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Phuc BH, Tuan VP, Binh TT, Tung PH, Tri TD, Dung HDQ, Thuan NPM, Fauzia KA, Tshibangu-Kabamba E, Alfaray RI, Saruuljavkhlan B, Matsumoto T, Akada J, Yamaoka Y. Comparative genomics of two Vietnamese Helicobacter pylori strains, CHC155 from a non-cardia gastric cancer patient and VN1291 from a duodenal ulcer patient. Sci Rep 2023; 13:8869. [PMID: 37258611 DOI: 10.1038/s41598-023-35527-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 05/19/2023] [Indexed: 06/02/2023] Open
Abstract
Helicobacter pylori is involved in the etiology and severity of several gastroduodenal diseases; however, plasticity of the H. pylori genome makes complete genome assembly difficult. We report here the full genomes of H. pylori strains CHC155 and VN1291 isolated from a non-cardia gastric cancer patient and a duodenal ulcer patient, respectively, and their virulence demonstrated by in vitro infection. Whole-genome sequences were obtained by combining long- and short-reads with a hybrid-assembly approach. Both CHC155 and VN1291 genome possessed four kinds of genomic island: a cag pathogenicity island (cagPAI), two type 4 secretion system islands within an integrative and conjugative element (tfs ICE), and prophage. CHC155 and VN1291 carried East Asian-type cagA and vacA s1m1, and outer membrane protein genes, including two copies of oipA. Corresponded to genetic determinants of antibiotic resistance, chromosomal mutations were identified in CHC155 (rdxA, gyrA, and 23S rRNA) and VN1291 (rdxA, 23S rRNA, and pbp1A). In vitro infection of AGS cells by both strains induced the cell scattering phenotype, tyrosine phosphorylation of CagA, and promoted high levels of IL8 secretion, indicating fully intact phenotypes of the cagPAI. Virulence genes in CHC155 and VN1291 genomes are crucial for H. pylori pathogenesis and are risk factors in the development of gastric cancer and duodenal ulcer. Our in vitro studies indicate that the strains CHC155 and VN1291 carry the pathogenic potential.
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Grants
- 21K08010 Ministry of Education, Culture, Sports, Science and Technology, Japan
- 21K07898 Ministry of Education, Culture, Sports, Science and Technology, Japan
- 221S0002 Ministry of Education, Culture, Sports, Science and Technology, Japan
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Affiliation(s)
- Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Faculty of Applied Technology, Van Lang University, Ho Chi Minh City, Vietnam
| | - Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | - Ho Dang Quy Dung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh City, Vietnam
| | | | - Kartika Afrida Fauzia
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Universitas Airlangga, Surabaya, 60115, Indonesia
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Evariste Tshibangu-Kabamba
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Department of Parasitology, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Ricky Indra Alfaray
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
- Helicobacter pylori and Microbiota Study Group, Institute of Tropical Disease, Universitas Airlangga, Surabaya, 60115, Indonesia
| | - Batsaikhan Saruuljavkhlan
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Oita, Japan.
- Research Center for GLOBAL and LOCAL Infectious Diseases, Oita University, Yufu, Oita, Japan.
- Department of Medicine, Gastroenterology and Hepatology Section, Baylor College of Medicine, Houston, TX, USA.
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Sung YJ, Song S, Sim SJ. A Rapid and High-Throughput Assay for Light Scattering of SARS-CoV-2 Virion-Sized Particulates via Microfluidic Spray Device Reveals the Protection Performance of Face Masks against Virus Infection. NANO LETTERS 2022; 22:6744-6752. [PMID: 35930264 DOI: 10.1021/acs.nanolett.2c02278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
To prevent interhuman transmission of viruses, new mask types─claiming improved filtration─require careful performance characterization. Here, a microfluidic spray device that can effectively simulate droplets emitted during coughing or sneezing was developed to spray droplets containing gold nanoparticles (AuNPs) that mimic SARS-CoV-2 to overcome the shortcomings associated with using biosamples. The light scattered by the AuNPs passing through the mask is successfully analyzed by using an automated scattering light mapping system within a duration of 2 min, thereby enabling high-throughput analysis of the filtering efficiency of various types of commercial masks. The differences in efficiency in terms of same mask type from different manufacturers, double masking, and prolonged usage, which are challenging to analyze with conventional testing systems, can also be assessed. AuNP-mediated mask performance evaluation enables the rapid determination of mask efficiency according to particle size and can contribute to the rapid response to counter new emerging infectious biohazards.
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Affiliation(s)
- Young Joon Sung
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sojin Song
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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3
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Ferreira R, Sousa C, Gonçalves RFS, Pinheiro AC, Oleastro M, Wagemans J, Lavigne R, Figueiredo C, Azeredo J, Melo LDR. Characterization and Genomic Analysis of a New Phage Infecting Helicobacter pylori. Int J Mol Sci 2022; 23:ijms23147885. [PMID: 35887231 PMCID: PMC9319048 DOI: 10.3390/ijms23147885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 02/04/2023] Open
Abstract
Helicobacter pylori, a significant human gastric pathogen, has been demonstrating increased antibiotic resistance, causing difficulties in infection treatment. It is therefore important to develop alternatives or complementary approaches to antibiotics to tackle H. pylori infections, and (bacterio)phages have proven to be effective antibacterial agents. In this work, prophage isolation was attempted using H. pylori strains and UV radiation. One phage was isolated and further characterized to assess potential phage-inspired therapeutic alternatives to H. pylori infections. HPy1R is a new podovirus prophage with a genome length of 31,162 bp, 37.1% GC, encoding 36 predicted proteins, of which 17 were identified as structural. Phage particles remained stable at 37 °C, from pH 3 to 11, for 24 h in standard assays. Moreover, when submitted to an in vitro gastric digestion model, only a small decrease was observed in the gastric phase, suggesting that it is adapted to the gastric tract environment. Together with its other characteristics, its capability to suppress H. pylori population levels for up to 24 h post-infection at multiplicities of infection of 0.01, 0.1, and 1 suggests that this newly isolated phage is a potential candidate for phage therapy in the absence of strictly lytic phages.
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Affiliation(s)
- Rute Ferreira
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal;
| | - Cláudia Sousa
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Raquel F. S. Gonçalves
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Ana Cristina Pinheiro
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Mónica Oleastro
- Department of Infectious Diseases, National Institute of Health Doctor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal;
| | - Jeroen Wagemans
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (J.W.); (R.L.)
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (J.W.); (R.L.)
| | - Ceu Figueiredo
- i3S—Instituto de Investigação e Inovação em Saúde, University of Porto, 4200-135 Porto, Portugal;
- Ipatimup—Institute of Molecular Pathology and Immunology of the University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Joana Azeredo
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
| | - Luís D. R. Melo
- CEB—Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal; (R.F.); (C.S.); (R.F.S.G.); (A.C.P.); (J.A.)
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
- Correspondence:
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Wang Y, Imran A, Shami A, Chaudhary AA, Khan S. Decipher the Helicobacter pylori Protein Targeting in the Nucleus of Host Cell and their Implications in Gallbladder Cancer: An insilico approach. J Cancer 2021; 12:7214-7222. [PMID: 34729122 PMCID: PMC8558644 DOI: 10.7150/jca.63517] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 10/03/2021] [Indexed: 12/26/2022] Open
Abstract
Gallbladder cancer (GBC) is one of the leading causes of cancer-related mortality worldwide. Researchers have investigated that specific strains of bacteria are connected with growth of different types of cancers in human. Some reports show possible implication of Helicobacter pylori (H. pylori) in the etiology of gallbladder cancer (GBC). Their enigmatic mechanisms, nevertheless, are not still well clear. We sought to predict whether various proteins of H. pylori targeted to nucleus of host cells and their implication in growth of gallbladder cancer. GBC is one of the leading causes of cancer mortality worldwide. We applied bioinformatics approach to analyze the H. pylori proteins targeting into the nucleus of host cells using different bioinformatics predictors including nuclear localization signal (NLS) mapper Balanced Subcellular Localization (BaCelLo) and Hum-mPLoc 2.0. Various nuclear targeting proteins may have a potential role in GBC etiology during intracellular infection. We identified 46 H. pylori proteins targeted into nucleus of host cell through bioinformatics tools. These H. pylori nucleus-targeting proteins might alter the normal function of host cells by disturbing the different pathways including replication, transcription, translation etc. Various nucleus-targeted proteins can affect the normal growth and development of infected cells. We propose that H. pylori proteins targeting into the nucleus of host cells regulate GBC growth using different strategies. These integrative bioinformatics research demonstrated several H. pylori proteins that may serve as possible targets or biomarkers for early cure and treatment or diagnosis GBC.
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Affiliation(s)
- Yunjian Wang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou City, Henan Province, 450008, China
| | - Ahamad Imran
- King Abdullah Institute for Nanotechnology, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ashwag Shami
- Department of Biology, College of Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11617, Saudi Arabia
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh 11623, Saudi Arabia
| | - Shahanavaj Khan
- Department of Health Sciences, Novel Global Community Educational Foundation, Australia.,Department of Bioscience, Shri Ram Group of College (SRGC), Muzaffarnagar, UP, India.,Department of Pharmaceutics, College of Pharmacy, PO Box 2457, King Saud University, Riyadh 11451, Saudi Arabia
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5
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Complete Genome Sequence of Helicobacter pylori Strain 3401, a Suitable Host for Bacteriophages KHP30 and KHP40. Microbiol Resour Announc 2021; 10:e0064721. [PMID: 34672714 PMCID: PMC8530030 DOI: 10.1128/mra.00647-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Helicobacter pylori 3401, isolated from a patient with duodenal ulcers in Japan, is susceptible to the bacteriophages KHP30 and KHP40. In this study, we report the complete genome sequence of H. pylori 3401. This study may lead to the establishment of phage therapy against H. pylori infection.
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Kamiya R, Uchiyama J, Matsuzaki S, Murata K, Iwasaki K, Miyazaki N. Acid-stable capsid structure of Helicobacter pylori bacteriophage KHP30 by single-particle cryoelectron microscopy. Structure 2021; 30:300-312.e3. [PMID: 34597601 DOI: 10.1016/j.str.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 07/04/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
The acid-stable capsid structures of Helicobacter pylori phages KHP30 and KHP40 are solved at 2.7 and 3.0 Å resolutions by cryoelectron microscopy, respectively. The capsids have icosahedral T = 9 symmetry and consist of each 540 copies of 2 structural proteins, a major capsid protein, and a cement protein. The major capsid proteins form 12 pentagonal capsomeres occupying icosahedral vertexes and 80 hexagonal capsomeres located at icosahedral faces and edges. The major capsid protein has a unique protruding loop extending to the neighboring subunit that stabilizes hexagonal capsomeres. Furthermore, the capsid is decorated with trimeric cement proteins with a jelly roll motif. The cement protein trimer sits on the quasi-three-fold axis formed by three major capsid protein capsomeres, thereby enhancing the particle stability by connecting these capsomeres. Sequence and structure comparisons between the related Helicobacter pylori phages suggest a possible mechanism of phage adaptation to the human gastric environment.
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Affiliation(s)
- Ryosuke Kamiya
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan
| | - Jumpei Uchiyama
- Laboratory of Veterinary Microbiology I, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan; Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Shigenobu Matsuzaki
- Department of Clinical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University, Kochi 780-0955, Japan
| | - Kazuyoshi Murata
- National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Kenji Iwasaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan
| | - Naoyuki Miyazaki
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8777, Japan.
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7
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Sousa C, Ferreira R, Azevedo NF, Oleastro M, Azeredo J, Figueiredo C, Melo LDR. Helicobacter pylori infection: from standard to alternative treatment strategies. Crit Rev Microbiol 2021; 48:376-396. [PMID: 34569892 DOI: 10.1080/1040841x.2021.1975643] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Helicobacter pylori is the major component of the gastric microbiome of infected individuals and one of the aetiological factors of chronic gastritis, peptic ulcer disease and gastric cancer. The increasing resistance to antibiotics worldwide has made the treatment of H. pylori infection a challenge. As a way to overhaul the efficacy of currently used H. pylori antibiotic-based eradication therapies, alternative treatment strategies are being devised. These include probiotics and prebiotics as adjuvants in H. pylori treatment, antimicrobial peptides as alternatives to antibiotics, photodynamic therapy ingestible devices, microparticles and nanoparticles applied as drug delivery systems, vaccines, natural products, and phage therapy. This review provides an updated synopsis of these emerging H. pylori control strategies and discusses the advantages, hurdles, and challenges associated with their development and implementation. An effective human vaccine would be a major achievement although, until now, projects regarding vaccine development have failed or were discontinued. Numerous natural products have demonstrated anti-H. pylori activity, mostly in vitro, but further clinical studies are needed to fully disclose their role in H. pylori eradication. Finally, phage therapy has the potential to emerge as a valid alternative, but major challenges remain, namely the isolation of more H. pylori strictly virulent bacterio(phages).
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Affiliation(s)
- Cláudia Sousa
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Rute Ferreira
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Nuno F Azevedo
- Faculty of Engineering, LEPABE - Department of Chemical Engineering, University of Porto, Porto, Portugal
| | - Mónica Oleastro
- Department of Infectious Diseases, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Ceu Figueiredo
- i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal.,Ipatimup - Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal.,Faculty of Medicine, Department of Pathology, University of Porto, Porto, Portugal
| | - Luís D R Melo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
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FBPAII and rpoBC, the Two Novel Secreted Proteins Identified by the Proteomic Approach from a Comparative Study between Antibiotic-Sensitive and Antibiotic-Resistant Helicobacter pylori-Associated Gastritis Strains. Infect Immun 2021; 89:IAI.00053-21. [PMID: 33782154 DOI: 10.1128/iai.00053-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/17/2021] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori infection is the leading cause of chronic gastritis, which can develop into gastric cancer. Eliminating H. pylori infection with antibiotics achieves the prevention of gastric cancer. Currently, the prevalence of H. pylori resistance to clarithromycin and metronidazole, and the dual resistance to metronidazole and clarithromycin (C_R, M_R, and C/M_R, respectively), remains at a high level worldwide. As a means of exploring new candidate proteins for the management of H. pylori infection, secreted proteins from antibiotic-susceptible and antibiotic-resistant H. pylori-associated gastritis strains were obtained by in-solution tryptic digestion coupled with nano-liquid chromatography tandem mass spectrometry (nano-LC-MS/MS). A total of 583, 582, 590, and 578 differential expressed proteins were identified from C_R, M_R, C/M_R, and antibiotic-sensitive strain (S_S) samples, respectively. Of these, 23 overlapping proteins were found by Venn diagram analysis. Based on heat map analyses, the most and least differing protein expressions were observed from C/M_R strains and S_S strains, respectively. Of the proteins secreted by the S_S strain, only nine were found. After predicting the protein interaction with metronidazole and clarithromycin via the STITCH database, the two most interesting proteins were found to be rpoBC and FBPAII. After quantitative real-time reverse transcription PCR (qRT-PCR) analysis, a downregulation of rpoB from M_R strains was observed, suggesting a relationship of rpoB to metronidazole sensitivity. Inversely, an upregulation of fba from C_R, M_R, and C/M_R strains was noticed, suggesting the paradoxical expression of FBPAII and the fba gene. This report is the first to demonstrate the association of these two novel secreted proteins, namely, rpoBC and FBPAII, with antibiotic-sensitive H. pylori -associated gastritis strains.
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Xu D, Zhao S, Dou J, Xu X, Zhi Y, Wen L. Engineered endolysin-based "artilysins" for controlling the gram-negative pathogen Helicobacter pylori. AMB Express 2021; 11:63. [PMID: 33913058 PMCID: PMC8081812 DOI: 10.1186/s13568-021-01222-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/17/2021] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori infection can cause a variety of gastrointestinal diseases. In severe cases, there is a risk of gastric cancer. Antibiotics are often used for clinical treatment of H. pylori infections. However, because of antibiotic overuse in recent years and the emergence of multidrug-resistant bacteria, there is an urgent need to develop new treatment methods and drugs to achieve complete eradication of H. pylori. Endolysins and holins encoded by bacterial viruses (i.e., phages) represent a promising avenue of investigation. These lyase-based antibacterial drugs act on the bacterial cell wall to destroy the bacteria. Currently, a type of endolysin that has been studied more frequently acts on the amide bond between peptidoglycans, and holin is a transmembrane protein that can punch holes in the cell membrane. However, as a Gram-negative bacterium, H. pylori possesses a layer of impermeable lipopolysaccharides on the cell wall, which prevents endolysin interaction with the cell wall. Therefore, we designed a genetic linkage between an endolysin enzyme and a holin enzyme with a section of polypeptides (e.g., polycations and hydrophobic peptides) that enable penetration of the outer membrane. These complexes were designated “artilysins” and were efficiently expressed in Escherichia coli. In vitro bacteriostasis experiments showed that the purified artilysins had strong bacteriostatic effects on H. pylori. In addition, the surface of H. pylori was perforated and destroyed, as confirmed by electron microscopy, which was proved that artilysins had bacteriolytic effect on H. pylori.
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10
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Muñoz AB, Trespalacios-Rangel AA, Vale FF. An American lineage of Helicobacter pylori prophages found in Colombia. Helicobacter 2021; 26:e12779. [PMID: 33400833 DOI: 10.1111/hel.12779] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/30/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Helicobacter pylori is a human gastric carcinogen that is highly prevalent in Latin American. The prophages of H. pylori show a structured population and contribute to the diversity of this bacterium. However, H. pylori prophages present in American strains have not been described to date. In this study, we identified, characterized, and present the phylogenetic analysis of the prophages present in Colombian H. pylori strains. METHODS To characterize Colombian H. pylori strains and their prophages, a Multilocus Sequences Typing (MLST) and a Prophage Sequences Typing (PST), using the integrase and holin genes, were performed. Furthermore, five Colombian H. pylori had their full genome sequenced, and six Colombian H.pylori retrieved from databases, allowing to determine the prophage complete genome and insertion site. RESULTS The integrase gene frequency was 12.6% (27/213), while both integrase and holin genes were present in 4.2% (9/213) of the samples analyzed. The PST analysis showed that Colombian prophages belong to different populations, including hpSWEurope, hpNEurope, hpAfrica1, and a new population, named hpColombia. The MLST analysis classified most of the Colombia strains in the hpEurope population. CONCLUSIONS The new H. pylori prophage population revealed that Colombian prophages follow a unique evolutionary trajectory, contributing to bacterial diversity. The global H. pylori prophage phylogeny highlighted five phylogenetic groups, one more than previously reported. After the arrival of Europeans, the Colombian H. pylori bacteria and their prophages formed an independent evolutionary line to adapt to the new environment and new human hosts.
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Affiliation(s)
- Angela B Muñoz
- Infectious Diseases Research Group, Microbiology Department, Sciences Faculty, Pontificia Universidad Javeriana, Bogotá, Colombia.,Host-Pathogen Interactions Unit, Faculdade de Farmácia, Research Institute for Medicines (iMed-ULisboa, Universidade de Lisboa, Lisbon, Portugal
| | - Alba A Trespalacios-Rangel
- Infectious Diseases Research Group, Microbiology Department, Sciences Faculty, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Faculdade de Farmácia, Research Institute for Medicines (iMed-ULisboa, Universidade de Lisboa, Lisbon, Portugal
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11
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Muñoz AB, Stepanian J, Trespalacios AA, Vale FF. Bacteriophages of Helicobacter pylori. Front Microbiol 2020; 11:549084. [PMID: 33281754 PMCID: PMC7688985 DOI: 10.3389/fmicb.2020.549084] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
The bacterium Helicobacter pylori colonize the stomach in approximately half of the world’s population. Infection with this bacterium is associated with gastritis, peptic ulcer, adenocarcinoma, and gastric mucosa-associated lymphoid tissue lymphoma. Besides being a pathogen with worldwide prevalence, H. pylori show increasingly high antibiotic resistance rates, making the development of new therapeutic strategies against this bacterium challenging. Furthermore, H. pylori is a genetically diverse bacterium, which may be influenced by the presence of mobile genomic elements, including prophages. In this review, we analyze these issues and summarize various reports and findings related to phages and H. pylori, discussing the relationship between the presence of these elements and the genomic diversity, virulence, and fitness of this bacterium. We also analyze the state of the knowledge on the potential utility of bacteriophages as a therapeutic strategy for H. pylori.
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Affiliation(s)
- Angela B Muñoz
- Infectious Diseases Research Group, Microbiology Department, Sciences Faculty, Pontificia Universidad Javeriana, Bogotá, Colombia.,Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Johanna Stepanian
- Infectious Diseases Research Group, Microbiology Department, Sciences Faculty, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Alba Alicia Trespalacios
- Infectious Diseases Research Group, Microbiology Department, Sciences Faculty, Pontificia Universidad Javeriana, Bogotá, Colombia
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
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12
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Yahara K, Lehours P, Vale FF. Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species. Microb Genom 2019; 5. [PMID: 31310202 PMCID: PMC6755498 DOI: 10.1099/mgen.0.000282] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages are the most prevalent biological entities impacting on the ecosystem and are characterized by their extensive diversity. However, there are two aspects of phages that have remained largely unexplored: genetic flux by recombination between phage populations and characterization of specific phages in terms of the pan-genome. Here, we examined the recombination and pan-genome in Helicobacter pylori prophages at both the genome and gene level. In the genome-level analysis, we applied, for the first time, chromosome painting and fineSTRUCTURE algorithms to a phage species, and showed novel trends in inter-population genetic flux. Notably, hpEastAsia is a phage population that imported a higher proportion of DNA fragments from other phages, whereas the hpSWEurope phages showed weaker signatures of inter-population recombination, suggesting genetic isolation. The gene-level analysis showed that, after parameter tuning of the prokaryote pan-genome analysis program, H. pylori phages have a pan-genome consisting of 75 genes and a soft-core genome of 10 genes, which includes genes involved in the lytic and lysogenic life cycles. Quantitative analysis of recombination events of the soft-core genes showed no substantial variation in the intensity of recombination across the genes, but rather equally frequent recombination among housekeeping genes that were previously reported to be less prone to recombination. The signature of frequent recombination appears to reflect the host–phage evolutionary arms race, either by contributing to escape from bacterial immunity or by protecting the host by producing defective phages.
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Affiliation(s)
- Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, 4-2-1 Aobacho, Higashimurayama, Tokyo 189-0002, Japan
| | - Philippe Lehours
- French National Reference Center for Campylobacters and Helicobacters, Bordeaux, France.,University of Bordeaux, INSERM, UMR1053 Bordeaux Research in Translational Oncology, BaRITOn, 33076 Bordeaux, France
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia da Universidade de Lisboa, Lisboa, Portugal
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13
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Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM. Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology. Viruses 2019; 11:E76. [PMID: 30669250 PMCID: PMC6356626 DOI: 10.3390/v11010076] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
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Affiliation(s)
- Sari Mäntynen
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Lotta-Riina Sundberg
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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14
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Vale FF, Lehours P. Relating Phage Genomes to Helicobacter pylori Population Structure: General Steps Using Whole-Genome Sequencing Data. Int J Mol Sci 2018; 19:ijms19071831. [PMID: 29933614 PMCID: PMC6073503 DOI: 10.3390/ijms19071831] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 05/30/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
The review uses the Helicobacter pylori, the gastric bacterium that colonizes the human stomach, to address how to obtain information from bacterial genomes about prophage biology. In a time of continuous growing number of genomes available, this review provides tools to explore genomes for prophage presence, or other mobile genetic elements and virulence factors. The review starts by covering the genetic diversity of H. pylori and then moves to the biologic basis and the bioinformatics approaches used for studding the H. pylori phage biology from their genomes and how this is related with the bacterial population structure. Aspects concerning H. pylori prophage biology, evolution and phylogeography are discussed.
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Affiliation(s)
- Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Faculdade de Farmácia, Universidade de Lisboa, 1649-003 Lisboa, Portugal.
| | - Philippe Lehours
- Laboratoire de Bacteriologie, Centre National de Référence des Campylobacters et Hélicobacters, Place Amélie Raba Léon, 33076 Bordeaux, France.
- INSERM U1053-UMR Bordeaux Research in Translational Oncology, BaRITOn, 33000 Bordeaux, France.
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15
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Takeuchi H, Kira M, Konishi S, Uchiyama J, Matsuzaki S, Matsumura Y. Polymorphisms in the Helicobacter pylori NY43 strain and its prophage-cured derivatives. MICROBIOLOGY-SGM 2018; 164:877-882. [PMID: 29738305 DOI: 10.1099/mic.0.000665] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This study aimed to determine the characteristics of the Helicobacter pylori host NY43 strain and its prophage-cured derivative. H. pylori colonizing the human stomach cause many diseases. They show high genetic diversity, allowing the development of mutant strains that can form bacterial communities adapted to specific environmental conditions. Bacteriophage activities are associated with bacterial evolution, including pathogenicity development. Herein, we reported the complete genome sequence and genomic organization of two H. pylori prophages, KHP30 and KHP40; the effects of KHP30 on the behaviours of NY43 are not yet known. We showed that approximately 57 % prophage-cured derivatives spontaneously appeared in the exponential phase during liquid culture, and the biological characteristics of these derivatives differed from those of the host NY43. KHP30 reinfected the cured derivatives, and the curing ratio was influenced by culture conditions. KHP30 was shown to promote the development of a flexible H. pylori community with variable characteristics.
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Affiliation(s)
- Hiroaki Takeuchi
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Mizuki Kira
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Sayuri Konishi
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Jumpei Uchiyama
- Laboratory of Veterinary Microbiology I, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Shigenobu Matsuzaki
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Yoshihisa Matsumura
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
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16
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Uchiyama J, Taniguchi M, Kurokawa K, Takemura-Uchiyama I, Ujihara T, Shimakura H, Sakaguchi Y, Murakami H, Sakaguchi M, Matsuzaki S. Adsorption of Staphylococcus viruses S13′ and S24-1 on Staphylococcus aureus strains with different glycosidic linkage patterns of wall teichoic acids. J Gen Virol 2017; 98:2171-2180. [DOI: 10.1099/jgv.0.000865] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Jumpei Uchiyama
- School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Maya Taniguchi
- School of Veterinary Medicine, Azabu University, Kanagawa, Japan
| | - Kenji Kurokawa
- Faculty of Pharmaceutical Sciences, Nagasaki International University, Nagasaki, Japan
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17
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Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical origins. Sci Rep 2017; 7:42471. [PMID: 28205536 PMCID: PMC5311958 DOI: 10.1038/srep42471] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 12/19/2022] Open
Abstract
Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6–33.0 Kbp, consisting of 27–39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3′ end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.
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18
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Uchiyama J, Takemura-Uchiyama I, Kato SI, Takeuchi H, Sakaguchi Y, Ujihara T, Daibata M, Shimakura H, Okamoto N, Sakaguchi M, Matsuzaki S. Screening of KHP30-like prophages among Japanese Helicobacter pylori strains, and genetic analysis of a defective KHP30-like prophage sequence integrated in the genome of the H. pylori strain NY40. FEMS Microbiol Lett 2016; 363:fnw157. [PMID: 27388014 DOI: 10.1093/femsle/fnw157] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/09/2016] [Indexed: 12/11/2022] Open
Abstract
We have recently reported the active Helicobacter pylori bacteriophages (phages), KHP30 and KHP40, the genomic DNAs of which exist as episomes in host bacterial strains isolated in Japan (i.e. pseudolysogeny). In this study, we examined the possibility of the lysogeny of active KHP30-like phages in Japanese H. pylori strains, because their genomes contain a putative integrase gene. Only the NY40 strain yielded partial detection of a KHP30-like prophage sequence in PCR among 174 Japanese H. pylori isolates, except for strains producing the above active phages. Next, according to the genomic analysis of the NY40 strain, the KHP30-like prophage sequence was found to be located from ca. 524 to 549 kb in the host chromosome. The attachment sites, attL and attR, in the NY40 genome showed almost the same genomic location and sequence as those detected in a French isolate B38, suggesting that an active parental KHP30-like phage had integrated into the ancestral NY40 genome in a site-specific manner. The prophage found in the NY40 genome was assumed to have been genetically modified, after site-specific integration. These, together with the data in the KHP30-like prophages of other H. pylori genomes, suggest that the lysogenic state of the KHP30-like phages is generally unstable.
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Affiliation(s)
- Jumpei Uchiyama
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Iyo Takemura-Uchiyama
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Shin-Ichiro Kato
- Research Institute of Molecular Genetics, Kochi University, Kochi 783-8502, Japan
| | - Hiroaki Takeuchi
- Department of Clinical Laboratory Medicine, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Yoshihiko Sakaguchi
- Department of Microbiology, Kitasato University School of Medicine, Kanagawa 252-0374, Japan
| | - Takako Ujihara
- Science Research Center, Kochi University, Kochi 783-8505, Japan
| | - Masanori Daibata
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
| | - Hidekatsu Shimakura
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Noriaki Okamoto
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Masahiro Sakaguchi
- Department of Veterinary Microbiology, School of Veterinary Medicine, Azabu University, Kanagawa 252-5201, Japan
| | - Shigenobu Matsuzaki
- Department of Microbiology and Infection, Kochi Medical School, Kochi University, Kochi 783-8505, Japan
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19
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Fan X, Li Y, He R, Li Q, He W. Comparative analysis of prophage-like elements in Helicobacter sp. genomes. PeerJ 2016; 4:e2012. [PMID: 27169002 PMCID: PMC4860318 DOI: 10.7717/peerj.2012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 04/14/2016] [Indexed: 12/11/2022] Open
Abstract
Prophages are regarded as one of the factors underlying bacterial virulence, genomic diversification, and fitness, and are ubiquitous in bacterial genomes. Information on Helicobacter sp. prophages remains scarce. In this study, sixteen prophages were identified and analyzed in detail. Eight of them are described for the first time. Based on a comparative genomic analysis, these sixteen prophages can be classified into four different clusters. Phylogenetic relationships of Cluster A Helicobacter prophages were investigated. Furthermore, genomes of Helicobacter prophages from Clusters B, C, and D were analyzed. Interestingly, some putative antibiotic resistance proteins and virulence factors were associated with Helicobacter prophages.
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Affiliation(s)
- Xiangyu Fan
- School of Biological Science and Technology, University of Jinan , Jinan , China
| | - Yumei Li
- School of Biological Science and Technology, University of Jinan , Jinan , China
| | - Rong He
- School of Biological Science and Technology, University of Jinan , Jinan , China
| | - Qiang Li
- School of Biological Science and Technology, University of Jinan , Jinan , China
| | - Wenxing He
- School of Biological Science and Technology, University of Jinan , Jinan , China
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20
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Lee WC, Anton BP, Wang S, Baybayan P, Singh S, Ashby M, Chua EG, Tay CY, Thirriot F, Loke MF, Goh KL, Marshall BJ, Roberts RJ, Vadivelu J. The complete methylome of Helicobacter pylori UM032. BMC Genomics 2015; 16:424. [PMID: 26031894 PMCID: PMC4450513 DOI: 10.1186/s12864-015-1585-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 04/27/2015] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome). RESULTS The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning. CONCLUSION Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori.
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Affiliation(s)
- Woon Ching Lee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Brian P Anton
- New England Biolabs, 240 County Road, Ipswich, MA, 01938, USA.
| | - Susana Wang
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA.
| | - Primo Baybayan
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA.
| | | | - Meredith Ashby
- Pacific Biosciences, 1380 Willow Road, Menlo Park, CA, 94025, USA.
| | - Eng Guan Chua
- Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia.
| | - Chin Yen Tay
- Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia.
| | - Fanny Thirriot
- Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia.
| | - Mun Fai Loke
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Khean Lee Goh
- Department of Medicine, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Barry J Marshall
- Marshall Centre, School of Pathology & Laboratory Medicine, The University of Western Australia, 6009, Perth, Australia.
| | | | - Jamuna Vadivelu
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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21
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You Y, He L, Zhang M, Zhang J. Comparative genomics of a Helicobacter pylori isolate from a Chinese Yunnan Naxi ethnic aborigine suggests high genetic divergence and phage insertion. PLoS One 2015; 10:e0120659. [PMID: 25799515 PMCID: PMC4370579 DOI: 10.1371/journal.pone.0120659] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Accepted: 01/07/2015] [Indexed: 02/07/2023] Open
Abstract
Helicobacter pylori is a common pathogen correlated with several severe digestive diseases. It has been reported that isolates associated with different geographic areas, different diseases and different individuals might have variable genomic features. Here, we describe draft genomic sequences of H. pylori strains YN4-84 and YN1-91 isolated from patients with gastritis from the Naxi and Han populations of Yunnan, China, respectively. The draft sequences were compared to 45 other publically available genomes, and a total of 1059 core genes were identified. Genes involved in restriction modification systems, type four secretion system three (TFS3) and type four secretion system four (TFS4), were identified as highly divergent. Both YN4-84 and YN1-91 harbor intact cag pathogenicity island (cagPAI) and have EPIYA-A/B/D type at the carboxyl terminal of cagA. The vacA gene type is s1m2i1. Another major finding was a 32.5-kb prophage integrated in the YN4-84 genome. The prophage shares most of its genes (30/33) with Helicobacter pylori prophage KHP30. Moreover, a 1,886 bp transposable sequence (IS605) was found in the prophage. Our results imply that the Naxi ethnic minority isolate YN4-84 and Han isolate YN1-91 belong to the hspEAsia subgroup and have diverse genome structure. The genome has been extensively modified in several regions involved in horizontal DNA transfer. The important roles played by phages in the ecology and microevolution of H. pylori were further emphasized. The current data will provide valuable information regarding the H. pylori genome based on historic human migrations and population structure.
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Affiliation(s)
- Yuanhai You
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Lihua He
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Maojun Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
| | - Jianzhong Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang, China
- * E-mail:
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22
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Atanasova NS, Senčilo A, Pietilä MK, Roine E, Oksanen HM, Bamford DH. Comparison of lipid-containing bacterial and archaeal viruses. Adv Virus Res 2015; 92:1-61. [PMID: 25701885 DOI: 10.1016/bs.aivir.2014.11.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Lipid-containing bacteriophages were discovered late and considered to be rare. After further phage isolations and the establishment of the domain Archaea, several new prokaryotic viruses with lipids were observed. Consequently, the presence of lipids in prokaryotic viruses is reasonably common. The wealth of information about how prokaryotic viruses use their lipids comes from a few well-studied model viruses (PM2, PRD1, and ϕ6). These bacteriophages derive their lipid membranes selectively from the host during the virion assembly process which, in the case of PM2 and PRD1, culminates in the formation of protein capsid with an inner membrane, and for ϕ6 an outer envelope. Several inner membrane-containing viruses have been described for archaea, and their lipid acquisition models are reminiscent to those of PM2 and PRD1. Unselective acquisition of lipids has been observed for bacterial mycoplasmaviruses and archaeal pleolipoviruses, which resemble each other by size, morphology, and life style. In addition to these shared morphotypes of bacterial and archaeal viruses, archaea are infected by viruses with unique morphotypes, such as lemon-shaped, helical, and globular ones. It appears that structurally related viruses may or may not have a lipid component in the virion, suggesting that the significance of viral lipids might be to provide viruses extended means to interact with the host cell.
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Affiliation(s)
- Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Ana Senčilo
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maija K Pietilä
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Elina Roine
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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23
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Lin D, Koskella B. Friend and foe: factors influencing the movement of the bacterium Helicobacter pylori along the parasitism-mutualism continuum. Evol Appl 2014; 8:9-22. [PMID: 25667600 PMCID: PMC4310578 DOI: 10.1111/eva.12231] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 10/14/2014] [Indexed: 12/11/2022] Open
Abstract
Understanding the transition of bacterial species from commensal to pathogen, or vice versa, is a key application of evolutionary theory to preventative medicine. This requires working knowledge of the molecular interaction between hosts and bacteria, ecological interactions among microbes, spatial variation in bacterial prevalence or host life history, and evolution in response to these factors. However, there are very few systems for which such broad datasets are available. One exception is the gram-negative bacterium, Helicobacter pylori, which infects upwards of 50% of the global human population. This bacterium is associated with a wide breadth of human gastrointestinal disease, including numerous cancers, inflammatory disorders, and pathogenic infections, but is also known to confer fitness benefits to its host both indirectly, through interactions with other pathogens, and directly. Outstanding questions are therefore why, when, and how this bacterium transitions along the parasitism–mutualism continuum. We examine known virulence factors, genetic predispositions of the host, and environmental contributors that impact progression of clinical disease and help define geographical trends in disease incidence. We also highlight the complexity of the interaction and discuss future therapeutic strategies for disease management and public health in light of the longstanding evolutionary history between the bacterium and its human host.
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24
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Quiles-Puchalt N, Martínez-Rubio R, Ram G, Lasa Í, Penadés JR. Unravelling bacteriophage ϕ11 requirements for packaging and transfer of mobile genetic elements inStaphylococcus aureus. Mol Microbiol 2014; 91:423-37. [DOI: 10.1111/mmi.12445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Nuria Quiles-Puchalt
- Instituto de Biomedicina de Valencia (IBV-CSIC); 46010 Valencia Spain
- Centro de Investigación y Tecnología Animal; Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA); 12400 Segorbe Castellón Spain
| | - Roser Martínez-Rubio
- Centro de Investigación y Tecnología Animal; Instituto Valenciano de Investigaciones Agrarias (CITA-IVIA); 12400 Segorbe Castellón Spain
- Cardenal Herrera-CEU University; 46113 Moncada Valencia Spain
| | - Geeta Ram
- Skirball Institute Program in Molecular Pathogenesis and Departments of Microbiology and Medicine; New York University Medical Center; New York NY 10016 USA
| | - Íñigo Lasa
- Instituto de Agrobiotecnología; CSIC-Universidad Pública de Navarra; 31006 Pamplona Navarra Spain
| | - José R. Penadés
- Instituto de Biomedicina de Valencia (IBV-CSIC); 46010 Valencia Spain
- Institute of Infection, Immunity and Inflammation; College of Medical; Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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25
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Abdel-Haliem MEF, Askora A. Isolation and characterization of bacteriophages of Helicobacter pylori isolated from Egypt. Future Virol 2013. [DOI: 10.2217/fvl.13.58] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aim: The aim of this work was to isolate and characterize bacteriophages from wastewater for the pathogenic bacteria Helicobacter pylori. Materials & methods: In this study, we isolated and characterized two phages against H. pylori isolated from gastric biopsies. The specific phages were isolated by the single plaque isolation technique, propagated by the liquid enrichment method and purified by the polyethylene glycol–dextran sulfate two-phase system. Results: The phages were designated as φHPE1 and φHPE2; φHPE1 had a head with a diameter of approximately 62 nm and short noncontractile tail with a length and width of approximately 12 × 6 nm and φHPE2 had an isometric head with a diameter of approximately 92.5 nm and a tail with a length of approximately 180 nm and width of approximately 15 nm. The host ranges were investigated with four strains of Helicobacter and all strains were susceptible to either φHPE1 or φHPE2. Conclusion: These results suggest that it may be possible to use this phage to control the disease caused by H. pylori.
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Affiliation(s)
| | - Ahmed Askora
- Department of Botany, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt
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