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Moulton KD, Adewale AP, Carol HA, Mikami SA, Dube DH. Metabolic Glycan Labeling-Based Screen to Identify Bacterial Glycosylation Genes. ACS Infect Dis 2020; 6:3247-3259. [PMID: 33186014 PMCID: PMC7808405 DOI: 10.1021/acsinfecdis.0c00612] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bacterial cell surface glycans are quintessential drug targets due to their critical role in colonization of the host, pathogen survival, and immune evasion. The dense cell envelope glycocalyx contains distinctive monosaccharides that are stitched together into higher order glycans to yield exclusively bacterial structures that are critical for strain fitness and pathogenesis. However, the systematic study and inhibition of bacterial glycosylation enzymes remains challenging. Bacteria produce glycans containing rare sugars refractory to traditional glycan analysis, complicating the study of bacterial glycans and the identification of their biosynthesis machinery. To ease the study of bacterial glycans in the absence of detailed structural information, we used metabolic glycan labeling to detect changes in glycan biosynthesis. Here, we screened wild-type versus mutant strains of the gastric pathogen Helicobacter pylori, ultimately permitting the identification of genes involved in glycoprotein and lipopolysaccharide biosynthesis. Our findings provide the first evidence that H. pylori protein glycosylation proceeds via a lipid carrier-mediated pathway that overlaps with lipopolysaccharide biosynthesis. Protein glycosylation mutants displayed fitness defects consistent with those induced by small molecule glycosylation inhibitors. Broadly, our results suggest a facile approach to screen for bacterial glycosylation genes and gain insight into their biosynthesis and functional importance, even in the absence of glycan structural information.
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Affiliation(s)
- Karen D. Moulton
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Adedunmola P. Adewale
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Hallie A. Carol
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Sage A. Mikami
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
| | - Danielle H. Dube
- Department of Chemistry & Biochemistry, Bowdoin College, 6600 College Station, Brunswick, ME 04011, USA
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In Vivo Genome and Methylome Adaptation of cag-Negative Helicobacter pylori during Experimental Human Infection. mBio 2020; 11:mBio.01803-20. [PMID: 32843556 PMCID: PMC7448279 DOI: 10.1128/mbio.01803-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Exceptional genetic diversity and variability are hallmarks of Helicobacter pylori, but the biological role of this plasticity remains incompletely understood. Here, we had the rare opportunity to investigate the molecular evolution during the first weeks of H. pylori infection by comparing the genomes and epigenomes of H. pylori strain BCS 100 used to challenge human volunteers in a vaccine trial with those of bacteria reisolated from the volunteers 10 weeks after the challenge. The data provide molecular insights into the process of establishment of this highly versatile pathogen in 10 different human individual hosts, showing, for example, selection for changes in host-interaction molecules as well as changes in epigenetic methylation patterns. The data provide important clues to the early adaptation of H. pylori to new host niches after transmission, which we believe is vital to understand its success as a chronic pathogen and develop more efficient treatments and vaccines. Multiple studies have demonstrated rapid bacterial genome evolution during chronic infection with Helicobacter pylori. In contrast, little was known about genetic changes during the first stages of infection, when selective pressure is likely to be highest. Using single-molecule, real-time (SMRT) and Illumina sequencing technologies, we analyzed genome and methylome evolution during the first 10 weeks of infection by comparing the cag pathogenicity island (cagPAI)-negative H. pylori challenge strain BCS 100 with pairs of H. pylori reisolates from gastric antrum and corpus biopsy specimens of 10 human volunteers who had been infected with this strain as part of a vaccine trial. Most genetic changes detected in the reisolates affected genes with a surface-related role or a predicted function in peptide uptake. Apart from phenotypic changes of the bacterial envelope, a duplication of the catalase gene was observed in one reisolate, which resulted in higher catalase activity and improved survival under oxidative stress conditions. The methylomes also varied in some of the reisolates, mostly by activity switching of phase-variable methyltransferase (MTase) genes. The observed in vivo mutation spectrum was remarkable for a very high proportion of nonsynonymous mutations. Although the data showed substantial within-strain genome diversity in the challenge strain, most antrum and corpus reisolates from the same volunteers were highly similar to each other, indicating that the challenge infection represents a major selective bottleneck shaping the transmitted population. Our findings suggest rapid in vivo selection of H. pylori during early-phase infection providing adaptation to different individuals by common mechanisms of genetic and epigenetic alterations.
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Li H, Marceau M, Yang T, Liao T, Tang X, Hu R, Xie Y, Tang H, Tay A, Shi Y, Shen Y, Yang T, Pi X, Lamichhane B, Luo Y, Debowski AW, Nilsson HO, Haslam SM, Mulloy B, Dell A, Stubbs KA, Marshall BJ, Benghezal M. East-Asian Helicobacter pylori strains synthesize heptan-deficient lipopolysaccharide. PLoS Genet 2019; 15:e1008497. [PMID: 31747390 PMCID: PMC6892558 DOI: 10.1371/journal.pgen.1008497] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 12/04/2019] [Accepted: 10/28/2019] [Indexed: 02/05/2023] Open
Abstract
The lipopolysaccharide O-antigen structure expressed by the European Helicobacter pylori model strain G27 encompasses a trisaccharide, an intervening glucan-heptan and distal Lewis antigens that promote immune escape. However, several gaps still remain in the corresponding biosynthetic pathway. Here, systematic mutagenesis of glycosyltransferase genes in G27 combined with lipopolysaccharide structural analysis, uncovered HP0102 as the trisaccharide fucosyltransferase, HP1283 as the heptan transferase, and HP1578 as the GlcNAc transferase that initiates the synthesis of Lewis antigens onto the heptan motif. Comparative genomic analysis of G27 lipopolysaccharide biosynthetic genes in strains of different ethnic origin revealed that East-Asian strains lack the HP1283/HP1578 genes but contain an additional copy of HP1105 and JHP0562. Further correlation of different lipopolysaccharide structures with corresponding gene contents led us to propose that the second copy of HP1105 and the JHP0562 may function as the GlcNAc and Gal transferase, respectively, to initiate synthesis of the Lewis antigen onto the Glc-Trio-Core in East-Asian strains lacking the HP1283/HP1578 genes. In view of the high gastric cancer rate in East Asia, the absence of the HP1283/HP1578 genes in East-Asian H. pylori strains warrants future studies addressing the role of the lipopolysaccharide heptan in pathogenesis.
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Affiliation(s)
- Hong Li
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
| | - Michael Marceau
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 8204—CIIL—Center for Infection and Immunity of Lille, Lille, France
| | - Tiandi Yang
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Tingting Liao
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
| | - Xiaoqiong Tang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Renwei Hu
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Yan Xie
- Department of Gastroenterology, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Tang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Alfred Tay
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
| | - Ying Shi
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Yalin Shen
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Tiankuo Yang
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Xuenan Pi
- Precision Medicine Key Laboratory of Sichuan Province & Precision Medicine Center, West China Hospital, Sichuan University, Chengdu, China
| | - Binit Lamichhane
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
| | - Yong Luo
- Key Laboratory of Geoscience Spatial Information Technology, Ministry of Land and Resources of the P.R.China, Chengdu University of Technology
| | - Aleksandra W. Debowski
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
- School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Hans-Olof Nilsson
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
| | - Stuart M. Haslam
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Barbara Mulloy
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Anne Dell
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, United Kingdom
| | - Keith A. Stubbs
- School of Molecular Sciences, University of Western Australia, Crawley, Australia
| | - Barry J. Marshall
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
- Ondek Pty Ltd, Rushcutters Bay, New South Wales, Australia
| | - Mohammed Benghezal
- West China Marshall Research Center for Infectious Diseases, Center of Infectious Diseases, Division of Infectious Diseases, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
- Helicobacter pylori Research Laboratory, School of Biomedical Sciences, Marshall Centre for Infectious Disease Research and Training, University of Western Australia, Nedlands, Australia
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Chua EG, Wise MJ, Khosravi Y, Seow SW, Amoyo AA, Pettersson S, Peters F, Tay CY, Perkins TT, Loke MF, Marshall BJ, Vadivelu J. Quantum changes in Helicobacter pylori gene expression accompany host-adaptation. DNA Res 2017; 24:37-49. [PMID: 27803027 PMCID: PMC5381349 DOI: 10.1093/dnares/dsw046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 09/23/2016] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori is a highly successful gastric pathogen. High genomic plasticity allows its adaptation to changing host environments. Complete genomes of H. pylori clinical isolate UM032 and its mice-adapted serial derivatives 298 and 299, generated using both PacBio RS and Illumina MiSeq sequencing technologies, were compared to identify novel elements responsible for host-adaptation. The acquisition of a jhp0562-like allele, which encodes for a galactosyltransferase, was identified in the mice-adapted strains. Our analysis implies a new β-1,4-galactosyltransferase role for this enzyme, essential for Ley antigen expression. Intragenomic recombination between babA and babB genes was also observed. Further, we expanded on the list of candidate genes whose expression patterns have been mediated by upstream homopolymer-length alterations to facilitate host adaption. Importantly, greater than four-fold reduction of mRNA levels was demonstrated in five genes. Among the down-regulated genes, three encode for outer membrane proteins, including BabA, BabB and HopD. As expected, a substantial reduction in BabA protein abundance was detected in mice-adapted strains 298 and 299 via Western analysis. Our results suggest that the expression of Ley antigen and reduced outer membrane protein expressions may facilitate H. pylori colonisation of mouse gastric epithelium.
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Affiliation(s)
- Eng-Guan Chua
- The Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia.,School of Computer Science and Software Engineering, The University of Western Australia, Australia
| | - Yalda Khosravi
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | | | | | - Sven Pettersson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.,LKC School of Medicine, Nanyang Technological University, Singapore.,SCELSE Microbiome Centre, Nanyang Technological University, Singapore
| | - Fanny Peters
- The Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Chin-Yen Tay
- The Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Timothy T Perkins
- The Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Mun-Fai Loke
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
| | - Barry J Marshall
- The Marshall Centre for Infectious Diseases Research and Training, School of Pathology and Laboratory Medicine, The University of Western Australia, Nedlands, Western Australia, Australia.,UM Marshall Centre, High Impact Research Building, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Jamuna Vadivelu
- Department of Medical Microbiology, University of Malaya, Kuala Lumpur, Malaysia
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Divergence between the Highly Virulent Zoonotic Pathogen Helicobacter heilmannii and Its Closest Relative, the Low-Virulence "Helicobacter ailurogastricus" sp. nov. Infect Immun 2015; 84:293-306. [PMID: 26527212 DOI: 10.1128/iai.01300-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 10/26/2015] [Indexed: 12/21/2022] Open
Abstract
Helicobacter heilmannii naturally colonizes the stomachs of dogs and cats and has been associated with gastric disorders in humans. Nine feline Helicobacter strains, classified as H. heilmannii based on ureAB and 16S rRNA gene sequences, were divided into a highly virulent and a low-virulence group. The genomes of these strains were sequenced to investigate their phylogenetic relationships, to define their gene content and diversity, and to determine if the differences in pathogenicity were associated with the presence or absence of potential virulence genes. The capacities of these helicobacters to bind to the gastric mucosa were investigated as well. Our analyses revealed that the low-virulence strains do not belong to the species H. heilmannii but to a novel, closely related species for which we propose the name Helicobacter ailurogastricus. Several homologs of H. pylori virulence factors, such as IceA1, HrgA, and jhp0562-like glycosyltransferase, are present in H. heilmannii but absent in H. ailurogastricus. Both species contain a VacA-like autotransporter, for which the passenger domain is remarkably larger in H. ailurogastricus than in H. heilmannii. In addition, H. ailurogastricus shows clear differences in binding to the gastric mucosa compared to H. heilmannii. These findings highlight the low-virulence character of this novel Helicobacter species.
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The Prevalence of Helicobacter pylori Virulence Factors in Bhutan, Vietnam, and Myanmar Is Related to Gastric Cancer Incidence. BIOMED RESEARCH INTERNATIONAL 2015; 2015:830813. [PMID: 26090448 PMCID: PMC4450262 DOI: 10.1155/2015/830813] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 01/26/2015] [Accepted: 01/31/2015] [Indexed: 12/24/2022]
Abstract
Gastric cancer is a significant health problem in Asia. Although the prevalence of Helicobacter pylori infection is similar in Bhutan, Vietnam, and Myanmar, the incidence of gastric cancer is highest in Bhutan, followed by Vietnam and Myanmar. We hypothesized that H. pylori virulence factors contribute to the differences. The status of cagA, vacA, jhp0562, and β-(1,3)galT(jhp0563) was examined in 371 H. pylori-infected patients from Bhutan, Vietnam, and Myanmar. Each virulence factor could not explain the difference of the incidence of gastric cancer. However, the prevalence of quadruple-positive for cagA, vacA s1, vacA m1, and jhp0562-positive/β-(1,3)galT-negative was significantly higher in Bhutan than in Vietnam and Myanmar and correlated with gastric cancer incidence. Moreover, gastritis-staging scores measured by histology of gastric mucosa were significantly higher in quadruple-positive strains. We suggest that the cagA, vacA s1, vacA m1, and jhp0562-positive/β-(1,3)galT-negative genotype may play a role in the development of gastric cancer.
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Rubin EJ, Trent MS. Colonize, evade, flourish: how glyco-conjugates promote virulence of Helicobacter pylori. Gut Microbes 2013; 4:439-53. [PMID: 23859890 PMCID: PMC3928157 DOI: 10.4161/gmic.25721] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Helicobacter pylori is an adapted gastric pathogen that colonizes the human stomach, causing severe gastritis and gastric cancer. A hallmark of infection is the ability of this organism to evade detection by the human immune system. H. pylori has evolved a number of features to achieve this, many of which involve glyco-conjugates including the lipopolysaccharide, peptidoglycan layer, glycoproteins, and glucosylated cholesterol. These major bacterial components possess unique features from those of other gram-negative organisms, including differences in structure, assembly, and modification. These defining characteristics of H. pylori glycobiology help the pathogen establish a long-lived infection by providing camouflage, modulating the host immune response, and promoting virulence mechanisms. In this way, glyco-conjugates are essential for H. pylori pathogenicity and survival, allowing it to carve out a niche in the formidable environment of the human stomach.
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Affiliation(s)
- Erica J Rubin
- Institute for Cellular and Molecular Biology; The University of Texas at Austin; Austin, TX USA
| | - M Stephen Trent
- Institute for Cellular and Molecular Biology; The University of Texas at Austin; Austin, TX USA,Department of Molecular Biosciences; The University of Texas at Austin; Austin, TX USA,Correspondence to: M Stephen Trent,
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Abstract
Although Helicobacter pylori infection is highly prevalent in the global human population, the majority of infected individuals remain asymptomatic. A complex combination of host, environmental, and bacterial factors are considered to determine susceptibility and severity of outcome in the subset of individuals that develop clinical disease. These factors collectively determine the ability of H. pylori to colonize the gastric mucosa and profoundly influence the nature of the interaction that ensues. Many studies over the last year provide new insight into H. pylori virulence strategies and the activities of critical bacterial determinants that modulate the host environment. These latter include the secreted proteins CagA and VacA and adhesins BabA and OipA, which directly interact with host tissues. Observations from several studies extend the functional repertoire of CagA and the cag type IV secretion system in particular, providing further mechanistic understanding of how these important determinants engage and activate host signalling pathways important in the development of disease.
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Affiliation(s)
- Robin M Delahay
- Centre for Biomolecular Sciences and Nottingham Digestive Diseases Centre, University of Nottingham, Nottingham, UK.
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