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Johnston EL, Guy-Von Stieglitz S, Zavan L, Cross J, Greening DW, Hill AF, Kaparakis-Liaskos M. The effect of altered pH growth conditions on the production, composition, and proteomes of Helicobacter pylori outer membrane vesicles. Proteomics 2024; 24:e2300269. [PMID: 37991474 DOI: 10.1002/pmic.202300269] [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: 06/30/2023] [Revised: 10/03/2023] [Accepted: 10/16/2023] [Indexed: 11/23/2023]
Abstract
Gram-negative bacteria release outer membrane vesicles (OMVs) that contain cargo derived from their parent bacteria. Helicobacter pylori is a Gram-negative human pathogen that produces urease to increase the pH of the surrounding environment to facilitate colonization of the gastric mucosa. However, the effect of acidic growth conditions on the production and composition of H. pylori OMVs is unknown. In this study, we examined the production, composition, and proteome of H. pylori OMVs produced during acidic and neutral pH growth conditions. H. pylori growth in acidic conditions reduced the quantity and size of OMVs produced. Additionally, OMVs produced during acidic growth conditions had increased protein, DNA, and RNA cargo compared to OMVs produced during neutral conditions. Proteomic analysis comparing the proteomes of OMVs to their parent bacteria demonstrated significant differences in the enrichment of beta-lactamases and outer membrane proteins between bacteria and OMVs, supporting that differing growth conditions impacts OMV composition. We also identified differences in the enrichment of proteins between OMVs produced during different pH growth conditions. Overall, our findings reveal that growth of H. pylori at different pH levels is a factor that alters OMV proteomes, which may affect their subsequent functions.
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Affiliation(s)
- Ella L Johnston
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
| | - Sebastian Guy-Von Stieglitz
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
| | - Lauren Zavan
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
| | - Jonathon Cross
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - David W Greening
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
- Baker Heart and Diabetes Institute, Melbourne, Australia
- Baker Department of Cardiometabolic Health, University of Melbourne, Melbourne, Australia
| | - Andrew F Hill
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
- Department of Biochemistry and Chemistry, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Australia
- Institute for Health and Sport, Victoria University, Melbourne, Victoria, Australia
| | - Maria Kaparakis-Liaskos
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Australia
- Research Centre for Extracellular Vesicles, La Trobe University, Bundoora, Australia
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2
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Zhao Q, Yao F, Li W, Liu S, Bi S. Identification of a dCache-type chemoreceptor in Campylobacter jejuni that specifically mediates chemotaxis towards methyl pyruvate. Front Microbiol 2024; 15:1400284. [PMID: 38784811 PMCID: PMC11111895 DOI: 10.3389/fmicb.2024.1400284] [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: 03/13/2024] [Accepted: 04/25/2024] [Indexed: 05/25/2024] Open
Abstract
The foodborne pathogenic bacterium Campylobacter jejuni utilizes chemotaxis to assist in the colonization of host niches. A key to revealing the relationship among chemotaxis and pathogenicity is the discovery of signaling molecules perceived by the chemoreceptors. The C. jejuni chemoreceptor Tlp11 is encoded by the highly infective C. jejuni strains. In the present study, we report that the dCache-type ligand-binding domain (LBD) of C. jejuni ATCC 33560 Tlp11 binds directly to novel ligands methyl pyruvate, toluene, and quinoline using the same pocket. Methyl pyruvate elicits a strong chemoattractant response, while toluene and quinoline function as the antagonists without triggering chemotaxis. The sensory LBD was used to control heterologous proteins by constructing chimeras, indicating that the signal induced by methyl pyruvate is transmitted across the membrane. In addition, bioinformatics and experiments revealed that the dCache domains with methyl pyruvate-binding sites and ability are widely distributed in the order Campylobacterales. This is the first report to identify the class of dCache chemoreceptors that bind to attractant methyl pyruvate and antagonists toluene and quinoline. Our research provides a foundation for understanding the chemotaxis and virulence of C. jejuni and lays a basis for the control of this foodborne pathogen.
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Affiliation(s)
- Qi Zhao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Fulian Yao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
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3
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Zhou X, Rahman MM, Bonny SQ, Xin Y, Liddelow N, Khan MF, Tikhomirova A, Homman-Ludiye J, Roujeinikova A. Pal power: Demonstration of the functional association of the Helicobacter pylori flagellar motor with peptidoglycan-associated lipoprotein (Pal) and its preliminary crystallographic analysis. Biosci Trends 2024; 17:491-498. [PMID: 38072447 DOI: 10.5582/bst.2023.01278] [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] [Indexed: 02/02/2024]
Abstract
The bacterial flagellar motor is a molecular nanomachine, the assembly and regulation of which requires many accessory proteins. Their identity, structure and function are often discovered through characterisation of mutants with impaired motility. Here, we demonstrate the functional association of the Helicobacter pylori peptidoglycan-associated lipoprotein (HpPal) with the flagellar motor by analysing the motility phenotype of the ∆pal mutant, and present the results of the preliminary X-ray crystallographic analysis of its globular C-terminal domain HpPal-C. Purified HpPal-C behaved as a dimer in solution. Crystals of HpPal-C were grown by the hanging drop vapour diffusion method using medium molecular weight polyethylene glycol (PEG) Smear as the precipitating agent. The crystals belong to the primitive orthorhombic space group P1 with unit cell parameters a = 50.7, b = 63.0, c = 75.1 Å. X-ray diffraction data were collected to 1.8 Å resolution on the Australian Synchrotron beamline MX2. Calculation of the Matthews coefficient (VM=2.24 Å3/Da) and molecular replacement showed that the asymmetric unit contains two protein subunits. This study is an important step towards elucidation of the non-canonical role of H. pylori Pal in the regulation, or function of, the flagellar motor.
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Affiliation(s)
- Xiaotian Zhou
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Mohammad M Rahman
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Sharmin Q Bonny
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Yue Xin
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Nikki Liddelow
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
| | - Mohammad F Khan
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Alexandra Tikhomirova
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Jihane Homman-Ludiye
- Monash Micro Imaging, Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
| | - Anna Roujeinikova
- Department of Microbiology, Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria, Australia
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4
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Matilla MA, Gavira JA, Krell T. Accessing nutrients as the primary benefit arising from chemotaxis. Curr Opin Microbiol 2023; 75:102358. [PMID: 37459734 DOI: 10.1016/j.mib.2023.102358] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 09/17/2023]
Abstract
About half of the known bacterial species perform chemotaxis that gains them access to sites that are optimal for growth and survival. The motility apparatus and chemotaxis signaling pathway impose a large energetic and metabolic burden on the cell. There is almost no limit to the type of chemoeffectors that are recognized by bacterial chemoreceptors. For example, they include hormones, neurotransmitters, quorum-sensing molecules, and inorganic ions. However, the vast majority of chemoeffectors appear to be of metabolic value. We review here the experimental evidence indicating that accessing nutrients is the main selective force that led to the evolution of chemotaxis.
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Affiliation(s)
- Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - José A Gavira
- Laboratory of Crystallographic Studies, IACT (CSIC-UGR), Armilla, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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5
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Suzuki S, Yokota K, Igimi S, Kajikawa A. Negative chemotaxis of Ligilactobacillus agilis BKN88 against gut-derived substances. Sci Rep 2023; 13:15632. [PMID: 37730901 PMCID: PMC10511705 DOI: 10.1038/s41598-023-42840-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 09/15/2023] [Indexed: 09/22/2023] Open
Abstract
Ligilactobacillus agilis is a motile lactic acid bacterium found in the gastrointestinal tracts of animals. The findings of our previous study suggest that the motility of L. agilis BKN88 enables gut colonization in murine models. However, the chemotactic abilities of motile lactobacilli remain unknown. This study aimed to identify the gut-derived chemoeffectors and their corresponding chemoreceptors in L. agilis BKN88. Chemotaxis assays with chemotactic and non-chemotactic (ΔcheA) L. agilis strains revealed that low pH, organic acids, and bile salts served as repellents. L. agilis BKN88 was more sensitive to bile and acid than the gut-derived non-motile lactobacilli, implying that L. agilis might utilize motility and chemotaxis instead of exhibiting stress tolerance/resistance. L. agilis BKN88 contains five putative chemoreceptor genes (mcp1-mcp5). Chemotaxis assays using a series of chemoreceptor mutants revealed that each of the five chemoreceptors could sense multiple chemoeffectors and that these chemoreceptors were functionally redundant. Mcp2 and Mcp3 sensed all tested chemoeffectors. This study provides further insights into the interactions between chemoreceptors and ligands of motile lactobacilli and the unique ecological and evolutionary features of motile lactobacilli, which may be distinct from those of non-motile lactobacilli.
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Affiliation(s)
- Shunya Suzuki
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Kenji Yokota
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Shizunobu Igimi
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan
| | - Akinobu Kajikawa
- Department of Agricultural Chemistry, Graduate School of Tokyo University of Agriculture, 1-1-1 Sakuragaoka, Setagaya, Tokyo, 156-8502, Japan.
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6
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Gupta N, Kumar A, Verma VK. Strategies adopted by gastric pathogen Helicobacter pylori for a mature biofilm formation: Antimicrobial peptides as a visionary treatment. Microbiol Res 2023; 273:127417. [PMID: 37267815 DOI: 10.1016/j.micres.2023.127417] [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: 03/13/2023] [Revised: 05/15/2023] [Accepted: 05/21/2023] [Indexed: 06/04/2023]
Abstract
Enormous efforts in recent past two decades to eradicate the pathogen that has been prevalent in half of the world's population have been problematic. The biofilm formed by Helicobacter pylori provides resistance towards innate immune cells, various combinatorial antibiotics, and human antimicrobial peptides, despite the fact that these all are potent enough to eradicate it in vitro. Biofilm provides the opportunity to secrete various virulence factors that strengthen the interaction between host and pathogen helping in evading the innate immune system and ultimately leading to persistence. To our knowledge, this review is the first of its kind to explain briefly the journey of H. pylori starting with the chemotaxis, the mechanism for selecting the site for colonization, the stress faced by the pathogen, and various adaptations to evade these stress conditions by forming biofilm and the morphological changes acquired by the pathogen in mature biofilm. Furthermore, we have explained the human GI tract antimicrobial peptides and the reason behind the failure of these AMPs, and how encapsulation of Pexiganan-A(MSI-78A) in a chitosan microsphere increases the efficiency of eradication.
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Affiliation(s)
- Nidhi Gupta
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India.
| | - Atul Kumar
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India
| | - Vijay Kumar Verma
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Marg, New Delhi 110021, India.
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7
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Beccaceci G, Sigal M. Unwelcome guests - the role of gland-associated Helicobacter pylori infection in gastric carcinogenesis. Front Oncol 2023; 13:1171003. [PMID: 37152042 PMCID: PMC10160455 DOI: 10.3389/fonc.2023.1171003] [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: 02/21/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Helicobacter pylori (H. pylori) are Gram-negative bacteria that cause chronic gastritis and are considered the main risk factor for the development of gastric cancer. H. pylori have evolved to survive the harsh luminal environment of the stomach and are known to cause damage and signaling aberrations in gastric epithelial cells, which can result in premalignant and malignant pathology. As well as colonizing the gastric mucus and surface epithelial cells, a subpopulation of H. pylori can invade deep into the gastric glands and directly interact with progenitor and stem cells. Gland colonization therefore bears the potential to cause direct injury to long-lived cells. Moreover, this bacterial subpopulation triggers a series of host responses that cause an enhanced proliferation of stem cells. Here, we review recent insights into how gastric gland colonization by H. pylori is established, the resulting pro-carcinogenic epithelial signaling alterations, as well as new insights into stem cell responses to infection. Together these point towards a critical role of gland-associated H. pylori in the development of gastric cancer.
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Affiliation(s)
- Giulia Beccaceci
- Medical Department, Division of Gastroenterology and Hepatology, Charité-Universtitätsmedizin Berlin, Berlin, Germany
- The Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Michael Sigal
- Medical Department, Division of Gastroenterology and Hepatology, Charité-Universtitätsmedizin Berlin, Berlin, Germany
- The Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine, Berlin, Germany
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8
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Yang H, Wang L, Zhang M, Hu B. The Role of Adhesion in Helicobacter pylori Persistent Colonization. Curr Microbiol 2023; 80:185. [PMID: 37071212 DOI: 10.1007/s00284-023-03264-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/10/2023] [Indexed: 04/19/2023]
Abstract
Helicobacter pylori (H. pylori) has coevolved with its human host for more than 100 000 years. It can safely colonize around the epithelium of gastric glands via their specific microstructures and proteins. Unless patients receive eradication treatment, H. pylori infection is always lifelong. However, few studies have discussed the reasons. This review will focus on the adhesion of H. pylori from the oral cavity to gastric mucosa and summarize the possible binding and translocation characteristics. Adhesion is the first step for persistent colonization after the directional motility, and factors related to adhesion are necessary. Outer membrane proteins, such as the blood group antigen binding adhesin (BabA) and the sialic acid binding adhesin (SabA), play pivotal roles in binding to human mucins and cellular surfaces. And this may offer different perspectives on eradication.
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Affiliation(s)
- Hang Yang
- Department of Gastroenterology, West China Hospital, Sichuan University, No.37, Guo Xue Alley, Wu Hou District, Chengdu City, 610041, Sichuan Province, China
| | - Lixia Wang
- The Second Department of Gastroenterology, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, China
| | - Miao Zhang
- Department of Gastroenterology, West China Hospital, Sichuan University, No.37, Guo Xue Alley, Wu Hou District, Chengdu City, 610041, Sichuan Province, China
| | - Bing Hu
- Department of Gastroenterology, West China Hospital, Sichuan University, No.37, Guo Xue Alley, Wu Hou District, Chengdu City, 610041, Sichuan Province, China.
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9
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Duan J, Zhao Q, Wang Y, Chi Z, Li W, Wang X, Liu S, Bi S. The dCache Domain of the Chemoreceptor Tlp1 in Campylobacter jejuni Binds and Triggers Chemotaxis toward Formate. mBio 2023:e0356422. [PMID: 37052512 DOI: 10.1128/mbio.03564-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Abstract
Chemotaxis is an important virulence factor in some enteric pathogens, and it is involved in the pathogenesis and colonization of the host. However, there is limited knowledge regarding the environmental signals that promote chemotactic behavior and the sensing of these signals by chemoreceptors. To date, there is no information on the ligand molecule that directly binds to and is sensed by Campylobacter jejuni Tlp1, which is a chemoreceptor with a dCache-type ligand-binding domain (LBD). dCache (double Calcium channels and chemotaxis receptor) is the largest group of sensory domains in bacteria, but the dCache-type chemoreceptor that directly binds to formate has not yet been discovered. In this study, formate was identified as a direct-binding ligand of C. jejuni Tlp1 with high sensing specificity. We used the strategy of constructing a functional hybrid receptor of C. jejuni Tlp1 and the Escherichia coli chemoreceptor Tar to screen for the potential ligand of Tlp1, with the binding of formate to Tlp1-LBD being verified using isothermal titration calorimetry. Molecular docking and experimental analyses indicated that formate binds to the membrane-proximal pocket of the dCache subdomain. Chemotaxis assays demonstrated that formate elicits robust attractant responses of the C. jejuni strain NCTC 11168, specifically via Tlp1. The chemoattraction effect of formate via Tlp1 promoted the growth of C. jejuni, especially when competing with Tlp1- or CheY-knockout strains. Our study reveals the molecular mechanisms by which C. jejuni mediates chemotaxis toward formate, and, to our knowledge, is the first report on the high-specificity binding of the dCache-type chemoreceptor to formate as well as the physiological role of chemotaxis toward formate. IMPORTANCE Chemotaxis is important for Campylobacter jejuni to colonize favorable niches in the gastrointestinal tract of its host. However, there is still a lack of knowledge about the ligand molecules for C. jejuni chemoreceptors. The dCache-type chemoreceptor, namely, Tlp1, is the most conserved chemoreceptor in C. jejuni strains; however, the direct-binding ligand(s) triggering chemotaxis has not yet been discovered. In the present study, we found that the ligand that binds directly to Tlp1-LBD with high specificity is formate. C. jejuni exhibits robust chemoattraction toward formate, primarily via Tlp1. Tlp1 is the first reported dCache-type chemoreceptor that specifically binds formate and triggers strong chemotaxis. We further demonstrated that the formate-mediated promotion of C. jejuni growth is correlated with Tlp1-mediated chemotaxis toward formate. Our work provides important insights into the mechanism and physiological function of chemotaxis toward formate and will facilitate further investigations into the involvement of microbial chemotaxis in pathogen-host interactions.
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Affiliation(s)
- Jingjing Duan
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Qi Zhao
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Yuxin Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Zhe Chi
- College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Wei Li
- Department of Clinical Laboratory, Qilu Hospital, Shandong University, Jinan, China
| | - Xue Wang
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
| | - Shuangjiang Liu
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Resources, and Environmental Microbiology Research Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shuangyu Bi
- State Key Laboratory of Microbial Biotechnology, Shandong University, Qingdao, China
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10
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Hu S, Ottemann KM. Helicobacter pylori initiates successful gastric colonization by utilizing L-lactate to promote complement resistance. Nat Commun 2023; 14:1695. [PMID: 36973281 PMCID: PMC10042806 DOI: 10.1038/s41467-023-37160-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The complement system has long been appreciated for its role in bloodborne infections, but its activities in other places, including the gastrointestinal tract, remain elusive. Here, we report that complement restricts gastric infection by the pathogen Helicobacter pylori. This bacterium colonized complement-deficient mice to higher levels than wild-type counterparts, particularly in the gastric corpus region. H. pylori uses uptake of the host molecule L-lactate to create a complement-resistant state that relies on blocking the deposition of the active complement C4b component on H. pylori's surface. H. pylori mutants unable to achieve this complement-resistant state have a significant mouse colonization defect that is largely corrected by mutational removal of complement. This work highlights a previously unknown role for complement in the stomach, and has revealed an unrecognized mechanism for microbial-derived complement resistance.
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Affiliation(s)
- Shuai Hu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA
| | - Karen M Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA, 95064, USA.
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11
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Helicobacter pylori Chronic-Stage Inflammation Undergoes Fluctuations That Are Altered in tlpA Mutants. Infect Immun 2023; 91:e0032222. [PMID: 36533917 PMCID: PMC9872690 DOI: 10.1128/iai.00322-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Helicobacter pylori colonizes half of the world's population and is responsible for a significant disease burden by causing gastritis, peptic ulcers, and gastric cancer. The development of host inflammation drives these diseases, but there are still open questions in the field about how H. pylori controls this process. We characterized H. pylori inflammation using an 8-month mouse infection time course and comparison of the wild type (WT) and a previously identified mutant lacking the TlpA chemoreceptor that causes elevated inflammation. Our work shows that H. pylori chronic-stage corpus inflammation undergoes surprising fluctuations, with changes in Th17 and eosinophil numbers. The H. pylori tlpA mutant changed the inflammation temporal characteristics, resulting in different inflammation from the wild type at some time points. tlpA mutants have equivalent total and gland colonization in late-stage infections. During early infection, in contrast, they show elevated gland and total colonization compared to those by WT. Our results suggest the chronic inflammation setting is dynamic and may be influenced by colonization properties of early infection.
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12
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Taha, Elgamoudi BA, Andrianova EP, Haselhorst T, Day CJ, Hartley-Tassell LE, King RM, Najnin T, Zhulin IB, Korolik V. Diverse Sensory Repertoire of Paralogous Chemoreceptors Tlp2, Tlp3, and Tlp4 in Campylobacter jejuni. Microbiol Spectr 2022; 10:e0364622. [PMID: 36374080 PMCID: PMC9769880 DOI: 10.1128/spectrum.03646-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 11/16/2022] Open
Abstract
Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). Here, we describe receptor-ligand interactions of a unique paralogue family of dCache_1 (double Calcium channels and chemotaxis) chemoreceptors: Tlp2, Tlp3, and Tlp4. Phylogenetic analysis revealed that Tlp2, Tlp3, and Tlp4 receptors may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently, and unexpectedly, responded to glycans, as well as multiple organic and amino acids with overlapping specificities. All three Tlps interacted with five monosaccharides and complex glycans, including Lewis's antigens, P antigens, and fucosyl GM1 ganglioside, indicating a potential role in host-pathogen interactions. Analysis of chemotactic motility of single, double, and triple mutants indicated that these chemoreceptors are likely to work together to balance responses to attractants and repellents to modulate chemotaxis in C. jejuni. Molecular docking experiments, in combination with saturation transfer difference nuclear magnetic resonance spectroscopy and competition surface plasmon resonance analysis, illustrated that the ligand-binding domain of Tlp3 possess one major binding pocket with two overlapping, but distinct binding sites able to interact with multiple ligands. A diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions. IMPORTANCE Campylobacter jejuni responds to extracellular stimuli via transducer-like chemoreceptors (Tlps). This remarkable sensory perception mechanism allows bacteria to sense environmental changes and avoid unfavorable conditions or to maneuver toward nutrient sources and host cells. Here, we describe receptor-ligand interactions of a unique paralogue family of chemoreceptors, Tlp2, Tlp3, and Tlp4, that may have arisen through domain duplications, followed by a divergent evolutionary drift, with Tlp3 emerging more recently. Unlike previous reports of ligands interacting with sensory proteins, Tlp2, Tlp3, and Tlp4 responded to many types of chemical compounds, including simple and complex sugars such as those present on human blood group antigens and gangliosides, indicating a potential role in host-pathogen interactions. Diverse sensory repertoire could provide C. jejuni with the ability to modulate responses to attractant and repellent signals and allow for adaptation in host-pathogen interactions.
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Affiliation(s)
- Taha
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Bassam A. Elgamoudi
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Ekaterina P. Andrianova
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Thomas Haselhorst
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Christopher J. Day
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | | | - Rebecca M. King
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Tahria Najnin
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Igor B. Zhulin
- Department of Microbiology and Translational Data Analytics Institute, The Ohio State University, Columbus, Ohio, USA
| | - Victoria Korolik
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
- School of Pharmacy and Medical Science, Griffith University, Gold Coast, Queensland, Australia
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13
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Somiah T, Gebremariam HG, Zuo F, Smirnova K, Jonsson AB. Lactate causes downregulation of Helicobacter pylori adhesin genes sabA and labA while dampening the production of proinflammatory cytokines. Sci Rep 2022; 12:20064. [PMID: 36414643 PMCID: PMC9681763 DOI: 10.1038/s41598-022-24311-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/14/2022] [Indexed: 11/24/2022] Open
Abstract
Chronic inflammation induced by Helicobacter pylori is strongly associated with gastric cancer development, which is influenced by both bacterial virulence and host genetics. The sialic acid-binding adhesin SabA and the MUC5AC-binding adhesin LabA are important H. pylori virulence factors that facilitate adhesion of the bacterium, which is a crucial step in colonization. Lactate utilization has been reported to play a key role in the pathogenicity of different bacterial species. However, this is poorly understood in H. pylori. In this study, we investigated the effect of lactate on H. pylori adhesin gene expression and the regulation of host inflammatory cytokines. We show that the bacterial adhesins SabA and LabA were downregulated at the transcriptional level during incubation of H. pylori with lactate. Downregulation of sabA required the involvement of the two-component system ArsRS, while labA was regulated via the CheA/CheY system, indicating differences in the regulation of these genes in response to lactate. The levels of the proinflammatory cytokines TNF and IL-6 in H. pylori-stimulated macrophages were reduced when lactate was present. Interestingly, glucose did not prevent the secretion of these cytokines. Taken together, our data suggest that lactate affects H. pylori adhesin gene expression and the host response upon infection.
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Affiliation(s)
- Tanvi Somiah
- grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Hanna G. Gebremariam
- grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Fanglei Zuo
- grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Ksenija Smirnova
- grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
| | - Ann-Beth Jonsson
- grid.10548.380000 0004 1936 9377Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20C, 10691 Stockholm, Sweden
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14
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Bacterial chemotaxis in human diseases. Trends Microbiol 2022; 31:453-467. [PMID: 36411201 DOI: 10.1016/j.tim.2022.10.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/16/2022] [Accepted: 10/18/2022] [Indexed: 11/21/2022]
Abstract
To infect and cause disease, bacterial pathogens must localize to specific regions of the host where they possess the metabolic and defensive acumen for survival. Motile flagellated pathogens exercise control over their localization through chemotaxis to direct motility based on the landscape of exogenous nutrients, toxins, and molecular cues sensed within the host. Here, we review advances in understanding the roles chemotaxis plays in human diseases. Chemotaxis drives pathogen colonization to sites of inflammation and injury and mediates fitness advantages through accessing host-derived nutrients from damaged tissue. Injury tropism may worsen clinical outcomes through instigating chronic inflammation and subsequent cancer development. Inhibiting bacterial chemotactic systems could act synergistically with antibacterial medicines for more effective and specific eradication.
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15
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Boyeldieu A, Poli J, Ali Chaouche A, Fierobe H, Giudici‐Orticoni M, Méjean V, Jourlin‐Castelli C. Multiple detection of both attractants and repellents by the dCache-chemoreceptor SO_1056 of Shewanella oneidensis. FEBS J 2022; 289:6752-6766. [PMID: 35668695 PMCID: PMC9796306 DOI: 10.1111/febs.16548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/17/2022] [Accepted: 06/06/2022] [Indexed: 01/01/2023]
Abstract
Chemoreceptors are usually transmembrane proteins dedicated to the detection of compound gradients or signals in the surroundings of a bacterium. After detection, they modulate the activation of CheA-CheY, the core of the chemotactic pathway, to allow cells to move upwards or downwards depending on whether the signal is an attractant or a repellent, respectively. Environmental bacteria such as Shewanella oneidensis harbour dozens of chemoreceptors or MCPs (methyl-accepting chemotaxis proteins). A recent study revealed that MCP SO_1056 of S. oneidensis binds chromate. Here, we show that this MCP also detects an additional attractant (l-malate) and two repellents (nickel and cobalt). The experiments were performed in vivo by the agarose-in-plug technique after overproducing MCP SO_1056 and in vitro, when possible, by submitting the purified ligand-binding domain (LBD) of SO_1056 to a thermal shift assay (TSA) coupled to isothermal titration calorimetry (ITC). ITC assays revealed a KD of 3.4 μm for l-malate and of 47.7 μm for nickel. We conclude that MCP SO_1056 binds attractants and repellents of unrelated composition. The LBD of SO_1056 belongs to the double Cache_1 family and is highly homologous to PctA, a chemoreceptor from Pseudomonas aeruginosa that detects several amino acids. Therefore, LBDs of the same family can bind diverse compounds, confirming that experimental approaches are required to define accurate LBD-binding molecules or signals.
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Affiliation(s)
- Anne Boyeldieu
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance,Present address:
Laboratoire de Microbiologie et de Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS)Université de Toulouse, UPSFrance
| | - Jean‐Pierre Poli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance,Université de Corse Pasquale PaoliCorteFrance
| | - Amine Ali Chaouche
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Henri‐Pierre Fierobe
- Laboratoire de Chimie Bactérienne (LCB, UMR7283), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Marie‐Thérèse Giudici‐Orticoni
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Vincent Méjean
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
| | - Cécile Jourlin‐Castelli
- Laboratoire de Bioénergétique et Ingénierie des Protéines (BIP, UMR7281), Centre National de la Recherche Scientifique, Institut de Microbiologie de la Méditerranée (IMM), Institut Microbiologie, Bioénergies et Biotechnologie (IM2B)Aix Marseille UniversitéFrance
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16
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Tetz V, Tetz G. Novel prokaryotic system employing previously unknown nucleic acids-based receptors. Microb Cell Fact 2022; 21:202. [PMID: 36195904 PMCID: PMC9531389 DOI: 10.1186/s12934-022-01923-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 09/16/2022] [Indexed: 12/26/2022] Open
Abstract
The present study describes a previously unknown universal system that orchestrates the interaction of bacteria with the environment, named the Teazeled receptor system (TR-system). The identical system was recently discovered within eukaryotes. The system includes DNA- and RNA-based molecules named "TezRs", that form receptor's network located outside the membrane, as well as reverse transcriptases and integrases. TR-system takes part in the control of all major aspects of bacterial behavior, such as intra cellular communication, growth, biofilm formation and dispersal, utilization of nutrients including xenobiotics, virulence, chemo- and magnetoreception, response to external factors (e.g., temperature, UV, light and gas content), mutation events, phage-host interaction, and DNA recombination activity. Additionally, it supervises the function of other receptor-mediated signaling pathways. Importantly, the TR-system is responsible for the formation and maintenance of cell memory to preceding cellular events, as well the ability to "forget" preceding events. Transcriptome and biochemical analysis revealed that the loss of different TezRs instigates significant alterations in gene expression and proteins synthesis.
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Affiliation(s)
- Victor Tetz
- Human Microbiology Institute, New York, NY, 10013, USA
| | - George Tetz
- Human Microbiology Institute, New York, NY, 10013, USA.
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17
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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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18
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Signal binding at both modules of its dCache domain enables the McpA chemoreceptor of Bacillus velezensis to sense different ligands. Proc Natl Acad Sci U S A 2022; 119:e2201747119. [PMID: 35858353 PMCID: PMC9303924 DOI: 10.1073/pnas.2201747119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Bacteria have evolved multiple signal transduction systems that permit an adaptation to changing environmental conditions. Chemoreceptor-based signaling cascades are very abundant in bacteria and are among the most complex signaling systems. Currently, our knowledge on the molecular features that determine signal recognition at chemoreceptors is limited. Chemoreceptor McpA of Bacillus velezensis SQR9 has been shown to mediate chemotaxis to a broad range of different ligands. Here we show that its ligand binding domain binds directly 13 chemoattractants. We provide support that organic acids and amino acids bind to the membrane-distal and membrane-proximal module of the dCache domain, respectively, whereas binding of sugars/sugar alcohols occurred at both modules. Structural biology studies combined with site-directed mutagenesis experiments have permitted to identify 10 amino acid residues that play key roles in the recognition of multiple ligands. Residues in membrane-distal and membrane-proximal regions were central for sensing organic acids and amimo acids, respectively, whereas all residues participated in sugars/sugar alcohol sensing. Most characterized chemoreceptors possess a narrow and well-defined ligand spectrum. We propose here a sensing mechanism involving both dCache modules that allows the integration of very diverse signals by a single chemoreceptor.
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19
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Koveal D, Rosen PC, Meyer DJ, Díaz-García CM, Wang Y, Cai LH, Chou PJ, Weitz DA, Yellen G. A high-throughput multiparameter screen for accelerated development and optimization of soluble genetically encoded fluorescent biosensors. Nat Commun 2022; 13:2919. [PMID: 35614105 PMCID: PMC9133083 DOI: 10.1038/s41467-022-30685-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/11/2022] [Indexed: 12/30/2022] Open
Abstract
Genetically encoded fluorescent biosensors are powerful tools used to track chemical processes in intact biological systems. However, the development and optimization of biosensors remains a challenging and labor-intensive process, primarily due to technical limitations of methods for screening candidate biosensors. Here we describe a screening modality that combines droplet microfluidics and automated fluorescence imaging to provide an order of magnitude increase in screening throughput. Moreover, unlike current techniques that are limited to screening for a single biosensor feature at a time (e.g. brightness), our method enables evaluation of multiple features (e.g. contrast, affinity, specificity) in parallel. Because biosensor features can covary, this capability is essential for rapid optimization. We use this system to generate a high-performance biosensor for lactate that can be used to quantify intracellular lactate concentrations. This biosensor, named LiLac, constitutes a significant advance in metabolite sensing and demonstrates the power of our screening approach.
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Affiliation(s)
- Dorothy Koveal
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Paul C Rosen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Dylan J Meyer
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Carlos Manlio Díaz-García
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yongcheng Wang
- Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou, 311121, China
| | - Li-Heng Cai
- Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
- Department of Materials Science and Engineering, University of Virginia, Charlottesville, VA, USA
| | - Peter J Chou
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - David A Weitz
- Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Gary Yellen
- Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
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20
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Gumerov VM, Andrianova EP, Matilla MA, Page KM, Monteagudo-Cascales E, Dolphin AC, Krell T, Zhulin IB. Amino acid sensor conserved from bacteria to humans. Proc Natl Acad Sci U S A 2022; 119:e2110415119. [PMID: 35238638 PMCID: PMC8915833 DOI: 10.1073/pnas.2110415119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 01/10/2022] [Indexed: 11/18/2022] Open
Abstract
SignificanceAmino acids are the building blocks of life and important signaling molecules. Despite their common structure, no universal mechanism for amino acid recognition by cellular receptors is currently known. We discovered a simple motif, which binds amino acids in various receptor proteins from all major life-forms. In humans, this motif is found in subunits of calcium channels that are implicated in pain and neurodevelopmental disorders. Our findings suggest that γ-aminobutyric acid-derived drugs bind to the same motif in human proteins that binds natural ligands in bacterial receptors, thus enabling future improvement of important drugs.
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Affiliation(s)
- Vadim M. Gumerov
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
| | - Ekaterina P. Andrianova
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
| | - Miguel A. Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain
| | - Karen M. Page
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain
| | - Annette C. Dolphin
- Department of Neuroscience, Physiology and Pharmacology, University College London, London WC1E 6BT, United Kingdom
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, E-18008 Granada, Spain
| | - Igor B. Zhulin
- Department of Microbiology, The Ohio State University, Columbus, OH 43210
- Translational Data Analytics Institute, The Ohio State University, Columbus, OH 43210
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21
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Phylogenetic Analysis with Prediction of Cofactor or Ligand Binding for Pseudomonas aeruginosa PAS and Cache Domains. Microbiol Spectr 2021; 9:e0102621. [PMID: 34937179 PMCID: PMC8694187 DOI: 10.1128/spectrum.01026-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PAS domains are omnipresent building blocks of multidomain proteins in all domains of life. Bacteria possess a variety of PAS domains in intracellular proteins and the related Cache domains in periplasmic or extracellular proteins. PAS and Cache domains are predominant in sensory systems, often carry cofactors or bind ligands, and serve as dimerization domains in protein association. To aid our understanding of the wide distribution of these domains, we analyzed the proteome of the opportunistic human pathogen Pseudomonas aeruginosa PAO1 in silico. The ability of this bacterium to survive under different environmental conditions, to switch between planktonic and sessile/biofilm lifestyle, or to evade stresses, notably involves c-di-GMP regulatory proteins or depends on sensory pathways involving multidomain proteins that possess PAS or Cache domains. Maximum likelihood phylogeny was used to group PAS and Cache domains on the basis of amino acid sequence. Conservation of cofactor- or ligand-coordinating amino acids aided by structure-based comparison was used to inform function. The resulting classification presented here includes PAS domains that are candidate binders of carboxylic acids, amino acids, fatty acids, flavin adenine dinucleotide (FAD), 4-hydroxycinnamic acid, and heme. These predictions are put in context to previously described phenotypic data, often generated from deletion mutants. The analysis predicts novel functions for sensory proteins and sheds light on functional diversification in a large set of proteins with similar architecture. IMPORTANCE To adjust to a variety of life conditions, bacteria typically use multidomain proteins, where the modular structure allows functional differentiation. Proteins responding to environmental cues and regulating physiological responses are found in chemotaxis pathways that respond to a wide range of stimuli to affect movement. Environmental cues also regulate intracellular levels of cyclic-di-GMP, a universal bacterial secondary messenger that is a key determinant of bacterial lifestyle and virulence. We study Pseudomonas aeruginosa, an organism known to colonize a broad range of environments that can switch lifestyle between the sessile biofilm and the planktonic swimming form. We have investigated the PAS and Cache domains, of which we identified 101 in 70 Pseudomonas aeruginosa PAO1 proteins, and have grouped these by phylogeny with domains of known structure. The resulting data set integrates sequence analysis and structure prediction to infer ligand or cofactor binding. With this data set, functional predictions for PAS and Cache domain-containing proteins are made.
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22
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Tuan VP, Yahara K, Dung HDQ, Binh TT, Huu Tung P, Tri TD, Thuan NPM, Khien VV, Trang TTH, Phuc BH, Tshibangu-Kabamba E, Matsumoto T, Akada J, Suzuki R, Okimoto T, Kodama M, Murakami K, Yano H, Fukuyo M, Takahashi N, Kato M, Nishiumi S, Azuma T, Ogura Y, Hayashi T, Toyoda A, Kobayashi I, Yamaoka Y. Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates. Microb Genom 2021; 7. [PMID: 34846284 PMCID: PMC8743543 DOI: 10.1099/mgen.0.000680] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWASs) can reveal genetic variations associated with a phenotype in the absence of any hypothesis of candidate genes. The problem of false-positive sites linked with the responsible site might be bypassed in bacteria with a high homologous recombination rate, such as Helicobacter pylori, which causes gastric cancer. We conducted a small-sample GWAS (125 gastric cancer cases and 115 controls) followed by prediction of gastric cancer and control (duodenal ulcer) H. pylori strains. We identified 11 single nucleotide polymorphisms (eight amino acid changes) and three DNA motifs that, combined, allowed effective disease discrimination. They were often informative of the underlying molecular mechanisms, such as electric charge alteration at the ligand-binding pocket, alteration in subunit interaction, and mode-switching of DNA methylation. We also identified three novel virulence factors/oncoprotein candidates. These results provide both defined targets for further informatic and experimental analyses to gain insights into gastric cancer pathogenesis and a basis for identifying a set of biomarkers for distinguishing these H. pylori-related diseases.
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Affiliation(s)
- Vo Phuoc Tuan
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Koji Yahara
- Antimicrobial Resistance ResearchCenter, National Institute of Infectious Diseases, Tokyo, Japan
- *Correspondence: Koji Yahara,
| | | | - Tran Thanh Binh
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Pham Huu Tung
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | - Tran Dinh Tri
- Department of Endoscopy, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Vu Van Khien
- Department of GI Endoscopy, 108 Central Hospital, Hanoi, Vietnam
| | | | - Bui Hoang Phuc
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Microbiology, Cho Ray Hospital, Ho Chi Minh, Vietnam
| | | | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
| | - Tadayoshi Okimoto
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Masaaki Kodama
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Kazunari Murakami
- Department of Gastroenterology, Oita University Faculty of Medicine, Yufu, Oita, Japan
| | - Hirokazu Yano
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Masaki Fukuyo
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Molecular Oncology, Chiba University, Chiba, Japan
| | - Noriko Takahashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
| | - Mototsugu Kato
- Division of Endoscopy, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
- Department of Gastroenterology, National Hospital Organization Hakodate Hospital, Hakodate, Hokkaido, Japan
| | - Shin Nishiumi
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
- Department of Omics Medicine, Hyogo College of Medicine, Hyogo, Japan
| | - Takashi Azuma
- Department of Gastroenterology, Graduate School of Medicine, Kobe University, Chuou-ku, Kobe, Hyogo, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
- Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Faculty of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Atsushi Toyoda
- Advanced GenomicsCenter, National Institute of Genetics, Shizuoka, Japan
| | - Ichizo Kobayashi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Tokyo, Japan
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
- Department of Infectious Diseases, Kyorin University School of Medicine, Mitaka City, Tokyo, Japan
- Research Center for Micro-Nano Technology, Hosei University, Tokyo, Japan
- *Correspondence: Ichizo Kobayashi, ;
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, Oita, Japan
- Department of Medicine, gastroenterology section, Baylor College of Medicine, Houston TX, USA
- *Correspondence: Yoshio Yamaoka,
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23
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Matilla MA, Velando F, Martín-Mora D, Monteagudo-Cascales E, Krell T. A catalogue of signal molecules that interact with sensor kinases, chemoreceptors and transcriptional regulators. FEMS Microbiol Rev 2021; 46:6356564. [PMID: 34424339 DOI: 10.1093/femsre/fuab043] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/10/2021] [Indexed: 12/12/2022] Open
Abstract
Bacteria have evolved many different signal transduction systems that sense signals and generate a variety of responses. Generally, most abundant are transcriptional regulators, sensor histidine kinases and chemoreceptors. Typically, these systems recognize their signal molecules with dedicated ligand-binding domains (LBDs), which, in turn, generate a molecular stimulus that modulates the activity of the output module. There are an enormous number of different LBDs that recognize a similarly diverse set of signals. To give a global perspective of the signals that interact with transcriptional regulators, sensor kinases and chemoreceptors, we manually retrieved information on the protein-ligand interaction from about 1,200 publications and 3D structures. The resulting 811 proteins were classified according to the Pfam family into 127 groups. These data permit a delineation of the signal profiles of individual LBD families as well as distinguishing between families that recognize signals in a promiscuous manner and those that possess a well-defined ligand range. A major bottleneck in the field is the fact that the signal input of many signaling systems is unknown. The signal repertoire reported here will help the scientific community design experimental strategies to identify the signaling molecules for uncharacterised sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Félix Velando
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Elizabet Monteagudo-Cascales
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain
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The dCache Chemoreceptor TlpA of Helicobacter pylori Binds Multiple Attractant and Antagonistic Ligands via Distinct Sites. mBio 2021; 12:e0181921. [PMID: 34340539 PMCID: PMC8406319 DOI: 10.1128/mbio.01819-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The Helicobacter pylori chemoreceptor TlpA plays a role in dampening host inflammation during chronic stomach colonization. TlpA has a periplasmic dCache_1 domain, a structure that is capable of sensing many ligands; however, the only characterized TlpA signals are arginine, bicarbonate, and acid. To increase our understanding of TlpA’s sensing profile, we screened for diverse TlpA ligands using ligand binding arrays. TlpA bound seven ligands with affinities in the low- to middle-micromolar ranges. Three of these ligands, arginine, fumarate, and cysteine, were TlpA-dependent chemoattractants, while the others elicited no response. Molecular docking experiments, site-directed point mutants, and competition surface plasmon resonance binding assays suggested that TlpA binds ligands via both the membrane-distal and -proximal dCache_1 binding pockets. Surprisingly, one of the nonactive ligands, glucosamine, acted as a chemotaxis antagonist, preventing the chemotaxis response to chemoattractant ligands, and acted to block the binding of ligands irrespective of whether they bound the membrane-distal or -proximal dCache_1 subdomains. In total, these results suggest that TlpA senses multiple attractant ligands as well as antagonist ones, an emerging theme in chemotaxis systems.
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25
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Feng H, Fu R, Hou X, Lv Y, Zhang N, Liu Y, Xu Z, Miao Y, Krell T, Shen Q, Zhang R. Chemotaxis of Beneficial Rhizobacteria to Root Exudates: The First Step towards Root-Microbe Rhizosphere Interactions. Int J Mol Sci 2021; 22:ijms22136655. [PMID: 34206311 PMCID: PMC8269324 DOI: 10.3390/ijms22136655] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 06/18/2021] [Accepted: 06/19/2021] [Indexed: 12/28/2022] Open
Abstract
Chemotaxis, the ability of motile bacteria to direct their movement in gradients of attractants and repellents, plays an important role during the rhizosphere colonization by rhizobacteria. The rhizosphere is a unique niche for plant-microbe interactions. Root exudates are highly complex mixtures of chemoeffectors composed of hundreds of different compounds. Chemotaxis towards root exudates initiates rhizobacteria recruitment and the establishment of bacteria-root interactions. Over the last years, important progress has been made in the identification of root exudate components that play key roles in the colonization process, as well as in the identification of the cognate chemoreceptors. In the first part of this review, we summarized the roles of representative chemoeffectors that induce chemotaxis in typical rhizobacteria and discussed the structure and function of rhizobacterial chemoreceptors. In the second part we reviewed findings on how rhizobacterial chemotaxis and other root-microbe interactions promote the establishment of beneficial rhizobacteria-plant interactions leading to plant growth promotion and protection of plant health. In the last part we identified the existing gaps in the knowledge and discussed future research efforts that are necessary to close them.
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Affiliation(s)
- Haichao Feng
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Ruixin Fu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Xueqin Hou
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Yu Lv
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Nan Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Yunpeng Liu
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zhihui Xu
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Youzhi Miao
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain;
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
| | - Ruifu Zhang
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-Based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing 210095, China; (H.F.); (R.F.); (X.H.); (Y.L.); (N.Z.); (Z.X.); (Y.M.); (Q.S.)
- Key Laboratory of Microbial Resources Collection and Preservation, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
- Correspondence: ; Tel.: +86-025-84396477
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26
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Matilla MA, Ortega Á, Krell T. The role of solute binding proteins in signal transduction. Comput Struct Biotechnol J 2021; 19:1786-1805. [PMID: 33897981 PMCID: PMC8050422 DOI: 10.1016/j.csbj.2021.03.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
The solute binding proteins (SBPs) of prokaryotes are present in the extracytosolic space. Although their primary function is providing substrates to transporters, SBPs also stimulate different signaling proteins, including chemoreceptors, sensor kinases, diguanylate cyclases/phosphodiesterases and Ser/Thr kinases, thereby causing a wide range of responses. While relatively few such systems have been identified, several pieces of evidence suggest that SBP-mediated receptor activation is a widespread mechanism. (1) These systems have been identified in Gram-positive and Gram-negative bacteria and archaea. (2) There is a structural diversity in the receptor domains that bind SBPs. (3) SBPs belonging to thirteen different families interact with receptor ligand binding domains (LBDs). (4) For the two most abundant receptor LBD families, dCache and four-helix-bundle, there are different modes of interaction with SBPs. (5) SBP-stimulated receptors carry out many different functions. The advantage of SBP-mediated receptor stimulation is attributed to a strict control of SBP levels, which allows a precise adjustment of the systeḿs sensitivity. We have compiled information on the effect of ligands on the transcript/protein levels of their cognate SBPs. In 87 % of the cases analysed, ligands altered SBP expression levels. The nature of the regulatory effect depended on the ligand family. Whereas inorganic ligands typically downregulate SBP expression, an upregulation was observed in response to most sugars and organic acids. A major unknown is the role that SBPs play in signaling and in receptor stimulation. This review attempts to summarize what is known and to present new information to narrow this gap in knowledge.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Regional Campus of International Excellence "Campus Mare Nostrum", Murcia, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada 18008, Spain
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27
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Antani JD, Sumali AX, Lele TP, Lele PP. Asymmetric random walks reveal that the chemotaxis network modulates flagellar rotational bias in Helicobacter pylori. eLife 2021; 10:63936. [PMID: 33493107 PMCID: PMC7834020 DOI: 10.7554/elife.63936] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 01/12/2021] [Indexed: 12/14/2022] Open
Abstract
The canonical chemotaxis network modulates the bias for a particular direction of rotation in the bacterial flagellar motor to help the cell migrate toward favorable chemical environments. How the chemotaxis network in Helicobacter pylori modulates flagellar functions is unknown, which limits our understanding of chemotaxis in this species. Here, we determined that H. pylori swim faster (slower) whenever their flagella rotate counterclockwise (clockwise) by analyzing their hydrodynamic interactions with bounding surfaces. This asymmetry in swimming helped quantify the rotational bias. Upon exposure to a chemo-attractant, the bias decreased and the cells tended to swim exclusively in the faster mode. In the absence of a key chemotaxis protein, CheY, the bias was zero. The relationship between the reversal frequency and the rotational bias was unimodal. Thus, H. pylori’s chemotaxis network appears to modulate the probability of clockwise rotation in otherwise counterclockwise-rotating flagella, similar to the canonical network.
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Affiliation(s)
- Jyot D Antani
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Anita X Sumali
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Tanmay P Lele
- Department of Biomedical Engineering, Texas A&M University, College Station, TX 77840, College Station, TX 77840, United States.,Department of Translational Medical Sciences, Texas A&M University, Houston, TX 77030, United States
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
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28
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Gasperotti AF, Herrera Seitz MK, Balmaceda RS, Prosa LM, Jung K, Studdert CA. Direct binding of benzoate derivatives to two chemoreceptors with Cache sensor domains in Halomonas titanicae KHS3. Mol Microbiol 2020; 115:672-683. [PMID: 33098326 DOI: 10.1111/mmi.14630] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/15/2020] [Accepted: 10/17/2020] [Indexed: 02/06/2023]
Abstract
Halomonas titanicae KHS3, isolated from a hydrocarbon-contaminated sea harbor in Argentina, is able to grow on aromatic hydrocarbons and displays chemotaxis toward those compounds. This behavior might contribute to the efficiency of its degradation capacity. Using high throughput screening, we identified two chemoreceptors (Htc1 and Htc2) that bind benzoate derivatives and other organic acids. Whereas Htc1 has a high affinity for benzoate (Kd 112 µM) and 2-hydroxybenzoate (Kd 83 µM), Htc2 binds 2-hydroxybenzoate with low affinity (Kd 3.25 mM), and also C3/C4 dicarboxylates. Both chemoreceptors are able to trigger a chemotactic response of E. coli cells to the specific ligands. A H. titanicae htc1 mutant has reduced chemotaxis toward benzoate, and is complemented upon expression of the corresponding receptor. Both chemoreceptors have a Cache-type sensor domain, double (Htc1) or single (Htc2), and their ability to bind aromatic compounds is reported here for the first time.
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Affiliation(s)
- Ana F Gasperotti
- Instituto de Investigaciones Biológicas, CONICET - Universidad Nacional de Mar del Plata, Mar del Plata, Argentina.,Department of Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - M Karina Herrera Seitz
- Instituto de Investigaciones Biológicas, CONICET - Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Rocío S Balmaceda
- Instituto de Agrobiotecnología del Litoral, CONICET - Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Luciano M Prosa
- Instituto de Investigaciones Biológicas, CONICET - Universidad Nacional de Mar del Plata, Mar del Plata, Argentina
| | - Kirsten Jung
- Department of Microbiology, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Claudia A Studdert
- Instituto de Agrobiotecnología del Litoral, CONICET - Universidad Nacional del Litoral, Santa Fe, Argentina
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29
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Fulgione A, Papaianni M, Cuomo P, Paris D, Romano M, Tuccillo C, Palomba L, Medaglia C, De Seta M, Esposito N, Motta A, Iannelli A, Iannelli D, Capparelli R. Interaction between MyD88, TIRAP and IL1RL1 against Helicobacter pylori infection. Sci Rep 2020; 10:15831. [PMID: 32985578 PMCID: PMC7522988 DOI: 10.1038/s41598-020-72974-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
The Toll-interleukin 1 receptor superfamily includes the genes interleukin 1 receptor-like 1 (IL1RL1), Toll like receptors (TLRs), myeloid differentiation primary-response 88 (MyD88), and MyD88 adaptor-like (TIRAP). This study describes the interaction between MyD88, TIRAP and IL1RL1 against Helicobacter pylori infection. Cases and controls were genotyped at the polymorphic sites MyD88 rs6853, TIRAP rs8177374 and IL1RL1 rs11123923. The results show that specific combinations of IL1RL1-TIRAP (AA-CT; P: 2,8 × 10–17) and MyD88-TIRAP-IL1RL1 (AA-CT-AA; P: 1,4 × 10–8) – but not MyD88 alone—act synergistically against Helicobacter pylori. Nuclear magnetic resonance (NMR) clearly discriminates cases from controls by highlighting significantly different expression levels of several metabolites (tyrosine, tryptophan, phenylalanine, branched-chain amino acids, short chain fatty acids, glucose, sucrose, urea, etc.). NMR also identifies the following dysregulated metabolic pathways associated to Helicobacter pylori infection: phenylalanine and tyrosine metabolism, pterine biosynthesis, starch and sucrose metabolism, and galactose metabolism. Furthermore, NMR discriminates between the cases heterozygous at the IL1RL1 locus from those homozygous at the same locus. Heterozygous patients are characterized by high levels of lactate, and IL1RL1—both associated with anti-inflammatory activity—and low levels of the pro-inflammatory molecules IL-1β, TNF-α, COX-2, and IL-6.
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Affiliation(s)
- Andrea Fulgione
- Department of Agriculture Sciences, University of Naples "Federico II", Via Università, 100, 80055, Portici, Naples, Italy.,Istituto Zooprofilattico Sperimentale del Mezzogiorno, Via Salute, 2, 80055, Portici, Naples, Italy
| | - Marina Papaianni
- Department of Agriculture Sciences, University of Naples "Federico II", Via Università, 100, 80055, Portici, Naples, Italy
| | - Paola Cuomo
- Department of Agriculture Sciences, University of Naples "Federico II", Via Università, 100, 80055, Portici, Naples, Italy
| | - Debora Paris
- Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Marco Romano
- Hepatogastroenterology Unit, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", via Pansini, 5, 80131, Naples, Italy
| | - Concetta Tuccillo
- Hepatogastroenterology Unit, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", via Pansini, 5, 80131, Naples, Italy
| | - Letizia Palomba
- Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Via Santa Chiara, 27, 61029, Urbino, Italy
| | - Chiara Medaglia
- Department of Microbiology and Molecular Medicine, University of Geneva Medical School, Rue du Général-Dufour, 24, 1211, Genève 4, Switzerland
| | | | - Nicolino Esposito
- Fondazione Evangelica Betania, Via Argine, 604, 80147, Naples, Italy
| | - Andrea Motta
- Institute of Biomolecular Chemistry, National Research Council, Via Campi Flegrei, 34, 80078, Pozzuoli, Naples, Italy
| | - Antonio Iannelli
- Université Côte D'Azur, Campus Valrose, Batiment L, Avenue de Valrose, 28, 06108, Nice CEDEX 2, France.,Centre Hospitalier Universitaire de Nice - Digestive Surgery and Liver Transplantation Unit, Archet 2 Hospital, Route Saint-Antoine de Ginestière 151, CS 23079, 06202, Nice CEDEX 3, France.,Inserm, U1065, Team 8 "Hepatic Complications of Obesity and Alcohol", Route Saint Antoine de Ginestière 151, BP 2 3194, 06204, Nice CEDEX 3, France
| | - Domenico Iannelli
- Department of Agriculture Sciences, University of Naples "Federico II", Via Università, 100, 80055, Portici, Naples, Italy.
| | - Rosanna Capparelli
- Department of Agriculture Sciences, University of Naples "Federico II", Via Università, 100, 80055, Portici, Naples, Italy
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30
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Pathways of Gastric Carcinogenesis, Helicobacter pylori Virulence and Interactions with Antioxidant Systems, Vitamin C and Phytochemicals. Int J Mol Sci 2020; 21:ijms21176451. [PMID: 32899442 PMCID: PMC7503565 DOI: 10.3390/ijms21176451] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 08/21/2020] [Accepted: 08/31/2020] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori is a class one carcinogen which causes chronic atrophic gastritis, gastric intestinal metaplasia, dysplasia and adenocarcinoma. The mechanisms by which H. pylori interacts with other risk and protective factors, particularly vitamin C in gastric carcinogenesis are complex. Gastric carcinogenesis includes metabolic, environmental, epigenetic, genomic, infective, inflammatory and oncogenic pathways. The molecular classification of gastric cancer subtypes has revolutionized the understanding of gastric carcinogenesis. This includes the tumour microenvironment, germline mutations, and the role of Helicobacter pylori bacteria, Epstein Barr virus and epigenetics in somatic mutations. There is evidence that ascorbic acid, phytochemicals and endogenous antioxidant systems can modify the risk of gastric cancer. Gastric juice ascorbate levels depend on dietary intake of ascorbic acid but can also be decreased by H. pylori infection, H. pylori CagA secretion, tobacco smoking, achlorhydria and chronic atrophic gastritis. Ascorbic acid may be protective against gastric cancer by its antioxidant effect in gastric cytoprotection, regenerating active vitamin E and glutathione, inhibiting endogenous N-nitrosation, reducing toxic effects of ingested nitrosodimethylamines and heterocyclic amines, and preventing H. pylori infection. The effectiveness of such cytoprotection is related to H. pylori strain virulence, particularly CagA expression. The role of vitamin C in epigenetic reprogramming in gastric cancer is still evolving. Other factors in conjunction with vitamin C also play a role in gastric carcinogenesis. Eradication of H. pylori may lead to recovery of vitamin C secretion by gastric epithelium and enable regression of premalignant gastric lesions, thereby interrupting the Correa cascade of gastric carcinogenesis.
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Wang W, Chen J, Zhu Y, Feng F. Activity prediction of aminoquinoline drugs based on deep learning. Biotechnol Appl Biochem 2020; 68:927-937. [PMID: 32865272 DOI: 10.1002/bab.2016] [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: 05/25/2020] [Accepted: 08/23/2020] [Indexed: 11/09/2022]
Abstract
The results of the traditional prediction method for the activity of aminoquinoline drugs are inaccurate, so the prediction method for the activity of aminoquinoline drugs based on the deep learning is designed. The molecular holographic distance vector method was used to describe the molecular structure of 40 aminoquinoline compounds, and the principal component regression method was used for modeling and quantitative analysis. Two methods were used to predict the activity of aminoquinoline drugs. The correlation coefficients of the results obtained from the two sets of activity data and the cross test were 0.9438 and 0.9737, and 0.8305 and 0.9098, respectively. Our data suggested that method for the activity prediction of aminoquinoline drugs based on deep learning studied in this paper can better predict the activity of aminoquinoline drugs and provide a strong basis for the activity prediction of aminoquinoline drugs.
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Affiliation(s)
- Wenle Wang
- Department of Mechanical and Electrical Engineering, Jiangsu Food & Pharmaceutical Science College, Huai'an, China
| | - Jinquan Chen
- Department of Mechanical and Electrical Engineering, Jiangsu Food & Pharmaceutical Science College, Huai'an, China
| | - Yujie Zhu
- Department of Mechanical and Electrical Engineering, Jiangsu Food & Pharmaceutical Science College, Huai'an, China
| | - Feng Feng
- Department of Mechanical and Electrical Engineering, Jiangsu Food & Pharmaceutical Science College, Huai'an, China
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32
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Matilla MA, Martín-Mora D, Krell T. The use of isothermal titration calorimetry to unravel chemotactic signalling mechanisms. Environ Microbiol 2020; 22:3005-3019. [PMID: 32329116 DOI: 10.1111/1462-2920.15035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/13/2022]
Abstract
Chemotaxis is based on the action of chemosensory pathways and is typically initiated by the recognition of chemoeffectors at chemoreceptor ligand-binding domains (LBD). Chemosensory signalling is highly complex; aspect that is not only reflected in the intricate interaction between many signalling proteins but also in the fact that bacteria frequently possess multiple chemosensory pathways and often a large number of chemoreceptors, which are mostly of unknown function. We review here the usefulness of isothermal titration calorimetry (ITC) to study this complexity. ITC is the gold standard for studying binding processes due to its precision and sensitivity, as well as its capability to determine simultaneously the association equilibrium constant, enthalpy change and stoichiometry of binding. There is now evidence that members of all major LBD families can be produced as individual recombinant proteins that maintain their ligand-binding properties. High-throughput screening of these proteins using thermal shift assays offer interesting initial information on chemoreceptor ligands, providing the basis for microcalorimetric analyses and microbiological experimentation. ITC has permitted the identification and characterization of many chemoreceptors with novel specificities. This ITC-based approach can also be used to identify signal molecules that stimulate members of other families of sensor proteins.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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33
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Khan MF, Machuca MA, Rahman MM, Koç C, Norton RS, Smith BJ, Roujeinikova A. Structure-Activity Relationship Study Reveals the Molecular Basis for Specific Sensing of Hydrophobic Amino Acids by the Campylobacter jejuni Chemoreceptor Tlp3. Biomolecules 2020; 10:biom10050744. [PMID: 32403336 PMCID: PMC7277094 DOI: 10.3390/biom10050744] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/04/2020] [Accepted: 05/08/2020] [Indexed: 12/16/2022] Open
Abstract
Chemotaxis is an important virulence factor of the foodborne pathogen Campylobacter jejuni. Inactivation of chemoreceptor Tlp3 reduces the ability of C. jejuni to invade human and chicken cells and to colonise the jejunal mucosa of mice. Knowledge of the structure of the ligand-binding domain (LBD) of Tlp3 in complex with its ligands is essential for a full understanding of the molecular recognition underpinning chemotaxis. To date, the only structure in complex with a signal molecule is Tlp3 LBD bound to isoleucine. Here, we used in vitro and in silico screening to identify eight additional small molecules that signal through Tlp3 as attractants by directly binding to its LBD, and determined the crystal structures of their complexes. All new ligands (leucine, valine, α-amino-N-valeric acid, 4-methylisoleucine, β-methylnorleucine, 3-methylisoleucine, alanine, and phenylalanine) are nonpolar amino acids chemically and structurally similar to isoleucine. X-ray crystallographic analysis revealed the hydrophobic side-chain binding pocket and conserved protein residues that interact with the ammonium and carboxylate groups of the ligands determine the specificity of this chemoreceptor. The uptake of hydrophobic amino acids plays an important role in intestinal colonisation by C. jejuni, and our study suggests that C. jejuni seeks out hydrophobic amino acids using chemotaxis.
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Affiliation(s)
- Mohammad F. Khan
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia; (M.F.K.); (M.A.M.); (M.M.R.); (C.K.)
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mayra A. Machuca
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia; (M.F.K.); (M.A.M.); (M.M.R.); (C.K.)
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mohammad M. Rahman
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia; (M.F.K.); (M.A.M.); (M.M.R.); (C.K.)
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Cengiz Koç
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia; (M.F.K.); (M.A.M.); (M.M.R.); (C.K.)
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia;
- ARC Centre for Fragment-Based Design, Monash University, Parkville, Victoria 3052, Australia
| | - Brian J. Smith
- La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria 3086, Australia;
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Clayton, Victoria 3800, Australia; (M.F.K.); (M.A.M.); (M.M.R.); (C.K.)
- Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- Correspondence: ; Tel.: +61-399029294
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Ud-Din AIMS, Khan MF, Roujeinikova A. Broad Specificity of Amino Acid Chemoreceptor CtaA of Pseudomonas fluorescens Is Afforded by Plasticity of Its Amphipathic Ligand-Binding Pocket. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2020; 33:612-623. [PMID: 31909676 DOI: 10.1094/mpmi-10-19-0277-r] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Motile bacteria follow gradients of nutrients or other environmental cues. Many bacterial chemoreceptors that sense exogenous amino acids contain a double Cache (dCache; calcium channels and chemotaxis receptors) ligand-binding domain (LBD). A growing number of studies suggest that broad-specificity dCache-type receptors that sense more than one amino acid are common. Here, we present an investigation into the mechanism by which the dCache LBD of the chemoreceptor CtaA from a plant growth-promoting rhizobacterium, Pseudomonas fluorescens, recognizes several chemically distinct amino acids. We established that amino acids that signal by directly binding to the CtaA LBD include ones with aliphatic (l-alanine, l-proline, l-leucine, l-isoleucine, l-valine), small polar (l-serine), and large charged (l-arginine) side chains. We determined the structure of CtaA LBD in complex with different amino acids, revealing that its ability to recognize a range of structurally and chemically distinct amino acids is afforded by its easily accessible plastic pocket, which can expand or contract according to the size of the ligand side chain. The amphipathic character of the pocket enables promiscuous interactions with both polar and nonpolar amino acids. The results not only clarify the means by which various amino acids are recognized by CtaA but also reveal that a conserved mobile lid over the ligand-binding pocket adopts the same conformation in all complexes, consistent with this being an important and invariant part of the signaling mechanism.
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Affiliation(s)
- Abu I M S Ud-Din
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Australia, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Mohammad F Khan
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Australia, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
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Structural basis of the binding affinity of chemoreceptors Mlp24p and Mlp37p for various amino acids. Biochem Biophys Res Commun 2020; 523:233-238. [PMID: 31862138 DOI: 10.1016/j.bbrc.2019.12.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 12/12/2019] [Accepted: 12/12/2019] [Indexed: 10/25/2022]
Abstract
Environmental sensing is crucial for bacterial survival and pathogenicity. Bacteria sense environmental chemicals using chemoreceptor proteins, such as Methyl-accepting Chemotaxis Proteins (MCPs). Vibrio cholerae, the etiological agent of cholera, has at least 44 chemoreceptor proteins homologous to MCP-Like Proteins (MLPs). Mlp24 and Mlp37 are dCACHE type chemoreceptors that senses various amino acids. Mlp24 is important for cholera toxin production, whereas Mlp37 is related to biofilm formation. The periplasmic ligand binding regions of Mlp24 and Mlp37 (Mlp24p and Mlp37p, respectively) share similar amino acid sequences, tertiary and quaternary structures, and a common mechanism for the ligand amino acid backbone recognition. However, Mlp37p recognizes various l-amino acids and taurine with similar affinity whereas Mlp24p shows different binding affinities for various l-amino acids and does not bind taurine. Here we solved the crystal structure of Mlp37p in complex with l-arginine and compared it with previously determined structures of Mlp37p, Mlp24p and their ligand complexes. We found that Mlp37p changes the conformation of the loop that forms the upper wall of the ligand binding pocket according to size and shape of the ligand, and thereby show similar affinity for various ligands.
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36
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The Mechanism of Bidirectional pH Taxis in Bacillus subtilis. J Bacteriol 2020; 202:JB.00491-19. [PMID: 31685537 DOI: 10.1128/jb.00491-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 10/30/2019] [Indexed: 01/19/2023] Open
Abstract
We investigated pH taxis in Bacillus subtilis This bacterium was found to perform bidirectional taxis in response to external pH gradients, enabling it to preferentially migrate to neutral environments. We next investigated the chemoreceptors involved in sensing pH gradients. We identified four chemoreceptors involved in sensing pH: McpA and TlpA for sensing acidic environments and McpB and TlpB for sensing alkaline ones. In addition, TlpA was found to also weakly sense alkaline environments. By analyzing chimeras between McpA and TlpB, the principal acid- and base-sensing chemoreceptors, we identified four critical amino acid residues-Thr199, Gln200, His273, and Glu274 on McpA and Lys199, Glu200, Gln273, and Asp274 on TlpB-involved in sensing pH. Swapping these four residues between McpA and TlpB converted the former into a base receptor and the latter into an acid receptor. Based on the results, we propose that disruption of hydrogen bonding between the adjacent residues upon pH changes induces signaling. Collectively, our results further our understanding of chemotaxis in B. subtilis and provide a new model for pH sensing in bacteria.IMPORTANCE Many bacteria can sense the pH in their environment and then use this information to direct their movement toward more favorable locations. In this study, we investigated the pH sensing mechanism in Bacillus subtilis This bacterium preferentially migrates to neutral environments. It employs four chemoreceptors to sense pH. Two are involved in sensing acidic environments, and two are involved in sensing alkaline ones. To identify the mechanism for pH sensing, we constructed receptor chimeras of acid- and base-sensing chemoreceptors. By analyzing the responses of these chimeric receptors, we were able to identify four critical amino acid residues involved in pH sensing and propose a model for the pH sensing mechanism in B. subtilis.
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37
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Abstract
Many bacteria possess a large number of chemoreceptors that recognize a variety of different compounds. More than 60% of the genomes analyzed in this study contain paralogous chemoreceptors, suggesting that they emerge with high frequency. We provide first insight on how paralogous receptors have evolved and show that two chemoreceptors with a narrow ligand range have evolved from an ancestral protein with a broad chemoeffector spectrum. Protein structures show that multiple changes in the ligand-binding site account for the differences in the ligand spectrum. This work lays the ground for further studies aimed at establishing whether the principles of ligand-binding evolution reported here can be generalized for a wider spectrum of sensory proteins in bacteria. Chemoreceptor-based signaling pathways are among the major modes of bacterial signal transduction, and Pseudomonas aeruginosa PAO1 is an important model to study their function. Of the 26 chemoreceptors of this strain, PctA has a broad ligand range and responds to most of the proteinogenic amino acids, whereas PctB and PctC have a much narrower range and show strong ligand preference for l-glutamine and γ-aminobutyrate, respectively. Using several comparative genomics approaches, we show that these receptors are paralogs: pctA gene duplication in the common ancestor of the genus Pseudomonas led to pctC, whereas pctB originated through another, independent pctA duplication in the common ancestor of P. aeruginosa. Thus, the broad-range amino acid chemoreceptor was evolutionarily older, and chemoreceptors that complemented “missing” amino acid sensing abilities arose later in specific Pseudomonas lineages. Using comparative sequence analysis, newly solved crystal structures of PctA, PctB, and PctC ligand-binding domains, and their molecular dynamics simulations, we identified a conserved amino acid recognition motif and changes in the ligand-binding pocket that led to novel ligand specificities. In addition, we determined major forces driving the evolution of this group of chemoreceptors.
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38
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Sweeney EG, Perkins A, Kallio K, James Remington S, Guillemin K. Structures of the ligand-binding domain of Helicobacter pylori chemoreceptor TlpA. Protein Sci 2019; 27:1961-1968. [PMID: 30171638 DOI: 10.1002/pro.3503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 12/21/2022]
Abstract
Bacteria use chemoreceptor proteins to sense and navigate their chemical environments. The most common class of chemoreceptors are transmembrane proteins that sense chemical cues through binding of a small-molecule ligand to a periplasmic domain, which modulates the receptor's ability to stimulate reversal of the cell's flagella motors. The prevalent gastric pathogen Helicobacter pylori uses such membrane-bound chemoreceptors, called transducer-like proteins (Tlp), to colonize and persist within the stomach. TlpA has been implicated in sensing arginine, bicarbonate, and acid, but no experimentally determined protein structures of TlpA were available to better understand ligand binding and signal transduction. Here, we report three crystal structures of the periplasmic portion of TlpA, which contains tandem PAS/Cache domains, similar to a recently published structure of the lactate-sensing chemoreceptor TlpC from H. pylori. These structures are the first to show a tandem PAS/Cache-form chemoreceptor in its native homo dimer oligomer, and we identify residues that are key contributers to the dimer interface. We performed sequence analyses to identify TlpA and TlpC homologs and used residue conservation among these homologs to implicate regions important for the general tandem PAS/Cache fold, and residues specific to TlpA function. Comparisons with TlpC show that despite high similarity across the general structure, TlpA lacks the residues required to bind lactate, and instead contains a pocket almost entirely hydrophobic in nature.
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Affiliation(s)
- Emily G Sweeney
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403
| | - Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403
| | - Karen Kallio
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403
| | | | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, 97403
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39
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Helicobacter pylori Uses the TlpB Receptor To Sense Sites of Gastric Injury. Infect Immun 2019; 87:IAI.00202-19. [PMID: 31262979 DOI: 10.1128/iai.00202-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/18/2019] [Indexed: 01/24/2023] Open
Abstract
Helicobacter pylori is a pathogen that chronically colonizes the stomachs of approximately half of the world's population and contributes to the development of gastric inflammation. We demonstrated previously in vivo that H. pylori uses motility to preferentially colonize injury sites in the mouse stomach. However, the chemoreceptor responsible for sensing gastric injury has not yet been identified. In this study, we utilized murine gastric organoids (gastroids) and mutant H. pylori strains to investigate the components necessary for H. pylori chemotaxis. High-intensity 730-nm light (two-photon photodamage) was used to cause single-cell damage in gastroids, and repair of the damage was monitored over time; complete repair occurred within ∼10 min in uninfected gastroids. Wild-type H. pylori accumulated at the damage site after gastric damage induction. In contrast, mutants lacking motility (ΔmotB) or chemotaxis (ΔcheY) did not accumulate at the injury site. Using mutants lacking individual chemoreceptors, we found that only TlpB was required for H. pylori accumulation, while TlpA, TlpC, and TlpD were dispensable. All strains that were able to accumulate at the damage site limited repair. When urea (an identified chemoattractant sensed by TlpB) was microinjected into the gastroid lumen, it prevented the accumulation of H. pylori at damage sites. Overall, our findings demonstrate that H. pylori colonizes and limits repair at damage sites via chemotactic motility that requires the TlpB chemoreceptor to sense signals generated by gastric epithelial cells.
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Perkins A, Tudorica DA, Amieva MR, Remington SJ, Guillemin K. Helicobacter pylori senses bleach (HOCl) as a chemoattractant using a cytosolic chemoreceptor. PLoS Biol 2019; 17:e3000395. [PMID: 31465435 PMCID: PMC6715182 DOI: 10.1371/journal.pbio.3000395] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022] Open
Abstract
The gastric pathogen Helicobacter pylori requires a noncanonical cytosolic chemoreceptor transducer-like protein D (TlpD) for efficient colonization of the mammalian stomach. Here, we reconstituted a complete chemotransduction signaling complex in vitro with TlpD and the chemotaxis (Che) proteins CheW and CheA, enabling quantitative assays for potential chemotaxis ligands. We found that TlpD is selectively sensitive at micromolar concentrations to bleach (hypochlorous acid, HOCl), a potent antimicrobial produced by neutrophil myeloperoxidase during inflammation. HOCl acts as a chemoattractant by reversibly oxidizing a conserved cysteine within a 3His/1Cys Zn-binding motif in TlpD that inactivates the chemotransduction signaling complex. We found that H. pylori is resistant to killing by millimolar concentrations of HOCl and responds to HOCl in the micromolar range by increasing its smooth-swimming behavior, leading to chemoattraction to HOCl sources. We show related protein domains from Salmonella enterica and Escherichia coli possess similar reactivity toward HOCl. We propose that this family of proteins enables host-associated bacteria to sense sites of tissue inflammation, a strategy that H. pylori uses to aid in colonizing and persisting in inflamed gastric tissue.
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Affiliation(s)
- Arden Perkins
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Dan A. Tudorica
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Manuel R. Amieva
- Departments of Pediatrics and of Microbiology & Immunology, Stanford University School of Medicine, Stanford, California, United States of America
| | - S. James Remington
- Department of Physics, University of Oregon, Eugene, Oregon, United States of America
| | - Karen Guillemin
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, United States of America
- Humans and the Microbiome Program, CIFAR, Toronto, Ontario, Canada
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41
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Ailloud F, Didelot X, Woltemate S, Pfaffinger G, Overmann J, Bader RC, Schulz C, Malfertheiner P, Suerbaum S. Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps. Nat Commun 2019; 10:2273. [PMID: 31118420 PMCID: PMC6531487 DOI: 10.1038/s41467-019-10050-1] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/10/2019] [Indexed: 02/07/2023] Open
Abstract
The human pathogen Helicobacter pylori displays extensive genetic diversity. While H. pylori is known to evolve during infection, population dynamics inside the gastric environment have not been extensively investigated. Here we obtained gastric biopsies from multiple stomach regions of 16 H. pylori-infected adults, and analyze the genomes of 10 H. pylori isolates from each biopsy. Phylogenetic analyses suggest location-specific evolution and bacterial migration between gastric regions. Migration is significantly more frequent between the corpus and the fundus than with the antrum, suggesting that physiological differences between antral and oxyntic mucosa contribute to spatial partitioning of H. pylori populations. Associations between H. pylori gene polymorphisms and stomach niches suggest that chemotaxis, regulatory functions and outer membrane proteins contribute to specific adaptation to the antral and oxyntic mucosa. Moreover, we show that antibiotics can induce severe population bottlenecks and likely play a role in shaping the population structure of H. pylori. Helicobacter pylori, a bacterial pathogen that infects human stomachs, has high genetic diversity across hosts. Here, Ailloud et al. reveal genetic structuring of H. pylori populations among different stomach regions of individual hosts and find signals of genetic associations with stomach region.
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Affiliation(s)
- Florent Ailloud
- Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336, Munich, Germany.,Institute of Medical Microbiology and Hospital Epidemiology, MHH Hannover Medical School, 30625, Hannover, Germany.,DZIF German Center for Infection Research, Munich Site, Munich, Germany.,DZIF German Center for Infection Research, Hannover-Braunschweig Site, Hannover, Germany
| | - Xavier Didelot
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK.,Department of Statistics, University of Warwick, Coventry, CV4 7AL, UK
| | - Sabrina Woltemate
- Institute of Medical Microbiology and Hospital Epidemiology, MHH Hannover Medical School, 30625, Hannover, Germany
| | - Gudrun Pfaffinger
- Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336, Munich, Germany
| | - Jörg Overmann
- DZIF German Center for Infection Research, Hannover-Braunschweig Site, Hannover, Germany.,Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany
| | - Ruth Christiane Bader
- Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336, Munich, Germany.,National Reference Center for Helicobacter pylori, Max von Pettenkofer Institute, 80336, Munich, Germany
| | - Christian Schulz
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University, 39106, Magdeburg, Germany.,Department of Medicine 2, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto von Guericke University, 39106, Magdeburg, Germany.,Department of Medicine 2, University Hospital, LMU Munich, 81377, Munich, Germany
| | - Sebastian Suerbaum
- Department of Medical Microbiology and Hospital Epidemiology, Max von Pettenkofer Institute, Faculty of Medicine, LMU Munich, 80336, Munich, Germany. .,Institute of Medical Microbiology and Hospital Epidemiology, MHH Hannover Medical School, 30625, Hannover, Germany. .,DZIF German Center for Infection Research, Munich Site, Munich, Germany. .,DZIF German Center for Infection Research, Hannover-Braunschweig Site, Hannover, Germany. .,National Reference Center for Helicobacter pylori, Max von Pettenkofer Institute, 80336, Munich, Germany.
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42
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Calcium Ions Modulate Amino Acid Sensing of the Chemoreceptor Mlp24 of Vibrio cholerae. J Bacteriol 2019; 201:JB.00779-18. [PMID: 30745373 DOI: 10.1128/jb.00779-18] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 02/01/2019] [Indexed: 12/16/2022] Open
Abstract
Bacteria sense environmental chemicals using chemosensor proteins, most of which are present in the cytoplasmic membrane. Canonical chemoreceptors bind their specific ligands in their periplasmic domain, and the ligand binding creates a molecular stimulus that is transmitted into the cytoplasm, leading to various cellular responses, such as chemotaxis and specific gene expression. Vibrio cholerae, the causative agent of cholera, contains about 44 putative sensor proteins, which are homologous to methyl-accepting chemotaxis proteins involved in chemotaxis. Two of them, Mlp24 and Mlp37, have been identified as chemoreceptors that mediate chemotactic responses to various amino acids. Although most of the residues of Mlp37 involved in ligand binding are conserved in Mlp24, these chemoreceptors bind the same ligands with different affinities. Moreover, they have distinct cellular roles. Here we determined a series of ligand complex structures of the periplasmic domains of Mlp24 (Mlp24p). The structures revealed that Ca2+ binds to the loop that forms the upper wall of the ligand-binding pocket. Ca2+ does not bind to the corresponding loop of Mlp37, implying that the structural difference of the loop may cause the ligand affinity difference. Isothermal titration calorimetry (ITC) measurements indicated that Ca2+ changes the ligand binding affinity of Mlp24p. Furthermore, Ca2+ affected chemotactic behaviors to various amino acids mediated by Mlp24. Thus, Ca2+ is suggested to serve as a cosignal for the primary signal mediated by Mlp24p, and V. cholerae fine-tunes its chemotactic behavior depending on the Ca2+ concentration by modulating the ligand sensitivity of Mlp24.IMPORTANCE Mlp24 and Mlp37 are homologous chemoreceptors of Vibrio cholerae that bind various amino acids. Although most of the residues involved in ligand interaction are conserved, these chemoreceptors show different affinities for the same ligand and play different cellular roles. A series of ligand complex structures of the periplasmic region of Mlp24 (Mlp24p) and following ITC analysis revealed that Ca2+ binds to the loop of Mlp24p and modulates the ligand binding affinity of Mlp24p. Moreover, Ca2+ changes the chemotactic behaviors mediated by Mlp24. We propose that Ca2+ acts as a cosignal that modulates the affinity of Mlp24 for the primary signal, thereby changing the chemotactic behavior of V. cholerae.
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43
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Structure of the sensory domain of McpX from Sinorhizobium meliloti, the first known bacterial chemotactic sensor for quaternary ammonium compounds. Biochem J 2018; 475:3949-3962. [PMID: 30442721 DOI: 10.1042/bcj20180769] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 11/07/2018] [Accepted: 11/14/2018] [Indexed: 02/01/2023]
Abstract
The α-proteobacterium Sinorhizobium meliloti can live freely in the soil or engage in a symbiosis with its legume host. S. meliloti facilitates nitrogen fixation in root nodules, thus providing pivotal, utilizable nitrogen to the host. The organism has eight chemoreceptors, namely McpT to McpZ and IcpA that facilitate chemotaxis. McpX is the first known bacterial sensor of quaternary ammonium compounds (QACs) such as choline and betaines. Because QACs are exuded at chemotaxis-relevant concentrations by germinating alfalfa seeds, McpX has been proposed to contribute to host-specific chemotaxis. We have determined the crystal structure of the McpX periplasmic region (McpXPR) in complex with the proline betaine at 2.7 Å resolution. In the crystal, the protein forms a symmetric dimer with one proline betaine molecule bound to each monomer of McpXPR within membrane-distal CACHE module. The ligand is bound through cation-πinteractions with four aromatic amino acid residues. Mutational analysis in conjunction with binding studies revealed that a conserved aspartate residue is pivotal for ligand binding. We discovered that, in a striking example of convergent evolution, the ligand-binding site of McpXPR resembles that of a group of structurally unrelated betaine-binding proteins including ProX and OpuAC. Through this comparison and docking studies, we rationalized the specificity of McpXPR for this specific group of ligands. Collectively, our structural, biochemical, and molecular docking data have revealed the molecular determinants in McpX that are crucial for its rare ligand specificity for QACs.
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44
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Abstract
Bacterial signal transduction systems are responsible for sensing environmental cues and adjusting the cellular behaviour and/or metabolism in response to these cues. They also monitor the intracellular conditions and the status of the cell envelope and the cytoplasmic membrane and trigger various stress responses to counteract adverse changes. This surveillance involves several classes of sensor proteins: histidine kinases; chemoreceptors; membrane components of the sugar phosphotransferase system; adenylate, diadenylate and diguanylate cyclases and certain cAMP, c-di-AMP and c-di-GMP phosphodiesterases; extracytoplasmic function sigma factors and Ser/Thr/Tyr protein kinases and phosphoprotein phosphatases. We have compiled a detailed listing of sensor proteins that are encoded in the genomes of Escherichia coli, Bacillus subtilis and 10 widespread pathogens: Chlamydia trachomatis, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, Mycoplasma pneumoniae, Neisseria gonorrhoeae, Porphyromonas gingivalis, Rickettsia typhi, Streptococcus pyogenes and Treponema pallidum, and checked what, if anything, is known about their functions. This listing shows significant gaps in the understanding of which environmental and intracellular cues are perceived by these bacteria and which cellular responses are triggered by the changes in the respective parameters. A better understanding of bacterial preferences may suggest new ways to modulate the expression of virulence factors and therefore decrease the reliance on antibiotics to fight infection.
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Affiliation(s)
- Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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45
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Blair KM, Mears KS, Taylor JA, Fero J, Jones LA, Gafken PR, Whitney JC, Salama NR. The Helicobacter pylori cell shape promoting protein Csd5 interacts with the cell wall, MurF, and the bacterial cytoskeleton. Mol Microbiol 2018; 110:114-127. [PMID: 30039535 DOI: 10.1111/mmi.14087] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2018] [Indexed: 12/17/2022]
Abstract
Chronic infection with Helicobacter pylori can lead to the development of gastric ulcers and stomach cancers. The helical cell shape of H. pylori promotes stomach colonization. Screens for loss of helical shape have identified several periplasmic peptidoglycan (PG) hydrolases and non-enzymatic putative scaffolding proteins, including Csd5. Both over and under expression of the PG hydrolases perturb helical shape, but the mechanism used to coordinate and localize their enzymatic activities is not known. Using immunoprecipitation and mass spectrometry we identified Csd5 interactions with cytosolic proteins CcmA, a bactofilin required for helical shape, and MurF, a PG precursor synthase, as well as the inner membrane spanning ATP synthase. A combination of Csd5 domain deletions, point mutations, and transmembrane domain chimeras revealed that the N-terminal transmembrane domain promotes MurF, CcmA, and ATP synthase interactions, while the C-terminal SH3 domain mediates PG binding. We conclude that Csd5 promotes helical shape as part of a membrane associated, multi-protein shape complex that includes interactions with the periplasmic cell wall, a PG precursor synthesis enzyme, the bacterial cytoskeleton, and ATP synthase.
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Affiliation(s)
- Kris M Blair
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA.,Molecular and Cellular Biology Ph.D. Program, University of Washington, 1959 NE Pacific Street, HSB T-466, Box 357275, Seattle, WA, 98195-7275, USA
| | - Kevin S Mears
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA
| | - Jennifer A Taylor
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA.,Department of Microbiology, University of Washington, 1705 NE Pacific St., HSB K-343, Box 357735, Seattle, WA, 98195-7735, USA
| | - Jutta Fero
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA
| | - Lisa A Jones
- Proteomics Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., DE-352, Seattle, WA, 98109-1024, USA
| | - Philip R Gafken
- Proteomics Facility, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., DE-352, Seattle, WA, 98109-1024, USA
| | - John C Whitney
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4K1, Canada
| | - Nina R Salama
- Division of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave, Seattle, WA, 98109, USA
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Gavira JA, Ortega Á, Martín-Mora D, Conejero-Muriel MT, Corral-Lugo A, Morel B, Matilla MA, Krell T. Structural Basis for Polyamine Binding at the dCACHE Domain of the McpU Chemoreceptor from Pseudomonas putida. J Mol Biol 2018; 430:1950-1963. [PMID: 29758259 DOI: 10.1016/j.jmb.2018.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 10/16/2022]
Abstract
Many bacteria can move chemotactically to a variety of compounds and the recognition of chemoeffectors by the chemoreceptor ligand binding domain (LBD) defines the specificity of response. Many chemoreceptors were found to recognize different amino and organic acids, but the McpU chemoreceptor from Pseudomonas putida was identified as the first chemoreceptor that bound specifically polyamines. We report here the three-dimensional structure of McpU-LBD in complex with putrescine at a resolution of 2.4 Å, which fitted well a solution structure generated by small-angle X-ray scattering. Putrescine bound to a negatively charged pocket in the membrane distal module of McpU-LBD. Similarities exist in the binding of putrescine to McpU-LBD and taurine to the LBD of the Mlp37 chemoreceptor of Vibrio cholerae. In both structures, the primary amino group of the respective ligand is recognized by hydrogen bonds established by two aspartate and a tyrosine side chain. This feature may be used to predict the ligands of chemoreceptors with unknown function. Analytical ultracentrifugation revealed that McpU-LBD is monomeric in solution and that ligand binding does not alter this oligomeric state. This sensing mode thus differs from that of the well-characterised four-helix bundle domains where ligands bind to two sites at the LBD dimer interface. Although there appear to be different sensing modes, results are discussed in the context of data, indicating that chemoreceptors employ the same mechanism of transmembrane signaling. This work enhances our understanding of CACHE domains, which are the most abundant sensor domains in bacterial chemoreceptors and sensor kinases.
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Affiliation(s)
- José Antonio Gavira
- Laboratory of Crystallographic Studies, IACT, (CSIC-UGR), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Álvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - María Teresa Conejero-Muriel
- Laboratory of Crystallographic Studies, IACT, (CSIC-UGR), Avenida de las Palmeras 4, 18100 Armilla, Granada, Spain
| | - Andrés Corral-Lugo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Bertrand Morel
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain.
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Greer-Phillips SE, Sukomon N, Chua TK, Johnson MS, Crane BR, Watts KJ. THE AER2 RECEPTOR FROM VIBRIO CHOLERAE IS A DUAL PAS-HEME OXYGEN SENSOR. Mol Microbiol 2018; 109:209-224. [PMID: 29719085 DOI: 10.1111/mmi.13978] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 04/28/2018] [Accepted: 04/29/2018] [Indexed: 12/16/2022]
Abstract
The diarrheal pathogen Vibrio cholerae navigates complex environments using three chemosensory systems and 44-45 chemoreceptors. Chemosensory cluster II modulates chemotaxis, whereas clusters I and III have unknown functions. Ligands have been identified for only five V. cholerae chemoreceptors. Here we report that the cluster III receptor, VcAer2, binds and responds to O2 . VcAer2 is an ortholog of Pseudomonas aeruginosa Aer2 (PaAer2), but differs in that VcAer2 has two, rather than one, N-terminal PAS domain. We have determined that both PAS1 and PAS2 form homodimers and bind penta-coordinate b-type heme via an Eη-His residue. Heme binding to PAS1 required the entire PAS core, but receptor function also required the N-terminal cap. PAS2 functioned as an O2 -sensor [Kd(O2) , 19 μM], utilizing the same Iβ Trp (W276) as PaAer2 to stabilize O2 . The crystal structure of PAS2-W276L was similar to that of PaAer2-PAS, but resided in an active conformation mimicking the ligand-bound state, consistent with its signal-on phenotype. PAS1 also bound O2 [Kd(O2), 12 μM], although O2 binding was stabilized by either a Trp or Tyr residue. Moreover, PAS1 appeared to function as a signal modulator, regulating O2 -mediated signaling from PAS2, and resulting in activation of the cluster III chemosensory pathway. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Suzanne E Greer-Phillips
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Nattakan Sukomon
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Teck Khiang Chua
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Mark S Johnson
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, USA
| | - Kylie J Watts
- Division of Microbiology and Molecular Genetics, Loma Linda University, Loma Linda, CA, 92350, USA
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