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Unravelling the specificity and mechanism of sialic acid recognition by the gut symbiont Ruminococcus gnavus. Nat Commun 2017; 8:2196. [PMID: 29259165 PMCID: PMC5736709 DOI: 10.1038/s41467-017-02109-8] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 11/07/2017] [Indexed: 02/08/2023] Open
Abstract
Ruminococcus gnavus is a human gut symbiont wherein the ability to degrade mucins is mediated by an intramolecular trans-sialidase (RgNanH). RgNanH comprises a GH33 catalytic domain and a sialic acid-binding carbohydrate-binding module (CBM40). Here we used glycan arrays, STD NMR, X-ray crystallography, mutagenesis and binding assays to determine the structure and function of RgNanH_CBM40 (RgCBM40). RgCBM40 displays the canonical CBM40 β-sandwich fold and broad specificity towards sialoglycans with millimolar binding affinity towards α2,3- or α2,6-sialyllactose. RgCBM40 binds to mucus produced by goblet cells and to purified mucins, providing direct evidence for a CBM40 as a novel bacterial mucus adhesin. Bioinformatics data show that RgCBM40 canonical type domains are widespread among Firmicutes. Furthermore, binding of R. gnavus ATCC 29149 to intestinal mucus is sialic acid mediated. Together, this study reveals novel features of CBMs which may contribute to the biogeography of symbiotic bacteria in the gut. The mucus layer is an important physical niche within the gut which harbours a distinct microbial community. Here the authors show that specific carbohydrate-binding modules associated with bacterial carbohydrate-active enzymes are mucus adhesins that target regions of the distal colon rich in sialomucins.
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Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med 2017. [PMID: 29183332 DOI: 10.1186/s13073-017-0490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. METHODS We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn. RESULTS We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut. CONCLUSIONS This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.
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Affiliation(s)
- Andrew Brantley Hall
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Moran Yassour
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Jenny Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Current address: Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Ashley Garner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Xiaofang Jiang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy Arthur
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Georgia K Lagoudas
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Nadine Fornelos
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Robin Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Madeline Bertha
- Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Melissa Cohen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - John Garber
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Hamed Khalili
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Current address: Janssen Human Microbiome Institute, Janssen Research & Development, Cambridge, MA, 02142, USA
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Subra Kugathasan
- Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02114, USA
| | - Paul Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, 02115, USA.
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103
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Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C. A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med 2017; 9:103. [PMID: 29183332 PMCID: PMC5704459 DOI: 10.1186/s13073-017-0490-5] [Citation(s) in RCA: 416] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/06/2017] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes. METHODS We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn. RESULTS We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut. CONCLUSIONS This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.
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Affiliation(s)
- Andrew Brantley Hall
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Moran Yassour
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Jenny Sauk
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Current address: Vatche and Tamar Manoukian Division of Digestive Disease, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Ashley Garner
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Xiaofang Jiang
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Timothy Arthur
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Georgia K Lagoudas
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Tommi Vatanen
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Nadine Fornelos
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Robin Wilson
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Madeline Bertha
- Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Melissa Cohen
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - John Garber
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Hamed Khalili
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Dirk Gevers
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
- Current address: Janssen Human Microbiome Institute, Janssen Research & Development, Cambridge, MA, 02142, USA
| | - Ashwin N Ananthakrishnan
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Subra Kugathasan
- Emory University School of Medicine, Emory University, Atlanta, GA, 30322, USA
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02114, USA
| | - Paul Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- MIT Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Hera Vlamakis
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Curtis Huttenhower
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, 02115, USA.
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104
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Different Inhibitory Potencies of Oseltamivir Carboxylate, Zanamivir, and Several Tannins on Bacterial and Viral Neuraminidases as Assessed in a Cell-Free Fluorescence-Based Enzyme Inhibition Assay. Molecules 2017; 22:molecules22111989. [PMID: 29149072 PMCID: PMC6150325 DOI: 10.3390/molecules22111989] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 11/14/2017] [Accepted: 11/15/2017] [Indexed: 02/07/2023] Open
Abstract
Neuraminidase is a key enzyme in the life cycle of influenza viruses and is present in some bacterial pathogens. We here assess the inhibitory potency of plant tannins versus clinically used inhibitors on both a viral and a bacterial model neuraminidase by applying the 2′-(4-methylumbelliferyl)-α-d-N-acetylneuraminic acid (MUNANA)-based activity assay. A range of flavan-3-ols, ellagitannins and chemically defined proanthocyanidin fractions was evaluated in comparison to oseltamivir carboxylate and zanamivir for their inhibitory activities against viral influenza A (H1N1) and bacterial Vibrio cholerae neuraminidase (VCNA). Compared to the positive controls, all tested polyphenols displayed a weak inhibition of the viral enzyme but similar or even higher potency on the bacterial neuraminidase. Structure–activity relationship analyses revealed the presence of galloyl groups and the hydroxylation pattern of the flavan skeleton to be crucial for inhibitory activity. The combination of zanamivir and EPs® 7630 (root extract of Pelargonium sidoides) showed synergistic inhibitory effects on the bacterial neuraminidase. Co-crystal structures of VCNA with oseltamivir carboxylate and zanamivir provided insight into bacterial versus viral enzyme-inhibitor interactions. The current data clearly indicate that inhibitor potency strongly depends on the biological origin of the enzyme and that results are not readily transferable. The therapeutic relevance of our findings is briefly discussed.
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105
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Monestier M, Latousakis D, Bell A, Tribolo S, Tailford LE, Colquhoun IJ, Le Gall G, Yu H, Chen X, Rejzek M, Dedola S, Field RA, Juge N. Membrane-enclosed multienzyme (MEME) synthesis of 2,7-anhydro-sialic acid derivatives. Carbohydr Res 2017; 451:110-117. [PMID: 28851488 PMCID: PMC5667892 DOI: 10.1016/j.carres.2017.08.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/16/2017] [Accepted: 08/17/2017] [Indexed: 12/05/2022]
Abstract
Naturally occurring 2,7-anhydro-alpha-N-acetylneuraminic acid (2,7-anhydro-Neu5Ac) is a transglycosylation product of bacterial intramolecular trans-sialidases (IT-sialidases). A facile one-pot two-enzyme approach has been established for the synthesis of 2,7-anhydro-sialic acid derivatives including those containing different sialic acid forms such as Neu5Ac and N-glycolylneuraminic acid (Neu5Gc). The approach is based on the use of Ruminoccocus gnavus IT-sialidase for the release of 2,7-anhydro-sialic acid from glycoproteins, and the conversion of free sialic acid by a sialic acid aldolase. This synthetic method, which is based on a membrane-enclosed enzymatic synthesis, can be performed on a preparative scale. Using fetuin as a substrate, high-yield and cost-effective production of 2,7-anhydro-Neu5Ac was obtained to high-purity. This method was also applied to the synthesis of 2,7-anhydro-Neu5Gc. The membrane-enclosed multienzyme (MEME) strategy reported here provides an efficient approach to produce a variety of sialic acid derivatives.
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Affiliation(s)
- Marie Monestier
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Dimitrios Latousakis
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Andrew Bell
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Sandra Tribolo
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Louise E Tailford
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Ian J Colquhoun
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Gwenaelle Le Gall
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK
| | - Hai Yu
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| | - Xi Chen
- Department of Chemistry, University of California-Davis, Davis, CA 95616, USA
| | - Martin Rejzek
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Simone Dedola
- Iceni Diagnostic Ltd, The Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK; Iceni Diagnostic Ltd, The Innovation Centre, Norwich Research Park, Norwich NR4 7GJ, UK
| | - Nathalie Juge
- Quadram Institute Bioscience, The Gut Health and Food Safety Institute Strategic Programme, Norwich Research Park, Norwich NR4 7UA, UK.
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106
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Zhang L, Wang Y, Xiayu X, Shi C, Chen W, Song N, Fu X, Zhou R, Xu YF, Huang L, Zhu H, Han Y, Qin C. Altered Gut Microbiota in a Mouse Model of Alzheimer’s Disease. J Alzheimers Dis 2017; 60:1241-1257. [DOI: 10.3233/jad-170020] [Citation(s) in RCA: 280] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ling Zhang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Ying Wang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Xia Xiayu
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Changhua Shi
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Wei Chen
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Nan Song
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Xinjing Fu
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Rui Zhou
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Yan-Feng Xu
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Lan Huang
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Hua Zhu
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Yunlin Han
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
| | - Chuan Qin
- Key Laboratory of Human Diseases Comparative Medicine, Ministry of Health, Institute of Medical Laboratory Animal Science, Chinese Academy of Medical Sciences (CAMS), Beijing, China
- Key Laboratory of Human Diseases Animal Models, State Administration of Traditional Chinese Medicine, Peking Union Medicine College (PUMC), Beijing, China
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107
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707682] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Serena Monaco
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
| | - Louise E. Tailford
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program; Quadram Institute of Bioscience; NR47UA Norwich Research Park Norwich UK
| | - Jesus Angulo
- School of Pharmacy; University of East Anglia; Norwich Research Park Norwich UK
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108
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Monaco S, Tailford LE, Juge N, Angulo J. Differential Epitope Mapping by STD NMR Spectroscopy To Reveal the Nature of Protein-Ligand Contacts. Angew Chem Int Ed Engl 2017; 56:15289-15293. [PMID: 28977722 PMCID: PMC5725711 DOI: 10.1002/anie.201707682] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/08/2017] [Indexed: 11/21/2022]
Abstract
Saturation transfer difference (STD) NMR spectroscopy is extensively used to obtain epitope maps of ligands binding to protein receptors, thereby revealing structural details of the interaction, which is key to direct lead optimization efforts in drug discovery. However, it does not give information about the nature of the amino acids surrounding the ligand in the binding pocket. Herein, we report the development of the novel method differential epitope mapping by STD NMR (DEEP‐STD NMR) for identifying the type of protein residues contacting the ligand. The method produces differential epitope maps through 1) differential frequency STD NMR and/or 2) differential solvent (D2O/H2O) STD NMR experiments. The two approaches provide different complementary information on the binding pocket. We demonstrate that DEEP‐STD NMR can be used to readily obtain pharmacophore information on the protein. Furthermore, if the 3D structure of the protein is known, this information also helps in orienting the ligand in the binding pocket.
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Affiliation(s)
- Serena Monaco
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
| | - Louise E Tailford
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Nathalie Juge
- The Gut Health And Food Safety Institute Strategic Program, Quadram Institute of Bioscience, NR47UA, Norwich Research Park, Norwich, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, UK
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109
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Cartmell A, Lowe EC, Baslé A, Firbank SJ, Ndeh DA, Murray H, Terrapon N, Lombard V, Henrissat B, Turnbull JE, Czjzek M, Gilbert HJ, Bolam DN. How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans. Proc Natl Acad Sci U S A 2017; 114:7037-7042. [PMID: 28630303 PMCID: PMC5502631 DOI: 10.1073/pnas.1704367114] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The human microbiota, which plays an important role in health and disease, uses complex carbohydrates as a major source of nutrients. Utilization hierarchy indicates that the host glycosaminoglycans heparin (Hep) and heparan sulfate (HS) are high-priority carbohydrates for Bacteroides thetaiotaomicron, a prominent member of the human microbiota. The sulfation patterns of these glycosaminoglycans are highly variable, which presents a significant enzymatic challenge to the polysaccharide lyases and sulfatases that mediate degradation. It is possible that the bacterium recruits lyases with highly plastic specificities and expresses a repertoire of enzymes that target substructures of the glycosaminoglycans with variable sulfation or that the glycans are desulfated before cleavage by the lyases. To distinguish between these mechanisms, the components of the B. thetaiotaomicron Hep/HS degrading apparatus were analyzed. The data showed that the bacterium expressed a single-surface endo-acting lyase that cleaved HS, reflecting its higher molecular weight compared with Hep. Both Hep and HS oligosaccharides imported into the periplasm were degraded by a repertoire of lyases, with each enzyme displaying specificity for substructures within these glycosaminoglycans that display a different degree of sulfation. Furthermore, the crystal structures of a key surface glycan binding protein, which is able to bind both Hep and HS, and periplasmic sulfatases reveal the major specificity determinants for these proteins. The locus described here is highly conserved within the human gut Bacteroides, indicating that the model developed is of generic relevance to this important microbial community.
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Affiliation(s)
- Alan Cartmell
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Elisabeth C Lowe
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Arnaud Baslé
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Susan J Firbank
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Didier A Ndeh
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Heath Murray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicolas Terrapon
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Vincent Lombard
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille University, F-13288 Marseille, France
- Institut National de la Recherche Agronomique, USC1408 Architecture et Fonction des Macromolécules Biologiques, F-13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Jeremy E Turnbull
- Centre for Glycobiology, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom
| | - Mirjam Czjzek
- Sorbonne Universités, Université Pierre-et-Marie-Curie, Université Paris 06, F-29688 Roscoff cedex, Bretagne, France
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff cedex, Bretagne, France
| | - Harry J Gilbert
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - David N Bolam
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;
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110
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Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J 2017; 474:1823-1836. [PMID: 28512250 PMCID: PMC5433529 DOI: 10.1042/bcj20160510] [Citation(s) in RCA: 1651] [Impact Index Per Article: 235.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 02/08/2023]
Abstract
The human gastrointestinal (GI) tract harbours a complex and dynamic population of microorganisms, the gut microbiota, which exert a marked influence on the host during homeostasis and disease. Multiple factors contribute to the establishment of the human gut microbiota during infancy. Diet is considered as one of the main drivers in shaping the gut microbiota across the life time. Intestinal bacteria play a crucial role in maintaining immune and metabolic homeostasis and protecting against pathogens. Altered gut bacterial composition (dysbiosis) has been associated with the pathogenesis of many inflammatory diseases and infections. The interpretation of these studies relies on a better understanding of inter-individual variations, heterogeneity of bacterial communities along and across the GI tract, functional redundancy and the need to distinguish cause from effect in states of dysbiosis. This review summarises our current understanding of the development and composition of the human GI microbiota, and its impact on gut integrity and host health, underlying the need for mechanistic studies focusing on host-microbe interactions.
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Affiliation(s)
- Elizabeth Thursby
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, U.K
| | - Nathalie Juge
- The Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, U.K.
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111
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Macke E, Tasiemski A, Massol F, Callens M, Decaestecker E. Life history and eco-evolutionary dynamics in light of the gut microbiota. OIKOS 2017. [DOI: 10.1111/oik.03900] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emilie Macke
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | | | - François Massol
- Univ. Lille; CNRS UMR 8198 Evo-Eco-Paleo SPICI group Lille France
| | - Martijn Callens
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
| | - Ellen Decaestecker
- Laboratory Aquatic Biology, KU Leuven (Kulak), Dept of Biology; E. Sabbelaan 53, BE-8500 Kortrijk Belgium
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112
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Abstract
Sialidases are a large group of enzymes, the majority of which catalyses the cleavage of terminal sialic acids from complex carbohydrates on glycoproteins or glycolipids. In the gastrointestinal (GI) tract, sialic acid residues are mostly found in terminal location of mucins via α2-3/6 glycosidic linkages. Many enteric commensal and pathogenic bacteria can utilize sialic acids as a nutrient source, but not all express the sialidases that are required to release free sialic acid. Sialidases encoded by gut bacteria vary in terms of their substrate specificity and their enzymatic reaction. Most are hydrolytic sialidases, which release free sialic acid from sialylated substrates. However, there are also examples with transglycosylation activities. Recently, a third class of sialidases, intramolecular trans-sialidase (IT-sialidase), has been discovered in gut microbiota, releasing (2,7-anhydro-Neu5Ac) 2,7-anydro-N-acetylneuraminic acid instead of sialic acid. Reaction specificity varies, with hydrolytic sialidases demonstrating broad activity against α2,3-, α2,6- and α2,8-linked substrates, whereas IT-sialidases tend to be specific for α2,3-linked substrates. In this mini-review, we summarize the current knowledge on the structural and biochemical properties of sialidases involved in the interaction between gut bacteria and epithelial surfaces.
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113
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Escherichia coli O157:H7 Strain EDL933 Harbors Multiple Functional Prophage-Associated Genes Necessary for the Utilization of 5-N-Acetyl-9-O-Acetyl Neuraminic Acid as a Growth Substrate. Appl Environ Microbiol 2016; 82:5940-50. [PMID: 27474715 DOI: 10.1128/aem.01671-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 07/14/2016] [Indexed: 12/20/2022] Open
Abstract
UNLABELLED Enterohemorrhagic Escherichia coli (EHEC) O157:H7 strain EDL933 harbors multiple prophage-associated open reading frames (ORFs) in its genome which are highly homologous to the chromosomal nanS gene. The latter is part of the nanCMS operon, which is present in most E. coli strains and encodes an esterase which is responsible for the monodeacetylation of 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac2). Whereas one prophage-borne ORF (z1466) has been characterized in previous studies, the functions of the other nanS-homologous ORFs are unknown. In the current study, the nanS-homologous ORFs of EDL933 were initially studied in silico Due to their homology to the chromosomal nanS gene and their location in prophage genomes, we designated them nanS-p and numbered the different nanS-p alleles consecutively from 1 to 10. The two alleles nanS-p2 and nanS-p4 were selected for production of recombinant proteins, their enzymatic activities were investigated, and differences in their temperature optima were found. Furthermore, a function of these enzymes in substrate utilization could be demonstrated using an E. coli C600ΔnanS mutant in a growth medium with Neu5,9Ac2 as the carbon source and supplementation with the different recombinant NanS-p proteins. Moreover, generation of sequential deletions of all nanS-p alleles in strain EDL933 and subsequent growth experiments demonstrated a gene dose effect on the utilization of Neu5,9Ac2 Since Neu5,9Ac2 is an important component of human and animal gut mucus and since the nutrient availability in the large intestine is limited, we hypothesize that the presence of multiple Neu5,9Ac2 esterases provides them a nutrient supply under certain conditions in the large intestine, even if particular prophages are lost. IMPORTANCE In this study, a group of homologous prophage-borne nanS-p alleles and two of the corresponding enzymes of enterohemorrhagic E. coli (EHEC) O157:H7 strain EDL933 that may be important to provide alternative genes for substrate utilization were characterized.
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114
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Nehra V, Allen JM, Mailing LJ, Kashyap PC, Woods JA. Gut Microbiota: Modulation of Host Physiology in Obesity. Physiology (Bethesda) 2016; 31:327-35. [PMID: 27511459 PMCID: PMC5005265 DOI: 10.1152/physiol.00005.2016] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Many factors are involved in weight gain and metabolic disturbances associated with obesity. The gut microbiota has been of particular interest in recent years, since both human and animal studies have increased our understanding of the delicate symbiosis between the trillions of microbes that reside in the GI tract and the host. It has been suggested that disruption of this mutual tolerance may play a significant role in modulating host physiology during obesity. Environmental influences such as diet, exercise, and early life exposures can significantly impact the composition of the microbiota, and this dysbiosis can in turn lead to increased host adiposity via a number of different mechanisms. The ability of the microbiota to regulate host fat deposition, metabolism, and immune function makes it an attractive target for achieving sustained weight loss.
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Affiliation(s)
- Vandana Nehra
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota;
| | - Jacob M Allen
- Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois; and
| | - Lucy J Mailing
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana Illinois
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota
| | - Jeffrey A Woods
- Kinesiology and Community Health, University of Illinois at Urbana-Champaign, Urbana, Illinois; and Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, Urbana Illinois
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115
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Ottman N, Huuskonen L, Reunanen J, Boeren S, Klievink J, Smidt H, Belzer C, de Vos WM. Characterization of Outer Membrane Proteome of Akkermansia muciniphila Reveals Sets of Novel Proteins Exposed to the Human Intestine. Front Microbiol 2016; 7:1157. [PMID: 27507967 PMCID: PMC4960237 DOI: 10.3389/fmicb.2016.01157] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/12/2016] [Indexed: 12/26/2022] Open
Abstract
Akkermansia muciniphila is a common member of the human gut microbiota and belongs to the Planctomycetes-Verrucomicrobia-Chlamydiae superphylum. Decreased levels of A. muciniphila have been associated with many diseases, and thus it is considered to be a beneficial resident of the intestinal mucus layer. Surface-exposed molecules produced by this organism likely play important roles in colonization and communication with other microbes and the host, but the protein composition of the outer membrane (OM) has not been characterized thus far. Herein we set out to identify and characterize A. muciniphila proteins using an integrated approach of proteomics and computational analysis. Sarkosyl extraction and sucrose density-gradient centrifugation methods were used to enrich and fractionate the OM proteome of A. muciniphila. Proteins from these fractions were identified by LC-MS/MS and candidates for OM proteins derived from the experimental approach were subjected to computational screening to verify their location in the cell. In total we identified 79 putative OM and membrane-associated extracellular proteins, and 23 of those were found to differ in abundance between cells of A. muciniphila grown on the natural substrate, mucin, and those grown on the non-mucus sugar, glucose. The identified OM proteins included highly abundant proteins involved in secretion and transport, as well as proteins predicted to take part in formation of the pili-like structures observed in A. muciniphila. The most abundant OM protein was a 95-kD protein, termed PilQ, annotated as a type IV pili secretin and predicted to be involved in the production of pili in A. muciniphila. To verify its location we purified the His-Tag labeled N-terminal domain of PilQ and generated rabbit polyclonal antibodies. Immunoelectron microscopy of thin sections immunolabeled with these antibodies demonstrated the OM localization of PilQ, testifying for its predicted function as a type IV pili secretin in A. muciniphila. As pili structures are known to be involved in the modulation of host immune responses, this provides support for the involvement of OM proteins in the host interaction of A. muciniphila. In conclusion, the characterization of A. muciniphila OM proteome provides valuable information that can be used for further functional and immunological studies.
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Affiliation(s)
- Noora Ottman
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Metapopulation Research Centre, University of HelsinkiHelsinki, Finland
| | - Laura Huuskonen
- Department of Veterinary Biosciences, University of Helsinki Helsinki, Finland
| | - Justus Reunanen
- Department of Veterinary Biosciences, University of HelsinkiHelsinki, Finland; Microbiology and Biotechnology, Department of Food and Environmental Sciences, University of HelsinkiHelsinki, Finland
| | - Sjef Boeren
- Laboratory of Biochemistry, Wageningen University Wageningen, Netherlands
| | - Judith Klievink
- Immunobiology, Department of Bacteriology and Immunology, and Research Programs Unit, University of Helsinki Helsinki, Finland
| | - Hauke Smidt
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University Wageningen, Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen UniversityWageningen, Netherlands; Department of Veterinary Biosciences, University of HelsinkiHelsinki, Finland; Immunobiology, Department of Bacteriology and Immunology, and Research Programs Unit, University of HelsinkiHelsinki, Finland
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116
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Crost EH, Tailford LE, Monestier M, Swarbreck D, Henrissat B, Crossman LC, Juge N. The mucin-degradation strategy of Ruminococcus gnavus: The importance of intramolecular trans-sialidases. Gut Microbes 2016; 7:302-312. [PMID: 27223845 PMCID: PMC4988440 DOI: 10.1080/19490976.2016.1186334] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/19/2016] [Accepted: 04/29/2016] [Indexed: 02/07/2023] Open
Abstract
We previously identified and characterized an intramolecular trans-sialidase (IT-sialidase) in the gut symbiont Ruminococcus gnavus ATCC 29149, which is associated to the ability of the strain to grow on mucins. In this work we have obtained and analyzed the draft genome sequence of another R. gnavus mucin-degrader, ATCC 35913, isolated from a healthy individual. Transcriptomics analyses of both ATCC 29149 and ATCC 35913 strains confirmed that the strategy utilized by R. gnavus for mucin-degradation is focused on the utilization of terminal mucin glycans. R. gnavus ATCC 35913 also encodes a predicted IT-sialidase and harbors a Nan cluster dedicated to sialic acid utilization. We showed that the Nan cluster was upregulated when the strains were grown in presence of mucin. In addition we demonstrated that both R. gnavus strains were able to grow on 2,7-anyhydro-Neu5Ac, the IT-sialidase transglycosylation product, as a sole carbon source. Taken together these data further support the hypothesis that IT-sialidase expressing gut microbes, provide commensal bacteria such as R. gnavus with a nutritional competitive advantage, by accessing and transforming a source of nutrient to their own benefit.
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Affiliation(s)
- Emmanuelle H. Crost
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Louise E. Tailford
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - Marie Monestier
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
| | - David Swarbreck
- The Genome Analysis Center, Norwich Research Park, Norwich, United Kingdom
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, Université Aix-Marseille, CNRS UMR 7257, France
- Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Denmark
| | - Lisa C. Crossman
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
- SequenceAnalysis.co.uk, NRP Innovation Center, Norwich, United Kingdom
| | - Nathalie Juge
- Institute of Food Research, The Gut Health and Food Safety Institute Strategic Program, Norwich Research Park, Norwich, United Kingdom
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117
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Dubinkina VB, Tyakht AV, Ilina EN, Ischenko DS, Kovarsky BA, Yarygin KS, Pavlenko AV, Popenko AS, Alexeev DG, Taraskina AE, Nasyrova RF, Krupitski EM, Skorodumova LO, Larin AK, Kostryukova ES, Govorun VM. [Metagenomic analysis of taxonomic and functional changes in gut microbiota of patients with alcoholic dependence syndrome]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 61:742-9. [PMID: 26716747 DOI: 10.18097/pbmc20156106742] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Here we present the first metagenomic study of gut microbiota in patients with alcohol dependence syndrome (ADS) performed in the whole-genome ("shotgun") format. Taxonomic analysis highlighted changes in community "drivers" abundance previously associated with inflammatory processes (including increase in Ruminococcus gnavus and torques, as well as decrease in Faecalibacterium and Akkermansia). Microbiota of alcoholics manifested presence of specific opportunistic pathogens rarely detected in healthy control subjects of the world. Differential analysis of metabolic potential basing on changes in KEGG Orthology groups abundance revealed increase in pathways associated with response to oxidative stress. Analysis of two specific gene groups--alcohol metabolism and virulence factors--also showed increase in comparison with the control groups. We suggest that gut microbiota distinct in alcoholics by both taxonomic and functional composition plays role in modulating the effect of alcohol on host organism.
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Affiliation(s)
- V B Dubinkina
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - A V Tyakht
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - E N Ilina
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - D S Ischenko
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - B A Kovarsky
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - K S Yarygin
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia
| | - A V Pavlenko
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - A S Popenko
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - D G Alexeev
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - A E Taraskina
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Saint-Petersburg, Russia
| | - R F Nasyrova
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Saint-Petersburg, Russia
| | - E M Krupitski
- Saint-Petersburg Bekhterev Psychoneurological Research Institute, Saint-Petersburg, Russia
| | - L O Skorodumova
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - A K Larin
- Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - E S Kostryukova
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
| | - V M Govorun
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russia; Scientific Research Institute of Physico-Chemical Medicine, Department of Molecular Biology and Genetics, Moscow, Russia
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118
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Derrien M, Belzer C, de Vos WM. Akkermansia muciniphila and its role in regulating host functions. Microb Pathog 2016; 106:171-181. [PMID: 26875998 DOI: 10.1016/j.micpath.2016.02.005] [Citation(s) in RCA: 624] [Impact Index Per Article: 78.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 02/07/2016] [Accepted: 02/09/2016] [Indexed: 02/08/2023]
Abstract
Akkermansia muciniphila is an intestinal bacterium that was isolated a decade ago from a human fecal sample. Its specialization in mucin degradation makes it a key organism at the mucosal interface between the lumen and host cells. Although it was isolated quite recently, it has rapidly raised significant interest as A. muciniphila is the only cultivated intestinal representative of the Verrucomicrobia, one of the few phyla in the human gut that can be easily detected in phylogenetic and metagenome analyses. There has also been a growing interest in A. muciniphila, due to its association with health in animals and humans. Notably, reduced levels of A. muciniphila have been observed in patients with inflammatory bowel diseases (mainly ulcerative colitis) and metabolic disorders, which suggests it may have potential anti-inflammatory properties. The aims of this review are to summarize the existing data on the intestinal distribution of A. muciniphila in health and disease, to provide insight into its ecology and its role in founding microbial networks at the mucosal interface, as well as to discuss recent research on its role in regulating host functions that are disturbed in various diseases, with a specific focus on metabolic disorders in both animals and humans.
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Affiliation(s)
- Muriel Derrien
- Danone Nutricia Research, Avenue de la Vauve, 91767 Palaiseau, France.
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Immunobiology Research Program, Department of Bacteriology and Immunology, Haartman Institute, University of Helsinki, Helsinki, Finland.
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119
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Lu S, Zuo T, Zhang N, Shi H, Liu F, Wu J, Wang Y, Xue C, Tang QJ. High throughput sequencing analysis reveals amelioration of intestinal dysbiosis by squid ink polysaccharide. J Funct Foods 2016. [DOI: 10.1016/j.jff.2015.11.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
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120
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Sagheddu V, Patrone V, Miragoli F, Puglisi E, Morelli L. Infant Early Gut Colonization by Lachnospiraceae: High Frequency of Ruminococcus gnavus. Front Pediatr 2016; 4:57. [PMID: 27313996 PMCID: PMC4889575 DOI: 10.3389/fped.2016.00057] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/19/2016] [Indexed: 12/28/2022] Open
Abstract
Lachnospiraceae is a bacterial family usually isolated from human and mammalian intestinal microbiota. However, its presence and role in the infant microbiota is not fully elucidated. This may be due to the strictly anaerobic behavior of its members that hampers the possibility of culture-dependent enumeration. Here, we report on the presence of this bacterial group, using biomolecular techniques, in stool samples from 25 babies aged between 1 and 24 months. Denaturing gradient gel electrophoresis (DGGE) was used as a first detection step, and data were confirmed by quantitative PCR (qPCR). The DGGE showed the presence of Lachnospiraceae in infant fecal specimens and indicated the prevalence of Ruminococcus gnavus (R. gnavus). The qPCR confirmed the presence of the Clostridium XVIa group, Blautia genus, and R. gnavus, which are the main members of this family. We detected R. gnavus in 22 of 25 (88%) samples with a qPCR probe assay. Despite the difficulties associated with their detection and enumeration, Lachnospiraceae, and in particular R. gnavus, should be included in future studies on the infant microbiota composition.
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Affiliation(s)
- Valeria Sagheddu
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore , Piacenza , Italy
| | - Vania Patrone
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore , Piacenza , Italy
| | - Francesco Miragoli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore , Piacenza , Italy
| | - Edoardo Puglisi
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore , Piacenza , Italy
| | - Lorenzo Morelli
- Facoltà di Scienze Agrarie, Alimentari e Ambientali, Istituto di Microbiologia, Università Cattolica del Sacro Cuore , Piacenza , Italy
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121
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Cook MD, Allen JM, Pence BD, Wallig MA, Gaskins HR, White BA, Woods JA. Exercise and gut immune function: evidence of alterations in colon immune cell homeostasis and microbiome characteristics with exercise training. Immunol Cell Biol 2015; 94:158-63. [PMID: 26626721 DOI: 10.1038/icb.2015.108] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 11/05/2015] [Accepted: 11/05/2015] [Indexed: 12/16/2022]
Abstract
There is robust evidence that habitual physical activity is anti-inflammatory and protective against developing chronic inflammatory disease. Much less is known about the effects of habitual moderate exercise in the gut, the compartment that has the greatest immunological responsibility and interactions with the intestinal microbiota. The link between the two has become evident, as recent studies have linked intestinal dysbiosis, or the disproportionate balance of beneficial to pathogenic microbes, with increased inflammatory disease susceptibility. Limited animal and human research findings imply that exercise may have a beneficial role in preventing and ameliorating such diseases by having an effect on gut immune function and, recently, microbiome characteristics. Emerging data from our laboratory show that different forms of exercise training differentially impact the severity of intestinal inflammation during an inflammatory insult (for example, ulcerative colitis) and may be jointly related to gut immune cell homeostasis and microbiota-immune interactions. The evidence we review and present will provide data in support of rigorous investigations concerning the effects of habitual exercise on gut health and disease.
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Affiliation(s)
- Marc D Cook
- Department of Kinesiology and Nutrition, University of Illinois at Chicago, Chicago, IL, USA
| | - Jacob M Allen
- Department of Kinesiology and Community Health, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Integrative Immunology and Behavior Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Brandt D Pence
- Department of Kinesiology and Community Health, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Integrative Immunology and Behavior Program, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Matthew A Wallig
- College of Veterinarian Medicine, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Pathobiology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - H Rex Gaskins
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Bryan A White
- Department of Animal Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL, USA
| | - Jeffrey A Woods
- Department of Kinesiology and Community Health, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Integrative Immunology and Behavior Program, University of Illinois Urbana-Champaign, Urbana, IL, USA.,Department of Nutritional Sciences, University of Illinois Urbana-Champaign, Urbana, IL, USA
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Owen CD, Lukacik P, Potter JA, Sleator O, Taylor GL, Walsh MA. Streptococcus pneumoniae NanC: STRUCTURAL INSIGHTS INTO THE SPECIFICITY AND MECHANISM OF A SIALIDASE THAT PRODUCES A SIALIDASE INHIBITOR. J Biol Chem 2015; 290:27736-48. [PMID: 26370075 PMCID: PMC4646021 DOI: 10.1074/jbc.m115.673632] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Indexed: 12/26/2022] Open
Abstract
Streptococcus pneumoniae is an important human pathogen that causes a range of disease states. Sialidases are important bacterial virulence factors. There are three pneumococcal sialidases: NanA, NanB, and NanC. NanC is an unusual sialidase in that its primary reaction product is 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (Neu5Ac2en, also known as DANA), a nonspecific hydrolytic sialidase inhibitor. The production of Neu5Ac2en from α2–3-linked sialosides by the catalytic domain is confirmed within a crystal structure. A covalent complex with 3-fluoro-β-N-acetylneuraminic acid is also presented, suggesting a common mechanism with other sialidases up to the final step of product formation. A conformation change in an active site hydrophobic loop on ligand binding constricts the entrance to the active site. In addition, the distance between the catalytic acid/base (Asp-315) and the ligand anomeric carbon is unusually short. These features facilitate a novel sialidase reaction in which the final step of product formation is direct abstraction of the C3 proton by the active site aspartic acid, forming Neu5Ac2en. NanC also possesses a carbohydrate-binding module, which is shown to bind α2–3- and α2–6-linked sialosides, as well as N-acetylneuraminic acid, which is captured in the crystal structure following hydration of Neu5Ac2en by NanC. Overall, the pneumococcal sialidases show remarkable mechanistic diversity while maintaining a common structural scaffold.
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Affiliation(s)
- C David Owen
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Petra Lukacik
- Diamond Light Source and Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA, United Kingdom, and
| | - Jane A Potter
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom
| | - Olivia Sleator
- the Medical Research Council France, c/o European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
| | - Garry L Taylor
- From the Biomedical Sciences Research Complex, University of St. Andrews, St. Andrews, Fife KY16 9ST, United Kingdom,
| | - Martin A Walsh
- Diamond Light Source and the Medical Research Council France, c/o European Synchrotron Radiation Facility, BP 220, 38043 Grenoble, France
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