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Sun X, Cao S, Mao C, Sun F, Zhang X, Song Y. Post-translational modifications of p65: state of the art. Front Cell Dev Biol 2024; 12:1417502. [PMID: 39050887 PMCID: PMC11266062 DOI: 10.3389/fcell.2024.1417502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
P65, a protein subunit of NF-κB, is a widely distributed transcription factor in eukaryotic cells and exerts diverse regulatory functions. Post-translational modifications such as phosphorylation, acetylation, methylation and ubiquitination modulate p65 transcriptional activity and function, impacting various physiological and pathological processes including inflammation, immune response, cell death, proliferation, differentiation and tumorigenesis. The intricate interplay between these modifications can be antagonistic or synergistic. Understanding p65 post-translational modifications not only elucidates NF-κB pathway regulation but also facilitates the identification of therapeutic targets and diagnostic markers for associated clinical conditions.
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Affiliation(s)
- Xutao Sun
- Department of Typhoid, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shuo Cao
- Department of Pharmacology, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Caiyun Mao
- Department of Pharmacology, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Fengqi Sun
- Department of Pathology, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xuanming Zhang
- Department of Orthopedics, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yunjia Song
- Department of Pharmacology, School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
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2
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Lehman SS, Verhoeve VI, Driscoll TP, Beckmann JF, Gillespie JJ. Metagenome diversity illuminates the origins of pathogen effectors. mBio 2024; 15:e0075923. [PMID: 38564675 PMCID: PMC11077975 DOI: 10.1128/mbio.00759-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 02/12/2024] [Indexed: 04/04/2024] Open
Abstract
Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.
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Affiliation(s)
- Stephanie S. Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, USA
| | - Victoria I. Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Timothy P. Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - John F. Beckmann
- Department of Microbiology and Immunology, University of South Alabama, Mobile, Alabama, USA
| | - Joseph J. Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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3
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Widen SA, Bes IC, Koreshova A, Pliota P, Krogull D, Burga A. Virus-like transposons cross the species barrier and drive the evolution of genetic incompatibilities. Science 2023; 380:eade0705. [PMID: 37384706 DOI: 10.1126/science.ade0705] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 05/17/2023] [Indexed: 07/01/2023]
Abstract
Horizontal gene transfer, the movement of genetic material between species, has been reported across all major eukaryotic lineages. However, the underlying mechanisms of transfer and their impact on genome evolution are still poorly understood. While studying the evolutionary origin of a selfish element in the nematode Caenorhabditis briggsae, we discovered that Mavericks, ancient virus-like transposons related to giant viruses and virophages, are one of the long-sought vectors of horizontal gene transfer. We found that Mavericks gained a novel herpesvirus-like fusogen in nematodes, leading to the widespread exchange of cargo genes between extremely divergent species, bypassing sexual and genetic barriers spanning hundreds of millions of years. Our results show how the union between viruses and transposons causes horizontal gene transfer and ultimately genetic incompatibilities in natural populations.
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Affiliation(s)
- Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Israel Campo Bes
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, A-1030 Vienna, Austria
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), 1030 Vienna, Austria
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4
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Verhoeve VI, Lehman SS, Driscoll TP, Beckmann JF, Gillespie JJ. Metagenome diversity illuminates origins of pathogen effectors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.26.530123. [PMID: 36909625 PMCID: PMC10002696 DOI: 10.1101/2023.02.26.530123] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.
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Affiliation(s)
- Victoria I Verhoeve
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Stephanie S Lehman
- Division of Molecular and Cellular Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Timothy P Driscoll
- Department of Biology, West Virginia University, Morgantown, West Virginia, USA
| | - John F Beckmann
- Microbiology and Immunology, University of South Alabama, Mobile, AL, USA
| | - Joseph J Gillespie
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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5
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Yamaguchi S, Nakashima H, Moriwaki Y, Terada T, Shimizu K. Prediction of protein mononucleotide binding sites using AlphaFold2 and machine learning. Comput Biol Chem 2022; 100:107744. [DOI: 10.1016/j.compbiolchem.2022.107744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/26/2022]
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6
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Vital JS, Tanoeiro L, Lopes-Oliveira R, Vale FF. Biomarker Characterization and Prediction of Virulence and Antibiotic Resistance from Helicobacter pylori Next Generation Sequencing Data. Biomolecules 2022; 12:691. [PMID: 35625618 PMCID: PMC9138241 DOI: 10.3390/biom12050691] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/07/2022] [Indexed: 02/06/2023] Open
Abstract
The Gram-negative bacterium Helicobacter pylori colonizes c.a. 50% of human stomachs worldwide and is the major risk factor for gastric adenocarcinoma. Its high genetic variability makes it difficult to identify biomarkers of early stages of infection that can reliably predict its outcome. Moreover, the increasing antibiotic resistance found in H. pylori defies therapy, constituting a major human health problem. Here, we review H. pylori virulence factors and genes involved in antibiotic resistance, as well as the technologies currently used for their detection. Furthermore, we show that next generation sequencing may lead to faster characterization of virulence factors and prediction of the antibiotic resistance profile, thus contributing to personalized treatment and management of H. pylori-associated infections. With this new approach, more and permanent data will be generated at a lower cost, opening the future to new applications for H. pylori biomarker identification and antibiotic resistance prediction.
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Affiliation(s)
- Joana S. Vital
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Ricardo Lopes-Oliveira
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (J.S.V.); (L.T.); (R.L.-O.)
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7
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Tegtmeyer N, Linz B, Yamaoka Y, Backert S. Unique TLR9 Activation by Helicobacter pylori Depends on the cag T4SS, But Not on VirD2 Relaxases or VirD4 Coupling Proteins. Curr Microbiol 2022; 79:121. [PMID: 35239059 PMCID: PMC8894178 DOI: 10.1007/s00284-022-02813-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 02/15/2022] [Indexed: 11/30/2022]
Abstract
The genomes of the gastric bacterial pathogen Helicobacter pylori harbor multiple type-IV secretion systems (T4SSs). Here we analyzed components of three T4SSs, the cytotoxin-associated genes (cag) T4SS, TFS3 and TFS4. The cag T4SS delivers the effector protein CagA and the LPS-metabolite ADP-heptose into gastric epithelial cells, which plays a pivotal role in chronic infection and development of gastric disease. In addition, the cag T4SS was reported to facilitate conjugative transport of chromosomal bacterial DNA into the host cell cytoplasm, where injected DNA activates intracellular toll-like receptor 9 (TLR9) and triggers anti-inflammatory signaling. Canonical DNA-delivering T4SSs in a variety of bacteria are composed of 11 VirB proteins (VirB1-11) which assemble and engage VirD2 relaxase and VirD4 coupling proteins that mediate DNA processing and guiding of the covalently bound DNA through the T4SS channel. Nevertheless, the role of the latter components in H. pylori is unclear. Here, we utilized isogenic knockout mutants of various virB (virB9 and virB10, corresponding to cagX and cagY), virD2 (rlx1 and rlx2), virD4 (cag5, traG1/2) and xerD recombinase genes in H. pylori laboratory strain P12 and studied their role in TLR9 activation by reporter assays. While inactivation of the structural cag T4SS genes cagX and cagY abolished TLR9 activation, the deletion of rlx1, rlx2, cag5, traG or xerD genes had no effect. The latter mutants activated TLR9 similar to wild-type bacteria, suggesting the presence of a unique non-canonical T4SS-dependent mechanism of TLR9 stimulation by H. pylori that is not mediated by VirD2, VirD4 and XerD proteins. These findings were confirmed by the analysis of TLR9 activation by H. pylori strains of worldwide origin that possess different sets of T4SS genes. The exact mechanism of TLR9 activation should be explored in future studies.
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Affiliation(s)
- Nicole Tegtmeyer
- Department of Biology, Chair of Microbiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Bodo Linz
- Department of Biology, Chair of Microbiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Steffen Backert
- Department of Biology, Chair of Microbiology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudtstr. 5, 91058, Erlangen, Germany.
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8
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Overview of protein phosphorylation in bacteria with a main focus on unusual protein kinases in Bacillus subtilis. Res Microbiol 2021; 172:103871. [PMID: 34500011 DOI: 10.1016/j.resmic.2021.103871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/12/2021] [Accepted: 07/22/2021] [Indexed: 12/21/2022]
Abstract
Protein phosphorylation is a post-translational modification that affects protein activity through the addition of a phosphate moiety by protein kinases or phosphotransferases. It occurs in all life forms. In addition to Hanks kinases found also in eukaryotes, bacteria encode membrane histidine kinases that, with their cognate response regulator, constitute two-component systems and phosphotransferases that phosphorylate proteins involved in sugar utilization on histidine and cysteine residues. In addition, they encode BY-kinases and arginine kinases that phosphorylate protein specifically on tyrosine and arginine residues respectively. They also possess unusual bacterial protein kinases illustrated here by examples from Bacillus subtilis.
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9
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Song X, He Y, Liu M, Yang Y, Yuan Y, Yan J, Zhang M, Huang J, Zhang S, Mo F. Mechanism underlying Polygonum capitatum effect on Helicobacter pylori-associated gastritis based on network pharmacology. Bioorg Chem 2021; 114:105044. [PMID: 34157554 DOI: 10.1016/j.bioorg.2021.105044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 05/24/2021] [Accepted: 05/28/2021] [Indexed: 02/07/2023]
Abstract
Helicobacter pylori (H. pylori) infection is a common disease that can cause H. pylori-associated gastritis (HAG), peptic ulcers, and gastric cancer. As a traditional Chinese medicine, Polygonum capitatum (PC) manifests its unique advantages in the prevention and treatment of complex diseases and chronic diseases, due to its ability to clear heat, detoxify and relieve pain, promote blood circulation, and remove blood stasis. In order to explore the molecular mechanism of PC for HAG, the study collected the predicted targets of active compounds, conducted functional analysis by the STRING database, collected HAG differential expression genes, and conducted KEGG enrichment analysis on the intersection of predicted targets and differential expression genes of gastritis by Cluego. The results show that PC works mainly by affecting phosphorylation of IκBα, NF-κB p65, p38MAPK, and ERK1/2 and nuclear transposition of NF-κB p65 and p-p38MAPK, which has been proved by in vivo and in vitro experiments. These results suggest that PC may act on HAG with multiple targets and pathways, and play a key role in the process of HAG treatment.
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Affiliation(s)
- Xiaohan Song
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Yun He
- Department of Clinical Laboratory, Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Street, Yunyan District, Guiyang 550004, China
| | - Min Liu
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Ye Yang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Yan Yuan
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Jiaoyan Yan
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Mengwei Zhang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China
| | - Jian Huang
- Department of Clinical Laboratory, Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Street, Yunyan District, Guiyang 550004, China
| | - Shu Zhang
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China; Department of Clinical Laboratory, Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Street, Yunyan District, Guiyang 550004, China.
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, No. 9 Beijing Road, Yunyan District, Guiyang 550004, China; Department of Clinical Laboratory, Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Street, Yunyan District, Guiyang 550004, China.
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10
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Millán C, Keegan RM, Pereira J, Sammito MD, Simpkin AJ, McCoy AJ, Lupas AN, Hartmann MD, Rigden DJ, Read RJ. Assessing the utility of CASP14 models for molecular replacement. Proteins 2021; 89:1752-1769. [PMID: 34387010 PMCID: PMC8881082 DOI: 10.1002/prot.26214] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/20/2021] [Accepted: 07/27/2021] [Indexed: 11/21/2022]
Abstract
The assessment of CASP models for utility in molecular replacement is a measure of their use in a valuable real‐world application. In CASP7, the metric for molecular replacement assessment involved full likelihood‐based molecular replacement searches; however, this restricted the assessable targets to crystal structures with only one copy of the target in the asymmetric unit, and to those where the search found the correct pose. In CASP10, full molecular replacement searches were replaced by likelihood‐based rigid‐body refinement of models superimposed on the target using the LGA algorithm, with the metric being the refined log‐likelihood‐gain (LLG) score. This enabled multi‐copy targets and very poor models to be evaluated, but a significant further issue remained: the requirement of diffraction data for assessment. We introduce here the relative‐expected‐LLG (reLLG), which is independent of diffraction data. This reLLG is also independent of any crystal form, and can be calculated regardless of the source of the target, be it X‐ray, NMR or cryo‐EM. We calibrate the reLLG against the LLG for targets in CASP14, showing that it is a robust measure of both model and group ranking. Like the LLG, the reLLG shows that accurate coordinate error estimates add substantial value to predicted models. We find that refinement by CASP groups can often convert an inadequate initial model into a successful MR search model. Consistent with findings from others, we show that the AlphaFold2 models are sufficiently good, and reliably so, to surpass other current model generation strategies for attempting molecular replacement phasing.
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Affiliation(s)
- Claudia Millán
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Ronan M Keegan
- Scientific Computing Dept., Science and Technologies Facilities Council, UK Research and Innovation, Didcot, Oxfordshire, United Kingdom
| | - Joana Pereira
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Massimo D Sammito
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Adam J Simpkin
- Institute of Systems, Molecular and Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7BE, United Kingdom
| | - Airlie J McCoy
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
| | - Andrei N Lupas
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Marcus D Hartmann
- Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, Germany
| | - Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7BE, United Kingdom
| | - Randy J Read
- Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Cambridge, United Kingdom
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11
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Evodiamine Inhibits Helicobacter pylori Growth and Helicobacter pylori-Induced Inflammation. Int J Mol Sci 2021; 22:ijms22073385. [PMID: 33806161 PMCID: PMC8036659 DOI: 10.3390/ijms22073385] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
Helicobacter pylori (H. pylori) classified as a class I carcinogen by the World Health Organization (WHO) plays an important role in the progression of chronic gastritis and the development of gastric cancer. A major bioactive component of Evodia rutaecarpa, evodiamine, has been known for its anti-bacterial effect and anti-cancer effects. However, the inhibitory effect of evodiamine against H. pylori is not yet known and the inhibitory mechanisms of evodiamine against gastric cancer cells are yet to be elucidated concretely. In this study, therefore, anti-bacterial effect of evodiamine on H. pylori growth and its inhibitory mechanisms as well as anti-inflammatory effects and its mechanisms of evodiamine on H. pylori-induced inflammation were investigated in vitr. Results of this study showed the growth of the H. pylori reference strains and clinical isolates were inhibited by evodiamine. It was considered one of the inhibitory mechanisms that evodiamine downregulated both gene expressions of replication and transcription machineries of H. pylori. Treatment of evodiamine also induced downregulation of urease and diminished translocation of cytotoxin-associated antigen A (CagA) and vacuolating cytotoxin A (VacA) proteins into gastric adenocarcinoma (AGS) cells. This may be resulted from the reduction of CagA and VacA expressions as well as the type IV secretion system (T4SS) components and secretion system subunit protein A (SecA) protein which are involved in translocation of CagA and VacA into host cells, respectively. In particular, evodiamine inhibited the activation of signaling proteins such as the nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB) and the mitogen-activated protein kinase (MAPK) pathway induced by H. pylori infection. It consequently might contribute to reduction of interleukin (IL)-8 production in AGS cells. Collectively, these results suggest anti-bacterial and anti-inflammatory effects of evodiamine against H. pylori.
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12
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Shang W, Wang Y, Liang X, Li T, Shao W, Liu F, Cui X, Wang Y, Lv L, Chai L, Qu L, Zheng L, Jia J. SETDB1 promotes gastric carcinogenesis and metastasis via upregulation of CCND1 and MMP9 expression. J Pathol 2021; 253:148-159. [PMID: 33044755 DOI: 10.1002/path.5568] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 09/20/2020] [Accepted: 10/07/2020] [Indexed: 12/19/2022]
Abstract
SETDB1 is a histone lysine methyltransferase that has critical roles in cancers. However, its potential role in gastric cancer (GC) remains obscure. Here, we mainly investigate the clinical significance and the possible role of SETDB1 in GC. We find that SETDB1 expression is upregulated in GC tissues and its high-level expression was a predictor of poor prognosis in patients. Overexpression of SETDB1 promoted cell proliferation and metastasis, while SETDB1 suppression had an opposite effect both in vitro and in vivo. Mechanistically, SETDB1 was shown to interact with ERG to promote the transcription of cyclin D1 (CCND1) and matrix metalloproteinase 9 (MMP9) through binding to their promoter regions. In addition, the expression of SETDB1 was also enhanced by the transcription factor TCF4 at the transcriptional level in GC. Furthermore, SETDB1 expression was found to be induced by Helicobacter pylori (H. pylori) infection in a TCF4-dependent manner. Taken together, our results indicate that SETDB1 is aberrantly overexpressed in GC and plays key roles in gastric carcinogenesis and metastasis via upregulation of CCND1 and MMP9. Our work also suggests that SETDB1 could be a potential oncogenic factor and a therapeutic target for GC. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Wenjing Shang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Yue Wang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Xiuming Liang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Shandong University-Karolinska Institute Collaborative Laboratory for Cancer Research, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Tongyu Li
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Wei Shao
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Fen Liu
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Xiujie Cui
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Yuanyuan Wang
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lin Lv
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Li Chai
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lingxin Qu
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Lixin Zheng
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
| | - Jihui Jia
- Department of Microbiology/Key Laboratory for Experimental Teratology of the Chinese Ministry of Education, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Key Laboratory of Infection and Immunity of Shandong Province, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
- Shandong University-Karolinska Institute Collaborative Laboratory for Cancer Research, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, PR China
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13
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Fischer W, Tegtmeyer N, Stingl K, Backert S. Four Chromosomal Type IV Secretion Systems in Helicobacter pylori: Composition, Structure and Function. Front Microbiol 2020; 11:1592. [PMID: 32754140 PMCID: PMC7366825 DOI: 10.3389/fmicb.2020.01592] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/18/2020] [Indexed: 12/14/2022] Open
Abstract
The pathogenic bacterium Helicobacter pylori is genetically highly diverse and a major risk factor for the development of peptic ulcer disease and gastric adenocarcinoma in humans. During evolution, H. pylori has acquired multiple type IV secretion systems (T4SSs), and then adapted for various purposes. These T4SSs represent remarkable molecular transporter machines, often associated with an extracellular pilus structure present in many bacteria, which are commonly composed of multiple structural proteins spanning the inner and outer membranes. By definition, these T4SSs exhibit central functions mediated through the contact-dependent conjugative transfer of mobile DNA elements, the contact-independent release and uptake of DNA into and from the extracellular environment as well as the secretion of effector proteins in mammalian host target cells. In recent years, numerous features on the molecular functionality of these T4SSs were disclosed. H. pylori encodes up to four T4SSs on its chromosome, namely the Cag T4SS present in the cag pathogenicity island (cagPAI), the ComB system, as well as the Tfs3 and Tfs4 T4SSs, some of which exhibit unique T4SS functions. The Cag T4SS facilitates the delivery of the CagA effector protein and pro-inflammatory signal transduction through translocated ADP-heptose and chromosomal DNA, while various structural pilus proteins can target host cell receptors such as integrins or TLR5. The ComB apparatus mediates the import of free DNA from the extracellular milieu, whereas Tfs3 may accomplish the secretion or translocation of effector protein CtkA. Both Tfs3 and Tfs4 are furthermore presumed to act as conjugative DNA transfer machineries due to the presence of tyrosine recombinases with cognate recognition sequences, conjugational relaxases, and potential origins of transfer (oriT) found within the tfs3 and tfs4 genome islands. In addition, some extrachromosomal plasmids, transposons and phages have been discovered in multiple H. pylori isolates. The genetic exchange mediated by DNA mobilization events of chromosomal genes and plasmids combined with recombination events could account for much of the genetic diversity found in H. pylori. In this review, we highlight our current knowledge on the four T4SSs and the involved mechanisms with consequences for H. pylori adaptation to the hostile environment in the human stomach.
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Affiliation(s)
- Wolfgang Fischer
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Medizinische Fakultät, LMU München, Munich, Germany
| | - Nicole Tegtmeyer
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Kerstin Stingl
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Steffen Backert
- Department Biologie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
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14
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Bleriot I, Trastoy R, Blasco L, Fernández-Cuenca F, Ambroa A, Fernández-García L, Pacios O, Perez-Nadales E, Torre-Cisneros J, Oteo-Iglesias J, Navarro F, Miró E, Pascual A, Bou G, Martínez-Martínez L, Tomas M. Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae. Microb Genom 2020; 6:e000369. [PMID: 32375972 PMCID: PMC7371120 DOI: 10.1099/mgen.0.000369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is the clinically most important species within the genus Klebsiella and, as a result of the continuous emergence of multi-drug resistant (MDR) strains, the cause of severe nosocomial infections. The decline in the effectiveness of antibiotic treatments for infections caused by MDR bacteria has generated particular interest in the study of bacteriophages. In this study, we characterized a total of 40 temperate bacteriophages (prophages) with a genome range of 11.454-84.199 kb, predicted from 16 carbapenemase-producing clinical strains of K. pneumoniae belonging to different sequence types, previously identified by multilocus sequence typing. These prophages were grouped into the three families in the order Caudovirales (27 prophages belonging to the family Myoviridae, 10 prophages belonging to the family Siphoviridae and 3 prophages belonging to the family Podoviridae). Genomic comparison of the 40 prophage genomes led to the identification of four prophages isolated from different strains and of genome sizes of around 33.3, 36.1, 39.6 and 42.6 kb. These prophages showed sequence similarities (query cover >90 %, identity >99.9 %) with international Microbe Versus Phage (MVP) (http://mvp.medgenius.info/home) clusters 4762, 4901, 3499 and 4280, respectively. Phylogenetic analysis revealed the evolutionary proximity among the members of the four groups of the most frequently identified prophages in the bacterial genomes studied (33.3, 36.1, 39.6 and 42.6 kb), with bootstrap values of 100 %. This allowed the prophages to be classified into three clusters: A, B and C. Interestingly, these temperate bacteriophages did not infect the highest number of strains as indicated by a host-range assay, these results could be explained by the development of superinfection exclusion mechanisms. In addition, bioinformatic analysis of the 40 identified prophages revealed the presence of 2363 proteins. In total, 59.7 % of the proteins identified had a predicted function, mainly involving viral structure, transcription, replication and regulation (lysogenic/lysis). Interestingly, some proteins had putative functions associated with bacterial virulence (toxin expression and efflux pump regulators), phage defence profiles such as toxin-antitoxin modules, an anti-CRISPR/Cas9 protein, TerB protein (from terZABCDE operon) and methyltransferase proteins.
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Affiliation(s)
- Ines Bleriot
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Rocío Trastoy
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Lucia Blasco
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Felipe Fernández-Cuenca
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Antón Ambroa
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Laura Fernández-García
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Olga Pacios
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Elena Perez-Nadales
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Julian Torre-Cisneros
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Jesús Oteo-Iglesias
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Ferran Navarro
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Elisenda Miró
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Alvaro Pascual
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - German Bou
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Luis Martínez-Martínez
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Maria Tomas
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
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15
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Excision and transfer of an integrating and conjugative element in a bacterial species with high recombination efficiency. Sci Rep 2019; 9:8915. [PMID: 31222169 PMCID: PMC6586827 DOI: 10.1038/s41598-019-45429-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 06/04/2019] [Indexed: 12/15/2022] Open
Abstract
Horizontal transfer of mobile genetic elements, such as integrating and conjugative elements (ICEs), plays an important role in generating diversity and maintaining comprehensive pan-genomes in bacterial populations. The human gastric pathogen Helicobacter pylori, which is known for its extreme genetic diversity, possesses highly efficient transformation and recombination systems to achieve this diversity, but it is unclear to what extent these systems influence ICE physiology. In this study, we have examined the excision/integration and horizontal transfer characteristics of an ICE (termed ICEHptfs4) in these bacteria. We show that transfer of ICEHptfs4 DNA during mating between donor and recipient strains is independent of its conjugation genes, and that homologous recombination is much more efficient than site-specific integration into the recipient chromosome. Nevertheless, ICEHptfs4 excision by site-specific recombination occurs permanently in a subpopulation of cells and involves relocation of a circularization-dependent promoter. Selection experiments for excision indicate that the circular form of ICEHptfs4 is not replicative, but readily reintegrates by site-specific recombination. Thus, although ICEHptfs4 harbours all essential transfer genes, and typical ICE functions such as site-specific integration are active in H. pylori, canonical ICE transfer is subordinate to the more efficient general DNA uptake and homologous recombination machineries in these bacteria.
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16
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Li N, Wang J, Yu W, Dong K, You F, Si B, Tang B, Zhang Y, Wang T, Qiao B. MicroRNA‑146a inhibits the inflammatory responses induced by interleukin‑17A during the infection of Helicobacter pylori. Mol Med Rep 2018; 19:1388-1395. [PMID: 30535468 DOI: 10.3892/mmr.2018.9725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 11/14/2018] [Indexed: 11/05/2022] Open
Abstract
Helicobacter pylori (H. pylori) infection is the major cause of chronic active gastritis and peptic ulcer disease. Upregulation of IL‑17A is associated with H. pylori infection in the gastric mucosa; however, the factors involved in the regulation of interleukin (IL)‑17A‑induced inflammatory responses in H. pylori‑associated gastritis remain unknown. MicroRNAs (miRNAs) serve as key post‑transcriptional regulators of gene expression and are associated with the H. pylori infection. The present study aimed to analyze the effects of IL‑17A on the expression of miR‑146a upon infection with H. pylori, as well as to identify the possible impact of miR‑146a dysregulation on the inflammatory response in vivo and in vitro. Reverse transcription‑quantitative polymerase chain reaction analysis was used to determine the expression levels of miR‑146a in gastric epithelial cells upon IL‑17A stimulation. The effects of miR‑146a mimics on IL‑17A‑induced inflammatory responses in SGC‑7901 cells were evaluated. The effects of miR‑146a mimics on the expression levels of IL‑1 receptor‑associated kinase 1 (IRAK1) and tumor necrosis factor receptor‑associated factor 6 (TRAF6) upon IL‑17A treatment were analyzed, and the IL‑17A‑stimulated inflammation following the silencing of IRAK1 and TRAF6 was observed. In addition, the correlation between miR‑146a and IL‑17A in human gastric mucosa with H. pylori was examined. The results indicated that IL‑17A‑induced miR‑146a may regulate the inflammatory response during the infection of H. pylori in a nuclear factor‑κB‑dependent manner. Furthermore, the expression of miR‑146a and IL‑17A are positively correlated in human gastric mucosa infected with H. pylori. These data suggested that miR‑146a may serve as a biomarker or therapeutic target in gastritis therapy.
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Affiliation(s)
- Na Li
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Jianlong Wang
- Department of Pediatrics, The First People's Hospital of Jining, Jining, Shandong 272000, P.R. China
| | - Wenqian Yu
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Kai Dong
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Feng You
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Biao Si
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Bin Tang
- Department of Clinical Microbiology and Immunology, Southwest Hospital and College of Medical Laboratory Science, The Third Military Medical University, Chongqing, Sichuan 400038, P.R. China
| | - Yan Zhang
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Tongjian Wang
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
| | - Bin Qiao
- Institute of Cardiovascular Disease, The 960th Hospital of Chinese PLA, Jinan, Shandong 250022, P.R. China
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17
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Induction of TNF, CXCL8 and IL-1β in macrophages by Helicobacter pylori secreted protein HP1173 occurs via MAP-kinases, NF-κB and AP-1 signaling pathways. Microb Pathog 2018; 125:295-305. [DOI: 10.1016/j.micpath.2018.09.037] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/06/2018] [Accepted: 09/24/2018] [Indexed: 02/07/2023]
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18
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A modified pectic polysaccharide from turmeric (Curcuma longa) with antiulcer effects via anti–secretary, mucoprotective and IL–10 mediated anti–inflammatory mechanisms. Int J Biol Macromol 2018; 118:864-880. [DOI: 10.1016/j.ijbiomac.2018.06.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 06/03/2018] [Accepted: 06/11/2018] [Indexed: 12/15/2022]
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19
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Yuan XY, Wang Y, Wang MY. The type IV secretion system in Helicobacter pylori. Future Microbiol 2018; 13:1041-1054. [PMID: 29927340 DOI: 10.2217/fmb-2018-0038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori (H. pylori) has an essential role in the pathogenesis of gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma and gastric cancer. The severity of the host inflammatory responses against the bacteria have been straightly associated with a special bacterial virulence factor, the cag pathogenicity island, which is a type IV secretion system (T4SS) to deliver CagA into the host cells. Besides cag-T4SS, the chromosomes of H. pylori can encode another three T4SSs, including comB, tfs3 and tfs4. In this review, we systematically reviewed the four T4SSs of H. pylori and explored their roles in the pathogenesis of gastroduodenal diseases. The information summarized in this review might provide valuable insights into the pathogenic mechanism for H. pylori.
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Affiliation(s)
- Xiao-Yan Yuan
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Ying Wang
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Ming-Yi Wang
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
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20
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Delahay RM, Croxall NJ, Stephens AD. Phylogeographic diversity and mosaicism of the Helicobacter pylori tfs integrative and conjugative elements. Mob DNA 2018; 9:5. [PMID: 29416569 PMCID: PMC5785829 DOI: 10.1186/s13100-018-0109-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/15/2018] [Indexed: 12/12/2022] Open
Abstract
Background The genome of the gastric pathogen Helicobacter pylori is characterised by considerable variation of both gene sequence and content, much of which is contained within three large genomic islands comprising the cag pathogenicity island (cagPAI) and two mobile integrative and conjugative elements (ICEs) termed tfs3 and tfs4. All three islands are implicated as virulence factors, although whereas the cagPAI is well characterised, understanding of how the tfs elements influence H. pylori interactions with different human hosts is significantly confounded by limited definition of their distribution, diversity and structural representation in the global H. pylori population. Results To gain a global perspective of tfs ICE population dynamics we established a bioinformatics workflow to extract and precisely define the full tfs pan-gene content contained within a global collection of 221 draft and complete H. pylori genome sequences. Complete (ca. 35-55kbp) and remnant tfs ICE clusters were reconstructed from a dataset comprising > 12,000 genes, from which orthologous gene complements and distinct alleles descriptive of different tfs ICE types were defined and classified in comparative analyses. The genetic variation within defined ICE modular segments was subsequently used to provide a complete description of tfs ICE diversity and a comprehensive assessment of their phylogeographic context. Our further examination of the apparent ICE modular types identified an ancient and complex history of ICE residence, mobility and interaction within particular H. pylori phylogeographic lineages and further, provided evidence of both contemporary inter-lineage and inter-species ICE transfer and displacement. Conclusions Our collective results establish a clear view of tfs ICE diversity and phylogeographic representation in the global H. pylori population, and provide a robust contextual framework for elucidating the functional role of the tfs ICEs particularly as it relates to the risk of gastric disease associated with different tfs ICE genotypes. Electronic supplementary material The online version of this article (10.1186/s13100-018-0109-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robin M Delahay
- 1Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Nicola J Croxall
- 1Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK
| | - Amberley D Stephens
- 1Nottingham Digestive Diseases Centre and National Institute for Health Research (NIHR) Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, UK.,2Present Address: Chemical Engineering and Biotechnology, University of Cambridge, Philippa Fawcette Drive, West Cambridge, Cambridge, CB3 0AS UK
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21
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Nishizuka SS, Tamura G, Nakatochi M, Fukushima N, Ohmori Y, Sumida C, Iwaya T, Takahashi T, Koeda K. Helicobacter pylori infection is associated with favorable outcome in advanced gastric cancer patients treated with S-1 adjuvant chemotherapy. J Surg Oncol 2018; 117:947-956. [PMID: 29355977 DOI: 10.1002/jso.24977] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND AND OBJECTIVES Limited information exists regarding beneficial effects of Helicobacter pylori. To examine the effect in advanced gastric cancer, we compared survival for patients treated with surgery-only or adjuvant chemotherapy on the basis of H. pylori infection status. METHODS A cohort of 491 patients who underwent R0 resection for locally advanced gastric cancer between 2000 and 2009 at 12 institutions in northern Japan was included. H. pylori infection status, was assessed from paraffin-embedded formalin-fixed samples. Overall survival (OS) and disease-free survival (DFS) in surgery-only (Surgery) and adjuvant chemotherapy (S-1) groups were analyzed. A propensity score matching was employed to correct for confounding factors by indication. RESULTS H. pylori infection was positive in 175 patients and negative in 316 patients. H. pylori-positive patients showed significantly better survival than H. pylori-negative patients in both OS (hazard ratio [HR] 0.593, 95% confidence interval [CI] 0.417-0.843; P = 0.003]) and DFS (HR 0.679, 95%CI 0.492-0.937; P = 0.018). Propensity score matching further confirmed that S-1 was virtually only effective when tumors were H. pylori-positive. CONCLUSIONS The favorable outcome of H. pylori-positive patients implies that the host immune system is modulated by H. pylori enhancing the chemotherapeutic efficacy.
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Affiliation(s)
- Satoshi S Nishizuka
- Molecular Therapeutics Laboratory, Iwate Medical University School of Medicine, Morioka, Japan.,Department of Surgery, Iwate Medical University School of Medicine, Morioka, Japan.,Division of Biomedical Research & Development, Institute of Biomedical Sciences, Iwate Medical University, Morioka, Japan.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia
| | - Gen Tamura
- Department of Laboratory Medicine, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Masahiro Nakatochi
- Statistical Analysis Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Norimasa Fukushima
- Department of Surgery, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Yukimi Ohmori
- Molecular Therapeutics Laboratory, Iwate Medical University School of Medicine, Morioka, Japan
| | - Chihiro Sumida
- Molecular Therapeutics Laboratory, Iwate Medical University School of Medicine, Morioka, Japan
| | - Takeshi Iwaya
- Molecular Therapeutics Laboratory, Iwate Medical University School of Medicine, Morioka, Japan.,Department of Surgery, Iwate Medical University School of Medicine, Morioka, Japan
| | - Takashi Takahashi
- Division of Molecular Carcinogenesis, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Koeda
- Department of Surgery, Iwate Medical University School of Medicine, Morioka, Japan
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22
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Alandiyjany MN, Croxall NJ, Grove JI, Delahay RM. A role for the tfs3 ICE-encoded type IV secretion system in pro-inflammatory signalling by the Helicobacter pylori Ser/Thr kinase, CtkA. PLoS One 2017; 12:e0182144. [PMID: 28759055 PMCID: PMC5536186 DOI: 10.1371/journal.pone.0182144] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/12/2017] [Indexed: 12/12/2022] Open
Abstract
Two distinct type IV secretion systems (T4SSs) can be identified in certain Helicobacter pylori strains, encoded on mobile genetic elements termed tfs3 and tfs4. Although their function remains unknown, both have been implicated in clinical outcomes of H. pylori infection. Here we provide evidence that the Tfs3 T4SS is required for activity of the pro-inflammatory Ser/Thr kinase protein, CtkA, in a gastric epithelial cell infection model. Previously, purified recombinant CtkA protein has been shown to upregulate NF-kappaB signalling and induce TNF-alpha and IL-8 cytokine secretion from cultured macrophages suggesting that it may potentiate the H. pylori-mediated inflammatory response. In this study, we show that CtkA expressed from its native host, H. pylori has a similar capacity for stimulation of a pro-inflammatory response from gastric epithelial cells. CtkA interaction was found to be dependent upon a complement of tfs3 T4SS genes, but independent of the T4SSs encoded by either tfs4 or the cag pathogenicity island. Moreover, the availability of CtkA for host cell interaction was shown to be conditional upon the carboxyl-terminus of CtkA, encoding a putative conserved secretion signal common to other variably encoded Tfs3 proteins. Collectively, our observations indicate a role for the Tfs3 T4SS in CtkA-mediated pro-inflammatory signalling by H. pylori and identify CtkA as a likely Tfs3 T4SS secretion substrate.
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Affiliation(s)
- Maher N. Alandiyjany
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Nicola J. Croxall
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Jane I. Grove
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
| | - Robin M. Delahay
- NIHR Nottingham Digestive Diseases Biomedical Research Unit, Nottingham University Hospitals NHS Trust and University of Nottingham, Nottingham, United Kingdom
- * E-mail:
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Kaplan-Türköz B. A putative Toll/interleukin-1 receptor domain protein fromHelicobacter pyloriis dimeric in solution and interacts with human Toll-like receptor adaptor myeloid differentiation primary response 88. Microbiol Immunol 2017; 61:85-91. [DOI: 10.1111/1348-0421.12469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/03/2017] [Accepted: 02/10/2017] [Indexed: 12/26/2022]
Affiliation(s)
- Burcu Kaplan-Türköz
- Department of Food Engineering; Faculty of Engineering; Ege University; 35100, Bornova İzmir Turkey
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Modulation of membrane phosphoinositide dynamics by the phosphatidylinositide 4-kinase activity of the Legionella LepB effector. Nat Microbiol 2016; 2:16236. [PMID: 27941800 DOI: 10.1038/nmicrobiol.2016.236] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 10/07/2016] [Indexed: 11/08/2022]
Abstract
Legionella pneumophila, the causative bacterium for Legionnaires' disease, hijacks host membrane trafficking for the maturation of the Legionella-containing vacuole (LCV). The LCV membrane mainly contains PtdIns4P, which is important for anchoring many secreted Legionella effectors onto the LCV. Here, we identify a cryptic functional domain (LepB_NTD) preceding the well-characterized RabGAP domain in the Legionella Dot/Icm type IV secretion system effector LepB. LepB_NTD alone is toxic to yeast and can disrupt the Golgi in mammalian cells. The crystal structure reveals an unexpected kinase fold and catalytic motif important for LepB_NTD function in eukaryotes. Cell biology-guided biochemical analyses uncovered a lipid kinase activity in LepB_NTD that specifically converts PtdIns3P into PtdIns(3,4)P2. PtdIns(3,4)P2 is efficiently hydrolysed into PtdIns4P by another Dot/Icm effector SidF that is known to possess phosphoinositide phosphatase activity. Consistently, SidF is capable of counteracting the cellular functions of LepB_NTD. Genetic analyses show a requirement for LepB kinase activity as well as lipid phosphatase activity of SidF for PtdIns4P biosynthesis on the LCV membrane. Our study identifies an unprecedented phosphatidylinositide 4-kinase activity from bacteria and highlights a sophisticated manipulation of host phosphoinositide metabolism by a bacterial pathogen.
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Phosphorylation of spore coat proteins by a family of atypical protein kinases. Proc Natl Acad Sci U S A 2016; 113:E3482-91. [PMID: 27185916 DOI: 10.1073/pnas.1605917113] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The modification of proteins by phosphorylation occurs in all life forms and is catalyzed by a large superfamily of enzymes known as protein kinases. We recently discovered a family of secretory pathway kinases that phosphorylate extracellular proteins. One member, family with sequence similarity 20C (Fam20C), is the physiological Golgi casein kinase. While examining distantly related protein sequences, we observed low levels of identity between the spore coat protein H (CotH), and the Fam20C-related secretory pathway kinases. CotH is a component of the spore in many bacterial and eukaryotic species, and is required for efficient germination of spores in Bacillus subtilis; however, the mechanism by which CotH affects germination is unclear. Here, we show that CotH is a protein kinase. The crystal structure of CotH reveals an atypical protein kinase-like fold with a unique mode of ATP binding. Examination of the genes neighboring cotH in B. subtilis led us to identify two spore coat proteins, CotB and CotG, as CotH substrates. Furthermore, we show that CotH-dependent phosphorylation of CotB and CotG is required for the efficient germination of B. subtilis spores. Collectively, our results define a family of atypical protein kinases and reveal an unexpected role for protein phosphorylation in spore biology.
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Ganguly M, Sarkar S, Ghosh P, Sarkar A, Alam J, Karmakar BC, De R, Saha DR, Mukhopadhyay AK. Helicobacter pylori plasticity region genes are associated with the gastroduodenal diseases manifestation in India. Gut Pathog 2016; 8:10. [PMID: 27006705 PMCID: PMC4802902 DOI: 10.1186/s13099-016-0093-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 03/02/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Almost all Helicobacter pylori infected person develop gastritis and severe gastritis is supposed to be the denominator of peptic ulcer diseases, which may lead to gastric cancer. However, it is still an enigma why few strains are associated with ulcer formation, while others are not related with any disease outcome. Although a number of putative virulence factors have been reported for H. pylori, there are contradictory results regarding their connotation with diseases. Recently, there has been a significant attention in strain-specific genes outside the cag pathogenicity island, especially genes within plasticity regions. Studies demonstrated that certain genes in this region may play important roles in the pathogenesis of H. pylori-associated diseases. The aim of this study was to assess the role of selected genes (jhp0940, jhp0945, jhp0947 and jhp0949) in the plasticity region in relation to risk of H. pylori-related diseases in Indian population. METHODS A total of 113 H. pylori strains isolated from duodenal ulcer (DU) (n = 61) and non-ulcer dyspepsia (NUD) subjects (n = 52) were screened by PCR and Dot-Blot to determine the presence of these genes. The comparative study of IL-8 production and apoptosis were also done by co-culturing the AGS cells with H. pylori strains of different genotype. RESULTS PCR and Dot-Blot results indicated that the prevalence rates of jhp0940, jhp0945, jhp0947 and jhp0949 in the H. pylori strains were 9.8, 47.5, 50.8, 40.9 % and 17.3, 28.8, 26.9, 19.2 % isolated from DU and NUD, respectively. IL-8 production and apoptotic cell death were significantly higher in H. pylori strains containing jhp0945, jhp0947 and jhp0949 than the strains lacking those genes. Results indicated that the prevalence of jhp0945, jhp0947 and jhp0949 are associated with increased risk of severe diseases in India. CONCLUSION Our study showed that presence of jhp0945, jhp0947 and jhp0949 were significantly associated with symptomatic expressions along with the increased virulence during in vitro study whereas jhp0940 seems to be negatively associated with the disease. These results suggest that jhp0945, jhp0947 and jhp0949 could be useful prognostic markers for the development of duodenal ulcer in India.
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Affiliation(s)
- Mou Ganguly
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India ; Department of Zoology, University of Calcutta, Kolkata, India
| | | | - Prachetash Ghosh
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
| | - Avijit Sarkar
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
| | - Jawed Alam
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
| | - Bipul Chandra Karmakar
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
| | - Ronita De
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
| | - Dhira Rani Saha
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
| | - Asish K Mukhopadhyay
- Division of Bacteriology, National Institute of Cholera and Enteric Diseases, P 33, CIT Road, Scheme XM, Beliaghata, Kolkata, 700010 India
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Zhao Z, Wang F, Fang C, Wang G, Shuang J, Chu G, Hu S, Chen L, Du J. A possible role of GDDR in the development of Helicobacter pylori-associated gastric cancer. Tumour Biol 2016; 37:10303-15. [PMID: 26842925 DOI: 10.1007/s13277-016-4862-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/13/2016] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection plays an important part in the development of gastric carcinoma. GDDR has been confirmed as a tumor suppressor gene in gastric tumorigenesis. However, the underlying mechanism of GDDR in H. pylori-induced carcinogenesis is not well known. The aim of this study is to investigate the clinicopathological significance and possible molecular mechanism of GDDR in gastric cancer associated with H. pylori. Western blot, real-time quantitative PCR (qRT-PCR), and immunohistochemistry were used to detect the expression level of GDDR with or without H. pylori infection. The function and possible related molecular mechanisms of GDDR were further explored in vitro and in vivo. The variability of GDDR expression appeared in the early stage of gastric carcinogenesis with positive H. pylori infection status. GDDR might inhibit the progression of normal gastric epithelial cells to cancer cells by suppressing NF-kappaB signaling pathway, which in turn could be regulated by H. pylori infection. Our results suggested, for the first time, that the gradual change in GDDR expression might not only be directly related to H. pylori infection but also be an early molecular event in the development of gastric carcinoma.
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Affiliation(s)
- Zhanwei Zhao
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Fei Wang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Cheng Fang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Gang Wang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Jianbo Shuang
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Guanghui Chu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Sijun Hu
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Lin Chen
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China
| | - Jianjun Du
- State Key Laboratory of Cancer Biology and Xijing Hospital of Digestive Diseases, The Fourth Military Medical University, 127 Changle Western Road, Xi'an, Shaanxi Province, 710032, China.
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Pachathundikandi SK, Müller A, Backert S. Inflammasome Activation by Helicobacter pylori and Its Implications for Persistence and Immunity. Curr Top Microbiol Immunol 2016; 397:117-31. [DOI: 10.1007/978-3-319-41171-2_6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Boura E, Nencka R. Phosphatidylinositol 4-kinases: Function, structure, and inhibition. Exp Cell Res 2015; 337:136-45. [DOI: 10.1016/j.yexcr.2015.03.028] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 03/12/2015] [Indexed: 02/07/2023]
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Flayhan A, Bergé C, Baïlo N, Doublet P, Bayliss R, Terradot L. The structure of Legionella pneumophila LegK4 type four secretion system (T4SS) effector reveals a novel dimeric eukaryotic-like kinase. Sci Rep 2015; 5:14602. [PMID: 26419332 PMCID: PMC4588518 DOI: 10.1038/srep14602] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 08/28/2015] [Indexed: 01/24/2023] Open
Abstract
Bacterial pathogens subvert signalling pathways to promote invasion and/or replication into the host. LegK1-4 proteins are eukaryotic-like serine/threonine kinases that are translocated by the Dot/Icm type IV secretion system (T4SS) of several Legionella pneumophila strains. We present the crystal structures of an active fragment of the LegK4 protein in apo and substrate-bound states. The structure of LegK41–445 reveals a eukaryotic-like kinase domain flanked by a novel cap domain and a four-helix bundle. The protein self-assembles through interactions mediated by helices αF and αG that generate a dimeric interface not previously observed in a protein kinase. The helix αG is displaced compared to previous kinase structures, and its role in stabilization of the activation loop is taken on by the dimerisation interface. The apo-form of the protein has an open conformation with a disordered P-loop but a structured activation segment in absence of targeted phosphorylation. The nucleotide-binding site of LegK4 contains an unusual set of residues that mediate non-canonical interactions with AMP-PNP. Nucleotide binding results in limited changes in the active site, suggesting that LegK4 constitutive kinase activity does not depend on phosphorylation of the activation loop but on the stabilizing effects of the dimer.
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Affiliation(s)
- Ali Flayhan
- UMR 5086 BMSSI CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Célia Bergé
- UMR 5086 BMSSI CNRS-Université de Lyon, Institut de Biologie et Chimie des Protéines, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Nathalie Baïlo
- Legionella Pathogenesis Group, International Center for Infectiology Research, Université de Lyon Lyon, France.,INSERM U1111 Lyon, France.,Ecole Normale Suptérieure de Lyon Lyon, France.,Centre International de Recherche en Infectiologie, Université Lyon 1 Lyon, France.,CNRS, UMR5308 Lyon, France
| | - Patricia Doublet
- Legionella Pathogenesis Group, International Center for Infectiology Research, Université de Lyon Lyon, France.,INSERM U1111 Lyon, France.,Ecole Normale Suptérieure de Lyon Lyon, France.,Centre International de Recherche en Infectiologie, Université Lyon 1 Lyon, France.,CNRS, UMR5308 Lyon, France
| | - Richard Bayliss
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
| | - Laurent Terradot
- Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom
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Klima M, Baumlova A, Chalupska D, Hřebabecký H, Dejmek M, Nencka R, Boura E. The high-resolution crystal structure of phosphatidylinositol 4-kinase IIβ and the crystal structure of phosphatidylinositol 4-kinase IIα containing a nucleoside analogue provide a structural basis for isoform-specific inhibitor design. ACTA ACUST UNITED AC 2015; 71:1555-63. [PMID: 26143926 DOI: 10.1107/s1399004715009505] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 05/18/2015] [Indexed: 11/10/2022]
Abstract
Phosphatidylinositol 4-phosphate (PI4P) is the most abundant monophosphoinositide in eukaryotic cells. Humans have four phosphatidylinositol 4-kinases (PI4Ks) that synthesize PI4P, among which are PI4K IIβ and PI4K IIα. In this study, two crystal structures are presented: the structure of human PI4K IIβ and the structure of PI4K IIα containing a nucleoside analogue. The former, a complex with ATP, is the first high-resolution (1.9 Å) structure of a PI4K. These structures reveal new details such as high conformational heterogeneity of the lateral hydrophobic pocket of the C-lobe and together provide a structural basis for isoform-specific inhibitor design.
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Affiliation(s)
- Martin Klima
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Adriana Baumlova
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Dominika Chalupska
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Hubert Hřebabecký
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Milan Dejmek
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Radim Nencka
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Evzen Boura
- Department of Biochemistry, Institute of Organic Chemistry and Biochemistry, Flemingovo nam. 2, 166 10 Prague, Czech Republic
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32
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Romo-González C, Consuelo-Sánchez A, Camorlinga-Ponce M, Velázquez-Guadarrama N, García-Zúñiga M, Burgueño-Ferreira J, Coria-Jiménez R. Plasticity Region Genes jhp0940, jhp0945, jhp0947, and jhp0949 of Helicobacter pylori in Isolates from Mexican Children. Helicobacter 2015; 20:231-7. [PMID: 25735460 DOI: 10.1111/hel.12194] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND The genes jhp0940, jhp0945, jhp0947, and jhp0949 belong to the plasticity region of the Helicobacter pylori genome. Due to their prevalence in isolates from patients with gastritis, duodenal ulcer, and gastric cancer, they have been proposed as markers of gastroduodenal diseases. These genes are associated with pro-inflammatory cytokine induction through the NF-κB activation pathway. Nevertheless, the status of these genes is unknown in H. pylori isolates from children. The aim of the present work was to determine the frequency of the jhp0940-jhp0945-jhp0947-jhp0949 genes in H. pylori isolates from children. MATERIALS AND METHODS We identified the jhp0940, jhp0945, jhp0947, and jhp0949 genes and the relationship of each with the virulence factors cagA, cagPAI, and dupA by PCR in 49 isolates of H. pylori from children. The results were corroborated using dot blots. In addition, we compared the prevalence of these genes with the prevalence in adults. RESULTS The prevalence of jhp0940 (53.1%), jhp0945 (44.9%), jhp0947 (77.6%), and jhp0949 (83.7%) was determined in the isolates from children, as was the prevalence of the virulence genes cagA (63.3%), cagPAI (71.4%), and dupA (37.5%). No association was found between the four genes of the plasticity region and the virulence genes. The presence of the intact locus integrated by jhp0940-jhp0945-jhp0947-jhp0949 was very common among the isolates from children. CONCLUSION The genes jhp0940, jhp0947, and jhp0949 were present in more than 50% of the H. pylori isolates, and the joint presence of jhp0940-jhp0945-jhp0947-jhp0949 was very frequent. The frequency of these genes in isolates from children could contribute to the virulence of H. pylori and the evolution of the infection.
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Affiliation(s)
| | - Alejandra Consuelo-Sánchez
- Gastroenterology & Nutrition Department, Children's Hospital of Mexico "Federico Gómez", SSA, México, D.F., México
| | - Margarita Camorlinga-Ponce
- Infectious Diseases Research Unit, Instituto Mexicano del Seguro Social, Mexico City, Mexico, CMN Siglo XXI, IMSS, México, D.F., México
| | | | | | - Juan Burgueño-Ferreira
- International Maize and Wheat Improvement Center, Biometrics and Statistics Unit, Mexico, Mexico
| | - Rafael Coria-Jiménez
- Experimental Bacteriology, National Institute of Pediatrics, SSA, México, D.F., México
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Baumlova A, Chalupska D, Róźycki B, Jovic M, Wisniewski E, Klima M, Dubankova A, Kloer DP, Nencka R, Balla T, Boura E. The crystal structure of the phosphatidylinositol 4-kinase IIα. EMBO Rep 2014; 15:1085-92. [PMID: 25168678 DOI: 10.15252/embr.201438841] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Phosphoinositides are a class of phospholipids generated by the action of phosphoinositide kinases with key regulatory functions in eukaryotic cells. Here, we present the atomic structure of phosphatidylinositol 4-kinase type IIα (PI4K IIα), in complex with ATP solved by X-ray crystallography at 2.8 Å resolution. The structure revealed a non-typical kinase fold that could be divided into N- and C-lobes with the ATP binding groove located in between. Surprisingly, a second ATP was found in a lateral hydrophobic pocket of the C-lobe. Molecular simulations and mutagenesis analysis revealed the membrane binding mode and the putative function of the hydrophobic pocket. Taken together, our results suggest a mechanism of PI4K IIα recruitment, regulation, and function at the membrane.
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Affiliation(s)
- Adriana Baumlova
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - Dominika Chalupska
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - Bartosz Róźycki
- Institute of Physics Polish Academy of Sciences, Warsaw, Poland
| | - Marko Jovic
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, NICHD NIH, Bethesda, MD, USA
| | - Eva Wisniewski
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, NICHD NIH, Bethesda, MD, USA
| | - Martin Klima
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - Anna Dubankova
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - Daniel P Kloer
- Syngenta Jealott's Hill Internation Research Centre, Bracknell, UK
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - Tamas Balla
- Section on Molecular Signal Transduction, Program for Developmental Neuroscience, NICHD NIH, Bethesda, MD, USA
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
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Tenguria S, Ansari SA, Khan N, Ranjan A, Devi S, Tegtmeyer N, Lind J, Backert S, Ahmed N. Helicobacter pylori cell translocating kinase (CtkA/JHP0940) is pro-apoptotic in mouse macrophages and acts as auto-phosphorylating tyrosine kinase. Int J Med Microbiol 2014; 304:1066-76. [PMID: 25172221 DOI: 10.1016/j.ijmm.2014.07.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/26/2014] [Accepted: 07/28/2014] [Indexed: 12/16/2022] Open
Abstract
The Helicobacter pylori gene JHP0940 has been shown to encode a serine/threonine kinase which can induce cytokines in gastric epithelial cells relevant to chronic gastric inflammation. Here we demonstrate that JHP0940 can be secreted by the bacteria, triggers apoptosis in cultured mouse macrophages and acts as an auto-phosphorylating tyrosine kinase. Recombinant JHP0940 protein was found to decrease the viability of RAW264.7 cells (a mouse macrophage cell line) up to 55% within 24h of co-incubation. The decreased cellular viability was due to apoptosis, which was confirmed by TUNEL assay and Fas expression analysis by flow-cytometry. Further, we found that caspase-1 and IL-1beta were activated upon treatment with JHP0940. These results point towards possible action through the host inflammasome. Our in vitro studies using tyrosine kinase assays further demonstrated that JHP0940 acts as auto-phosphorylating tyrosine kinase and induces pro-inflammatory cytokines in RAW264.7 cells. Upon exposure with JHP0940, these cells secreted IL-1beta, TNF-alpha and IL-6, in a dose- and time-dependent manner, as detected by ELISA and transcript profiling by q-RT-PCR. The pro-inflammatory, pro-apoptotic and other regulatory responses triggered by JHP0940 lead to the assumption of its possible role in inducing chronic inflammation for enhanced bacterial persistence and escape from host innate immune responses by apoptosis of macrophages.
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Affiliation(s)
- Shivendra Tenguria
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India
| | - Suhail A Ansari
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India
| | - Nooruddin Khan
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India
| | - Amit Ranjan
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India
| | - Savita Devi
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India
| | - Nicole Tegtmeyer
- Division of Microbiology, Department of Biology, Friedrich Alexander University Nuremberg, D-91058 Erlangen, Germany
| | - Judith Lind
- Division of Microbiology, Department of Biology, Friedrich Alexander University Nuremberg, D-91058 Erlangen, Germany
| | - Steffen Backert
- Division of Microbiology, Department of Biology, Friedrich Alexander University Nuremberg, D-91058 Erlangen, Germany
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad 500046, India.
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Fischer W, Breithaupt U, Kern B, Smith SI, Spicher C, Haas R. A comprehensive analysis of Helicobacter pylori plasticity zones reveals that they are integrating conjugative elements with intermediate integration specificity. BMC Genomics 2014; 15:310. [PMID: 24767410 PMCID: PMC4234485 DOI: 10.1186/1471-2164-15-310] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 04/16/2014] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The human gastric pathogen Helicobacter pylori is a paradigm for chronic bacterial infections. Its persistence in the stomach mucosa is facilitated by several mechanisms of immune evasion and immune modulation, but also by an unusual genetic variability which might account for the capability to adapt to changing environmental conditions during long-term colonization. This variability is reflected by the fact that almost each infected individual is colonized by a genetically unique strain. Strain-specific genes are dispersed throughout the genome, but clusters of genes organized as genomic islands may also collectively be present or absent. RESULTS We have comparatively analysed such clusters, which are commonly termed plasticity zones, in a high number of H. pylori strains of varying geographical origin. We show that these regions contain fixed gene sets, rather than being true regions of genome plasticity, but two different types and several subtypes with partly diverging gene content can be distinguished. Their genetic diversity is incongruent with variations in the rest of the genome, suggesting that they are subject to horizontal gene transfer within H. pylori populations. We identified 40 distinct integration sites in 45 genome sequences, with a conserved heptanucleotide motif that seems to be the minimal requirement for integration. CONCLUSIONS The significant number of possible integration sites, together with the requirement for a short conserved integration motif and the high level of gene conservation, indicates that these elements are best described as integrating conjugative elements (ICEs) with an intermediate integration site specificity.
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Affiliation(s)
- Wolfgang Fischer
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität, D-80336 Munich, Germany.
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Yoon JY, Lee SJ, Kim DJ, Lee BJ, Yang JK, Suh SW. Crystal structure of JHP933 fromHelicobacter pyloriJ99 shows two-domain architecture with a DUF1814 family nucleotidyltransferase domain and a helical bundle domain. Proteins 2014; 82:2275-81. [DOI: 10.1002/prot.24572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/03/2014] [Accepted: 03/21/2014] [Indexed: 01/26/2023]
Affiliation(s)
- Ji Young Yoon
- Department of Chemistry; College of Natural Sciences, Seoul National University; Seoul 151-742 Republic of Korea
| | - Sang Jae Lee
- The Research Institute of Pharmaceutical Sciences; College of Pharmacy, Seoul National University, Gwanak-gu; Seoul 151-742 Republic of Korea
| | - Do Jin Kim
- Department of Chemistry; College of Natural Sciences, Seoul National University; Seoul 151-742 Republic of Korea
| | - Bong-Jin Lee
- The Research Institute of Pharmaceutical Sciences; College of Pharmacy, Seoul National University, Gwanak-gu; Seoul 151-742 Republic of Korea
| | - Jin Kuk Yang
- Department of Chemistry; College of Natural Sciences, Soongsil University; Seoul 156-743 Republic of Korea
| | - Se Won Suh
- Department of Chemistry; College of Natural Sciences, Seoul National University; Seoul 151-742 Republic of Korea
- Department of Biophysics and Chemical Biology; College of Natural Sciences, Seoul National University; Seoul 151-742 Republic of Korea
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Hosoda F, Arai Y, Okada N, Shimizu H, Miyamoto M, Kitagawa N, Katai H, Taniguchi H, Yanagihara K, Imoto I, Inazawa J, Ohki M, Shibata T. Integrated genomic and functional analyses reveal glyoxalase I as a novel metabolic oncogene in human gastric cancer. Oncogene 2014; 34:1196-206. [PMID: 24662817 DOI: 10.1038/onc.2014.57] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 11/15/2013] [Accepted: 12/16/2013] [Indexed: 02/07/2023]
Abstract
Chromosomal abnormalities are good guideposts when hunting for cancer-related genes. We analyzed copy number alterations of 163 primary gastric cancers using array-based comparative genomic hybridization and simultaneously performed a genome-wide integrated analysis of copy number and gene expression using microarray data for 58 tumors. We showed that chromosome 6p21 amplification frequently occurred secondary to ERBB2 amplification, was associated with poorer prognosis and caused overexpression of half of the genes mapped. A comprehensive small interfering RNA knockdown of 58 genes overexpressed in tumors identified 32 genes that reduced gastric cancer cell growth. Enforced expression of 16 of these genes promoted cell growth in vitro, and six genes showing more than two-fold activity conferred tumor-forming ability in vivo. Among these six candidates, GLO1, encoding a detoxifying enzyme glyoxalase I (GLO1), exhibited the strongest tumor-forming activity. Coexpression of other genes with GLO1 enhanced growth-stimulating activity. A GLO1 inhibitor, S-p-bromobenzyl glutathione cyclopentyl diester, inhibited the growth of two-thirds of 24 gastric cancer cell lines examined. The efficacy was found to be associated with the mRNA expression ratio of GLO1 to GLO2, encoding glyoxalase II (GLO2), another constituent of the glyoxalase system. GLO1 downregulation affected cell growth through inactivating central carbon metabolism and reduced the transcriptional activities of nuclear factor kappa B and activator protein-1. Our study demonstrates that GLO1 is a novel metabolic oncogene of the 6p21 amplicon, which promotes tumor growth and aberrant transcriptional signals via regulating cellular metabolic activities for energy production and could be a potential therapeutic target in gastric cancer.
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Affiliation(s)
- F Hosoda
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Y Arai
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - N Okada
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - H Shimizu
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - M Miyamoto
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - N Kitagawa
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - H Katai
- Division of Gastric Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - H Taniguchi
- Division of Clinical Laboratory, National Cancer Center Hospital, Tokyo, Japan
| | - K Yanagihara
- Division of Translational Research, Exploratory Oncology Research & Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - I Imoto
- 1] Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan [2] Department of Human Genetics and Public Health, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - J Inazawa
- Department of Molecular Cytogenetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - M Ohki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - T Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
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Devi S, Ansari SA, Vadivelu J, Mégraud F, Tenguria S, Ahmed N. Helicobacter pylori antigen HP0986 (TieA) interacts with cultured gastric epithelial cells and induces IL8 secretion via NF-κB mediated pathway. Helicobacter 2014; 19:26-36. [PMID: 24205801 DOI: 10.1111/hel.12100] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND The envisaged roles and partly understood functional properties of Helicobacter pylori protein HP0986 are significant in the context of proinflammatory and or proapoptotic activities, the two important facilitators of pathogen survival and persistence. In addition, sequence analysis of this gene predicts a restriction endonuclease function which remained unknown thus far. To evaluate the role of HP0986 in gastric inflammation, we studied its expression profile using a large number of clinical isolates but a limited number of biopsies and patient sera. Also, we studied antigenic role of HP0986 in altering cytokine responses of human gastric epithelial (AGS) cells including its interaction with and localization within the AGS cells. MATERIALS AND METHODS For in vitro expression study of HP0986, 110 H. pylori clinical isolates were cultured from patients with functional dyspepsia. For expression analysis by qRT PCR of HP0986, 10 gastric biopsy specimens were studied. HP0986 was also used to detect antibodies in patient sera. AGS cells were incubated with recombinant HP0986 to determine cytokine response and NF-κB activation. Transient transfection with HP0986 cloned in pEGFPN1 was used to study its subcellular localization or homing in AGS cells. RESULTS Out of 110 cultured H. pylori strains, 34 (31%) were positive for HP0986 and this observation was correlated with in vitro expression profiles. HP0986 mRNA was detected in 7 of the 10 biopsy specimens. Further, HP0986 induced IL-8 secretion in gastric epithelial cells in a dose and time-dependent manner via NF-κB pathway. Serum antibodies against HP0986 were positively associated with H. pylori positive patients. Transient transfection of AGS cells revealed both cytoplasmic and nuclear localization of HP0986. CONCLUSION HP0986 was moderately prevalent in clinical isolates and its expression profile in cultures and gastric biopsies points to its being naturally expressed. Collective observations including the induction of IL-8 via TNFR1 and NF-κB, subcellular localization, and seropositivity data point to a significant role of HP0986 in gastroduodenal inflammation. We propose to name the HP0986 gene/protein as 'TNFR1 interacting endonuclease A (TieA or tieA)'.
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Affiliation(s)
- Savita Devi
- Pathogen Biology Laboratory, Department of Biotechnology and Bioinformatics, University of Hyderabad, Hyderabad, 500046, India
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Abstract
The family with sequence similarity 20 (Fam20) kinases phosphorylate extracellular substrates and play important roles in biomineralization. Fam20C is the Golgi casein kinase that phosphorylates secretory pathway proteins within Ser-x-Glu/pSer motifs. Mutations in Fam20C cause Raine syndrome, an osteosclerotic bone dysplasia. Here we report the crystal structure of the Fam20C ortholog from Caenorhabditis elegans. The nucleotide-free and Mn/ADP-bound structures unveil an atypical protein kinase-like fold and highlight residues critical for activity. The position of the regulatory αC helix and the lack of an activation loop indicate an architecture primed for efficient catalysis. Furthermore, several distinct elements, including the presence of disulfide bonds, suggest that the Fam20 family diverged early in the evolution of the protein kinase superfamily. Our results reinforce the structural diversity of protein kinases and have important implications for patients with disorders of biomineralization.
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Kang Y, Wang F, Lu Z, Ying H, Zhang H, Ding W, Wang C, Shi L. MAPK kinase 3 potentiates Chlamydia HSP60-induced inflammatory response through distinct activation of NF-κB. THE JOURNAL OF IMMUNOLOGY 2013; 191:386-94. [PMID: 23729445 DOI: 10.4049/jimmunol.1300481] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Chlamydia pneumonia (C. pneumonia) remains one of the leading causes of bacterial pneumonia and has been implicated in the pathogenesis of some inflammation-related diseases, such as asthma, chronic obstructive pulmonary disease, and vascular diseases. Heat shock protein 60 is one of the pathogenic components of C. pneumonia that is closely associated with the inflammatory disorders. However, the molecular basis for the immunopathologic property of chlamydial heat shock protein (cHSP60) has not been elucidated. In this article, we report that MAPK kinase 3 (MKK3) is essential for cHSP60-induced lung inflammation, because MKK3-knockout mice displayed significantly reduced lung neutrophil accumulation and decreased production of proinflammatory mediators, correlating with the alleviated inflammatory response in lung tissues. Mechanistically, p38 kinase was selectively activated by MKK3 in response to cHSP60 and activated NF-κB by stimulating the nuclear kinase, mitogen- and stress-activated protein kinase 1. The specific knockdown of mitogen- and stress-activated protein kinase 1 in macrophages resulted in a defective phosphorylation of NF-κB/RelA at Ser(276) but had no apparent effect on RelA translocation. Furthermore, TGF-β-activated kinase 1 was found to relay the signal to MKK3 from TLR4, the major receptor that sensed cHSP60 in the initiation of the inflammatory response. Thus, we establish a critical role for MKK3 signaling in cHSP60 pathology and suggest a novel mechanism underlying C. pneumonia-associated inflammatory disorders.
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Affiliation(s)
- Yanhua Kang
- Department of Basic Medical Science, Key Laboratory of Immunology and Molecular Medicine, School of Medicine, Hangzhou Normal University, Hangzhou, Zhejiang 310036, China
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Zhang H, Pelech S. Using protein microarrays to study phosphorylation-mediated signal transduction. Semin Cell Dev Biol 2012; 23:872-82. [DOI: 10.1016/j.semcdb.2012.05.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 05/30/2012] [Accepted: 05/30/2012] [Indexed: 01/18/2023]
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Takeuchi H, Zhang YN, Israel DA, Peek Jr RM, Kamioka M, Yanai H, Morimoto N, Sugiura T. Effect of Helicobacter pylori cdrA on interleukin-8 secretions and nuclear factor kappa B activation. World J Gastroenterol 2012; 18:425-34. [PMID: 22346248 PMCID: PMC3270507 DOI: 10.3748/wjg.v18.i5.425] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 05/19/2011] [Accepted: 05/26/2011] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate genetic diversity of Helicobacter pylori (H. pylori) cell division-related gene A (cdrA) and its effect on the host response.
METHODS: Inactivation of H. pylori cdrA, which is involved in cell division and morphological elongation, has a role in chronic persistent infections. Genetic property of H. pylori cdrA was evaluated using polymerase chain reaction and sequencing in 128 (77 American and 51 Japanese) clinical isolates obtained from 48 and 51 patients, respectively. Enzyme-linked immunosorbent assay was performed to measure interleukin-8 (IL-8) secretion with gastric biopsy specimens obtained from American patients colonized with cdrA-positive or -negative strains and AGS cells co-cultured with wild-type HPK5 (cdrA-positive) or its derivative HPKT510 (cdrA-disruptant). Furthermore, the cytotoxin-associated gene A (cagA) status (translocation and phosphorylation) and kinetics of transcription factors [nuclear factor-kappa B (NF-κB) and inhibition kappa B] were investigated in AGS cells co-cultured with HPK5, HPKT510 and its derivative HPK5CA (cagA-disruptant) by western blotting analysis with immunoprecipitation.
RESULTS: Genetic diversity of the H. pylori cdrA gene demonstrated that the cdrA status segregated into two categories including four allele types, cdrA-positive (allele types;Iand II) and cdrA-negative (allele types; III and IV) categories, respectively. Almost all Japanese isolates were cdrA-positive (I: 7.8% and II: 90.2%), whereas 16.9% of American isolates were cdrA-positive (II) and 83.1% were cdrA-negative (III: 37.7% and IV: 45.5%), indicating extended diversity of cdrA in individual American isolates. Comparison of each isolate from different regions (antrum and corpus) in the stomach of 29 Americans revealed that cdrA status was identical in both isolates from different regions in 17 cases. However, 12 cases had a different cdrA allele and 6 of them exhibited a different cdrA category between two regions in the stomach. Furthermore, in 5 of the 6 cases possessing a different cdrA category, cdrA-negative isolate existed in the corpus, suggesting that cdrA-negative strain is more adaptable to colonization in the corpus. IL-8 secretions from AGS revealed that IL-8 levels induced by a cdrA-disrupted HPKT510 was significantly lower (P < 0.01) compared to wild-type HPK5: corresponding to 50%-60% of those of wild-type HPK5. These data coincided with in vivo data that an average value of IL-8 in biopsy specimens from cdrA-positive and cdrA-negative groups was 215.6 and 135.9 pg/mL, respectively. Western blotting analysis documented that HPKT510 had no effect on CagA translocation and phosphorylation, however, nuclear accumulation of NF-κB was lower by HPKT510 compared to HPK5.
CONCLUSION: Colonization by a cdrA-negative or cdrA-dysfunctional strain resulted in decreased IL-8 production and repression of NF-κB, and hence, attenuate the host immunity leading to persistent infection.
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Abstract
PURPOSE OF REVIEW Helicobacter pylori is implicated in numerous gastric pathologies; however, the prevalence of infection is declining in developed countries. Therefore, it is important to understand the complex mechanism of its interaction with the host and how the changing epidemiology of infection may impact on disease. In this review, we systemically revisit the major novel discoveries of the last year relating to H. pylori disease pathogenesis. RECENT FINDINGS Novel pathways have been implicated in H. pylori cytotoxin-associated gene (CagA) mediated carcinogenesis, highlighting the aberrant regulation of proliferation and apoptosis. Furthermore, the human microbiome was implicated as having a key role in H. pylori-related disease development. Several studies have begun to delineate the mechanisms behind the epidemiologically inverse correlation of H. pylori infection with asthma and inflammatory bowel disease. SUMMARY The recent findings enable researchers to focus on novel and previously unsuspected mechanisms in the development of disease, and prompt further research into possible therapeutic approaches. The potential beneficial aspects of H. pylori colonization and the role bacterial flora play in promoting disease have yet to be elucidated, but promise to have a great impact on patient care.
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Role of Helicobacter pylori plasticity region genes in development of gastroduodenal diseases. J Clin Microbiol 2011; 50:441-8. [PMID: 22116145 DOI: 10.1128/jcm.00906-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The plasticity region of Helicobacter pylori is a large chromosomal segment including isolate-specific open reading frames with characteristics of pathogenicity islands. It remains unclear whether genes in the plasticity region play a role in the pathogenesis of gastric mucosal inflammation and gastroduodenal disease. Our aim was to assess the role of selected genes in the plasticity region in relation to risk of H. pylori-related disease and the severity of gastric mucosal damage. We used PCR to study the relation of disease outcome and mucosal damage with four genes in the H. pylori plasticity region (jhp0940, jhp0945, jhp0947, and jhp0949) from isolates obtained from both Western (n = 296) and East Asian (n = 217) patients. The prevalence of jhp0945, jhp0947, and jhp0949 differed significantly between Western and East Asian isolates. In Western isolates, the presence of jhp0945 was significantly associated with gastric ulcer, duodenal ulcer, and gastric cancer (odds ratios [95% confidence intervals]: 2.27 [1.04 to 4.98], 1.86 [1.03 to 3.34], and 1.92 [1.03 to 3.56], respectively). jhp0940-positive Western isolates were significantly associated with absence of gastric ulcer or duodenal ulcer (0.21 [0.05 to 0.94] and 0.31 [0.12 to 0.78], respectively). No significant difference was observed between inflammatory cell infiltration or atrophy and the presence or absence of plasticity region genes. The outcome of H. pylori infections varies widely geographically. These data suggest a possible role for difference in the prevalence of plasticity region genes in the geographic variation in H. pylori-related diseases.
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