bacillus velezensis SQR9 and Their Effect on Root Colonization. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2022; 35:64-72. [PMID: 34698535 DOI: 10.1094/mpmi-09-21-0234-r] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Probiotic Bacillus colonization of plant root surfaces has been reported to improve its beneficial effect. Chemotaxis, adhesion, aggregation, and biofilm formation are the four steps of root colonization by plant growth-promoting rhizobacteria (PGPRs). Compared with the other three well-studied processes, adhesion of PGPRs is less known. In this study, using mutant strains deleted for potential adhesin genes in PGPR strain Bacillus velezensis SQR9, adherence to both cucumber root surface and abiotic surface by those strains was evaluated. Results showed that deletion mutations ΔlytB, ΔV529_10500, ΔfliD, ΔyhaN, and ΔsacB reduced the adhesion to root surfaces, while, among them, only ΔfliD had significant defects in adhesion to abiotic surfaces (glass and polystyrene). In addition, B. velevzensis SQR9 mutants defective in adhesion to root surfaces showed a deficiency in rhizosphere colonization. Among the encoded proteins, FliD and YhaN played vital roles in root adhesion. This research systematically explored the potential adhesins in a well-studied PGPR strain and also indicated that adhesion progress was required for root colonization, which will help to enhance rhizosphere colonization and beneficial function of PGPRs in agricultural production.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Collapse
Affiliation(s)
- Rong Huang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Haichao Feng
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Zhihui Xu
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Nan Zhang
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| | - Jiahui Shao
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Qirong Shen
- Jiangsu Provincial Key Lab of Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center of Solid Organic Wastes, Nanjing Agricultural University, Nanjing 210095, Jiangsu, P.R. China
| | - Ruifu Zhang
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R. China
| |
Collapse
|
5
|
Yang W, Sheng L, Su L, Chen S, Wu J. Directed Mutation of Two Key Amino Acid Residues Alters the Product Structure of the New 4,6-α-Glucanotransferase from Bacillus sporothermodurans. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14680-14688. [PMID: 34845909 DOI: 10.1021/acs.jafc.1c05263] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
4,6-α-Glucanotransferases (4,6-α-GTs) convert amylose V into two types of differently structured products: a linear product connected by continuous α,1 → 6 bonds, such as isomalto/malto-polysaccharide (IMMP), and a highly branched product connected by alternating α,1 → 4 and α,1 → 6 bonds, such as reuteran-like polysaccharide (RLP). The synthesis process of 4,6-α-GT products is unclear, and exploring this process is significant for producing dietary fibers with potential applications. This study identified and expressed Geobacillus sp. 12AMOR1 GtfD-ΔC and Bacillus sporothermodurans GtfC-ΔC. After characterizing their products through 1H NMR and enzymatic fingerprinting, we found that GtfD-ΔC synthesized RLP with 29% α,1 → 6 bonds, and GtfC-ΔC synthesized IMMP with 71% α,1 → 6 bonds. The maltoheptaose incubation experiment showed different chain-length transfer patterns of two 4,6-α-GTs, GtfC-ΔC and GtfD-ΔC, transferring single and multiple glucose residues in each transglycosylation reaction, respectively. Site-directed mutagenesis confirmed that positions S345 and I347 influence the product structure of GtfC-ΔC, and the S345T/I347V mutation changed the GtfC-ΔC product to a linear product connected by alternating α,1 → 4 and α,1 → 6 bonds (pullulan-like polysaccharide) and altered the chain-length transfer pattern of GtfC-ΔC. We proposed that different chain-length transfer patterns between GtfD-ΔC and GtfC-ΔC may explain their differences in product structures. These findings are significant for obtaining the desired dietary fiber by engineering 4,6-α-GT.
Collapse
Affiliation(s)
- Weikang Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lufei Sheng
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Lingqia Su
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
- International Joint Laboratory on Food Safety, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| |
Collapse
|
6
|
Chatterjee S, Basak AJ, Nair AV, Duraivelan K, Samanta D. Immunoglobulin-fold containing bacterial adhesins: molecular and structural perspectives in host tissue colonization and infection. FEMS Microbiol Lett 2021; 368:6045506. [PMID: 33355339 DOI: 10.1093/femsle/fnaa220] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/21/2020] [Indexed: 12/16/2022] Open
Abstract
Immunoglobulin (Ig) domains are one of the most widespread protein domains encoded by the human genome and are present in a large array of proteins with diverse biological functions. These Ig domains possess a central structure, the immunoglobulin-fold, which is a sandwich of two β sheets, each made up of anti-parallel β strands, surrounding a central hydrophobic core. Apart from humans, proteins containing Ig-like domains are also distributed in a vast selection of organisms including vertebrates, invertebrates, plants, viruses and bacteria where they execute a wide array of discrete cellular functions. In this review, we have described the key structural deviations of bacterial Ig-folds when compared to the classical eukaryotic Ig-fold. Further, we have comprehensively grouped all the Ig-domain containing adhesins present in both Gram-negative and Gram-positive bacteria. Additionally, we describe the role of these particular adhesins in host tissue attachment, colonization and subsequent infection by both pathogenic and non-pathogenic Escherichia coli as well as other bacterial species. The structural properties of these Ig-domain containing adhesins, along with their interactions with specific Ig-like and non Ig-like binding partners present on the host cell surface have been discussed in detail.
Collapse
Affiliation(s)
- Shruti Chatterjee
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Aditya J Basak
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Asha V Nair
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Kheerthana Duraivelan
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| | - Dibyendu Samanta
- School of Bioscience, Indian Institute of Technology Kharagpur, Kharagpur-721302, West Bengal, India
| |
Collapse
|
7
|
Petruschke H, Schori C, Canzler S, Riesbeck S, Poehlein A, Daniel R, Frei D, Segessemann T, Zimmerman J, Marinos G, Kaleta C, Jehmlich N, Ahrens CH, von Bergen M. Discovery of novel community-relevant small proteins in a simplified human intestinal microbiome. MICROBIOME 2021; 9:55. [PMID: 33622394 PMCID: PMC7903761 DOI: 10.1186/s40168-020-00981-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 12/16/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND The intestinal microbiota plays a crucial role in protecting the host from pathogenic microbes, modulating immunity and regulating metabolic processes. We studied the simplified human intestinal microbiota (SIHUMIx) consisting of eight bacterial species with a particular focus on the discovery of novel small proteins with less than 100 amino acids (= sProteins), some of which may contribute to shape the simplified human intestinal microbiota. Although sProteins carry out a wide range of important functions, they are still often missed in genome annotations, and little is known about their structure and function in individual microbes and especially in microbial communities. RESULTS We created a multi-species integrated proteogenomics search database (iPtgxDB) to enable a comprehensive identification of novel sProteins. Six of the eight SIHUMIx species, for which no complete genomes were available, were sequenced and de novo assembled. Several proteomics approaches including two earlier optimized sProtein enrichment strategies were applied to specifically increase the chances for novel sProtein discovery. The search of tandem mass spectrometry (MS/MS) data against the multi-species iPtgxDB enabled the identification of 31 novel sProteins, of which the expression of 30 was supported by metatranscriptomics data. Using synthetic peptides, we were able to validate the expression of 25 novel sProteins. The comparison of sProtein expression in each single strain versus a multi-species community cultivation showed that six of these sProteins were only identified in the SIHUMIx community indicating a potentially important role of sProteins in the organization of microbial communities. Two of these novel sProteins have a potential antimicrobial function. Metabolic modelling revealed that a third sProtein is located in a genomic region encoding several enzymes relevant for the community metabolism within SIHUMIx. CONCLUSIONS We outline an integrated experimental and bioinformatics workflow for the discovery of novel sProteins in a simplified intestinal model system that can be generically applied to other microbial communities. The further analysis of novel sProteins uniquely expressed in the SIHUMIx multi-species community is expected to enable new insights into the role of sProteins on the functionality of bacterial communities such as those of the human intestinal tract. Video abstract.
Collapse
Affiliation(s)
- Hannes Petruschke
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian Schori
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Sebastian Canzler
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Sarah Riesbeck
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Anja Poehlein
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Institute of Microbiology and Genetics, Department of Genomic and Applied Microbiology, Georg-August University of Göttingen, Göttingen, Germany
| | - Daniel Frei
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Tina Segessemann
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland
| | - Johannes Zimmerman
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Georgios Marinos
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Christoph Kaleta
- Research Group Medical Systems Biology, Institute for Experimental Medicine, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Nico Jehmlich
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics and SIB Swiss Institute of Bioinformatics, Wädenswil, Switzerland.
| | - Martin von Bergen
- Department of Molecular Systems Biology, Helmholtz-Centre for Environmental Research - UFZ GmbH, Leipzig, Germany.
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, University of Leipzig, Leipzig, Germany.
| |
Collapse
|
8
|
Haake DA, Matsunaga J. Leptospiral Immunoglobulin-Like Domain Proteins: Roles in Virulence and Immunity. Front Immunol 2021; 11:579907. [PMID: 33488581 PMCID: PMC7821625 DOI: 10.3389/fimmu.2020.579907] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/05/2020] [Indexed: 02/03/2023] Open
Abstract
The virulence mechanisms required for infection and evasion of immunity by pathogenic Leptospira species remain poorly understood. A number of L. interrogans surface proteins have been discovered, lying at the interface between the pathogen and host. Among these proteins, the functional properties of the Lig (leptospiral immunoglobulin-like domain) proteins have been examined most thoroughly. LigA, LigB, and LigC contain a series of, 13, 12, and 12 closely related domains, respectively, each containing a bacterial immunoglobulin (Big) -like fold. The multidomain region forms a mostly elongated structure that exposes a large surface area. Leptospires wield the Lig proteins to promote interactions with a range of specific host proteins, including those that aid evasion of innate immune mechanisms. These diverse binding events mediate adhesion of L. interrogans to the extracellular matrix, inhibit hemostasis, and inactivate key complement proteins. These interactions may help L. interrogans overcome the physical, hematological, and immunological barriers that would otherwise prevent the spirochete from establishing a systemic infection. Despite significant differences in the affinities of the LigA and LigB proteins for host targets, their functions overlap during lethal infection of hamsters; virulence is lost only when both ligA and ligB transcription is knocked down simultaneously. Lig proteins have been shown to be promising vaccine antigens through evaluation of a variety of different adjuvant strategies. This review serves to summarize current knowledge of Lig protein roles in virulence and immunity and to identify directions needed to better understand the precise functions of the Lig proteins during infection.
Collapse
Affiliation(s)
- David A. Haake
- Division of Infectious Diseases, VA Greater Los Angeles Healthcare System, Los Angeles, CA, United States
- Departments of Medicine, and Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| | - James Matsunaga
- Research Service, VA Greater Los Angeles Healthcare System, Los Angeles, CA, United States
- Department of Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, United States
| |
Collapse
|
9
|
The extracellular juncture domains in the intimin passenger adopt a constitutively extended conformation inducing restraints to its sphere of action. Sci Rep 2020; 10:21249. [PMID: 33277518 PMCID: PMC7718877 DOI: 10.1038/s41598-020-77706-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 11/05/2020] [Indexed: 02/06/2023] Open
Abstract
Enterohemorrhagic and enteropathogenic Escherichia coli are among the most important food-borne pathogens, posing a global health threat. The virulence factor intimin is essential for the attachment of pathogenic E. coli to the intestinal host cell. Intimin consists of four extracellular bacterial immunoglobulin-like (Big) domains, D00–D2, extending into the fifth lectin subdomain (D3) that binds to the Tir-receptor on the host cell. Here, we present the crystal structures of the elusive D00–D0 domains at 1.5 Å and D0–D1 at 1.8 Å resolution, which confirms that the passenger of intimin has five distinct domains. We describe that D00–D0 exhibits a higher degree of rigidity and D00 likely functions as a juncture domain at the outer membrane-extracellular medium interface. We conclude that D00 is a unique Big domain with a specific topology likely found in a broad range of other inverse autotransporters. The accumulated data allows us to model the complete passenger of intimin and propose functionality to the Big domains, D00–D0–D1, extending directly from the membrane.
Collapse
|
10
|
Hua Y, Bai X, Zhang J, Jernberg C, Chromek M, Hansson S, Frykman A, Yang X, Xiong Y, Wan C, Matussek A. Molecular characteristics of eae-positive clinical Shiga toxin-producing Escherichia coli in Sweden. Emerg Microbes Infect 2020; 9:2562-2570. [PMID: 33179570 PMCID: PMC7733975 DOI: 10.1080/22221751.2020.1850182] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/08/2020] [Indexed: 12/19/2022]
Abstract
Shiga toxin (Stx)-producing Escherichia coli (STEC) can cause a wide range of symptoms from asymptomatic carriage, mild diarrhea to bloody diarrhea (BD) and hemolytic uremic syndrome (HUS). Intimin, encoded by the eae gene, also plays a critical role in STEC pathogenesis. Herein, we investigated the prevalence and genetic diversity of eae among clinical STEC isolates from patients with diarrhea, BD, HUS as well as from asymptomatic STEC-positive individuals in Sweden with whole-genome sequencing. We found that 173 out of 239 (72.4%) of clinical STEC strains were eae positive. Six eae subtypes (ϵ1, γ1, β3, θ, ζ and ρ) were identified eae and its subtype γ1 were significantly overrepresented in O157:H7 strains isolated from BD and HUS patients. ϵ1 was associated with O121:H19 and O103:H2 strains, and β3 to O26:H11 strains. The combination of eae subtype γ1 and stx subtype (stx 2 or stx 1+stx 2) is more likely to cause severe disease, suggesting the possibility of using eae genotypes in risk assessment of STEC infection. In summary, this study demonstrated a high prevalence of eae in clinical STEC strains and considerable genetic diversity of eae in STEC strains in Sweden from 1994 through 2018, and revealed association between eae subtypes and disease severity.
Collapse
Affiliation(s)
- Ying Hua
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Xiangning Bai
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Huddinge, Sweden
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Ji Zhang
- mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | | | - Milan Chromek
- Division of Pediatrics, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sverker Hansson
- Department of Pediatrics, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Anne Frykman
- Department of Pediatrics, Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Xi Yang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanwen Xiong
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Chengsong Wan
- Department of Microbiology, School of Public Health, Southern Medical University, Guangzhou, People’s Republic of China
| | - Andreas Matussek
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Sweden
- Laboratory Medicine, Jönköping Region County, Jönköping, Sweden
- Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
- Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
- Division of Laboratory Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
11
|
Jung DH, Seo DH, Kim YJ, Chung WH, Nam YD, Park CS. The presence of resistant starch-degrading amylases in Bifidobacterium adolescentis of the human gut. Int J Biol Macromol 2020; 161:389-397. [DOI: 10.1016/j.ijbiomac.2020.05.235] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/25/2020] [Accepted: 05/26/2020] [Indexed: 01/11/2023]
|
12
|
Computational analysis of phylogenetic, functional and structural features of Bacillus hyaluronate lyases. Biologia (Bratisl) 2020. [DOI: 10.2478/s11756-020-00580-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
13
|
Ting SY, Martínez-García E, Huang S, Bertolli SK, Kelly KA, Cutler KJ, Su ED, Zhi H, Tang Q, Radey MC, Raffatellu M, Peterson SB, de Lorenzo V, Mougous JD. Targeted Depletion of Bacteria from Mixed Populations by Programmable Adhesion with Antagonistic Competitor Cells. Cell Host Microbe 2020; 28:313-321.e6. [PMID: 32470328 PMCID: PMC7725374 DOI: 10.1016/j.chom.2020.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/21/2020] [Accepted: 05/06/2020] [Indexed: 01/15/2023]
Abstract
Selective and targeted removal of individual species or strains of bacteria from complex communities can be desirable over traditional, broadly acting antibacterials in several contexts. However, generalizable strategies that accomplish this with high specificity have been slow to emerge. Here we develop programmed inhibitor cells (PICs) that direct the potent antibacterial activity of the type VI secretion system (T6SS) against specified target cells. The PICs express surface-displayed nanobodies that mediate antigen-specific cell-cell adhesion to effectively overcome the barrier to T6SS activity in fluid conditions. We demonstrate the capacity of PICs to efficiently deplete low-abundance target bacteria without significant collateral damage to complex microbial communities. The only known requirements for PIC targeting are a Gram-negative cell envelope and a unique cell surface antigen; therefore, this approach should be generalizable to a wide array of bacteria and find application in medical, research, and environmental settings.
Collapse
Affiliation(s)
- See-Yeun Ting
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | - Shuo Huang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Savannah K Bertolli
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katherine A Kelly
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Kevin J Cutler
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Elizabeth D Su
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Hui Zhi
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Qing Tang
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Matthew C Radey
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Manuela Raffatellu
- Division of Host-Microbe Systems & Therapeutics, Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy, and Vaccines (CU-UCSD cMAV), La Jolla, CA 92093, USA
| | - S Brook Peterson
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Víctor de Lorenzo
- System Biology Program, National Center of Biotechnology CSIC, 28049 Madrid, Spain
| | - Joseph D Mougous
- Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, USA; Department of Biochemistry, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
| |
Collapse
|
14
|
Methylation of Salmonella Typhimurium flagella promotes bacterial adhesion and host cell invasion. Nat Commun 2020; 11:2013. [PMID: 32332720 PMCID: PMC7181671 DOI: 10.1038/s41467-020-15738-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/13/2020] [Indexed: 11/09/2022] Open
Abstract
The long external filament of bacterial flagella is composed of several thousand copies of a single protein, flagellin. Here, we explore the role played by lysine methylation of flagellin in Salmonella, which requires the methylase FliB. We show that both flagellins of Salmonella enterica serovar Typhimurium, FliC and FljB, are methylated at surface-exposed lysine residues by FliB. A Salmonella Typhimurium mutant deficient in flagellin methylation is outcompeted for gut colonization in a gastroenteritis mouse model, and methylation of flagellin promotes bacterial invasion of epithelial cells in vitro. Lysine methylation increases the surface hydrophobicity of flagellin, and enhances flagella-dependent adhesion of Salmonella to phosphatidylcholine vesicles and epithelial cells. Therefore, posttranslational methylation of flagellin facilitates adhesion of Salmonella Typhimurium to hydrophobic host cell surfaces, and contributes to efficient gut colonization and host infection. Flagellin proteins of Salmonella flagella are methylated. Here, the authors show that flagellin methylation facilitates adhesion of Salmonella to hydrophobic host-cell surfaces, and contributes to efficient gut colonization and host infection.
Collapse
|
15
|
Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense. mSystems 2020; 5:5/1/e00650-19. [PMID: 31992632 PMCID: PMC6989131 DOI: 10.1128/msystems.00650-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
In this study, we examine the impact of transcriptional network rearrangements driven by horizontal gene acquisition in PhoP and SlyA regulons using as a case study a phytopathosystem comprised of potato tubers and the soft-rot pathogen Pectobacterium brasiliense 1692 (Pb1692). Genome simulations and statistical analyses uncovered the tendency of PhoP and SlyA networks to mobilize lineage-specific traits predicted as horizontal gene transfer at late infection, highlighting the prominence of regulatory network rearrangements in this stage of infection. The evidence further supports the circumscription of two horizontally acquired quorum-sensing regulators (carR and expR1) by the PhoP network. By recruiting carR and expR1, the PhoP network also impacts certain host adaptation- and bacterial competition-related systems, seemingly in a quorum sensing-dependent manner, such as the type VI secretion system, carbapenem biosynthesis, and plant cell wall-degrading enzymes (PCWDE) like cellulases and pectate lyases. Conversely, polygalacturonases and the type III secretion system (T3SS) exhibit a transcriptional pattern that suggests quorum-sensing-independent regulation by the PhoP network. This includes an uncharacterized novel phage-related gene family within the T3SS gene cluster that has been recently acquired by two Pectobacterium species. The evidence further suggests a PhoP-dependent regulation of carbapenem- and PCWDE-encoding genes based on the synthesized products' optimum pH. The PhoP network also controls slyA expression in planta, which seems to impact carbohydrate metabolism regulation, especially at early infection, when 76.2% of the SlyA-regulated genes from that category also require PhoP to achieve normal expression levels.IMPORTANCE Exchanging genetic material through horizontal transfer is a critical mechanism that drives bacteria to efficiently adapt to host defenses. In this report, we demonstrate that a specific plant-pathogenic species (from the Pectobacterium genus) successfully integrated a population density-based behavior system (quorum sensing) acquired through horizontal transfer into a resident stress-response gene regulatory network controlled by the PhoP protein. Evidence found here underscores that subsets of bacterial weaponry critical for colonization, typically known to respond to quorum sensing, are also controlled by PhoP. Some of these traits include different types of enzymes that can efficiently break down plant cell walls depending on the environmental acidity level. Thus, we hypothesize that PhoP's ability to elicit regulatory responses based on acidity and nutrient availability fluctuations has strongly impacted the fixation of its regulatory connection with quorum sensing. In addition, another global gene regulator, known as SlyA, was found under the PhoP regulatory network. The SlyA regulator controls a series of carbohydrate metabolism-related traits, which also seem to be regulated by PhoP. By centralizing quorum sensing and slyA under PhoP scrutiny, Pectobacterium cells added an advantageous layer of control over those two networks that potentially enhances colonization efficiency.
Collapse
|
16
|
Okumura R, Kodama T, Hsu CC, Sahlgren BH, Hamano S, Kurakawa T, Iida T, Takeda K. Lypd8 inhibits attachment of pathogenic bacteria to colonic epithelia. Mucosal Immunol 2020; 13:75-85. [PMID: 31659301 DOI: 10.1038/s41385-019-0219-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 10/04/2019] [Accepted: 10/13/2019] [Indexed: 02/04/2023]
Abstract
Mucosal barriers segregate commensal microbes from the intestinal epithelia to maintain gut homeostasis. Ly6/Plaur domain-containing 8 (Lypd8), a highly glycosylated glycosylphosphatidylinositol-anchored protein selectively expressed on colonic enterocytes, promotes this segregation by inhibiting bacterial invasion of the inner mucus layer and colonic epithelia. However, it remains unclear whether Lypd8 prevents infection with enteric bacterial pathogens. Here, we demonstrate that Lypd8 strongly contributes to early-phase defense against Citrobacter rodentium, which causes colitis by inducing attachment and effacement (A/E) lesions on colonic epithelia. Lypd8 inhibits C. rodentium attachment to intestinal epithelial cells by binding to intimin, thereby suppressing the interaction between intimin and translocated intimin receptor. Lypd8 deficiency leads to rapid C. rodentium colonization in the colon, resulting in severe colitis with Th17-cell and neutrophil expansion in the lamina propria. This study identifies a novel function for Lypd8 against A/E bacteria and highlights the role of enterocytes as crucial players in innate immunity for protection against enteric bacterial pathogens.
Collapse
Affiliation(s)
- Ryu Okumura
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Toshio Kodama
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Chiao-Ching Hsu
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan.,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Benjamin Heller Sahlgren
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Shota Hamano
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Takashi Kurakawa
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tetsuya Iida
- Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Kiyoshi Takeda
- Department of Microbiology and Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, 565-0871, Japan. .,WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, 565-0871, Japan. .,Institute for Open and Transdisciplinary Research Initiative, Osaka University, Suita, Osaka, 565-0871, Japan.
| |
Collapse
|
17
|
Jarocki P, Komoń-Janczara E, Podleśny M, Kholiavskyi O, Pytka M, Kordowska-Wiater M. Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen. Viruses 2019; 11:E1163. [PMID: 31888239 PMCID: PMC6950654 DOI: 10.3390/v11121163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/10/2019] [Accepted: 12/13/2019] [Indexed: 02/06/2023] Open
Abstract
Lactobacillus rhamnosus Pen is a human endogenous strain used for the production of probiotic formula, which is effective in the prevention of antibiotic-associated diarrhoea. Our study showed that this probiotic strain releases bacteriophage BH1 without the addition of any inducing agent. Our research revealed that phage BH1 has a circular genome with a length of 40721 nt and a GC content of 44.8%. The genome of phage BH1 possesses 57 open reading frames which could be divided into functional modules associated with DNA packaging, morphogenesis, lysis, integration, genetic switch, and replication. In spite of similarity in morphology and genomic organization, comparative analysis revealed substantial genetic diversity and mosaic genomic architecture among phages described for the Lactobacillus casei group. Additionally, qPCR and ddPCR analysis confirmed earlier microscopic observations indicating that L. rhamnosus Pen liberates bacteriophage particles during growth. This occurs spontaneously, and is not a result of external inducing factors. For samples collected after 4 and 24 h of L. rhamnosus Pen culture, the number of attB and attP copies increased 2.5 and 12 times, respectively. This phenomenon, by introducing resistance to other phages or enhancing the biofilm-forming capabilities, may increase the survivability of microorganisms in their natural ecological niche. Conversely, spontaneous phage induction may be an important virulence factor for bacteria, posing a potential threat for the human host.
Collapse
Affiliation(s)
- Piotr Jarocki
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Elwira Komoń-Janczara
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Marcin Podleśny
- Process and Development Department, Al. Tysiąclecia Państwa Polskiego 13, Grupa Azoty Zakłady Azotowe “Puławy” S.A, 24-110 Puławy, Poland
| | - Oleksandr Kholiavskyi
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Monika Pytka
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| | - Monika Kordowska-Wiater
- Department of Biotechnology, Microbiology and Human Nutrition, University of Life Sciences in Lublin, 8 Skromna St., 20-704 Lublin, Poland
| |
Collapse
|
18
|
Nguyen SN, Flores A, Talamantes D, Dar F, Valdez A, Schwans J, Berlemont R. GeneHunt for rapid domain-specific annotation of glycoside hydrolases. Sci Rep 2019; 9:10137. [PMID: 31300677 PMCID: PMC6626019 DOI: 10.1038/s41598-019-46290-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/26/2019] [Indexed: 12/20/2022] Open
Abstract
The identification of glycoside hydrolases (GHs) for efficient polysaccharide deconstruction is essential for the development of biofuels. Here, we investigate the potential of sequential HMM-profile identification for the rapid and precise identification of the multi-domain architecture of GHs from various datasets. First, as a validation, we successfully reannotated >98% of the biochemically characterized enzymes listed on the CAZy database. Next, we analyzed the 43 million non-redundant sequences from the M5nr data and identified 322,068 unique GHs. Finally, we searched 129 assembled metagenomes retrieved from MG-RAST for environmental GHs and identified 160,790 additional enzymes. Although most identified sequences corresponded to single domain enzymes, many contained several domains, including known accessory domains and some domains never identified in association with GH. Several sequences displayed multiple catalytic domains and few of these potential multi-activity proteins combined potentially synergistic domains. Finally, we produced and confirmed the biochemical activities of a GH5-GH10 cellulase-xylanase and a GH11-CE4 xylanase-esterase. Globally, this "gene to enzyme pipeline" provides a rationale for mining large datasets in order to identify new catalysts combining unique properties for the efficient deconstruction of polysaccharides.
Collapse
Affiliation(s)
- S N Nguyen
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Flores
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - D Talamantes
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - F Dar
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - A Valdez
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA
| | - J Schwans
- Department of Chemistry and Biochemistry, California State University Long Beach, Long Beach, California, USA
| | - R Berlemont
- Department of Biological Sciences, California State University Long Beach, Long Beach, California, USA.
| |
Collapse
|
19
|
Eble JA. Structurally Robust and Functionally Highly Versatile-C-Type Lectin (-Related) Proteins in Snake Venoms. Toxins (Basel) 2019; 11:toxins11030136. [PMID: 30823637 PMCID: PMC6468738 DOI: 10.3390/toxins11030136] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 02/19/2019] [Accepted: 02/20/2019] [Indexed: 12/31/2022] Open
Abstract
Snake venoms contain an astounding variety of different proteins. Among them are numerous C-type lectin family members, which are grouped into classical Ca2+- and sugar-binding lectins and the non-sugar-binding snake venom C-type lectin-related proteins (SV-CLRPs), also called snaclecs. Both groups share the robust C-type lectin domain (CTLD) fold but differ in a long loop, which either contributes to a sugar-binding site or is expanded into a loop-swapping heterodimerization domain between two CLRP subunits. Most C-type lectin (-related) proteins assemble in ordered supramolecular complexes with a high versatility of subunit numbers and geometric arrays. Similarly versatile is their ability to inhibit or block their target molecules as well as to agonistically stimulate or antagonistically blunt a cellular reaction triggered by their target receptor. By utilizing distinct interaction sites differentially, SV-CLRPs target a plethora of molecules, such as distinct coagulation factors and receptors of platelets and endothelial cells that are involved in hemostasis, thrombus formation, inflammation and hematogenous metastasis. Because of their robust structure and their high affinity towards their clinically relevant targets, SV-CLRPs are and will potentially be valuable prototypes to develop new diagnostic and therapeutic tools in medicine, provided that the molecular mechanisms underlying their versatility are disclosed.
Collapse
Affiliation(s)
- Johannes A Eble
- Institute of Physiological Chemistry and Pathobiochemistry, University of Münster, Waldeyerstr. 15, 48149 Münster, Germany.
| |
Collapse
|
20
|
Libreros-Zúñiga GA, dos Santos Silva C, Salgado Ferreira R, Dias MVB. Structural Basis for the Interaction and Processing of β-Lactam Antibiotics by l,d-Transpeptidase 3 (Ldt Mt3) from Mycobacterium tuberculosis. ACS Infect Dis 2019; 5:260-271. [PMID: 30556998 DOI: 10.1021/acsinfecdis.8b00244] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting Mycobacterium tuberculosis peptidoglycans with β-lactam antibiotics represents a strategy to address increasing resistance to antitubercular drugs. β-Lactams inhibit peptidoglycan synthases such as l,d-transpeptidases, a group of carbapenem-sensitive enzymes that stabilize peptidoglycans through 3 → 3 cross-links. M. tuberculosis encodes five l,d-transpeptidases (LdtMt1-5), of which LdtMt3 is one of the less understood. Herein, we structurally characterized the apo and faropenem-acylated forms of LdtMt3 at 1.3 and 1.8 Å resolution, respectively. These structures revealed a fold and catalytic diad similar to those of other LdtsMt enzymes, supporting its involvement in transpeptidation reactions despite divergences in active site size and charges. The LdtMt3-faropenem structure indicated that faropenem is degraded after Cys-246 acylation, and possibly only a β-OH-butyrate or an acetyl group (C2H3O) covalently attached to the enzyme remains, an observation that strongly supports the notion that LdtMt3 is inactivated by β-lactams. Docking simulations with intact β-lactams predicted key LdtMt3 residues that interact with these antibiotics. We also characterized the heat of acylation involved in the binding and reaction of LdtMt3 for ten β-lactams belonging to four different classes, and imipenem had the highest inactivation constant. This work provides key insights into the structure, binding mechanisms, and degradation of β-lactams by LdtMt3, which may be useful for the development of additional β-lactams with potential antitubercular activity.
Collapse
Affiliation(s)
- Gerardo Andrés Libreros-Zúñiga
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 São José do Rio Preto, Brazil
- Departamento de Microbiología, Facultad de Salud, Universidad del Valle, Calle 4B No. 36-00 Cali, Colombia
| | - Catharina dos Santos Silva
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627 Belo Horizonte, Brazil
| | - Marcio Vinicius Bertacine Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, Avenida Prof. Lineu Prestes, 1374 São Paulo, Brazil
- Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual Paulista, Rua Cristóvão Colombo, 2265 São José do Rio Preto, Brazil
| |
Collapse
|
21
|
Leth ML, Ejby M, Workman C, Ewald DA, Pedersen SS, Sternberg C, Bahl MI, Licht TR, Aachmann FL, Westereng B, Abou Hachem M. Differential bacterial capture and transport preferences facilitate co-growth on dietary xylan in the human gut. Nat Microbiol 2018; 3:570-580. [PMID: 29610517 DOI: 10.1038/s41564-018-0132-8] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/19/2018] [Indexed: 12/11/2022]
Abstract
Metabolism of dietary glycans is pivotal in shaping the human gut microbiota. However, the mechanisms that promote competition for glycans among gut commensals remain unclear. Roseburia intestinalis, an abundant butyrate-producing Firmicute, is a key degrader of the major dietary fibre xylan. Despite the association of this taxon to a healthy microbiota, insight is lacking into its glycan utilization machinery. Here, we investigate the apparatus that confers R. intestinalis growth on different xylans. R. intestinalis displays a large cell-attached modular xylanase that promotes multivalent and dynamic association to xylan via four xylan-binding modules. This xylanase operates in concert with an ATP-binding cassette transporter to mediate breakdown and selective internalization of xylan fragments. The transport protein of R. intestinalis prefers oligomers of 4-5 xylosyl units, whereas the counterpart from a model xylan-degrading Bacteroides commensal targets larger ligands. Although R. intestinalis and the Bacteroides competitor co-grew in a mixed culture on xylan, R. intestinalis dominated on the preferred transport substrate xylotetraose. These findings highlight the differentiation of capture and transport preferences as a possible strategy to facilitate co-growth on abundant dietary fibres and may offer a unique route to manipulate the microbiota based on glycan transport preferences in therapeutic interventions to boost distinct taxa.
Collapse
Affiliation(s)
- Maria Louise Leth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Morten Ejby
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Christopher Workman
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - David Adrian Ewald
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Signe Schultz Pedersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Claus Sternberg
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Martin Iain Bahl
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Tine Rask Licht
- National Food Institute, Technical University of Denmark, Lyngby, Denmark
| | - Finn Lillelund Aachmann
- NOBIPOL, Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, Trondheim, Norway
| | - Bjørge Westereng
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
| |
Collapse
|
22
|
Porayath C, Suresh MK, Biswas R, Nair BG, Mishra N, Pal S. Autolysin mediated adherence of Staphylococcus aureus with Fibronectin, Gelatin and Heparin. Int J Biol Macromol 2018; 110:179-184. [PMID: 29398086 PMCID: PMC5864509 DOI: 10.1016/j.ijbiomac.2018.01.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 12/20/2017] [Accepted: 01/08/2018] [Indexed: 12/21/2022]
Abstract
Major autolysin (Atl) of Staphylococcus aureusis a cell surface associated peptidoglycan hydrolase with amidase and glucosaminidase domains. Atl enzymes (amidase and glucosaminidase) are known to participate in biofilm formation and also can bind with host matrices. Earlier studies demonstrated the binding of Atlwithfibronectin, thrombospondin 1, vitronectin and heat shock cognate protein Hsc70. Here, we have shown, Atl mediates attachment of S.aureus to heparin and gelatine as well. The atl mutant strain demonstrated around 2.5 fold decreased adherence with fibronectin, gelatin and heparin coated microtiter plates. The microscopic studies confirmed the reduced binding of atl mutant with them compared to its parental wild type and complemented mutant strains. Amidase and glucosaminidase were expressed as N-terminal histidine tagged proteins from Escherichia coli, purified and refolded. We found refolded amidase bind with fibronectin, gelatin and heparin; whereas refolded glucosaminidase binds with only fibronectin and heparin but not gelatin. These results reemphasize Atl as one of the crucial proteins from Staphylococcus that facilitate their binding with multiple host cellular components during colonization and infection.
Collapse
Affiliation(s)
- Chandni Porayath
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, Kerala, India
| | - Maneesha K Suresh
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Cochin 682041, Kerala, India
| | - Raja Biswas
- Centre for Nanosciences and Molecular Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Cochin 682041, Kerala, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, Kerala, India
| | - Nandita Mishra
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, Kerala, India
| | - Sanjay Pal
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, Kerala, India.
| |
Collapse
|
23
|
Salema V, Fernández LÁ. Escherichia coli surface display for the selection of nanobodies. Microb Biotechnol 2017; 10:1468-1484. [PMID: 28772027 PMCID: PMC5658595 DOI: 10.1111/1751-7915.12819] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 07/12/2017] [Accepted: 07/13/2017] [Indexed: 12/29/2022] Open
Abstract
Nanobodies (Nbs) are the smallest functional antibody fragments known in nature and have multiple applications in biomedicine or environmental monitoring. Nbs are derived from the variable segment of camelid heavy chain-only antibodies, known as VHH. For selection, libraries of VHH gene segments from naïve, immunized animals or of synthetic origin have been traditionally cloned in E. coli phage display or yeast display systems, and clones binding the target antigen recovered, usually from plastic surfaces with the immobilized antigen (phage display) or using fluorescence-activated cell sorting (FACS; yeast display). This review briefly describes these conventional approaches and focuses on the distinct properties of an E. coli display system developed in our laboratory, which combines the benefits of both phage display and yeast display systems. We demonstrate that E. coli display using an N-terminal domain of intimin is an effective platform for the surface display of VHH libraries enabling selection of high-affinity Nbs by magnetic cell sorting and direct selection on live mammalian cells displaying the target antigen on their surface. Flow cytometry analysis of E. coli bacteria displaying the Nbs on their surface allows monitoring of the selection process, facilitates screening, characterization of antigen-binding clones, specificity, ligand competition and estimation of the equilibrium dissociation constant (KD ).
Collapse
Affiliation(s)
- Valencio Salema
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| | - Luis Ángel Fernández
- Department of Microbial BiotechnologyCentro Nacional de Biotecnología (CNB)Consejo Superior de Investigaciones Científicas (CSIC)MadridSpain
| |
Collapse
|
24
|
Comparative genomics of Vibrio campbellii strains and core species of the Vibrio Harveyi clade. Sci Rep 2017; 7:41394. [PMID: 28145490 PMCID: PMC5286417 DOI: 10.1038/srep41394] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 01/09/2023] Open
Abstract
The core of the Vibrio Harveyi clade contains V. harveyi, V. campbellii, V. owensii, V. jasicida, and V. rotiferianus. They are well recognized aquatic animal pathogens, but misclassification has been common due to similarities in their rDNA sequences and phenotypes. To better understand their evolutionary relationships and functional features, we sequenced a shrimp pathogen strain V. harveyi 1114GL, reclassified it as V. campbellii and compared this and 47 other sequenced Vibrio genomes in the Harveryi clade. A phylogeny based on 1,775 genes revealed that both V. owensii and V. jasicida were closer to V. campbellii than to V. harveyi and that V. campbellii strains can be divided into two distinct groups. Species-specific genes such as intimin and iron acquisition genes were identified in V. campbellii. In particular, the 1114GL strain contains two bacterial immunoglobulin-like genes for cell adhesion with 22 Big_2 domains that have been extensively reshuffled and are by far the most expanded among all species surveyed in this study. The 1114GL strain differed from ATCC BAA-1116 by ~9% at the synonymous sites, indicating high diversity within V. campbellii. Our study revealed the characteristics of V. campbellii in the Harveyi clade and the genetic basis for their wide-spread pathogenicity.
Collapse
|
25
|
Abstract
Type V secretion denotes a variety of secretion systems that cross the outer membrane in Gram-negative bacteria but that depend on the Sec machinery for transport through the inner membrane. They are possibly the simplest bacterial secretion systems, because they consist only of a single polypeptide chain (or two chains in the case of two-partner secretion). Their seemingly autonomous transport through the outer membrane has led to the term "autotransporters" for various subclasses of type V secretion. In this chapter, we review the structure and function of these transporters and review recent findings on additional factors involved in the secretion process, which have put the term "autotransporter" to debate.
Collapse
|
26
|
Leo JC, Oberhettinger P, Yoshimoto S, Udatha DBRKG, Morth JP, Schütz M, Hori K, Linke D. Secretion of the Intimin Passenger Domain Is Driven by Protein Folding. J Biol Chem 2016; 291:20096-112. [PMID: 27466361 DOI: 10.1074/jbc.m116.731497] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Intimin is an essential adhesin of attaching and effacing organisms such as entropathogenic Escherichia coli It is also the prototype of type Ve secretion or inverse autotransport, where the extracellular C-terminal region or passenger is exported with the help of an N-terminal transmembrane β-barrel domain. We recently reported a stalled secretion intermediate of intimin, where the passenger is located in the periplasm but the β-barrel is already inserted into the membrane. Stalling of this mutant is due to the insertion of an epitope tag at the very N terminus of the passenger. Here, we examined how this insertion disrupts autotransport and found that it causes misfolding of the N-terminal immunoglobulin (Ig)-like domain D00. We could also stall the secretion by making an internal deletion in D00, and introducing the epitope tag into the second Ig-like domain, D0, also resulted in reduced passenger secretion. In contrast to many classical autotransporters, where a proximal folding core in the passenger is required for secretion, the D00 domain is dispensable, as the passenger of an intimin mutant lacking D00 entirely is efficiently exported. Furthermore, the D00 domain is slightly less stable than the D0 and D1 domains, unfolding at ∼200 piconewtons (pN) compared with ∼250 pN for D0 and D1 domains as measured by atomic force microscopy. Our results support a model where the secretion of the passenger is driven by sequential folding of the extracellular Ig-like domains, leading to vectorial transport of the passenger domain across the outer membrane in an N to C direction.
Collapse
Affiliation(s)
- Jack C Leo
- From the Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Philipp Oberhettinger
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Shogo Yoshimoto
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and
| | - D B R K Gupta Udatha
- From the Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | | | - Monika Schütz
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Katsutoshi Hori
- Department of Biotechnology, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603, Japan, and
| | - Dirk Linke
- From the Evolution and Genetics, Department of Biosciences, University of Oslo, 0316 Oslo, Norway,
| |
Collapse
|
27
|
Heinz E, Stubenrauch CJ, Grinter R, Croft NP, Purcell AW, Strugnell RA, Dougan G, Lithgow T. Conserved Features in the Structure, Mechanism, and Biogenesis of the Inverse Autotransporter Protein Family. Genome Biol Evol 2016; 8:1690-705. [PMID: 27190006 PMCID: PMC4943183 DOI: 10.1093/gbe/evw112] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The bacterial cell surface proteins intimin and invasin are virulence factors that share a common domain structure and bind selectively to host cell receptors in the course of bacterial pathogenesis. The β-barrel domains of intimin and invasin show significant sequence and structural similarities. Conversely, a variety of proteins with sometimes limited sequence similarity have also been annotated as “intimin-like” and “invasin” in genome datasets, while other recent work on apparently unrelated virulence-associated proteins ultimately revealed similarities to intimin and invasin. Here we characterize the sequence and structural relationships across this complex protein family. Surprisingly, intimins and invasins represent a very small minority of the sequence diversity in what has been previously the “intimin/invasin protein family”. Analysis of the assembly pathway for expression of the classic intimin, EaeA, and a characteristic example of the most prevalent members of the group, FdeC, revealed a dependence on the translocation and assembly module as a common feature for both these proteins. While the majority of the sequences in the grouping are most similar to FdeC, a further and widespread group is two-partner secretion systems that use the β-barrel domain as the delivery device for secretion of a variety of virulence factors. This comprehensive analysis supports the adoption of the “inverse autotransporter protein family” as the most accurate nomenclature for the family and, in turn, has important consequences for our overall understanding of the Type V secretion systems of bacterial pathogens.
Collapse
Affiliation(s)
- Eva Heinz
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Christopher J Stubenrauch
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Rhys Grinter
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia Institute of Microbiology and Infection, School of Immunity and Infection, University of Birmingham, Birmingham, United Kingdom
| | - Nathan P Croft
- Department of Biochemistry and Molecular Biology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Anthony W Purcell
- Department of Biochemistry and Molecular Biology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| | - Richard A Strugnell
- Department of Microbiology & Immunology, University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Trevor Lithgow
- Department of Microbiology, Infection & Immunity Program, Biomedicine Discovery Institute, Monash University, Clayton, Australia
| |
Collapse
|
28
|
Abstract
Proteinaceous components of the biofilm matrix include secreted extracellular proteins, cell surface adhesins, and protein subunits of cell appendages such as flagella and pili. Biofilm matrix proteins play diverse roles in biofilm formation and dissolution. They are involved in attaching cells to surfaces, stabilizing the biofilm matrix via interactions with exopolysaccharide and nucleic acid components, developing three-dimensional biofilm architectures, and dissolving biofilm matrix via enzymatic degradation of polysaccharides, proteins, and nucleic acids. In this article, we will review functions of matrix proteins in a selected set of microorganisms, studies of the matrix proteomes of Vibrio cholerae and Pseudomonas aeruginosa, and roles of outer membrane vesicles and of nucleoid-binding proteins in biofilm formation.
Collapse
|
29
|
The Locus of Enterocyte Effacement and Associated Virulence Factors of Enterohemorrhagic Escherichia coli. Microbiol Spectr 2016; 2:EHEC-0007-2013. [PMID: 26104209 DOI: 10.1128/microbiolspec.ehec-0007-2013] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A subset of Shiga toxin-producing Escherichia coli strains, termed enterohemorrhagic E. coli (EHEC), is defined in part by the ability to produce attaching and effacing (A/E) lesions on intestinal epithelia. Such lesions are characterized by intimate bacterial attachment to the apical surface of enterocytes, cytoskeletal rearrangements beneath adherent bacteria, and destruction of proximal microvilli. A/E lesion formation requires the locus of enterocyte effacement (LEE), which encodes a Type III secretion system that injects bacterial proteins into host cells. The translocated proteins, termed effectors, subvert a plethora of cellular pathways to the benefit of the pathogen, for example, by recruiting cytoskeletal proteins, disrupting epithelial barrier integrity, and interfering with the induction of inflammation, phagocytosis, and apoptosis. The LEE and selected effectors play pivotal roles in intestinal persistence and virulence of EHEC, and it is becoming clear that effectors may act in redundant, synergistic, and antagonistic ways during infection. Vaccines that target the function of the Type III secretion system limit colonization of reservoir hosts by EHEC and may thus aid control of zoonotic infections. Here we review the features and functions of the LEE-encoded Type III secretion system and associated effectors of E. coli O157:H7 and other Shiga toxin-producing E. coli strains.
Collapse
|
30
|
The Exiguobacterium sibiricum 255-15 GtfC Enzyme Represents a Novel Glycoside Hydrolase 70 Subfamily of 4,6-α-Glucanotransferase Enzymes. Appl Environ Microbiol 2015; 82:756-66. [PMID: 26590275 DOI: 10.1128/aem.03420-15] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 11/13/2015] [Indexed: 11/20/2022] Open
Abstract
The glycoside hydrolase 70 (GH70) family originally was established for glucansucrase enzymes found solely in lactic acid bacteria synthesizing α-glucan polysaccharides from sucrose (e.g., GtfA). In recent years, we have characterized GtfB and related Lactobacillus enzymes as 4,6-α-glucanotransferase enzymes. These GtfB-type enzymes constitute the first GH70 subfamily of enzymes that are unable to act on sucrose as a substrate but are active with maltodextrins and starch, cleave α1→4 linkages, and synthesize linear α1→6-glucan chains. The GtfB disproportionating type of activity results in the conversion of malto-oligosaccharides into isomalto/malto-polysaccharides with a relatively high percentage of α1→6 linkages. This paper reports the identification of the members of a second GH70 subfamily (designated GtfC enzymes) and the characterization of the Exiguobacterium sibiricum 255-15 GtfC enzyme, which is also inactive with sucrose and displays 4,6-α-glucanotransferase activity with malto-oligosaccharides. GtfC differs from GtfB in synthesizing isomalto/malto-oligosaccharides. Biochemically, the GtfB- and GtfC-type enzymes are related, but phylogenetically, they clearly constitute different GH70 subfamilies, displaying only 30% sequence identity. Whereas the GtfB-type enzyme largely has the same domain order as glucansucrases (with α-amylase domains A, B, and C plus domains IV and V), this GtfC-type enzyme differs in the order of these domains and completely lacks domain V. In GtfC, the sequence of conserved regions I to IV of clan GH-H is identical to that in GH13 (I-II-III-IV) but different from that in GH70 (II-III-IV-I because of a circular permutation of the (β/α)8 barrel. The GtfC 4,6-α-glucanotransferase enzymes thus represent structurally and functionally very interesting evolutionary intermediates between α-amylase and glucansucrase enzymes.
Collapse
|
31
|
Abstract
Enteropathogenic Escherichia coli (EPEC) strains induce morphological changes in infected epithelial cells. The resulting attaching and effacing (A/E) lesion is characterized by intimate bacterial adherence to epithelial cells, with microvillus destruction, cytoskeletal rearrangement, and aggregation of host cytoskeletal proteins. This review presents an overview of the adhesion mechanisms used for the colonization of the human gastrointestinal tract by EPEC. The mechanisms underlying EPEC adhesion, prior to and during the formation of the A/E lesion, and the host cytosolic responses to bacterial infection leading to diarrheal disease are discussed.
Collapse
|
32
|
McNeilly TN, Mitchell MC, Corbishley A, Nath M, Simmonds H, McAteer SP, Mahajan A, Low JC, Smith DGE, Huntley JF, Gally DL. Optimizing the Protection of Cattle against Escherichia coli O157:H7 Colonization through Immunization with Different Combinations of H7 Flagellin, Tir, Intimin-531 or EspA. PLoS One 2015; 10:e0128391. [PMID: 26020530 PMCID: PMC4447243 DOI: 10.1371/journal.pone.0128391] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/24/2015] [Indexed: 11/19/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) are important human pathogens, causing hemorrhagic colitis and hemolytic uraemic syndrome in humans. E. coli O157:H7 is the most common serotype associated with EHEC infections worldwide, although other non-O157 serotypes cause life-threatening infections. Cattle are a main reservoir of EHEC and intervention strategies aimed at limiting EHEC excretion from cattle are predicted to lower the risk of human infection. We have previously shown that immunization of calves with recombinant versions of the type III secretion system (T3SS)-associated proteins EspA, intimin and Tir from EHEC O157:H7 significantly reduced shedding of EHEC O157 from experimentally-colonized calves, and that protection could be augmented by the addition of H7 flagellin to the vaccine formulation. The main aim of the present study was to optimize our current EHEC O157 subunit vaccine formulations by identifying the key combinations of these antigens required for protection. A secondary aim was to determine if vaccine-induced antibody responses exhibited cross-reactive potential with antigens from other EHEC serotypes. Immunization with EspA, intimin and Tir resulted in a reduction in mean EHEC O157 shedding following challenge, but not the mean proportion of calves colonized. Removal of Tir resulted in more prolonged shedding compared with all other groups, whereas replacement of Tir with H7 flagellin resulted in the highest levels of protection, both in terms of reducing both mean EHEC O157 shedding and the proportion of colonized calves. Immunization of calves with recombinant EHEC O157 EspA, intimin and Tir resulted in the generation of antibodies capable of cross-reacting with antigens from non-O157 EHEC serotypes, suggesting that immunization with these antigens may provide a degree of cross-protection against other EHEC serotypes. Further studies are now required to test the efficacy of these vaccines in the field, and to formally test the cross-protective potential of the vaccines against other non-O157 EHEC.
Collapse
Affiliation(s)
- Tom N. McNeilly
- Moredun Research Institute, Edinburgh, United Kingdom
- * E-mail:
| | | | - Alexander Corbishley
- Moredun Research Institute, Edinburgh, United Kingdom
- Division of Immunity and Infection, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Mintu Nath
- Biomathematics and Statistics Scotland, Edinburgh, United Kingdom
| | - Hannah Simmonds
- Division of Immunity and Infection, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Sean P. McAteer
- Division of Immunity and Infection, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Arvind Mahajan
- Division of Immunity and Infection, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - J. Christopher Low
- Division of Immunity and Infection, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - David G. E. Smith
- Moredun Research Institute, Edinburgh, United Kingdom
- Institute of Infection, Immunity & Inflammation, University of Glasgow, Glasgow, United Kingdom
| | | | - David L. Gally
- Division of Immunity and Infection, The Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
| |
Collapse
|
33
|
Abstract
Adhesins are a group of proteins in enterohemorrhagic Escherichia coli (EHEC) that are involved in the attachment or colonization of this pathogen to abiotic (plastic or steel) and biological surfaces, such as those found in bovine and human intestines. This review provides the most up-to-date information on these essential adhesion factors, summarizing important historical discoveries and analyzing the current and future state of this research. In doing so, the proteins intimin and Tir are discussed in depth, especially regarding their role in the development of attaching and effacing lesions and in EHEC virulence. Further, a series of fimbrial proteins (Lpf1, Lpf2, curli, ECP, F9, ELF, Sfp, HCP, and type 1 fimbriae) are also described, emphasizing their various contributions to adherence and colonization of different surfaces and their potential use as genetic markers in detection and classification of different EHEC serotypes. This review also discusses the role of several autotransporter proteins (EhaA-D, EspP, Saa and Sab, and Cah), as well as other proteins associated with adherence, such as flagella, EibG, Iha, and OmpA. While these proteins have all been studied to varying degrees, all of the adhesins summarized in this chapter have been linked to different stages of the EHEC life cycle, making them good targets for the development of more effective diagnostics and therapeutics.
Collapse
Affiliation(s)
- Brian D. McWilliams
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, 77555. USA
| | - Alfredo G. Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, 77555. USA
- Department of Pathology and Sealy Center for Vaccine Development, University of Texas Medical Branch, Galveston, Texas, 77555. USA
| |
Collapse
|
34
|
Leo JC, Oberhettinger P, Schütz M, Linke D. The inverse autotransporter family: intimin, invasin and related proteins. Int J Med Microbiol 2014; 305:276-82. [PMID: 25596886 DOI: 10.1016/j.ijmm.2014.12.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Intimin and invasin are adhesins and central virulence factors of attaching and effacing bacteria, such as enterohaemorrhagic Escherichia coli, and enteropathogenic Yersiniae, respectively. These proteins are prototypes of a large family of adhesins distributed widely in Gram-negative bacteria. It is now evident that this protein family represents a previously unrecognized autotransporter secretion system, termed type Ve secretion. In contrast to classical autotransport, where the transmembrane β-barrel domain or translocation unit is C-terminal to the extracellular region or passenger domain, type Ve-secreted proteins have an inverted topology with the passenger domain C-terminal to the translocation unit; hence the term inverse autotransporter. This minireview covers the recent advances in elucidating the structure and biogenesis of inverse autotransporters.
Collapse
Affiliation(s)
- Jack C Leo
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Philipp Oberhettinger
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Monika Schütz
- Interfaculty Institute for Microbiology and Infection Medicine, University Clinics Tübingen, 72076 Tübingen, Germany
| | - Dirk Linke
- Department of Biosciences, University of Oslo, 0316 Oslo, Norway; Max Planck Institute for Developmental Biology, Department of Protein Evolution, 72076 Tübingen, Germany.
| |
Collapse
|
35
|
Leo JC, Oberhettinger P, Chaubey M, Schütz M, Kühner D, Bertsche U, Schwarz H, Götz F, Autenrieth IB, Coles M, Linke D. The Intimin periplasmic domain mediates dimerisation and binding to peptidoglycan. Mol Microbiol 2014; 95:80-100. [PMID: 25353290 DOI: 10.1111/mmi.12840] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2014] [Indexed: 12/21/2022]
Abstract
Intimin and Invasin are prototypical inverse (Type Ve) autotransporters and important virulence factors of enteropathogenic Escherichia coli and Yersinia spp. respectively. In addition to a C-terminal extracellular domain and a β-barrel transmembrane domain, both proteins also contain a short N-terminal periplasmic domain that, in Intimin, includes a lysin motif (LysM), which is thought to mediate binding to peptidoglycan. We show that the periplasmic domain of Intimin does bind to peptidoglycan both in vitro and in vivo, but only under acidic conditions. We were able to determine a dissociation constant of 0.8 μM for this interaction, whereas the Invasin periplasmic domain, which lacks a LysM, bound only weakly in vitro and failed to bind peptidoglycan in vivo. We present the solution structure of the Intimin LysM, which has an additional α-helix conserved within inverse autotransporter LysMs but lacking in others. In contrast to previous reports, we demonstrate that the periplasmic domain of Intimin mediates dimerisation. We further show that dimerisation and peptidoglycan binding are general features of LysM-containing inverse autotransporters. Peptidoglycan binding by the periplasmic domain in the infection process may aid in resisting mechanical and chemical stress during transit through the gastrointestinal tract.
Collapse
Affiliation(s)
- Jack C Leo
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Ptak CP, Hsieh CL, Lin YP, Maltsev AS, Raman R, Sharma Y, Oswald RE, Chang YF. NMR solution structure of the terminal immunoglobulin-like domain from the leptospira host-interacting outer membrane protein, LigB. Biochemistry 2014; 53:5249-60. [PMID: 25068811 PMCID: PMC4139157 DOI: 10.1021/bi500669u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A number of surface proteins specific to pathogenic strains of Leptospira have been identified. The Lig protein family has shown promise as a marker in typing leptospiral isolates for pathogenesis and as an antigen in vaccines. We used NMR spectroscopy to solve the solution structure of the twelfth immunoglobulin-like (Ig-like) repeat domain from LigB (LigB-12). The fold is similar to that of other bacterial Ig-like domains and comprised mainly of β-strands that form a β-sandwich based on a Greek-key folding arrangement. Based on sequence analysis and conservation of structurally important residues, homology models for the other LigB Ig-like domains were generated. The set of LigB models illustrates the electrostatic differences between the domains as well as the possible interactions between neighboring domains. Understanding the structure of the extracellular portion of LigB and related proteins is important for developing diagnostic methods and new therapeutics directed toward leptospirosis.
Collapse
Affiliation(s)
- Christopher P Ptak
- Department of Population Medicine and Diagnostic Sciences and ‡Department of Molecular Medicine, College of Veterinary Medicine, Cornell University , Ithaca, New York 14853, United States
| | | | | | | | | | | | | | | |
Collapse
|
37
|
Contribution of the highly conserved EaeH surface protein to enterotoxigenic Escherichia coli pathogenesis. Infect Immun 2014; 82:3657-66. [PMID: 24935979 DOI: 10.1128/iai.01890-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) strains are among the most common causes of diarrheal illness worldwide. These pathogens disproportionately afflict children in developing countries, where they cause substantial morbidity and are responsible for hundreds of thousands of deaths each year. Although these organisms are important targets for enteric vaccines, most development efforts to date have centered on a subset of plasmid-encoded fimbrial adhesins known as colonization factors and heat-labile toxin (LT). Emerging data suggest that ETEC undergoes considerable changes in its surface architecture, sequentially deploying a number of putative adhesins during its interactions with the host. We demonstrate here that one putative highly conserved, chromosomally encoded adhesin, EaeH, engages the surfaces of intestinal epithelial cells and contributes to bacterial adhesion, LT delivery, and colonization of the small intestine.
Collapse
|
38
|
Structural features of the Pseudomonas fluorescens biofilm adhesin LapA required for LapG-dependent cleavage, biofilm formation, and cell surface localization. J Bacteriol 2014; 196:2775-88. [PMID: 24837291 DOI: 10.1128/jb.01629-14] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The localization of the LapA protein to the cell surface is a key step required by Pseudomonas fluorescens Pf0-1 to irreversibly attach to a surface and form a biofilm. LapA is a member of a diverse family of predicted bacterial adhesins, and although lacking a high degree of sequence similarity, family members do share common predicted domains. Here, using mutational analysis, we determine the significance of each domain feature of LapA in relation to its export and localization to the cell surface and function in biofilm formation. Our previous work showed that the N terminus of LapA is required for cleavage by the periplasmic cysteine protease LapG and release of the adhesin from the cell surface under conditions unfavorable for biofilm formation. We define an additional critical region of the N terminus of LapA required for LapG proteolysis. Furthermore, our results suggest that the domains within the C terminus of LapA are not absolutely required for biofilm formation, export, or localization to the cell surface, with the exception of the type I secretion signal, which is required for LapA export and cell surface localization. In contrast, deletion of the central repetitive region of LapA, consisting of 37 repeats of 100 amino acids, results in an inability to form a biofilm. We also used single-molecule atomic force microscopy to further characterize the role of these domains in biofilm formation on hydrophobic and hydrophilic surfaces. These studies represent the first detailed analysis of the domains of the LapA family of biofilm adhesin proteins.
Collapse
|
39
|
Ganz HH, Law C, Schmuki M, Eichenseher F, Calendar R, Loessner MJ, Getz WM, Korlach J, Beyer W, Klumpp J. Novel giant siphovirus from Bacillus anthracis features unusual genome characteristics. PLoS One 2014; 9:e85972. [PMID: 24475065 PMCID: PMC3903500 DOI: 10.1371/journal.pone.0085972] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 12/03/2013] [Indexed: 12/05/2022] Open
Abstract
Here we present vB_BanS-Tsamsa, a novel temperate phage isolated from Bacillus anthracis, the agent responsible for anthrax infections in wildlife, livestock and humans. Tsamsa phage is a giant siphovirus (order Caudovirales), featuring a long, flexible and non-contractile tail of 440 nm (not including baseplate structure) and an isometric head of 82 nm in diameter. We induced Tsamsa phage in samples from two different carcass sites in Etosha National Park, Namibia. The Tsamsa phage genome is the largest sequenced Bacillus siphovirus, containing 168,876 bp and 272 ORFs. The genome features an integrase/recombinase enzyme, indicative of a temperate lifestyle. Among bacterial strains tested, the phage infected only certain members of the Bacillus cereus sensu lato group (B. anthracis, B. cereus and B. thuringiensis) and exhibited moderate specificity for B. anthracis. Tsamsa lysed seven out of 25 B. cereus strains, two out of five B. thuringiensis strains and six out of seven B. anthracis strains tested. It did not lyse B. anthracis PAK-1, an atypical strain that is also resistant to both gamma phage and cherry phage. The Tsamsa endolysin features a broader lytic spectrum than the phage host range, indicating possible use of the enzyme in Bacillus biocontrol.
Collapse
Affiliation(s)
- Holly H Ganz
- University of California, Berkeley, Department of Environmental Science, Policy & Management, Berkeley, California, United States of America
| | - Christina Law
- University of California, Berkeley, Department of Environmental Science, Policy & Management, Berkeley, California, United States of America
| | - Martina Schmuki
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Fritz Eichenseher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Richard Calendar
- University of California, Berkeley, Department of Molecular and Cellular Biology, Berkeley, California, United States of America
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Wayne M Getz
- University of California, Berkeley, Department of Environmental Science, Policy & Management, Berkeley, California, United States of America ; School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Wolfgang Beyer
- University of Hohenheim, Institute of Environmental and Animal Hygiene, Stuttgart, Germany
| | - Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| |
Collapse
|
40
|
Han Q, Liu N, Robinson H, Cao L, Qian C, Wang Q, Xie L, Ding H, Wang Q, Huang Y, Li J, Zhou Z. Biochemical characterization and crystal structure of a GH10 xylanase from termite gut bacteria reveal a novel structural feature and significance of its bacterial Ig-like domain. Biotechnol Bioeng 2013; 110:3093-103. [PMID: 23794438 DOI: 10.1002/bit.24982] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/15/2013] [Accepted: 06/10/2013] [Indexed: 11/11/2022]
Abstract
Bacterial Ig-like (Big) domains are commonly distributed in glycoside hydrolases (GH), but their structure and function remains undefined. Xylanase is a GH, and catalyzes the hydrolysis of the internal β-xylosidic linkages of xylan. In this study, we report the molecular cloning, biochemical and biophysical characterization, and crystal structure of a termite gut bacterial xylanase, Xyl-ORF19, which was derived from gut bacteria of a wood-feeding termite (Globitermes brachycerastes). The protein architecture of Xyl-ORF19 reveals that it has two domains, a C-terminal GH10 catalytic domain and an N-terminal Big_2 non-catalytic domain. The catalytic domain folds in an (α/β)8 barrel as most GH10 xylanases do, but it has two extra β-strands. The non-catalytic domain is structurally similar to an immunoglobulin-like domain of intimins. The recombinant enzyme without the non-catalytic domain has fairly low catalytic activity, and is different from the full-length enzyme in kinetic parameters, pH and temperature profiles, which suggests the non-catalytic domain could affect the enzyme biochemical and biophysical properties as well as the role for enzyme localization. This study provides a molecular basis for future efforts in xylanase bioengineering.
Collapse
Affiliation(s)
- Qian Han
- Department of Biochemistry, Virginia Tech, Blacksburg, Virginia, 24061
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Adhesion of Diarrheagenic Escherichia coli and Inhibition by Glycocompounds Engaged in the Mucosal Innate Immunity. BIOLOGY 2013; 2:810-31. [PMID: 24832810 PMCID: PMC3960885 DOI: 10.3390/biology2020810] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/18/2013] [Accepted: 05/22/2013] [Indexed: 11/17/2022]
Abstract
Escherichia coli colonizes the human intestine shortly after birth, with most strains engaging in a commensal relationship. However, some E. coli strains have evolved toward acquiring genetic traits associated with virulence. Currently, five categories of enteroadherent E. coli strains are well-recognized, and are classified in regard to expressed adhesins and the strategy used during the colonization. The high morbidity associated with diarrhea has motivated investigations focusing on E. coli adhesins, as well on factors that inhibit bacterial adherence. Breastfeeding has proved to be the most effective strategy for preventing diarrhea in children. Aside from the immunoglobulin content, glycocompounds and oligosaccharides in breast milk play a critical role in the innate immunity against diarrheagenic E. coli strains. This review summarizes the colonization factors and virulence strategies exploited by diarrheagenic E. coli strains, addressing the inhibitory effects that oligosaccharides and glycocompounds, such as lactoferrin and free secretory components, exert on the adherence and virulence of these strains. This review thus provides an overview of experimental data indicating that human milk glycocompounds are responsible for the universal protective effect of breastfeeding against diarrheagenic E. coli pathotypes.
Collapse
|
42
|
Kamneva OK, Knight SJ, Liberles DA, Ward NL. Analysis of genome content evolution in pvc bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol Evol 2013; 4:1375-90. [PMID: 23221607 PMCID: PMC3542564 DOI: 10.1093/gbe/evs113] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Planctomycetes, Verrucomicrobia, Chlamydiae (PVC) super-phylum contains bacteria with either complex cellular organization or simple cell structure; it also includes organisms of different lifestyles (pathogens, mutualists, commensal, and free-living). Genome content evolution of this group has not been studied in a systematic fashion, which would reveal genes underlying the emergence of PVC-specific phenotypes. Here, we analyzed the evolutionary dynamics of 26 PVC genomes and several outgroup species. We inferred HGT, duplications, and losses by reconciliation of 27,123 gene trees with the species phylogeny. We showed that genome expansion and contraction have driven evolution within Planctomycetes and Chlamydiae, respectively, and balanced each other in Verrucomicrobia and Lentisphaerae. We also found that for a large number of genes in PVC genomes the most similar sequences are present in Acidobacteria, suggesting past and/or current ecological interaction between organisms from these groups. We also found evidence of shared ancestry between carbohydrate degradation genes in the mucin-degrading human intestinal commensal Akkermansia muciniphila and sequences from Acidobacteria and Bacteroidetes, suggesting that glycoside hydrolases are transferred laterally between gut microbes and that the process of carbohydrate degradation is crucial for microbial survival within the human digestive system. Further, we identified a highly conserved genetic module preferentially present in compartmentalized PVC species and possibly associated with the complex cell plan in these organisms. This conserved machinery is likely to be membrane targeted and involved in electron transport, although its exact function is unknown. These genes represent good candidates for future functional studies.
Collapse
Affiliation(s)
- Olga K Kamneva
- Department of Molecular Biology, University of Wyoming, WY, USA
| | | | | | | |
Collapse
|
43
|
Bodelón G, Palomino C, Fernández LÁ. Immunoglobulin domains inEscherichia coliand other enterobacteria: from pathogenesis to applications in antibody technologies. FEMS Microbiol Rev 2013; 37:204-50. [DOI: 10.1111/j.1574-6976.2012.00347.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 06/07/2012] [Accepted: 06/14/2012] [Indexed: 11/28/2022] Open
|
44
|
Oberhettinger P, Schütz M, Leo JC, Heinz N, Berger J, Autenrieth IB, Linke D. Intimin and invasin export their C-terminus to the bacterial cell surface using an inverse mechanism compared to classical autotransport. PLoS One 2012; 7:e47069. [PMID: 23056583 PMCID: PMC3467248 DOI: 10.1371/journal.pone.0047069] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 09/07/2012] [Indexed: 11/19/2022] Open
Abstract
Invasin and intimin are major virulence factors of enteropathogenic Yersiniae and Escherichia coli, mediating invasion into and intimate adherence to host cells, respectively. Several studies have hinted that extracellular portion of these homologous proteins might be exported via an autotransport mechanism, but rigorous experimental proof has been lacking. Here, we present a topology model for invasin and intimin, consistent with the hypothesis that the N-terminal β-barrel domain acts as a translocation pore to secrete the C-terminal passenger domain. We confirmed this topology model by inserting epitope tags into the loops of the β-barrel. We further show that obstructing the pore of β-barrel hinders the export of the passenger domain. As for classical autotransport, the biogenesis of invasin and intimin is dependent on the Bam complex and the periplasmic chaperone SurA, whereas the chaperone/protease DegP is involved in quality control. However, compared to classical autotransporters (Type Va secretion), the domain structure of intimin and invasin is inverted. We conclude that proteins of the intimin and invasin family constitute a novel group of autotransported proteins, and propose that this class of autotransporters be termed Type Ve secretion.
Collapse
Affiliation(s)
- Philipp Oberhettinger
- Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Monika Schütz
- Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Jack C. Leo
- Abteilung 1, Max Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Nadja Heinz
- Abteilung 1, Max Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Jürgen Berger
- Abteilung 1, Max Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| | - Ingo B. Autenrieth
- Institut für Medizinische Mikrobiologie und Hygiene, Universität Tübingen, Tübingen, Germany
| | - Dirk Linke
- Abteilung 1, Max Planck Institut für Entwicklungsbiologie, Tübingen, Germany
| |
Collapse
|
45
|
Strong PCR, Hinchliffe SJ, Patrick H, Atkinson S, Champion OL, Wren BW. Identification and characterisation of a novel adhesin Ifp in Yersinia pseudotuberculosis. BMC Microbiol 2011; 11:85. [PMID: 21527009 PMCID: PMC3102037 DOI: 10.1186/1471-2180-11-85] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2011] [Accepted: 04/28/2011] [Indexed: 11/23/2022] Open
Abstract
Background In order to identify new virulence determinants in Y. pseudotuberculosis a comparison between its genome and that of Yersinia pestis was undertaken. This reveals dozens of pseudogenes in Y. pestis, which are still putatively functional in Y. pseudotuberculosis and may be important in the enteric lifestyle. One such gene, YPTB1572 in the Y. pseudotuberculosis IP32953 genome sequence, encodes a protein with similarity to invasin, a classic adhesion/invasion protein, and to intimin, the attaching and effacing protein from enteropathogenic (EPEC) and enterohaemorraghic (EHEC) Escherichia coli. Results We termed YPTB1572 Ifp (Intimin family protein) and show that it is able to bind directly to human HEp-2 epithelial cells. Cysteine and tryptophan residues in the C-terminal region of intimin that are essential for function in EPEC and EHEC are conserved in Ifp. Protein binding occurred at distinct foci on the HEp-2 cell surface and can be disrupted by mutation of a single cysteine residue at the C-terminus of the protein. Temporal expression analysis using lux reporter constructs revealed that ifp is expressed at late log phase at 37°C in contrast to invasin, suggesting that Ifp is a late stage adhesin. An ifp defined mutant showed a reduction in adhesion to HEp-2 cells and was attenuated in the Galleria mellonella infection model. Conclusion A new Y. pseudotuberculosis adhesin has been identified and characterised. This Ifp is a new member in the family of invasin/intimin outer membrane adhesins.
Collapse
Affiliation(s)
- Philippa C R Strong
- Pathogen Molecular Biology Unit, Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | | | | | | | | | | |
Collapse
|
46
|
Sasaki H, Ishikawa H, Sato T, Sekiguchi S, Amao H, Kawamoto E, Matsumoto T, Shirama K. Molecular and virulence characteristics of an outer membrane-associated RTX exoprotein in Pasteurella pneumotropica. BMC Microbiol 2011; 11:55. [PMID: 21410992 PMCID: PMC3075217 DOI: 10.1186/1471-2180-11-55] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2010] [Accepted: 03/17/2011] [Indexed: 11/18/2022] Open
Abstract
Background Pasteurella pneumotropica is a ubiquitous bacterium that is frequently isolated from laboratory rodents and causes various clinical symptoms in immunodeficient animals. Currently two RTX toxins, PnxIA and PnxIIA, which are similar to hemolysin-like high-molecular-weight exoproteins are known in this species. In this study, we identified and analyzed a further RTX toxin named PnxIIIA and the corresponding type I secretion system. Results The RTX exoprotein, PnxIIIA, contains only a few copies of the RTX repeat-like sequence and 3 large repeat sequences that are partially similar to the outer membrane protein found in several prokaryotes. Recombinant PnxIIIA protein (rPnxIIIA) was cytotoxic toward J774A.1 mouse macrophage cells, whereas cytotoxicity was attenuated by the addition of anti-CD11a monoclonal antibody. rPnxIIIA could bind to extracellular matrices (ECMs) and cause hemagglutination of sheep erythrocytes. Binding was dependent on the 3 large repeat sequences in PnxIIIA. Protein interaction analyses indicated that PnxIIIA is mainly localized in the outer membrane of P. pneumotropica ATCC 35149 in a self-assembled oligomeric form. PnxIIIA is less cytotoxic to J774A.1 cells than PnxIA and PnxIIA. Conclusions The results implicate that PnxIIIA is located on the cell surface and participates in adhesion to ECMs and enhanced hemagglutination in the rodent pathogen P. pneumotropica.
Collapse
Affiliation(s)
- Hiraku Sasaki
- Animal Research Center, Tokyo Medical University, Shinjuku, Tokyo, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
47
|
Shewmaker F. The application of NMR techniques to bacterial adhesins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 715:241-56. [PMID: 21557068 DOI: 10.1007/978-94-007-0940-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular adhesins frequently compose large, highly-ordered structural assemblies that project away from the bacterial surface. These assemblies, known as pili or fimbriae, are rod-like polymeric structures that in some cases can extend up to several micrometers from the cell surface. Because these adhesin structures are critical to bacterial colonization of host cell surfaces, there is an incentive to understand their structure, assembly and mechanism of host cell attachment. Various methods in Nuclear Magnetic Resonance (NMR) spectroscopy have been used to address these topics, yielding structural information at the atomic level. Also, new methods in solid-state NMR spectroscopy have thus far been under-utilized in the study of large adhesin structures and offer a powerful approach to overcoming problems with crystallization to better understand the structures of these complexes. The following is a brief overview of the contributions of NMR to the study of bacterial adhesins with an emphasis on the future potential of solid-state NMR.
Collapse
Affiliation(s)
- Frank Shewmaker
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
| |
Collapse
|
48
|
Tsai JC, Yen MR, Castillo R, Leyton DL, Henderson IR, Saier MH. The bacterial intimins and invasins: a large and novel family of secreted proteins. PLoS One 2010; 5:e14403. [PMID: 21203509 PMCID: PMC3008723 DOI: 10.1371/journal.pone.0014403] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2010] [Accepted: 10/14/2010] [Indexed: 11/26/2022] Open
Abstract
Background Gram-negative bacteria have developed a limited repertoire of solutions for secreting proteins from the cytoplasmic compartment to the exterior of the cell. Amongst the spectrum of secreted proteins are the intimins and invasins (the Int/Inv family; TC# 1.B.54) which are characterized by an N-terminal β-barrel domain and a C-terminal surface localized passenger domain. Despite the important role played by members of this family in diseases mediated by several species of the Enterobacteriaceae, there has been little appreciation for the distribution and diversity of these proteins amongst Gram-negative bacteria. Furthermore, there is little understanding of the molecular events governing secretion of these proteins to the extracellular milieu. Principal Findings In silico approaches were used to analyze the domain organization and diversity of members of this secretion family. Proteins belonging to this family are predominantly associated with organisms from the γ-proteobacteria. Whilst proteins from the Chlamydia, γ-, β- and ε-proteobacteria possess β-barrel domains and passenger domains of various sizes, Int/Inv proteins from the α-proteobacteria, cyanobacteria and chlorobi possess only the predicted β-barrel domains. Phylogenetic analyses revealed that with few exceptions these proteins cluster according to organismal type, indicating that divergence occurred contemporaneously with speciation, and that horizontal transfer was limited. Clustering patterns of the β-barrel domains correlate well with those of the full-length proteins although the passenger domains do so with much less consistency. The modular subdomain design of the passenger domains suggests that subdomain duplication and deletion have occurred with high frequency over evolutionary time. However, all repeated subdomains are found in tandem, suggesting that subdomain shuffling occurred rarely if at all. Topological predictions for the β-barrel domains are presented. Conclusion Based on our in silico analyses we present a model for the biogenesis of these proteins. This study is the first of its kind to describe this unusual family of bacterial adhesins.
Collapse
Affiliation(s)
- Jennifer C. Tsai
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Ming-Ren Yen
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Rostislav Castillo
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
| | - Denisse L. Leyton
- The School of Immunity and Infection, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Ian R. Henderson
- The School of Immunity and Infection, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Milton H. Saier
- Department of Molecular Biology, University of California at San Diego, La Jolla, California, United States of America
- * E-mail:
| |
Collapse
|
49
|
Affiliation(s)
- Ashu Sharma
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, 311 Foster Hall, 3435 Main Street, Buffalo, NY 14214-8013, USA, Phone: 716-829-2759; Fax: 716-829-3942
| |
Collapse
|
50
|
Brochothrix thermosphacta bacteriophages feature heterogeneous and highly mosaic genomes and utilize unique prophage insertion sites. J Bacteriol 2010; 192:5441-53. [PMID: 20709901 DOI: 10.1128/jb.00709-10] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Brochothrix belongs to the low-GC branch of Gram-positive bacteria (Firmicutes), closely related to Listeria, Staphylococcus, Clostridium, and Bacillus. Brochothrix thermosphacta is a nonproteolytic food spoilage organism, adapted to growth in vacuum-packaged meats. We report the first genome sequences and characterization of Brochothrix bacteriophages. Phage A9 is a myovirus with an 89-nm capsid diameter and a 171-nm contractile tail; it belongs to the Spounavirinae subfamily and shares significant homologies with Listeria phage A511, Staphylococcus phage Twort, and others. The A9 unit genome is 127 kb long with 11-kb terminal redundancy; it encodes 198 proteins and 6 tRNAs. Phages BL3 and NF5 are temperate siphoviruses with a head diameter of 56 to 59 nm. The BL3 tail is 270 nm long, whereas NF5 features a short tail of only 94 nm. The NF5 genome (36.95 kb) encodes 57 gene products, BL3 (41.52 kb) encodes 65 products, and both are arranged in life cycle-specific modules. Surprisingly, BL3 and NF5 show little relatedness to Listeria phages but rather demonstrate relatedness to lactococcal phages. Peptide mass fingerprinting of viral proteins indicate programmed -1 translational frameshifts in the NF5 capsid and the BL3 major tail protein. Both NF5 and BL3 feature circularly permuted, terminally redundant genomes, packaged by a headful mechanism, and integrases of the serine (BL3) and tyrosine (NF5) types. They utilize unique target sequences not previously described: BL3 inserts into the 3' end of a RNA methyltransferase, whereas NF5 integrates into the 5'-terminal part of a putative histidinol-phosphatase. Interestingly, both genes are reconstituted by phage sequence.
Collapse
|