1
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Åberg A, Gideonsson P, Bhat A, Ghosh P, Arnqvist A. Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori. Nucleic Acids Res 2024:gkae188. [PMID: 38499492 DOI: 10.1093/nar/gkae188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
Adaptation to variations in pH is crucial for the ability of Helicobacter pylori to persist in the human stomach. The acid responsive two-component system ArsRS, constitutes the global regulon that responds to acidic conditions, but molecular details of how transcription is affected by the ArsR response regulator remains poorly understood. Using a combination of DNA-binding studies, in vitro transcription assays, and H. pylori mutants, we demonstrate that phosphorylated ArsR (ArsR-P) forms an active protein complex that binds DNA with high specificity in order to affect transcription. Our data showed that DNA topology is key for DNA binding. We found that AT-rich DNA sequences direct ArsR-P to specific sites and that DNA-bending proteins are important for the effect of ArsR-P on transcription regulation. The repression of sabA transcription is mediated by ArsR-P with the support of Hup and is affected by simple sequence repeats located upstream of the sabA promoter. Here stochastic events clearly contribute to the fine-tuning of pH-dependent gene regulation. Our results reveal important molecular aspects for how ArsR-P acts to repress transcription in response to acidic conditions. Such transcriptional control likely mediates shifts in bacterial positioning in the gastric mucus layer.
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Affiliation(s)
- Anna Åberg
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Pär Gideonsson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Abhayprasad Bhat
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Prachetash Ghosh
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Anna Arnqvist
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
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2
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Wang H, Yang K, Huang H, Guo L, He X. Development of Simple Sequence Repeat Markers and Genetic Diversity Evaluation of Mycocentrospora acerina in Yunnan Province, China. J Fungi (Basel) 2023; 9:944. [PMID: 37755052 PMCID: PMC10532959 DOI: 10.3390/jof9090944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023] Open
Abstract
Round spot is a destructive disease that limits of Panax notoginseng production in China. However, the genetic diversity of its etiological agent Mycocentrospora acerina has yet to be studied. In this work, firstly, we developed 32 M. acerina polymorphic microsatellite markers using MISA and CERVUS 3.0 and selected 14 for further analysis. Then, we studied the genetic diversity of 187 isolates collected from P. notoginseng round spot using simple sequence repeat markers and polyacrylamide gel electrophoresis. The genetic diversity ranged from 0.813 to 0.946, with 264 alleles detected at the 14 microsatellite loci. The expected average heterozygosity was 0.897.
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Affiliation(s)
- Huiling Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (K.Y.); (H.H.)
| | - Kuan Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (K.Y.); (H.H.)
| | - Hongping Huang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (K.Y.); (H.H.)
| | - Liwei Guo
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (K.Y.); (H.H.)
| | - Xiahong He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China; (H.W.); (K.Y.); (H.H.)
- School of Landscape and Horticulture, Southwest Forestry University, Kunming 650224, China
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3
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Yuan C, Yu C, Sun Q, Xiong M, Zhou S, Zeng M, Song H. Research on antibiotic resistance in Helicobacter pylori: a bibliometric analysis of the past decade. Front Microbiol 2023; 14:1208157. [PMID: 37389333 PMCID: PMC10301835 DOI: 10.3389/fmicb.2023.1208157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/25/2023] [Indexed: 07/01/2023] Open
Abstract
Resistance of Helicobacter pylori (H. pylori) to antibiotics has reached alarming levels worldwide, and the efficacy of the H. pylori eradication treatment has decreased dramatically because of antibiotic resistance. To gain a more comprehensive understanding of the development status, research hotspots, and future trends related to H. pylori antibiotic resistance, we conducted a thorough retrospective analysis via the bibliometrics method. We searched the Science Citation Index Expanded of the Web of Science Core Collection for all pertinent articles on H. pylori antibiotic resistance from 2013 to 2022. R-bibliometrix, CiteSpace, and VOSviewer tools were utilized to depict statistical evaluations in order to provide an unbiased presentation and forecasts in the field. We incorporated a total of 3,509 articles related to H. pylori antibiotic resistance. Publications were inconsistent prior to 2017, but steadily increased after 2017. China generated the most papers and the United States of America received the most citations and the highest H-index. Baylor College of Medicine was the most influential institution in this field, with the highest number of publications and citations, as well as the highest H-index. Helicobacter was the most productive journal, followed by the World Journal of Gastroenterology and Frontiers in Microbiology. The World Journal of Gastroenterology had the highest citation. Graham, David Y was the most productive and cited author. Clarithromycin resistance, prevalence, gastric cancer, quadruple therapy, sequential therapy, 23S rRNA, whole genome sequencing, bismuth, and probiotics appeared with a high frequency in the keywords. The top keywords with the highest citation bursts were vonoprazan, RdxA, biofilm formation, and fatty acid chain. Our research illustrated a multi-dimensional facet and a holistic knowledge structure for H. pylori antibiotic resistance research over the past decade, which can serve as a guide for the H. pylori research community to conduct in-depth investigations in the future.
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Affiliation(s)
- Chengzhi Yuan
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
- School of Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Chang Yu
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Qifang Sun
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Meng Xiong
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Sainan Zhou
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Meiyan Zeng
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Houpan Song
- Hunan Provincial Key Laboratory of Traditional Chinese Medicine Diagnostics, Hunan University of Chinese Medicine, Changsha, Hunan, China
- School of Traditional Chinese Medicine, Hunan University of Chinese Medicine, Changsha, Hunan, China
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4
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Kesharwani A, Dighe OR, Lamture Y. Role of Helicobacter pylori in Gastric Carcinoma: A Review. Cureus 2023; 15:e37205. [PMID: 37159779 PMCID: PMC10163845 DOI: 10.7759/cureus.37205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/06/2023] [Indexed: 04/08/2023] Open
Abstract
Gastric cancer (GC) is one of the leading causes of cancer-related deaths globally. Gastritis caused by Helicobacter pylori (H. pylori) is a potent cause of gastrointestinal malignancies. The majority of all humans on the planet have H. pylori invasion in their stomachs, yet only a few diseased people develop GC. The human gastrointestinal system contains a broad population of microorganisms in addition to H. pylori. H. pylori heterogeneity has been studied because not all H. pylori diseases result in cancer. Individuals in the adult age group account for the bulk of gastric carcinoma cases. H. pylori has various strains, which is beneficial for its survival in host cell epithelium for a longer duration of time. Along with H. pylori, oral microbes have a major role in the pathogenicity of gastric carcinoma. The complex ecology of oral microbiota helps to defend against infections, preserve homeostasis, and regulate the immune system. In contrast, oral microbiota is involved in various mechanisms like anti-apoptotic activity, suppression of the immune system of the host, and initiation of chronic inflammation. These oral microbes are also responsible for the development of mutations. Interactions between the host immune system and bacteria promote the progression of cancer. For this review, various research articles were studied, and information was collected using databases like PubMed and Google Scholar. This review emphasizes on the role of H. pylori in gastric carcinoma, its pathogenesis, the role of various virulence factors and risk factors related to it, the role of oral microbiota in gastric carcinoma pathogenesis, diagnostic modalities, treatment options, and preventive measures for gastric carcinoma.
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5
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Dooyema SD, Noto JM, Wroblewski LE, Piazuelo MB, Krishna U, Suarez G, Romero-Gallo J, Delgado AG, Peek RM. Helicobacter pylori actively suppresses innate immune nucleic acid receptors. Gut Microbes 2022; 14:2105102. [PMID: 35905376 PMCID: PMC9341374 DOI: 10.1080/19490976.2022.2105102] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Chronic mucosal pathogens have evolved multiple strategies to manipulate the host immune response; consequently, microbes contribute to the development of >2 million cases of cancer/year. Gastric adenocarcinoma is the fourth leading cause of cancer-related death and Helicobacter pylori confers the highest risk for this disease. Gastric innate immune effectors can either eliminate bacteria or mobilize adaptive immune responses including Toll-like receptors (TLRs), and cytosolic DNA sensor/adaptor proteins (e.g., stimulator of interferon genes, STING). The H. pylori strain-specific cag type IV secretion system (T4SS) augments gastric cancer risk and translocates DNA into epithelial cells where it activates the microbial DNA sensor TLR9 and suppresses injury in vivo; however, the ability of H. pylori to suppress additional nucleic acid PRRs within the context of chronic gastric inflammation and injury remains undefined. In this study, in vitro and ex vivo experiments identified a novel mechanism through which H. pylori actively suppresses STING and RIG-I signaling via downregulation of IRF3 activation. In vivo, the use of genetically deficient mice revealed that Th17 inflammatory responses are heightened following H. pylori infection within the context of Sting deficiency in conjunction with increased expression of a known host immune regulator, Trim30a. This novel mechanism of immune suppression by H. pylori is likely a critical component of a finely tuned rheostat that not only regulates the initial innate immune response, but also drives chronic gastric inflammation and injury.
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Affiliation(s)
- Samuel D.R. Dooyema
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Microbe-Host Interactions Training Program, Vanderbilt University, Nashville, Tennessee, USA
| | - Jennifer M. Noto
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lydia E. Wroblewski
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M. Blanca Piazuelo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Uma Krishna
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Giovanni Suarez
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judith Romero-Gallo
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alberto G. Delgado
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard M. Peek
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA,CONTACT Richard M. Peek Vanderbilt University Medical Center, Division of Gastroenterology, 2215 Garland Avenue, 1030C Medical Research Building IV, Nashville, TN37232, USA
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6
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Kim A, Lai J, Merrell DS, Kim JH, Su H, Cha JH. Geographic diversity in Helicobacter pylori oipA genotype between Korean and United States isolates. J Microbiol 2021; 59:1125-1132. [PMID: 34718962 DOI: 10.1007/s12275-021-1450-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 09/15/2021] [Accepted: 09/23/2021] [Indexed: 12/30/2022]
Abstract
Helicobacter pylori outer membrane inflammatory protein A (OipA) was originally named for its role in inducing inflammation in the host, as evidenced by high mucosal IL-8 levels. Expression of OipA is regulated by phase variation of a CT dinucleotide-repeat located in the 5' region of the gene. However, little is known about OipA geographic diversity across isolates. To address this gap, we conducted a large-scale molecular epidemiologic analysis using H. pylori clinical isolates obtained from two geographically distinct populations: Korea and the United States (US). Most Korean isolates (98.7%) possessed two copies of oipA located at two specific loci (A and B) while all US isolates contained only one copy of oipA at locus A. Furthermore, most Korean oipA (94.8%) possessed three or less CT repeats while most US oipA (96.6%) contained five or more CT repeats. Among the two copies, all Korean H. pylori possessed at least one oipA 'on' phase variant while the single copy of oipA in US isolates showed 56.2% 'on' and 43.8% 'off.' Thus, host differences seem to have driven geographic diversification of H. pylori across these populations such that OipA expression in US isolates is still regulated by phase variation with 5 or more CT repeats, while Korean isolates always express OipA; duplication of the oipA combined with a reduction of CT repeats to three or less ensures continued expression. En masse, these findings suggest that diversity in the oipA gene copy number, CT repeats, and phase variation among H. pylori from different populations may confer a benefit in adaptation to particular host populations.
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Affiliation(s)
- Aeryun Kim
- Department of Oral Biology, Oral Science Research Center, Department of Applied Life Science, The Graduate School, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea.,Department of Dental Hygiene, Gangdong University, Eumseong, 27600, Republic of Korea
| | - Jing Lai
- Department of Oral Biology, Oral Science Research Center, Department of Applied Life Science, The Graduate School, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, USA
| | - Ji-Hye Kim
- Department of Dental Hygiene, Baekseok University, Cheonan, 31065, Republic of Korea.
| | - Hanfu Su
- Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, P. R. China.
| | - Jeong-Heon Cha
- Department of Oral Biology, Oral Science Research Center, Department of Applied Life Science, The Graduate School, BK21 FOUR Project, Yonsei University College of Dentistry, Seoul, 03722, Republic of Korea. .,Guangzhou Key Laboratory of Basic and Applied Research of Oral Regenerative Medicine, Affiliated Stomatology Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510182, P. R. China.
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7
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Keikha M, Karbalaei M. EPIYA motifs of Helicobacter pylori cagA genotypes and gastrointestinal diseases in the Iranian population: a systematic review and meta-analysis. New Microbes New Infect 2021; 41:100865. [PMID: 33912350 PMCID: PMC8066700 DOI: 10.1016/j.nmni.2021.100865] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 03/01/2021] [Accepted: 03/07/2021] [Indexed: 02/08/2023] Open
Abstract
Helicobacter pylori is one of the best risk factors for gastric cancer. Recent studies have examined the relationship between virulence factors, in particular CagA toxin, and the development of gastrointestinal diseases. According to the literature, there is a significant relationship between the polymorphism of cagA-EPIYA motifs and progression to severe clinical outcomes. The main goal of our study was to determine the possible association between cagA genotypes and the risk of severe clinical outcomes in the Iranian population. We investigated these ambiguities using a comprehensive meta-analysis study, in which we evaluated data from 1762 Iranian patients for a potential correlation between all cagA gene genotypes and gastrointestinal diseases. According to statistical analysis, the frequencies of cagA genotypes including ABC, ABCC, AB and ABCCC in the Iranian population were estimated at 80.18%, 22.81%, 5.52% and 2.76%, respectively; the ABD genotype was not detected in these PCR-based studies. There was a significant relationship between cagA genotypes ABCC and ABCCC and severe clinical outcomes of infection such as peptic ulcer and gastric cancer. Overall, it can be concluded that there is a positive correlation with the number of copies of EPIYA-C and the increase of gastric cancer. Therefore, according to our results, it seems that the EPIYA-ABCCC motif has a strong positive relationship with gastric cancer in the Iranian population.
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Affiliation(s)
- M. Keikha
- Department of Microbiology and Virology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Student Research Committee, Mashhad University of Medical Sciences, Mashhad, Iran
| | - M. Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
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8
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He H, Liu J, Li L, Qian G, Hao D, Li M, Zhang Y, Hong X, Xu J, Yan D. Helicobacter pylori CagA Interacts with SHP-1 to Suppress the Immune Response by Targeting TRAF6 for K63-Linked Ubiquitination. THE JOURNAL OF IMMUNOLOGY 2021; 206:1161-1170. [PMID: 33568397 DOI: 10.4049/jimmunol.2000234] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 10/14/2020] [Indexed: 01/09/2023]
Abstract
Helicobacter pylori is the major etiological agent for most gastric cancer. CagA has been reported to be an important virulence factor of H. pylori, but its effect on the immune response is not yet clear. In this study, wild-type C57BL/6 mice and Ptpn6me-v/me-v mice were randomly assigned for infection with H. pylori We demonstrated that CagA suppressed H. pylori-stimulated expression of proinflammatory cytokines in vivo. Besides, we infected mouse peritoneal macrophages RAW264.7 and AGS with H. pylori Our results showed that CagA suppressed expression of proinflammatory cytokines through inhibiting the MAPKs and NF-κB pathways activation in vitro. Mechanistically, we found that CagA interacted with the host cellular tyrosine phosphatase SHP-1, which facilitated the recruitment of SHP-1 to TRAF6 and inhibited the K63-linked ubiquitination of TRAF6, which obstructed the transmission of signal downstream. Taken together, these findings reveal a previously unknown mechanism by which CagA negatively regulates the posttranslational modification of TRAF6 in innate antibacterial immune response and provide molecular basis for new therapeutics to treat microbial infection.
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Affiliation(s)
- Huan He
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jing Liu
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Liuyan Li
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Gui Qian
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Doudou Hao
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Manman Li
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yihua Zhang
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaowu Hong
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jianqing Xu
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Dapeng Yan
- Shanghai Public Health Clinical Center and Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
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9
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Roszczenko-Jasińska P, Wojtyś MI, Jagusztyn-Krynicka EK. Helicobacter pylori treatment in the post-antibiotics era-searching for new drug targets. Appl Microbiol Biotechnol 2020; 104:9891-9905. [PMID: 33052519 PMCID: PMC7666284 DOI: 10.1007/s00253-020-10945-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 09/28/2020] [Accepted: 10/04/2020] [Indexed: 12/14/2022]
Abstract
Abstract Helicobacter pylori, a member of Epsilonproteobacteria, is a Gram-negative microaerophilic bacterium that colonizes gastric mucosa of about 50% of the human population. Although most infections caused by H. pylori are asymptomatic, the microorganism is strongly associated with serious diseases of the upper gastrointestinal tract such as chronic gastritis, peptic ulcer, duodenal ulcer, and gastric cancer, and it is classified as a group I carcinogen. The prevalence of H. pylori infections varies worldwide. The H. pylori genotype, host gene polymorphisms, and environmental factors determine the type of induced disease. Currently, the most common therapy to treat H. pylori is the first line clarithromycin–based triple therapy or a quadruple therapy replacing clarithromycin with new antibiotics. Despite the enormous recent effort to introduce new therapeutic regimens to combat this pathogen, treatment for H. pylori still fails in more than 20% of patients, mainly due to the increased prevalence of antibiotic resistant strains. In this review we present recent progress aimed at designing new anti-H. pylori strategies to combat this pathogen. Some novel therapeutic regimens will potentially be used as an extra constituent of antibiotic therapy, and others may replace current antibiotic treatments. Key points • Attempts to improve eradication rate of H. pylori infection. • Searching for new drug targets in anti-Helicobacter therapies.
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Affiliation(s)
- Paula Roszczenko-Jasińska
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, Univeristy of Warsaw, Miecznikowa 1, 02-096, Warszawa, Poland
| | - Marta Ilona Wojtyś
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, Univeristy of Warsaw, Miecznikowa 1, 02-096, Warszawa, Poland.,Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, Univeristy of Warsaw, Pasteura 5, 02-093, Warszawa, Poland
| | - Elżbieta K Jagusztyn-Krynicka
- Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, Univeristy of Warsaw, Miecznikowa 1, 02-096, Warszawa, Poland.
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10
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Nemoto TK, Ohara Nemoto Y. Dipeptidyl-peptidases: Key enzymes producing entry forms of extracellular proteins in asaccharolytic periodontopathic bacterium Porphyromonas gingivalis. Mol Oral Microbiol 2020; 36:145-156. [PMID: 33006264 PMCID: PMC8048996 DOI: 10.1111/omi.12317] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 09/17/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023]
Abstract
Porphyromonas gingivalis, a pathogen of chronic periodontitis, is an asaccharolytic microorganism that solely utilizes nutritional amino acids as its energy source and cellular constituents. The bacterium is considered to incorporate proteinaceous nutrients mainly as dipeptides, thus exopeptidases that produce dipeptides from polypeptides are critical for survival and proliferation. We present here an overview of dipeptide production by P. gingivalis mediated by dipeptidyl-peptidases (DPPs), e.g., DPP4, DPP5, DPP7, and DPP11, serine exopeptidases localized in periplasm, which release dipeptides from the N-terminus of polypeptides. Additionally, two other exopeptidases, acylpeptidyl-oligopeptidase (AOP) and prolyl tripeptidyl-peptidase A (PTP-A), which liberate N-terminal acylated di-/tri-peptides and tripeptides with Pro at the third position, respectively, provide polypeptides in an acceptable form for DPPs. Hence, a large fraction of dipeptides is produced from nutritional polypeptides by DPPs with differential specificities in combination with AOP and PTP-A. The resultant dipeptides are then incorporated across the inner membrane mainly via a proton-dependent oligopeptide transporter (POT), a member of the major facilitator superfamily. Recent studies also indicate that DPP4 and DPP7 directly link between periodontal and systemic diseases, such as type 2 diabetes mellitus and coagulation abnormality, respectively. Therefore, these dipeptide-producing and incorporation molecules are considered to be potent targets for prevention and treatment of periodontal and related systemic diseases.
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Affiliation(s)
- Takayuki K Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuko Ohara Nemoto
- Department of Oral Molecular Biology, Course of Medical and Dental Sciences, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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11
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Salama NR. Cell morphology as a virulence determinant: lessons from Helicobacter pylori. Curr Opin Microbiol 2020; 54:11-17. [PMID: 32014717 PMCID: PMC7247928 DOI: 10.1016/j.mib.2019.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/30/2019] [Indexed: 02/06/2023]
Abstract
A genetic screen for colonization factors of the human stomach pathogen Helicobacter pylori took a surprising turn with the discovery that some colonization mutants had lost helical cell morphology. Further pursuit of direct morphology screens revealed a large H. pylori 'shapesome' complex consisting of peptidoglycan modification and precursor synthesis enzymes, a cytoskeletal element and putative scaffold or regulatory proteins that promote enhanced asymmetric cell wall growth. Functional characterization of H. pylori shape mutants indicates multiple roles for cell shape during colonization of mucosal surfaces. Conservation of both the molecular constituents of the H. pylori cell shape program and a newly appreciated enrichment of this morphotype at mucosal surface suggests that helical organisms may be particularly well poised to exploit host perturbations to become pathogens.
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Affiliation(s)
- Nina R Salama
- Human Biology Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, United States.
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12
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Salerian AJ. Burn wound infections and Pseudomonas aeruginosa. Burns 2019; 46:257-258. [PMID: 31859094 DOI: 10.1016/j.burns.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/03/2019] [Indexed: 01/28/2023]
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13
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Establishment of serine protease htrA mutants in Helicobacter pylori is associated with secA mutations. Sci Rep 2019; 9:11794. [PMID: 31409845 PMCID: PMC6692382 DOI: 10.1038/s41598-019-48030-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 07/29/2019] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori plays an essential role in the pathogenesis of gastritis, peptic ulcer disease, and gastric cancer. The serine protease HtrA, an important secreted virulence factor, disrupts the gastric epithelium, which enables H. pylori to transmigrate across the epithelium and inject the oncogenic CagA protein into host cells. The function of periplasmic HtrA for the H. pylori cell is unknown, mainly due to unavailability of the htrA mutants. In fact, htrA has been described as an essential gene in this bacterium. We have screened 100 worldwide H. pylori isolates and show that only in the N6 strain it was possible to delete htrA or mutate the htrA gene to produce proteolytically inactive HtrA. We have sequenced the wild-type and mutant chromosomes and we found that inactivation of htrA is associated with mutations in SecA – a component of the Sec translocon apparatus used to translocate proteins from the cytoplasm into the periplasm. The cooperation of SecA and HtrA has been already suggested in Streptococcus pneumonia, in which these two proteins co-localize. Hence, our results pinpointing a potential functional relationship between HtrA and the Sec translocon in H. pylori possibly indicate for the more general mechanism responsible to maintain bacterial periplasmic homeostasis.
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Whitmire JM, Merrell DS. Helicobacter pylori Genetic Polymorphisms in Gastric Disease Development. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1149:173-194. [DOI: 10.1007/5584_2019_365] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Waskito LA, Yih-Wu J, Yamaoka Y. The role of integrating conjugative elements in Helicobacter pylori: a review. J Biomed Sci 2018; 25:86. [PMID: 30497458 PMCID: PMC6264033 DOI: 10.1186/s12929-018-0489-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 11/16/2018] [Indexed: 12/15/2022] Open
Abstract
The genome of Helicobacter pylori contains many putative genes, including a genetic region known as the Integrating Conjugative Elements of H. pylori type four secretion system (ICEHptfs). This genetic regions were originally termed as "plasticity zones/regions" due to the great genetic diversity between the original two H. pylori whole genome sequences. Upon analysis of additional genome sequences, the regions were reported to be extremely common within the genome of H. pylori. Moreover, these regions were also considered conserved rather than genetically plastic and were believed to act as mobile genetic elements transferred via conjugation. Although ICEHptfs(s) are highly conserved, these regions display great allele diversity, especially on ICEHptfs4, with three different subtypes: ICEHptfs4a, 4b, and 4c. ICEHptfs were also reported to contain a novel type 4 secretion system (T4SS) with both epidemiological and in vitro infection model studies highlighting that this novel T4SS functions primarily as a virulence factor. However, there is currently no information regarding the structure, the genes responsible for forming the T4SS, and the interaction between this T4SS and other virulence genes. Unlike the cag pathogenicity island (PAI), which contains CagA, a gene found to be essential for H. pylori virulence, these novel T4SSs have not yet been reported to contain genes that contribute significant effects to the entire system. This notion prompted the hypothesis that these novel T4SSs may have different mechanisms involving cag PAI.
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Affiliation(s)
- Langgeng Agung Waskito
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu City, Oita, Japan.,Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Jeng Yih-Wu
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University, Faculty of Medicine, Yufu City, Oita, Japan. .,Department of Medicine, Gastroenterology Section, Baylor College of Medicine, Houston, TX, USA. .,Global Oita Medical Advanced Research Center for Health, Yufu City, Oita, Japan.
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Noto JM, Chopra A, Loh JT, Romero-Gallo J, Piazuelo MB, Watson M, Leary S, Beckett AC, Wilson KT, Cover TL, Mallal S, Israel DA, Peek RM. Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments. Gut 2018; 67:1793-1804. [PMID: 28924022 PMCID: PMC5857411 DOI: 10.1136/gutjnl-2017-313863] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 06/30/2017] [Accepted: 07/15/2017] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Helicobacter pylori is the strongest risk factor for gastric cancer; however, the majority of infected individuals do not develop disease. Pathological outcomes are mediated by complex interactions among bacterial, host and environmental constituents, and two dietary factors linked with gastric cancer risk are iron deficiency and high salt. We hypothesised that prolonged adaptation of H. pylori to in vivo carcinogenic microenvironments results in genetic modification important for disease. DESIGN Whole genome sequencing of genetically related H. pylori strains that differ in virulence and targeted H. pylori sequencing following prolonged exposure of bacteria to in vitro carcinogenic conditions were performed. RESULTS A total of 180 unique single nucleotide polymorphisms (SNPs) were identified among the collective genomes when compared with a reference H. pylori genome. Importantly, common SNPs were identified in isolates harvested from iron-depleted and high salt carcinogenic microenvironments, including an SNP within fur (FurR88H). To investigate the direct role of low iron and/or high salt, H. pylori was continuously cultured in vitro under low iron or high salt conditions to assess fur genetic variation. Exposure to low iron or high salt selected for the FurR88H variant after only 5 days. To extend these results, fur was sequenced in 339 clinical H. pylori strains. Among the isolates examined, 17% (40/232) of strains isolated from patients with premalignant lesions harboured the FurR88H variant, compared with only 6% (6/107) of strains from patients with non-atrophic gastritis alone (p=0.0034). CONCLUSION These results indicate that specific genetic variation arises within H. pylori strains during in vivo adaptation to conditions conducive for gastric carcinogenesis.
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Affiliation(s)
- Jennifer M Noto
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Abha Chopra
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - John T Loh
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Judith Romero-Gallo
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - M Blanca Piazuelo
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Mark Watson
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Shay Leary
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia
| | - Amber C Beckett
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Keith T Wilson
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Timothy L Cover
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Veterans Affairs, Tennessee Valley Healthcare System, Nashville, Tennessee, USA,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, Australia,Department of Medicine, Division of Infectious Diseases, Vanderbilt University, Nashville, Tennessee, USA
| | - Dawn A Israel
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Richard M Peek
- Department of Medicine, Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA,Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Jaiswal N, Raikwal N, Pandey H, Agarwal N, Arora A, Poluri KM, Kumar D. NMR elucidation of monomer-dimer transition and conformational heterogeneity in histone-like DNA binding protein of Helicobacter pylori. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2018; 56:285-299. [PMID: 29241299 DOI: 10.1002/mrc.4701] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 05/25/2023]
Abstract
Helicobacter pylori (H. pylori) colonizes under harsh acidic/oxidative stress conditions of human gastrointestinal tract and can survive there for infinitely longer durations of host life. The bacterium expresses several harbinger proteins to facilitate its persistent colonization under such conditions. One such protein in H. pylori is histone-like DNA binding protein (Hup), which in its homo-dimeric form binds to DNA to perform various DNA dependent cellular activities. Further, it also plays an important role in protecting the genomic DNA from oxidative stress and acidic denaturation. Legitimately, if the binding of Hup to DNA is suppressed, it will directly impact on the survival of the bacterium, thus making Hup a potential therapeutic target for developing new anti-H. pylori agents. However, to inhibit the binding of Hup to DNA, it is necessary to gain detailed insights into the molecular and structural basis of Hup-dimerization and its binding mechanism to DNA. As a first step in this direction, we report here the nuclear magnetic resonance (NMR) assignments and structural features of Hup at pH 6.0. The study revealed the occurrence of dynamic equilibrium between its monomer and dimer conformations. The dynamic equilibrium was found to shifting towards dimer both at low temperature and low pH; whereas DNA binding studies evidenced that the protein binds to DNA in its dimeric form. These preliminary investigations correlate very well with the diverse functionality of protein and will form the basis for future studies aiming to develop novel anti-H. pylori agents employing structure-based-rational drug discovery approach.
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Affiliation(s)
- Nancy Jaiswal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
- Dr. APJ Abdul Kalam Technical University, IET Campus, Sitapur Road, Lucknow, 226021, Uttar Pradesh, India
| | - Nisha Raikwal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
| | - Himanshu Pandey
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Nipanshu Agarwal
- Department of Biotechnology and Centre for Nanotechnology Indian Institute of Technology Roorkee, 247667, Uttarakhand, India
| | - Ashish Arora
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow, 226 031, India
| | - Krishna Mohan Poluri
- Department of Biotechnology and Centre for Nanotechnology Indian Institute of Technology Roorkee, 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow, 226014, India
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18
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Chung JW, Jeong SH, Lee SM, Pak JH, Lee GH, Jeong JY, Kim JH. Expression of MicroRNA in Host Cells Infected with Helicobacter pylori. Gut Liver 2018; 11:392-400. [PMID: 28208005 PMCID: PMC5417782 DOI: 10.5009/gnl16265] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/17/2016] [Accepted: 09/05/2016] [Indexed: 12/16/2022] Open
Abstract
Background/Aims MicroRNAs (miRNAs) regulate gene expression. We assess miRNA regulation by Helicobacter pylori infection and elucidate their role in H. pylori-infected gastric epithelial cells. Methods The relationship between miRNA expression and DNA methylation was examined. Cells were treated with the nuclear factor-kappaB (NF-κB) inhibitor Bay 11-7082 to determine the relationship between miRNA expression and NF-κB signal transduction. Results In the negative control cells infected with H. pylori 26695, the expression of six miRNAs was increased, whereas the expression of five miRNAs was decreased. The expression of upregulated miRNAs was increased when the host cells were treated with H. pylori and an NF-κB inhibitor. miR-127-5p, -155, and -181 were associated with increased interleukin 6 (IL-6) secretion in H. pylori infected cells treated with anti-miRNA. The expression of miR-155, -127-5p, -195, -216, -206, and -488 increased by approximately 3-fold following treatment with the methylation inhibitor Aza. Conclusions We found novel miRNAs in H. pylori-infected negative control cells using miRNA microarrays. Upregulated miRNA expression was inversely related to the transcription of NF-κB. miR-195 and miR-488 appear to play a pivotal role in controlling IL-6 activity in H. pylori infection. miRNA expression in H. pylori infection was affected by methylation.
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Affiliation(s)
- Jun-Won Chung
- Department of Internal Medicine, Gachon University Gil Medical Center, Incheon, Korea
| | - Seok Hoo Jeong
- Department of Internal Medicine, Catholic Kwandong University International St. Mary's Hospital, Incheon, Korea
| | - Sun Mi Lee
- Department of Convergence Medicine and Asan Institute for Life Sciences, Seoul, Korea
| | - Jhang Ho Pak
- Department of Convergence Medicine and Asan Institute for Life Sciences, Seoul, Korea
| | - Gin Hyug Lee
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jin-Yong Jeong
- Department of Convergence Medicine and Asan Institute for Life Sciences, Seoul, Korea
| | - Jin-Ho Kim
- Department of Gastroenterology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
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Papizadeh M, Rohani M, Nahrevanian H, Javadi A, Pourshafie MR. Probiotic characters of Bifidobacterium and Lactobacillus are a result of the ongoing gene acquisition and genome minimization evolutionary trends. Microb Pathog 2017; 111:118-131. [DOI: 10.1016/j.micpath.2017.08.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Revised: 08/12/2017] [Accepted: 08/16/2017] [Indexed: 02/07/2023]
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20
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Blum FC, Hu HQ, Servetas SL, Benoit SL, Maier RJ, Maroney MJ, Merrell DS. Structure-function analyses of metal-binding sites of HypA reveal residues important for hydrogenase maturation in Helicobacter pylori. PLoS One 2017; 12:e0183260. [PMID: 28809946 PMCID: PMC5557546 DOI: 10.1371/journal.pone.0183260] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 08/01/2017] [Indexed: 01/18/2023] Open
Abstract
The nickel-containing enzymes of Helicobacter pylori, urease and hydrogenase, are essential for efficient colonization in the human stomach. The insertion of nickel into urease and hydrogenase is mediated by the accessory protein HypA. HypA contains an N-terminal nickel-binding site and a dynamic structural zinc-binding site. The coordination of nickel and zinc within HypA is known to be critical for urease maturation and activity. Herein, we test the hydrogenase activity of a panel of H. pylori mutant strains containing point mutations within the nickel- and zinc-binding sites. We found that the residues that are important for hydrogenase activity are those that were similarly vital for urease activity. Thus, the zinc and metal coordination sites of HypA play similar roles in urease and hydrogenase maturation. In other pathogenic bacteria, deletion of hydrogenase leads to a loss in acid resistance. Thus, the acid resistance of two strains of H. pylori containing a hydrogenase deletion was also tested. These mutant strains demonstrated wild-type levels of acid resistance, suggesting that in H. pylori, hydrogenase does not play a role in acid resistance.
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Affiliation(s)
- Faith C. Blum
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Heidi Q. Hu
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, United States of America
| | - Stephanie L. Servetas
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
| | - Stéphane L. Benoit
- Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Robert J. Maier
- Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Michael J. Maroney
- Department of Chemistry and Program in Molecular and Cellular Biology, University of Massachusetts Amherst, Amherst, MA, United States of America
- * E-mail: (MJM); (DSM)
| | - D. Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America
- * E-mail: (MJM); (DSM)
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21
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Abadi ATB. Strategies used by helicobacter pylori to establish persistent infection. World J Gastroenterol 2017; 23:2870-2882. [PMID: 28522905 PMCID: PMC5413782 DOI: 10.3748/wjg.v23.i16.2870] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/01/2017] [Accepted: 02/17/2017] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) is a Gram-negative and motile bacterium that colonizes the hostile microniche of the human stomach, then persists for the host’s entire life, if not effectively treated. Clinically, H. pylori plays a causative role in the development of a wide spectrum of diseases including chronic active gastritis, peptic ulceration, gastric adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Due to the global distribution of H. pylori, it is no exaggeration to conclude that smart strategies are contributing to adaptation of the bacterium to its permanent host. Thirty-four years after the discovery of this bacterium, there are still many unanswered questions. For example, which strategies help the bacterium to survive in this inhospitable microniche? This question is slightly easier to answer if we presume the same clinical concept for both persistent infection and disease. Understanding the mechanisms governing H. pylori persistence will improve identification of the increased risk of diseases such as gastric cancer in patients infected with this bacterium. A well-defined and long-term equilibrium between the human host and H. pylori allows bacterial persistence in the gastric microniche; although this coexistence leads to a high risk of severe diseases such as gastric cancer. To escape the bactericidal activity of stomach acid, H. pylori secretes large amounts of surface-associated and cytosolic urease. The potential to avoid acidic conditions and immune evasion are discussed in order to explain the persistence of H. pylori colonization in the gastric mucosa, and data on bacterial genetic diversity are included. Information on the mechanisms related to H. pylori persistence can also provide the direction for future research concerning effective therapy and management of gastroduodenal disorders. The topics presented in the current review are important for elucidating the strategies used by H. pylori to help the bacterium persist in relation to the immune system and the many unfavorable features of living in the gastric microniche.
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22
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Singh G, Singh V. Functional elucidation of hypothetical proteins for their indispensable roles toward drug designing targets from Helicobacter pylori strain HPAG1. J Biomol Struct Dyn 2017; 36:906-918. [DOI: 10.1080/07391102.2017.1302361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Gagandeep Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, TAB, Shahpur 176206, India
| | - Vikram Singh
- Centre for Computational Biology and Bioinformatics, School of Life Sciences, Central University of Himachal Pradesh, TAB, Shahpur 176206, India
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Noecker C, McNally CP, Eng A, Borenstein E. High-resolution characterization of the human microbiome. Transl Res 2017; 179:7-23. [PMID: 27513210 PMCID: PMC5164958 DOI: 10.1016/j.trsl.2016.07.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/12/2016] [Accepted: 07/15/2016] [Indexed: 12/29/2022]
Abstract
The human microbiome plays an important and increasingly recognized role in human health. Studies of the microbiome typically use targeted sequencing of the 16S rRNA gene, whole metagenome shotgun sequencing, or other meta-omic technologies to characterize the microbiome's composition, activity, and dynamics. Processing, analyzing, and interpreting these data involve numerous computational tools that aim to filter, cluster, annotate, and quantify the obtained data and ultimately provide an accurate and interpretable profile of the microbiome's taxonomy, functional capacity, and behavior. These tools, however, are often limited in resolution and accuracy and may fail to capture many biologically and clinically relevant microbiome features, such as strain-level variation or nuanced functional response to perturbation. Over the past few years, extensive efforts have been invested toward addressing these challenges and developing novel computational methods for accurate and high-resolution characterization of microbiome data. These methods aim to quantify strain-level composition and variation, detect and characterize rare microbiome species, link specific genes to individual taxa, and more accurately characterize the functional capacity and dynamics of the microbiome. These methods and the ability to produce detailed and precise microbiome information are clearly essential for informing microbiome-based personalized therapies. In this review, we survey these methods, highlighting the challenges each method sets out to address and briefly describing methodological approaches.
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Affiliation(s)
- Cecilia Noecker
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Colin P McNally
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Alexander Eng
- Department of Genome Sciences, University of Washington, Seattle, WA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA
- Santa Fe Institute, Santa Fe, NM
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van Vliet AHM. Use of pan-genome analysis for the identification of lineage-specific genes of Helicobacter pylori. FEMS Microbiol Lett 2016; 364:fnw296. [PMID: 28011701 DOI: 10.1093/femsle/fnw296] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 09/08/2016] [Accepted: 12/22/2016] [Indexed: 12/23/2022] Open
Abstract
The human bacterial pathogen Helicobacter pylori has a highly variable genome, with significant allelic and sequence diversity between isolates and even within well-characterised strains, hampering comparative genomics of H. pylori In this study, pan-genome analysis has been used to identify lineage-specific genes of H. pylori A total of 346 H. pylori genomes spanning the hpAfrica1, hpAfrica2, hpAsia2, hpEurope, hspAmerind and hspEAsia multilocus sequence typing (MLST) lineages were searched for genes specifically overrepresented or underrepresented in MLST lineages or associated with the cag pathogenicity island. The only genes overrepresented in cag-positive genomes were the cag pathogenicity island genes themselves. In contrast, a total of 125 genes were either overrepresented or underrepresented in one or more MLST lineages. Of these 125 genes, alcohol/aldehyde-reducing enzymes linked with acid resistance and production of toxic aldehydes were found to be overrepresented in African lineages. Conversely, the FecA2 ferric citrate receptor was missing from hspAmerind genomes, but present in all other lineages. This work shows the applicability of pan-genome analysis for identification of lineage-specific genes of H. pylori, facilitating further investigation to allow linkage of differential distribution of genes with disease outcome or virulence of H. pylori.
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Affiliation(s)
- Arnoud H M van Vliet
- School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7AD, UK
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Flint A, Stintzi A, Saraiva LM. Oxidative and nitrosative stress defences of Helicobacter and Campylobacter species that counteract mammalian immunity. FEMS Microbiol Rev 2016; 40:938-960. [PMID: 28201757 PMCID: PMC5091033 DOI: 10.1093/femsre/fuw025] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/29/2016] [Accepted: 07/02/2016] [Indexed: 12/18/2022] Open
Abstract
Helicobacter and Campylobacter species are Gram-negative microaerophilic host-associated heterotrophic bacteria that invade the digestive tract of humans and animals. Campylobacter jejuni is the major worldwide cause of foodborne gastroenteritis in humans, while Helicobacter pylori is ubiquitous in over half of the world's population causing gastric and duodenal ulcers. The colonisation of the gastrointestinal system by Helicobacter and Campylobacter relies on numerous cellular defences to sense the host environment and respond to adverse conditions, including those imposed by the host immunity. An important antimicrobial tool of the mammalian innate immune system is the generation of harmful oxidative and nitrosative stresses to which pathogens are exposed during phagocytosis. This review summarises the regulators, detoxifying enzymes and subversion mechanisms of Helicobacter and Campylobacter that ultimately promote the successful infection of humans.
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Affiliation(s)
- Annika Flint
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Alain Stintzi
- Ottawa Institute of Systems Biology, Faculty of Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Lígia M. Saraiva
- Instituto de Tecnologia Química e Biológica, NOVA, Av. da República, 2780-157 Oeiras, Portugal
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Zhang Y, Sun H, Chen X, Li J, Zhao H, Geng L, Li B. Functional profile of gastric epithelial cells infected with Helicobacter pylori strains. Microb Pathog 2016; 95:77-81. [DOI: 10.1016/j.micpath.2016.03.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 03/21/2016] [Accepted: 03/22/2016] [Indexed: 12/13/2022]
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Helicobacter pylori vacA Genotypes in Chronic Gastritis and Gastric Carcinoma Patients from Macau, China. Toxins (Basel) 2016; 8:toxins8050142. [PMID: 27164143 PMCID: PMC4885057 DOI: 10.3390/toxins8050142] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2016] [Revised: 04/11/2016] [Accepted: 04/29/2016] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori is the major triggering factor for gastric carcinoma, but only a small proportion of infected patients develop this disease. Differences in virulence observed among H. pylori strains, namely in the vacuolating cytotoxin vacA gene, may contribute to this discrepancy. Infection with vacA s1, i1 and m1 strains increases the risk for progression of gastric premalignant lesions and for gastric carcinoma. However, in East Asian countries most of the H. pylori strains are vacA s1, regardless of the patients’ clinical status, and the significance of the vacA i1 and m1 genotypes for gastric carcinoma in this geographic area remains to be fully elucidated. The aim of the present study was to investigate this relationship in 290 patients from Macau, China. Using very sensitive and accurate genotyping methods, we detected infection with vacA i1 and with vacA m1 strains in, respectively, 85.2% and 52.6% of the patients that were infected with single genotypes. The prevalence of cagA-positive strains was 87.5%. No significant associations were observed between vacA genotypes or cagA and gastric carcinoma. It is worth noting that 37.5% of the infected patients had coexistence of H. pylori strains with different vacA genotypes. Additional studies directed to other H. pylori virulence factors should be performed to identify high risk patients in East Asia.
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Talebi Bezmin Abadi A. Vaccine against Helicobacter pylori: Inevitable approach. World J Gastroenterol 2016; 22:3150-3157. [PMID: 27003991 PMCID: PMC4789989 DOI: 10.3748/wjg.v22.i11.3150] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/05/2016] [Accepted: 01/30/2016] [Indexed: 02/06/2023] Open
Abstract
Over three decades have passed since the discovery of Helicobacter pylori (H. pylori), and yet many questions about its treatment remain unanswered. For example, there is no certainty regarding continued use of current antibiotic therapy against H. pylori. The bad news is that even combined regimens are also unable to eradicate bacterial colonization. The worst problem with H. pylori chemotherapy is that even if we identify the most successful regimen, it cannot eliminate the risk of re-infection. This problem is further complicated by the fact that clinicians have no information as to whether probiotics are useful or not. Moreover, to date, we have no large scale produced vaccine effective against H. pylori. Due to the relatively rapid and abundant dissemination of guidelines globally reported concerning management of gastric cancer prevention and therapeutic regimens, clinicians may choose a vaccine as better effective weapon against H. pylori. Therefore, a radical shift in adopted strategies is needed to guide ultimate decisions regarding H. pylori management. In light of failures in vaccine projects, we should identify better vaccine design targeting conserved/essential genes. The unique character and persistence of H. pylori pose obstacles to making an effective vaccine. Preferably, in developing countries, the best reasonable and logical approach is to recommend prophylactic H. pylori vaccine among children as an obligatory national program to limit primary colonization. Trying to produce a therapeutic vaccine would be postponed until later. In reality, we should not forget to prescribe narrow spectrum antibiotics. In the current review, I draw a route to define the best adopted strategy against this rogue bacterium.
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Xuan SH, Wu LP, Zhou YG, Xiao MB. Detection of clarithromycin-resistant Helicobacter pylori in clinical specimens by molecular methods: A review. J Glob Antimicrob Resist 2016; 4:35-41. [PMID: 27436390 DOI: 10.1016/j.jgar.2016.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 12/17/2022] Open
Abstract
Various molecular methods have been developed to rapidly detect clarithromycin (CLR) resistance in Helicobacter pylori isolates in clinical specimens. All of these assays for detecting CLR resistance in H. pylori are based on detection of mutations in the 23S rRNA gene. In this article, we summarise current knowledge regarding the detection of H. pylori CLR resistance in clinical specimens by molecular tests. The available data showed that restriction fragment length polymorphism (RFLP), 3'-mismatch PCR, DNA sequencing, the PCR line probe assay (PCR-LiPA) and fluorescence in situ hybridisation assay (FISH) are able to detect CLR-resistant H. pylori in clinical specimens with excellent specificity and sensitivity. However, several factors limit their clinical application, including fastidious, time-consuming preparation and low-throughput as well as carrying a risk of contamination. Furthermore, as an invasive method, FISH is not suitable for children or the elderly. Among the molecular methods, one that is most promising for the future is real-time PCR probe hybridisation technology using fluorescence resonance energy transfer (FRET) probes, which can rapidly detect CLR resistance with high sensitivity and specificity in biopsies and stool specimens, even though mixed infections are present in clinical specimens. Moreover, due to the advantages that this method is simple, rapid and economical, real-time PCR is technically feasible for clinical application in small- and medium-sized hospitals in developing countries. Second, with high sensitivity, specificity and throughput, DNA chips will also be a valuable tool for detecting resistant H. pylori isolates from cultures and clinical specimens.
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Affiliation(s)
- Shi-Hai Xuan
- Department of Clinical Laboratory, The Affiliated Dongtai Hospital of Nantong University, Dongtai 224200, China
| | - Li-Pei Wu
- Department of Clinical Laboratory, The Affiliated Dongtai Hospital of Nantong University, Dongtai 224200, China
| | - Yu-Gui Zhou
- Department of Clinical Laboratory, The Affiliated Dongtai Hospital of Nantong University, Dongtai 224200, China
| | - Ming-Bing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Nantong 226001, China.
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Abstract
BACKGROUND Helicobacter pylori is a bacterial carcinogen that is supposed to have the highest known level of risk for the development of gastric cancer, a disease that claims hundreds of thousands of lives per year. Approximately 89% of the global gastric cancer burden and 5.5% of malignancies worldwide are attributed to H. pylori-induced inflammation and injury. However, only a fraction of colonized persons ever develop neoplasia, and disease risk involves well-choreographed interactions between pathogen and host, which are dependent upon strain-specific bacterial factors, host genotypic traits, and/or environmental conditions. KEY MESSAGES One H. pylori strain-specific virulence determinant that augments the risk for gastric cancer is the cag pathogenicity island, a secretion system that injects the bacterial oncoprotein CagA into host cells. Host polymorphisms within genes that regulate immunity and oncogenesis also heighten the risk for gastric cancer, in conjunction with H. pylori strain-specific constituents. Further, conditions such as iron deficiency and high salt intake can influence H. pylori phenotypes that lower the threshold for disease. CONCLUSIONS Delineation of bacterial, host, and environmental mediators that augment gastric cancer risk has profound ramifications for both physicians and biomedical researchers as such findings will not only focus prevention approaches that target H. pylori-infected human populations at increased risk for stomach cancer, but will also provide mechanistic insights into inflammatory carcinomas that develop beyond the gastric niche.
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Affiliation(s)
- Richard M. Peek
- Division of Gastroenterology, Department of Medicine, Vanderbilt University School of Medicine, 2215B Garland Ave Suite 1030C, 37232 Nashville, TN USA
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31
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Grine FE. The Late Quaternary Hominins of Africa: The Skeletal Evidence from MIS 6-2. AFRICA FROM MIS 6-2 2016. [DOI: 10.1007/978-94-017-7520-5_17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Vorwerk H, Huber C, Mohr J, Bunk B, Bhuju S, Wensel O, Spröer C, Fruth A, Flieger A, Schmidt-Hohagen K, Schomburg D, Eisenreich W, Hofreuter D. A transferable plasticity region in Campylobacter coli allows isolates of an otherwise non-glycolytic food-borne pathogen to catabolize glucose. Mol Microbiol 2015; 98:809-30. [PMID: 26259566 DOI: 10.1111/mmi.13159] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2015] [Indexed: 12/31/2022]
Abstract
Thermophilic Campylobacter species colonize the intestine of agricultural and domestic animals commensally but cause severe gastroenteritis in humans. In contrast to other enteropathogenic bacteria, Campylobacter has been considered to be non-glycolytic, a metabolic property originally used for their taxonomic classification. Contrary to this dogma, we demonstrate that several Campylobacter coli strains are able to utilize glucose as a growth substrate. Isotopologue profiling experiments with (13) C-labeled glucose suggested that these strains catabolize glucose via the pentose phosphate and Entner-Doudoroff (ED) pathways and use glucose efficiently for de novo synthesis of amino acids and cell surface carbohydrates. Whole genome sequencing of glycolytic C. coli isolates identified a genomic island located within a ribosomal RNA gene cluster that encodes for all ED pathway enzymes and a glucose permease. We could show in vitro that a non-glycolytic C. coli strain could acquire glycolytic activity through natural transformation with chromosomal DNA of C. coli and C. jejuni subsp. doylei strains possessing the ED pathway encoding plasticity region. These results reveal for the first time the ability of a Campylobacter species to catabolize glucose and provide new insights into how genetic macrodiversity through intra- and interspecies gene transfer expand the metabolic capacity of this food-borne pathogen.
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Affiliation(s)
- Hanne Vorwerk
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Claudia Huber
- Lehrstuhl für Biochemie, Technische Universität München, Garching, Germany
| | - Juliane Mohr
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Sabin Bhuju
- Department of Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Olga Wensel
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Centre of Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Angelika Fruth
- Division of Enteropathogenic Bacteria and Legionella (FG11), German National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch-Institute, Wernigerode, Germany
| | - Antje Flieger
- Division of Enteropathogenic Bacteria and Legionella (FG11), German National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch-Institute, Wernigerode, Germany
| | - Kerstin Schmidt-Hohagen
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | - Dietmar Schomburg
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Braunschweig, Germany
| | | | - Dirk Hofreuter
- Institute for Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
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Molina-Sánchez MD, López-Contreras JA, Toro N, Fernández-López M. Genomic characterization of Sinorhizobium meliloti AK21, a wild isolate from the Aral Sea Region. SPRINGERPLUS 2015; 4:259. [PMID: 26090306 PMCID: PMC4468178 DOI: 10.1186/s40064-015-1062-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/26/2015] [Indexed: 11/10/2022]
Abstract
The symbiotic, nitrogen-fixing bacterium Sinorhizobium meliloti has been widely studied due to its ability to improve crop yields through direct interactions with leguminous plants. S. meliloti AK21 is a wild type strain that forms nodules on Medicago plants in saline and drought conditions in the Aral Sea Region. The aim of this work was to establish the genetic similarities and differences between S. meliloti AK21 and the reference strain S. meliloti 1021. Comparative genome hybridization with the model reference strain S. meliloti 1021 yielded 365 variable genes, grouped into 11 regions in the three main replicons in S. meliloti AK21. The most extensive regions of variability were found in the symbiotic plasmid pSymA, which also contained the largest number of orthologous and polymorphic sequences identified by suppression subtractive hybridization. This procedure identified a large number of divergent sequences and others without homology in the databases, the further investigation of which could provide new insight into the alternative metabolic pathways present in S. meliloti AK21. We identified a plasmid replication module from the repABC replicon family, together with plasmid mobilization-related genes (traG and a VirB9-like protein), which suggest that this indigenous isolate harbors an accessory plasmid. Furthermore, the transcriptomic profiles reflected differences in gene content and regulation between S. meliloti AK21 and S. meliloti 1021 (ExpR and PhoB regulons), but provided evidence for an as yet unknown, alternative mechanism involving activation of the cbb3 terminal oxidase. Finally, phenotypic microarrays characterization revealed a greater versatility of substrate use and chemical degradation than for S. meliloti 1021.
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Affiliation(s)
- María Dolores Molina-Sánchez
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
| | - José Antonio López-Contreras
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Nicolás Toro
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
| | - Manuel Fernández-López
- Grupo de Ecología Genética, Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, CSIC, Calle Profesor Albareda 1, 18008 Granada, Spain
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Romo-González C, Consuelo-Sánchez A, Camorlinga-Ponce M, Velázquez-Guadarrama N, García-Zúñiga M, Burgueño-Ferreira J, Coria-Jiménez R. Plasticity Region Genes jhp0940, jhp0945, jhp0947, and jhp0949 of Helicobacter pylori in Isolates from Mexican Children. Helicobacter 2015; 20:231-7. [PMID: 25735460 DOI: 10.1111/hel.12194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND The genes jhp0940, jhp0945, jhp0947, and jhp0949 belong to the plasticity region of the Helicobacter pylori genome. Due to their prevalence in isolates from patients with gastritis, duodenal ulcer, and gastric cancer, they have been proposed as markers of gastroduodenal diseases. These genes are associated with pro-inflammatory cytokine induction through the NF-κB activation pathway. Nevertheless, the status of these genes is unknown in H. pylori isolates from children. The aim of the present work was to determine the frequency of the jhp0940-jhp0945-jhp0947-jhp0949 genes in H. pylori isolates from children. MATERIALS AND METHODS We identified the jhp0940, jhp0945, jhp0947, and jhp0949 genes and the relationship of each with the virulence factors cagA, cagPAI, and dupA by PCR in 49 isolates of H. pylori from children. The results were corroborated using dot blots. In addition, we compared the prevalence of these genes with the prevalence in adults. RESULTS The prevalence of jhp0940 (53.1%), jhp0945 (44.9%), jhp0947 (77.6%), and jhp0949 (83.7%) was determined in the isolates from children, as was the prevalence of the virulence genes cagA (63.3%), cagPAI (71.4%), and dupA (37.5%). No association was found between the four genes of the plasticity region and the virulence genes. The presence of the intact locus integrated by jhp0940-jhp0945-jhp0947-jhp0949 was very common among the isolates from children. CONCLUSION The genes jhp0940, jhp0947, and jhp0949 were present in more than 50% of the H. pylori isolates, and the joint presence of jhp0940-jhp0945-jhp0947-jhp0949 was very frequent. The frequency of these genes in isolates from children could contribute to the virulence of H. pylori and the evolution of the infection.
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Affiliation(s)
| | - Alejandra Consuelo-Sánchez
- Gastroenterology & Nutrition Department, Children's Hospital of Mexico "Federico Gómez", SSA, México, D.F., México
| | - Margarita Camorlinga-Ponce
- Infectious Diseases Research Unit, Instituto Mexicano del Seguro Social, Mexico City, Mexico, CMN Siglo XXI, IMSS, México, D.F., México
| | | | | | - Juan Burgueño-Ferreira
- International Maize and Wheat Improvement Center, Biometrics and Statistics Unit, Mexico, Mexico
| | - Rafael Coria-Jiménez
- Experimental Bacteriology, National Institute of Pediatrics, SSA, México, D.F., México
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35
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Analysis of a single Helicobacter pylori strain over a 10-year period in a primate model. Int J Med Microbiol 2015; 305:392-403. [PMID: 25804332 DOI: 10.1016/j.ijmm.2015.03.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/30/2015] [Accepted: 03/01/2015] [Indexed: 12/18/2022] Open
Abstract
Helicobacter pylori from different individuals exhibits substantial genetic diversity. However, the kinetics of bacterial diversification after infection with a single strain is poorly understood. We investigated evolution of H. pylori following long-term infection in the primate stomach; Rhesus macaques were infected with H. pylori strain USU101 and then followed for 10 years. H. pylori was regularly cultured from biopsies, and single colony isolates were analyzed. At 1-year, DNA fingerprinting showed that all output isolates were identical to the input strain; however, at 5-years, different H. pylori fingerprints were observed. Microarray-based comparative genomic hybridization revealed that long term persistence of USU101 in the macaque stomach was associated with specific whole gene changes. Further detailed investigation showed that levels of the BabA protein were dramatically reduced within weeks of infection. The molecular mechanisms behind this reduction were shown to include phase variation and gene loss via intragenomic rearrangement, suggesting strong selective pressure against BabA expression in the macaque model. Notably, although there is apparently strong selective pressure against babA, babA is required for establishment of infection in this model as a strain in which babA was deleted was unable to colonize experimentally infected macaques.
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36
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Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets. BIOMED RESEARCH INTERNATIONAL 2015; 2015:139580. [PMID: 25705648 PMCID: PMC4325212 DOI: 10.1155/2015/139580] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 12/23/2022]
Abstract
Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.
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37
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Greenblum S, Carr R, Borenstein E. Extensive strain-level copy-number variation across human gut microbiome species. Cell 2015; 160:583-594. [PMID: 25640238 DOI: 10.1016/j.cell.2014.12.038] [Citation(s) in RCA: 153] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 10/30/2014] [Accepted: 12/24/2014] [Indexed: 12/22/2022]
Abstract
Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear. Here, we present a comprehensive large-scale analysis of intra-species copy-number variation in the gut microbiome, introducing a rigorous computational pipeline for detecting such variation directly from shotgun metagenomic data. We uncover a large set of variable genes in numerous species and demonstrate that this variation has significant functional and clinically relevant implications. We additionally infer intra-species compositional profiles, identifying population structure shifts and the presence of yet uncharacterized variants. Our results highlight the complex relationship between microbiome composition and functional capacity, linking metagenome-level compositional shifts to strain-level variation.
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Affiliation(s)
- Sharon Greenblum
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Rogan Carr
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA; Santa Fe Institute, Santa Fe, NM 87501, USA.
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Yamaoka Y, Miftahussurur M. Helicobacter pylori virulence genes and host genetic polymorphisms as risk factors for peptic ulcer disease. Expert Rev Gastroenterol Hepatol 2015; 9:1535-47. [PMID: 26470920 PMCID: PMC5332543 DOI: 10.1586/17474124.2015.1095089] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Helicobacter pylori infection plays an important role in the pathogenesis of peptic ulcer disease (PUD). Several factors have been proposed as possible H. pylori virulence determinants; for example, bacterial adhesins and gastric inflammation factors are associated with an increased risk of PUD. However, differences in bacterial virulence factors alone cannot explain the opposite ends of the PUD disease spectrum, that is duodenal and gastric ulcers; presumably, both bacterial and host factors contribute to the differential response. Carriers of the high-producer alleles of the pro-inflammatory cytokines IL-1B, IL-6, IL-8, IL-10, and TNF-α who also carry low-producer allele of anti-inflammatory cytokines have severe gastric mucosal inflammation, whereas carriers of the alternative alleles have mild inflammation. Recent reports have suggested that the PSCA and CYP2C19 ultra-rapid metabolizer genotypes are also associated with PUD.
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Affiliation(s)
- Yoshio Yamaoka
- Oita University, Baylor College of Medicine Houston United States
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39
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Rhee KH, Park JS, Cho MJ. Helicobacter pylori: bacterial strategy for incipient stage and persistent colonization in human gastric niches. Yonsei Med J 2014; 55:1453-66. [PMID: 25323880 PMCID: PMC4205683 DOI: 10.3349/ymj.2014.55.6.1453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Helicobacter pylori (H. pylori) undergoes decades long colonization of the gastric mucosa of half the population in the world to produce acute and chronic gastritis at the beginning of infection, progressing to more severe disorders, including peptic ulcer disease and gastric cancer. Prolonged carriage of H. pylori is the most crucial factor for the pathogenesis of gastric maladies. Bacterial persistence in the gastric mucosa depends on bacterial factors as well as host factors. Herein, the host and bacterial components responsible for the incipient stages of H. pylori infection are reviewed and discussed. Bacterial adhesion and adaptation is presented to explain the persistence of H. pylori colonization in the gastric mucosa, in which bacterial evasion of host defense systems and genomic diversity are included.
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Affiliation(s)
- Kwang-Ho Rhee
- Department of Microbiology, Gyeongsang National University College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Jin-Sik Park
- Department of Microbiology, Gyeongsang National University College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, Korea
| | - Myung-Je Cho
- Department of Microbiology, Gyeongsang National University College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, Korea.
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40
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Kodaman N, Sobota RS, Mera R, Schneider BG, Williams SM. Disrupted human-pathogen co-evolution: a model for disease. Front Genet 2014; 5:290. [PMID: 25202324 PMCID: PMC4142859 DOI: 10.3389/fgene.2014.00290] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/05/2014] [Indexed: 02/06/2023] Open
Abstract
A major goal in infectious disease research is to identify the human and pathogenic genetic variants that explain differences in microbial pathogenesis. However, neither pathogenic strain nor human genetic variation in isolation has proven adequate to explain the heterogeneity of disease pathology. We suggest that disrupted co-evolution between a pathogen and its human host can explain variation in disease outcomes, and that genome-by-genome interactions should therefore be incorporated into genetic models of disease caused by infectious agents. Genetic epidemiological studies that fail to take both the pathogen and host into account can lead to false and misleading conclusions about disease etiology. We discuss our model in the context of three pathogens, Helicobacter pylori, Mycobacterium tuberculosis and human papillomavirus, and generalize the conditions under which it may be applicable.
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Affiliation(s)
- Nuri Kodaman
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA ; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center Nashville, TN, USA
| | - Rafal S Sobota
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA ; Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center Nashville, TN, USA
| | - Robertino Mera
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, USA
| | - Barbara G Schneider
- Division of Gastroenterology, Department of Medicine, Vanderbilt University Medical Center Nashville, TN, USA
| | - Scott M Williams
- Department of Genetics, Geisel School of Medicine, Dartmouth College Hanover, NH, USA
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Prevalence of the Helicobacter pylori babA2 gene and correlation with the degree of gastritis in infected Slovenian children. Antonie van Leeuwenhoek 2014; 106:637-45. [PMID: 25055876 DOI: 10.1007/s10482-014-0234-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 07/07/2014] [Indexed: 12/16/2022]
Abstract
The aims of our study were to determine the prevalence of the babA2 gene within Helicobacter pylori strains circulating in the Slovenian pediatric population, to further clarify its significance in causing inflammation of gastric mucosa in children and to verify whether cagA, vacA, iceA and babA genes work independently or synergistically in causing gastritis. A total of 163 H. pylori isolates obtained from the same number of children were tested for the presence of cagA, vacA and iceA genes using previously established methods, while the babA2 gene was determined using novel polymerase chain reaction assay targeting a 139-bp fragment of the central region of babA2. The babA2 gene was detected in 47.9% of H. pylori samples. The presence of the babA2 gene was strongly associated with cagA, vacA s1 and vacA m1 genotype. The babA2 status correlated positively with bacterial density score, activity of inflammation and chronic inflammation of gastric mucosa. No significant correlation was found between the babA2 status and the presence of atrophy or intestinal metaplasia. In addition, the activity of gastric inflammation and density score were significantly associated with the coexpression of the cagA, vacA s1, vacA m1 and babA2 genes. The study, which included the largest number of pediatric H. pylori samples to date, confirmed that babA2 gene plays an important role in the pathogenesis of H. pylori gastritis in children. Furthermore, our results suggest that babA2, cagA and vacA s1 and m1 gene products may work synergistically in worsening the inflammation of gastric mucosa.
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42
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Kilb N, Burger J, Roth G. Protein microarray generation by in situ protein expression from template DNA. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Normann Kilb
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
| | - Jürgen Burger
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- Laboratory for MEMS Applications, Department of Microsystems Engineering—IMTEK University of Freiburg Freiburg Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- BIOSS—Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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43
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A repetitive DNA element regulates expression of the Helicobacter pylori sialic acid binding adhesin by a rheostat-like mechanism. PLoS Pathog 2014; 10:e1004234. [PMID: 24991812 PMCID: PMC4081817 DOI: 10.1371/journal.ppat.1004234] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Accepted: 05/21/2014] [Indexed: 12/12/2022] Open
Abstract
During persistent infection, optimal expression of bacterial factors is required to match the ever-changing host environment. The gastric pathogen Helicobacter pylori has a large set of simple sequence repeats (SSR), which constitute contingency loci. Through a slipped strand mispairing mechanism, the SSRs generate heterogeneous populations that facilitate adaptation. Here, we present a model that explains, in molecular terms, how an intergenically located T-tract, via slipped strand mispairing, operates with a rheostat-like function, to fine-tune activity of the promoter that drives expression of the sialic acid binding adhesin, SabA. Using T-tract variants, in an isogenic strain background, we show that the length of the T-tract generates multiphasic output from the sabA promoter. Consequently, this alters the H. pylori binding to sialyl-Lewis x receptors on gastric mucosa. Fragment length analysis of post-infection isolated clones shows that the T-tract length is a highly variable feature in H. pylori. This mirrors the host-pathogen interplay, where the bacterium generates a set of clones from which the best-fit phenotypes are selected in the host. In silico and functional in vitro analyzes revealed that the length of the T-tract affects the local DNA structure and thereby binding of the RNA polymerase, through shifting of the axial alignment between the core promoter and UP-like elements. We identified additional genes in H. pylori, with T- or A-tracts positioned similar to that of sabA, and show that variations in the tract length likewise acted as rheostats to modulate cognate promoter output. Thus, we propose that this generally applicable mechanism, mediated by promoter-proximal SSRs, provides an alternative mechanism for transcriptional regulation in bacteria, such as H. pylori, which possesses a limited repertoire of classical trans-acting regulatory factors.
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Wang S, Hao B, Li J, Gu H, Peng J, Xie F, Zhao X, Frech C, Chen N, Ma B, Li Y. Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics. BMC Genomics 2014; 15:440. [PMID: 24906389 PMCID: PMC4072884 DOI: 10.1186/1471-2164-15-440] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
Background Evidence based on genomic sequences is urgently needed to confirm the phylogenetic relationship between Mesorhizobium strain MAFF303099 and M. huakuii. To define underlying causes for the rather striking difference in host specificity between M. huakuii strain 7653R and MAFF303099, several probable determinants also require comparison at the genomic level. An improved understanding of mobile genetic elements that can be integrated into the main chromosomes of Mesorhizobium to form genomic islands would enrich our knowledge of how genome dynamics may contribute to Mesorhizobium evolution in general. Results In this study, we sequenced the complete genome of 7653R and compared it with five other Mesorhizobium genomes. Genomes of 7653R and MAFF303099 were found to share a large set of orthologs and, most importantly, a conserved chromosomal backbone and even larger perfectly conserved synteny blocks. We also identified candidate molecular differences responsible for the different host specificities of these two strains. Finally, we reconstructed an ancestral Mesorhizobium genomic island that has evolved into diverse forms in different Mesorhizobium species. Conclusions Our ortholog and synteny analyses firmly establish MAFF303099 as a strain of M. huakuii. Differences in nodulation factors and secretion systems T3SS, T4SS, and T6SS may be responsible for the unique host specificities of 7653R and MAFF303099 strains. The plasmids of 7653R may have arisen by excision of the original genomic island from the 7653R chromosome. Electronic supplementary material The online version of this article (doi: 10.1186/1471-2164-15-440) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Nansheng Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei, P, R, China.
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Sagar V, Bergmann R, Nerlich A, McMillan DJ, Nitsche-Schmitz DP, Fulde M, Talay S, Geffers R, Hoe N, Kumar R, Rohde M, Chakraborti A, Chhatwal GS. Differences in virulence repertoire and cell invasive potential of group A Streptococcus emm1-2 in comparison to emm1 genotype. Int J Med Microbiol 2014; 304:685-95. [PMID: 24856243 DOI: 10.1016/j.ijmm.2014.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 04/24/2014] [Accepted: 04/27/2014] [Indexed: 11/26/2022] Open
Abstract
Group A streptococcus (GAS, Streptococcus pyogenes) type emm1 is widely associated with streptococcal invasive disease. This type is prevalent worldwide but is rare in India. Instead, emm1-2 type which is closely related to emm1 but is a distinct type is more prevalent. Although emm1 has been well characterized, information available on emm1-2 is rare. In this study we present a comparative study of both types. DNA microarray analysis showed segregation of emm1 and emm1-2 isolates into two distinct clusters. Out of 229 arrayed genes, 83-87% were present, 6-9% absent and 4-8% genes were ambiguous in emm1 isolates. emm1-2 strains harboured only 68-77%, 11-13% were absent and 10-20% ambiguous genes. Fourteen genes, present in all emm1, were completely absent in the emm1-2 isolates. sfb1 is a gene which encodes for Streptococcal fibronectin binding adhesin and invasin which has restricted distribution among different emm types of GAS. A variant of sfb1 (sfb1-2) was the only gene which was present in all emm1-2 isolates, but absent from all emm1 strains. Sfb1 and Sfb1-2 differ in sequences in the aromatic domain and the proline rich repeat region, whereas the fibronectin binding region was conserved and exhibited similar fibronectin binding activity. The presence of Sfb1-2 in emm1-2 strains was concomitant with significantly higher fibronectin-binding and invasion efficiency of HEp-2 cells when compared to emm1 isolates. The role of Sfb1-2 in invasion was confirmed by latex bead assay. emm1-2 isolates follow membrane ruffling mechanism during invasion and intracellularly follow classical endocytic pathway. Further studies are required to understand the correlation between the presence of emm1-2 isolates and the disease pattern in North India.
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Affiliation(s)
- Vivek Sagar
- Helmholtz Centre for Infection Research, Braunschweig, Germany; Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Rene Bergmann
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Andreas Nerlich
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - David J McMillan
- Bacterial Pathogenesis Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia and Inflammation and Healing Research Cluster, School of Health and Sport Sciences, University of the Sunshine Coast, Sippy Downs, Australia
| | | | - Marcus Fulde
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Susanne Talay
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Robert Geffers
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Nancy Hoe
- National Institute of Health, Hamilton, USA
| | - Rajesh Kumar
- Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Braunschweig, Germany
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Fernandez-Gonzalez E, Backert S. DNA transfer in the gastric pathogen Helicobacter pylori. J Gastroenterol 2014; 49:594-604. [PMID: 24515309 DOI: 10.1007/s00535-014-0938-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 01/16/2014] [Indexed: 02/08/2023]
Abstract
The gastric pathogen Helicobacter pylori is one of the most genetically diverse bacteria. Recombination and DNA transfer contribute to its genetic variability and enhance host adaptation. Among the strategies described to increase genetic diversity in bacteria, DNA transfer by conjugation is one of the best characterized. Using this mechanism, a fragment of DNA from a donor cell can be transferred to a recipient, always mediated by a conjugative nucleoprotein complex, which is evolutionarily related to type IV secretion systems (T4SSs). Interestingly, the H. pylori chromosomes can encode up to four T4SSs, including the cagPAI, comB, tfs3, and tfs4 genes, some of which are known to promote chronic H. pylori infection. The T4SS encoded by the cagPAI mediates the injection of the effector protein CagA and proinflammatory signaling, and the comB system is involved in DNA uptake from the environment. However, the role of tfs3 and tfs4 is not yet clear. The presence of a functional XerD tyrosine recombinase and 5'AAAGAATG-3' border sequences as well as two putative conjugative relaxases (Rlx1 and Rlx2), a coupling protein (TraG), and a chromosomal region carrying a putative origin of transfer (oriT) suggest the existence of a DNA transfer apparatus in tfs4. Moreover, a conjugation-like DNA transfer mechanism in H. pylori has already been described in vitro, but whether this occurs in vivo is still unknown. Some extrachromosomal plasmids and phages are also present in various H. pylori strains. Genetic exchange among plasmids and chromosomes, and involved DNA mobilization events, could explain part of H. pylori's genetic diversity. Here, we review our knowledge about the possible DNA transfer mechanisms in H. pylori and its implications in bacterial adaptation to the host environment.
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Affiliation(s)
- Esther Fernandez-Gonzalez
- Division of Microbiology, Department of Biology, Friedrich Alexander University Erlangen/Nuremberg, Staudtstr. 5, 91058, Erlangen, Germany
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Raghwan, Chowdhury R. Host cell contact induces fur-dependent expression of virulence factors CagA and VacA in Helicobacter pylori. Helicobacter 2014; 19:17-25. [PMID: 24020886 DOI: 10.1111/hel.12087] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Helicobacter pylori, a gram negative bacterium, colonizes the stomach in a majority of the world population. The two major virulence factors of H. pylori VacA and CagA, thought to be associated with chronic inflammation and disease, have been extensively studied, but the regulation of the expression of these virulence genes in H. pylori remains poorly understood. METHODS qRT-PCR was performed to quantify gene expression in unadhered and AGS-adhered H. pylori. Δfur mutant was constructed by splicing by overlap extension PCR and allelic exchange. RESULTS Adherence of H. pylori to the gastric epithelial cell line AGS strongly induces the expression of both cagA and vacA. Induction of cagA and vacA in the AGS cell-adhered H. pylori Δfur mutant strain was consistently lower than in the adhered parent strain. However, expression of the genes was similar between the wild-type and Δfur mutant strains in the unadhered state, suggesting that Fur has a role in the upregulation of cagA and vacA expression, especially in AGS-adhered H. pylori. Consistent with these results, microscopic observations revealed that infection of AGS cells with H. pylori Δfur mutant strain produced much less damage as compared to that produced by the wild-type H. pylori strain. CONCLUSIONS These results suggested that cagA and vacA gene expression is upregulated in H. pylori, especially by host cell contact, and Fur has a role in the upregulation.
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Affiliation(s)
- Raghwan
- Infectious Diseases and Immunology Division, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, India
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Belogolova E, Bauer B, Pompaiah M, Asakura H, Brinkman V, Ertl C, Bartfeld S, Nechitaylo TY, Haas R, Machuy N, Salama N, Churin Y, Meyer TF. Helicobacter pylori outer membrane protein HopQ identified as a novel T4SS-associated virulence factor. Cell Microbiol 2013; 15:1896-912. [PMID: 23782461 DOI: 10.1111/cmi.12158] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 06/11/2013] [Accepted: 06/11/2013] [Indexed: 12/13/2022]
Abstract
Helicobacter pylori is a bacterial pathogen that colonizes the gastric niche of ∼ 50% of the human population worldwide and is known to cause peptic ulceration and gastric cancer. Pathology of infection strongly depends on a cag pathogenicity island (cagPAI)-encoded type IV secretion system (T4SS). Here, we aimed to identify as yet unknown bacterial factors involved in cagPAI effector function and performed a large-scale screen of an H. pylori transposon mutant library using activation of the pro-inflammatory transcription factor NF-κB in human gastric epithelial cells as a measure of T4SS function. Analysis of ∼ 3000 H. pylori mutants revealed three non-cagPAI genes that affected NF-κB nuclear translocation. Of these, the outer membrane protein HopQ from H. pylori strain P12 was essential for CagA translocation and for CagA-mediated host cell responses such as formation of the hummingbird phenotype and cell scattering. Besides that, deletion of hopQ reduced T4SS-dependent activation of NF-κB, induction of MAPK signalling and secretion of interleukin 8 (IL-8) in the host cells, but did not affect motility or the quantity of bacteria attached to host cells. Hence, we identified HopQ as a non-cagPAI-encoded cofactor of T4SS function.
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Affiliation(s)
- Elena Belogolova
- Department of Molecular Biology, Max Planck Institute for Infection Biology, D-10117, Berlin, Germany
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Dutilh BE, Backus L, Edwards RA, Wels M, Bayjanov JR, van Hijum SAFT. Explaining microbial phenotypes on a genomic scale: GWAS for microbes. Brief Funct Genomics 2013; 12:366-80. [PMID: 23625995 PMCID: PMC3743258 DOI: 10.1093/bfgp/elt008] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
There is an increasing availability of complete or draft genome sequences for microbial organisms. These data form a potentially valuable resource for genotype-phenotype association and gene function prediction, provided that phenotypes are consistently annotated for all the sequenced strains. In this review, we address the requirements for successful gene-trait matching. We outline a basic protocol for microbial functional genomics, including genome assembly, annotation of genotypes (including single nucleotide polymorphisms, orthologous groups and prophages), data pre-processing, genotype-phenotype association, visualization and interpretation of results. The methodologies for association described herein can be applied to other data types, opening up possibilities to analyze transcriptome-phenotype associations, and correlate microbial population structure or activity, as measured by metagenomics, to environmental parameters.
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Affiliation(s)
- Bas E Dutilh
- CMBI, NCMLS, Radboud University Medical Centre. Geert Grooteplein 28, 6525 GA Nijmegen, The Netherlands.
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50
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Barrozo RM, Cooke CL, Hansen LM, Lam AM, Gaddy JA, Johnson EM, Cariaga TA, Suarez G, Peek RM, Cover TL, Solnick JV. Functional plasticity in the type IV secretion system of Helicobacter pylori. PLoS Pathog 2013; 9:e1003189. [PMID: 23468628 PMCID: PMC3585145 DOI: 10.1371/journal.ppat.1003189] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2012] [Accepted: 12/20/2012] [Indexed: 12/13/2022] Open
Abstract
Helicobacter pylori causes clinical disease primarily in those individuals infected with a strain that carries the cytotoxin associated gene pathogenicity island (cagPAI). The cagPAI encodes a type IV secretion system (T4SS) that injects the CagA oncoprotein into epithelial cells and is required for induction of the pro-inflammatory cytokine, interleukin-8 (IL-8). CagY is an essential component of the H. pylori T4SS that has an unusual sequence structure, in which an extraordinary number of direct DNA repeats is predicted to cause rearrangements that invariably yield in-frame insertions or deletions. Here we demonstrate in murine and non-human primate models that immune-driven host selection of rearrangements in CagY is sufficient to cause gain or loss of function in the H. pylori T4SS. We propose that CagY functions as a sort of molecular switch or perhaps a rheostat that alters the function of the T4SS and “tunes” the host inflammatory response so as to maximize persistent infection. Helicobacter pylori is a bacterium that colonizes the stomach of about half the world's population, most of whom are asymptomatic. However, some strains of H. pylori express a bacterial secretion system, a sort of molecular syringe that injects a bacterial protein inside the gastric cells and causes inflammation that can lead to peptic ulcer disease or gastric cancer. One of the essential components of the H. pylori secretion system is CagY, which is unusual because it contains a series of repetitive amino acid motifs that are encoded by a very large number of direct DNA repeats. Here we have shown that DNA recombination in cagY changes the protein motif structure and alters the function of the secretion system—turning it on or off. Using mouse and non-human primate models, we have demonstrated that CagY is a molecular switch that “tunes” the host inflammatory response, and likely contributes to persistent infection. Determining the mechanism by which CagY functions will enhance our understanding of the effects of H. pylori on human health, and could lead to novel applications for the modulation of host cell function.
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Affiliation(s)
- Roberto M. Barrozo
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Cara L. Cooke
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Lori M. Hansen
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Anna M. Lam
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Jennifer A. Gaddy
- Department of Medicine, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States of America
| | - Elizabeth M. Johnson
- Department of Medicine, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States of America
| | - Taryn A. Cariaga
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
| | - Giovanni Suarez
- Department of Medicine, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States of America
| | - Richard M. Peek
- Department of Medicine, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States of America
| | - Timothy L. Cover
- Department of Medicine, Vanderbilt University, School of Medicine, Nashville, Tennessee, United States of America
- Department of Microbiology and Immunology, Vanderbilt University, Nashville, Tennessee, United States of America
- Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
| | - Jay V. Solnick
- Center for Comparative Medicine, University of California Davis, Davis, California, United States of America
- Department of Medicine, University of California Davis, School of Medicine, Davis, California, United States of America
- Department of Microbiology and Immunology, University of California Davis, School of Medicine, Davis, California, United States of America
- California National Primate Research Center, University of California Davis, Davis School of Medicine, Davis, California, United States of America
- * E-mail:
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