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Wang B, Luan J, Zhao W, Yu J, Li A, Li X, Zhong X, Cao H, Wang R, Liu B, Lu S, Shi M. Comprehensive multiomics analysis of the signatures of gastric mucosal bacteria and plasma metabolites across different stomach microhabitats in the development of gastric cancer. Cell Oncol (Dordr) 2024:10.1007/s13402-024-00965-3. [PMID: 38963518 DOI: 10.1007/s13402-024-00965-3] [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] [Accepted: 05/30/2024] [Indexed: 07/05/2024] Open
Abstract
PURPOSE As an important component of the microenvironment, the gastric microbiota and its metabolites are associated with tumour occurrence, progression, and metastasis. However, the relationship between the gastric microbiota and the development of gastric cancer is unclear. The present study investigated the role of the gastric mucosa microbiome and metabolites as aetiological factors in gastric carcinogenesis. METHODS Gastric biopsies from different stomach microhabitats (n = 70) were subjected to 16S rRNA gene sequencing, and blood samples (n = 95) were subjected to untargeted metabolome (gas chromatography‒mass spectrometry, GC‒MS) analyses. The datasets were analysed using various bioinformatics approaches. RESULTS The microbiota diversity and community composition markedly changed during gastric carcinogenesis. High Helicobacter. pylori colonization modified the overall diversity and composition of the microbiota associated with gastritis and cancer in the stomach. Most importantly, analysis of the functional features of the microbiota revealed that nitrate reductase genes were significantly enriched in the tumoral microbiota, while urease-producing genes were significantly enriched in the microbiota of H. pylori-positive patients. A panel of 81 metabolites was constructed to discriminate gastric cancer patients from gastritis patients, and a panel of 15 metabolites was constructed to discriminate H. pylori-positive patients from H. pylori-negative patients. receiver operator characteristic (ROC) curve analysis identified a series of gastric microbes and plasma metabolites as potential biomarkers of gastric cancer. CONCLUSION The present study identified a series of signatures that may play important roles in gastric carcinogenesis and have the potential to be used as biomarkers for diagnosis and for the surveillance of gastric cancer patients with minimal invasiveness.
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Affiliation(s)
- Bingsen Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
| | - Jiahui Luan
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of Clinical Microbiology, Zibo City Key Laboratory of Respiratory Infection and Clinical Microbiology, Zibo City Engineering Technology Research Center of Etiology Molecular Diagnosis, Zibo Municipal Hospital, Zibo, 255400, China
| | - Weidong Zhao
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of gastroenterology, Zibo Municipal Hospital, Zibo, 255400, China
| | - Junbao Yu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
| | - Anqing Li
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of gastroenterology, Zibo Municipal Hospital, Zibo, 255400, China
| | - Xinxin Li
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of gastroenterology, Zibo Municipal Hospital, Zibo, 255400, China
| | - Xiaoqin Zhong
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of gastroenterology, Zibo Municipal Hospital, Zibo, 255400, China
| | - Hongyun Cao
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of Clinical Microbiology, Zibo City Key Laboratory of Respiratory Infection and Clinical Microbiology, Zibo City Engineering Technology Research Center of Etiology Molecular Diagnosis, Zibo Municipal Hospital, Zibo, 255400, China
| | - Ruicai Wang
- Department of Pathology, Zibo Municipal Hospital, Zibo, 255400, China
| | - Bo Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
- Department of Clinical Microbiology, Zibo City Key Laboratory of Respiratory Infection and Clinical Microbiology, Zibo City Engineering Technology Research Center of Etiology Molecular Diagnosis, Zibo Municipal Hospital, Zibo, 255400, China
- Department of Pulmonary and Critical Care Medicine, Shandong Institute of Respiratory Diseases, The First Affiliated Hospital of Shandong First Medical University, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, 250014, China
| | - Shiyong Lu
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China
| | - Mei Shi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
- Shandong University-Zibo Municipal Hospital Research Center of Human Microbiome and Health, Zibo, 255400, China.
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Ghasemifar S, Chabak O, Piri-Gharaghie T, Doosti A. PIRES2-EGFP/CTB-UreI vaccination activated a mixed Th1/Th2/Th17 immune system defense towards Helicobacter pylori infection in the BALB/c mice model. Vaccine 2024:S0264-410X(24)00209-3. [PMID: 38453620 DOI: 10.1016/j.vaccine.2024.02.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 02/01/2024] [Accepted: 02/17/2024] [Indexed: 03/09/2024]
Abstract
The occurrence of gastritis, gastric ulcers, distal gastric cancer, and gastric mucosal lymphoma in humans is strongly associated with Helicobacter pylori (H. pylori). Vaccination is an effective preventive measure due to the increasing prevalence of antibiotic resistance. Fusion vaccination is a potentially practical approach. A fusion vaccine was created in this study by combining the cholera toxin B subunit (CTB) with the antigenic H. pylori urease I subunit (CTB-UreI). The CTB-UreI DNA vaccine was chemically cloned into pIRES2-EGFP, and the success of the cloning was validated using PCR and restriction enzyme digestion. An investigation was conducted on the induction of CTB-UreI in Escherichia coli BL21(DE3). The immunogenicity and immune-protective efficacy of the vaccination were assessed in BALB/c mice. The Western blot assay successfully identified the activation of CTB-UreI. In comparison, BALB/c mice receiving pIRES2-EGFP/CTB-UreI vaccination exhibited higher IgG, IgA, IFN-γ, IL-4, and IL-17 levels in their blood samples. In addition, there was a decrease in stomach injuries and bacterial loads. Furthermore, BALB/c mice inoculated with pIRES2-EGFP/CTB-UreI showed a high level of immunity (100%) against the H. pylori challenge. The pIRES2-EGFP/CTB-UreI elicited a combination of Th1/Th2/Th17 immune responses, possibly contributing to an effective defence mechanism. Our data suggests that using this fusion vaccine to prevent H. pylori infection is a promising option.
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Affiliation(s)
- Sana Ghasemifar
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Omid Chabak
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Tohid Piri-Gharaghie
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran; Department of Biotechnology, Faculty of Basic Sciences, East-Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Abbas Doosti
- Biotechnology Research Center, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
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Chi G, Dietz L, Tang H, Snee M, Scacioc A, Wang D, Mckinley G, Mukhopadhyay SM, Pike AC, Chalk R, Burgess-Brown NA, Timmermans JP, van Putte W, Robinson CV, Dürr KL. Structural characterization of human urea transporters UT-A and UT-B and their inhibition. SCIENCE ADVANCES 2023; 9:eadg8229. [PMID: 37774028 PMCID: PMC10541013 DOI: 10.1126/sciadv.adg8229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/30/2023] [Indexed: 10/01/2023]
Abstract
In this study, we present the structures of human urea transporters UT-A and UT-B to characterize them at molecular level and to detail the mechanism of UT-B inhibition by its selective inhibitor, UTBinh-14. High-resolution structures of both transporters establish the structural basis for the inhibitor's selectivity to UT-B, and the identification of multiple binding sites for the inhibitor will aid with the development of drug lead molecules targeting both transporters. Our study also discovers phospholipids associating with the urea transporters by combining structural observations, native MS, and lipidomics analysis. These insights improve our understanding of urea transporter function at a molecular level and provide a blueprint for a structure-guided design of therapeutics targeting these transporters.
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Affiliation(s)
- Gamma Chi
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Larissa Dietz
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Haiping Tang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Matthew Snee
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Andreea Scacioc
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Dong Wang
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Gavin Mckinley
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Shubhashish M. M. Mukhopadhyay
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Ashley C. W. Pike
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Rod Chalk
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Nicola A. Burgess-Brown
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
| | - Jean-Pierre Timmermans
- Laboratory of Cell Biology and Histology (CBH) at Antwerp Centre for Advanced Microscopy (ACAM), Department of Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
| | - Wouter van Putte
- Laboratory of Cell Biology and Histology (CBH) at Antwerp Centre for Advanced Microscopy (ACAM), Department of Veterinary Sciences, University of Antwerp, Groenenborgerlaan 171, 2020 Antwerp, Belgium
- PUXANO, Ottergemsesteenweg Zuid 713, 9000 Gent, Belgium
| | - Carol V. Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
- Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford OX1 3QU, UK
| | - Katharina L. Dürr
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Nuffield Department of Medicine Research Building, Oxford OX3 7FZ, UK
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Wang C, Zhu WJ, Ding HT, Liu NH, Cao HY, Suo CL, Liu ZK, Zhang Y, Sun ML, Fu HH, Li CY, Chen XL, Zhang YZ, Wang P. Structural and molecular basis for urea recognition by Prochlorococcus. J Biol Chem 2023; 299:104958. [PMID: 37380083 PMCID: PMC10392092 DOI: 10.1016/j.jbc.2023.104958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 06/09/2023] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
Nitrogen (N) is an essential element for microbial growth and metabolism. The growth and reproduction of microorganisms in more than 75% of areas of the ocean are limited by N. Prochlorococcus is numerically the most abundant photosynthetic organism on the planet. Urea is an important and efficient N source for Prochlorococcus. However, how Prochlorococcus recognizes and absorbs urea still remains unclear. Prochlorococcus marinus MIT 9313, a typical Cyanobacteria, contains an ABC-type transporter, UrtABCDE, which may account for the transport of urea. Here, we heterologously expressed and purified UrtA, the substrate-binding protein of UrtABCDE, detected its binding affinity toward urea, and further determined the crystal structure of the UrtA/urea complex. Molecular dynamics simulations indicated that UrtA can alternate between "open" and "closed" states for urea binding. Based on structural and biochemical analyses, the molecular mechanism for urea recognition and binding was proposed. When a urea molecule is bound, UrtA undergoes a state change from open to closed surrounding the urea molecule, and the urea molecule is further stabilized by the hydrogen bonds supported by the conserved residues around it. Moreover, bioinformatics analysis showed that ABC-type urea transporters are widespread in bacteria and probably share similar urea recognition and binding mechanisms as UrtA from P. marinus MIT 9313. Our study provides a better understanding of urea absorption and utilization in marine bacteria.
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Affiliation(s)
- Chen Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Wen-Jing Zhu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Hai-Tao Ding
- Antarctic Great Wall Ecology National Observation and Research Station, Polar Research Institute of China, Shanghai, China
| | - Ning-Hua Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Hai-Yan Cao
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Chuan-Lei Suo
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Ze-Kun Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yi Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Mei-Ling Sun
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Hui-Hui Fu
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chun-Yang Li
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yu-Zhong Zhang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China; Marine Biotechnology Research Center, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Peng Wang
- MOE Key Laboratory of Evolution and Marine Biodiversity, Frontiers Science Center for Deep Ocean Multispheres and Earth System & College of Marine Life Sciences, Ocean University of China, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China.
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5
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Malfertheiner P, Camargo MC, El-Omar E, Liou JM, Peek R, Schulz C, Smith SI, Suerbaum S. Helicobacter pylori infection. Nat Rev Dis Primers 2023; 9:19. [PMID: 37081005 DOI: 10.1038/s41572-023-00431-8] [Citation(s) in RCA: 119] [Impact Index Per Article: 119.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/17/2023] [Indexed: 04/22/2023]
Abstract
Helicobacter pylori infection causes chronic gastritis, which can progress to severe gastroduodenal pathologies, including peptic ulcer, gastric cancer and gastric mucosa-associated lymphoid tissue lymphoma. H. pylori is usually transmitted in childhood and persists for life if untreated. The infection affects around half of the population in the world but prevalence varies according to location and sanitation standards. H. pylori has unique properties to colonize gastric epithelium in an acidic environment. The pathophysiology of H. pylori infection is dependent on complex bacterial virulence mechanisms and their interaction with the host immune system and environmental factors, resulting in distinct gastritis phenotypes that determine possible progression to different gastroduodenal pathologies. The causative role of H. pylori infection in gastric cancer development presents the opportunity for preventive screen-and-treat strategies. Invasive, endoscopy-based and non-invasive methods, including breath, stool and serological tests, are used in the diagnosis of H. pylori infection. Their use depends on the specific individual patient history and local availability. H. pylori treatment consists of a strong acid suppressant in various combinations with antibiotics and/or bismuth. The dramatic increase in resistance to key antibiotics used in H. pylori eradication demands antibiotic susceptibility testing, surveillance of resistance and antibiotic stewardship.
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Affiliation(s)
- Peter Malfertheiner
- Medical Department II, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany.
- Medical Department Klinik of Gastroenterology, Hepatology and Infectiology, Otto-von-Guericke Universität, Magdeburg, Germany.
| | - M Constanza Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Emad El-Omar
- Microbiome Research Centre, St George & Sutherland Clinical Campuses, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, New South Wales, Australia
| | - Jyh-Ming Liou
- Department of Internal Medicine, National Taiwan University Cancer Center, National Taiwan University Hospital, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Richard Peek
- Division of Gastroenterology, Hepatology, and Nutrition, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christian Schulz
- Medical Department II, University Hospital, Ludwig-Maximilians-Universität, Munich, Germany
- DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Munich, Germany
| | - Stella I Smith
- Department of Molecular Biology and Biotechnology, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Sebastian Suerbaum
- DZIF Deutsches Zentrum für Infektionsforschung, Partner Site Munich, Munich, Germany
- Max von Pettenkofer Institute, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
- National Reference Center for Helicobacter pylori, Munich, Germany
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Abstract
In recent years, protein structure analysis using cryo-electron microscopy(cryo-EM) has expanded and improved. In this review, we discuss many recent improvements to the field, the problems those improvements hope to solve, and some of the still unanswered questions. Most notably, this review will discuss improvements in resolving small or fragmented protein structures, as well as methods to improve the signal-to-noise ratio of the data by increasing image contrast using carbon-based systems. We will also describe how, in the last 5 years, methodological improvements have allowed for better 3D image resolution by capturing a continuum of 3D images. We will provide examples of these methods in practice and discuss how these improved methods may be used in small-molecule drug discovery and development. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Angela Cabral
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Julia Elise Cabral
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
| | - Reginald McNulty
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, California, USA
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Ghasemi A, Wang S, Sahay B, Abbott JR, Curtiss R. Protective immunity enhanced Salmonella vaccine vectors delivering Helicobacter pylori antigens reduce H. pylori stomach colonization in mice. Front Immunol 2022; 13:1034683. [DOI: 10.3389/fimmu.2022.1034683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 10/31/2022] [Indexed: 11/21/2022] Open
Abstract
Helicobacter pylori is a major cause of gastric mucosal inflammation, peptic ulcers, and gastric cancer. Emerging antimicrobial-resistant H. pylori has hampered the effective eradication of frequent chronic infections. Moreover, a safe vaccine is highly demanded due to the absence of effective vaccines against H. pylori. In this study, we employed a new innovative Protective Immunity Enhanced Salmonella Vaccine (PIESV) vector strain to deliver and express multiple H. pylori antigen genes. Immunization of mice with our vaccine delivering the HpaA, Hp-NAP, UreA and UreB antigens, provided sterile protection against H. pylori SS1 infection in 7 out of 10 tested mice. In comparison to the control groups that had received PBS or a PIESV carrying an empty vector, immunized mice exhibited specific and significant cellular recall responses and antigen-specific serum IgG1, IgG2c, total IgG and gastric IgA antibody titers. In conclusion, an improved S. Typhimurium-based live vaccine delivering four antigens shows promise as a safe and effective vaccine against H. pylori infection.
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Andrei IM, Barboiu M. Biomimetic Artificial Proton Channels. Biomolecules 2022; 12:biom12101473. [PMID: 36291682 PMCID: PMC9599858 DOI: 10.3390/biom12101473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/07/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
One of the most common biochemical processes is the proton transfer through the cell membranes, having significant physiological functions in living organisms. The proton translocation mechanism has been extensively studied; however, mechanistic details of this transport are still needed. During the last decades, the field of artificial proton channels has been in continuous growth, and understanding the phenomena of how confined water and channel components mediate proton dynamics is very important. Thus, proton transfer continues to be an active area of experimental and theoretical investigations, and acquiring insights into the proton transfer mechanism is important as this enlightenment will provide direct applications in several fields. In this review, we present an overview of the development of various artificial proton channels, focusing mostly on their design, self-assembly behavior, proton transport activity performed on bilayer membranes, and comparison with protein proton channels. In the end, we discuss their potential applications as well as future development and perspectives.
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Gössweiner-Mohr N, Siligan C, Pluhackova K, Umlandt L, Koefler S, Trajkovska N, Horner A. The Hidden Intricacies of Aquaporins: Remarkable Details in a Common Structural Scaffold. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2202056. [PMID: 35802902 DOI: 10.1002/smll.202202056] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Evolution turned aquaporins (AQPs) into the most efficient facilitators of passive water flow through cell membranes at no expense of solute discrimination. In spite of a plethora of solved AQP structures, many structural details remain hidden. Here, by combining extensive sequence- and structural-based analysis of a unique set of 20 non-redundant high-resolution structures and molecular dynamics simulations of four representatives, key aspects of AQP stability, gating, selectivity, pore geometry, and oligomerization, with a potential impact on channel functionality, are identified. The general view of AQPs possessing a continuous open water pore is challenged and it is depicted that AQPs' selectivity is not exclusively shaped by pore-lining residues but also by the relative arrangement of transmembrane helices. Moreover, this analysis reveals that hydrophobic interactions constitute the main determinant of protein thermal stability. Finally, a numbering scheme of the conserved AQP scaffold is established, facilitating direct comparison of, for example, disease-causing mutations and prediction of potential structural consequences. Additionally, the results pave the way for the design of optimized AQP water channels to be utilized in biotechnological applications.
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Affiliation(s)
| | - Christine Siligan
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Kristyna Pluhackova
- Stuttgart Center for Simulation Science, University of Stuttgart, Cluster of Excellence EXC 2075, Universitätsstr. 32, 70569, Stuttgart, Germany
| | - Linnea Umlandt
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Sabina Koefler
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Natasha Trajkovska
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
| | - Andreas Horner
- Institute of Biophysics, Johannes Kepler University Linz, Gruberstr. 40, Linz, 4020, Austria
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Kumar S, Vinella D, De Reuse H. Nickel, an essential virulence determinant of Helicobacter pylori: Transport and trafficking pathways and their targeting by bismuth. Adv Microb Physiol 2022; 80:1-33. [PMID: 35489790 DOI: 10.1016/bs.ampbs.2022.01.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. Nickel is required for the pathogenicity of H. pylori. This bacterial pathogen colonizes the stomach of about half of the human population worldwide and is associated with gastric cancer that is responsible for 800,000 deaths per year. H. pylori possesses two nickel-enzymes that are essential for in vivo colonization, a [NiFe] hydrogenase and an abundant urease responsible for resistance to gastric acidity. Because of these two enzymes, survival of H. pylori relies on an important supply of nickel, implying tight control strategies to avoid its toxic accumulation or deprivation. H. pylori possesses original mechanisms for nickel uptake, distribution, storage and trafficking that will be discussed in this review. During evolution, acquisition of nickel transporters and specific nickel-binding proteins has been a decisive event to allow Helicobacter species to become able to colonize the stomach. Accordingly, many of the factors involved in these mechanisms are required for mouse colonization by H. pylori. These mechanisms are controlled at different levels including protein interaction networks, transcriptional, post-transcriptional and post-translational regulation. Bismuth is another metal used in combination with antibiotics to efficiently treat H. pylori infections. Although the precise mode of action of bismuth is unknown, many targets have been identified in H. pylori and there is growing evidence that bismuth interferes with the essential nickel pathways. Understanding the metal pathways will help improve treatments against H. pylori and other pathogens.
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Affiliation(s)
- Sumith Kumar
- Unité Pathogenèse de Helicobacter, CNRS UMR6047, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Daniel Vinella
- Unité Pathogenèse de Helicobacter, CNRS UMR6047, Département de Microbiologie, Institut Pasteur, Paris, France
| | - Hilde De Reuse
- Unité Pathogenèse de Helicobacter, CNRS UMR6047, Département de Microbiologie, Institut Pasteur, Paris, France.
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11
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Hailemariam S, Zhao S, He Y, Wang J. Urea transport and hydrolysis in the rumen: A review. ANIMAL NUTRITION (ZHONGGUO XU MU SHOU YI XUE HUI) 2021; 7:989-996. [PMID: 34738029 PMCID: PMC8529027 DOI: 10.1016/j.aninu.2021.07.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Inefficient dietary nitrogen (N) conversion to microbial proteins, and the subsequent use by ruminants, is a major research focus across different fields. Excess bacterial ammonia (NH3) produced due to degradation or hydrolyses of N containing compounds, such as urea, leads to an inefficiency in a host's ability to utilize nitrogen. Urea is a non-protein N containing compound used by ruminants as an ammonia source, obtained from feed and endogenous sources. It is hydrolyzed by ureases from rumen bacteria to produce NH3 which is used for microbial protein synthesis. However, lack of information exists regarding urea hydrolysis in ruminal bacteria, and how urea gets to hydrolysis sites. Therefore, this review describes research on sites of urea hydrolysis, urea transport routes towards these sites, the role and structure of urea transporters in rumen epithelium and bacteria, the composition of ruminal ureolytic bacteria, mechanisms behind urea hydrolysis by bacterial ureases, and factors influencing urea hydrolysis. This review explores the current knowledge on the structure and physiological role of urea transport and ureolytic bacteria, for the regulation of urea hydrolysis and recycling in ruminants. Lastly, underlying mechanisms of urea transportation in rumen bacteria and their physiological importance are currently unknown, and therefore future research should be directed to this subject.
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Affiliation(s)
- Samson Hailemariam
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
- Dilla University, College of Agriculture and Natural Resource, Dilla P. O. Box 419, Ethiopia
| | - Shengguo Zhao
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yue He
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Jiaqi Wang
- State Key Laboratory of Animal Nutrition, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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12
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Kell DB. A protet-based, protonic charge transfer model of energy coupling in oxidative and photosynthetic phosphorylation. Adv Microb Physiol 2021; 78:1-177. [PMID: 34147184 DOI: 10.1016/bs.ampbs.2021.01.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Textbooks of biochemistry will explain that the otherwise endergonic reactions of ATP synthesis can be driven by the exergonic reactions of respiratory electron transport, and that these two half-reactions are catalyzed by protein complexes embedded in the same, closed membrane. These views are correct. The textbooks also state that, according to the chemiosmotic coupling hypothesis, a (or the) kinetically and thermodynamically competent intermediate linking the two half-reactions is the electrochemical difference of protons that is in equilibrium with that between the two bulk phases that the coupling membrane serves to separate. This gradient consists of a membrane potential term Δψ and a pH gradient term ΔpH, and is known colloquially as the protonmotive force or pmf. Artificial imposition of a pmf can drive phosphorylation, but only if the pmf exceeds some 150-170mV; to achieve in vivo rates the imposed pmf must reach 200mV. The key question then is 'does the pmf generated by electron transport exceed 200mV, or even 170mV?' The possibly surprising answer, from a great many kinds of experiment and sources of evidence, including direct measurements with microelectrodes, indicates it that it does not. Observable pH changes driven by electron transport are real, and they control various processes; however, compensating ion movements restrict the Δψ component to low values. A protet-based model, that I outline here, can account for all the necessary observations, including all of those inconsistent with chemiosmotic coupling, and provides for a variety of testable hypotheses by which it might be refined.
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Affiliation(s)
- Douglas B Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative, Biology, University of Liverpool, Liverpool, United Kingdom; The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.
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13
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Cunha ES, Chen X, Sanz-Gaitero M, Mills DJ, Luecke H. Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution. Nat Commun 2021; 12:230. [PMID: 33431861 PMCID: PMC7801526 DOI: 10.1038/s41467-020-20485-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 12/04/2020] [Indexed: 02/08/2023] Open
Abstract
Infection of the human stomach by Helicobacter pylori remains a worldwide problem and greatly contributes to peptic ulcer disease and gastric cancer. Without active intervention approximately 50% of the world population will continue to be infected with this gastric pathogen. Current eradication, called triple therapy, entails a proton-pump inhibitor and two broadband antibiotics, however resistance to either clarithromycin or metronidazole is greater than 25% and rising. Therefore, there is an urgent need for a targeted, high-specificity eradication drug. Gastric infection by H. pylori depends on the expression of a nickel-dependent urease in the cytoplasm of the bacteria. Here, we report the 2.0 Å resolution structure of the 1.1 MDa urease in complex with an inhibitor by cryo-electron microscopy and compare it to a β-mercaptoethanol-inhibited structure at 2.5 Å resolution. The structural information is of sufficient detail to aid in the development of inhibitors with high specificity and affinity.
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Affiliation(s)
- Eva S. Cunha
- grid.5510.10000 0004 1936 8921Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Xiaorui Chen
- grid.266093.80000 0001 0668 7243Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697 USA ,grid.506938.10000 0004 0633 8088Present Address: Genomics Research Center, Academia Sinica, 128 Academia Road, Sect. 2, Nankang District, Taipei, Taiwan
| | - Marta Sanz-Gaitero
- grid.5510.10000 0004 1936 8921Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318 Oslo, Norway
| | - Deryck J. Mills
- grid.419494.50000 0001 1018 9466Department of Structural Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Hartmut Luecke
- Structural Biology and Drug Discovery Group, Centre for Molecular Medicine Norway, Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, 0318, Oslo, Norway. .,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA. .,Department of Medical Biochemistry, University of Oslo and Oslo University Hospital, 0372, Oslo, Norway. .,Department of Physiology and Biophysics, University of California, Irvine, CA, 92697, USA.
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14
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Pseudo-Symmetric Assembly of Protodomains as a Common Denominator in the Evolution of Polytopic Helical Membrane Proteins. J Mol Evol 2020; 88:319-344. [PMID: 32189026 PMCID: PMC7162841 DOI: 10.1007/s00239-020-09934-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 02/16/2020] [Indexed: 11/05/2022]
Abstract
The polytopic helical membrane proteome is dominated by proteins containing seven transmembrane helices (7TMHs). They cannot be grouped under a monolithic fold or superfold. However, a parallel structural analysis of folds around that magic number of seven in distinct protein superfamilies (SWEET, PnuC, TRIC, FocA, Aquaporin, GPCRs) reveals a common homology, not in their structural fold, but in their systematic pseudo-symmetric construction during their evolution. Our analysis leads to guiding principles of intragenic duplication and pseudo-symmetric assembly of ancestral transmembrane helical protodomains, consisting of 3 (or 4) helices. A parallel deconstruction and reconstruction of these domains provides a structural and mechanistic framework for their evolutionary paths. It highlights the conformational plasticity inherent to fold formation itself, the role of structural as well as functional constraints in shaping that fold, and the usefulness of protodomains as a tool to probe convergent vs divergent evolution. In the case of FocA vs. Aquaporin, this protodomain analysis sheds new light on their potential divergent evolution at the protodomain level followed by duplication and parallel evolution of the two folds. GPCR domains, whose function does not seem to require symmetry, nevertheless exhibit structural pseudo-symmetry. Their construction follows the same protodomain assembly as any other pseudo-symmetric protein suggesting their potential evolutionary origins. Interestingly, all the 6/7/8TMH pseudo-symmetric folds in this study also assemble as oligomeric forms in the membrane, emphasizing the role of symmetry in evolution, revealing self-assembly and co-evolution not only at the protodomain level but also at the domain level.
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15
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Prinz C, Weber D. MicroRNA (miR) dysregulation during Helicobacter pylori-induced gastric inflammation and cancer development: critical importance of miR-155. Oncotarget 2020; 11:894-904. [PMID: 32206186 PMCID: PMC7075464 DOI: 10.18632/oncotarget.27520] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 02/06/2020] [Indexed: 02/03/2023] Open
Abstract
Dysregulation of noncoding microRNA molecules has been associated with immune cell activation in the context of Helicobacter pylori induced gastric inflammation as well as carcinogenesis, but also with downregulation of mismatch repair genes, and may interfere with immune checkpoint proteins that lead to the overexpression of antigens on gastric tumor cells. Numerous miR-molecules have been described as important tools and markers in gastric inflammation and cancer development -including miR-21, miR-143, miR-145, miR-201, and miR-335- all of which are downregulated in gastric tumors, and involved in cell cycle growth or tumor invasion. Among the many microRNAs involved in gastric inflammation, adenocarcinoma development and immune checkpoint regulation, miR-155 is notable in that its upregulation is considered a key marker of chronic gastric inflammation that predisposes a patient to gastric carcinogenesis. Among various other miRs, miR-155 is highly expressed in activated B and T cells and in monocytes/macrophages present in chronic gastric inflammation. Notably, miR-155 was shown to downregulate the expression of certain MMR genes, such as MLH1, MSH2, and MSH6. In tumor-infiltrating miR-155-deficient CD8+ T cells, antibodies against immune checkpoint proteins restored the expression of several derepressed miR-155 targets, suggesting that miR-155 may regulate overlapping pathways to promote antitumor immunity. It may thus be of high clinical impact that gastric pathologies mediated by miR-155 result from its overexpression. This suggests that it may be possible to therapeutically attenuate miR-155 levels for gastric cancer treatment and/or to prevent the progression of chronic gastric inflammation into cancer.
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Affiliation(s)
- Christian Prinz
- Lehrstuhl für Innere Medizin1, University of Witten gGmbH, Helios Universitätsklinikum, D-42283 Wuppertal, Germany
| | - David Weber
- Lehrstuhl für Innere Medizin1, University of Witten gGmbH, Helios Universitätsklinikum, D-42283 Wuppertal, Germany
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16
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Zhang F, Wang F, Chen C, Wang T, Hu J, Su R, Li X, Gu B, Tang S, Chen H, Li Y. Prediction of progression of chronic atrophic gastritis with Helicobacter pylori and poor prognosis of gastric cancer by CYP3A4. J Gastroenterol Hepatol 2020; 35:425-432. [PMID: 31441961 DOI: 10.1111/jgh.14844] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM It has been well documented that Helicobacter pylori (H. pylori) infection is a risk factor for aggravating gastric mucosal atrophy. However, the exact molecular mechanism mediating this process is not fully elucidated. The purpose of this study was to identify biomarkers, which may predict the risk for progression of chronic atrophic gastritis (CAG) with H. pylori. METHODS GSE27411 was downloaded from the Gene Expression Omnibus. The differentially expressed genes (DEGs) between H. pylori-infected samples without CAG and H. pylori-infected CAG samples were analyzed. Gene Ontology and pathway enrichment analyses were performed, followed by protein-protein interaction network construction. We used immunohistochemistry analysis to identify DEGs in 20 chronic gastritis, 20 CAG, and 22 gastric cancer (GC) specimens. RESULTS A total of 303 upregulated and 26 downregulated DEGs were identified. The pathways enriched by upregulated DEGs were mainly related to fat digestion and absorption, peroxisome proliferator-activated receptor signaling pathway, and chemical carcinogenesis. Cytochrome P450, family 3, subfamily A, polypeptide 4 (CYP3A4) had the highest degrees in protein-protein interaction network. Moreover, the positive rates of CYP3A4 protein expression in chronic gastritis, CAG, and GC were 10% (2/20), 55% (11/20), and 77.3% (17/22), respectively (P < 0.001). The Kaplan-Meier analysis revealed that elevated expression of CYP3A4 was significantly associated with worse overall survival and first progression, respectively (P < 0.0001). CONCLUSION According to the findings of this study, the expression of CYP3A4 might be related to the potential carcinogenic transformation of CAG to GC. Therefore, CYP3A4 may be biomarkers to predict progression of CAG and poor prognosis of gastric cancer.
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Affiliation(s)
- Fan Zhang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Furong Wang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Cong Chen
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Tianyu Wang
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Jike Hu
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Ruiliang Su
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Xuemei Li
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Baohong Gu
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Shaojun Tang
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, District of Columbia, USA.,Department of Oncology, Georgetown University Medical Center, Washington, District of Columbia, USA
| | - Hao Chen
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
| | - Yumin Li
- Lanzhou University Second Hospital, Lanzhou, Gansu, China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou, Gansu, China
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17
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Raghunathan S, Jaganade T, Priyakumar UD. Urea-aromatic interactions in biology. Biophys Rev 2020; 12:65-84. [PMID: 32067192 PMCID: PMC7040157 DOI: 10.1007/s12551-020-00620-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.
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Affiliation(s)
- Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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18
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Zhang F, Chen C, Hu J, Su R, Zhang J, Han Z, Chen H, Li Y. Molecular mechanism of Helicobacter pylori-induced autophagy in gastric cancer. Oncol Lett 2019; 18:6221-6227. [PMID: 31788098 DOI: 10.3892/ol.2019.10976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
Helicobacter pylori (H. pylori) is a gram-negative pathogen that colonizes gastric epithelial cells. The drug resistance rates of H. pylori have dramatically increased, causing persistent infections. Chronic infection by H. pylori is a critical cause of gastritis, peptic ulcers and even gastric cancer. In host cells, autophagy is stimulated to maintain cellular homeostasis following intracellular pathogen recognition by the innate immune defense system. However, H. pylori-induced autophagy is not consistent during acute and chronic infection. Therefore, a deeper understanding of the association between H. pylori infection and autophagy in gastric epithelial cells could aid the understanding of the mechanisms of persistent infection and the identification of autophagy-associated therapeutic targets for H. pylori infection. The present review describes the role of H. pylori and associated virulence factors in the induction of autophagy by different signaling pathways during acute infection. Additionally, the inhibition of autophagy in gastric epithelial cells during chronic infection was discussed. The present review summarized H. pylori-mediated autophagy and provided insights into its mechanism of action, suggesting the induction of autophagy as a novel therapeutic target for persistent H. pylori infection.
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Affiliation(s)
- Fan Zhang
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Cong Chen
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Jike Hu
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Ruiliang Su
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Junqiang Zhang
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Zhijian Han
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Hao Chen
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Yumin Li
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
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19
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Suzuki R, Satou K, Shiroma A, Shimoji M, Teruya K, Matsumoto T, Akada J, Hirano T, Yamaoka Y. Genome-wide mutation analysis of Helicobacter pylori after inoculation to Mongolian gerbils. Gut Pathog 2019; 11:45. [PMID: 31558915 PMCID: PMC6754630 DOI: 10.1186/s13099-019-0326-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 09/12/2019] [Indexed: 12/23/2022] Open
Abstract
Background Helicobacter pylori is a pathogenic bacterium that causes various gastrointestinal diseases in the human stomach. H. pylori is well adapted to the human stomach but does not easily infect other animals. As a model animal, Mongolian gerbils are often used, however, the genome of the inoculated H. pylori may accumulate mutations to adapt to the new host. To investigate mutations occurring in H. pylori after infection in Mongolian gerbils, we compared the whole genome sequence of TN2 wild type strain (TN2wt) and next generation sequencing data of retrieved strains from the animals after different lengths of infection. Results We identified mutations in 21 loci of 17 genes of the post-inoculation strains. Of the 17 genes, five were outer membrane proteins that potentially influence on the colonization and inflammation. Missense and nonsense mutations were observed in 15 and 6 loci, respectively. Multiple mutations were observed in three genes. Mutated genes included babA, tlpB, and gltS, which are known to be associated with adaptation to murine. Other mutations were involved with chemoreceptor, pH regulator, and outer membrane proteins, which also have potential to influence on the adaptation to the new host. Conclusions We confirmed mutations in genes previously reported to be associated with adaptation to Mongolian gerbils. We also listed up genes that mutated during the infection to the gerbils, though it needs experiments to prove the influence on adaptation.
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Affiliation(s)
- Rumiko Suzuki
- 1Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, Okinawa 904-2234 Japan
| | - Akino Shiroma
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, Okinawa 904-2234 Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, Okinawa 904-2234 Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, Okinawa 904-2234 Japan
| | - Takashi Matsumoto
- 1Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
| | - Junko Akada
- 1Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma, Okinawa 904-2234 Japan
| | - Yoshio Yamaoka
- 1Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan.,3Department of Medicine-Gastroenterology, Baylor College of Medicine, 2002 Holcombe Blvd., Houston, TX 77030 USA.,Global Oita Medical Advanced Research Center for Health, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593 Japan
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20
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Xiong Y, Yang Z, Zhang J, Li J, Chen P, Xiang Y. Panning using a phage-displayed random peptide library to identify peptides that antagonize the Helicobacter pylori ArsS acid-sensing domain. Microb Pathog 2019; 135:103614. [PMID: 31255726 DOI: 10.1016/j.micpath.2019.103614] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/27/2019] [Accepted: 06/26/2019] [Indexed: 01/01/2023]
Abstract
Helicobacter pylori is an important etiological factor involved in chronic gastritis, peptic ulcer, and gastric cancer. There are currently no optimal preventive or therapeutic interventions for H. pylori infection. H. pylori survives in the stomach by sensing and adapting to the highly acidic environment by using the two-component signal transduction system that contains the most widely known gastric acid receptor, ArsRS (which is composed of ArsS and ArsR). This study aimed to identify peptides that antagonize the acid-sensing domain of H. pylori ArsS. These peptides could be used to block the acid-sensing signal and thereby hinder H. pylori adaption to acidic environments to prevent its survival. Using proSite, the functional domains (including the N-terminal acid-sensing domain) of H. pylori J99 ArsS were predicted. The purified recombinant ArsS N-terminal acid-sensing protein (P-ArsS-A) was used as the target in a panning protocol in which peptides from the Ph.D.-7 Phage Display Peptide Library that could bind to P-ArsS-A were identified. As a result, eight phage clones that could specifically bind to P-ArsS-A were obtained and five amino acid sequences were identified, including P03 (MMSYPKH) and P06 (LTPMPNW). An in vitro minimum inhibitory concentration (MIC) evaluation showed that P03 and P06 significantly inhibited the growth of H. pylori J99. The MIC of P03 was 8 μM, and the MIC of P06 was >16 μM, indicating that P03 is a stronger inhibitor compared to P06. This was confirmed by colony counting on blood agar plates after P03 and P06 administration. Using homology modeling and molecular docking analysis, it was shown that P03 and P06 could bind to the ArsS N-terminal domain, and there were four shared binding sites: TYR25, ASN39, ARG73, and GLU74. Additionally, one hydrogen bond was found between P03 and ArsS, which is more cohesive than other forms of bonding (van der Waals force, other non-covalent bonds).
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Affiliation(s)
- Yuxia Xiong
- Department of Pathogenic Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Zhibang Yang
- Department of Pathogenic Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Jin Zhang
- Department of Pathogenic Biology, College of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Jinyang Li
- College of Clinical Medicine, Chongqing Medical University, Chongqing, 400016, China.
| | - Pu Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
| | - Yu Xiang
- Department of Clinical Laboratory, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China.
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21
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Cong Y, Geng J, Wang H, Su J, Arif M, Dong Q, Chi Z, Liu C. Ureido-modified carboxymethyl chitosan-graft-stearic acid polymeric nano-micelles as a targeted delivering carrier of clarithromycin for Helicobacter pylori: Preparation and in vitro evaluation. Int J Biol Macromol 2019; 129:686-692. [DOI: 10.1016/j.ijbiomac.2019.01.227] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/06/2019] [Accepted: 01/16/2019] [Indexed: 12/11/2022]
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22
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Enkavi G, Javanainen M, Kulig W, Róg T, Vattulainen I. Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance. Chem Rev 2019; 119:5607-5774. [PMID: 30859819 PMCID: PMC6727218 DOI: 10.1021/acs.chemrev.8b00538] [Citation(s) in RCA: 173] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Biological
membranes are tricky to investigate. They are complex
in terms of molecular composition and structure, functional
over a wide range of time scales, and characterized
by nonequilibrium conditions. Because of all of these
features, simulations are a great technique to study biomembrane
behavior. A significant part of the functional processes
in biological membranes takes place at the molecular
level; thus computer simulations are the method of
choice to explore how their properties emerge from specific
molecular features and how the interplay among the numerous
molecules gives rise to function over spatial and
time scales larger than the molecular ones. In this
review, we focus on this broad theme. We discuss the current
state-of-the-art of biomembrane simulations that, until
now, have largely focused on a rather narrow picture
of the complexity of the membranes. Given this, we
also discuss the challenges that we should unravel in the
foreseeable future. Numerous features such as the actin-cytoskeleton
network, the glycocalyx network, and nonequilibrium
transport under ATP-driven conditions have so far
received very little attention; however, the potential
of simulations to solve them would be exceptionally high. A
major milestone for this research would be that one day
we could say that computer simulations genuinely research
biological membranes, not just lipid bilayers.
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Affiliation(s)
- Giray Enkavi
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Matti Javanainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Flemingovo naḿesti 542/2 , 16610 Prague , Czech Republic.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Waldemar Kulig
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland
| | - Tomasz Róg
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland
| | - Ilpo Vattulainen
- Department of Physics , University of Helsinki , P.O. Box 64, FI-00014 Helsinki , Finland.,Computational Physics Laboratory , Tampere University , P.O. Box 692, FI-33014 Tampere , Finland.,MEMPHYS-Center for Biomembrane Physics
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23
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Wu M, Sun L, Zhou Q, Peng Y, Liu Z, Zhao S. Molecular Mechanism of Acetate Transport through the Acetate Channel SatP. J Chem Inf Model 2019; 59:2374-2382. [DOI: 10.1021/acs.jcim.8b00975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Meng Wu
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- University of Chinese
Academy of Sciences, No. 19A, Yuquan Road, Beijing 100049, China
| | - Liping Sun
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Qingtong Zhou
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yao Peng
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Zhijie Liu
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Suwen Zhao
- iHuman Institute, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
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24
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Cui Y, Zhou K, Strugatsky D, Wen Y, Sachs G, Zhou ZH, Munson K. pH-dependent gating mechanism of the Helicobacter pylori urea channel revealed by cryo-EM. SCIENCE ADVANCES 2019; 5:eaav8423. [PMID: 30906870 PMCID: PMC6426461 DOI: 10.1126/sciadv.aav8423] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/31/2019] [Indexed: 06/09/2023]
Abstract
The urea channel of Helicobacter pylori (HpUreI) is an ideal drug target for preventing gastric cancer but incomplete understanding of its gating mechanism has hampered development of inhibitors for the eradication of H. pylori. Here, we present the cryo-EM structures of HpUreI in closed and open conformations, both at a resolution of 2.7 Å. Our hexameric structures of this small membrane protein (~21 kDa/protomer) resolve its periplasmic loops and carboxyl terminus that close and open the channel, and define a gating mechanism that is pH dependent and requires cooperativity between protomers in the hexamer. Gating is further associated with well-resolved changes in the channel-lining residues that modify the shape and length of the urea pore. Site-specific mutations in the periplasmic domain and urea pore identified key residues important for channel function. Drugs blocking the urea pore based on our structures should lead to a new strategy for H. pylori eradication.
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Affiliation(s)
- Yanxiang Cui
- California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Kang Zhou
- California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - David Strugatsky
- Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yi Wen
- David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA
| | - George Sachs
- David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA
| | - Z. Hong Zhou
- California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA
- Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Keith Munson
- David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA
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25
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Wang G, Pang J, Hu X, Nie T, Lu X, Li X, Wang X, Lu Y, Yang X, Jiang J, Li C, Xiong YQ, You X. Daphnetin: A Novel Anti- Helicobacter pylori Agent. Int J Mol Sci 2019; 20:ijms20040850. [PMID: 30781382 PMCID: PMC6412720 DOI: 10.3390/ijms20040850] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/02/2019] [Accepted: 02/12/2019] [Indexed: 02/08/2023] Open
Abstract
Background: Antibiotic-resistant H. pylori was increasingly found in infected individuals, which resulted in treatment failure and required alternative therapeutic strategies. Daphnetin, a coumarin-derivative compound, has multiple pharmacological activities. Methods: The mechanism of daphnetin on H. pylori was investigated focusing on its effect on cell morphologies, transcription of genes related to virulence, adhesion, and cytotoxicity to human gastric epithelial (GES-1) cell line. Results: Daphnetin showed good activities against multidrug resistant (MDR) H. pylori clinical isolates, with minimal inhibitory concentration (MIC) values ranging from 25 to 100 μg/mL. In addition, daphnetin exposure resulted in H. pylori morphological changes. Moreover, daphnetin caused increased translocation of phosphatidylserine (PS), DNA damage, and recA expression, and RecA protein production vs. control group. Of great importance, daphnetin significantly decreased H. pylori adhesion to GES-1 cell line vs. control group, which may be related to the reduced expression of colonization related genes (e.g., babA and ureI). Conclusions: These results suggested that daphnetin has good activity against MDR H. pylori. The mechanism(s) of daphnetin against H. pylori were related to change of membrane structure, increase of DNA damage and PS translocation, and decrease of H. pylori attachment to GES-1 cells.
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Affiliation(s)
- Genzhu Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Jing Pang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xinxin Hu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Tongying Nie
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xi Lu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xue Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xiukun Wang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Yun Lu
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Xinyi Yang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Jiandong Jiang
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Congran Li
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
| | - Yan Q Xiong
- Los Angeles Biomedical Research Institute, Harbor-UCLA Medical Center, Torrance, CA 90502, USA.
- David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA.
| | - Xuefu You
- Beijing Key Laboratory of Antimicrobial Agents, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China.
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26
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Sun P, Li J, Zhang X, Guan Z, Xiao Q, Zhao C, Song M, Zhou Y, Mou L, Ke M, Guo L, Geng J, Deng D. Crystal structure of the bacterial acetate transporter SatP reveals that it forms a hexameric channel. J Biol Chem 2018; 293:19492-19500. [PMID: 30333234 DOI: 10.1074/jbc.ra118.003876] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 10/15/2018] [Indexed: 02/05/2023] Open
Abstract
Acetate is found ubiquitously in the natural environment and can be used as an exogenous carbon source by bacteria, fungi, and mammalian cells. A representative member of the acetate uptake transporter (AceTr) family named SatP (also yaaH) has been preliminarily identified as a succinate-acetate/proton symporter in Escherichia coli However, the molecular mechanism of acetate uptake by SatP still remains elusive. Here, we report the crystal structure of SatP from E. coli at 2.8 Å resolution, determined with a molecular replacement approach using a previously developed predicted model algorithm, which revealed a hexameric UreI-like channel structure. Structural analysis identified six transmembrane (TM) helices surrounding the central channel pore in each protomer and three conserved hydrophobic residues, FLY, located in the middle of the TM region for pore constriction. According to single-channel conductance recordings, performed with purified SatP reconstituted into lipid bilayer, three conserved polar residues in the TM1 facing to the periplasmic side are closely associated with acetate translocation activity. These analyses provide critical insights into the mechanism of acetate translocation in bacteria and a first glimpse of a structure of an AceTr family transporter.
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Affiliation(s)
- Pengcheng Sun
- the School of Life Sciences, Tsinghua University, Beijing 100084, China, and
| | - Jialu Li
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and
| | - Xialin Zhang
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and.,the Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Zeyuan Guan
- the National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingjie Xiao
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and
| | - Changjian Zhao
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and.,the Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mengxiao Song
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and.,the Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yanxia Zhou
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and
| | - Luqiu Mou
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and
| | - Meng Ke
- the School of Life Sciences, Tsinghua University, Beijing 100084, China, and
| | - Li Guo
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and
| | - Jia Geng
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and .,the Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Dong Deng
- From the Division of Obstetrics, Key Laboratory of Birth Defects and Related Disease of Women and Children of MOE, State Key Laboratory of Biotherapy, West China Second Hospital, and
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27
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Pan X, Ke H, Niu X, Li S, Lv J, Pan L. Protection Against Helicobacter pylori Infection in BALB/c Mouse Model by Oral Administration of Multivalent Epitope-Based Vaccine of Cholera Toxin B Subunit-HUUC. Front Immunol 2018; 9:1003. [PMID: 29867978 PMCID: PMC5951970 DOI: 10.3389/fimmu.2018.01003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/23/2018] [Indexed: 12/20/2022] Open
Abstract
Vaccination is an increasingly important alternative approach to control Helicobacter pylori infection, since H. pylori resistance to previously efficacious antibiotic regimens is increased, and H. pylori eradication treatment for upper gastrointestinal diseases is becoming less successful. Fortunately, an efficient oral monovalent H. pylori vaccine has been developed. However, compared with monovalent vaccines, multivalent vaccines have the potential to induce more effective and comprehensive protection against H. pylori infection. In this study, we designed and produced a multivalent epitope-based vaccine cholera toxin B subunit (CTB)-HUUC with the intramucosal adjuvant CTB and tandem copies of B-cell epitopes (HpaA132-141, UreA183-203, and UreB321-339) and T-cell epitopes (HpaA88-100, UreA27-53, UreB229-251, UreB317-329, UreB373-385, UreB438-452, UreB546-561, CagA149-164, and CagA196-217) from H. pylori adhesion A subunit (HpaA), urease A subunit (UreA), urease B subunit (UreB), and cytotoxin-associated antigen (CagA). Serum IgG, stomach, and intestine mucosal sIgA from mice after CTB-HUUC vaccination neutralized H. pylori urease activity in vitro. CTB-HUUC vaccination promoted H. pylori-specific lymphocyte responses and a mixed CD4+ T cell immune response as indicated by IFN-γ, interleukin-4, and interleukin-17 production in mice. Both oral prophylactic and therapeutic CTB-HUUC vaccinations reduced gastric urease activity and H. pylori infection and protected stomachs in mice. Taken together, CTB-HUUC is a promising potent and safe multivalent vaccine in controlling H. pylori infection in BALB/c mouse model.
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Affiliation(s)
- Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Hong Ke
- Department of Hemotology, People's Hospital, Hubei University of Medicine, Shiyan, China
| | - Xiaojuan Niu
- Department of Pharmacology, Hubei University of Medicine, Shiyan, China
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Jun Lv
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Longrui Pan
- Department of Pharmacology, Hubei University of Medicine, Shiyan, China
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28
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Qiu B, Xia B, Zhou Q, Lu Y, He M, Hasegawa K, Ma Z, Zhang F, Gu L, Mao Q, Wang F, Zhao S, Gao Z, Liao J. Succinate-acetate permease from Citrobacter koseri is an anion channel that unidirectionally translocates acetate. Cell Res 2018; 28:644-654. [PMID: 29588525 DOI: 10.1038/s41422-018-0032-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 02/08/2018] [Accepted: 03/01/2018] [Indexed: 12/13/2022] Open
Abstract
Acetate is an important metabolite in metabolism and cell signaling. Succinate-Acetate Permease (SatP) superfamily proteins are known to be responsible for acetate transport across membranes, but the nature of this transport remains unknown. Here, we show that the SatP homolog from Citrobacter koseri (SatP_Ck) is an anion channel that can unidirectionally translocate acetate at rates of the order of ~107 ions/s. Crystal structures of SatP_Ck in complex with multiple acetates at 1.8 Å reveal that the acetate pathway consists of four acetate-binding sites aligned in a single file that are interrupted by three hydrophobic constrictions. The bound acetates at the four sites are each orientated differently. The acetate at the cytoplasmic vestibule is partially dehydrated, whereas those in the main pore body are fully dehydrated. Aromatic residues within the substrate pathway may coordinate translocation of acetates via anion-π interactions. SatP_Ck reveals a new type of selective anion channel and provides a structural and functional template for understanding organic anion transport.
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Affiliation(s)
- Biao Qiu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Bingqing Xia
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Qingtong Zhou
- iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Yan Lu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Miaomiao He
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
| | - Kazuya Hasegawa
- Protein Crystal Analysis Division, Japan Synchrotron Radiation Research Institute, Hyogo, 679-5198, Japan
| | - Zhiqiang Ma
- Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, Guangzhou, Guangdong, 510640, China
| | - Fengyu Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, 250100, China
| | - Lichuan Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong, 250100, China
| | - Qionglei Mao
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.,University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Feng Wang
- Wuxi Biortus Biosciences Co., Ltd, Wuxi, Jiangsu, 214437, China
| | - Suwen Zhao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,iHuman Institute, ShanghaiTech University, Shanghai, 201210, China
| | - Zhaobing Gao
- CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
| | - Jun Liao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China.
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29
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THE CASE OF FALSE NEGATIVE RESULT OF HELIK-TEST OF PATIENT WITH CHRONIC NON - ATROPHIC GASTRITIS WITH INTRACELLULAR "DEPOT" HELICOBACTER PYLORI INFECTION. WORLD OF MEDICINE AND BIOLOGY 2018. [DOI: 10.26724/2079-8334-2018-2-64-9-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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30
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Goyal S, Chattopadhyay A, Kasavajhala K, Priyakumar UD. Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State. J Am Chem Soc 2017; 139:14931-14946. [DOI: 10.1021/jacs.7b05463] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Siddharth Goyal
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Aditya Chattopadhyay
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - Koushik Kasavajhala
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
| | - U. Deva Priyakumar
- Center for Computational
Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500 032, India
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31
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Zhang HT, Wang Z, Yu T, Sang JP, Zou XW, Zou X. Modeling of flux, binding and substitution of urea molecules in the urea transporter dvUT. J Mol Graph Model 2017; 76:504-511. [PMID: 28506671 PMCID: PMC5685562 DOI: 10.1016/j.jmgm.2017.04.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Revised: 04/19/2017] [Accepted: 04/20/2017] [Indexed: 11/28/2022]
Abstract
Urea transporters (UTs) are transmembrane proteins that transport urea molecules across cell membranes and play a crucial role in urea excretion and water balance. Modeling the functional characteristics of UTs helps us understand how their structures accomplish the functions at the atomic level, and facilitates future therapeutic design targeting the UTs. This study was based on the crystal structure of Desulfovibrio vulgaris urea transporter (dvUT). To model the binding behavior of urea molecules in dvUT, we constructed a cooperative binding model. To model the substitution of urea by the urea analogue N,N'-dimethylurea (DMU) in dvUT, we calculated the occupation probability of DMU along the urea pore and the ratio of the occupation probabilities of DMU at the external (Sext) and internal (Sint) binding sites, and we established the mutual substitution rule for binding and substitution of urea and DMU. Based on these calculations and modelings, together with the use of the Monte Carlo (MC) method, we further modeled the urea flux in dvUT, equilibrium urea binding to dvUT, and the substitution of urea by DMU in the dvUT. Our modeling results are in good agreement with the existing experimental functional data. Furthermore, the modelings have discovered the microscopic process and mechanisms of those functional characteristics. The methods and the results would help our future understanding of the underlying mechanisms of the diseases associated with impaired UT functions and rational drug design for the treatment of these diseases.
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Affiliation(s)
- Hai-Tian Zhang
- Department of Physics, Wuhan University, Wuhan 430072, China
| | - Zhe Wang
- Department of Physics, Wuhan University, Wuhan 430072, China; Department of Physics and Department of Medical Imaging, Jianghan University, Wuhan 430056, China
| | - Tao Yu
- Department of Physics, Wuhan University, Wuhan 430072, China; Department of Physics and Department of Medical Imaging, Jianghan University, Wuhan 430056, China
| | - Jian-Ping Sang
- Department of Physics, Wuhan University, Wuhan 430072, China; Department of Physics and Department of Medical Imaging, Jianghan University, Wuhan 430056, China.
| | - Xian-Wu Zou
- Department of Physics, Wuhan University, Wuhan 430072, China
| | - Xiaoqin Zou
- Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry and Informatics Institute, University of Missouri, Columbia, MO 65211, United States.
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32
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Tepeš B, Malfertheiner P, Labenz J, Aygen S. Modified Helicobacter test using a new test meal and a 13C-urea breath test in Helicobacter pylori positive and negative dyspepsia patients on proton pump inhibitors. World J Gastroenterol 2017; 23:5954-5961. [PMID: 28932087 PMCID: PMC5583580 DOI: 10.3748/wjg.v23.i32.5954] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 03/25/2017] [Accepted: 06/01/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To determine the sensitivity and specificity of the 13C-urea breath test (UBT) in patients taking proton pump inhibitors (PPIs), using a new test meal Refex.
METHODS One hundred and fourteen consecutive patients with dyspepsia, 53 Helicobacter pylori (H. pylori) positive, 49 H. pylori negative, were included in the study. The patients were then given esomeprazole 40 mg for 29 consecutive days, and the 13C-UBT with the new test meal was performed the next morning.
RESULTS The sensitivity of the 13C-UBT with a cut off 2.5‰ was 92.45% (95%CI: 81.79%-97.91%) by per-protocol (PP) analysis and 78.13% (95%CI: 66.03%-87.49%) by intention-to-treat (ITT) analysis. The specificity of the 13C-UBT test was 96.00% in the ITT population (95%CI: 86.29%-99.51%) and 97.96% in the PP population (95%CI: 89.15%-99.95%).
CONCLUSION The new test meal based 13C-UBT is highly accurate in patients on PPIs and can be used in those unable to stop their PPI treatment.
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Affiliation(s)
- Bojan Tepeš
- AM DC Rogaška, Prvomajska 29 A, 3250 Rogaška Slatina, Slovenia
| | - Peter Malfertheiner
- Universitätsklinikum Magdeburg A. ö. R Klinik für Gastroenterologie, Hepatologie und Infektiologie, 39120 Magdeburg, Germany
| | - Joachim Labenz
- Department of Internal Medicine and Gastroenterology, Diakonie Klinikum, Jung-Stilling Hospital, 57074 Siegen, Germany
| | - Sitke Aygen
- Institut für Biomedizinische Analytik und NMR-Imaging GmbH (INFAI), Gottfried-Hagen-Str. 6062, 51105 Köln, Germany
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Saidijam M, Azizpour S, Patching SG. Comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in prokaryotic, eukaryotic and viral integral membrane proteins of high-resolution structure. J Biomol Struct Dyn 2017; 36:443-464. [PMID: 28150531 DOI: 10.1080/07391102.2017.1285725] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We report a comprehensive analysis of the numbers, lengths and amino acid compositions of transmembrane helices in 235 high-resolution structures of integral membrane proteins. The properties of 1551 transmembrane helices in the structures were compared with those obtained by analysis of the same amino acid sequences using topology prediction tools. Explanations for the 81 (5.2%) missing or additional transmembrane helices in the prediction results were identified. Main reasons for missing transmembrane helices were mis-identification of N-terminal signal peptides, breaks in α-helix conformation or charged residues in the middle of transmembrane helices and transmembrane helices with unusual amino acid composition. The main reason for additional transmembrane helices was mis-identification of amphipathic helices, extramembrane helices or hairpin re-entrant loops. Transmembrane helix length had an overall median of 24 residues and an average of 24.9 ± 7.0 residues and the most common length was 23 residues. The overall content of residues in transmembrane helices as a percentage of the full proteins had a median of 56.8% and an average of 55.7 ± 16.0%. Amino acid composition was analysed for the full proteins, transmembrane helices and extramembrane regions. Individual proteins or types of proteins with transmembrane helices containing extremes in contents of individual amino acids or combinations of amino acids with similar physicochemical properties were identified and linked to structure and/or function. In addition to overall median and average values, all results were analysed for proteins originating from different types of organism (prokaryotic, eukaryotic, viral) and for subgroups of receptors, channels, transporters and others.
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Affiliation(s)
- Massoud Saidijam
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Sonia Azizpour
- a Department of Molecular Medicine and Genetics, Research Centre for Molecular Medicine, School of Medicine , Hamadan University of Medical Sciences , Hamadan , Iran
| | - Simon G Patching
- b School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology , University of Leeds , Leeds , UK
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Padhi S, Priyakumar UD. Urea-Aromatic Stacking and Concerted Urea Transport: Conserved Mechanisms in Urea Transporters Revealed by Molecular Dynamics. J Chem Theory Comput 2016; 12:5190-5200. [PMID: 27576044 DOI: 10.1021/acs.jctc.6b00602] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Urea transporters are membrane proteins that selectively allow urea molecules to pass through. It is not clear how these transporters allow rapid conduction of urea, a polar molecule, in spite of the presence of a hydrophobic constriction lined by aromatic rings. The current study elucidates the mechanism that is responsible for this rapid conduction by performing free energy calculations on the transporter dvUT with a cumulative sampling time of about 1.3 μs. A parallel arrangement of aromatic rings in the pore enables stacking of urea with these rings, which, in turn, lowers the energy barrier for urea transport. Such interaction of the rings with urea is proposed to be a conserved mechanism across all urea-conducting proteins. The free energy landscape for the permeation of multiple urea molecules reveals an interplay between interurea interaction and the solvation state of the urea molecules. This is for the first time that multiple molecule permeation through any small molecule transporter has been modeled.
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Affiliation(s)
- Siladitya Padhi
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032, India
| | - U Deva Priyakumar
- Centre for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology , Hyderabad 500032, India
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Jeon WJ, Dong HJ, Shin JH, Kim IY, Ho H, Oh SH, Yoon YM, Choi YK, Suh JG, Nam KH, Kim HC, Cho S, Seong JK. Helicobacter apodemus sp. nov., a new Helicobacter species identified from the gastrointestinal tract of striped field mice in Korea. J Vet Sci 2016; 16:475-81. [PMID: 25797297 PMCID: PMC4701740 DOI: 10.4142/jvs.2015.16.4.475] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/02/2015] [Accepted: 03/07/2015] [Indexed: 01/23/2023] Open
Abstract
A novel Helicobacter species was identified from the gastrointestinal tract of the Korean striped field mouse (Apodemus agrarius). Biochemical testing, ultrastructure characterization, and 16S rRNA gene sequence analysis suggested that this bacterium represents a distinct taxon. The bacterium was positive for urease activity, susceptible to cephalothin and nalidixic acid, and weakly positive for oxidase and catalase activity. Electron microscopy revealed that the bacterium has spirally curved rod morphology with singular bipolar nonsheathed flagella. Genotypically, the isolated bacterial strains (YMRC 000215, YMRC 000216, and YMRC 000419) were most closely related to a reference strain of Helicobacter mesocricetorum (97.25%, 97.32%, and 97.03% 16S rRNA sequence similarities, respectively). The 16S rRNA sequences of these strains were deposited into GenBank under accession numbers AF284754, AY009129, and AY009130, respectively. We propose the name Helicobacter apodemus for this novel species.
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Affiliation(s)
- Woo Jin Jeon
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program fo.,Incheon International Airport Imported Food Inspection Center, Gyeongin Regional Food and Drug Administration, Ministry of Food and Drug Safety, Incheon 22382, Korea
| | - Hee-Jin Dong
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program for Creative
| | - Jae Hoon Shin
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program fo
| | - Il Yong Kim
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program fo
| | - Hungwui Ho
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program for Creative
| | - Seung Hyun Oh
- College of Pharmacy, Gachon University, Incheon 21936, Korea
| | - Young Min Yoon
- College of Veterinary Medicine, Jeju National University, Jeju 63241, Korea
| | - Yang-Kyu Choi
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
| | - Jun Gyo Suh
- Department of Medical Genetics, College of Medicine, Hallym University, Chuncheon 24252, Korea
| | - Ki-Hoan Nam
- Biomedical Mouse Resource Center, Korea Research Institute for Bioscience and Biotechnology, Ochang 34141, Korea
| | - Hyoung-Chin Kim
- Biomedical Mouse Resource Center, Korea Research Institute for Bioscience and Biotechnology, Ochang 34141, Korea
| | - Seongbeom Cho
- Laboratory of Veterinary Public Health, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program for Creative
| | - Je Kyung Seong
- Laboratory of Developmental Biology and Genomics, College of Veterinary Medicine, BIO-MAX Institute, Program for Cancer Biology, and Interdisciplinary Program for Bioinformatics, BK21Plus Program fo
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Role of VicRKX and GlnR in pH-Dependent Regulation of the Streptococcus salivarius 57.I Urease Operon. mSphere 2016; 1:mSphere00033-16. [PMID: 27303745 PMCID: PMC4888889 DOI: 10.1128/msphere.00033-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 04/20/2016] [Indexed: 11/20/2022] Open
Abstract
Dental plaque rich in alkali-producing bacteria is less cariogenic, and thus, urease-producing Streptococcus salivarius has been considered as a therapeutic agent for dental caries control. Being one of the few ureolytic microbes in the oral cavity, S. salivarius strain 57.I promotes its competitiveness by mass-producing urease only at acidic growth pH. Here, we demonstrated that the downregulation of the transcription of the ure operon at neutral pH is controlled by a two-component system, VicRKX, whereas the upregulation at acidic pH is mediated by the global transcription regulator of nitrogen metabolism, GlnR. In the absence of VicR-mediated repression, the α subunit of RNA polymerase gains access to interact with the AT-rich sequence within the operator of VicR, leading to further activation of transcription. The overall regulation provides an advantage for S. salivarius to cope with the fluctuation of environmental pH, allowing it to persist in the mouth successfully. Ureolysis by Streptococcus salivarius is critical for pH homeostasis of dental plaque and prevention of dental caries. The expression of S. salivarius urease is induced by acidic pH and carbohydrate excess. The differential expression is mainly controlled at the transcriptional level from the promoter 5′ to ureI (pureI). Our previous study demonstrates that CodY represses pureI by binding to a CodY box 5′ to pureI, and the repression is more pronounced in cells grown at pH 7 than in cells grown at pH 5.5. Recent sequence analysis revealed a putative VicR consensus and two GlnR boxes 5′ to the CodY box. The results of DNA affinity precipitation assay, electrophoretic mobility shift assay, and chromatin immunoprecipitation-PCR analysis confirmed that both GlnR and VicR interact with the predicted binding sites in pureI. Isogenic mutant strains (vicRKX null and glnR null) and their derivatives (harboring S. salivariusvicRKX and glnR, respectively) were generated in a recombinant Streptococcus gordonii strain harboring a pureI-chloramphenicol acetyltransferase gene fusion on gtfG to investigate the regulation of VicR and GlnR. The results indicated that GlnR activates, whereas VicR represses, pureI expression. The repression by VicR is more pronounced at pH 7, whereas GlnR is more active at pH 5.5. Furthermore, the VicR box acts as an upstream element to enhance pureI expression in the absence of the cognate regulator. The overall regulation by CodY, VicR, and GlnR in response to pH ensures an optimal expression of urease in S. salivarius when the enzyme is most needed. IMPORTANCE Dental plaque rich in alkali-producing bacteria is less cariogenic, and thus, urease-producing Streptococcus salivarius has been considered as a therapeutic agent for dental caries control. Being one of the few ureolytic microbes in the oral cavity, S. salivarius strain 57.I promotes its competitiveness by mass-producing urease only at acidic growth pH. Here, we demonstrated that the downregulation of the transcription of the ure operon at neutral pH is controlled by a two-component system, VicRKX, whereas the upregulation at acidic pH is mediated by the global transcription regulator of nitrogen metabolism, GlnR. In the absence of VicR-mediated repression, the α subunit of RNA polymerase gains access to interact with the AT-rich sequence within the operator of VicR, leading to further activation of transcription. The overall regulation provides an advantage for S. salivarius to cope with the fluctuation of environmental pH, allowing it to persist in the mouth successfully.
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Kao CY, Sheu BS, Wu JJ. Helicobacter pylori infection: An overview of bacterial virulence factors and pathogenesis. Biomed J 2016; 39:14-23. [PMID: 27105595 PMCID: PMC6138426 DOI: 10.1016/j.bj.2015.06.002] [Citation(s) in RCA: 252] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 06/08/2015] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori pathogenesis and disease outcomes are mediated by a complex interplay between bacterial virulence factors, host, and environmental factors. After H. pylori enters the host stomach, four steps are critical for bacteria to establish successful colonization, persistent infection, and disease pathogenesis: (1) Survival in the acidic stomach; (2) movement toward epithelium cells by flagella-mediated motility; (3) attachment to host cells by adhesins/receptors interaction; (4) causing tissue damage by toxin release. Over the past 20 years, the understanding of H. pylori pathogenesis has been improved by studies focusing on the host and bacterial factors through epidemiology researches and molecular mechanism investigations. These include studies identifying the roles of novel virulence factors and their association with different disease outcomes, especially the bacterial adhesins, cag pathogenicity island, and vacuolating cytotoxin. Recently, the development of large-scale screening methods, including proteomic, and transcriptomic tools, has been used to determine the complex gene regulatory networks in H. pylori. In addition, a more available complete genomic database of H. pylori strains isolated from patients with different gastrointestinal diseases worldwide is helpful to characterize this bacterium. This review highlights the key findings of H. pylori virulence factors reported over the past 20 years.
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Affiliation(s)
- Cheng-Yen Kao
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bor-Shyang Sheu
- Department of Internal Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jiunn-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Biotechnology and Laboratory Science in Medicine, School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan.
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Abstract
Helicobacter pylori is a ubiquitous gastropathogen infecting more than half of the world population. It is associated with dyspepsia, gastritis, gastroduodenal ulcers, mucus-associated lymphoid tissue lymphoma and gastric carcinoma. Current recommended therapy does not eradicate infection in all treated cases and at least 20% post-treatment patients continue to suffer. Salvage therapy helps some of these nonresponders, but resistance to available antibiotics is mounting. Hence, its treatment still remains a daunting task for the practicing physician. Novel medications with improved efficacy and tolerability and with less chances of resistance are required. The present review attempts to discuss the newer patents in this field, which demonstrate a promising future role in the management of H. pylori infection and its consequent problems.
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39
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Naylor CE, Bagnéris C, DeCaen PG, Sula A, Scaglione A, Clapham DE, Wallace BA. Molecular basis of ion permeability in a voltage-gated sodium channel. EMBO J 2016; 35:820-30. [PMID: 26873592 PMCID: PMC4972137 DOI: 10.15252/embj.201593285] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/18/2016] [Indexed: 12/20/2022] Open
Abstract
Voltage‐gated sodium channels are essential for electrical signalling across cell membranes. They exhibit strong selectivities for sodium ions over other cations, enabling the finely tuned cascade of events associated with action potentials. This paper describes the ion permeability characteristics and the crystal structure of a prokaryotic sodium channel, showing for the first time the detailed locations of sodium ions in the selectivity filter of a sodium channel. Electrostatic calculations based on the structure are consistent with the relative cation permeability ratios (Na+ ≈ Li+ ≫ K+, Ca2+, Mg2+) measured for these channels. In an E178D selectivity filter mutant constructed to have altered ion selectivities, the sodium ion binding site nearest the extracellular side is missing. Unlike potassium ions in potassium channels, the sodium ions in these channels appear to be hydrated and are associated with side chains of the selectivity filter residues, rather than polypeptide backbones.
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Affiliation(s)
- Claire E Naylor
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
| | - Claire Bagnéris
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
| | - Paul G DeCaen
- Department of Cardiology, Howard Hughes Medical Institute Boston Children's Hospital, Boston, MA, USA Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Altin Sula
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
| | - Antonella Scaglione
- Department of Cardiology, Howard Hughes Medical Institute Boston Children's Hospital, Boston, MA, USA Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - David E Clapham
- Department of Cardiology, Howard Hughes Medical Institute Boston Children's Hospital, Boston, MA, USA Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck College University of London, London, UK
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40
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Abstract
Symmetry is a common feature among natural systems, including protein structures. A strong propensity toward symmetric architectures has long been recognized for water-soluble proteins, and this propensity has been rationalized from an evolutionary standpoint. Proteins residing in cellular membranes, however, have traditionally been less amenable to structural studies, and thus the prevalence and significance of symmetry in this important class of molecules is not as well understood. In the past two decades, researchers have made great strides in this area, and these advances have provided exciting insights into the range of architectures adopted by membrane proteins. These structural studies have revealed a similarly strong bias toward symmetric arrangements, which were often unexpected and which occurred despite the restrictions imposed by the membrane environment on the possible symmetry groups. Moreover, membrane proteins disproportionately contain internal structural repeats resulting from duplication and fusion of smaller segments. This article discusses the types and origins of symmetry in membrane proteins and the implications of symmetry for protein function.
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Affiliation(s)
- Lucy R Forrest
- Computational Structural Biology Group, Porter Neuroscience Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20852;
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41
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Farrugia MA, Wang B, Feig M, Hausinger RP. Mutational and Computational Evidence That a Nickel-Transfer Tunnel in UreD Is Used for Activation of Klebsiella aerogenes Urease. Biochemistry 2015; 54:6392-401. [PMID: 26401965 DOI: 10.1021/acs.biochem.5b00942] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nickel-containing urease from Klebsiella aerogenes requires four accessory proteins for proper active site metalation. The metallochaperone UreE delivers nickel to UreG, a GTPase that forms a UreD/UreF/UreG complex, which binds to urease apoprotein via UreD. Prior in silico analysis of the homologous, structurally characterized UreH/UreF/UreG complex from Helicobacter pylori identified a water tunnel originating at a likely nickel-binding motif in UreG, passing through UreF, and exiting UreH, suggestive of a role for the channel in providing the metal to urease apoprotein for its activation; however, no experimental support was reported for the significance of this tunnel. Here, specific variants were designed to disrupt a comparable 34.6 Å predicted internal tunnel, alternative channels, and surface sites for UreD. Cells producing a set of tunnel-disrupting variants of UreD exhibited greatly reduced urease specific activities, whereas other mutants had no appreciable effect on activity. Affinity pull-down studies of cell-free extracts from tunnel-disrupting mutant cultures showed no loss of UreD interactions with urease or UreF/UreG. The nickel contents of urease samples enriched from activity-deficient cultures were decreased, while zinc and iron incorporation increased. Molecular dynamics simulations revealed size restrictions in the internal channels of the UreD variants. These findings support the role of a molecular tunnel in UreD as a direct facilitator of nickel transfer into urease, illustrating a new paradigm in active site metallocenter assembly.
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Affiliation(s)
- Mark A Farrugia
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Beibei Wang
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
| | - Robert P Hausinger
- Department of Biochemistry and Molecular Biology, ‡Department of Chemistry, and §Department of Microbiology and Molecular Genetics, Michigan State University , East Lansing, Michigan 48824, United States
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Expanded metabolic versatility of ubiquitous nitrite-oxidizing bacteria from the genus Nitrospira. Proc Natl Acad Sci U S A 2015; 112:11371-6. [PMID: 26305944 DOI: 10.1073/pnas.1506533112] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrospira are a diverse group of nitrite-oxidizing bacteria and among the environmentally most widespread nitrifiers. However, they remain scarcely studied and mostly uncultured. Based on genomic and experimental data from Nitrospira moscoviensis representing the ubiquitous Nitrospira lineage II, we identified ecophysiological traits that contribute to the ecological success of Nitrospira. Unexpectedly, N. moscoviensis possesses genes coding for a urease and cleaves urea to ammonia and CO2. Ureolysis was not observed yet in nitrite oxidizers and enables N. moscoviensis to supply ammonia oxidizers lacking urease with ammonia from urea, which is fully nitrified by this consortium through reciprocal feeding. The presence of highly similar urease genes in Nitrospira lenta from activated sludge, in metagenomes from soils and freshwater habitats, and of other ureases in marine nitrite oxidizers, suggests a wide distribution of this extended interaction between ammonia and nitrite oxidizers, which enables nitrite-oxidizing bacteria to indirectly use urea as a source of energy. A soluble formate dehydrogenase lends additional ecophysiological flexibility and allows N. moscoviensis to use formate, with or without concomitant nitrite oxidation, using oxygen, nitrate, or both compounds as terminal electron acceptors. Compared with Nitrospira defluvii from lineage I, N. moscoviensis shares the Nitrospira core metabolism but shows substantial genomic dissimilarity including genes for adaptations to elevated oxygen concentrations. Reciprocal feeding and metabolic versatility, including the participation in different nitrogen cycling processes, likely are key factors for the niche partitioning, the ubiquity, and the high diversity of Nitrospira in natural and engineered ecosystems.
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Cáceres-Delpiano J, Teneb J, Mansilla R, García A, Salas-Burgos A. Variations in periplasmic loop interactions determine the pH-dependent activity of the hexameric urea transporter UreI from Helicobacter pylori: a molecular dynamics study. BMC STRUCTURAL BIOLOGY 2015; 15:11. [PMID: 26112768 PMCID: PMC4482100 DOI: 10.1186/s12900-015-0038-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Accepted: 06/15/2015] [Indexed: 11/17/2022]
Abstract
Background Helicobacter pylori is an important factor in the development of diseases such as ulcer and gastric cancer. This bacterium uses a periplasmic transporter, UreI, to deliver urea to the intracelullar space, where later it is transformed into ammonia by the cytoplasmic enzyme urease to survive the acidic condition of the human stomach. The UreI transporter presents a pH-dependent activity, where this pH-dependence remains unknown at a structural level. Althought the existance of several protonable residues in the periplasmic loops are related to the pH-dependent activity, we find interesting to have a clear view of the conformational changes involved in this phenomena through a molecular dynamic study. Results Molecular dynamic simulations of the UreI transporter at three different pH conditions were performed, revealing two main pH-dependent conformations, which we present as the open and close states. We find that salt bridges between the periplasmic loops are crucial interactions that stabilize these conformations. Besides, a cooperative behaviour exists between the six subunits of the system that is necessary to fulfill the activity of this transporter. Conclusions We found different pH-dependent conformations of the urea transporter UreI from Helicobacter pylori, which are related to salt-bridge interactions in the periplasmic regions. The behaviour of every channel in the system is not independent, given the existance of a cooperative behaviour through the formation of salt-bridges between the subunits of the hexameric system. We believe that our results will be related to the generation of new eradication therapies using this transporter as an attractive target, denoting that the knowledge of the possible pH-dependent conformations adopted for this transporter are important for the development of rational drug design approximations. Electronic supplementary material The online version of this article (doi:10.1186/s12900-015-0038-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Javier Cáceres-Delpiano
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Jaime Teneb
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Rodrigo Mansilla
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Apolinaria García
- Department of Microbiology, School of Sciences, University of Concepción, Concepción, Chile.
| | - Alexis Salas-Burgos
- Department of Pharmacology, School of Sciences, University of Concepción, Concepción, Chile.
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44
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Scaria J, Suzuki H, Ptak CP, Chen JW, Zhu Y, Guo XK, Chang YF. Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference. BMC Genomics 2015; 16:448. [PMID: 26059449 PMCID: PMC4462011 DOI: 10.1186/s12864-015-1663-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 05/29/2015] [Indexed: 01/05/2023] Open
Abstract
Background Clostridium difficile and C. sordellii are two anaerobic, spore forming, gram positive pathogens with a broad host range and the ability to cause lethal infections. Despite strong similarities between the two Clostridial strains, differences in their host tissue preference place C. difficile infections in the gastrointestinal tract and C. sordellii infections in soft tissues. Results In this study, to improve our understanding of C. sordellii and C. difficile virulence and pathogenesis, we have performed a comparative genomic and phenomic analysis of the two. The global phenomes of C. difficile and C. sordellii were compared using Biolog Phenotype microarrays. When compared to C. difficile, C. sordellii was found to better utilize more complex sources of carbon and nitrogen, including peptides. Phenotype microarray comparison also revealed that C. sordellii was better able to grow in acidic pH conditions. Using next generation sequencing technology, we determined the draft genome of C. sordellii strain 8483 and performed comparative genome analysis with C. difficile and other Clostridial genomes. Comparative genome analysis revealed the presence of several enzymes, including the urease gene cluster, specific to the C. sordellii genome that confer the ability of expanded peptide utilization and survival in acidic pH. Conclusions The identified phenotypes of C. sordellii might be important in causing wound and vaginal infections respectively. Proteins involved in the metabolic differences between C. sordellii and C. difficile should be targets for further studies aimed at understanding C. difficile and C. sordellii infection site specificity and pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1663-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joy Scaria
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA. .,Department of Veterinary and Biomedical Sciences, South Dakota State University, Brookings, SD, 57007, USA.
| | - Haruo Suzuki
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA. .,Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi, Japan.
| | - Christopher P Ptak
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Jenn-Wei Chen
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Yongzhang Zhu
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA. .,Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Xiao-Kui Guo
- Department of Medical Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Yung-Fu Chang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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45
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Wang Z, Yu T, Sang JP, Zou XW, Yan C, Zou X. Computation and simulation of the structural characteristics of the kidney urea transporter and behaviors of urea transport. J Phys Chem B 2015; 119:5124-31. [PMID: 25781365 DOI: 10.1021/jp511300u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Urea transporters are a family of membrane proteins that transport urea molecules across cell membranes and play important roles in a variety of physiological processes. Although the crystal structure of bacterial urea channel dvUT has been solved, there lacks an understanding of the dynamics of urea transport in dvUT. In this study, by using molecular dynamics simulations, Monte Carlo methods, and the adaptive biasing force approach, we built the equilibrium structure of dvUT, calculated the variation in the free energy of urea, determined the urea-binding sites of dvUT, gained insight into the microscopic process of urea transport, and studied the water permeability in dvUT including the analysis of a water chain in the pore. The strategy used in this work can be applied to studying transport behaviors of other membrane proteins.
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Affiliation(s)
- Zhe Wang
- †Department of Physics, Wuhan University, Wuhan 430072, China
| | - Tao Yu
- †Department of Physics, Wuhan University, Wuhan 430072, China
- ‡Department of Physics, Jianghan University, Wuhan 430056, China
| | - Jian-Ping Sang
- †Department of Physics, Wuhan University, Wuhan 430072, China
- ‡Department of Physics, Jianghan University, Wuhan 430056, China
| | - Xian-Wu Zou
- †Department of Physics, Wuhan University, Wuhan 430072, China
| | - Chengfei Yan
- §Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
| | - Xiaoqin Zou
- §Dalton Cardiovascular Research Center, Department of Physics and Astronomy, Department of Biochemistry, and Informatics Institute, University of Missouri, Columbia, Missouri 65211, United States
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46
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Yang J, Dai LX, Pan X, Wang H, Li B, Zhu J, Li MY, Shi XL, Wang BN. Protection against Helicobacter pylori infection in BALB/c mice by oral administration of multi-epitope vaccine of CTB-UreI-UreB. Pathog Dis 2015; 73:ftv026. [PMID: 25846576 DOI: 10.1093/femspd/ftv026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2015] [Indexed: 12/26/2022] Open
Abstract
Chronic gastric infection by the Gram-negative bacterium Helicobacter pylori (H. pylori) is strongly associated with gastritis, gastric ulcer and the development of distal gastric carcinoma and gastric mucosal lymphoma in humans. Antibiotic treatment of H. pylori is becoming less effective because of increasing antibiotic resistance; other treatment approaches such as specifically targeted methods, etc. to destroy this organism would be beneficial. An epitope vaccine is a promising option for protection against H. pylori infection. In this study, a multi-epitope vaccine was constructed by linking cholera toxin B subunit (CTB), two antigenic fragments of H. pylori urease I subunit (UreI20-29, UreI98-107) and four antigenic fragments of H. pylori urease B subunit (UreB12-23, UreB229-251, UreB327-400, UreB515-561), resulting in the recombinant CTB-UreI-UreB (BIB). Its protective effect against H. pylori infection was evaluated in BALB/c mice. Significant protection against H. pylori challenge was achieved in BALB/c mice immunized with BIB (15/18, 83.3%), rIB plus rCTB (6/18, 33.3%) and rIB (2/18, 11.1%) separately, while no protective effect was found in the mice immunized with either adjuvant rCTB alone or PBS. The induction of significant protection against H. pylori is possibly mediated by specific serum IgA and mucosal sIgA antibodies, and a mixed Th1/Th2/Th17 cells response. This multi-epitope vaccine might be a promising vaccine candidate that helps to control H. pylori infection.
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Affiliation(s)
- Jing Yang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Sichuan Vaccine Technology Co. Ltd, Chengdu, Sichuan 610041, People's Republic of China Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, People's Republic of China Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Lv-xia Dai
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Experiment Teaching Center of Clinical Medicine, Chengdu College of Medicine, Chengdu, Sichuan 610500, People's Republic of China
| | - Xing Pan
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Sichuan Vaccine Technology Co. Ltd, Chengdu, Sichuan 610041, People's Republic of China
| | - Hongren Wang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Bei Li
- Department of Infectious Disease, Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei 442000, People's Republic of China Department of Microbiology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, People's Republic of China
| | - Jie Zhu
- Sichuan Vaccine Technology Co. Ltd, Chengdu, Sichuan 610041, People's Republic of China
| | - Ming-yuan Li
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
| | - Xin-Li Shi
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China Department of Pathobiology and Immunology, Hebei University of Chinese Medicine, Shijiazhuang 050200, People's Republic of China
| | - Bao-ning Wang
- Department of Microbiology, West China School of Preclinical and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, People's Republic of China
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47
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Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends Biotechnol 2015; 33:237-46. [DOI: 10.1016/j.tibtech.2015.02.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/02/2015] [Indexed: 02/06/2023]
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48
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Wang J, Yu X, Hu B, Zheng J, Xiao W, Hao Y, Liu W, Wang D. Physicochemical evolution and molecular adaptation of the cetacean osmoregulation-related gene UT-A2 and implications for functional studies. Sci Rep 2015; 5:8795. [PMID: 25762239 PMCID: PMC4357013 DOI: 10.1038/srep08795] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 02/04/2015] [Indexed: 12/15/2022] Open
Abstract
Cetaceans have an enigmatic evolutionary history of re-invading aquatic habitats. One of their essential adaptabilities that has enabled this process is their homeostatic strategy adjustment. Here, we investigated the physicochemical evolution and molecular adaptation of the cetacean urea transporter UT-A2, which plays an important role in urine concentration and water homeostasis. First, we cloned UT-A2 from the freshwater Yangtze finless porpoise, after which bioinformatics analyses were conducted based on available datasets (including freshwater baiji and marine toothed and baleen whales) using MEGA, PAML, DataMonkey, TreeSAAP and Consurf. Our findings suggest that the UT-A2 protein shows folding similar to that of dvUT and UT-B, whereas some variations occurred in the functional So and Si regions of the selectivity filter. Additionally, several regions of the cetacean UT-A2 protein have experienced molecular adaptations. We suggest that positive-destabilizing selection could contribute to adaptations by influencing its biochemical and conformational character. The conservation of amino acid residues within the selectivity filter of the urea conduction pore is likely to be necessary for urea conduction, whereas the non-conserved amino acid replacements around the entrance and exit of the conduction pore could potentially affect the activity, which could be interesting target sites for future mutagenesis studies.
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Affiliation(s)
- Jingzhen Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - Xueying Yu
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Bo Hu
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Jinsong Zheng
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Wuhan Xiao
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Yujiang Hao
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
| | - Wenhua Liu
- Marine Biology Institute, Shantou University, Shantou, Guangdong 515063, China
| | - Ding Wang
- Key Laboratory of Aquatic Biodiversity and Conservation of the Chinese Academy of Sciences; Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei 430072, China
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49
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Lee JY, Kim N. Diagnosis of Helicobacter pylori by invasive test: histology. ANNALS OF TRANSLATIONAL MEDICINE 2015; 3:10. [PMID: 25705642 DOI: 10.3978/j.issn.2305-5839.2014.11.03] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 09/26/2014] [Indexed: 12/31/2022]
Abstract
The accurate detection of Helicobacter pylori (H. pylori), a major cause of gastric cancer, is essential for managing infected patients. Among various diagnostic methods, histology plays a pivotal role in detecting H. pylori and it also provided more information about the degree of inflammation and associated pathology, such as, atrophic gastritis (AG), intestinal metaplasia (IM), and gastric cancer. The diagnosis of H. pylori could be performed in hematoxylin and eosin (H&E) staining, however the specificity can be improved by special stains such as modified Giemsa, Warthin-Starry silver, Genta, and immunohistochemical (IHC) stains. Thus, at least two kinds of stain methods are recommended for diagnosis in practice; H&E staining is routine and Giemsa stain seems to have advantage over other stains because of its simplicity and consistency. IHC stain may be useful in special situations. However, histology has several limitations, including higher cost, longer turnaround time, dependence on the skills of the operator, and interobserver variability in assessment. Furthermore, the density of H. pylori can vary at different sites, possibly leading to sampling error, and the sensitivity of histology may decrease in patients taking proton pump inhibitor (PPI). The updated Sydney system recommend to take five biopsy specimens from different sites; however if this is not possible, the gastric body greater curvature could be a better site to detect current H. pylori infections, especially in the presence of peptic ulcer bleeding, AG and IM, or gastric cancer. In the presence of peptic ulcer bleeding, histology is also the most reliable test. PPIs can affect the result of histology and should be stopped 2 weeks before testing. Postbiopsy bleeding may be increased in patients with anticoagulation therapy, so careful precautions should be taken.
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Affiliation(s)
- Ju Yup Lee
- 1 Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea ; 2 Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Nayoung Kim
- 1 Department of Internal Medicine, Seoul National University Bundang Hospital, Seoungnam, Gyeonggi-do, Korea ; 2 Department of Internal Medicine and Liver Research Institute, Seoul National University College of Medicine, Seoul, Korea
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50
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Lv M, He B, Liu Z, Xiu P, Tu Y. Charge-signal multiplication mediated by urea wires inside Y-shaped carbon nanotubes. J Chem Phys 2014; 141:044707. [DOI: 10.1063/1.4890725] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Mei Lv
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
| | - Bing He
- School of Computer Engineering and Science, Shanghai University, Shanghai 200444, China
| | - Zengrong Liu
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
| | - Peng Xiu
- Department of Engineering Mechanics, and Soft Matter Research Center, Zhejiang University, Hangzhou 310027, China
| | - Yusong Tu
- Department of Mathematics, and Institute of Systems Biology, Shanghai University, Shanghai 200444, China
- College of Physics Science and Technology, Yangzhou University, Yangzhou 225009, China
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