1
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Xu G, Yang S. Evolution of orphan and atypical histidine kinases and response regulators for microbial signaling diversity. Int J Biol Macromol 2024:133635. [PMID: 38964677 DOI: 10.1016/j.ijbiomac.2024.133635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 06/22/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024]
Abstract
Two-component signaling systems (TCS) are the predominant means of microbes for sensing and responding to environmental stimuli. Typically, TCS is comprised of a sensor histidine kinase (HK) and a cognate response regulator (RR), which might have coevolved together. They usually involve the phosphoryl transfer signaling mechanism. However, there are also some orphan and atypical HK and RR homologs, and their evolutionary origins are still not very clear. They are not associated with cognate pairs or lack the conserved residues for phosphoryl transfer, but they could receive or respond to signals from other regulators. The objective of this study is to reveal the evolutionary history of these orphan and atypical HK and RR homologs. Structural, domain, sequence, and phylogenetic analyses indicated that their evolution process might undergo gene duplication, divergence, and domain shuffling. Meanwhile, lateral gene transfer might also be involved for their gene distribution. Evolution of orphan and atypical HK and RR homologs have increased their signaling diversity, which could be helpful for microbial adaption in complex environments.
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Affiliation(s)
- Gangming Xu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Suiqun Yang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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2
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Vannini A, Pinatel E, Costantini PE, Pelliciari S, Roncarati D, Puccio S, De Bellis G, Scarlato V, Peano C, Danielli A. (Re)-definition of the holo- and apo-Fur direct regulons of Helicobacter pylori. J Mol Biol 2024; 436:168573. [PMID: 38626867 DOI: 10.1016/j.jmb.2024.168573] [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: 12/13/2023] [Revised: 04/09/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Iron homeostasis is a critical process for living organisms because this metal is an essential co-factor for fundamental biochemical activities, like energy production and detoxification, albeit its excess quickly leads to cell intoxication. The protein Fur (ferric uptake regulator) controls iron homeostasis in bacteria by switching from its apo- to holo-form as a function of the cytoplasmic level of ferrous ions, thereby modulating gene expression. The Helicobacter pylori HpFur protein has the rare ability to operate as a transcriptional commutator; apo- and holo-HpFur function as two different repressors with distinct DNA binding recognition properties for specific sets of target genes. Although the regulation of apo- and holo-HpFur in this bacterium has been extensively investigated, we propose a genome-wide redefinition of holo-HpFur direct regulon in H. pylori by integration of RNA-seq and ChIP-seq data, and a large extension of the apo-HpFur direct regulon. We show that in response to iron availability, new coding sequences, non-coding RNAs, toxin-antitoxin systems, and transcripts within open reading frames are directly regulated by apo- or holo-HpFur. These new targets and the more thorough validation and deeper characterization of those already known provide a complete and updated picture of the direct regulons of this two-faced transcriptional regulator.
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Affiliation(s)
- Andrea Vannini
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Eva Pinatel
- Institute of Biomedical Technologies - National Research Council, Via Fratelli Cervi 93, 20054 Segrate (MI), Italy.
| | - Paolo Emidio Costantini
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Simone Pelliciari
- Human Genetic Unit, Institute of Genetic and Cancer - University of Edinburgh, Crewe Road, Edinburgh EH4 2XU, UK.
| | - Davide Roncarati
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Simone Puccio
- Institute of Genetics and Biomedical Research, UoS Milan - National Research Council, Via Manzoni 113, 20089 Rozzano (MI), Italy; Humanitas Clinical and Research Center, Via Manzoni 56, 20089 Rozzano (MI), Italy.
| | - Gianluca De Bellis
- Institute of Biomedical Technologies - National Research Council, Via Fratelli Cervi 93, 20054 Segrate (MI), Italy.
| | - Vincenzo Scarlato
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
| | - Clelia Peano
- Institute of Genetics and Biomedical Research, UoS Milan - National Research Council, Via Manzoni 113, 20089 Rozzano (MI), Italy; Human Technopole, Via Rita Levi Montalcini 1, 20157 Milan, Italy.
| | - Alberto Danielli
- University of Bologna Department of Pharmacy and Biotechnology, Via Selmi 3, 40126 Bologna, Italy.
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3
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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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4
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Liu Y, Shi Y, Han R, Liu C, Qin X, Li P, Gu R. Signaling pathways of oxidative stress response: the potential therapeutic targets in gastric cancer. Front Immunol 2023; 14:1139589. [PMID: 37143652 PMCID: PMC10151477 DOI: 10.3389/fimmu.2023.1139589] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/20/2023] [Indexed: 05/06/2023] Open
Abstract
Gastric cancer is one of the top causes of cancer-related death globally. Although novel treatment strategies have been developed, attempts to eradicate gastric cancer have been proven insufficient. Oxidative stress is continually produced and continually present in the human body. Increasing evidences show that oxidative stress contributes significantly to the development of gastric cancer, either through initiation, promotion, and progression of cancer cells or causing cell death. As a result, the purpose of this article is to review the role of oxidative stress response and the subsequent signaling pathways as well as potential oxidative stress-related therapeutic targets in gastric cancer. Understanding the pathophysiology of gastric cancer and developing new therapies for gastric cancer depends on more researches focusing on the potential contributors to oxidative stress and gastric carcinogenesis.
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Affiliation(s)
- Yingying Liu
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- Institute for Immunology and School of Medicine, Tsinghua University, Beijing, China
| | - Yu Shi
- Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ruiqin Han
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Chaoge Liu
- Department of Oromaxillofacial - Head and Neck Surgery, Tianjin Stomatological Hospital, School of Medicine, Nankai University, Tianjin, China
- Tianjin Key Laboratory of Oral and Maxillofacial Function Reconstruction, Tianjin, China
| | - Xiaogang Qin
- Traditional Chinese Medicine Hospital of Tongzhou District, Nantong, Jiangsu, China
- *Correspondence: Renjun Gu, ; Pengfei Li, ; Xiaogang Qin,
| | - Pengfei Li
- Department of Clinical Laboratory, Jiangsu Province Hospital of Chinese Medicine, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Renjun Gu, ; Pengfei Li, ; Xiaogang Qin,
| | - Renjun Gu
- School of Chinese Medicine & School of Integrated Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Renjun Gu, ; Pengfei Li, ; Xiaogang Qin,
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5
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Insights into the Orchestration of Gene Transcription Regulators in Helicobacter pylori. Int J Mol Sci 2022; 23:ijms232213688. [PMID: 36430169 PMCID: PMC9696931 DOI: 10.3390/ijms232213688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
Bacterial pathogens employ a general strategy to overcome host defenses by coordinating the virulence gene expression using dedicated regulatory systems that could raise intricate networks. During the last twenty years, many studies of Helicobacter pylori, a human pathogen responsible for various stomach diseases, have mainly focused on elucidating the mechanisms and functions of virulence factors. In parallel, numerous studies have focused on the molecular mechanisms that regulate gene transcription to attempt to understand the physiological changes of the bacterium during infection and adaptation to the environmental conditions it encounters. The number of regulatory proteins deduced from the genome sequence analyses responsible for the correct orchestration of gene transcription appears limited to 14 regulators and three sigma factors. Furthermore, evidence is accumulating for new and complex circuits regulating gene transcription and H. pylori virulence. Here, we focus on the molecular mechanisms used by H. pylori to control gene transcription as a function of the principal environmental changes.
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Ivyna de Araújo Rêgo R, Guedes Silvestre GF, Ferreira de Melo D, Albino SL, Pimentel MM, Silva Costa Cruz SB, Silva Wurzba SD, Rodrigues WF, Goulart de Lima Damasceno BP, Cançado Castellano LR. Flavonoids-Rich Plant Extracts Against Helicobacter pylori Infection as Prevention to Gastric Cancer. Front Pharmacol 2022; 13:951125. [PMID: 36120379 PMCID: PMC9470917 DOI: 10.3389/fphar.2022.951125] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/20/2022] [Indexed: 11/15/2022] Open
Abstract
Gastric cancer is the fifth most common and fourth type to cause the highest mortality rates worldwide. The leading cause is related to Helicobacter pylori (H. pylori) infection. Unfortunately, current treatments have low success rates, highlighting the need for alternative treatments against carcinogenic agents, specifically H. pylori. Noteworthy, natural origin products contain pharmacologically active metabolites such as flavonoids, with potential antimicrobial applications. Objective: This article overviews flavonoid-rich extracts’ biological and pharmacological activities. It focuses on using these substances against Helicobacter pylori infection to prevent gastric cancer. For this, PubMed and Science Direct databases were searched for studies that reported the activity of flavonoids against H. pylori, published within a 10-year time frame (2010 to August 2020). It resulted in 1,773 publications, of which 44 were selected according to the search criteria. The plant family primarily found in publications was Fabaceae (9.61%). Among the flavonoids identified after extraction, the most prevalent were quercetin (19.61%), catechin (13.72), epicatechin (11.76), and rutin (11.76). The potential mechanisms associated with anti-H. pylori activity to the extracts were: inhibition of urease, damage to genetic material, inhibition of protein synthesis, and adhesion of the microorganism to host cells. Conclusion: Plant extracts rich in flavonoids with anti-H. pylori potential proved to be a promising alternative therapy source, reinforcing the relevance of studies with natural products.
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Affiliation(s)
- Renaly Ivyna de Araújo Rêgo
- Human Immunology Research and Education Group-GEPIH, Federal University of Paraiba, João Pessoa, Brazil
- Postgraduate Program of Pharmaceutical Sciences, State University of Paraíba, Campina Grande, Brazil
- Postgraduate Program of Science and Technology in Health, State University of Paraíba, Campina Grande, Brazil
| | | | - Demis Ferreira de Melo
- Postgraduate Program of Pharmaceutical Sciences, State University of Paraíba, Campina Grande, Brazil
| | - Sonaly Lima Albino
- Postgraduate Program of Therapeutic Innovation, Federal University of Pernambuco, Recife, Brazil
| | - Marcela Monteiro Pimentel
- Postgraduate Program of Science and Technology in Health, State University of Paraíba, Campina Grande, Brazil
| | - Sara Brito Silva Costa Cruz
- Postgraduate Program in Dentistry, Federal University of Paraíba, João Pessoa, Brazil
- Department of Otolaryngology and Head and Neck Surgery, McGill University, Montreal, QC, Canada
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Sabrina Daniela Silva Wurzba
- Department of Otolaryngology and Head and Neck Surgery, McGill University, Montreal, QC, Canada
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | | | | | - Lúcio Roberto Cançado Castellano
- Human Immunology Research and Education Group-GEPIH, Federal University of Paraiba, João Pessoa, Brazil
- Postgraduate Program of Pharmaceutical Sciences, State University of Paraíba, Campina Grande, Brazil
- Postgraduate Program in Dentistry, Federal University of Paraíba, João Pessoa, Brazil
- Department of Otolaryngology and Head and Neck Surgery, McGill University, Montreal, QC, Canada
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Departments of Medicine and Oncology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- *Correspondence: Lúcio Roberto Cançado Castellano,
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7
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Casado J, Lanas Á, González A. Two-component regulatory systems in Helicobacter pylori and Campylobacter jejuni: Attractive targets for novel antibacterial drugs. Front Cell Infect Microbiol 2022; 12:977944. [PMID: 36093179 PMCID: PMC9449129 DOI: 10.3389/fcimb.2022.977944] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
Two-component regulatory systems (TCRS) are ubiquitous signal transduction mechanisms evolved by bacteria for sensing and adapting to the constant changes that occur in their environment. Typically consisting of two types of proteins, a membrane sensor kinase and an effector cytosolic response regulator, the TCRS modulate via transcriptional regulation a plethora of key physiological processes, thereby becoming essential for bacterial viability and/or pathogenicity and making them attractive targets for novel antibacterial drugs. Some members of the phylum Campylobacterota (formerly Epsilonproteobacteria), including Helicobacter pylori and Campylobacter jejuni, have been classified by WHO as “high priority pathogens” for research and development of new antimicrobials due to the rapid emergence and dissemination of resistance mechanisms against first-line antibiotics and the alarming increase of multidrug-resistant strains worldwide. Notably, these clinically relevant pathogens express a variety of TCRS and orphan response regulators, sometimes unique among its phylum, that control transcription, translation, energy metabolism and redox homeostasis, as well as the expression of relevant enzymes and virulence factors. In the present mini-review, we describe the signalling mechanisms and functional diversity of TCRS in H. pylori and C. jejuni, and provide an overview of the most recent findings in the use of these microbial molecules as potential novel therapeutic targets for the development of new antibiotics.
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Affiliation(s)
- Javier Casado
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Zaragoza, Spain
| | - Ángel Lanas
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa, Zaragoza, Spain
| | - Andrés González
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
- *Correspondence: Andrés González,
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González A, Casado J, Gündüz MG, Santos B, Velázquez-Campoy A, Sarasa-Buisan C, Fillat MF, Montes M, Piazuelo E, Lanas Á. 1,4-Dihydropyridine as a Promising Scaffold for Novel Antimicrobials Against Helicobacter pylori. Front Microbiol 2022; 13:874709. [PMID: 35694298 PMCID: PMC9174938 DOI: 10.3389/fmicb.2022.874709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 05/03/2022] [Indexed: 12/19/2022] Open
Abstract
The increasing occurrence of multidrug-resistant strains of the gastric carcinogenic bacterium Helicobacter pylori threatens the efficacy of current eradication therapies. In a previous work, we found that several 1,4-dihydropyridine (DHP)-based antihypertensive drugs exhibited strong bactericidal activities against H. pylori by targeting the essential response regulator HsrA. To further evaluate the potential of 1,4-DHP as a scaffold for novel antimicrobials against H. pylori, we determined the antibacterial effects of 12 novel DHP derivatives that have previously failed to effectively block L- and T-type calcium channels. Six of these molecules exhibited potent antimicrobial activities (MIC ≤ 8 mg/L) against three different antibiotic-resistant strains of H. pylori, while at least one compound resulted as effective as metronidazole. Such antimicrobial actions appeared to be specific against Epsilonproteobacteria, since no deleterious effects were appreciated on Escherichia coli and Staphylococcus epidermidis. The new bactericidal DHP derivatives targeted the H. pylori regulator HsrA and inhibited its DNA binding activity according to both in vitro and in vivo analyses. Molecular docking predicted a potential druggable binding pocket in HsrA, which could open the door to structure-based design of novel anti-H. pylori drugs.
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Affiliation(s)
- Andrés González
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
- *Correspondence: Andrés González,
| | - Javier Casado
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
| | - Miyase Gözde Gündüz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - Brisa Santos
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
- Fundación Agencia Aragonesa para la Investigación y el Desarrollo (ARAID), Zaragoza, Spain
| | - Cristina Sarasa-Buisan
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
| | - María F. Fillat
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Zaragoza, Spain
- Department of Biochemistry and Molecular and Cellular Biology, University of Zaragoza, Zaragoza, Spain
| | - Milagrosa Montes
- Department of Microbiology, Donostia University Hospital-Biodonostia Health Research Institute, San Sebastian, Spain
- Biomedical Research Networking Center in Respiratory Diseases (CIBERES), Madrid, Spain
| | - Elena Piazuelo
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
- Aragón Health Sciences Institute (IACS), Zaragoza, Spain
| | - Ángel Lanas
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Zaragoza, Spain
- Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa, Zaragoza, Spain
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Antoniciello F, Roncarati D, Zannoni A, Chiti E, Scarlato V, Chiappori F. Targeting the Essential Transcription Factor HP1043 of Helicobacter pylori: A Drug Repositioning Study. Front Mol Biosci 2022; 9:887564. [PMID: 35647033 PMCID: PMC9135449 DOI: 10.3389/fmolb.2022.887564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 04/07/2022] [Indexed: 12/13/2022] Open
Abstract
Antibiotic-resistant bacterial pathogens are a very challenging problem nowadays. Helicobacter pylori is one of the most widespread and successful human pathogens since it colonizes half of the world population causing chronic and atrophic gastritis, peptic ulcer, mucosa-associated lymphoid tissue-lymphoma, and even gastric adenocarcinoma. Moreover, it displays resistance to numerous antibiotics. One of the H. pylori pivotal transcription factors, HP1043, plays a fundamental role in regulating essential cellular processes. Like other bacterial transcription factors, HP1043 does not display a eukaryote homolog. These characteristics make HP1043 a promising candidate to develop novel antibacterial strategies. Drug repositioning is a relatively recent strategy employed in drug development; testing approved drugs on new targets considerably reduces the time and cost of this process. The combined computational and in vitro approach further reduces the number of compounds to be tested in vivo. Our aim was to identify a subset of known drugs able to prevent HP1043 binding to DNA promoters. This result was reached through evaluation by molecular docking the binding capacity of about 14,350 molecules on the HP1043 dimer in both conformations, bound and unbound to the DNA. Employing an ad hoc pipeline including MMGBSA molecular dynamics, a selection of seven drugs was obtained. These were tested in vitro by electrophoretic mobility shift assay to evaluate the HP1043–DNA interaction. Among these, three returned promising results showing an appreciable reduction of the DNA-binding activity of HP1043. Overall, we applied a computational methodology coupled with experimental validation of the results to screen a large number of known drugs on one of the H. pylori essential transcription factors. This methodology allowed a rapid reduction of the number of drugs to be tested, and the drug repositioning approach considerably reduced the drug design costs. Identified drugs do not belong to the same pharmaceutical category and, by computational analysis, bound different cavities, but all display a reduction of HP1043 binding activity on the DNA.
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Affiliation(s)
- Federico Antoniciello
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Annamaria Zannoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Elena Chiti
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Federica Chiappori
- Istituto di Tecnologie Biomediche–Consiglio Nazionale Delle Ricerche (ITB-CNR), Segrate (Mi), Italy
- *Correspondence: Federica Chiappori,
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10
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Insights into the Virulence of Campylobacter jejuni Associated with Two-Component Signal Transduction Systems and Single Regulators. MICROBIOLOGY RESEARCH 2022. [DOI: 10.3390/microbiolres13020016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Campylobacter jejuni is one of the major aetiologies of diarrhoea. Understanding the processes and virulence factors contributing to C. jejuni fitness is a cornerstone for developing mitigation strategies. Two-component signal transduction systems, known as two-component systems (TCSs), along with single regulators with no obvious cognate histidine kinase, help pathogens in interacting with their environments, but the available literature on C. jejuni is limited. A typical TCS possesses histidine kinase and response regulator proteins. The objective of this review was to provide insights into the virulence of C. jejuni associated with TCSs and single regulators. Despite limited research, TCSs are important contributors to the pathogenicity of C. jejuni by influencing motility (FlgSR), colonisation (DccRS), nutrient acquisition (PhosSR and BumSR), and stress response (RacRS). Of the single regulators, CbrR and CosR are involved in bile resistance and oxidative stress response, respectively. Cross-talks among TCSs complicate the full elucidation of their molecular mechanisms. Although progress has been made in characterising C. jejuni TCSs, shortfalls such as triggering signals, inability to induce mutations in some genes, or developing suitable in vivo models are still being encountered. Further research is expected to shed light on the unexplored sides of the C. jejuni TCSs, which may allow new drug discoveries and better control strategies.
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11
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Han L, Shu X, Wang J. Helicobacter pylori-Mediated Oxidative Stress and Gastric Diseases: A Review. Front Microbiol 2022; 13:811258. [PMID: 35211104 PMCID: PMC8860906 DOI: 10.3389/fmicb.2022.811258] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
Gastric cancer is considered to be a type of gastrointestinal tumor and is mostly accompanied by Helicobacter pylori (HP) infection at the early stage. Hence, the long-term colonization of the gastric mucosa by HP as a causative factor for gastrointestinal diseases cannot be ignored. The virulence factors secreted by the bacterium activate the signaling pathway of oxidative stress and mediate chronic inflammatory response in the host cells. The virulence factors also thwart the antibacterial effect of neutrophils. Subsequently, DNA methylation is induced, which causes continuous cell proliferation and evolution toward low-grade-differentiated gastric cells. This process provides the pathological basis for the occurrence of progressive gastric cancer. Therefore, this review aims to summarize the oxidative stress response triggered by HP in the gastric mucosa and the subsequent signaling pathways. The findings are expected to help in the formulation of new targeted drugs for preventing the occurrence of early gastric cancer and its progression to middle and advanced cancer.
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Affiliation(s)
- Lu Han
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Clinical Research Center for Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xu Shu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Clinical Research Center for Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jian Wang
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China.,Jiangxi Clinical Research Center for Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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12
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Roncarati D, Scarlato V, Vannini A. Targeting of Regulators as a Promising Approach in the Search for Novel Antimicrobial Agents. Microorganisms 2022; 10:microorganisms10010185. [PMID: 35056634 PMCID: PMC8777881 DOI: 10.3390/microorganisms10010185] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Since the discovery of penicillin in the first half of the last century, antibiotics have become the pillars of modern medicine for fighting bacterial infections. However, pathogens resistant to antibiotic treatment have increased in recent decades, and efforts to discover new antibiotics have decreased. As a result, it is becoming increasingly difficult to treat bacterial infections successfully, and we look forward to more significant efforts from both governments and the scientific community to research new antibacterial drugs. This perspective article highlights the high potential of bacterial transcriptional and posttranscriptional regulators as targets for developing new drugs. We highlight some recent advances in the search for new compounds that inhibit their biological activity and, as such, appear very promising for treating bacterial infections.
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Affiliation(s)
- Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
- Correspondence: (D.R.); (V.S.); (A.V.)
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy
- Correspondence: (D.R.); (V.S.); (A.V.)
| | - Andrea Vannini
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40126 Bologna, Italy
- Correspondence: (D.R.); (V.S.); (A.V.)
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13
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Versace G, Palombo M, Menon A, Scarlato V, Roncarati D. Feeling the Heat: The Campylobacter jejuni HrcA Transcriptional Repressor Is an Intrinsic Protein Thermosensor. Biomolecules 2021; 11:biom11101413. [PMID: 34680046 PMCID: PMC8533110 DOI: 10.3390/biom11101413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/14/2021] [Accepted: 09/22/2021] [Indexed: 01/16/2023] Open
Abstract
The heat-shock response, a universal protective mechanism consisting of a transcriptional reprogramming of the cellular transcriptome, results in the accumulation of proteins which counteract the deleterious effects of heat-stress on cellular polypeptides. To quickly respond to thermal stress and trigger the heat-shock response, bacteria rely on different mechanisms to detect temperature variations, which can involve nearly all classes of biological molecules. In Campylobacter jejuni the response to heat-shock is transcriptionally controlled by a regulatory circuit involving two repressors, HspR and HrcA. In the present work we show that the heat-shock repressor HrcA acts as an intrinsic protein thermometer. We report that a temperature upshift up to 42 °C negatively affects HrcA DNA-binding activity to a target promoter, a condition required for de-repression of regulated genes. Furthermore, we show that this impairment of HrcA binding at 42 °C is irreversible in vitro, as DNA-binding was still not restored by reversing the incubation temperature to 37 °C. On the other hand, we demonstrate that the DNA-binding activity of HspR, which controls, in combination with HrcA, the transcription of chaperones' genes, is unaffected by heat-stress up to 45 °C, portraying this master repressor as a rather stable protein. Additionally, we show that HrcA binding activity is enhanced by the chaperonin GroE, upon direct protein-protein interaction. In conclusion, the results presented in this work establish HrcA as a novel example of intrinsic heat-sensing transcriptional regulator, whose DNA-binding activity is positively modulated by the GroE chaperonin.
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Affiliation(s)
| | | | | | - Vincenzo Scarlato
- Correspondence: (V.S.); (D.R.); Tel.: +39-051-209-4204 (V.S.); +39-051-209-9320 (D.R.)
| | - Davide Roncarati
- Correspondence: (V.S.); (D.R.); Tel.: +39-051-209-4204 (V.S.); +39-051-209-9320 (D.R.)
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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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Zannoni A, Pelliciari S, Musiani F, Chiappori F, Roncarati D, Scarlato V. Definition of the Binding Architecture to a Target Promoter of HP1043, the Essential Master Regulator of Helicobacter pylori. Int J Mol Sci 2021; 22:ijms22157848. [PMID: 34360614 PMCID: PMC8345958 DOI: 10.3390/ijms22157848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 07/13/2021] [Accepted: 07/14/2021] [Indexed: 11/30/2022] Open
Abstract
HP1043 is an essential orphan response regulator of Helicobacter pylori orchestrating multiple crucial cellular processes. Classified as a member of the OmpR/PhoB family of two-component systems, HP1043 exhibits a highly degenerate receiver domain and evolved to function independently of phosphorylation. Here, we investigated the HP1043 binding mode to a target sequence in the hp1227 promoter (Php1227). Scanning mutagenesis of HP1043 DNA-binding domain and consensus sequence led to the identification of residues relevant for the interaction of the protein with a target DNA. These determinants were used as restraints to guide a data-driven protein-DNA docking. Results suggested that, differently from most other response regulators of the same family, HP1043 binds in a head-to-head conformation to the Php1227 target promoter. HP1043 interacts with DNA largely through charged residues and contacts with both major and minor grooves of the DNA are required for a stable binding. Computational alanine scanning on molecular dynamics trajectory was performed to corroborate our findings. Additionally, in vitro transcription assays confirmed that HP1043 positively stimulates the activity of RNA polymerase.
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Affiliation(s)
- Annamaria Zannoni
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Simone Pelliciari
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Francesco Musiani
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
| | - Federica Chiappori
- Istituto di Tecnologie Biomediche-Consiglio Nazionale delle Ricerche (ITB-CNR), 20054 Segrate, Italy;
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
- Correspondence: (D.R.); (V.S.)
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40126 Bologna, Italy; (A.Z.); (S.P.); (F.M.)
- Correspondence: (D.R.); (V.S.)
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16
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González A, Casado J, Lanas Á. Fighting the Antibiotic Crisis: Flavonoids as Promising Antibacterial Drugs Against Helicobacter pylori Infection. Front Cell Infect Microbiol 2021; 11:709749. [PMID: 34354964 PMCID: PMC8329489 DOI: 10.3389/fcimb.2021.709749] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/05/2021] [Indexed: 12/12/2022] Open
Abstract
Over half of the world’s population is estimated to be infected with Helicobacter pylori. Chronic infection with this microbial class I carcinogen is considered the most important risk factor for developing gastric cancer. The increasing antimicrobial resistance to first-line antibiotics mainly causes the failure of current eradication therapies, inducing refractory infections. The alarming increase in multidrug resistance in H. pylori isolates worldwide is already beginning to limit the efficacy of existing treatments. Consequently, the World Health Organization (WHO) has included H. pylori in its list of “priority pathogens” for which new antibiotics are urgently needed. Novel strategies must be followed to fight this antibiotic crisis, including properly exploiting the proven therapeutic potential of medicinal plants and plant-derived phytochemicals. In this mini-review, we overview the impressive properties of naturally occurring flavonoids as effective antimicrobial agents against H. pylori, which support the use of these plant-derived bioactive compounds as promising drug candidates for inclusion in novel and personalized combinatory therapies against H. pylori infection.
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Affiliation(s)
- Andrés González
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain.,Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Zaragoza, Spain.,Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain
| | - Javier Casado
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain.,Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Zaragoza, Spain
| | - Ángel Lanas
- Group of Translational Research in Digestive Diseases, Institute for Health Research Aragón (IIS Aragón), Zaragoza, Spain.,Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Zaragoza, Spain.,Biomedical Research Networking Center in Hepatic and Digestive Diseases (CIBERehd), Madrid, Spain.,Digestive Diseases Service, University Clinic Hospital Lozano Blesa, Zaragoza, Spain
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17
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Cooperative Regulation of Campylobacter jejuni Heat-Shock Genes by HspR and HrcA. Microorganisms 2020; 8:microorganisms8081161. [PMID: 32751623 PMCID: PMC7464140 DOI: 10.3390/microorganisms8081161] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/24/2020] [Accepted: 07/27/2020] [Indexed: 01/17/2023] Open
Abstract
The heat-shock response is defined by the transient gene-expression program that leads to the rapid accumulation of heat-shock proteins. This evolutionary conserved response aims at the preservation of the intracellular environment and represents a crucial pathway during the establishment of host–pathogen interaction. In the food-borne pathogen Campylobacter jejuni two transcriptional repressors, named HspR and HrcA, are involved in the regulation of the major heat-shock genes. However, the molecular mechanism underpinning HspR and HrcA regulatory function has not been defined yet. In the present work, we assayed and mapped the HspR and HrcA interactions on heat-shock promoters by high-resolution DNase I footprintings, defining their regulatory circuit, which governs C. jejuni heat-shock response. We found that, while DNA-binding of HrcA covers a compact region enclosing a single inverted repeat similar to the so-called Controlling Inverted Repeat of Chaperone Expression (CIRCE) sequence, HspR interacts with multiple high- and low-affinity binding sites, which contain HspR Associated Inverted Repeat (HAIR)-like sequences. We also explored the DNA-binding properties of the two repressors competitively on their common targets and observed, for the first time, that HrcA and HspR can directly interact and their binding on co-regulated promoters occurs in a cooperative manner. This mutual cooperative mechanism of DNA binding could explain the synergic repressive effect of HspR and HrcA observed in vivo on co-regulated promoters. Peculiarities of the molecular mechanisms exerted by HspR and HrcA in C. jejuni are compared to the closely related bacterium H. pylori that uses homologues of the two regulators.
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18
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Rajeev L, Garber ME, Mukhopadhyay A. Tools to map target genes of bacterial two-component system response regulators. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:267-276. [PMID: 32212247 PMCID: PMC7318608 DOI: 10.1111/1758-2229.12838] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/17/2020] [Accepted: 03/18/2020] [Indexed: 05/05/2023]
Abstract
Studies on bacterial physiology are incomplete without knowledge of the signalling and regulatory systems that a bacterium uses to sense and respond to its environment. Two-component systems (TCSs) are among the most prevalent bacterial signalling systems, and they control essential and secondary physiological processes; however, even in model organisms, we lack a complete understanding of the signals sensed, the phosphotransfer partners and the functions regulated by these systems. In this review, we discuss several tools to map the genes targeted by transcriptionally acting TCSs. Many of these tools have been used for studying individual TCSs across diverse species, but systematic approaches to delineate entire signalling networks have been very few. Since genome sequences and high-throughput technologies are now readily available, the methods presented here can be applied to characterize the entire DNA-binding TCS signalling network in any bacterial species and are especially useful for non-model environmental bacteria.
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Affiliation(s)
- Lara Rajeev
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Megan E. Garber
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
- Department of Comparative BiochemistryUniversity of CaliforniaBerkeleyCA94720USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
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19
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Flavodoxins as Novel Therapeutic Targets against Helicobacter pylori and Other Gastric Pathogens. Int J Mol Sci 2020; 21:ijms21051881. [PMID: 32164177 PMCID: PMC7084853 DOI: 10.3390/ijms21051881] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/04/2020] [Accepted: 03/06/2020] [Indexed: 02/06/2023] Open
Abstract
Flavodoxins are small soluble electron transfer proteins widely present in bacteria and absent in vertebrates. Flavodoxins participate in different metabolic pathways and, in some bacteria, they have been shown to be essential proteins representing promising therapeutic targets to fight bacterial infections. Using purified flavodoxin and chemical libraries, leads can be identified that block flavodoxin function and act as bactericidal molecules, as it has been demonstrated for Helicobacter pylori (Hp), the most prevalent human gastric pathogen. Increasing antimicrobial resistance by this bacterium has led current therapies to lose effectiveness, so alternative treatments are urgently required. Here, we summarize, with a focus on flavodoxin, opportunities for pharmacological intervention offered by the potential protein targets described for this bacterium and provide information on other gastrointestinal pathogens and also on bacteria from the gut microbiota that contain flavodoxin. The process of discovery and development of novel antimicrobials specific for Hp flavodoxin that is being carried out in our group is explained, as it can be extrapolated to the discovery of inhibitors specific for other gastric pathogens. The high specificity for Hp of the antimicrobials developed may be of help to reduce damage to the gut microbiota and to slow down the development of resistant Hp mutants.
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20
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SrnR from Streptomyces griseus is a nickel-binding transcriptional activator. J Biol Inorg Chem 2019; 25:187-198. [PMID: 31853648 DOI: 10.1007/s00775-019-01751-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/25/2019] [Indexed: 01/24/2023]
Abstract
Nickel ions are crucial components for the catalysis of biological reactions in prokaryotic organisms. As an uncontrolled nickel trafficking is toxic for living organisms, nickel-dependent bacteria have developed tightly regulated strategies to maintain the correct intracellular metal ion quota. These mechanisms require transcriptional regulator proteins that respond to nickel concentration, activating or repressing the expression of specific proteins related to Ni(II) metabolism. In Streptomyces griseus, a Gram-positive bacterium used for antibiotic production, SgSrnR and SgSrnQ regulate the nickel-dependent antagonistic expression of two superoxide dismutase (SOD) enzymes, a Ni-SOD and a FeZn-SOD. According to a previously proposed model, SgSrnR and SgSrnQ form a protein complex in which SgSrnR works as repressor, binding directly to the promoter of the gene coding for FeZn-SOD, while SgSrnQ is the Ni(II)-dependent co-repressor. The present work focuses on the determination of the biophysical and functional properties of SgSrnR. The protein was heterologously expressed and purified from Escherichia coli. The structural and metal-binding analysis, carried out by circular dichroism, light scattering, fluorescence and isothermal titration calorimetry, showed that the protein is a well-structured homodimer, able to bind nickel with moderate affinity. DNase I footprinting and β-galactosidase gene reporter assays revealed that apo-SgSrnR is able to bind its DNA operator and activates a transcriptional response. The structural and functional properties of this protein are discussed relatively to its role as a Ni(II)-dependent sensor.
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21
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González A, Casado J, Chueca E, Salillas S, Velázquez-Campoy A, Espinosa Angarica V, Bénejat L, Guignard J, Giese A, Sancho J, Lehours P, Lanas Á. Repurposing Dihydropyridines for Treatment of Helicobacter pylori Infection. Pharmaceutics 2019; 11:pharmaceutics11120681. [PMID: 31847484 PMCID: PMC6969910 DOI: 10.3390/pharmaceutics11120681] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 12/11/2022] Open
Abstract
Antibiotic resistance is a major cause of the increasing failures in the current eradication therapies against Helicobacter pylori. In this scenario, repurposing drugs could be a valuable strategy to fast-track novel antimicrobial agents. In the present study, we analyzed the inhibitory capability of 1,4-dihydropyridine (DHP) antihypertensive drugs on the essential function of the H. pylori response regulator HsrA and investigated both the in vitro antimicrobial activities and the in vivo efficacy of DHP treatments against H. pylori. Six different commercially available and highly prescribed DHP drugs-namely, Nifedipine, Nicardipine, Nisoldipine, Nimodipine, Nitrendipine, and Lercanidipine-noticeably inhibited the DNA binding activity of HsrA and exhibited potent bactericidal activities against both metronidazole- and clarithromycin-resistant strains of H. pylori, with minimal inhibitory concentration (MIC) values in the range of 4 to 32 mg/L. The dynamics of the decline in the bacterial counts at 2 × MIC appeared to be correlated with the lipophilicity of the drugs, suggesting different translocation efficiencies of DHPs across the bacterial membrane. Oral treatments with 100 mg/kg/day of marketed formulations of Nimodipine or Nitrendipine in combination with omeprazole significantly reduced the H. pylori gastric colonization in mice. The results presented here support a novel therapeutic solution for treatment of antibiotic-resistant H. pylori infections.
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Affiliation(s)
- Andrés González
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34-976-762807
| | - Javier Casado
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Eduardo Chueca
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
| | - Sandra Salillas
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
- ARAID Foundation, Government of Aragon, Ranillas 1-D, 50018 Zaragoza, Spain
| | - Vladimir Espinosa Angarica
- Cancer Science Institute, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore
| | - Lucie Bénejat
- UMR1053 Bordeaux Research in Translational Oncology, INSERM, Université Bordeaux, BaRITOn, 33000 Bordeaux, France
- French National Reference Center for Campylobacters & Helicobacters, 33000 Bordeaux, France
| | - Jérome Guignard
- UMR1053 Bordeaux Research in Translational Oncology, INSERM, Université Bordeaux, BaRITOn, 33000 Bordeaux, France
| | - Alban Giese
- UMR1053 Bordeaux Research in Translational Oncology, INSERM, Université Bordeaux, BaRITOn, 33000 Bordeaux, France
| | - Javier Sancho
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems (BIFI), Mariano Esquilor (Edif. I+D), 50018 Zaragoza, Spain
- Department of Biochemistry and Molecular & Cellular Biology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Philippe Lehours
- UMR1053 Bordeaux Research in Translational Oncology, INSERM, Université Bordeaux, BaRITOn, 33000 Bordeaux, France
- French National Reference Center for Campylobacters & Helicobacters, 33000 Bordeaux, France
| | - Ángel Lanas
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009 Zaragoza, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Monforte de Lemos 3-5, 28029 Madrid, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa; San Juan Bosco 15, 50009 Zaragoza, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Pedro Cerbuna 12, 50009 Zaragoza, Spain
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22
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Helicobacter pylori Stress-Response: Definition of the HrcA Regulon. Microorganisms 2019; 7:microorganisms7100436. [PMID: 31614448 PMCID: PMC6843607 DOI: 10.3390/microorganisms7100436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/03/2019] [Accepted: 10/08/2019] [Indexed: 12/12/2022] Open
Abstract
Bacteria respond to different environmental stresses by reprogramming the transcription of specific genes whose proper expression is critical for their survival. In this regard, the heat-shock response, a widespread protective mechanism, triggers a sudden increase in the cellular concentration of different proteins, including molecular chaperones and proteases, to preserve protein folding and maintain cellular homeostasis. In the medically important gastric pathogen Helicobacter pylori the regulation of the principal heat-shock genes is under the transcriptional control of two repressor proteins named HspR and HrcA. To define the HrcA regulon, we carried out whole transcriptome analysis through RNA-sequencing, comparing the transcriptome of the H. pylori G27 wild type strain to that of the isogenic hrcA-knockout strain. Overall, differential gene expression analysis outlined 49 genes to be deregulated upon hrcA gene inactivation. Interestingly, besides controlling the transcription of genes coding for molecular chaperones and stress-related mediators, HrcA is involved in regulating the expression of proteins whose function is linked to several cellular processes crucial for bacterial survival and virulence. These include cell motility, membrane transporters, Lipopolysaccharide modifiers and adhesins. The role of HrcA as a central regulator of H. pylori transcriptome, as well as its interconnections with the HspR regulon are here analyzed and discussed. As the HrcA protein acts as a pleiotropic regulator, influencing the expression of several stress-unrelated genes, it may be considered a promising target for the design of new antimicrobial strategies.
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González A, Salillas S, Velázquez-Campoy A, Espinosa Angarica V, Fillat MF, Sancho J, Lanas Á. Identifying potential novel drugs against Helicobacter pylori by targeting the essential response regulator HsrA. Sci Rep 2019; 9:11294. [PMID: 31383920 PMCID: PMC6683298 DOI: 10.1038/s41598-019-47746-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023] Open
Abstract
The increasing antibiotic resistance evolved by Helicobacter pylori has alarmingly reduced the eradication rates of first-line therapies. To overcome the current circulating resistome, we selected a novel potential therapeutic target in order to identify new candidate drugs for treating H. pylori infection. We screened 1120 FDA-approved drugs for molecules that bind to the essential response regulator HsrA and potentially inhibit its biological function. Seven natural flavonoids were identified as HsrA binders. All of these compounds noticeably inhibited the in vitro DNA binding activity of HsrA, but only four of them, apigenin, chrysin, kaempferol and hesperetin, exhibited high bactericidal activities against H. pylori. Chrysin showed the most potent bactericidal activity and the most synergistic effect in combination with clarithromycin or metronidazole. Flavonoid binding to HsrA occurs preferably at its C-terminal effector domain, interacting with amino acid residues specifically involved in forming the helix-turn-helix DNA binding motif. Our results validate the use of HsrA as a novel and effective therapeutic target in H. pylori infection and provide molecular evidence of a novel antibacterial mechanism of some natural flavonoids against H. pylori. The results further support the valuable potential of natural flavonoids as candidate drugs for novel antibacterial strategies.
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Affiliation(s)
- Andrés González
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009, Zaragoza, Spain.
- Institute for Biocomputation and Physics of Complex Systems, Mariano Esquillor (Edif. I + D), 50018, Zaragoza, Spain.
| | - Sandra Salillas
- Institute for Biocomputation and Physics of Complex Systems, Mariano Esquillor (Edif. I + D), 50018, Zaragoza, Spain
- Department of Biochemistry & Molecular and Cell Biology, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Institute for Biocomputation and Physics of Complex Systems, Mariano Esquillor (Edif. I + D), 50018, Zaragoza, Spain
- CIBERehd, Monforte de Lemos 3-5, 28029, Madrid, Spain
- ARAID Foundation, Ranillas 1-D, 500018, Zaragoza, Spain
| | - Vladimir Espinosa Angarica
- Cancer Science Institute, National University of Singapore, 14 Medical Drive, #12-01, 117599, Singapore, Singapore
| | - María F Fillat
- Institute for Biocomputation and Physics of Complex Systems, Mariano Esquillor (Edif. I + D), 50018, Zaragoza, Spain
- Department of Biochemistry & Molecular and Cell Biology, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Javier Sancho
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009, Zaragoza, Spain
- Institute for Biocomputation and Physics of Complex Systems, Mariano Esquillor (Edif. I + D), 50018, Zaragoza, Spain
- Department of Biochemistry & Molecular and Cell Biology, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Ángel Lanas
- Aragon Institute for Health Research (IIS Aragón), San Juan Bosco 13, 50009, Zaragoza, Spain
- CIBERehd, Monforte de Lemos 3-5, 28029, Madrid, Spain
- Department of Medicine, Psychiatry and Dermatology, University of Zaragoza, Pedro Cerbuna 12, 50009, Zaragoza, Spain
- Digestive Diseases Service, University Clinic Hospital Lozano Blesa, San Juan Bosco 15, 50009, Zaragoza, Spain
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Type I Toxin-Antitoxin Systems: Regulating Toxin Expression via Shine-Dalgarno Sequence Sequestration and Small RNA Binding. Microbiol Spectr 2019; 6. [PMID: 30051800 DOI: 10.1128/microbiolspec.rwr-0030-2018] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Toxin-antitoxin (TA) systems are small genetic loci composed of two adjacent genes: a toxin and an antitoxin that prevents toxin action. Despite their wide distribution in bacterial genomes, the reasons for TA systems being on chromosomes remain enigmatic. In this review, we focus on type I TA systems, composed of a small antisense RNA that plays the role of an antitoxin to control the expression of its toxin counterpart. It does so by direct base-pairing to the toxin-encoding mRNA, thereby inhibiting its translation and/or promoting its degradation. However, in many cases, antitoxin binding is not sufficient to avoid toxicity. Several cis-encoded mRNA elements are also required for repression, acting to uncouple transcription and translation via the sequestration of the ribosome binding site. Therefore, both antisense RNA binding and compact mRNA folding are necessary to tightly control toxin synthesis and allow the presence of these toxin-encoding systems on bacterial chromosomes.
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Pepe S, Pinatel E, Fiore E, Puccio S, Peano C, Brignoli T, Vannini A, Danielli A, Scarlato V, Roncarati D. The Helicobacter pylori Heat-Shock Repressor HspR: Definition of Its Direct Regulon and Characterization of the Cooperative DNA-Binding Mechanism on Its Own Promoter. Front Microbiol 2018; 9:1887. [PMID: 30154784 PMCID: PMC6102357 DOI: 10.3389/fmicb.2018.01887] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 07/27/2018] [Indexed: 12/12/2022] Open
Abstract
The ability of pathogens to perceive environmental conditions and modulate gene expression accordingly is a crucial feature for bacterial survival. In this respect, the heat-shock response, a universal cellular response, allows cells to adapt to hostile environmental conditions and to survive during stress. In the major human pathogen Helicobacter pylori the expression of chaperone-encoding operons is under control of two auto-regulated transcriptional repressors, HrcA and HspR, with the latter acting as the master regulator of the regulatory circuit. To further characterize the HspR regulon in H. pylori, we used global transcriptome analysis (RNA-sequencing) in combination with Chromatin Immunoprecipitation coupled with deep sequencing (ChIP-sequencing) of HspR genomic binding sites. Intriguingly, these analyses showed that HspR is involved in the regulation of different crucial cellular functions through a limited number of genomic binding sites. Moreover, we further characterized HspR-DNA interactions through hydroxyl-radical footprinting assays. This analysis in combination with a nucleotide sequence alignment of HspR binding sites, revealed a peculiar pattern of DNA protection and highlighted sequence conservation with the HAIR motif (an HspR-associated inverted repeat of Streptomyces spp.). Site-directed mutagenesis demonstrated that the HAIR motif is fundamental for HspR binding and that additional nucleotide determinants flanking the HAIR motif are required for complete binding of HspR to its operator sequence spanning over 70 bp of DNA. This finding is compatible with a model in which possibly a dimer of HspR recognizes the HAIR motif overlapping its promoter for binding and in turn cooperatively recruits two additional dimers on both sides of the HAIR motif.
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Affiliation(s)
- Simona Pepe
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Eva Pinatel
- Institute of Biomedical Technologies, National Research Council, Milan, Italy
| | - Elisabetta Fiore
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Simone Puccio
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy
| | - Clelia Peano
- Institute of Biomedical Technologies, National Research Council, Milan, Italy.,Humanitas Clinical and Research Center, Milan, Italy.,Institute of Genetic and Biomedical Research, National Research Council, Milan, Italy
| | - Tarcisio Brignoli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Andrea Vannini
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Alberto Danielli
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | - Davide Roncarati
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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26
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Yuan XY, Wang Y, Wang MY. The type IV secretion system in Helicobacter pylori. Future Microbiol 2018; 13:1041-1054. [PMID: 29927340 DOI: 10.2217/fmb-2018-0038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Helicobacter pylori (H. pylori) has an essential role in the pathogenesis of gastritis, peptic ulcer disease, mucosa-associated lymphoid tissue lymphoma and gastric cancer. The severity of the host inflammatory responses against the bacteria have been straightly associated with a special bacterial virulence factor, the cag pathogenicity island, which is a type IV secretion system (T4SS) to deliver CagA into the host cells. Besides cag-T4SS, the chromosomes of H. pylori can encode another three T4SSs, including comB, tfs3 and tfs4. In this review, we systematically reviewed the four T4SSs of H. pylori and explored their roles in the pathogenesis of gastroduodenal diseases. The information summarized in this review might provide valuable insights into the pathogenic mechanism for H. pylori.
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Affiliation(s)
- Xiao-Yan Yuan
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Ying Wang
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
| | - Ming-Yi Wang
- Department of Central Lab, Weihai Municipal Hospital Affiliated to Dalian Medical University, Weihai, Shandong, 264200, PR China
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27
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Abstract
Antibiotics have saved millions of lives over the past decades. However, the accumulation of so many antibiotic resistance genes by some clinically relevant pathogens has begun to lead to untreatable infections worldwide. The current antibiotic resistance crisis will require greater efforts by governments and the scientific community to increase the research and development of new antibacterial drugs with new mechanisms of action. A major challenge is the identification of novel microbial targets, essential for in vivo growth or pathogenicity, whose inhibitors can overcome the currently circulating resistome of human pathogens. In this article, we focus on the potential high value of bacterial transcriptional regulators as targets for the development of new antibiotics, discussing in depth the molecular role of these regulatory proteins in bacterial physiology and pathogenesis. Recent advances in the search for novel compounds that inhibit the biological activity of relevant transcriptional regulators in pathogenic bacteria are reviewed.
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28
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Abstract
As Helicobacter pylori infects half the world's population and displays an extensive intraspecies diversity, genomics is a powerful tool to understand evolution and disease, to identify factors that confer higher risk of severe sequelae, and to find new approaches for therapy both among bacterial and host targets. In line with these objectives, this review article summarizes the major findings in Helicobacter genomics in papers published between April 2016 and March 2017.
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Affiliation(s)
- Kaisa Thorell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm, Sweden
| | - Philippe Lehours
- INSERM, Univ. Bordeaux, UMR1053 Bordeaux Research In Translational Oncology, BaRITOn, Bordeaux, France
| | - Filipa F Vale
- Faculty of Pharmacy, Host-Pathogen Interactions Unit, Research Institute for Medicines (iMed-ULisboa), Universidade de Lisboa, Lisbon, Portugal
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29
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Abstract
Helicobacter pylori is responsible for the most commonly found infection in the world's population. It is the major risk factor for gastric cancer development. Numerous studies published over the last year provide new insights into the strategies employed by H. pylori to adapt to the extreme acidic conditions of the gastric environment, to establish persistent infection and to deregulate host functions, leading to gastric pathogenesis and cancer. In this review, we report recent data on the mechanisms involved in chemotaxis, on the essential role of nickel in acid resistance and gastric colonization, on the importance of adhesins and Hop proteins and on the role of CagPAI-components and CagA. Among the host functions, a special focus has been made on the escape from immune response, the ability of bacteria to induce genetic instability and modulate telomeres, the mechanism of autophagy and the deregulation of micro RNAs.
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Affiliation(s)
- Vania Camilo
- Pasteur Institute, Department of Microbiology, Helicobacter Pathogenesis Unit, Paris Cedex 15, France.,INSERM U1173, Faculty of Health Sciences Simone Veil, Université Versailles-Saint-Quentin, Saint Quentin en Yvelines, France
| | - Toshiro Sugiyama
- Graduate School of Medicine and Pharmaceutical Sciences, Department of Gastroenterology, University of Toyama, Sugitani, Toyama, Japan
| | - Eliette Touati
- Pasteur Institute, Department of Microbiology, Helicobacter Pathogenesis Unit, Paris Cedex 15, France
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30
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Campilongo R, Fung RKY, Little RH, Grenga L, Trampari E, Pepe S, Chandra G, Stevenson CEM, Roncarati D, Malone JG. One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet 2017; 13:e1006839. [PMID: 28658302 PMCID: PMC5489143 DOI: 10.1371/journal.pgen.1006839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 12/04/2022] Open
Abstract
Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate. Here we show how Pseudomonas controls multiple different primary carbon metabolism pathways by sensing levels of KDPG, an Entner Doudoroff (ED) pathway intermediate. KDPG binds to two highly similar transcription factors; the ED regulator HexR and the previously uncharacterised protein RccR. RccR inversely controls the glyoxylate shunt, gluconeogenesis and pyruvate metabolism, suppressing the first two pathways as pyruvate metabolism genes are expressed, and vice versa. This complex regulation is enabled by two distinct RccR-binding consensus sequences in the RccR regulon promoters. KDPG binding simultaneously increases RccR affinity for the glyoxylate shunt and gluconeogenesis promoters, and releases repression of pyruvate metabolism. This elegant two-regulator circuit allows Pseudomonas to rapidly respond to carbon source availability by sensing a single key intermediate, KDPG.
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Affiliation(s)
- Rosaria Campilongo
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- Istituto Pasteur- Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘C. Darwin”, Sapienza Universita`di Roma, Roma, Italy
| | - Rowena K. Y. Fung
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Richard H. Little
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Lucia Grenga
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Eleftheria Trampari
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Simona Pepe
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Davide Roncarati
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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