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Pan J, Li J, Zhang T, Liu T, Xu K, Wang C, Zheng M. Complete ammonia oxidation (comammox) at pH 3-4 supports stable production of ammonium nitrate from urine. WATER RESEARCH 2024; 257:121686. [PMID: 38705065 DOI: 10.1016/j.watres.2024.121686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 04/23/2024] [Accepted: 04/27/2024] [Indexed: 05/07/2024]
Abstract
This study developed a new process that stably produced ammonium nitrate (NH4NO3), an important and commonly used fertilizer, from the source-separated urine by comammox Nitrospira. In the first stage, the complete conversion of ammonium to nitrate was achieved by comammox Nitrospira. In this scenario, the pH was maintained at 6 by adding external alkali, which also provided sufficient alkalinity for full nitrification. In the second stage, the NH4NO3 was produced directly by comammox Nitropsira by converting half of the ammonium in urine into nitrate. In this case, no alkali was added and pH automatically dropped and self-maintained at an extremely acidic level (pH 3-4). In both scenarios, negligible nitrite accumulation was observed, while the final product of the second stage contained ammonium and nitrate at the molar ratio of 1:1. The dominance of comammox Nitrospira over canonical ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) was systematically proved by the combination of 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction, and metagenomics. Notably, metagenomic sequencing suggested that the relative abundance of comammox Nitrospira was over 20 % under the acidic condition at pH 3-4, while canonical AOB and NOB were undetectable. Batch experiments showed that the optimal pH for the enriched comammox Nitrospira was ∼7, which could sustain their activity in a wider pH range from 4 to 8 surprisingly but lost activity at pH 3 and 9. The findings not only present an application potential of comammox Nitrospira in nitrogen recovery from urine wastewater but also report the survivability of comammox bacteria in acidic environments.
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Affiliation(s)
- Junhao Pan
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiyun Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tingting Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Tao Liu
- Australian Centre for Water and Environmental Biotechnology, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Kangning Xu
- Beijing Key Laboratory for Source Control Technology of Water Pollution, College of Environmental Science and Engineering, Beijing Forestry University, Beijing, China
| | - Chengwen Wang
- School of Environment, Tsinghua University, Beijing 100084, China.
| | - Min Zheng
- Water Research Centre, School of Civil and Environmental Engineering, University of New South Wales, Sydney, New South Wales 2052, Australia.
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Åberg A, Gideonsson P, Bhat A, Ghosh P, Arnqvist A. Molecular insights into the fine-tuning of pH-dependent ArsR-mediated regulation of the SabA adhesin in Helicobacter pylori. Nucleic Acids Res 2024; 52:5572-5595. [PMID: 38499492 PMCID: PMC11162790 DOI: 10.1093/nar/gkae188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 02/28/2024] [Accepted: 03/12/2024] [Indexed: 03/20/2024] Open
Abstract
Adaptation to variations in pH is crucial for the ability of Helicobacter pylori to persist in the human stomach. The acid responsive two-component system ArsRS, constitutes the global regulon that responds to acidic conditions, but molecular details of how transcription is affected by the ArsR response regulator remains poorly understood. Using a combination of DNA-binding studies, in vitro transcription assays, and H. pylori mutants, we demonstrate that phosphorylated ArsR (ArsR-P) forms an active protein complex that binds DNA with high specificity in order to affect transcription. Our data showed that DNA topology is key for DNA binding. We found that AT-rich DNA sequences direct ArsR-P to specific sites and that DNA-bending proteins are important for the effect of ArsR-P on transcription regulation. The repression of sabA transcription is mediated by ArsR-P with the support of Hup and is affected by simple sequence repeats located upstream of the sabA promoter. Here stochastic events clearly contribute to the fine-tuning of pH-dependent gene regulation. Our results reveal important molecular aspects for how ArsR-P acts to repress transcription in response to acidic conditions. Such transcriptional control likely mediates shifts in bacterial positioning in the gastric mucus layer.
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Affiliation(s)
- Anna Åberg
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Pär Gideonsson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Abhayprasad Bhat
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Prachetash Ghosh
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Anna Arnqvist
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
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Huang TT, Liu YN, Huang JX, Yan PP, Wang JJ, Cao YX, Cao L. Sodium sulfite-driven Helicobacter pylori eradication: Unraveling oxygen dynamics through multi-omics investigation. Biochem Pharmacol 2024; 222:116055. [PMID: 38354959 DOI: 10.1016/j.bcp.2024.116055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/05/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
Due to the emergence and spread of multidrug resistance in Helicobacter pylori (H. pylori), its eradication has become difficult. Sodium sulfite (SS), a widely used food additive for ensuring food safety and storage, has been recognized as an effective nonbactericidal agent for H. pylori eradication. However, the mechanism by which H. pylori adapts and eventually succumbs under low- or no-oxygen conditions remains unknown. In this study, we aimed to evaluate the anti-H. pylori effect of SS and investigated the multiomics mechanism by which SS kills H. pylori. The results demonstrated that SS effectively eradicated H. pylori both in vitro and in vivo. H. pylori responds to the oxygen changes regulated by SS, downregulates the HcpE gene, which is responsible for redox homeostasis in bacteria, decreases the activities of enzymes related to oxidative stress, and disrupts the outer membrane structure, increasing susceptibility to oxidative stress. Furthermore, SS downregulates the content of cytochrome C in the microaerobic respiratory chain, leading to a sharp decrease in ATP synthesis. Consequently, the accumulation of triglycerides (TGs) in bacteria due to oxidative stress supports anaerobic respiration, meeting their energy requirements. The multifaceted death of H. pylori caused by SS does not result in drug resistance. Thus, screening of the redox homeostasis of HcpE as a new target for H. pylori infection treatment could lead to the development of a novel approach for H. pylori eradication therapy.
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Affiliation(s)
- Ting-Ting Huang
- Department of Pharmacology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an 710061, Shaanxi, China
| | - Yan-Ni Liu
- Department of Pharmacology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an 710061, Shaanxi, China
| | - Jin-Xian Huang
- Software Department, East China University of Technology, Nanchang 330032, Jiangxi, China
| | - Ping-Ping Yan
- Department of Pharmacology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an 710061, Shaanxi, China
| | - Ji-Jing Wang
- Department of Medical Biophysics and Biochemistry, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Yong-Xiao Cao
- Department of Pharmacology, School of Basic Medical Science, Xi'an Jiaotong University Health Science Center, Xi'an 710061, Shaanxi, China.
| | - Lei Cao
- Precision Medical Institute, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710004, Shaanxi, China.
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Zimmerman EH, Ramsey EL, Hunter KE, Villadelgado SM, Phillips CM, Shipman RT, Forsyth MH. The Helicobacter pylori methylome is acid-responsive due to regulation by the two-component system ArsRS and the type I DNA methyltransferase HsdM1 (HP0463). J Bacteriol 2024; 206:e0030923. [PMID: 38179929 PMCID: PMC10810217 DOI: 10.1128/jb.00309-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
In addition to its role in genome protection, DNA methylation can regulate gene expression. In this study, we characterized the impact of acidity, phase variation, and the ArsRS TCS on the expression of the Type I m6A DNA methyltransferase HsdM1 (HP0463) of Helicobacter pylori 26695 and their subsequent effects on the methylome. Transcription of hsdM1 increases at least fourfold in the absence of the sensory histidine kinase ArsS, the major acid-sensing protein of H. pylori. hsdM1 exists in the phase-variable operon hsdR1-hsdM1. Phase-locking hsdR1 (HP0464), the restriction endonuclease gene, has significant impacts on the transcription of hsdM1. To determine the impacts of methyltransferase transcription patterns on the methylome, we conducted methylome sequencing on samples cultured at pH 7 or pH 5. We found differentially methylated motifs between these growth conditions and that deletions of arsS and/or hsdM1 interfere with the epigenetic acid response. Deletion of arsS leads to altered activity of HsdM1 and multiple other methyltransferases under both pH conditions indicating that the ArsRS TCS, in addition to direct effects on regulon transcription during acid acclimation, may also indirectly impact gene expression via regulation of the methylome. We determined the target motif of HsdM1 (HP0463) to be the complementary bipartite sequence pair 5'-TCAm6AVN6TGY-3' and 3'-AGTN6GAm6ACA-5'. This complex regulation of DNA methyltransferases, and thus differential methylation patterns, may have implications for the decades-long persistent infection by H. pylori. IMPORTANCE This study expands the possibilities for complex, epigenomic regulation in Helicobacter pylori. We demonstrate that the H. pylori methylome is plastic and acid sensitive via the two-component system ArsRS and the DNA methyltransferase HsdM1. The control of a methyltransferase by ArsRS may allow for a layered response to changing acidity. Likely, an early response whereby ArsR~P affects regulon expression, including the methyltransferase hsdM1. Then, a somewhat later effect as the altered methylome, due to altered HsdM1 expression, subsequently alters the expression of other genes involved in acclimation. The intermediate methylation of certain motifs supports the hypothesis that methyltransferases play a regulatory role. Untangling this additional web of regulation could play a key role in understanding H. pylori colonization and persistence.
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Affiliation(s)
| | - Erin L. Ramsey
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | | | | | | | - Ryan T. Shipman
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
| | - Mark H. Forsyth
- Department of Biology, William & Mary, Williamsburg, Virginia, USA
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Rezaei F, Alebouyeh M, Mirbagheri SZ, Ebrahimi A, Foroushani AR, Bakhtiari R. Transcriptional analysis of Helicobacter pylori cytotoxic-associated gene-pathogenicity island in response to different pH levels and proton pump inhibitor exposure. Indian J Gastroenterol 2023; 42:686-693. [PMID: 37665542 DOI: 10.1007/s12664-023-01422-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 06/21/2023] [Indexed: 09/05/2023]
Abstract
BACKGROUND Long-term use of proton pump inhibitors (PPIs) can increase the risk of gastric cancer in Helicobacter pylori-infected patients; nevertheless, there is no data about their impact on the pathogenicity of H. pylori. This study aimed at investigating the transcriptional alteration of key gene mediators of cytotoxin-associated gene-pathogenicity island (cag-PAI) among clinical H. pylori isolates in response to omeprazole at different pH levels. METHODS Accordingly, H. pylori isolates with the same virulence genotypes selected from the gastric biopsies of patients and transcriptional alteration in the cag-PAI genes studied in the presence or absence of omeprazole (2 mg/mL) at pH 2.0, 4.0 and 7.0 after 30 and 90 minutes of the treatment. Relative changes in the transcriptional levels were recorded in each assay, separately. RESULTS Of 18 H. pylori isolates, the cag-PAI empty site was detected in four strains, while the presence of cagA, cagL and cagY was characterized in 77.7%, 83.3% and 83.3% of the cag-PAI-positive strains, respectively. Transcriptional analysis of the selected strains showed up-regulation of cagA and cagL, mainly at pH 2.0 and 4.0 after 30 and 90-minute exposure. A diversity in the expression levels of cag-PAI genes was seen among the strains at the extent and time of induction. CONCLUSION Our results showed that omeprazole could increase the expression of H. pylori cagA and cagL at acidic pH. Heterogeneity among the strains probably has an impact on the extent of their interplay with PPIs. Further studies are needed to establish this correlation.
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Affiliation(s)
- Fatemeh Rezaei
- Department of Pathobiology, School of Public Health and Institute Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Alebouyeh
- Pediatric Infections Research Centre, Research Institute for Children's Health, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyedeh Zohre Mirbagheri
- Department of Pathobiology, School of Public Health and Institute Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Ebrahimi
- Department of Pathobiology, School of Public Health and Institute Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health and Institute Health Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Ronak Bakhtiari
- Department of Pathobiology, School of Public Health and Institute Health Research, Tehran University of Medical Sciences, Tehran, Iran.
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Taya T, Teruyama F, Gojo S. Host-directed therapy for bacterial infections -Modulation of the phagolysosome pathway. Front Immunol 2023; 14:1227467. [PMID: 37841276 PMCID: PMC10570837 DOI: 10.3389/fimmu.2023.1227467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 09/11/2023] [Indexed: 10/17/2023] Open
Abstract
Bacterial infections still impose a significant burden on humanity, even though antimicrobial agents have long since been developed. In addition to individual severe infections, the f fatality rate of sepsis remains high, and the threat of antimicrobial-resistant bacteria grows with time, putting us at inferiority. Although tremendous resources have been devoted to the development of antimicrobial agents, we have yet to recover from the lost ground we have been driven into. Looking back at the evolution of treatment for cancer, which, like infectious diseases, has the similarity that host immunity eliminates the lesion, the development of drugs to eliminate the tumor itself has shifted from a single-minded focus on drug development to the establishment of a treatment strategy in which the de-suppression of host immunity is another pillar of treatment. In infectious diseases, on the other hand, the development of therapies that strengthen and support the immune system has only just begun. Among innate immunity, the first line of defense that bacteria encounter after invading the host, the molecular mechanisms of the phagolysosome pathway, which begins with phagocytosis to fusion with lysosome, have been elucidated in detail. Bacteria have a large number of strategies to escape and survive the pathway. Although the full picture is still unfathomable, the molecular mechanisms have been elucidated for some of them, providing sufficient clues for intervention. In this article, we review the host defense mechanisms and bacterial evasion mechanisms and discuss the possibility of host-directed therapy for bacterial infection by intervening in the phagolysosome pathway.
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Affiliation(s)
- Toshihiko Taya
- Department of Cardiovascular Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Fumiya Teruyama
- Pharmacology Research Department, Tokyo New Drug Research Laboratories, Kowa Company, Ltd., Tokyo, Japan
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Gojo
- Department of Regenerative Medicine, Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
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Ramoneda J, Stallard-Olivera E, Hoffert M, Winfrey CC, Stadler M, Niño-García JP, Fierer N. Building a genome-based understanding of bacterial pH preferences. SCIENCE ADVANCES 2023; 9:eadf8998. [PMID: 37115929 PMCID: PMC10146879 DOI: 10.1126/sciadv.adf8998] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The environmental preferences of many microbes remain undetermined. This is the case for bacterial pH preferences, which can be difficult to predict a priori despite the importance of pH as a factor structuring bacterial communities in many systems. We compiled data on bacterial distributions from five datasets spanning pH gradients in soil and freshwater systems (1470 samples), quantified the pH preferences of bacterial taxa across these datasets, and compiled genomic data from representative bacterial taxa. While taxonomic and phylogenetic information were generally poor predictors of bacterial pH preferences, we identified genes consistently associated with pH preference across environments. We then developed and validated a machine learning model to estimate bacterial pH preferences from genomic information alone, a model that could aid in the selection of microbial inoculants, improve species distribution models, or help design effective cultivation strategies. More generally, we demonstrate the value of combining biogeographic and genomic data to infer and predict the environmental preferences of diverse bacterial taxa.
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Affiliation(s)
- Josep Ramoneda
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Corresponding author. (J.R.); (N.F.)
| | - Elias Stallard-Olivera
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Michael Hoffert
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Claire C. Winfrey
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Masumi Stadler
- Département des Sciences Biologiques, Université du Québec à Montréal, Case Postale 8888, Succursale Centre-Ville, Montréal, QC H3C 3P8, Canada
| | - Juan Pablo Niño-García
- Département des Sciences Biologiques, Université du Québec à Montréal, Case Postale 8888, Succursale Centre-Ville, Montréal, QC H3C 3P8, Canada
- Escuela de Microbiología, Universidad de Antioquia, Ciudad Universitaria Calle 67 No 12 53-108, Medellín, Colombia
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Corresponding author. (J.R.); (N.F.)
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8
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Li D, Ren Z, Zhou Y, Jiang L, Zheng M, Liu G. Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations. Appl Environ Microbiol 2023; 89:e0004723. [PMID: 36912626 PMCID: PMC10056971 DOI: 10.1128/aem.00047-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/31/2023] [Indexed: 03/14/2023] Open
Abstract
Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.
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Affiliation(s)
- Deyong Li
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Zhichang Ren
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yangqi Zhou
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Lugao Jiang
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Min Zheng
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), University of Queensland, St. Lucia, Brisbane, Queensland, Australia
| | - Guoqiang Liu
- Center for Environmental Microplastics Studies, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, and School of Environment, Jinan University, Guangzhou, and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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9
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Schwarz J, Schumacher K, Brameyer S, Jung K. Bacterial battle against acidity. FEMS Microbiol Rev 2022; 46:6652135. [PMID: 35906711 DOI: 10.1093/femsre/fuac037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/11/2022] [Accepted: 07/27/2022] [Indexed: 01/09/2023] Open
Abstract
The Earth is home to environments characterized by low pH, including the gastrointestinal tract of vertebrates and large areas of acidic soil. Most bacteria are neutralophiles, but can survive fluctuations in pH. Herein, we review how Escherichia, Salmonella, Helicobacter, Brucella, and other acid-resistant Gram-negative bacteria adapt to acidic environments. We discuss the constitutive and inducible defense mechanisms that promote survival, including proton-consuming or ammonia-producing processes, cellular remodeling affecting membranes and chaperones, and chemotaxis. We provide insights into how Gram-negative bacteria sense environmental acidity using membrane-integrated and cytosolic pH sensors. Finally, we address in more detail the powerful proton-consuming decarboxylase systems by examining the phylogeny of their regulatory components and their collective functionality in a population.
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Affiliation(s)
- Julia Schwarz
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kilian Schumacher
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Sophie Brameyer
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
| | - Kirsten Jung
- Faculty of Biology, Microbiology, Ludwig-Maximilians-University München, Großhaderner Str. 2-4, 82152 Martinsried, Germany
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10
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Xia X. Multiple regulatory mechanisms for pH homeostasis in the gastric pathogen, Helicobacter pylori. ADVANCES IN GENETICS 2022; 109:39-69. [PMID: 36334916 DOI: 10.1016/bs.adgen.2022.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Acid-resistance in gastric pathogen Helicobacter pylori requires the coordination of four essential processes to regulate urease activity. Firstly, urease expression above a base level needs to be finely tuned at different ambient pH. Secondly, as nickel is needed to activate urease, nickel homeostasis needs to be maintained by proteins that import and export nickel ions, and sequester, store and release nickel when needed. Thirdly, urease accessary proteins that activate urease activity by nickel insertion need to be expressed. Finally, a reliable source of urea needs to be maintained by both intrinsic and extrinsic sources of urea. Two-component systems (arsRS and flgRS), as well as a nickel response regulator (NikR), sense the change in pH and act on a variety of genes to accomplish the function of acid resistance without causing cellular overalkalization and nickel toxicity. Nickel storage proteins also feature built-in switches to store nickel at neutral pH and release nickel at low pH. This review summarizes the current status of H. pylori research and highlights a number of hypotheses that need to be tested.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, Canada; Ottawa Institute of Systems Biology, Ottawa, Canada.
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11
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Lazar JT, Tabor JJ. Bacterial two-component systems as sensors for synthetic biology applications. CURRENT OPINION IN SYSTEMS BIOLOGY 2021; 28:100398. [PMID: 34917859 PMCID: PMC8670732 DOI: 10.1016/j.coisb.2021.100398] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Two-component systems (TCSs) are a ubiquitous family of signal transduction pathways that enable bacteria to sense and respond to diverse physical, chemical, and biological stimuli outside and inside the cell. Synthetic biologists have begun to repurpose TCSs for applications in optogenetics, materials science, gut microbiome engineering, and soil nutrient biosensing, among others. New engineering methods including genetic refactoring, DNA-binding domain swapping, detection threshold tuning, and phosphorylation cross-talk insulation are being used to increase the reliability of TCS sensor performance and tailor TCS signaling properties to the requirements of specific applications. There is now potential to combine these methods with large-scale gene synthesis and laboratory screening to discover the inputs sensed by many uncharacterized TCSs and develop a large new family of genetically-encoded sensors that respond to an unrivaled breadth of stimuli.
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Affiliation(s)
- John T Lazar
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA
| | - Jeffrey J Tabor
- Department of Bioengineering, Rice University, Houston, TX, USA
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, TX, USA
- Department of Biosciences, Rice University, Houston, TX, USA
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12
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Agarwal N, Jaiswal N, Gulati K, Gangele K, Nagar N, Kumar D, Poluri KM. Molecular Insights into Conformational Heterogeneity and Enhanced Structural Integrity of Helicobacter pylori DNA Binding Protein Hup at Low pH. Biochemistry 2021; 60:3236-3252. [PMID: 34665609 DOI: 10.1021/acs.biochem.1c00395] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The summarized amalgam of internal relaxation modulations and external forces like pH, temperature, and solvent conditions determine the protein structure, stability, and function. In a free-energy landscape, although conformers are arranged in vertical hierarchy, there exist several adjacent parallel sets with conformers occupying equivalent energy cleft. Such conformational states are pre-requisites for the functioning of proteins that have oscillating environmental conditions. As these conformational changes have utterly small re-arrangements, nuclear magnetic resonance (NMR) spectroscopy is unique in elucidating the structure-dynamics-stability-function relationships for such conformations. Helicobacter pylori survives and causes gastric cancer at extremely low pH also. However, least is known as to how the genome of the pathogen is protected from reactive oxygen species (ROS) scavenging in the gut at low pH under acidic stress. In the current study, biophysical characteristics of H. pylori DNA binding protein (Hup) have been elucidated at pH 2 using a combination of circular dichroism, fluorescence, NMR spectroscopy, and molecular dynamics simulations. Interestingly, the protein was found to have conserved structural features, differential backbone dynamics, enhanced stability, and DNA binding ability at low pH as well. In summary, the study suggests the partaking of Hup protein even at low pH in DNA protection for maintaining the genome integrity.
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Affiliation(s)
- Nipanshu Agarwal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Nancy Jaiswal
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Krishnakant Gangele
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Nupur Nagar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India.,Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667 Uttarakhand, India
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13
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Fujii S, Kobayashi S, Tettey PA, Lisdiana L, Saito H, Kawai K, Sambongi Y. Transcriptome analysis of Chironomus sulfurosus larvae living in acidic environments: Insights into molecular mechanisms for acid tolerance. JOURNAL OF INSECT PHYSIOLOGY 2021; 133:104288. [PMID: 34343520 DOI: 10.1016/j.jinsphys.2021.104288] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Larvae of chironomid Chironomus sulfurosus mainly live in acidic rivers near hot springs, suggesting that they naturally select acidic environments as preferred habitats. Here we showed that C. sulfurosus larvae moved toward acidic areas and stayed alive on agar gels with a pH gradient of H2SO4, and the body fluid pH of the homogenized larvae was near neutral even acclimated under the acidic conditions, indicating mechanisms for acid tolerance. In order to gain insights into this mechanism at the molecular level, de novo RNA-seq analysis was performed on C. sulfurosus larvae. As a result, 1,208 genes were found to be significantly up-regulated in larvae acclimated at pH 2.0 compared to controls at pH 7.0. Among the up-regulated genes, ones encoding cuticle proteins, peritrophic matrix proteins, mucus-forming proteins, F-type ATPase subunits, glutathione S transferases, β-1,3-D-glucan synthetase, hemoglobin, and cytochrome P450 were identified. This transcriptome analysis in conjunction with behavioral and biochemical assays expands our knowledge of gene expression in C. sulfurosus larvae living in acidic environments, which will provide a basis for further studies to elucidate the molecular mechanisms for acid tolerance employed by organisms in nature.
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Affiliation(s)
- Sotaro Fujii
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan.
| | - Satoru Kobayashi
- Graduate School of Biosphere Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Pamela A Tettey
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Lisa Lisdiana
- Department of Biology, Universitas Negeri Surabaya, Kampus Unesa Ketintang, Surabaya 60231, Indonesia
| | - Hidetoshi Saito
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Koichiro Kawai
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Yoshihiro Sambongi
- Graduate School of Integrated Sciences for Life, Hiroshima University, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan.
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14
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Szczepanowski P, Noszka M, Żyła-Uklejewicz D, Pikuła F, Nowaczyk-Cieszewska M, Krężel A, Stingl K, Zawilak-Pawlik A. HP1021 is a redox switch protein identified in Helicobacter pylori. Nucleic Acids Res 2021; 49:6863-6879. [PMID: 34139017 PMCID: PMC8266642 DOI: 10.1093/nar/gkab440] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/26/2021] [Accepted: 05/06/2021] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a gram-negative, microaerophilic, pathogenic bacterium and a widespread colonizer of humans. H. pylori has developed mechanisms that enable it to overcome the harsh environment of the human stomach, including reactive oxygen species (ROS). Interestingly, up to now no typical regulator dedicated to the oxidative-stress response has been discovered. In this work, we reveal that the inhibitor of replication initiation HP1021 functions as a redox switch protein in H. pylori and plays an important role in response to oxidative stress of the gastric pathogen. Each of the two predicted HP1021 domains contains three cysteine residues. We show that the cysteine residues of HP1021 are sensitive to oxidation both in vitro and in vivo, and we demonstrate that HP1021 DNA-binding activity to oriC depends on the redox state of the protein. Moreover, Zn2+ modulates HP1021 affinity towards oriC template DNA. Transcription analysis of selected H. pylori genes by RT-qPCR indicated that HP1021 is directly involved in the oxygen-dependent control of H. pylori fecA3 and gluP genes, which are implicated in response to oxidative stress. In conclusion, HP1021 is a redox switch protein and could be a target for H. pylori control strategies.
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Affiliation(s)
- Piotr Szczepanowski
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław 53-114, Poland
| | - Mateusz Noszka
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław 53-114, Poland
| | - Dorota Żyła-Uklejewicz
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław 53-114, Poland
| | - Fabian Pikuła
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław 53-114, Poland
| | - Malgorzata Nowaczyk-Cieszewska
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław 53-114, Poland
| | - Artur Krężel
- Department of Chemical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław 50-383, Poland
| | - Kerstin Stingl
- Department of Biological Safety, National Reference Laboratory for Campylobacter, German Federal Institute for Risk Assessment, Berlin 12277, Germany
| | - Anna Zawilak-Pawlik
- Department of Microbiology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wrocław 53-114, Poland
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15
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In Vitro Framework to Assess the Anti- Helicobacter pylori Potential of Lactic Acid Bacteria Secretions as Alternatives to Antibiotics. Int J Mol Sci 2021; 22:ijms22115650. [PMID: 34073352 PMCID: PMC8198849 DOI: 10.3390/ijms22115650] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/20/2021] [Accepted: 05/20/2021] [Indexed: 12/31/2022] Open
Abstract
Helicobacter pylori is a prevalent bacterium that can cause gastric ulcers and cancers. Lactic acid bacteria (LAB) ameliorate treatment outcomes against H. pylori, suggesting that they could be a source of bioactive molecules usable as alternatives to current antibiotics for which resistance is mounting. We developed an in vitro framework to compare the anti-H. pylori properties of 25 LAB and their secretions against H. pylori. All studies were done at acidic and neutralized pH, with or without urea to mimic various gastric compartments. Eighteen LAB strains secreted molecules that curtailed the growth of H. pylori and the activity was urea-resistant in five LAB. Several LAB supernatants also reduced the urease activity of H. pylori. Pre-treatment of H. pylori with acidic LAB supernatants abrogated its flagella-mediated motility and decreased its ability to elicit pro-inflammatory IL-8 cytokine from human gastric cells, without reverting the H. pylori-induced repression of other pro-inflammatory cytokines. This study identified the LAB that have the most anti-H. pylori effects, decreasing its viability, its production of virulence factors, its motility and/or its ability to elicit pro-inflammatory IL-8 from gastric cells. Once identified, these molecules can be used as alternatives or complements to current antibiotics to fight H. pylori infections.
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16
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Delineation of the pH-Responsive Regulon Controlled by the Helicobacter pylori ArsRS Two-Component System. Infect Immun 2021; 89:IAI.00597-20. [PMID: 33526561 DOI: 10.1128/iai.00597-20] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/09/2021] [Indexed: 12/22/2022] Open
Abstract
Helicobacter pylori encounters a wide range of pH within the human stomach. In a comparison of H. pylori cultured in vitro under neutral or acidic conditions, about 15% of genes are differentially expressed, and corresponding changes are detectable for many of the encoded proteins. The ArsRS two-component system (TCS), comprised of the sensor kinase ArsS and its cognate response regulator ArsR, has an important role in mediating pH-responsive changes in H. pylori gene expression. In this study, we sought to delineate the pH-responsive ArsRS regulon and further define the role of ArsR in pH-responsive gene expression. We compared H. pylori strains containing an intact ArsRS system with an arsS null mutant or strains containing site-specific mutations of a conserved aspartate residue (D52) in ArsR, which is phosphorylated in response to signals relayed by the cognate sensor kinase ArsS. We identified 178 genes that were pH-responsive in strains containing an intact ArsRS system but not in ΔarsS or arsR mutants. These constituents of the pH-responsive ArsRS regulon include genes involved in acid acclimatization (ureAB, amidases), oxidative stress responses (katA, sodB), transcriptional regulation related to iron or nickel homeostasis (fur, nikR), and genes encoding outer membrane proteins (including sabA, alpA, alpB, hopD [labA], and horA). When comparing H. pylori strains containing an intact ArsRS TCS with arsRS mutants, each cultured at neutral pH, relatively few genes are differentially expressed. Collectively, these data suggest that ArsRS-mediated gene regulation has an important role in H. pylori adaptation to changing pH conditions.
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17
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Dey R, Rieger A, Banting G, Ashbolt NJ. Role of amoebae for survival and recovery of 'non-culturable' Helicobacter pylori cells in aquatic environments. FEMS Microbiol Ecol 2021; 96:5902844. [PMID: 32897313 PMCID: PMC7494403 DOI: 10.1093/femsec/fiaa182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022] Open
Abstract
Helicobacter pylori is a fastidious Gram-negative bacterium that infects over half of the world's population, causing chronic gastritis and is a risk factor for stomach cancer. In developing and rural regions where prevalence rate exceeds 60%, persistence and waterborne transmission are often linked to poor sanitation conditions. Here we demonstrate that H. pylori not only survives but also replicates within acidified free-living amoebal phagosomes. Bacterial counts of the clinical isolate H. pylori G27 increased over 50-fold after three days in co-culture with amoebae. In contrast, a H. pylori mutant deficient in a cagPAI gene (cagE) showed little growth within amoebae, demonstrating the likely importance of a type IV secretion system in H. pylori for amoebal infection. We also demonstrate that H. pylori can be packaged by amoebae and released in extracellular vesicles. Furthermore, and for the first time, we successfully demonstrate the ability of two free-living amoebae to revert and recover viable but non-cultivable coccoid (VBNC)-H. pylori to a culturable state. Our studies provide evidence to support the hypothesis that amoebae and perhaps other free-living protozoa contribute to the replication and persistence of human-pathogenic H. pylori by providing a protected intracellular microenvironment for this pathogen to persist in natural aquatic environments and engineered water systems, thereby H. pylori potentially uses amoeba as a carrier and a vector of transmission.
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Affiliation(s)
- Rafik Dey
- School of Public Health, University of Alberta,11405-87 Avenue, Edmonton, Alberta T6G 1C9, Canada.,Deparment of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Aja Rieger
- Deparment of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada
| | - Graham Banting
- School of Public Health, University of Alberta,11405-87 Avenue, Edmonton, Alberta T6G 1C9, Canada
| | - Nicholas J Ashbolt
- School of Public Health, University of Alberta,11405-87 Avenue, Edmonton, Alberta T6G 1C9, Canada.,Deparment of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta T6G 2E1, Canada.,Provincial Laboratory for Public Health (ProvLab), Alberta Health Services, Edmonton, Canada.,School of Environmental, Sciense and Engineering, Southern Cross University, Lismore NSW, Australia
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18
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Jaboulay C, Godeux AS, Doublet P, Vianney A. Regulatory Networks of the T4SS Control: From Host Cell Sensing to the Biogenesis and the Activity during the Infection. J Mol Biol 2021; 433:166892. [PMID: 33636165 DOI: 10.1016/j.jmb.2021.166892] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/17/2021] [Accepted: 02/17/2021] [Indexed: 02/03/2023]
Abstract
Delivery of effectors, DNA or proteins, that hijack host cell processes to the benefit of bacteria is a mechanism widely used by bacterial pathogens. It is achieved by complex effector injection devices, the secretion systems, among which Type 4 Secretion Systems (T4SSs) play a key role in bacterial virulence of numerous animal and plant pathogens. Considerable progress has recently been made in the structure-function analyses of T4SSs. Nevertheless, the signals and processes that trigger machine assembly and activity during infection, as well as those involved in substrate recognition and transfer, are complex and still poorly understood. In this review, we aim at summarizing the last updates of the knowledge on signaling pathways that regulate the biogenesis and the activity of T4SSs in important bacterial pathogens.
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Affiliation(s)
- C Jaboulay
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France.
| | - A S Godeux
- CIRI, Centre International de Recherche en Infectiologie, (Team: Horigene), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - P Doublet
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
| | - A Vianney
- CIRI, Centre International de Recherche en Infectiologie, (Team: Legionella pathogenesis), Univ Lyon, Inserm, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007 Lyon, France
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19
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Panwar H, Rokana N, Aparna SV, Kaur J, Singh A, Singh J, Singh KS, Chaudhary V, Puniya AK. Gastrointestinal stress as innate defence against microbial attack. J Appl Microbiol 2020; 130:1035-1061. [PMID: 32869386 DOI: 10.1111/jam.14836] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/09/2020] [Accepted: 08/21/2020] [Indexed: 12/13/2022]
Abstract
The human gastrointestinal (GI) tract has been bestowed with the most difficult task of protecting the underlying biological compartments from the resident commensal flora and the potential pathogens in transit through the GI tract. It has a unique environment in which several defence tactics are at play while maintaining homeostasis and health. The GI tract shows myriad number of environmental extremes, which includes pH variations, anaerobic conditions, nutrient limitations, elevated osmolarity etc., which puts a check to colonization and growth of nonfriendly microbial strains. The GI tract acts as a highly selective barrier/platform for ingested food and is the primary playground for balance between the resident and uninvited organisms. This review focuses on antimicrobial defense mechanisms of different sections of human GI tract. In addition, the protective mechanisms used by microbes to combat the human GI defence systems are also discussed. The ability to survive this innate defence mechanism determines the capability of probiotic or pathogen strains to confer health benefits or induce clinical events respectively.
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Affiliation(s)
- H Panwar
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - N Rokana
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - S V Aparna
- Department of Dairy Microbiology, College of Dairy Science and Technology, Kerala Veterinary and Animal Science University, Mannuthy, Thrissur, India
| | - J Kaur
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - A Singh
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - J Singh
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - K S Singh
- Structure and Function of Proteins, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - V Chaudhary
- Department of Microbiology, Punjab Agriculture University, Ludhiana, Punjab, India
| | - A K Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, Haryana, India
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20
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Kornspan D, Zahavi T, Salmon-Divon M. The Acidic Stress Response of the Intracellular Pathogen Brucella melitensis: New Insights from a Comparative, Genome-Wide Transcriptome Analysis. Genes (Basel) 2020; 11:genes11091016. [PMID: 32872264 PMCID: PMC7563570 DOI: 10.3390/genes11091016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 11/30/2022] Open
Abstract
The intracellular pathogenic bacteria belonging to the genus Brucella must cope with acidic stress as they penetrate the host via the gastrointestinal route, and again during the initial stages of intracellular infection. A transcription-level regulation has been proposed to explain this but the specific molecular mechanisms are yet to be determined. We recently reported a comparative transcriptomic analysis of the attenuated vaccine Brucella melitensis strain Rev.1 against the virulent strain 16M in cultures grown under either neutral or acidic conditions. Here, we re-analyze the RNA-seq data of 16M from our previous study and compare it to published transcriptomic data of this strain from both an in cellulo and an in vivo model. We identify 588 genes that are exclusively differentially expressed in 16M grown under acidic versus neutral pH conditions, including 286 upregulated genes and 302 downregulated genes that are not differentially expressed in either the in cellulo or the in vivo model. Of these, we highlight 13 key genes that are known to be associated with a bacterial response to acidic stress and, in our study, were highly upregulated under acidic conditions. These genes provide new molecular insights into the mechanisms underlying the acid-resistance of Brucella within its host.
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Affiliation(s)
- David Kornspan
- Department of Bacteriology, Kimron Veterinary Institute, Bet Dagan 50250, Israel
- Correspondence: ; Tel.: +972-3-968-1745
| | - Tamar Zahavi
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel 40700, Israel; (T.Z.); (M.S.-D.)
| | - Mali Salmon-Divon
- Genomic Bioinformatics Laboratory, Department of Molecular Biology, Ariel University, Ariel 40700, Israel; (T.Z.); (M.S.-D.)
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel
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21
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Marcus EA, Tokhtaeva E, Jimenez JL, Wen Y, Naini BV, Heard AN, Kim S, Capri J, Cohn W, Whitelegge JP, Vagin O. Helicobacter pylori infection impairs chaperone-assisted maturation of Na-K-ATPase in gastric epithelium. Am J Physiol Gastrointest Liver Physiol 2020; 318:G931-G945. [PMID: 32174134 PMCID: PMC7272721 DOI: 10.1152/ajpgi.00266.2019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 03/06/2020] [Accepted: 03/10/2020] [Indexed: 01/31/2023]
Abstract
Helicobacter pylori infection always induces gastritis, which may progress to ulcer disease or cancer. The mechanisms underlying mucosal injury by the bacteria are incompletely understood. Here, we identify a novel pathway for H. pylori-induced gastric injury, the impairment of maturation of the essential transport enzyme and cell adhesion molecule, Na-K-ATPase. Na-K-ATPase comprises α- and β-subunits that assemble in the endoplasmic reticulum (ER) before trafficking to the plasma membrane. Attachment of H. pylori to gastric epithelial cells increased Na-K-ATPase ubiquitylation, decreased its surface and total levels, and impaired ion balance. H. pylori did not alter degradation of plasmalemma-resident Na-K-ATPase subunits or their mRNA levels. Infection decreased association of α- and β-subunits with ER chaperone BiP and impaired assembly of α/β-heterodimers, as was revealed by quantitative mass spectrometry and immunoblotting of immunoprecipitated complexes. The total level of BiP was not altered, and the decrease in interaction with BiP was not observed for other BiP client proteins. The H. pylori-induced decrease in Na-K-ATPase was prevented by BiP overexpression, stopping protein synthesis, or inhibiting proteasomal, but not lysosomal, protein degradation. The results indicate that H. pylori impairs chaperone-assisted maturation of newly made Na-K-ATPase subunits in the ER independently of a generalized ER stress and induces their ubiquitylation and proteasomal degradation. The decrease in Na-K-ATPase levels is also seen in vivo in the stomachs of gerbils and chronically infected children. Further understanding of H. pylori-induced Na-K-ATPase degradation will provide insights for protection against advanced disease.NEW & NOTEWORTHY This work provides evidence that Helicobacter pylori decreases levels of Na-K-ATPase, a vital transport enzyme, in gastric epithelia, both in acutely infected cultured cells and in chronically infected patients and animals. The bacteria interfere with BiP-assisted folding of newly-made Na-K-ATPase subunits in the endoplasmic reticulum, accelerating their ubiquitylation and proteasomal degradation and decreasing efficiency of the assembly of native enzyme. Decreased Na-K-ATPase expression contributes to H. pylori-induced gastric injury.
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Affiliation(s)
- Elizabeth A Marcus
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
| | - Elmira Tokhtaeva
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, California
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
| | - Jossue L Jimenez
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
| | - Yi Wen
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, California
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
| | - Bita V Naini
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Ashley N Heard
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
| | - Samuel Kim
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
| | - Joseph Capri
- Pasarow Mass Spectrometry Laboratory, The Neuropsychiatric Insititute-Semel Institute, University of California, Los Angeles, California
| | - Whitaker Cohn
- Pasarow Mass Spectrometry Laboratory, The Neuropsychiatric Insititute-Semel Institute, University of California, Los Angeles, California
| | - Julian P Whitelegge
- Pasarow Mass Spectrometry Laboratory, The Neuropsychiatric Insititute-Semel Institute, University of California, Los Angeles, California
| | - Olga Vagin
- Department of Physiology, David Geffen School of Medicine, University of California, Los Angeles, California
- Veterans Affairs Greater Los Angeles Health Care System, Los Angeles, California
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22
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Mechanisms of the Epithelial-Mesenchymal Transition and Tumor Microenvironment in Helicobacter pylori-Induced Gastric Cancer. Cells 2020; 9:cells9041055. [PMID: 32340207 PMCID: PMC7225971 DOI: 10.3390/cells9041055] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/11/2022] Open
Abstract
Helicobacter pylori (H. pylori) is one of the most common human pathogens, affecting half of the world’s population. Approximately 20% of the infected patients develop gastric ulcers or neoplastic changes in the gastric stroma. An infection also leads to the progression of epithelial–mesenchymal transition within gastric tissue, increasing the probability of gastric cancer development. This paper aims to review the role of H. pylori and its virulence factors in epithelial–mesenchymal transition associated with malignant transformation within the gastric stroma. The reviewed factors included: CagA (cytotoxin-associated gene A) along with induction of cancer stem-cell properties and interaction with YAP (Yes-associated protein pathway), tumor necrosis factor α-inducing protein, Lpp20 lipoprotein, Afadin protein, penicillin-binding protein 1A, microRNA-29a-3p, programmed cell death protein 4, lysosomal-associated protein transmembrane 4β, cancer-associated fibroblasts, heparin-binding epidermal growth factor (HB-EGF), matrix metalloproteinase-7 (MMP-7), and cancer stem cells (CSCs). The review summarizes the most recent findings, providing insight into potential molecular targets and new treatment strategies for gastric cancer.
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23
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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Narayanan N, Banerjee A, Jain D, Kulkarni DS, Sharma R, Nirwal S, Rao DN, Nair DT. Tetramerization at Low pH Licenses DNA Methylation Activity of M.HpyAXI in the Presence of Acid Stress. J Mol Biol 2020; 432:324-342. [DOI: 10.1016/j.jmb.2019.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2019] [Revised: 10/01/2019] [Accepted: 10/01/2019] [Indexed: 11/25/2022]
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Belova AM, Basmanov DV, Prusakov KA, Lazarev VN, Klinov DV. A Microfluidic Platform for the Development of a Biosensor Based on Genetically Modified Helicobacter pylori Single Cells. Biophysics (Nagoya-shi) 2019. [DOI: 10.1134/s0006350918050020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
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Spronk CAEM, Żerko S, Górka M, Koźmiński W, Bardiaux B, Zambelli B, Musiani F, Piccioli M, Basak P, Blum FC, Johnson RC, Hu H, Merrell DS, Maroney M, Ciurli S. Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools. J Biol Inorg Chem 2018; 23:1309-1330. [PMID: 30264175 DOI: 10.1007/s00775-018-1616-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Accepted: 09/05/2018] [Indexed: 01/03/2023]
Abstract
Helicobacter pylori HypA (HpHypA) is a metallochaperone necessary for maturation of [Ni,Fe]-hydrogenase and urease, the enzymes required for colonization and survival of H. pylori in the gastric mucosa. HpHypA contains a structural Zn(II) site and a unique Ni(II) binding site at the N-terminus. X-ray absorption spectra suggested that the Zn(II) coordination depends on pH and on the presence of Ni(II). This study was performed to investigate the structural properties of HpHypA as a function of pH and Ni(II) binding, using NMR spectroscopy combined with DFT and molecular dynamics calculations. The solution structure of apo,Zn-HpHypA, containing Zn(II) but devoid of Ni(II), was determined using 2D, 3D and 4D NMR spectroscopy. The structure suggests that a Ni-binding and a Zn-binding domain, joined through a short linker, could undergo mutual reorientation. This flexibility has no physiological effect on acid viability or urease maturation in H. pylori. Atomistic molecular dynamics simulations suggest that Ni(II) binding is important for the conformational stability of the N-terminal helix. NMR chemical shift perturbation analysis indicates that no structural changes occur in the Zn-binding domain upon addition of Ni(II) in the pH 6.3-7.2 range. The structure of the Ni(II) binding site was probed using 1H NMR spectroscopy experiments tailored to reveal hyperfine-shifted signals around the paramagnetic metal ion. On this basis, two possible models were derived using quantum-mechanical DFT calculations. The results provide a comprehensive picture of the Ni(II) mode to HpHypA, important to rationalize, at the molecular level, the functional interactions of this chaperone with its protein partners.
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Affiliation(s)
- Chris A E M Spronk
- JSC Spronk, Vilnius, Lithuania.,Department of Molecular and Cell Biology, Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, UK
| | - Szymon Żerko
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Michał Górka
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland.,Faculty of Physics, Division of Biophysics, Institute of Experimental Physics, University of Warsaw, Pasteura 5, 02-093, Warsaw, Poland
| | - Wiktor Koźmiński
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089, Warsaw, Poland
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Barbara Zambelli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Mario Piccioli
- Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy
| | - Priyanka Basak
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - Faith C Blum
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ryan C Johnson
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Heidi Hu
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA
| | - D Scott Merrell
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Michael Maroney
- Department of Chemistry, University of Massachusetts, Amherst, MA, 01003, USA.
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy. .,Center for Magnetic Resonance, Department of Chemistry, University of Florence, Florence, Italy.
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Molina-Castro S, Ramírez-Mayorga V, Alpízar-Alpízar W. Priming the seed: Helicobacter pylori alters epithelial cell invasiveness in early gastric carcinogenesis. World J Gastrointest Oncol 2018; 10:231-243. [PMID: 30254719 PMCID: PMC6147766 DOI: 10.4251/wjgo.v10.i9.231] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/13/2018] [Accepted: 06/27/2018] [Indexed: 02/05/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection is a well-established risk factor for the development of gastric cancer (GC), one of the most common and deadliest neoplasms worldwide. H. pylori infection induces chronic inflammation in the gastric mucosa that, in the absence of treatment, may progress through a series of steps to GC. GC is only one of several clinical outcomes associated with this bacterial infection, which may be at least partially attributed to the high genetic variability of H. pylori. The biological mechanisms underlying how and under what circumstances H. pylori alters normal physiological processes remain enigmatic. A key aspect of carcinogenesis is the acquisition of traits that equip preneoplastic cells with the ability to invade. Accumulating evidence implicates H. pylori in the manipulation of cellular and molecular programs that are crucial for conferring cells with invasive capabilities. We present here an overview of the main findings about the involvement of H. pylori in the acquisition of cell invasive behavior, specifically focusing on the epithelial-to-mesenchymal transition, changes in cell polarity, and deregulation of molecules that control extracellular matrix remodeling.
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Affiliation(s)
- Silvia Molina-Castro
- Cancer Epidemiology Research Program, Health Research Institute, University of Costa Rica, San José 2060, Costa Rica
- Clinical Department, School of Medicine, University of Costa Rica, San José 2060, Costa Rica
| | - Vanessa Ramírez-Mayorga
- Cancer Epidemiology Research Program, Health Research Institute, University of Costa Rica, San José 2060, Costa Rica
- Public Nutrition Section, School of Nutrition, University of Costa Rica, San José 2060, Costa Rica
| | - Warner Alpízar-Alpízar
- Center for Research in Microscopic Structures, University of Costa Rica, San José 2060, Costa Rica
- Department of Biochemistry, School of Medicine, University of Costa Rica, San José 2060, Costa Rica
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Jones MD, Li Y, Zamble DB. Acid-responsive activity of the Helicobacter pylori metalloregulator NikR. Proc Natl Acad Sci U S A 2018; 115:8966-8971. [PMID: 30126985 PMCID: PMC6130374 DOI: 10.1073/pnas.1808393115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Helicobacter pylori is a human pathogen that infects the stomach, where it experiences variable pH. To survive the acidic gastric conditions, H. pylori produces large quantities of urease, a nickel enzyme that hydrolyzes urea to ammonia, which neutralizes the local environment. One of the regulators of urease expression in H. pylori is HpNikR, a nickel-responsive transcription factor. Here we show that HpNikR also regulates urease expression in response to changes in pH, linking acid adaptation and nickel homeostasis. Upon measuring the cytosolic pH of H. pylori exposed to an external pH of 2, similar to the acidic shock conditions that occur in the human stomach, a significant drop in internal pH was observed. This decrease in internal pH resulted in HpNikR-dependent activation of ureA transcription. Furthermore, analysis of a slate of H. pylori genes encoding other acid adaptation or nickel homeostasis components revealed HpNikR-dependent regulation in response to acid shock. This regulation was consistent with pH-dependent DNA binding to the corresponding promoter sequences observed in vitro with purified HpNikR. These results demonstrate that HpNikR can directly respond to changes in cytosolic pH during acid acclimation and illustrate the exquisitely coordinated regulatory networks that support H. pylori infections in the harsh environment of the human stomach.
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Affiliation(s)
- Michael D Jones
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Yanjie Li
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
| | - Deborah B Zamble
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
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Saylor Z, Maier R. Helicobacter pylori nickel storage proteins: recognition and modulation of diverse metabolic targets. Microbiology (Reading) 2018; 164:1059-1068. [DOI: 10.1099/mic.0.000680] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Zachary Saylor
- Department of Microbiology and Center for Metalloprotein Studies, University of Georgia, Athens, GA, USA
| | - Robert Maier
- Department of Microbiology and Center for Metalloprotein Studies, University of Georgia, Athens, GA, USA
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Abstract
Codon usage depends on mutation bias, tRNA-mediated selection, and the need for high efficiency and accuracy in translation. One codon in a synonymous codon family is often strongly over-used, especially in highly expressed genes, which often leads to a high dN/dS ratio because dS is very small. Many different codon usage indices have been proposed to measure codon usage and codon adaptation. Sense codon could be misread by release factors and stop codons misread by tRNAs, which also contribute to codon usage in rare cases. This chapter outlines the conceptual framework on codon evolution, illustrates codon-specific and gene-specific codon usage indices, and presents their applications. A new index for codon adaptation that accounts for background mutation bias (Index of Translation Elongation) is presented and contrasted with codon adaptation index (CAI) which does not consider background mutation bias. They are used to re-analyze data from a recent paper claiming that translation elongation efficiency matters little in protein production. The reanalysis disproves the claim.
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Measurement of Internal pH in Helicobacter pylori by Using Green Fluorescent Protein Fluorimetry. J Bacteriol 2018; 200:JB.00178-18. [PMID: 29735759 DOI: 10.1128/jb.00178-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/01/2018] [Indexed: 11/20/2022] Open
Abstract
Helicobacter pylori is an organism known to colonize the normal human stomach. Previous studies have shown that the bacterium does this by elevating its periplasmic pH via the hydrolysis of urea. However, the value of the periplasmic pH was calculated indirectly from the proton motive force equation. To measure the periplasmic pH directly in H. pylori, we fused enhanced green fluorescent protein (EGFP) to the predicted twin-arginine signal peptides of HydA and KapA from H. pylori and TorA from Escherichia coli The fusion proteins were expressed in the H. pylori genome under the control of the cagA promoter. Confocal microscopic and cell fractionation/immunoblotting analyses detected TorA-EGFP in the periplasm and KapA-EGFP in both the periplasm and cytoplasm, while the mature form of HydA-EGFP was seen at low levels in the periplasm, with major cytoplasmic retention of the precursor form. With H. pylori expressing TorA-EGFP, we established a system to directly measure periplasmic pH based on the pH-sensitive fluorimetry of EGFP. These measurements demonstrated that the addition of 5 mM urea has little effect on the periplasmic pH at a medium pH higher than pH 6.5 but rapidly increases the periplasmic pH to pH 6.1 at an acidic medium pH (pH 5.0), corresponding to the opening of the proton-gated channel, UreI, and confirming the basis of gastric colonization. Measurements of the periplasmic pH in an HP0244 (FlgS)-deficient mutant of H. pylori expressing TorA-EGFP revealed a significant loss of the urea-dependent increase in the periplasmic pH at an acidic medium pH, providing additional evidence that FlgS is responsible for recruitment of urease to the inner membrane in association with UreI.IMPORTANCEHelicobacter pylori has been identified as the major cause of chronic superficial gastritis and peptic ulcer disease. In addition, persistent infection with H. pylori, which, if untreated, lasts for the lifetime of an infected individual, predisposes one to gastric malignancies, such as adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma. A unique feature of the neutralophilic bacterium H. pylori is its ability to survive in the extremely acidic environment of the stomach through its acid acclimation mechanism. The presented results on measurements of periplasmic pH in H. pylori based on fluorimetry of fully active green fluorescent protein fusion proteins exported with the twin-arginine translocase system provide a reliable and rapid tool for the investigation of acid acclimation in H. pylori.
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Marcus EA, Sachs G, Scott DR. Acid-regulated gene expression of Helicobacter pylori: Insight into acid protection and gastric colonization. Helicobacter 2018; 23:e12490. [PMID: 29696729 PMCID: PMC5980792 DOI: 10.1111/hel.12490] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND The pathogen Helicobacter pylori encounters many stressors as it transits to and infects the gastric epithelium. Gastric acidity is the predominate stressor encountered by the bacterium during initial infection and establishment of persistent infection. H. pylori initiates a rapid response to acid to maintain intracellular pH and proton motive force appropriate for a neutralophile. However, acid sensing by H. pylori may also serve as a transcriptional trigger to increase the levels of other pathogenic factors needed to subvert host defenses such as acid acclimation, antioxidants, flagellar synthesis and assembly, and CagA secretion. MATERIALS AND METHODS Helicobacter pylori were acid challenged at pH 3.0, 4.5, 6.0 vs nonacidic pH for 4 hours in the presence of urea, followed by RNA-seq analysis and qPCR. Cytoplasmic pH was monitored under the same conditions. RESULTS About 250 genes were induced, and an equal number were repressed at acidic pHs. Genes encoding for antioxidant proteins, flagellar structural proteins, particularly class 2 genes, T4SS/Cag-PAI, Fo F1 -ATPase, and proteins involved in acid acclimation were highly expressed at acidic pH. Cytoplasmic pH decreased from 7.8 at pHout of 8.0 to 6.0 at pHout of 3.0. CONCLUSIONS These results suggest that increasing extracellular or intracellular acidity or both are detected by the bacterium and serve as a signal to initiate increased production of protective and pathogenic factors needed to counter host defenses for persistent infection. These changes are dependent on degree of acidity and time of acid exposure, triggering a coordinated response to the environment required for colonization.
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Affiliation(s)
- Elizabeth A. Marcus
- Department of Pediatrics, David Geffen School of Medicine at UCLA,VA GLAHS, Los Angeles, CA
| | - George Sachs
- Department Medicine, David Geffen School of Medicine at UCLA,Department Physiology, David Geffen School of Medicine at UCLA,VA GLAHS, Los Angeles, CA
| | - David R. Scott
- Department Physiology, David Geffen School of Medicine at UCLA,VA GLAHS, Los Angeles, CA,Corresponding author: David R. Scott, Department of Physiology, DGSOM at UCLA, VA GLAHS, Bldg 113, Rm 324, 11301 Wilshire Blvd, Los Angeles, CA 90073, , phone: 310-478-3711 x42046; Fax: 310-312-9478
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Hu HQ, Huang HT, Maroney MJ. The Helicobacter pylori HypA·UreE 2 Complex Contains a Novel High-Affinity Ni(II)-Binding Site. Biochemistry 2018; 57:2932-2942. [PMID: 29708738 DOI: 10.1021/acs.biochem.8b00127] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Helicobacter pylori is a human pathogen that colonizes the stomach, is the major cause of ulcers, and has been associated with stomach cancers. To survive in the acidic environment of the stomach, H. pylori uses urease, a nickel-dependent enzyme, to produce ammonia for maintenance of cellular pH. The bacteria produce apo-urease in large quantities and activate it by incorporating nickel under acid shock conditions. Urease nickel incorporation requires the urease-specific metallochaperone UreE and the (UreFGH)2 maturation complex. In addition, the H. pylori nickel urease maturation pathway recruits accessory proteins from the [NiFe] hydrogenase maturation pathway, namely, HypA and HypB. HypA and UreE dimers (UreE2) are known to form a protein complex, the role of which in urease maturation is largely unknown. Herein, we examine the nickel-binding properties and protein-protein interactions of HypA and UreE2 using isothermal titration calorimetry and fluorometric methods under neutral and acidic pH conditions to gain insight into the roles played by HypA in urease maturation. The results reveal that HypA and UreE2 form a stable complex with micromolar affinity that protects UreE from hydrolytic degradation. The HypA·UreE2 complex contains a unique high-affinity (nanomolar) Ni2+-binding site that is maintained under conditions designed to mimic acid shock (pH 6.3). The data are interpreted in terms of a proposed mechanism wherein HypA and UreE2 act as co-metallochaperones that target the delivery of Ni2+ to apo-urease with high fidelity.
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Guerrero-Castro J, Lozano L, Sohlenkamp C. Dissecting the Acid Stress Response of Rhizobium tropici CIAT 899. Front Microbiol 2018; 9:846. [PMID: 29760688 PMCID: PMC5936775 DOI: 10.3389/fmicb.2018.00846] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 04/12/2018] [Indexed: 11/27/2022] Open
Abstract
Rhizobium tropici CIAT899 is a nodule-forming α-proteobacterium displaying intrinsic resistance to several abiotic stress conditions such as low pH and high temperatures, which are common in tropical environments. It is a good competitor for Phaseolus vulgaris (common bean) nodule occupancy at low pH values, however little is known about the genetic and physiological basis of the tolerance to acidic conditions. To identify genes in R. tropici involved in pH stress response we combined two different approaches: (1) A Tn5 mutant library of R. tropici CIAT899 was screened and 26 acid-sensitive mutants were identified. For 17 of these mutants, the transposon insertion sites could be identified. (2) We also studied the transcriptomes of cells grown under different pH conditions using RNA-Seq. RNA was extracted from cells grown for several generations in minimal medium at 6.8 or 4.5 (adapted cells). In addition, we acid-shocked cells pre-grown at pH 6.8 for 45 min at pH 4.5. Of the 6,289 protein-coding genes annotated in the genome of R. tropici CIAT 899, 383 were differentially expressed under acidic conditions (pH 4.5) vs. control condition (pH 6.8). Three hundred and fifty one genes were induced and 32 genes were repressed; only 11 genes were induced upon acid shock. The acid stress response of R. tropici CIAT899 is versatile: we found genes encoding response regulators and membrane transporters, enzymes involved in amino acid and carbohydrate metabolism and proton extrusion, in addition to several hypothetical genes. Our findings enhance our understanding of the core genes that are important during the acid stress response in R. tropici.
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Affiliation(s)
- Julio Guerrero-Castro
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico.,Programa de Doctorado en Ciencias Biomédicas, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis Lozano
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Christian Sohlenkamp
- Programa de Ecología Genómica, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Sasaki M, Kodama Y, Shimoyama Y, Ishikawa T, Kimura S. Aciduricity and acid tolerance mechanisms of Streptococcus anginosus. J GEN APPL MICROBIOL 2018; 64:174-179. [PMID: 29669961 DOI: 10.2323/jgam.2017.11.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Although Streptococcus anginosus constitutes a proportion of the normal flora of the gastrointestinal and genital tracts, and the oral cavity, it has been reported that S. anginosus infection could be closely associated with abscesses at various body sites, infective endocarditis, and upper gastrointestinal cancers. The colonization in an acidic environment due to the aciduricity of S. anginosus could be the etiology of the systemic infection of the bacteria. To elucidate the aciduricity and acid tolerance mechanisms of the microbe, we examined the viability and growth of S. anginosus under acidic conditions. The viabilities of S. anginosus NCTC 10713 and Streptococcus mutans ATCC 25175 at pH 4.0 showed as being markedly higher than those of Streptococcus sanguinis ATCC 10556, Streptococcus gordonii ATCC 10558, and Streptococcus mitis ATCC 49456; however, the viability was partially inhibited by dicyclohexylcarbodiimide, an H+-ATPase inhibitor, suggesting that H+-ATPase could play a role in the viability of S. anginosus under acidic conditions. In addition, S. anginosus NCTC 10713 could grow at pH 5.0 and showed a marked arginine deiminase (ADI) activity, unlike its ΔarcA mutant, deficient in the gene encoding ADI, and other streptococcal species, which indicated that ADI could also be associated with aciduricity. These results suggest that S. anginosus has significant aciduric properties, which can be attributed to these enzyme activities.
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Affiliation(s)
- Minoru Sasaki
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University School of Dentistry
| | - Yoshitoyo Kodama
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University School of Dentistry
| | - Yu Shimoyama
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University School of Dentistry
| | - Taichi Ishikawa
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University School of Dentistry
| | - Shigenobu Kimura
- Division of Molecular Microbiology, Department of Microbiology, Iwate Medical University School of Dentistry
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Pereira V, Abraham P, Nallapeta S, Shetty A. Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy. BMC Gastroenterol 2018; 18:20. [PMID: 29373960 PMCID: PMC5787260 DOI: 10.1186/s12876-018-0744-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/14/2018] [Indexed: 02/06/2023] Open
Abstract
Background The gastric microbiota has recently been implicated in the causation of organic/structural gastroduodenal diseases (gastric and duodenal ulcers, gastric cancer) in patients with Helicobacter pylori (H. pylori) infection. We aimed to ascertain, in patients harbouring H. pylori, the role of the gastric microbiota in the causation of symptoms (chronic dyspepsia) in the absence of organic disease. Methods Seventy-four gastric biopsy samples obtained at endoscopy from patients with (n = 21) or without (n = 53) chronic dyspepsia, and that tested positive by the bedside rapid urease test for H. pylori infection, were cultured for detection of H. pylori and non-H. pylori organisms. The cultured organisms were identified by matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI-TOF MS). Results A total of 106 non-H. pylori isolates were obtained from 74 patients’ samples. This included 33 isolates (median 2, range 1–2 per patient) from dyspeptic and 73 (median 2, range 1–2 per patient) from non-dyspeptic patients. These were identified from the Bruker Biotyper 2 database as Staphylococcus spp., Streptococcus spp., Lactobacillus spp., Micrococcus spp., Enterococcus spp., Pseudomonas spp., Escherichia spp., Klebsiella spp. and Bacillus spp., Staphylococcus and Lactobacillus were identified significantly more commonly in dyspeptics and Streptococcus, Pseudomonas, Escherichia coli and Klebsiella pneumoniae in non-dyspeptics. All identified organisms belonged to the phyla Firmicutes and Proteobacteria. Conclusions There is a qualitative difference in the gastric microbial spectrum between patients harbouring H. pylori with and without chronic dyspepsia. Whether these organisms have an independent role in the development or prevention of dyspepsia or act in concurrence with H. pylori needs study.
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Affiliation(s)
- Verima Pereira
- Division of Gastroenterology, P D Hinduja Hospital, V S Marg, Mahim, Mumbai, 400016, India
| | - Philip Abraham
- Division of Gastroenterology, P D Hinduja Hospital, V S Marg, Mahim, Mumbai, 400016, India.
| | | | - Anjali Shetty
- Division of Microbiology, P D Hinduja Hospital, Mumbai, India
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Li N, Cao M, Yi S, Cheng J, Wang L, Tao Y, Wu D, Peng J, Zhang M, Qi P, Zhao J. Effects of the RNA-binding protein, KSRP, on innate immune response against Helicobacter pylori infection in mice. Biochem Biophys Res Commun 2017; 495:1573-1579. [PMID: 29222050 DOI: 10.1016/j.bbrc.2017.12.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022]
Abstract
Helicobacter pylori (H. pylori) contributes to various gastric diseases such as chronic gastritis, gastric ulcer, and gastric carcinoma. Host innate immune response against the pathogen plays a significant role in elimination of pathogen infection. Importantly, pathogen elimination is closely related to numerous inflammatory-related genes that participate in complex biological response of cells to harmful stimuli. Here we studied effects of the KH-type splicing regulatory protein (KSRP), a RNA-binding protein, on innate immune response against H. pylori infection. We found that H. pylori infection downregulated KSRP expression directly, and that KSRP overexpression repressed upregulation of CXCL-2 expression induced by H. pylori and facilitated H. pylori proliferation in vitro. Similarly, KSRP overexpression in H. pylori mice also facilitated H. pylori proliferation and colonization, and induced more severe gastric mucosal damage. Intriguingly, CXCL-2 and HMOX-1 were upregulated in H. pylori infected mice after KSRP overexpression. This difference in expression of these genes implicated that KSRP was closely associated with and directly participated in the innate immune response against H. pylori. These results were beneficial for understanding the in vivo function of KSRP on innate immune response against pathogen infection.
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Affiliation(s)
- Ningzhe Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Mei Cao
- Core Laboratory, School of Medicine, Sichuan Provincial People's Hospital Affiliated to University of Electronic Science and Technology of China, Chengdu 610072, PR China
| | - Sijun Yi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Juan Cheng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Lei Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Yuwei Tao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Daoyan Wu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jingshan Peng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Mao Zhang
- Core Laboratory, School of Medicine, Sichuan Provincial People's Hospital Affiliated to University of Electronic Science and Technology of China, Chengdu 610072, PR China
| | - Panpan Qi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China
| | - Jian Zhao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, Sichuan, PR China.
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Helicobacter pylori antigenic Lpp20 is a structural homologue of Tipα and promotes epithelial-mesenchymal transition. Biochim Biophys Acta Gen Subj 2017; 1861:3263-3271. [PMID: 28947343 DOI: 10.1016/j.bbagen.2017.09.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 09/07/2017] [Accepted: 09/21/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Helicobacter pylori is a bacterium that affects about 50% of the world population and, despite being often asymptomatic, it is responsible of several gastric diseases, from gastritis to gastric cancer. The protein Lpp20 (HP1456) plays an important role in bacterium survival and host colonization, but the possibility that it might be involved in the etiology of H. pylori-related disorders is an unexplored issue. Lpp20 is a lipoprotein bound to the external membrane of the bacterium, but it is also secreted inside vesicles along with other two proteins of the same operon, i.e. HP1454 and HP1457. RESULTS In this study we determined the crystal structure of Lpp20 and we found that it has a fold similar to a carcinogenic factor released by H. pylori, namely Tipα. We demonstrate that Lpp20 promotes cell migration and E-cadherin down-regulation in gastric cancer cells, two events recalling the epithelial-mesenchymal transition (EMT) process. Differently from Tipα, Lpp20 also stimulates cell proliferation. CONCLUSIONS This identifies Lpp20 as a new pathogenic factor produced by H. pylori that promotes EMT and thereby the progression of cancer to the metastatic state.
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Kissing S, Saftig P, Haas A. Vacuolar ATPase in phago(lyso)some biology. Int J Med Microbiol 2017; 308:58-67. [PMID: 28867521 DOI: 10.1016/j.ijmm.2017.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/28/2017] [Accepted: 08/23/2017] [Indexed: 12/23/2022] Open
Abstract
Many eukaryotic cells ingest extracellular particles in a process termed phagocytosis which entails the generation of a new intracellular compartment, the phagosome. Phagosomes change their composition over time and this maturation process culminates in their fusion with acidic, hydrolase-rich lysosomes. During the maturation process, degradation and, when applicable, killing of the cargo may ensue. Many of the events that are pathologically relevant depend on strong acidification of phagosomes by the 'vacuolar' ATPase (V-ATPase). This protein complex acidifies the lumen of some intracellular compartments at the expense of ATP hydrolysis. We discuss here the roles and importance of V-ATPase in intracellular trafficking, its distribution, inhibition and activities, its role in the defense against microorganisms and the counteractivities of pathogens.
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Affiliation(s)
- Sandra Kissing
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany
| | - Paul Saftig
- Institut für Biochemie, Christian-Albrechts-Universität zu Kiel, Olshausenstrasse 40, D-24098 Kiel, Germany.
| | - Albert Haas
- Institut für Zellbiologie, Friedrich-Wilhelms-Universität Bonn, Ulrich-Haberland-Str. 61A, D-53121 Bonn, Germany.
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Álvarez A, Toledo H. The histone-like protein HU has a role in gene expression during the acid adaptation response in Helicobacter pylori. Helicobacter 2017; 22. [PMID: 28244177 DOI: 10.1111/hel.12381] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Gastritis, ulcers, and gastric malignancy have been linked to human gastric epithelial colonization by Helicobacter pylori. Characterization of the mechanisms by which H. pylori adapts to the human stomach environment is of crucial importance to understand H. pylori pathogenesis. MATERIAL AND METHODS In an effort to extend our knowledge of these mechanisms, we used proteomic analysis and qRT-PCR to characterize the role of the histone-like protein HU in the response of H. pylori to low pH. RESULTS Proteomic analysis revealed that genes involved in chemotaxis, oxidative stress, or metabolism are under control of the HU protein. Also, expression of the virulence factors Ggt and NapA is affected by the null mutation of hup gene both at neutral and acid pH, as evidenced by qRT-PCR analysis. CONCLUSIONS Those results showed that H. pylori gene expression is altered by shift to low pH, thus confirming that acid exposure leads to profound changes in genomic expression, and suggest that the HU protein is a regulator that may help the bacterium adapt to the acid stress. In accordance with previous reports, we found that the HU protein participates in gene expression regulation when the microorganism is exposed to acid stress. Such transcriptional regulation underlies protein accumulation in the H. pylori cell.
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Affiliation(s)
- Alhejandra Álvarez
- Laboratory of Molecular Microbiology, Department of Molecular and Cellular Biology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile
| | - Héctor Toledo
- Laboratory of Molecular Microbiology, Department of Molecular and Cellular Biology, Faculty of Medicine, ICBM, University of Chile, Santiago, Chile
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Abstract
BACKGROUND Helicobacter pylori is well adapted to colonize the epithelial surface of the human gastric mucosa and can cause persistent infections. In order to infect the gastric mucosa, it has to survive in the gastric acidic pH. This organism has well developed mechanisms to neutralize the effects of acidic pH. OBJECTIVE This review article was designed to summarize the various functional and molecular aspects by which the bacterium can combat and survive the gastric acidic pH in order to establish the persistent infections. METHODS We used the keywords (acid acclimation, gastric acidic environment, H. pylori and survival) in combination or alone for pubmed search of recent scientific literatures. One hundred and forty one papers published between 1989 and 2016 were sorted out. The articles published with only abstracts, other than in English language, case reports and reviews were excluded. RESULTS Many literatures describing the role of several factors in acid survival were found. Recently, the role of several other factors has been claimed to participate in acid survival. CONCLUSION In conclusion, this organism has well characterized mechanisms for acid survival.
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Affiliation(s)
- Shamshul Ansari
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Yufu, Japan,Department of Medicine-Gastroenterology, Baylor College of Medicine, Houston, Texas, USA,Corresponding author: Yoshio Yamaoka, MD, PhD, Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu-City, Oita 879-5593, Japan, Tel: +81-97-586-5740; Fax: +81-97-586-5749,
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Silva B, Nunes A, Vale FF, Rocha R, Gomes JP, Dias R, Oleastro M. The expression of Helicobacter pylori tfs plasticity zone cluster is regulated by pH and adherence, and its composition is associated with differential gastric IL-8 secretion. Helicobacter 2017; 22. [PMID: 28436598 DOI: 10.1111/hel.12390] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
BACKGROUND Helicobacter pylori virulence is associated with different clinical outcomes. The existence of an intact dupA gene from tfs4b cluster has been suggested as a predictor for duodenal ulcer development. However, the role of tfs plasticity zone clusters in the development of ulcers remains unclear. We studied several H. pylori strains to characterize the gene arrangement of tfs3 and tfs4 clusters and their impact in the inflammatory response by infected gastric cells. METHODS The genome of 14 H. pylori strains isolated from Western patients, pediatric (n=10) and adult (n=4), was fully sequenced using the Illumina platform MiSeq, in addition to eight pediatric strains previously sequenced. These strains were used to infect human gastric cells, and the secreted interleukin-8 (IL-8) was quantified by ELISA. The expression of virB2, dupA, virB8, virB10, and virB6 was assessed by quantitative PCR in adherent and nonadherent fractions of H. pylori during in vitro co-infection, at different pH values. RESULTS We have found that cagA-positive H. pylori strains harboring a complete tfs plasticity zone cluster significantly induce increased production of IL-8 from gastric cells. We have also found that the region spanning from virB2 to virB10 genes constitutes an operon, whose expression is increased in the adherent fraction of bacteria during infection, as well as in both adherent and nonadherent fractions at acidic conditions. CONCLUSIONS A complete tfs plasticity zone cluster is a virulence factor that may be important for the colonization of H. pylori and to the development of severe outcomes of the infection with cagA-positive strains.
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Affiliation(s)
- Bruno Silva
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Filipa F Vale
- Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Instituto de Medicina Molecular, Faculdade de Farmácia da Universidade de Lisboa, Lisbon, Portugal
| | - Raquel Rocha
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
| | - Ricardo Dias
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Mónica Oleastro
- National Reference Laboratory for Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health, Lisbon, Portugal
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Zhang H, Au SWN. Helicobacter pylori does not use spermidine synthase to produce spermidine. Biochem Biophys Res Commun 2017. [PMID: 28648602 DOI: 10.1016/j.bbrc.2017.06.132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Helicobacter pylori is the primary pathogen associated to gastritis and gastric cancer. Growth of H. pylori depends on the availability of spermidine in vivo. Interestingly, the genome of H. pylori contains an incomplete set of genes for the classical pathway of spermidine biosynthesis. It is thus not clear whether some other genes remained in the pathway would have any functions in spermidine biosynthesis. Here, we study spermidine synthase, which is responsible for the final catalytic process in the classical route. Protein sequence alignment reveals that H. pylori SpeE (HpSpeE) lacks key residues for substrate binding. By using isothermal titration calorimetry, we show that purified recombinant HpSpeE does not interact with the putative substrates putrescine and decarboxylated S-adenosylmethionine, and the product spermidine. High performance liquid chromatography analysis further demonstrates that HpSpeE has no detectable in vitro enzymatic activity. Additionally, intracellular spermidine level in speE-null mutant strain is comparable to that in the wild type strain. Collectively, our results suggest that HpSpeE is functionally distinct from spermidine production. H. pylori may instead employ the alternative pathway for spermidine synthesis which is dominantly exploited by other human gut microbes.
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Affiliation(s)
- Huawei Zhang
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Shannon Wing Ngor Au
- Centre for Protein Science and Crystallography, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong.
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The Bifunctional Enzyme SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471. Antimicrob Agents Chemother 2017; 61:AAC.02011-16. [PMID: 28242673 PMCID: PMC5404559 DOI: 10.1128/aac.02011-16] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 02/21/2017] [Indexed: 01/30/2023] Open
Abstract
Clarithromycin (CLA) is a commonly recommended drug for Helicobacter pylori eradication. However, the prevalence of CLA-resistant H. pylori is increasing. Although point mutations in the 23S rRNA are key factors for CLA resistance, other factors, including efflux pumps and regulation genes, are also involved in the resistance of H. pylori to CLA. Guanosine 3′-diphosphate 5′-triphosphate and guanosine 3′,5′-bispyrophosphate [(p)ppGpp)], which are synthesized by the bifunctional enzyme SpoT in H. pylori, play an important role for some bacteria to adapt to antibiotic pressure. Nevertheless, no related research involving H. pylori has been reported. In addition, transporters have been found to be related to bacterial drug resistance. Therefore, this study investigated the function of SpoT in H. pylori resistance to CLA by examining the shifts in the expression of transporters and explored the role of transporters in the CLA resistance of H. pylori. A ΔspoT strain was constructed in this study, and it was shown that SpoT is involved in H. pylori tolerance of CLA by upregulating the transporters HP0939, HP1017, HP0497, and HP0471. This was assessed using a series of molecular and biochemical experiments and a cDNA microarray. Additionally, the knockout of genes hp0939, hp0471, and hp0497 in the resistant strains caused a reduction or loss (the latter in the Δhp0497 strain) of resistance to CLA. Furthermore, the average expression levels of these four transporters in clinical CLA-resistant strains were considerably higher than those in clinical CLA-sensitive strains. Taken together, our results revealed a novel molecular mechanism of H. pylori adaption to CLA stress.
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De la Cruz MA, Ares MA, von Bargen K, Panunzi LG, Martínez-Cruz J, Valdez-Salazar HA, Jiménez-Galicia C, Torres J. Gene Expression Profiling of Transcription Factors of Helicobacter pylori under Different Environmental Conditions. Front Microbiol 2017; 8:615. [PMID: 28443084 PMCID: PMC5385360 DOI: 10.3389/fmicb.2017.00615] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 03/27/2017] [Indexed: 12/22/2022] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that colonizes the human gastric mucosa and causes peptic ulcers and gastric carcinoma. H. pylori strain 26695 has a small genome (1.67 Mb), which codes for few known transcriptional regulators that control bacterial metabolism and virulence. We analyzed by qRT-PCR the expression of 16 transcriptional regulators in H. pylori 26695, including the three sigma factors under different environmental conditions. When bacteria were exposed to acidic pH, urea, nickel, or iron, the sigma factors were differentially expressed with a particularly strong induction of fliA. The regulatory genes hrcA, hup, and crdR were highly induced in the presence of urea, nickel, and iron. In terms of biofilm formation fliA, flgR, hp1021, fur, nikR, and crdR were induced in sessile bacteria. Transcriptional expression levels of rpoD, flgR, hspR, hp1043, and cheY were increased in contact with AGS epithelial cells. Kanamycin, chloramphenicol, and tetracycline increased or decreased expression of regulatory genes, showing that these antibiotics affect the transcription of H. pylori. Our data indicate that environmental cues which may be present in the human stomach modulate H. pylori transcription.
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Affiliation(s)
- Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro SocialMexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro SocialMexico City, Mexico
| | | | - Leonardo G Panunzi
- CNRS UMR7280, Inserm, U1104, Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2Marseille, France
| | - Jessica Martínez-Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro SocialMexico City, Mexico
| | - Hilda A Valdez-Salazar
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro SocialMexico City, Mexico
| | - César Jiménez-Galicia
- Laboratorio Clínico, Unidad Médica de Alta Especialidad, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro SocialMexico City, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro SocialMexico City, Mexico
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Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability. BIOMED RESEARCH INTERNATIONAL 2016; 2016:6106029. [PMID: 28078297 PMCID: PMC5203880 DOI: 10.1155/2016/6106029] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/17/2016] [Accepted: 10/11/2016] [Indexed: 01/05/2023]
Abstract
The genus Helicobacter is a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species. Helicobacter pylori (H. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings of H. pylori that are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representative H. pylori and 24 non-pylori Helicobacter genomes. There were 1173 conserved protein families of H. pylori and 673 of all 99 Helicobacter genus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of the H. pylori but lacked in non-pylori Helicobacter species. The operons, genes, and sRNAs within the H. pylori unique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship.
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Koh HY, Park H, Lee JH, Han SJ, Sohn YC, Lee SG. Proteomic and transcriptomic investigations on cold-responsive properties of the psychrophilic Antarctic bacterium Psychrobacter sp. PAMC 21119 at subzero temperatures. Environ Microbiol 2016; 19:628-644. [PMID: 27750393 DOI: 10.1111/1462-2920.13578] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 10/12/2016] [Indexed: 11/28/2022]
Abstract
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ twofold, P <0.005) by RNA-seq. Genes for translation, ribosomal structure and biogenesis were upregulated, and lipid transport and metabolism was downregulated at low temperatures. A total of 60 protein spots (≥ 1.8 fold, P < 0.005) showed differential expression on two-dimensional gel electrophoresis and the proteins were identified by mass spectrometry. The most prominent upregulated proteins in response to cold were involved in metabolite transport, protein folding and membrane fluidity. Proteins involved in energy production and conversion, and heme protein synthesis were downregulated. Moreover, isoform exchange of cold-shock proteins was detected at both temperatures. Interestingly, pathways for acetyl-CoA metabolism, putrescine synthesis and amino acid metabolism were upregulated. This study highlights some of the strategies and different physiological states that Psychrobacter sp. PAMC 21119 has developed to adapt to the cold environment in Antarctica.
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Affiliation(s)
- Hye Yeon Koh
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Hyun Park
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Se Jong Han
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
| | - Young Chang Sohn
- Department of Marine Molecular Biotechnology, Gangneung-Wonju National University, Gangneung, South Korea
| | - Sung Gu Lee
- Unit of Polar Genomics Korea Polar Research Institute, Incheon, South Korea.,Department of Polar Sciences, University of Science and Technology, Incheon, South Korea
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Cheng L, Mirko R, Sara L, Medea P, Caroline B, Eva B, Myrthe J, Bram F, Wim VDB, Richard D, Freddy H, Annemieke S. The Helicobacter heilmannii hofE and hofF Genes are Essential for Colonization of the Gastric Mucosa and Play a Role in IL-1β-Induced Gastric MUC13 Expression. Helicobacter 2016; 21:504-522. [PMID: 26935145 DOI: 10.1111/hel.12307] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Helicobacter heilmannii is a zoonotic bacterium associated with gastric disease in humans. We recently showed that H. heilmannii binds to human gastric mucins and epithelial cells and highlighted a potential role for the murine Muc13 mucin in gastric Helicobacter colonization. The aims of this study were to investigate the role of the H. heilmannii hof gene locus encoding HofH/F/E/G/C/D in adhesion to the gastric mucosa and induction of increased gastric Muc13 expression. METHODS Bacterial hof gene and host gene expression experiments, Helicobacter binding assays and experimental infection studies in mice were performed. H. pylori and its ΔhofF mutant were included for comparison. RESULTS Helicobacter heilmannii strains lacking HofE or HofF showed a clear decrease in binding to gastric mucins and epithelial cells as well as a lower gastric colonization level in the stomach of Balb/c mice at 4 and 9 weeks post-infection compared to the H. heilmannii wildtype strain. Interestingly, H. heilmannii ΔhofE and ΔhofF and H. pylori ΔhofF did not induce an increased expression of MUC13 in human gastric epithelial cells and of Muc13 in the stomach of mice. Finally, we demonstrated that IL-1β is induced in the stomach as a response to Helicobacter colonization which on its turn is involved in the expression of MUC13/Muc13 in the gastric epithelium. CONCLUSION These novel results in Helicobacter research identified H. heilmannii HofE and HofF as adhesins and suggest an important role of H. heilmannii HofE and HofF and H. pylori HofF in IL-1β-induced gastric MUC13/Muc13 expression.
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Affiliation(s)
- Liu Cheng
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Rossi Mirko
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Lindén Sara
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Padra Medea
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Blaecher Caroline
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bauwens Eva
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Joosten Myrthe
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Flahou Bram
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Van den Broeck Wim
- Department of Morphology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ducatelle Richard
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Haesebrouck Freddy
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Smet Annemieke
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Cárdenas-Mondragón MG, Ares MA, Panunzi LG, Pacheco S, Camorlinga-Ponce M, Girón JA, Torres J, De la Cruz MA. Transcriptional Profiling of Type II Toxin-Antitoxin Genes of Helicobacter pylori under Different Environmental Conditions: Identification of HP0967-HP0968 System. Front Microbiol 2016; 7:1872. [PMID: 27920769 PMCID: PMC5118875 DOI: 10.3389/fmicb.2016.01872] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 11/07/2016] [Indexed: 12/24/2022] Open
Abstract
Helicobacter pylori is a Gram-negative bacterium that colonizes the human gastric mucosa and is responsible for causing peptic ulcers and gastric carcinoma. The expression of virulence factors allows the persistence of H. pylori in the stomach, which results in a chronic, sometimes uncontrolled inflammatory response. Type II toxin-antitoxin (TA) systems have emerged as important virulence factors in many pathogenic bacteria. Three type II TA systems have previously been identified in the genome of H. pylori 26695: HP0315-HP0316, HP0892-HP0893, and HP0894-HP0895. Here we characterized a heretofore undescribed type II TA system in H. pylori, HP0967-HP0968, which is encoded by the bicistronic operon hp0968-hp0967 and belongs to the Vap family. The predicted HP0967 protein is a toxin with ribonuclease activity whereas HP0968 is an antitoxin that binds to its own regulatory region. We found that all type II TA systems were expressed in H. pylori during early stationary growth phase, and differentially expressed in the presence of urea, nickel, and iron, although, the hp0968-hp0967 pair was the most affected under these environmental conditions. Transcription of hp0968-hp0967 was strongly induced in a mature H. pylori biofilm and when the bacteria interacted with AGS epithelial cells. Kanamycin and chloramphenicol considerably boosted transcription levels of all the four type II TA systems. The hp0968-hp0967 TA system was the most frequent among 317 H. pylori strains isolated from all over the world. This study is the first report on the transcription of type II TA genes in H. pylori under different environmental conditions. Our data show that the HP0967 and HP0968 proteins constitute a bona fide type II TA system in H. pylori, whose expression is regulated by environmental cues, which are relevant in the context of infection of the human gastric mucosa.
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Affiliation(s)
- María G Cárdenas-Mondragón
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, IMSS Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, IMSS Mexico City, Mexico
| | - Leonardo G Panunzi
- Centre d'Immunologie de Marseille-Luminy, Aix Marseille Université UM2, Inserm, U1104, CNRS UMR7280 Marseille, France
| | - Sabino Pacheco
- Departamento de Microbiología Molecular, Instituto de Biotecnología UNAM Cuernavaca, Mexico
| | - Margarita Camorlinga-Ponce
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, IMSS Mexico City, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla Puebla, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, IMSS Mexico City, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatria, Centro Médico Nacional Siglo XXI, IMSS Mexico City, Mexico
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Karlsson R, Thorell K, Hosseini S, Kenny D, Sihlbom C, Sjöling Å, Karlsson A, Nookaew I. Comparative Analysis of Two Helicobacter pylori Strains using Genomics and Mass Spectrometry-Based Proteomics. Front Microbiol 2016; 7:1757. [PMID: 27891114 PMCID: PMC5104757 DOI: 10.3389/fmicb.2016.01757] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 10/19/2016] [Indexed: 12/20/2022] Open
Abstract
Helicobacter pylori, a gastroenteric pathogen believed to have co-evolved with humans over 100,000 years, shows significant genetic variability. This motivates the study of different H. pylori strains and the diseases they cause in order to identify determinants for disease evolution. In this study, we used proteomics tools to compare two H. pylori strains. Nic25_A was isolated in Nicaragua from a patient with intestinal metaplasia, and P12 was isolated in Europe from a patient with duodenal ulcers. Differences in the abundance of surface proteins between the two strains were determined with two mass spectrometry-based methods, label-free quantification (MaxQuant) or the use of tandem mass tags (TMT). Each approach used a lipid-based protein immobilization (LPITM) technique to enrich peptides of surface proteins. Using the MaxQuant software, we found 52 proteins that differed significantly in abundance between the two strains (up- or downregulated by a factor of 1.5); with TMT, we found 18 proteins that differed in abundance between the strains. Strain P12 had a higher abundance of proteins encoded by the cag pathogenicity island, while levels of the acid response regulator ArsR and its regulatory targets (KatA, AmiE, and proteins involved in urease production) were higher in strain Nic25_A. Our results show that differences in protein abundance between H. pylori strains can be detected with proteomic approaches; this could have important implications for the study of disease progression.
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Affiliation(s)
- Roger Karlsson
- Nanoxis Consulting ABGothenburg, Sweden; Department of Infectious Diseases, Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
| | - Kaisa Thorell
- Department of Microbiology and Immunology, University of GothenburgGothenburg, Sweden; Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden
| | - Shaghayegh Hosseini
- Department of Biology and Biological Engineering, Chalmers University of Technology Gothenburg, Sweden
| | - Diarmuid Kenny
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Carina Sihlbom
- Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg Gothenburg, Sweden
| | - Åsa Sjöling
- Department of Microbiology and Immunology, University of Gothenburg Gothenburg, Sweden
| | | | - Intawat Nookaew
- Department of Biology and Biological Engineering, Chalmers University of TechnologyGothenburg, Sweden; Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little RockAR, USA
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