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Akbari A, Noorbakhsh Varnosfaderani SM, Haeri MS, Fathi Z, Aziziyan F, Yousefi Rad A, Zalpoor H, Nabi-Afjadi M, Malekzadegan Y. Autophagy induced by Helicobacter Pylori infection can lead to gastric cancer dormancy, metastasis, and recurrence: new insights. Hum Cell 2024; 37:139-153. [PMID: 37924488 DOI: 10.1007/s13577-023-00996-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
According to the findings of recent research, Helicobacter Pylori (H. pylori) infection is not only the primary cause of gastric cancer (GC), but it is also linked to the spread and invasion of GC through a number of processes and factors that contribute to virulence. In this study, we discussed that H. pylori infection can increase autophagy in GC tumor cells, leading to poor prognosis in such patients. Until now, the main concerns have been focused on H. pylori's role in GC development. According to our hypothesis, however, H. pylori infection may also lead to GC dormancy, metastasis, and recurrence by stimulating autophagy. Therefore, understanding how H. pylori possess these processes through its virulence factors and various microRNAs can open new windows for providing new prevention and/or therapeutic approaches to combat GC dormancy, metastasis, and recurrence which can occur in GC patients with H. pylori infection with targeting autophagy and eradicating H. pylori infection.
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Affiliation(s)
- Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | | | - Melika Sadat Haeri
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zeinab Fathi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Aziziyan
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Yousefi Rad
- Department of Biochemistry, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Mohsen Nabi-Afjadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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2
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Jala I, Almanfaluthi ML, Laha T, Kanthawong S, Tangkawattana S, Saichua P, Suttiprapa S, Sripa B. Helicobacter pylori GroEL Seropositivity Is Associated with an Increased Risk of Opisthorchis viverrini-Associated Hepatobiliary Abnormalities and Cholangiocarcinoma. THE KOREAN JOURNAL OF PARASITOLOGY 2021; 59:363-368. [PMID: 34470087 PMCID: PMC8413853 DOI: 10.3347/kjp.2021.59.4.363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/02/2021] [Indexed: 11/23/2022]
Abstract
Despite the synergistic effect of Opisthorchis viverrini and Helicobacter pylori co-infection on pathogenesis of severe hepatobiliary abnormalities (HBA) including advanced periductal fibrosis and replace with cholangiocarcinoma (CCA) have been established, the immune response to H. pylori in O. viverrini infected population has never been explored. Hence, this study aimed to investigate the antibody responses to 2 immunogenic H. pylori proteins in O. viverrini-infected patients with HBA and CCA. The risk analysis by multinomial logistic regression revealed that GroEL seropositivity was associated with higher risks of hepatobiliary abnormalities and CCA with adjusted odds ratios (95% confidence intervals) of 2.11 (95% CI=1.20-3.71, P=0.008) and 2.13 (95% CI=1.21-3.75, P=0.009), respectively. These findings indicate that GroEL seropositivity might be a biomarker for early detection of O. viverrini associated HBA and CCA.
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Affiliation(s)
- Isabelle Jala
- Tropical Medicine Graduate Program (International Program), Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Muhammad Luthfi Almanfaluthi
- Tropical Medicine Graduate Program (International Program), Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Thewarach Laha
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sakawrat Kanthawong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sirikachorn Tangkawattana
- WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathobiology, Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Prasert Saichua
- Tropical Medicine Graduate Program (International Program), Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sutas Suttiprapa
- Tropical Medicine Graduate Program (International Program), Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Banchob Sripa
- WHO Collaborating Centre for Research and Control of Opisthorchiasis (Southeast Asian Liver Fluke Disease), Tropical Disease Research Centre, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Department of Pathology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
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3
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Wang Z, Lv Z, Xu Q, Sun L, Yuan Y. Identification of differential proteomics in Epstein-Barr virus-associated gastric cancer and related functional analysis. Cancer Cell Int 2021; 21:368. [PMID: 34247602 PMCID: PMC8274036 DOI: 10.1186/s12935-021-02077-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/05/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Epstein-Barr virus-associated gastric cancer (EBVaGC) is the most common EBV-related malignancy. A comprehensive research for the protein expression patterns in EBVaGC established by high-throughput assay remains lacking. In the present study, the protein profile in EBVaGC tissue was explored and related functional analysis was performed. METHODS Epstein-Barr virus-encoded RNA (EBER) in situ hybridization (ISH) was applied to EBV detection in GC cases. Data-independent acquisition (DIA) mass spectrometry (MS) was performed for proteomics assay of EBVaGC. Functional analysis of identified proteins was conducted with bioinformatics methods. Immunohistochemistry (IHC) staining was employed to detect protein expression in tissue. RESULTS The proteomics study for EBVaGC was conducted with 7 pairs of GC cases. A total of 137 differentially expressed proteins in EBV-positive GC group were identified compared with EBV-negative GC group. A PPI network was constructed for all of them, and several proteins with relatively high interaction degrees could be the hub genes in EBVaGC. Gene enrichment analysis showed they might be involved in the biological pathways related to energy and biochemical metabolism. Combined with GEO datasets, a highly associated protein (GBP5) with EBVaGC was screened out and validated with IHC staining. Further analyses demonstrated that GBP5 protein might be associated with clinicopathological parameters and EBV infection in GC. CONCLUSIONS The newly identified proteins with significant differences and potential central roles could be applied as diagnostic markers of EBVaGC. Our study would provide research clues for EBVaGC pathogenesis as well as novel targets for the molecular-targeted therapy of EBVaGC.
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Affiliation(s)
- Zeyang Wang
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Zhi Lv
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Qian Xu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Liping Sun
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, Liaoning Province, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China
| | - Yuan Yuan
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, No.155 NanjingBei Street, Heping District, Shenyang, 110001, Liaoning Province, China. .,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, The First Hospital of China Medical University, Shenyang, 110001, China. .,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, The First Hospital of China Medical University, Shenyang, 110001, China.
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Lettl C, Haas R, Fischer W. Kinetics of CagA type IV secretion by Helicobacter pylori and the requirement for substrate unfolding. Mol Microbiol 2021; 116:794-807. [PMID: 34121254 DOI: 10.1111/mmi.14772] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 06/02/2021] [Accepted: 06/12/2021] [Indexed: 12/27/2022]
Abstract
Type IV secretion of effector proteins is an important principle for interaction of human pathogens with their target cells. The corresponding secretion systems may transport a multitude of effector proteins that have to be deployed in the respective spatiotemporal context, or only a single translocated protein, as in the case of the CagA effector protein produced by the human gastric pathogen Helicobacter pylori. For a more detailed analysis of the kinetics and mode of action of CagA type IV secretion by H. pylori, we describe here, a novel, highly sensitive split luciferase-based translocation reporter which can be easily adapted to different end-point or real-time measurements. Using this reporter, we showed that H. pylori cells are able to rapidly inject a limited amount of their CagA supply into cultured gastric epithelial cells. We have further employed the reporter system to address the question whether CagA has to be unfolded prior to translocation by the type IV secretion system. We showed that protein domains co-translocated with CagA as protein fusions are more readily tolerated as substrates than in other secretion systems, but also provide evidence that unfolding of effector proteins is a prerequisite for their transport.
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Affiliation(s)
- Clara Lettl
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Munich, Germany.,Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Munich, Germany.,Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
| | - Wolfgang Fischer
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Medical Faculty, LMU Munich, Munich, Germany.,Partner Site Munich, German Center for Infection Research (DZIF), Munich, Germany
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5
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Zhang F, Chen C, Hu J, Su R, Zhang J, Han Z, Chen H, Li Y. Molecular mechanism of Helicobacter pylori-induced autophagy in gastric cancer. Oncol Lett 2019; 18:6221-6227. [PMID: 31788098 DOI: 10.3892/ol.2019.10976] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 07/26/2019] [Indexed: 12/14/2022] Open
Abstract
Helicobacter pylori (H. pylori) is a gram-negative pathogen that colonizes gastric epithelial cells. The drug resistance rates of H. pylori have dramatically increased, causing persistent infections. Chronic infection by H. pylori is a critical cause of gastritis, peptic ulcers and even gastric cancer. In host cells, autophagy is stimulated to maintain cellular homeostasis following intracellular pathogen recognition by the innate immune defense system. However, H. pylori-induced autophagy is not consistent during acute and chronic infection. Therefore, a deeper understanding of the association between H. pylori infection and autophagy in gastric epithelial cells could aid the understanding of the mechanisms of persistent infection and the identification of autophagy-associated therapeutic targets for H. pylori infection. The present review describes the role of H. pylori and associated virulence factors in the induction of autophagy by different signaling pathways during acute infection. Additionally, the inhibition of autophagy in gastric epithelial cells during chronic infection was discussed. The present review summarized H. pylori-mediated autophagy and provided insights into its mechanism of action, suggesting the induction of autophagy as a novel therapeutic target for persistent H. pylori infection.
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Affiliation(s)
- Fan Zhang
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Cong Chen
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Jike Hu
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Ruiliang Su
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Junqiang Zhang
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Zhijian Han
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Hao Chen
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
| | - Yumin Li
- Department of Oncology Surgery, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China.,Key Laboratory of Digestive System Tumors of Gansu Province, Lanzhou University Second Hospital, Lanzhou, Gansu 730030, P.R. China
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6
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Kim SH. Comparative Proteome Analysis of Zerumbone-treated Helicobacter pylori. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2018. [DOI: 10.15324/kjcls.2018.50.3.275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sa-Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon, Korea
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7
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Liao HY, Chien CC, Tang P, Chen CC, Chen CY, Chen SC. The integrated analysis of transcriptome and proteome for exploring the biodegradation mechanism of 2, 4, 6-trinitrotoluene by Citrobacter sp. JOURNAL OF HAZARDOUS MATERIALS 2018; 349:79-90. [PMID: 29414755 DOI: 10.1016/j.jhazmat.2018.01.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 01/16/2018] [Accepted: 01/21/2018] [Indexed: 06/08/2023]
Abstract
Citrobacter sp. has been shown to degrade 2,4,6-trinitrotoluene (TNT). However, the mechanism of its TNT biodegradation is poorly understood. An integrated proteome and transcriptome analysis was performed for investigating the differential genes and differential proteins in bacterial growth at the onset of experiments and after 12 h treatment with TNT. With the RNA sequencing, we found a total of 3792 transcripts and 569 differentially expressed genes (≥2 fold, P < 0.05) by. Genes for amino acid transport, cellular metabolism and stress-shock proteins were up-regulated, while carbohydrate transport and metabolism were down-regulated. A total of 42 protein spots (≥1.5 fold, P < 0.05) showed differential expression on two-dimensional gel electrophoresis and these proteins were identified by mass spectrometry. The most prominent proteins up-regulated were involved in energy production and conversion, amino acid transport and metabolism, posttranslational modification, protein turnover and chaperones. Proteins involved in carbohydrate transport and metabolism were down-regulated. Most notably, we observed that nemA encoding N-ethylmaleimide reductase was the most up-regulated gene involved in TNT degradation, and further proved that it can transform TNT to 4-amino-2,6-dinitrotoluene (4-ADNT) and 2-amino-4,6-dinitrotoluene (2-ADNT). This study highlights the molecular mechanisms of Citrobacter sp. for TNT removal.
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Affiliation(s)
- Hung-Yu Liao
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Chih-Ching Chien
- Graduate School of Biotechnology and Bioengineering, Yuan Ze University, No. 135, Yuantung Rd., Jhongli City, Taoyuan, 32003, Taiwan
| | - Petrus Tang
- Department of Parasitology, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dis., Taoyuan City, 33302, Taiwan
| | - Chien-Cheng Chen
- Department of Biotechnology, National Kaohsiung Normal University, No.116, Heping 1st Rd., Lingya District, Kaohsiung City, 80201, Taiwan
| | - Chin-Yu Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan
| | - Ssu-Ching Chen
- Department of Life Sciences, National Central University, No. 300, Jhing-da Rd., Jhongli City, Taoyuan, 32001, Taiwan.
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8
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Wuchty S, Müller SA, Caufield JH, Häuser R, Aloy P, Kalkhof S, Uetz P. Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. Mol Cell Proteomics 2018; 17:961-973. [PMID: 29414760 DOI: 10.1074/mcp.ra117.000474] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/25/2018] [Indexed: 01/17/2023] Open
Abstract
Helicobacter pylori is a common pathogen that is estimated to infect half of the human population, causing several diseases such as duodenal ulcer. Despite one of the first pathogens to be sequenced, its proteome remains poorly characterized as about one-third of its proteins have no functional annotation. Here, we integrate and analyze known protein interactions with proteomic and genomic data from different sources. We find that proteins with similar abundances tend to interact. Such an observation is accompanied by a trend of interactions to appear between proteins of similar functions, although some show marked cross-talk to others. Protein function prediction with protein interactions is significantly improved when interactions from other bacteria are included in our network, allowing us to obtain putative functions of more than 300 poorly or previously uncharacterized proteins. Proteins that are critical for the topological controllability of the underlying network are significantly enriched with genes that are up-regulated in the spiral compared with the coccoid form of H. pylori Determining their evolutionary conservation, we present evidence that 80 protein complexes are identical in composition with their counterparts in Escherichia coli, while 85 are partially conserved and 120 complexes are completely absent. Furthermore, we determine network clusters that coincide with related functions, gene essentiality, genetic context, cellular localization, and gene expression in different cellular states.
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Affiliation(s)
- Stefan Wuchty
- From the ‡Dept. of Computer Science.,§Center for Computational Science.,¶Dept. of Biology.,‖Sylvester Comprehensive Cancer Center, Univ. of Miami, Miami, FL 33156
| | - Stefan A Müller
- **German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany
| | - J Harry Caufield
- ‡‡Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VI 23284
| | - Roman Häuser
- §§German Cancer Research Center, 69120 Heidelberg, Germany
| | - Patrick Aloy
- ¶¶Joint IRB-BSC-CRG Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona) and the Barcelona Institute of Science and Technology. Barcelona, Catalonia, Spain.,‖‖Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
| | - Stefan Kalkhof
- Department of Molecular Systems Biology, UFZ, Helmholtz-Centre for Environmental Research Leipzig, 04318 Leipzig, Germany.,Institute of Bioanalysis, University of Applied Sciences and Arts of Coburg, Friedrich-Streib-Str. 2, 96450 Coburg, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Therapy Validation, 04103 Leipzig, Germany
| | - Peter Uetz
- ‡‡Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VI 23284
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9
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Horvatić A, Kuleš J, Guillemin N, Galan A, Mrljak V, Bhide M. High-throughput proteomics and the fight against pathogens. MOLECULAR BIOSYSTEMS 2017; 12:2373-84. [PMID: 27227577 DOI: 10.1039/c6mb00223d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pathogens pose a major threat to human and animal welfare. Understanding the interspecies host-pathogen protein-protein interactions could lead to the development of novel strategies to combat infectious diseases through the rapid development of new therapeutics. The first step in understanding the host-pathogen crosstalk is to identify interacting proteins in order to define crucial hot-spots in the host-pathogen interactome, such as the proposed pharmaceutical targets by means of high-throughput proteomic methodologies. In order to obtain holistic insight into the inter- and intra-species bimolecular interactions, apart from the proteomic approach, sophisticated in silico modeling is used to correlate the obtained large data sets with other omics data and clinical outcomes. Since the main focus in this area has been directed towards human medicine, it is time to extrapolate the existing expertise to a new emerging field: the 'systems veterinary medicine'. Therefore, this review addresses high-throughput mass spectrometry-based technology for monitoring protein-protein interactions in vitro and in vivo and discusses pathogen cultivation, model host cells and available bioinformatic tools employed in vaccine development.
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Affiliation(s)
- Anita Horvatić
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Josipa Kuleš
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Nicolas Guillemin
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Asier Galan
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Vladimir Mrljak
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia.
| | - Mangesh Bhide
- ERA Chair VetMedZg Project, Internal Diseases Clinic, Faculty of Veterinary Medicine, University of Zagreb, Heinzelova 55, 10 000 Zagreb, Croatia. and Laboratory of Biomedical Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Kosice, Slovakia and Institute of Neuroimmunology, Slovakia Academy of Sciences, Bratislava, Slovakia
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10
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Bernardini G, Figura N, Ponzetto A, Marzocchi B, Santucci A. Application of proteomics to the study of Helicobacter pylori and implications for the clinic. Expert Rev Proteomics 2017; 14:477-490. [PMID: 28513226 DOI: 10.1080/14789450.2017.1331739] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Helicobacter pylori (H. pylori) is a gram-negative bacterium that colonizes the gastric epithelium and mucous layer of more than half the world's population. H. pylori is a primary human pathogen, responsible for the development of chronic gastritis, peptic ulceration and gastric cancer. Proteomics is impacting several aspects of medical research: understanding the molecular basis of infection and disease manifestation, identification of therapeutic targets and discovery of clinically relevant biomarkers. Areas covered: The main aim of the present review is to provide a comprehensive overview of the contribution of proteomics to the study of H. pylori infection pathophysiology. In particular, we focused on the role of the bacterium and its most important virulence factor, CagA, in the progression of gastric cells transformation and cancer progression. We also discussed the proteomic approaches aimed at the investigation of the host response to bacterial infection. Expert commentary: In the field of proteomics of H. pylori, comprehensive analysis of clinically relevant proteins (functional proteomics) rather than entire proteomes will result in important medical outcomes. Finally, we provided an outlook on the potential development of proteomics in H. pylori research.
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Affiliation(s)
- Giulia Bernardini
- a Dipartimento di Biotecnologie , Chimica e Farmacia, Università degli Studi di Siena , Siena , Italy
| | - Natale Figura
- a Dipartimento di Biotecnologie , Chimica e Farmacia, Università degli Studi di Siena , Siena , Italy
| | - Antonio Ponzetto
- b Dipartimento di Scienze Mediche , Università degli Studi di Torino , Torino , Italy
| | - Barbara Marzocchi
- a Dipartimento di Biotecnologie , Chimica e Farmacia, Università degli Studi di Siena , Siena , Italy
| | - Annalisa Santucci
- a Dipartimento di Biotecnologie , Chimica e Farmacia, Università degli Studi di Siena , Siena , Italy
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11
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De Re V, Repetto O, Zanussi S, Casarotto M, Caggiari L, Canzonieri V, Cannizzaro R. Protein signature characterizing Helicobacter pylori strains of patients with autoimmune atrophic gastritis, duodenal ulcer and gastric cancer. Infect Agent Cancer 2017; 12:22. [PMID: 28465717 PMCID: PMC5408474 DOI: 10.1186/s13027-017-0133-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 04/13/2017] [Indexed: 12/12/2022] Open
Abstract
Background Helicobacter pylori (H. pylori) represents a key factor in the etiology of autoimmune atrophic gastritis (AAG), duodenal ulcer (DU) and gastric cancer (GC). The aim of this study was to characterize the differential protein expression of H. pylori isolated from gastric biopsies of patients affected by either AAG, DU or GC. Methods The H. pylori strains were isolated from endoscopic biopsies from the stomach of patients with gastric disease. Protein profiles of H. pylori were compared by two-dimensional difference in gel electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) for the identification of significantly different spots (Student t-test, p < 0.05). Results A total of 47 differentially expressed spots were found between H. pylori isolated from patients with either DU or AAG diseases and those isolated from patients with GC (Anova < 0.05, log fold change >1.5). These spots corresponded to 35 unique proteins. The identity of 7 protein spots was validated after one-dimensional electrophoresis and MS/MS analyses of excised gel portions. In H. pylori isolated from DU-patients a significant increase in proteins with antioxidant activity emerged (AroQ, AspA, FldA, Icd, OorA and ScoB), together with a higher content of proteins counteracting the high acid environment (KatA and NapA). In H. pylori isolated from AAG-patients proteins neutralizing hydrogen concentrations through organic substance metabolic processes decreased (GroL, TrxB and Tuf). In addition, a reduction of bacterial motility (FlhA) was found to be associated with AAG-H. pylori isolates. In GC-H. pylori strains it was found an increase in nucleic acid-binding proteins (e.g. DnaG, Tuf, RpoA, RplU) which may be involved in a higher demand of DNA- and protein-related processes. Conclusion Our data suggest the presence of specific protein signatures discriminating among H. pylori isolated from either AAG, DU or GC. Changes in protein expression profiles evaluated by DIGE succeeded in deciphering part of the molecular scenarios associated with the different H. pylori-related gastric diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13027-017-0133-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Valli De Re
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, Via F. Gallini 2, 33081 Aviano, Italy
| | - Ombretta Repetto
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, Via F. Gallini 2, 33081 Aviano, Italy
| | - Stefania Zanussi
- Microbiology-Immunology and Virology, IRCCS CRO National Cancer Institute, Aviano, Italy
| | - Mariateresa Casarotto
- Microbiology-Immunology and Virology, IRCCS CRO National Cancer Institute, Aviano, Italy
| | - Laura Caggiari
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, Via F. Gallini 2, 33081 Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology Gastroenterology, IRCCS CRO National Cancer Institute, Aviano, Italy
| | - Renato Cannizzaro
- Facility of Bio-Proteomics, Immunopathology and Cancer Biomarkers, IRCCS CRO National Cancer Institute, Via F. Gallini 2, 33081 Aviano, Italy.,Microbiology-Immunology and Virology, IRCCS CRO National Cancer Institute, Aviano, Italy.,Pathology Gastroenterology, IRCCS CRO National Cancer Institute, Aviano, Italy.,Gastroenterology, IRCCS CRO National Cancer Institute, Aviano, Italy
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12
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Gobert AP, Wilson KT. Polyamine- and NADPH-dependent generation of ROS during Helicobacter pylori infection: A blessing in disguise. Free Radic Biol Med 2017; 105:16-27. [PMID: 27682363 PMCID: PMC5366100 DOI: 10.1016/j.freeradbiomed.2016.09.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/16/2016] [Accepted: 09/23/2016] [Indexed: 12/20/2022]
Abstract
Helicobacter pylori is a Gram-negative bacterium that specifically colonizes the gastric ecological niche. During the infectious process, which results in diseases ranging from chronic gastritis to gastric cancer, the host response is characterized by the activation of the innate immunity of gastric epithelial cells and macrophages. These cells thus produce effector molecules such as reactive oxygen species (ROS) to counteract the infection. The generation of ROS in response to H. pylori involves two canonical pathways: 1) the NADPH-dependent reduction of molecular oxygen to generate O2•-, which can dismute to generate ROS; and 2) the back-conversion of the polyamine spermine into spermidine through the enzyme spermine oxidase, leading to H2O2 production. Although these products have the potential to affect the survival of bacteria, H. pylori has acquired numerous strategies to counteract their deleterious effects. Nonetheless, ROS-mediated oxidative DNA damage and mutations may participate in the adaptation of H. pylori to its ecological niche. Lastly, ROS have been shown to play a major role in the development of the inflammation and carcinogenesis. It is the purpose of this review to summarize the literature about the production of ROS during H. pylori infection and their role in this infectious gastric disease.
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Affiliation(s)
- Alain P Gobert
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, United States; Center for Mucosal Inflammation and Cancer, United States
| | - Keith T Wilson
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Medicine, United States; Department of Pathology, Microbiology, and Immunology, United States; Department of Cancer Biology, United States; Center for Mucosal Inflammation and Cancer, United States; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, United States; Veterans Affairs Tennessee Valley Healthcare System, Nashville, TN 37212, United States.
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13
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Mendoza JA, Weinberger KK, Swan MJ. The Hsp60 protein of helicobacter pylori displays chaperone activity under acidic conditions. Biochem Biophys Rep 2016; 9:95-99. [PMID: 28955994 PMCID: PMC5614549 DOI: 10.1016/j.bbrep.2016.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/17/2016] [Accepted: 11/23/2016] [Indexed: 10/26/2022] Open
Abstract
The heat shock protein, Hsp60, is one of the most abundant proteins in Helicobacter pylori. Given its sequence homology to the Escherichia coli Hsp60 or GroEL, Hsp60 from H. pylori would be expected to function as a molecular chaperone in this organism. H. pylori is an organism that grows on the gastric epithelium, where the pH can fluctuate between neutral and 4.5 and the intracellular pH can be as low as 5.0. This study was performed to test the ability of Hsp60 from H. pylori to function as a molecular chaperone under mildly acidic conditions. We report here that Hsp60 could suppress the acid-induced aggregation of alcohol dehydrogenase (ADH) in the 7.0-5.0 pH range. Hsp60 was found to undergo a conformational change within this pH range. It was also found that exposure of hydrophobic surfaces of Hsp60 is significant and that their exposure is increased under acidic conditions. Although, alcohol dehydrogenase does not contain exposed hydrophobic surfaces, we found that their exposure is triggered at low pH. Our results demonstrate that Hsp60 from H. pylori can function as a molecular chaperone under acidic conditions and that the interaction between Hsp60 and other proteins may be mediated by hydrophobic interactions.
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Affiliation(s)
- Jose A Mendoza
- Department of Chemistry and Biochemistry, California State University San Marcos, CA 92096-0001, United States
| | - Kevin K Weinberger
- Department of Chemistry and Biochemistry, California State University San Marcos, CA 92096-0001, United States
| | - Matthew J Swan
- Department of Chemistry and Biochemistry, California State University San Marcos, CA 92096-0001, United States
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14
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Chiu KH, Wang LH, Tsai TT, Lei HY, Liao PC. Secretomic Analysis of Host-Pathogen Interactions Reveals That Elongation Factor-Tu Is a Potential Adherence Factor of Helicobacter pylori during Pathogenesis. J Proteome Res 2016; 16:264-273. [PMID: 27764940 DOI: 10.1021/acs.jproteome.6b00584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The secreted proteins of bacteria are usually accompanied by virulence factors, which can cause inflammation and damage host cells. Identifying the secretomes arising from the interactions of bacteria and host cells could therefore increase understanding of the mechanisms during initial pathogenesis. The present study used a host-pathogen coculture system of Helicobacter pylori and monocytes (THP-1 cells) to investigate the secreted proteins associated with initial H. pylori pathogenesis. The secreted proteins from the conditioned media from H. pylori, THP-1 cells, and the coculture were collected and analyzed using SDS-PAGE and LC-MS/MS. Results indicated the presence of 15 overexpressed bands in the coculture. Thirty-one proteins were identified-11 were derived from THP-1 cells and 20 were derived from H. pylori. A potential adherence factor from H. pylori, elongation factor-Tu (EF-Tu), was selected for investigation of its biological function. Results from confocal microscopic and flow cytometric analyses indicated the contribution of EF-Tu to the binding ability of H. pylori in THP-1. The data demonstrated that fluorescence of EF-Tu on THP-1 cells increased after the addition of the H. pylori-conditioned medium. This study reports a novel secretory adherence factor in H. pylori, EF-Tu, and further elucidates mechanisms of H. pylori adaptation for host-pathogen interaction during pathogenesis.
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Affiliation(s)
- Kuo-Hsun Chiu
- Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University , Kaohsiung 81157, Taiwan
| | - Ling-Hui Wang
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University , Tainan 70428, Taiwan
| | - Tsung-Ting Tsai
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University , Tainan 70101, Taiwan
| | - Huan-Yao Lei
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University , Tainan 70101, Taiwan
| | - Pao-Chi Liao
- Department of Environmental and Occupational Health, College of Medicine, National Cheng Kung University , Tainan 70428, Taiwan
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15
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Dantas GC, Martins PMM, Martins DAB, Gomes E, Ferreira H. A protein expression system for tandem affinity purification in Xanthomonas citri subsp. citri. Braz J Microbiol 2016; 47:518-26. [PMID: 26991273 PMCID: PMC4874617 DOI: 10.1016/j.bjm.2016.01.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 10/23/2015] [Indexed: 11/30/2022] Open
Abstract
Citrus canker, caused by the Gram-negative bacterium Xanthomonas citri subsp. citri (Xac), is one of the most devastating diseases to affect citrus crops. There is no treatment for citrus canker; effective control against the spread of Xac is usually achieved by the elimination of affected plants along with that of asymptomatic neighbors. An in depth understanding of the pathogen is the keystone for understanding of the disease; to this effect we are committed to the development of strategies to ease the study of Xac. Genome sequencing and annotation of Xac revealed that ∼37% of the genome is composed of hypothetical ORFs. To start a systematic characterization of novel factors encoded by Xac, we constructed integrative-vectors for protein expression specific to this bacterium. The vectors allow for the production of TAP-tagged proteins in Xac under the regulation of the xylose promoter. In this study, we show that a TAP-expression vector, integrated into the amy locus of Xac, does not compromise its virulence. Furthermore, our results also demonstrate that the polypeptide TAP can be overproduced in Xac and purified from the soluble phase of cell extracts. Our results substantiate the use of our vectors for protein expression in Xac thus contributing a novel tool for the characterization of proteins and protein complexes generated by this bacterium in vivo.
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Affiliation(s)
- Giordanni C Dantas
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Paula M M Martins
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil
| | - Daniela A B Martins
- Depto. de Bioquímica e Tecnologia Química, Instituto de Química, Universidade Estadual Paulista, Araraquara, SP, Brazil
| | - Eleni Gomes
- Depto. de Biologia, Universidade Estadual Paulista, São Jose do Rio Preto, SP, Brazil
| | - Henrique Ferreira
- Depto. de Bioquimica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista, Rio Claro, SP, Brazil.
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16
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Jiménez-Soto LF, Haas R. The CagA toxin of Helicobacter pylori: abundant production but relatively low amount translocated. Sci Rep 2016; 6:23227. [PMID: 26983895 PMCID: PMC4794710 DOI: 10.1038/srep23227] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 03/02/2016] [Indexed: 02/07/2023] Open
Abstract
CagA is one of the most studied pathogenicity factors of the bacterial pathogen Helicobacter pylori. It is injected into host cells via the H. pylori cag-Type IV secretion system. Due to its association with gastric cancer, CagA is classified as oncogenic protein. At the same time CagA represents the 4th most abundant protein produced by H. pylori, suggesting that high amounts of toxin are required to cause the physiological changes or damage observed in cells. We were able to quantify the injection of CagA into gastric AGS epithelial cells in vitro by the adaptation of a novel protease-based approach to remove the tightly adherent extracellular bacteria. After one hour of infection only 1.5% of the total CagA available was injected by the adherent bacteria, whereas after 3 hours 7.5% was found within the host cell. Thus, our data show that only a surprisingly small amount of the CagA available in the infection is finally injected under in vitro infection conditions.
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Affiliation(s)
- Luisa F Jiménez-Soto
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität, Pettenkoferstraße 9a, D-80336 München, Germany
| | - Rainer Haas
- Max von Pettenkofer-Institut für Hygiene und Medizinische Mikrobiologie, Ludwig-Maximilians-Universität, Pettenkoferstraße 9a, D-80336 München, Germany.,German Center for Infection Research (DZIF), LMU Munich, Germany
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17
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Kim SH, Kim JB. Comparative Proteome Analysis of Cyanidin 3-O-glucoside Treated Helicobacter pylori. ACTA ACUST UNITED AC 2015. [DOI: 10.15616/bsl.2015.21.4.233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sa-Hyun Kim
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Korea
| | - Jong-Bae Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju 26493, Korea
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18
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Vinella D, Fischer F, Vorontsov E, Gallaud J, Malosse C, Michel V, Cavazza C, Robbe-Saule M, Richaud P, Chamot-Rooke J, Brochier-Armanet C, De Reuse H. Evolution of Helicobacter: Acquisition by Gastric Species of Two Histidine-Rich Proteins Essential for Colonization. PLoS Pathog 2015; 11:e1005312. [PMID: 26641249 PMCID: PMC4671568 DOI: 10.1371/journal.ppat.1005312] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 11/05/2015] [Indexed: 02/07/2023] Open
Abstract
Metal acquisition and intracellular trafficking are crucial for all cells and metal ions have been recognized as virulence determinants in bacterial pathogens. Virulence of the human gastric pathogen Helicobacter pylori is dependent on nickel, cofactor of two enzymes essential for in vivo colonization, urease and [NiFe] hydrogenase. We found that two small paralogous nickel-binding proteins with high content in Histidine (Hpn and Hpn-2) play a central role in maintaining non-toxic intracellular nickel content and in controlling its intracellular trafficking. Measurements of metal resistance, intracellular nickel contents, urease activities and interactomic analysis were performed. We observed that Hpn acts as a nickel-sequestration protein, while Hpn-2 is not. In vivo, Hpn and Hpn-2 form homo-multimers, interact with each other, Hpn interacts with the UreA urease subunit while Hpn and Hpn-2 interact with the HypAB hydrogenase maturation proteins. In addition, Hpn-2 is directly or indirectly restricting urease activity while Hpn is required for full urease activation. Based on these data, we present a model where Hpn and Hpn-2 participate in a common pathway of controlled nickel transfer to urease. Using bioinformatics and top-down proteomics to identify the predicted proteins, we established that Hpn-2 is only expressed by H. pylori and its closely related species Helicobacter acinonychis. Hpn was detected in every gastric Helicobacter species tested and is absent from the enterohepatic Helicobacter species. Our phylogenomic analysis revealed that Hpn acquisition was concomitant with the specialization of Helicobacter to colonization of the gastric environment and the duplication at the origin of hpn-2 occurred in the common ancestor of H. pylori and H. acinonychis. Finally, Hpn and Hpn-2 were found to be required for colonization of the mouse model by H. pylori. Our data show that during evolution of the Helicobacter genus, acquisition of Hpn and Hpn-2 by gastric Helicobacter species constituted a decisive evolutionary event to allow Helicobacter to colonize the hostile gastric environment, in which no other bacteria persistently thrives. This acquisition was key for the emergence of one of the most successful bacterial pathogens, H. pylori. Helicobacter pylori is a bacterium that persistently colonizes the stomach of half of the human population. Infection by H. pylori is associated with gastritis, peptic ulcer disease and adenocarcinoma. To resist gastric acidity and proliferate in the stomach, H. pylori relies on urease, an enzyme that contains a nickel-metallocenter at its active site. Thus, nickel is a virulence determinant for H. pylori. Our aim is to characterize how H. pylori controls the intracellular nickel concentration to avoid toxicity, which protein partners are involved, and how they impact urease activity and virulence. We characterized two H. pylori proteins, Hpn and Hpn-2 that are rich in Histidine residues. We demonstrated that Hpn is involved in nickel sequestration, that the two proteins interact with each other and that their combined activities participate in a nickel transfer pathway to urease. Hpn is only expressed in gastric Helicobacter species able to colonize the stomach and Hpn-2 is restricted to the H. pylori and its close relative H. acinonychis. We found that both proteins are essential for colonization of a mouse model by H. pylori. We conclude that during evolution, the acquisition of Hpn and Hpn-2 by gastric Helicobacter species was decisive for their capacity to colonize the stomach.
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Affiliation(s)
- Daniel Vinella
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | - Frédéric Fischer
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | - Egor Vorontsov
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, Paris, France
| | - Julien Gallaud
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Christian Malosse
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, Paris, France
| | - Valérie Michel
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | | | - Marie Robbe-Saule
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
| | - Pierre Richaud
- CEA, DSV, IBEB, SBVME and CNRS, UMR 7265 Biol Veget & Microbiol Environ, Saint-Paul-lez-Durance, France and Aix Marseille Université, BVME UMR7265, Marseille, France
| | - Julia Chamot-Rooke
- Institut Pasteur, Département de Biologie Structurale et Chimie, Unité Spectrométrie de Masse Structurale et Protéomique, CNRS UMR 3528, Paris, France
| | - Céline Brochier-Armanet
- Université de Lyon, Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France
| | - Hilde De Reuse
- Institut Pasteur, Département de Microbiologie, Unité Pathogenèse de Helicobacter, ERL CNRS 3526, Paris, France
- * E-mail:
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19
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Amilon KR, Letley DP, Winter JA, Robinson K, Atherton JC. Expression of the Helicobacter pylori virulence factor vacuolating cytotoxin A (vacA) is influenced by a potential stem-loop structure in the 5' untranslated region of the transcript. Mol Microbiol 2015; 98:831-46. [PMID: 26259667 PMCID: PMC4843948 DOI: 10.1111/mmi.13160] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2015] [Indexed: 01/03/2023]
Abstract
The vacuolating cytotoxin, VacA, is an important virulence factor secreted by the gastric pathogen Helicobacter pylori. Certain vacA genotypes are strongly associated with disease risk, but the association is not absolute. The factors determining vacA gene expression are not fully understood, and the mechanisms of its regulation are elusive. We have identified a potential mRNA stem‐loop forming structure in the 5′ untranslated region (UTR) of the vacA transcript. Using site‐directed mutagenesis, we found that disruption of the stem‐loop structure reduced steady‐state mRNA levels between two‐ and sixfold (P = 0.0005) and decreased mRNA half‐life compared with wild type (P = 0.03). This led to a marked reduction in VacA protein levels and overall toxin activity. Additionally, during stressful environmental conditions of acid pH or high environmental salt concentrations, when general transcription of vacA was decreased or increased respectively, the stabilising effects of the stem‐loop were even more pronounced. Our results suggest that the stem‐loop structure in the vacA 5′ UTR is an important determinant of vacA expression through stabilisation of the vacA mRNA transcript and that the stabilising effect is of particular importance during conditions of environmental stress.
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Affiliation(s)
- Karin R Amilon
- Nottingham Digestive Diseases Biomedical Research Unit, School of Medicine, University of Nottingham, Nottingham, UK
| | - Darren P Letley
- Nottingham Digestive Diseases Biomedical Research Unit, School of Medicine, University of Nottingham, Nottingham, UK
| | - Jody A Winter
- Nottingham Digestive Diseases Biomedical Research Unit, School of Medicine, University of Nottingham, Nottingham, UK
| | - Karen Robinson
- Nottingham Digestive Diseases Biomedical Research Unit, School of Medicine, University of Nottingham, Nottingham, UK
| | - John C Atherton
- Nottingham Digestive Diseases Biomedical Research Unit, School of Medicine, University of Nottingham, Nottingham, UK
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20
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Wang MY, Liu XF, Gao XZ. Helicobacter pylori virulence factors in development of gastric carcinoma. Future Microbiol 2015; 10:1505-16. [PMID: 26346770 DOI: 10.2217/fmb.15.72] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Helicobacter pylori plays a vital role in the pathogenesis of gastric carcinoma. However, only a relatively small proportion of individuals infected with H. pylori develop gastric carcinoma. Differences in the incidence of gastric carcinoma among infected individuals can be explained, at least partly, by the different genotypes of H. pylori virulence factors. Thus far, many virulence factors of H. pylori, such as Cag PAI, VacA, OMPs and DupA, have been reported to be involved in the development of gastric cancer. The risk of developing gastric cancer during H. pylori infection is affected by specific host-microbe interactions that are independent of H. pylori virulence factors. In this review, we discuss virulence factors of H. pylori and their role in the development of gastric carcinoma that will provide further understanding of the biological interactions of H. pylori with the host.
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Affiliation(s)
- Ming-Yi Wang
- Department of Clinical Lab, Weihai Municipal Hospital, Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Xiao-Fei Liu
- Department of Laboratory Medicine, General Hospital of Ji'nan Military Region of PLA, Ji'nan, Shandong Province, 250031, PR China
| | - Xiao-Zhong Gao
- Department of Gastroenterology, Weihai Municipal Hospital, Dalian Medical University, Weihai, Shandong, 264200, PR China
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21
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Stable isotope labeling by amino acids in cell culture based proteomics reveals differences in protein abundances between spiral and coccoid forms of the gastric pathogen Helicobacter pylori. J Proteomics 2015; 126:34-45. [DOI: 10.1016/j.jprot.2015.05.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 04/20/2015] [Accepted: 05/11/2015] [Indexed: 02/07/2023]
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22
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De Falco M, Lucariello A, Iaquinto S, Esposito V, Guerra G, De Luca A. Molecular Mechanisms of Helicobacter pylori Pathogenesis. J Cell Physiol 2015; 230:1702-7. [PMID: 25639461 DOI: 10.1002/jcp.24933] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 01/16/2015] [Indexed: 12/12/2022]
Abstract
Helicobacter pylori infects 50% of mankind. The vast majority of H. pylori infection occurs in the developing countries where up to 80% of the middle-aged adults may be infected. Bacterial infection causes an inflammatory response that proceeds through a series of intermediated stages of precancerous lesions (gastritis, atrophy, intestinal metaplasia, and dysplasia). Among infected individuals, approximately 10% develops severe gastric lesions such as peptic ulcer disease, 1-3% progresses to gastric cancer (GC) with a low 5-year survival rate, and 0.1% develops mucosa-associated lymphoid tissue (MALT). GC is one of the most common cancer and the third leading cause of cancer-related deaths worldwide. In this review, we have summarized the most recent papers about molecular mechanisms of H. pylori pathogenesis. The main important steps of H. pylori infection such as adhesion, entry in epithelial gastric cells, activation of intracellular pathways until epigenetic modifications have been described.
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Affiliation(s)
- Maria De Falco
- Department of Biology, University Federico II of Naples, Naples, Italy; National Institute of Biostructures and Biosystems (INBB), Rome, Italy
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23
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Akada J, Okuda M, Hiramoto N, Kitagawa T, Zhang X, Kamei S, Ito A, Nakamura M, Uchida T, Hiwatani T, Fukuda Y, Nakazawa T, Kuramitsu Y, Nakamura K. Proteomic characterization of Helicobacter pylori CagA antigen recognized by child serum antibodies and its epitope mapping by peptide array. PLoS One 2014; 9:e104611. [PMID: 25141238 PMCID: PMC4139317 DOI: 10.1371/journal.pone.0104611] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 07/09/2014] [Indexed: 12/12/2022] Open
Abstract
Serum antibodies against pathogenic bacteria play immunologically protective roles, and can be utilized as diagnostic markers of infection. This study focused on Japanese child serum antibodies against Helicobacter pylori, a chronically-infected gastric bacterium which causes gastric cancer in adults. Serological diagnosis for H. pylori infection is well established for adults, but it needs to be improved for children. Serum samples from 24 children, 22 H. pylori (Hp)-positive and 2 Hp-negative children, were used to catalogue antigenic proteins of a Japanese strain CPY2052 by two-dimensional electrophoresis followed by immunoblot and LC-MS/MS analysis. In total, 24 proteins were identified as candidate antigen proteins. Among these, the major virulence factor, cytotoxin-associated gene A protein (CagA) was the most reactive antigen recognized by all the Hp-positive sera even from children under the age of 3 years. The major antigenic part of CagA was identified in the middle region, and two peptides containing CagA epitopes were identified using a newly developed peptide/protein-combined array chip method, modified from our previous protein chip method. Each of the epitopes was found to contain amino acid residue(s) unique to East Asian CagA. Epitope analysis of CagA indicated importance of the regional CagA antigens for serodiagnosis of H. pylori infection in children.
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Affiliation(s)
- Junko Akada
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
- * E-mail: (JA); (KN)
| | - Masumi Okuda
- Sasayama Medical Center, Hyogo College of Medicine, Sasayama, Hyogo, Japan
- Department of General Medicine and Community Health Science, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Narumi Hiramoto
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Takao Kitagawa
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Xiulian Zhang
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Shuichi Kamei
- Technical Research Laboratory, Toyo Kohan Company, Ltd., Kudamatsu, Yamaguchi, Japan
| | - Akane Ito
- Technical Research Laboratory, Toyo Kohan Company, Ltd., Kudamatsu, Yamaguchi, Japan
| | - Mikiko Nakamura
- Innovation Center with University-Industry-Public Cooperation, Organization for Research Initiatives, Yamaguchi University, Tokiwadai, Ube, Yamaguchi, Japan
| | - Tomohisa Uchida
- Department of Molecular Pathology, Oita University, Faculty of Medicine, Oita University, Yufu, Oita, Japan
| | | | - Yoshihiro Fukuda
- Sasayama Medical Center, Hyogo College of Medicine, Sasayama, Hyogo, Japan
- Department of General Medicine and Community Health Science, Hyogo College of Medicine, Nishinomiya, Hyogo, Japan
| | - Teruko Nakazawa
- Department of Microbiology and Immunology, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Yasuhiro Kuramitsu
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Kazuyuki Nakamura
- Department of Biochemistry and Functional Proteomics, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
- * E-mail: (JA); (KN)
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Lopes AI, Vale FF, Oleastro M. Helicobacter pylori infection - recent developments in diagnosis. World J Gastroenterol 2014; 20:9299-9313. [PMID: 25071324 PMCID: PMC4110561 DOI: 10.3748/wjg.v20.i28.9299] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 04/16/2014] [Indexed: 02/06/2023] Open
Abstract
Considering the recommended indications for Helicobacter pylori (H. pylori) eradication therapy and the broad spectrum of available diagnostic methods, a reliable diagnosis is mandatory both before and after eradication therapy. Only highly accurate tests should be used in clinical practice, and the sensitivity and specificity of an adequate test should exceed 90%. The choice of tests should take into account clinical circumstances, the likelihood ratio of positive and negative tests, the cost-effectiveness of the testing strategy and the availability of the tests. This review concerns some of the most recent developments in diagnostic methods of H. pylori infection, namely the contribution of novel endoscopic evaluation methodologies for the diagnosis of H. pylori infection, such as magnifying endoscopy techniques and chromoendoscopy. In addition, the diagnostic contribution of histology and the urea breath test was explored recently in specific clinical settings and patient groups. Recent studies recommend enhancing the number of biopsy fragments for the rapid urease test. Bacterial culture from the gastric biopsy is the gold standard technique, and is recommended for antibiotic susceptibility test. Serology is used for initial screening and the stool antigen test is particularly used when the urea breath test is not available, while molecular methods have gained attention mostly for detecting antibiotic resistance.
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25
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Repetto O, Zanussi S, Casarotto M, Canzonieri V, De Paoli P, Cannizzaro R, De Re V. Differential proteomics of Helicobacter pylori associated with autoimmune atrophic gastritis. Mol Med 2014; 20:57-71. [PMID: 24395566 DOI: 10.2119/molmed.2013.00076] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Accepted: 12/23/2013] [Indexed: 12/20/2022] Open
Abstract
Atrophic autoimmune gastritis (AAG) is a condition of chronic inflammation and atrophy of stomach mucosa, for which development can be partially triggered by the bacterial pathogen Helicobacter pylori (HP). HP can cause a variety of gastric diseases, such as duodenal ulcer (DU) or gastric cancer (GC). In this study, a comparative proteomic approach was used by two-dimensional fluorescence difference gel electrophoresis (DIGE) to identify differentially expressed proteins of HP strains isolated from patients with AAG, to identify markers of HP strain associated with AAG. Proteome profiles of HP isolated from GC or DU were used as a reference to compare proteomic levels. Proteomics analyses revealed 27 differentially expressed spots in AAG-associated HP in comparison with GC, whereas only 9 differential spots were found in AAG-associated HP profiles compared with DU. Proteins were identified after matrix-assisted laser desorption ionization (MALDI)-TOF and peptide mass fingerprinting. Some AAG-HP differential proteins were common between DU- and GC-HP (peroxiredoxin, heat shock protein 70 [HSP70], adenosine 5'-triphosphate [ATP] synthase subunit α, flagellin A). Our results presented here may suggest that comparative proteomes of HP isolated from AAG and DU share more common protein expression than GC and provide subsets of putative AAG-specific upregulated or downregulated proteins that could be proposed as putative markers of AAG-associated HP. Other comparative studies by two-dimensional maps integrated with functional genomics of candidate proteins will undoubtedly contribute to better decipher the biology of AAG-associated HP strains.
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Affiliation(s)
- Ombretta Repetto
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Stefania Zanussi
- Microbiology-Immunology and Virology, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Mariateresa Casarotto
- Microbiology-Immunology and Virology, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Vincenzo Canzonieri
- Pathology Unit, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Paolo De Paoli
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Renato Cannizzaro
- Gastroenterology Unit, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
| | - Valli De Re
- Facility of Bio-Proteomics, Centro di Riferimento Oncologico (CRO), Aviano National Cancer Institute, Aviano, Italy
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26
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High natural variability bacteria identification and typing: Helicobacter pylori analysis based on peptide mass fingerprinting. J Proteomics 2014; 98:112-22. [DOI: 10.1016/j.jprot.2013.11.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 11/04/2013] [Accepted: 11/22/2013] [Indexed: 01/18/2023]
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27
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Bernardini G, Braconi D, Lusini P, Santucci A. Helicobacter pylori: immunoproteomics related to different pathologies. Expert Rev Proteomics 2014; 4:679-89. [DOI: 10.1586/14789450.4.5.679] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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28
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Comparative analysis of explosive RDX-induced proteomes in the Pseudomonas sp. HK-6 wild-type strain and its rpoH mutant strain. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-013-0249-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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29
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Alkyl hydroperoxide reductase repair by Helicobacter pylori methionine sulfoxide reductase. J Bacteriol 2013; 195:5396-401. [PMID: 24097943 DOI: 10.1128/jb.01001-13] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Protein exposure to oxidants such as HOCl leads to formation of methionine sulfoxide (MetSO) residues, which can be repaired by methionine sulfoxide reductase (Msr). A Helicobacter pylori msr strain was more sensitive to HOCl-mediated killing than the parent. Because of its abundance in H. pylori and its high methionine content, alkyl hydroperoxide reductase C (AhpC) was hypothesized to be prone to methionine oxidation. AhpC was expressed as a recombinant protein in Escherichia coli. AhpC activity was abolished by HOCl, while all six methionine residues of the enzyme were fully to partially oxidized. Upon incubation with a Msr repair mixture, AhpC activity was restored to nonoxidized levels and the MetSO residues were repaired to methionine, albeit to different degrees. The two most highly oxidized and then Msr-repaired methionine residues in AhpC, Met101 and Met133, were replaced with isoleucine residues by site-directed mutagenesis, either individually or together. E. coli cells expressing variant versions were more sensitive to t-butyl hydroperoxide than cells expressing native protein, and purified AhpC variant proteins had 5% to 39% of the native enzyme activity. Variant proteins were still able to oligomerize like the native version, and circular dichroism (CD) spectra of variant proteins revealed no significant change in AhpC conformation, indicating that the loss of activity in these variants was not related to major structural alterations. Our results suggest that both Met101 and Met133 residues are important for AhpC catalytic activity and that their integrity relies on the presence of a functional Msr.
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Cho YT, Kuo CH, Wang SS, Chen YS, Weng BC, Lee YC, Cheng CN, Shiea J, Wu DC. Differentiation of virulence of Helicobacter pylori by matrix-assisted laser desorption/ionization mass spectrometry and multivariate analyses. Clin Chim Acta 2013; 424:123-30. [DOI: 10.1016/j.cca.2013.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 05/18/2013] [Accepted: 05/20/2013] [Indexed: 02/01/2023]
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31
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Fowsantear W, Argo E, Pattinson C, Cash P. Comparative proteomics of Helicobacter species: the discrimination of gastric and enterohepatic Helicobacter species. J Proteomics 2013; 97:245-55. [PMID: 23899588 DOI: 10.1016/j.jprot.2013.07.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 07/11/2013] [Accepted: 07/14/2013] [Indexed: 12/26/2022]
Abstract
UNLABELLED Helicobacter pylori is a major human pathogen that infects the gastric mucosa and is responsible for a range of infections including gastritis and gastric carcinoma. Although other bacteria within the Helicobacter genus can also infect the gastric mucosa, there are Helicobacter species that infect alternative sites within the gastrointestinal (GI) tract. Two-dimensional gel electrophoresis was used to compare the cellular proteomes of seven non-pylori Helicobacters (H. mustelae, H. felis, H. cinaedi, H. hepaticus, H. fennelliae, H. bilis and H. cholecystus) against the more extensively characterised H. pylori. The different Helicobacter species showed distinctive 2D protein profiles, it was possible to combine them into a single dataset using Progenesis SameSpots software. Principal Component Analysis was used to search for correlations between the bacterial proteomes and their sites of infection. This approach clearly discriminated between gastric (i.e. those which infect in the gastric mucosa) and enterohepatic Helicobacter species (i.e. those bacteria that infect the small intestine and hepatobillary regions of the GI tract). Selected protein spots showing significant differences in abundance between these two groups of bacteria were identified by LC-MS. The data provide an initial insight into defining those features of the bacterial proteome that influence the sites of bacterial infection. BIOLOGICAL SIGNIFICANCE This study demonstrated that representative members of the Helicobacter genus were readily discriminated from each other on the basis of their in vitro whole cell proteomes determined using 2D gel electrophoresis. Despite the intra-species heterogeneity observed it was possible, to demonstrate that the enterohepatic (represented by H. bilis, H. hepaticus, H. fennelliae, H. cinaedi and H. cholecystus) and gastric (represented by H. pylori, H. mustelae, and H. felis) Helicobacters formed discrete groups based on their 2D protein profiles. A provisional proteomic signature was identified that correlated with the typical sites of colonisation of these members of the Helicobacter genus. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Winita Fowsantear
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Evelyn Argo
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Craig Pattinson
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom
| | - Phillip Cash
- Division of Applied Medicine, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen AB25 2ZD, United Kingdom.
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32
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Lange S, Rosenkrands I, Stein R, Andersen P, Kaufmann SHE, Jungblut PR. Analysis of protein species differentiation among mycobacterial low-Mr-secreted proteins by narrow pH range Immobiline gel 2-DE-MALDI-MS. J Proteomics 2013; 97:235-44. [PMID: 23856608 DOI: 10.1016/j.jprot.2013.06.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 06/11/2013] [Accepted: 06/29/2013] [Indexed: 12/25/2022]
Abstract
UNLABELLED Secreted proteins of bacteria are preferentially capable of interacting with host cells and are therefore of special biological and medical interest. Narrow pH range 2-DE and MALDI-TOFTOF-MS combine high-resolution protein separation with highly sensitive identification of proteins. Secreted proteins of Mycobacterium tuberculosis were separated at the protein species level, distinguishing different protein species of one protein. We focused on the pI range 4.0-4.7 and the Mr range 6-20kDa of the 2-DE pattern. Out of 128 analyzed spots, 121 were identified resulting in 33 different proteins with 277 different protein species, accumulating in a mean of 8.4 protein species per protein. Overrepresentation was found for the protein classes "virulence, detoxification, adaption", "information pathways", "cell wall and cell processes" and "intermediary metabolism and respiration". Thus far, 15 protein species of the ESX-1 family are characterized with 100% sequence coverage. More automated 2-DE procedures and more sensitive identification techniques are required for complete characterization of all of the protein species even in highly enriched samples, such as culture filtrates. Only then the functional level of proteomics will be achieved and potential biomarkers can be postulated at the molecular level. BIOLOGICAL SIGNIFICANCE Proteomics is dominated by bottom-up approaches largely ignoring protein speciation. A prerequisite to reach the protein species level is to obtain 100% sequence coverage, which is a major challenge in proteomics. Here we show complete sequence information with a 2-DE-MS approach for 15 protein species. Acetylation of the N-terminus of ESAT-6 inhibits interaction with CFP-10, with direct consequences for pathogen-host interaction. This article is part of a Special Issue entitled: Trends in Microbial Proteomics.
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Affiliation(s)
- Sabine Lange
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany
| | - Ida Rosenkrands
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | | | - Peter Andersen
- Department of Infectious Disease Immunology, Statens Serum Institut, Copenhagen, Denmark
| | - Stefan H E Kaufmann
- Max Planck Institute for Infection Biology, Department of Immunology, Berlin, Germany
| | - Peter R Jungblut
- Max Planck Institute for Infection Biology, Core Facility Protein Analysis, Berlin, Germany.
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33
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Two-dimensional gel electrophoresis in bacterial proteomics. Protein Cell 2012; 3:346-63. [PMID: 22610887 DOI: 10.1007/s13238-012-2034-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Accepted: 02/22/2012] [Indexed: 02/01/2023] Open
Abstract
Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.
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Ameri Shah Reza M, Mousavi Gargari SL, Rasooli I, Jalali Nadoushan M, Ebrahimizadeh W. Inhibition of H. pylori colonization and prevention of gastritis in murine model. World J Microbiol Biotechnol 2012; 28:2513-9. [PMID: 22806157 DOI: 10.1007/s11274-012-1059-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 04/14/2012] [Indexed: 01/15/2023]
Abstract
Helicobacter pylori is a Gram-negative spiral bacterium that colonizes human gastric mucosa causing infection. In this study aiming at inhibition of H. pylori infection we made an attempt to evaluate immunogenicity of the total (UreC) and C-terminal (UreCc) fragments of H. pylori urease. Total UreC and its C-terminal fragment were expressed in E. coli. Recombinant proteins were analyzed by SDS-PAGE and western blot and then purified by Ni-NTA affinity chromatography. Female C57BL6/j mice were immunized with the purified proteins (UreC and UreCc). Antibody titers from isolated sera were measured by ELISA. Immunized mice were then challenged by oral gavage with live H. pylori Sydney strain SS1. Total of 109 CFU were inoculated into stomach of immunized and unimmunized healthy mice three times each at one day interval. Eight weeks after the last inoculation, the blood sample was collected and the serum antibody titer was estimated by ELISA. Stomach tissues from control and experimental animal groups were studied histopathologically. UreC and UreCc yielded recombinant proteins of 61 and 31 kDa respectively. ELIZA confirmed establishment of immunity and the antibodies produced thereby efficiently recognized H. pylori and inhibited its colonization in vivo. Pathological analysis did not reveal established infection in immunized mice challenged with H. pylori. The results support the idea that UreC and UreCc specific antibodies contribute to protection against H. pylori infections.
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35
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Lin LL, Huang HC, Juan HF. Discovery of biomarkers for gastric cancer: a proteomics approach. J Proteomics 2012; 75:3081-97. [PMID: 22498886 DOI: 10.1016/j.jprot.2012.03.046] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 03/10/2012] [Accepted: 03/25/2012] [Indexed: 01/06/2023]
Abstract
Gastric cancer is the second leading cause of cancer-related deaths worldwide. Although many treatment options exist for patients with gastric tumors, the incidence and mortality rate of gastric cancer are on the rise. The early stages of gastric cancer are non-symptomatic, and the treatment response is unpredictable. This situation is further aggravated by a lack of diagnostic biomarkers that can aid in the early detection and prognosis of gastric cancer and in the prediction of chemoresistance. Moreover, clinical surgical specimens are rarely obtained, and traditional biomarkers of gastric cancer are not very effective. Many studies in the field of proteomics have contributed to the discovery and establishment of powerful diagnostic tools (e.g., ProteinChip array) in the management of cancer. The evolution in proteomic technologies has not only enabled the screening of a large number of samples but also enabled the identification of pathologically significant proteins, such as phosphoproteins, and the quantitation of difference in protein expression under different conditions. Multiplexed assays are used widely to accurately fractionate various complex samples such as blood, tissue, cells, and Helicobacter pylori-infected specimens to identify differentially expressed proteins. Biomarker detection studies have substantially contributed to the areas of secretome, metabolome, and phosphoproteome. Here, we review the development of potential biomarkers in the natural history of gastric cancer, with specific emphasis on the characteristics of target protein convergence.
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Affiliation(s)
- Li-Ling Lin
- Institute of Molecular and Cellular Biology and Department of Life Science, National Taiwan University, Taipei, Taiwan
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36
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Zhang YN, Ding SG, Huang LH, Zhang J, Shi YY, Zhong LJ. Comparative proteome analysis of Helicobacter pylori clinical strains by two-dimensional gel electrophoresis. J Zhejiang Univ Sci B 2012; 12:820-7. [PMID: 21960345 DOI: 10.1631/jzus.b1000445] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
OBJECTIVE To investigate the pathogenic properties of Helicobacter pylori by comparing the proteome map of H. pylori clinical strains. METHODS Two wild-type H. pylori strains, YN8 (isolated from biopsy tissue of a gastric cancer patient) and YN14 (isolated from biopsy tissue of a gastritis and duodenal ulcer patient), were used. Proteomic analysis, using a pH range of 3-10 and 5-8, was performed. The individual proteins were identified by quadrupole time-of-flight (Q-TOF) mass spectrometer and protein database search. RESULTS Variation in spot patterns directed towards differential protein expression levels was observed between the strains. The gel revealed prominent proteins with several protein "families". The comparison of protein expressions of the two strains reveals a high variability. Differentially present or absent spots were observed. Nine differentially expressed protein spots identified by Q-TOF included adenosine triphosphate (ATP)-binding protein, disulfide oxidoreductase B (DsbB)-like protein, N utilization substance A (NusA), ATP-dependent protease binding subunit/heat shock protein, hydantoin utilization protein A, seryl-tRNA synthetase, molybdenum ABC transporter ModD, and hypothetical proteins. CONCLUSIONS This study suggests that H. pylori strains express/repress protein variation, not only in terms of the virulence proteins, but also in terms of physiological proteins, when they infect a human host. The difference of protein expression levels between H. pylori strains isolated from gastric cancer and gastritis may be the initiator of inflammation, and result in the different clinical presentation. In this preliminary study, we report seven differential proteins between strains, with molecule weights from approximately 10 kDa to approximately 40 kDa. Further studies are needed to investigate those proteins and their function associated with H. pylori colonization and adaptation to host environment stress.
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Affiliation(s)
- Ya-nan Zhang
- Department of Laboratory, Beijing Tiantan Hospital affiliated to Capital Medical University, Beijing, China
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37
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A proteome reference map and virulence factors analysis of Yersinia pestis 91001. J Proteomics 2012; 75:894-907. [DOI: 10.1016/j.jprot.2011.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Revised: 09/27/2011] [Accepted: 10/08/2011] [Indexed: 01/06/2023]
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38
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Abstract
The recent detection and isolation of the aflagellate Campylobacter ureolyticus (previously known as Bacteroides ureolyticus) from intestinal biopsy specimens and fecal samples of children with newly diagnosed Crohn's disease led us to investigate the pathogenic potential of this bacterium. Adherence and gentamicin protection assays were employed to quantify the levels of adherence to and invasion into host cells. C. ureolyticus UNSWCD was able to adhere to the Caco-2 intestinal epithelial cell line with a value of 5.341% ± 0.74% but was not able to invade the Caco-2 cells. The addition of two proinflammatory cytokines, tumor necrosis factor alpha (TNF-α) and gamma interferon (IFN-γ), to the cell line did not affect attachment or invasion, with attachment levels being 4.156% ± 0.61% (P = 0.270) for TNF-α and 6.472% ± 0.61% (P = 0.235) for IFN-γ. Scanning electron microscopy visually confirmed attachment and revealed that C. ureolyticus UNSWCD colonizes and adheres to intestinal cells, inducing cellular damage and microvillus degradation. Purification and identification of the C. ureolyticus UNSWCD secretome detected a total of 111 proteins, from which 29 were bioinformatically predicted to be secretory proteins. Functional classification revealed three putative virulence and colonization factors: the surface antigen CjaA, an outer membrane fibronectin binding protein, and an S-layer RTX toxin. These results suggest that C. ureolyticus has the potential to be a pathogen of the gastrointestinal tract.
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39
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Cash P. Investigating pathogen biology at the level of the proteome. Proteomics 2011; 11:3190-202. [DOI: 10.1002/pmic.201100029] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Revised: 04/04/2011] [Accepted: 04/19/2011] [Indexed: 11/12/2022]
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40
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Holland C, Schmid M, Zimny-Arndt U, Rohloff J, Stein R, Jungblut PR, Meyer TF. Quantitative phosphoproteomics reveals link between Helicobacter pylori infection and RNA splicing modulation in host cells. Proteomics 2011; 11:2798-811. [DOI: 10.1002/pmic.201000793] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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41
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Valenzuela M, Albar JP, Paradela A, Toledo H. Helicobacter pylori exhibits a fur-dependent acid tolerance response. Helicobacter 2011; 16:189-99. [PMID: 21585604 DOI: 10.1111/j.1523-5378.2011.00824.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BACKGROUND Helicobacter pylori colonizes the acid environment of the gastric mucosa. Like other enteric bacterial pathogens, including Salmonella enterica, which must survive a brief exposure to that environment, H. pylori displays a rapid response to subtle changes in pH, which confers an increased ability to survive at more extreme acidic pH. This two-step acid tolerance response (ATR) requires de novo protein synthesis and is dependent on the function of the global regulatory protein Fur. OBJECTIVE We have explored the physiological bases of the ATR in H. pylori. MATERIALS AND METHODS Proteomic analysis of phenotypes of H. pylori and fur mutant strains show that subtle pH changes elicit significant changes in the pattern of proteins synthesized. RESULTS A loss-of-function mutation in the fur gene, obtained by insertion of an antibiotic resistance cassette, indicated that Fur regulates the expression of a fraction of H. pylori proteins. CONCLUSION A subset of proteins is involved in the ATR and confer a negative ATR phenotype.
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Affiliation(s)
- Manuel Valenzuela
- Programa de Biología Celular y Molecular, ICBM, Facultad de Medicina, Universidad de Chile, Casilla 70086, Santiago-7, Chile
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Dmitriev A, Mohapatra SS, Chong P, Neely M, Biswas S, Biswas I. CovR-controlled global regulation of gene expression in Streptococcus mutans. PLoS One 2011; 6:e20127. [PMID: 21655290 PMCID: PMC3105014 DOI: 10.1371/journal.pone.0020127] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2011] [Accepted: 04/13/2011] [Indexed: 12/15/2022] Open
Abstract
CovR/S is a two-component signal transduction system (TCS) that controls the expression of various virulence related genes in many streptococci. However, in the dental pathogen Streptococcus mutans, the response regulator CovR appears to be an orphan since the cognate sensor kinase CovS is absent. In this study, we explored the global transcriptional regulation by CovR in S. mutans. Comparison of the transcriptome profiles of the wild-type strain UA159 with its isogenic covR deleted strain IBS10 indicated that at least 128 genes (∼6.5% of the genome) were differentially regulated. Among these genes, 69 were down regulated, while 59 were up regulated in the IBS10 strain. The S. mutans CovR regulon included competence genes, virulence related genes, and genes encoded within two genomic islands (GI). Genes encoded by the GI TnSmu2 were found to be dramatically reduced in IBS10, while genes encoded by the GI TnSmu1 were up regulated in the mutant. The microarray data were further confirmed by real-time RT-PCR analyses. Furthermore, direct regulation of some of the differentially expressed genes was demonstrated by electrophoretic mobility shift assays using purified CovR protein. A proteomic study was also carried out that showed a general perturbation of protein expression in the mutant strain. Our results indicate that CovR truly plays a significant role in the regulation of several virulence related traits in this pathogenic streptococcus.
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Affiliation(s)
- Alexander Dmitriev
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- Department of Molecular Microbiology, Institute of Experimental Medicine, Saint-Petersburg, Russia
| | - Saswat S. Mohapatra
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Patrick Chong
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Melody Neely
- Department of Microbiology and Immunology, Wayne State School of Medicine, Detroit, Michigan, United States of America
| | - Saswati Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
- * E-mail:
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Vitoriano I, Rocha-Gonçalves A, Carvalho T, Oleastro M, Calado CRC, Roxo-Rosa M. Antigenic diversity among Portuguese clinical isolates of Helicobacter pylori. Helicobacter 2011; 16:153-68. [PMID: 21435094 DOI: 10.1111/j.1523-5378.2011.00825.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND The human gastroduodenal pathogen, Helicobacter pylori, is characterized by an unusual extent of genetic heterogeneity. This dictates differences in the antigenic pattern of strains resulting in heterogeneous human humoral immune responses. Here, we examined the antigenic variability among a group of 10 strains isolated from Portuguese patients differing in age, gender, and H. pylori-associated gastric diseases. MATERIAL AND METHODS Immunoassays were performed on two-dimensional electrophoresis gels obtained for the proteome of each strain, using a commercial pool of antibodies produced in rabbit, against the whole cell lysate of an Australian H. pylori strain. Relevant proteins were identified by mass spectrometry. RESULTS Immunoproteomes of the Portuguese strains showed no correlation between the number of antigenic proteins or the antigenic profile, and the disease to which each strain was associated. The Heat shock protein B was the unique immunoreactive protein common to all of them. Additionally, seven proteins were found to be antigenic in at least 80% of strains: enoyl-(acyl-carrier-protein) reductase (NADH); Catalase; Flagellin A; 2 isoforms of alkyl hydroperoxide reductase; succinyl-CoA transferase subunit B; and an unidentified protein. These proteins were present in the proteome of all tested strains, suggesting that differences in their antigenicity are related to antigenic variance. CONCLUSIONS This study showed evidence of the variability of antigenic pattern among H. pylori strains. We believe that this fact contributes to the failure of anti-H. pylori vaccines and the low accuracy of serological tests based on a low number of proteins or antigens of only one strain.
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Affiliation(s)
- Inês Vitoriano
- Faculdade de Engenharia, Universidade Católica Portuguesa, Rio de Mouro, Portugal Chymiotechnon, Departamento de Química, Universidade de Coimbra, Coimbra, Portugal
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Bernarde C, Lehours P, Lasserre JP, Castroviejo M, Bonneu M, Mégraud F, Ménard A. Complexomics study of two Helicobacter pylori strains of two pathological origins: potential targets for vaccine development and new insight in bacteria metabolism. Mol Cell Proteomics 2010; 9:2796-826. [PMID: 20610778 PMCID: PMC3101863 DOI: 10.1074/mcp.m110.001065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Indexed: 12/12/2022] Open
Abstract
Helicobacter pylori infection plays a causal role in the development of gastric mucosa-associated lymphoid tissue (MALT) lymphoma (LG-MALT) and duodenal ulcer (DU). Although many virulence factors have been associated with DU, many questions remain unanswered regarding the evolution of the infection toward this exceptional event, LG-MALT. The present study describes and compares the complexome of two H. pylori strains, strain J99 associated with DU and strain B38 associated with LG-MALT, using the two-dimensional blue native/SDS-PAGE method. It was possible to identify 90 different complexes (49 and 41 in the B38 and J99 strains, respectively); 12 of these complexes were common to both strains (seven and five in the membrane and cytoplasm, respectively), reflecting the variability of H. pylori strains. The 44 membrane complexes included numerous outer membrane proteins, such as the major adhesins BabA and SabA retrieved from a complex in the B38 strain, and also proteins from the hor family rarely studied. BabA and BabB adhesins were found to interact independently with HopM/N in the B38 and J99 strains, respectively. The 46 cytosolic complexes essentially comprised proteins involved in H. pylori physiology. Some orphan proteins were retrieved from heterooligomeric complexes, and a function could be proposed for a number of them via the identification of their partners, such as JHP0119, which may be involved in the flagellar function. Overall, this study gave new insights into the membrane and cytoplasm structure, and those which could help in the design of molecules for vaccine and/or antimicrobial agent development are highlighted.
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Affiliation(s)
- Cédric Bernarde
- From ‡INSERM U853, 33076 Bordeaux, France and
- §Laboratoire de Bactériologie
| | - Philippe Lehours
- From ‡INSERM U853, 33076 Bordeaux, France and
- §Laboratoire de Bactériologie
| | - Jean-Paul Lasserre
- From ‡INSERM U853, 33076 Bordeaux, France and
- §Laboratoire de Bactériologie
| | - Michel Castroviejo
- ‖Laboratoire de Microbiologie Cellulaire et Moléculaire et Pathogénicité, UMR CNRS 5234, and
| | - Marc Bonneu
- **Pôle Protéomique, Plateforme Génomique Fonctionnelle, Université Victor Segalen Bordeaux 2, Bordeaux, F 33076 France
| | - Francis Mégraud
- From ‡INSERM U853, 33076 Bordeaux, France and
- §Laboratoire de Bactériologie
| | - Armelle Ménard
- From ‡INSERM U853, 33076 Bordeaux, France and
- §Laboratoire de Bactériologie
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Pleissner KP, Eifert T, Jungblut PR. A European pathogenic microorganism proteome database: construction and maintenance. Comp Funct Genomics 2010; 3:97-100. [PMID: 18628887 PMCID: PMC2447247 DOI: 10.1002/cfg.165] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2002] [Accepted: 02/19/2005] [Indexed: 11/21/2022] Open
Abstract
A relational database structure based on MS-Access and MySQL to store and manage
proteomics data was established. This system may be used to publish two-dimensional
electrophoretic proteomics data, and also may be accessed by external users who want to
compare their own data with those in the databases. The maintenance of the database is
managed centrally. The producers of proteomics data do not need to construct a database
themselves. Users can introduce mass spectra into the database, which allows the searching
of peptide mass fingerprints against their own protein sequence databases. The first release
published in January 2002 contains data from Mycobacterium tuberculosis, Helicobacter
pylori, Borrelia garinii, Francisella tularensis, Chlamydia pneumoniae, Mycoplasma pneumoniae,
Jurkat T-cells and mouse mammary gland projects (http://www.mpiib-berlin.
mpg.de/2D-PAGE/).
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Affiliation(s)
- Klaus-Peter Pleissner
- Max Planck Institute for Infection Biology, Core Facility Bioinformatics, Berlin, Germany
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Lahner E, Bernardini G, Santucci A, Annibale B. Helicobacter pylori immunoproteomics in gastric cancer and gastritis of the carcinoma phenotype. Expert Rev Proteomics 2010; 7:239-48. [PMID: 20377390 DOI: 10.1586/epr.10.5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Helicobacter pylori infection is linked to the development of gastric cancer. Atrophic body gastritis is considered the first important step in the histogenesis of such neoplasia. H. pylori infection is involved in the induction of atrophic body gastritis, but documentation of H. pylori infection is difficult because of the progressive disappearance of the bacterium. Host-pathogen interactions may be investigated by means of immunoproteomics, which provides global information regarding the host humoral response to H. pylori infection and allows the identification of relevant specific and nonspecific antigens, and can be used for diagnostic or prognostic purposes. In the present review, we describe how several research groups used H. pylori immunoproteomics to investigate highly immunoreactive bacterial antigens related to the development of gastric cancer.
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Affiliation(s)
- Edith Lahner
- Digestive and Liver Disease Unit, University La Sapienza, Dipartimento di Scienze Cliniche, Ospedale Sant'Andrea, Rome, Italy
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Jungblut PR, Schiele F, Zimny-Arndt U, Ackermann R, Schmid M, Lange S, Stein R, Pleissner KP. Helicobacter pylori proteomics by 2-DE/MS, 1-DE-LC/MS and functional data mining. Proteomics 2010; 10:182-93. [PMID: 19941309 DOI: 10.1002/pmic.200900361] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
With its predicted proteome of 1550 proteins (data set Etalon) Helicobacter pylori 26695 represents a perfect model system of medium complexity for investigating basic questions in proteomics. We analyzed urea-solubilized proteins by 2-DE/MS (data set 2-DE) and by 1-DE-LC/MS (Supprot); proteins insoluble in 9 M urea but solubilized by SDS (Pellet); proteins precipitating in the Sephadex layer at the application side of IEF (Sephadex) by 1-DE-LC/MS; and proteins precipitating close to the application side within the IEF gel by LC/MS (Startline). The experimental proteomics data of H. pylori comprising 567 proteins (protein coverage: 36.6%) were stored in the Proteome Database System for Microbial Research (http://www.mpiib-berlin.mpg.de/2D-PAGE/), which gives access to raw mass spectra (MALDI-TOF/TOF) in T2D format, as well as to text files of peak lists. For data mining the protein mapping and comparison tool PROMPT (http://webclu.bio.wzw.tum.de/prompt/) was used. The percentage of proteins with transmembrane regions, relative to all proteins detected, was 0, 0.2, 0, 0.5, 3.8 and 6.3% for 2-DE, Supprot, Startline, Sephadex, Pellet, and Etalon, respectively. 2-DE does not separate membrane proteins because they are insoluble in 9 M urea/70 mM DTT and 2% CHAPS. SDS solubilizes a considerable portion of the urea-insoluble proteins and makes them accessible for separation by SDS-PAGE and LC. The 2-DE/MS analysis with urea-solubilized proteins and the 1-DE-LC/MS analysis with the urea-insoluble protein fraction (Pellet) are complementary procedures in the pursuit of a complete proteome analysis. Access to the PROMPT-generated diagrams in the Proteome Database allows the mining of experimental data with respect to other functional aspects.
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Affiliation(s)
- Peter R Jungblut
- Core Facility Protein Analysis, Max Planck Institute for Infection Biology, 10117 Berlin, Germany.
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O'Toole PW, Snelling WJ, Canchaya C, Forde BM, Hardie KR, Josenhans C, Graham RL, McMullan G, Parkhill J, Belda E, Bentley SD. Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen. BMC Genomics 2010; 11:164. [PMID: 20219135 PMCID: PMC2846917 DOI: 10.1186/1471-2164-11-164] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2009] [Accepted: 03/10/2010] [Indexed: 12/11/2022] Open
Abstract
Background Helicobacter mustelae causes gastritis, ulcers and gastric cancer in ferrets and other mustelids. H. mustelae remains the only helicobacter other than H. pylori that causes gastric ulceration and cancer in its natural host. To improve understanding of H. mustelae pathogenesis, and the ulcerogenic and carcinogenic potential of helicobacters in general, we sequenced the H. mustelae genome, and identified 425 expressed proteins in the envelope and cytosolic proteome. Results The H. mustelae genome lacks orthologs of major H. pylori virulence factors including CagA, VacA, BabA, SabA and OipA. However, it encodes ten autotransporter surface proteins, seven of which were detected in the expressed proteome, and which, except for the Hsr protein, are of unknown function. There are 26 putative outer membrane proteins in H. mustelae, some of which are most similar to the Hof proteins of H. pylori. Although homologs of putative virulence determinants of H. pylori (NapA, plasminogen adhesin, collagenase) and Campylobacter jejuni (CiaB, Peb4a) are present in the H. mustelae genome, it also includes a distinct complement of virulence-related genes including a haemagglutinin/haemolysin protein, and a glycosyl transferase for producing blood group A/B on its lipopolysaccharide. The most highly expressed 264 proteins in the cytosolic proteome included many corresponding proteins from H. pylori, but the rank profile in H. mustelae was distinctive. Of 27 genes shown to be essential for H. pylori colonization of the gerbil, all but three had orthologs in H. mustelae, identifying a shared set of core proteins for gastric persistence. Conclusions The determination of the genome sequence and expressed proteome of the ulcerogenic species H mustelae provides a comparative model for H. pylori to investigate bacterial gastric carcinogenesis in mammals, and to suggest ways whereby cag minus H. pylori strains might cause ulceration and cancer. The genome sequence was deposited in EMBL/GenBank/DDBJ under accession number FN555004.
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Affiliation(s)
- Paul W O'Toole
- Department of Microbiology, & Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
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Kaakoush NO, Man SM, Lamb S, Raftery MJ, Wilkins MR, Kovach Z, Mitchell H. The secretome of Campylobacter concisus. FEBS J 2010; 277:1606-17. [PMID: 20148967 DOI: 10.1111/j.1742-4658.2010.07587.x] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A higher prevalence of Campylobacter concisus and higher levels of IgG antibodies specific to C. concisus in Crohn's disease patients than in controls were recently detected. In this study, 1D and 2D gel electrophoresis coupled with LTQ FT-MS and QStar tandem MS, respectively, were performed to characterize the secretome of a C. concisus strain isolated from a Crohn's disease patient. Two hundred and one secreted proteins were identified, of which 86 were bioinformatically predicted to be secreted. Searches were performed on the genome of C. concisus strain 13826, and 25 genes that have been associated with virulence or colonization in other organisms were identified. The zonula occludens toxin was found only in C. concisus among the Campylobacterales, although expanded searches revealed that this protein was present in two epsilon-proteobacterial species from extreme marine environments. Alignments and structural threading indicated that this toxin shared features with that of other virulent pathogens, including Neisseria meningitidis and Vibrio cholerae. Further comparative analyses identified several associations between the secretome of C. consisus and putative virulence factors of this bacterium. This study has identified several factors putatively associated with disease outcome, suggesting that C. concisus is a pathogen of the gastrointestinal tract.
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Affiliation(s)
- Nadeem O Kaakoush
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
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50
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Momynaliev KT, Kashin SV, Chelysheva VV, Selezneva OV, Demina IA, Serebryakova MV, Alexeev D, Ivanisenko VA, Aman E, Govorun VM. Functional Divergence of Helicobacter pylori Related to Early Gastric Cancer. J Proteome Res 2009; 9:254-67. [DOI: 10.1021/pr900586w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Kuvat T. Momynaliev
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Sergey V. Kashin
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Vera V. Chelysheva
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Oksana V. Selezneva
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Irina A. Demina
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Marya V. Serebryakova
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Dmitry Alexeev
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Vladimir A. Ivanisenko
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Ewgeniya Aman
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
| | - Vadim M. Govorun
- Research Institute for Physico-Chemical Medicine, Moscow, Russia, Endoscopy, Yaroslavl Regional Oncologic Hospital, Yaroslavl, Russia, Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia, and Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia
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