1
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Scheidweiler D, Bordoloi AD, Jiao W, Sentchilo V, Bollani M, Chhun A, Engel P, de Anna P. Spatial structure, chemotaxis and quorum sensing shape bacterial biomass accumulation in complex porous media. Nat Commun 2024; 15:191. [PMID: 38167276 PMCID: PMC10761857 DOI: 10.1038/s41467-023-44267-y] [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: 03/28/2023] [Accepted: 12/06/2023] [Indexed: 01/05/2024] Open
Abstract
Biological tissues, sediments, or engineered systems are spatially structured media with a tortuous and porous structure that host the flow of fluids. Such complex environments can influence the spatial and temporal colonization patterns of bacteria by controlling the transport of individual bacterial cells, the availability of resources, and the distribution of chemical signals for communication. Yet, due to the multi-scale structure of these complex systems, it is hard to assess how different biotic and abiotic properties work together to control the accumulation of bacterial biomass. Here, we explore how flow-mediated interactions allow the gut commensal Escherichia coli to colonize a porous structure that is composed of heterogenous dead-end pores (DEPs) and connecting percolating channels, i.e. transmitting pores (TPs), mimicking the structured surface of mammalian guts. We find that in presence of flow, gradients of the quorum sensing (QS) signaling molecule autoinducer-2 (AI-2) promote E. coli chemotactic accumulation in the DEPs. In this crowded environment, the combination of growth and cell-to-cell collision favors the development of suspended bacterial aggregates. This results in hot-spots of resource consumption, which, upon resource limitation, triggers the mechanical evasion of biomass from nutrients and oxygen depleted DEPs. Our findings demonstrate that microscale medium structure and complex flow coupled with bacterial quorum sensing and chemotaxis control the heterogenous accumulation of bacterial biomass in a spatially structured environment, such as villi and crypts in the gut or in tortuous pores within soil and filters.
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Affiliation(s)
- David Scheidweiler
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland.
| | - Ankur Deep Bordoloi
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Wenqiao Jiao
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Vladimir Sentchilo
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | | | - Audam Chhun
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Philipp Engel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Pietro de Anna
- Institute of Earth Sciences, University of Lausanne, CH-1015, Lausanne, Switzerland.
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2
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Buchinger TJ, Li W. Chemical communication and its role in sexual selection across Animalia. Commun Biol 2023; 6:1178. [PMID: 37985853 PMCID: PMC10662023 DOI: 10.1038/s42003-023-05572-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023] Open
Abstract
Sexual selection has been studied as a major evolutionary driver of animal diversity for roughly 50 years. Much evidence indicates that competition for mates favors elaborate signaling traits. However, this evidence comes primarily from a few taxa, leaving sexual selection as a salient evolutionary force across Animalia largely untested. Here, we reviewed the evidence for sexual selection on communication across all animal phyla, classes, and orders with emphasis on chemoreception, the only sense shared across lifeforms. An exhaustive literature review documented evidence for sexual selection on chemosensory traits in 10 of 34 animal phyla and indications of sexual selection on chemosensory traits in an additional 13 phyla. Potential targets of sexual selection include structures and processes involved in production, delivery, and detection of chemical signals. Our review suggests sexual selection plays a widespread role in the evolution of communication and highlights the need for research that better reflects animal diversity.
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Affiliation(s)
- Tyler J Buchinger
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.
- Biology Department, Albion College, Albion, MI, USA.
| | - Weiming Li
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA
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3
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Xie LY, Xu YB, Ding XQ, Liang S, Li DL, Fu AK, Zhan XA. Itaconic acid and dimethyl itaconate exert antibacterial activity in carbon-enriched environments through the TCA cycle. Biomed Pharmacother 2023; 167:115487. [PMID: 37713987 DOI: 10.1016/j.biopha.2023.115487] [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: 07/09/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023] Open
Abstract
Itaconic acid (IA), a metabolite generated by the tricarboxylic acid (TCA) cycle in eukaryotic immune cells, and its derivative dimethyl itaconate (DI) exert antibacterial functions in intracellular environments. Previous studies suggested that IA and DI only inhibit bacterial growth in carbon-limited environments; however, whether IA and DI maintain antibacterial activity in carbon-enriched environments remains unknown. Here, IA and DI inhibited the bacteria with minimum inhibitory concentrations of 24.02 mM and 39.52 mM, respectively, in a carbon-enriched environment. The reduced bacterial pathogenicity was reflected in cell membrane integrity, motility, biofilm formation, AI-2/luxS, and virulence. Mechanistically, succinate dehydrogenase (SDH) activity and fumaric acid levels decreased in the IA and DI treatments, while isocitrate lyase (ICL) activity was upregulated. Inhibited TCA circulation was also observed through untargeted metabolomics. In addition, energy-related aspartate metabolism and lysine degradation were suppressed. In summary, these results indicated that IA and DI reduced bacterial pathogenicity while exerting antibacterial functions by inhibiting TCA circulation. This study enriches knowledge on the inhibition of bacteria by IA and DI in a carbon-mixed environment, suggesting an alternative method for treating bacterial infections by immune metabolites.
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Affiliation(s)
- L Y Xie
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - Y B Xu
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - X Q Ding
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - S Liang
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - D L Li
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - A K Fu
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China
| | - X A Zhan
- Key Laboratory of Animal Nutrition and Feed in East China, Ministry of Agriculture and Key Laboratory of Animal Feed and Nutrition of Zhejiang Province, Feed Science Institute, College of Animal Science, Zhejiang University, Hangzhou 310058, China.
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4
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Shoup D, Ursell T. Bacterial bioconvection confers context-dependent growth benefits and is robust under varying metabolic and genetic conditions. J Bacteriol 2023; 205:e0023223. [PMID: 37787517 PMCID: PMC10601612 DOI: 10.1128/jb.00232-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 08/17/2023] [Indexed: 10/04/2023] Open
Abstract
Microbes often respond to environmental cues by adopting collective behaviors-like biofilms or swarming-that benefit the population. During "bioconvection," microbes gather in dense groups and plume downward through fluid environments, driving flow and mixing on the scale of millions of cells. Though bioconvection was observed a century ago, the effects of differing physical and chemical inputs and its potential selective advantages for different species of microbes remain largely unexplored. In Bacillus subtilis, vertical oxygen gradients that originate from air-liquid interfaces create cell-density inversions that drive bioconvection. Here, we develop Escherichia coli as a complementary model for the study of bioconvection. In the context of a still fluid, we found that motile and chemotactic genotypes of both E. coli and B. subtilis bioconvect and show increased growth compared to immotile or non-chemotactic genotypes, whereas in a well-mixed fluid, there is no growth advantage to motility or chemotaxis. We found that fluid depth, cell concentration, and carbon availability affect the emergence and timing of bioconvective patterns. Also, whereas B. subtilis requires oxygen gradients to bioconvect, E. coli deficient in aerotaxis (Δaer) or energy-taxis (Δtsr) still bioconvects, as do cultures that lack an air-liquid interface. Thus, in two distantly related microbes, bioconvection may confer context-dependent growth benefits, and E. coli bioconvection is robustly elicited by multiple types of chemotaxis. These results greatly expand the set of physical and metabolic conditions in which this striking collective behavior can be expected and demonstrate its potential to be a generic force for behavioral selection across ecological contexts. IMPORTANCE Individual microorganisms frequently move in response to gradients in their fluid environment, with corresponding metabolic benefits. At a population level, such movements can create density variations in a fluid that couple to gravity and drive large-scale convection and mixing called bioconvection. In this work, we provide evidence that this collective behavior confers a selective benefit on two distantly related species of bacteria. We develop new methods for quantifying this behavior and show that bioconvection in Escherichia coli is surprisingly robust to changes in cell concentration, fluid depth, interface conditions, metabolic sensing, and carbon availability. These results greatly expand the set of conditions known to elicit this collective behavior and indicate its potential to be a selective pressure across ecological contexts.
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Affiliation(s)
- Daniel Shoup
- Department of Physics, University of Oregon, Eugene, Oregon, USA
- Rocky Mountain National Laboratories (NIH), Hamilton, Montana, USA
| | - Tristan Ursell
- Department of Physics, University of Oregon, Eugene, Oregon, USA
- Material Science Institute, Eugene, Oregon, USA
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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5
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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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6
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Cerna‐Vargas JP, Sánchez‐Romera B, Matilla MA, Ortega Á, Krell T. Sensing preferences for prokaryotic solute binding protein families. Microb Biotechnol 2023; 16:1823-1833. [PMID: 37547952 PMCID: PMC10443332 DOI: 10.1111/1751-7915.14292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 05/25/2023] [Indexed: 08/08/2023] Open
Abstract
Solute binding proteins (SBPs) are of central physiological relevance for prokaryotes. These proteins present substrates to transporters, but they also stimulate different signal transduction receptors. SBPs form a superfamily of at least 33 protein Pfam families. To assess possible links between SBP sequence and the ligand recognized, we have inspected manually all SBP three-dimensional structures deposited in the protein data bank and retrieved 748 prokaryotic structures that have been solved in complex with bound ligand. These structures were classified into 26 SBP Pfam families. The analysis of the ligands recognized revealed that most families possess a preference for a compound class. There were three families each that bind preferentially saccharides and amino acids. In addition, we identified families that bind preferentially purines, quaternary amines, iron and iron-chelating compounds, oxoanions, bivalent metal ions or phosphates. Phylogenetic analyses suggest convergent evolutionary events that lead to families that bind the same ligand. The functional link between chemotaxis and compound uptake is reflected in similarities in the ligands recognized by SBPs and chemoreceptors. Associating Pfam families with ligand profiles will be of help to design experimental strategies aimed at the identification of ligands for uncharacterized SBPs.
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Affiliation(s)
- Jean Paul Cerna‐Vargas
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
- Centro de Biotecnología y Genómica de Plantas CBGPUniversidad Politécnica de Madrid‐Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria/CSIC, Parque Científico y Tecnológico de la UPMMadridSpain
| | - Beatriz Sánchez‐Romera
- Scientific Instrumentation ServiceEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology B and Immunology, Faculty of ChemistryUniversity of MurciaMurciaSpain
| | - Tino Krell
- Department of Biotechnology and Environmental ProtectionEstación Experimental del Zaidín, Consejo Superior de Investigaciones CientíficasGranadaSpain
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7
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Oxendine A, Walsh AA, Young T, Dixon B, Hoke A, Rogers EE, Lee MD, Maurer JJ. Conditions Necessary for the Transfer of Antimicrobial Resistance in Poultry Litter. Antibiotics (Basel) 2023; 12:1006. [PMID: 37370325 DOI: 10.3390/antibiotics12061006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/23/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Animal manures contain a large and diverse reservoir of antimicrobial resistance (AMR) genes that could potentially spillover into the general population through transfer of AMR to antibiotic-susceptible pathogens. The ability of poultry litter microbiota to transmit AMR was examined in this study. Abundance of phenotypic AMR was assessed for litter microbiota to the antibiotics: ampicillin (Ap; 25 μg/mL), chloramphenicol (Cm; 25 μg/mL), streptomycin (Sm; 100 μg/mL), and tetracycline (Tc; 25 μg/mL). qPCR was used to estimate gene load of streptomycin-resistance and sulfonamide-resistance genes aadA1 and sul1, respectively, in the poultry litter community. AMR gene load was determined relative to total bacterial abundance using 16S rRNA qPCR. Poultry litter contained 108 CFU/g, with Gram-negative enterics representing a minor population (<104 CFU/g). There was high abundance of resistance to Sm (106 to 107 CFU/g) and Tc (106 to 107 CFU/g) and a sizeable antimicrobial-resistance gene load in regards to gene copies per bacterial genome (aadA1: 0.0001-0.0060 and sul1: 0.0355-0.2455). While plasmid transfer was observed from Escherichia coli R100, as an F-plasmid donor control, to the Salmonella recipient in vitro, no AMR Salmonella were detected in a poultry litter microcosm with the inclusion of E. coli R100. Confirmatory experiments showed that isolated poultry litter bacteria were not interfering with plasmid transfer in filter matings. As no R100 transfer was observed at 25 °C, conjugative plasmid pRSA was chosen for its high plasmid transfer frequency (10-4 to 10-5) at 25 °C. While E. coli strain background influenced the persistence of pRSA in poultry litter, no plasmid transfer to Salmonella was ever observed. Although poultry litter microbiota contains a significant AMR gene load, potential to transmit resistance is low under conditions commonly used to assess plasmid conjugation.
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Affiliation(s)
- Aaron Oxendine
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Allison A Walsh
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Tamesha Young
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Brandan Dixon
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Alexa Hoke
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Eda Erdogan Rogers
- Department of Biomedical Science and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - Margie D Lee
- Department of Biomedical Science and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
| | - John J Maurer
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24060, USA
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8
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Oliveira RA, Cabral V, Torcato I, Xavier KB. Deciphering the quorum-sensing lexicon of the gut microbiota. Cell Host Microbe 2023; 31:500-512. [PMID: 37054672 DOI: 10.1016/j.chom.2023.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
The enduring coexistence between the gut microbiota and the host has led to a symbiotic relationship that benefits both parties. In this complex, multispecies environment, bacteria can communicate through chemical molecules to sense and respond to the chemical, physical, and ecological properties of the surrounding environment. One of the best-studied cell-to-cell communication mechanisms is quorum sensing. Chemical signaling through quorum sensing is involved in regulating the bacterial group behaviors, often required for host colonization. However, most microbial-host interactions regulated by quorum sensing are studied in pathogens. Here, we will focus on the latest reports on the emerging studies of quorum sensing in the gut microbiota symbionts and on group behaviors adopted by these bacteria to colonize the mammalian gut. Moreover, we address the challenges and approaches to uncover molecule-mediated communication mechanisms, which will allow us to unravel the processes that drive the establishment of gut microbiota.
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Affiliation(s)
| | - Vitor Cabral
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
| | - Inês Torcato
- Instituto Gulbenkian de Ciência, 2780-156 Oeiras, Portugal
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9
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Laganenka L, Lee JW, Malfertheiner L, Dieterich CL, Fuchs L, Piel J, von Mering C, Sourjik V, Hardt WD. Chemotaxis and autoinducer-2 signalling mediate colonization and contribute to co-existence of Escherichia coli strains in the murine gut. Nat Microbiol 2023; 8:204-217. [PMID: 36624229 DOI: 10.1038/s41564-022-01286-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 11/09/2022] [Indexed: 01/11/2023]
Abstract
Bacteria communicate and coordinate their behaviour at the intra- and interspecies levels by producing and sensing diverse extracellular small molecules called autoinducers. Autoinducer 2 (AI-2) is produced and detected by a variety of bacteria and thus plays an important role in interspecies communication and chemotaxis. Although AI-2 is a major autoinducer molecule present in the mammalian gut and can influence the composition of the murine gut microbiota, its role in bacteria-bacteria and bacteria-host interactions during gut colonization remains unclear. Combining competitive infections in C57BL/6 mice with microscopy and bioinformatic approaches, we show that chemotaxis (cheY) and AI-2 signalling (via lsrB) promote gut colonization by Escherichia coli, which is in turn connected to the ability of the bacteria to utilize fructoselysine (frl operon). We further show that the genomic diversity of E. coli strains with respect to AI-2 signalling allows ecological niche segregation and stable co-existence of different E. coli strains in the mammalian gut.
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Affiliation(s)
- Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Jae-Woo Lee
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany
| | - Lukas Malfertheiner
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | | | - Lea Fuchs
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Jörn Piel
- Institute of Microbiology, D-BIOL, ETH Zurich, Zurich, Switzerland
| | - Christian von Mering
- Department of Molecular Life Sciences and Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology, Marburg, Germany
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10
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Rodrigues MV, Kis P, Xavier KB, Ventura MR. Synthesis and potential of Autoinducer‐2 and analogs to manipulate inter‐species Quorum Sensing. Isr J Chem 2023. [DOI: 10.1002/ijch.202200091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Miguel V. Rodrigues
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
| | - Peter Kis
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
- Institute of Chemistry Slovak Academy of Sciences 845 38 Bratislava Slovakia
| | | | - M. Rita Ventura
- Instituto de Tecnologia Química e Biológica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras Portugal
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11
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Matilla MA, Monteagudo-Cascales E, Krell T. Advances in the identification of signals and novel sensing mechanisms for signal transduction systems. Environ Microbiol 2023; 25:79-86. [PMID: 35896893 DOI: 10.1111/1462-2920.16142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/16/2022] [Indexed: 01/21/2023]
Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Elizabet Monteagudo-Cascales
- 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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12
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Singh PK, Cecchini G, Nakagawa T, Iverson TM. CryoEM structure of a post-assembly MS-ring reveals plasticity in stoichiometry and conformation. PLoS One 2023; 18:e0285343. [PMID: 37205674 DOI: 10.1371/journal.pone.0285343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/20/2023] [Indexed: 05/21/2023] Open
Abstract
The flagellar motor supports bacterial chemotaxis, a process that allows bacteria to move in response to their environment. A central feature of this motor is the MS-ring, which is composed entirely of repeats of the FliF subunit. This MS-ring is critical for the assembly and stability of the flagellar switch and the entire flagellum. Despite multiple independent cryoEM structures of the MS-ring, there remains a debate about the stoichiometry and organization of the ring-building motifs (RBMs). Here, we report the cryoEM structure of a Salmonella MS-ring that was purified from the assembled flagellar switch complex (MSC-ring). We term this the 'post-assembly' state. Using 2D class averages, we show that under these conditions, the post-assembly MS-ring can contain 32, 33, or 34 FliF subunits, with 33 being the most common. RBM3 has a single location with C32, C33, or C34 symmetry. RBM2 is found in two locations with RBM2inner having C21 or C22 symmetry and an RBM2outer-RBM1 having C11 symmetry. Comparison to previously reported structures identifies several differences. Most strikingly, we find that the membrane domain forms 11 regions of discrete density at the base of the structure rather than a contiguous ring, although density could not be unambiguously interpreted. We further find density in some previously unresolved areas, and we assigned amino acids to those regions. Finally, we find differences in interdomain angles in RBM3 that affect the diameter of the ring. Together, these investigations support a model of the flagellum with structural plasticity, which may be important for flagellar assembly and function.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, United States of America
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, United States of America
| | - Terunaga Nakagawa
- Department of Molecular Physiology and Biophysics, Vanderbilt University, School of Medicine, Nashville, TN, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, United States of America
- Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States of America
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, United States of America
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13
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Laganenka L, Sourjik V. Bacterial Quorum Sensing Signals at the Interdomain Interface. Isr J Chem 2022. [DOI: 10.1002/ijch.202200080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO) Marburg Germany
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14
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Shu R, Yuan C, Liu B, Song Y, Hou L, Ren P, Wang H, Cui C. PAS Domain-Containing Chemoreceptors Influence the Signal Sensing and Intestinal Colonization of Vibrio cholerae. Genes (Basel) 2022; 13:genes13122224. [PMID: 36553491 PMCID: PMC9777591 DOI: 10.3390/genes13122224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/11/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Bacterial chemotaxis is the phenomenon in which bacteria migrate toward a more favorable niche in response to chemical cues in the environment. The methyl-accepting chemotaxis proteins (MCPs) are the principal sensory receptors of the bacterial chemotaxis system. Aerotaxis is a special form of chemotaxis in which oxygen serves as the signaling molecule; the process is dependent on the aerotaxis receptors (Aer) containing the Per-Arnt-Sim (PAS) domain. Over 40 MCPs are annotated on the genome of Vibrio cholerae; however, little is known about their functions. We investigated six MCPs containing the PAS domain in V. cholerae El Tor C6706, namely aer2, aer3, aer4, aer5, aer6, and aer7. Deletion analyses of each aer homolog gene indicated that these Aer receptors are involved in aerotaxis, chemotaxis, biofilm formation, and intestinal colonization. Swarming motility assay indicated that the aer2 gene was responsible for sensing the oxygen gradient independent of the other five homologs. When bile salts and mucin were used as chemoattractants, each Aer receptor influenced the chemotaxis differently. Biofilm formation was enhanced by overexpression of the aer6 and aer7 genes. Moreover, deletion of the aer2 gene resulted in better bacterial colonization of the mutant in adult mice; however, virulence gene expression was unaffected. These data suggest distinct roles for different Aer homologs in V. cholerae physiology.
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Affiliation(s)
- Rundong Shu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Chaoqun Yuan
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Bojun Liu
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Yang Song
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Leqi Hou
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Panpan Ren
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Hui Wang
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (H.W.); (C.C.); Tel.: +86-25-84396645 (H.W.)
| | - Chunhong Cui
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (H.W.); (C.C.); Tel.: +86-25-84396645 (H.W.)
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15
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Ortega Á, Matilla MA, Krell T. The Repertoire of Solute-Binding Proteins of Model Bacteria Reveals Large Differences in Number, Type, and Ligand Range. Microbiol Spectr 2022; 10:e0205422. [PMID: 36121253 PMCID: PMC9602780 DOI: 10.1128/spectrum.02054-22] [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: 06/07/2022] [Accepted: 08/24/2022] [Indexed: 12/31/2022] Open
Abstract
Solute-binding proteins (SBPs) are of central physiological relevance for bacteria. They are located in the extracytosolic space, where they present substrates to transporters but also stimulate different types of transmembrane receptors coordinating compound uptake with signal transduction. SBPs are a superfamily composed of proteins recognized by 45 Pfam profiles. The definition of SBP profiles for bacteria is hampered by the fact that these Pfam profiles recognize sensor domains for different types of signaling proteins or cytosolic proteins with alternative functions. We report here the retrieval of the SBPs from 49 bacterial model strains with different lifestyles and phylogenetic distributions. Proteins were manually curated, and the ligands recognized were predicted bioinformatically. There were very large differences in the number and type of SBPs between strains, ranging from 7 SBPs in Helicobacter pylori 26695 to 189 SBPs in Sinorhizobium meliloti 1021. SBPs were found to represent 0.22 to 5.13% of the total protein-encoding genes. The abundance of SBPs was largely determined by strain phylogeny, and no obvious link with the bacterial lifestyle was noted. Most abundant (36%) were SBPs predicted to recognize amino acids or peptides, followed by those expected to bind different sugars (18%). To the best of our knowledge, this is the first comparative study of bacterial SBP repertoires. Given the importance of SBPs in nutrient uptake and signaling, this study enhances the knowledge of model bacteria and will permit the definition of SBP profiles of other strains. IMPORTANCE SBPs are essential components for many transporters, but multiple pieces of more recent evidence indicate that the SBP-mediated stimulation of different transmembrane receptors is a general and widespread signal transduction mechanism in bacteria. The double function of SBPs in coordinating transport with signal transduction remains to a large degree unexplored and represents a major research need. The definition of the SBP repertoire of the 49 bacterial model strains examined here, along with information on their cognate ligand profiles forms the basis to close this gap in knowledge. Furthermore, this study provides information on the forces that have driven the evolution of transporters with different ligand specificities in bacteria that differ in phylogenetics and lifestyle. This article is also a first step in setting up automatic algorithms that permit the large-scale identification of the SBP repertoire in proteomes.
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Affiliation(s)
- 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
| | - 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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16
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Sahreen S, Mukhtar H, Imre K, Morar A, Herman V, Sharif S. Exploring the Function of Quorum Sensing Regulated Biofilms in Biological Wastewater Treatment: A Review. Int J Mol Sci 2022; 23:ijms23179751. [PMID: 36077148 PMCID: PMC9456111 DOI: 10.3390/ijms23179751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 08/21/2022] [Accepted: 08/26/2022] [Indexed: 11/26/2022] Open
Abstract
Quorum sensing (QS), a type of bacterial cell–cell communication, produces autoinducers which help in biofilm formation in response to cell population density. In this review, biofilm formation, the role of QS in biofilm formation and development with reference to biological wastewater treatment are discussed. Autoinducers, for example, acyl-homoserine lactones (AHLs), auto-inducing oligo-peptides (AIPs) and autoinducer 2, present in both Gram-negative and Gram-positive bacteria, with their mechanism, are also explained. Over the years, wastewater treatment (WWT) by QS-regulated biofilms and their optimization for WWT have gained much attention. This article gives a comprehensive review of QS regulation methods, QS enrichment methods and QS inhibition methods in biological waste treatment systems. Typical QS enrichment methods comprise adding QS molecules, adding QS accelerants and cultivating QS bacteria, while typical QS inhibition methods consist of additions of quorum quenching (QQ) bacteria, QS-degrading enzymes, QS-degrading oxidants, and QS inhibitors. Potential applications of QS regulated biofilms for WWT have also been summarized. At last, the knowledge gaps present in current researches are analyzed, and future study requirements are proposed.
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Affiliation(s)
- Sania Sahreen
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
| | - Hamid Mukhtar
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
- Correspondence: (H.M.); (K.I.); Tel.: +92-3334245581 (H.M.); +40-256277186 (K.I.)
| | - Kálmán Imre
- Department of Animal Production and Veterinary Public Health, Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania”, 300645 Timisoara, Romania
- Correspondence: (H.M.); (K.I.); Tel.: +92-3334245581 (H.M.); +40-256277186 (K.I.)
| | - Adriana Morar
- Department of Animal Production and Veterinary Public Health, Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania”, 300645 Timisoara, Romania
| | - Viorel Herman
- Department of Infectious Diseases and Preventive Medicine, Faculty of Veterinary Medicine, Banat’s University of Agricultural Sciences and Veterinary Medicine “King Michael I of Romania”, 300645 Timisoara, Romania
| | - Sundas Sharif
- Institute of Industrial Biotechnology, Government College University, Lahore 54000, Pakistan
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17
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Chen X, Bi S, Ma X, Sourjik V, Lai L. Discovery of a New Chemoeffector for Escherichia coli Chemoreceptor Tsr and Identification of a Molecular Mechanism of Repellent Sensing. ACS BIO & MED CHEM AU 2022; 2:386-394. [PMID: 37102165 PMCID: PMC10125284 DOI: 10.1021/acsbiomedchemau.1c00055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Motile bacteria use chemotaxis to search for nutrients and escape from harmful chemicals. While the sensing mechanisms for chemical attractants are well established, the molecular details of chemorepellent detection are poorly understood. Here, by using combined computational and experimental approaches to screen potential chemoeffectors for the Escherichia coli chemoreceptor Tsr, we identified a specific chemorepellent, 1-aminocyclohexanecarboxylic acid (ACHC). Our study strongly suggests that ACHC directly binds to the periplasmic sensory domain of Tsr and competes with l-serine, the amino acid attractant of Tsr. We further characterized the binding features of l-serine, ACHC, and l-leucine (a natural repellent that binds Tsr) and found that Asn68 plays a key role in mediating chemotactic response. Mutating Asn68 to Ala inverted the response to l-leucine from a repellent to an attractant. Our study provides important insights into the molecular mechanisms of ligand sensing via bacterial chemoreceptors.
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Affiliation(s)
- Xi Chen
- BNLMS,
Peking-Tsinghua Center for Life Sciences at College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Shuangyu Bi
- Max
Planck Institute for Terrestrial Microbiology & LOEWE Center for
Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
- State
Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiaomin Ma
- BNLMS,
Peking-Tsinghua Center for Life Sciences at College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Victor Sourjik
- Max
Planck Institute for Terrestrial Microbiology & LOEWE Center for
Synthetic Microbiology (SYNMIKRO), Marburg 35043, Germany
| | - Luhua Lai
- BNLMS,
Peking-Tsinghua Center for Life Sciences at College of Chemistry and
Molecular Engineering, Peking University, Beijing 100871, China
- Center
for Quantitative Biology, Academy of Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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18
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Mishra S, Huang Y, Li J, Wu X, Zhou Z, Lei Q, Bhatt P, Chen S. Biofilm-mediated bioremediation is a powerful tool for the removal of environmental pollutants. CHEMOSPHERE 2022; 294:133609. [PMID: 35051518 DOI: 10.1016/j.chemosphere.2022.133609] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Biofilm-mediated bioremediation is an attractive approach for the elimination of environmental pollutants, because of its wide adaptability, biomass, and excellent capacity to absorb, immobilize, or degrade contaminants. Biofilms are assemblages of individual or mixed microbial cells adhering to a living or non-living surface in an aqueous environment. Biofilm-forming microorganisms have excellent survival under exposure to harsh environmental stressors, can compete for nutrients, exhibit greater tolerance to pollutants compared to free-floating planktonic cells, and provide a protective environment for cells. Biofilm communities are thus capable of sorption and metabolization of organic pollutants and heavy metals through a well-controlled expression pattern of genes governed by quorum sensing. The involvement of quorum sensing and chemotaxis in biofilms can enhance the bioremediation kinetics with the help of signaling molecules, the transfer of genetic material, and metabolites. This review provides in-depth knowledge of the process of biofilm formation in microorganisms, their regulatory mechanisms of interaction, and their importance and application as powerful bioremediation agents in the biodegradation of environmental pollutants, including hydrocarbons, pesticides, and heavy metals.
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Affiliation(s)
- Sandhya Mishra
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Yaohua Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiayi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Xiaozhen Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Zhe Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Qiqi Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Pankaj Bhatt
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Shaohua Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Provincial Key Laboratory of Agricultural & Rural Pollution Abatement and Environmental Safety, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
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19
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Liu Q, Lin B, Tao Y. Improved methylation in E. coli via an efficient methyl supply system driven by betaine. Metab Eng 2022; 72:46-55. [DOI: 10.1016/j.ymben.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 01/28/2022] [Accepted: 02/16/2022] [Indexed: 12/21/2022]
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20
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Rico-Jiménez M, Roca A, Krell T, Matilla MA. A bacterial chemoreceptor that mediates chemotaxis to two different plant hormones. Environ Microbiol 2022; 24:3580-3597. [PMID: 35088505 PMCID: PMC9543091 DOI: 10.1111/1462-2920.15920] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/14/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Indole-3-acetic acid (IAA) is the main naturally occurring auxin and is produced by organisms of all kingdoms of life. In addition to the regulation of plant growth and development, IAA plays an important role in the interaction between plants and growth-promoting and phytopathogenic bacteria by regulating bacterial gene expression and physiology. We show here that a IAA metabolizing plant-associated Pseudomonas putida isolate exhibits chemotaxis to IAA that is independent of auxin metabolism. We found that IAA chemotaxis is based on the activity of the PcpI chemoreceptor and heterologous expression of pcpI conferred IAA taxis to different environmental and human pathogenic isolates of the Pseudomonas genus. Using ligand screening, microcalorimetry and quantitative chemotaxis assays, we found that PcpI failed to bind IAA directly, but recognized and mediated chemoattractions to various aromatic compounds, including the phytohormone salicylic acid. The expression of pcpI and its role in the interactions with plants was also investigated. PcpI extends the range of central signal molecules recognized by chemoreceptors. To our knowledge, this is the first report on a bacterial receptor that responds to two different phytohormones. Our study reinforces the multifunctional role of IAA and salicylic acid as intra- and inter-kingdom signal molecules. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Miriam Rico-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Amalia Roca
- Department of Microbiology, Facultad de Farmacia, Campus Universitario de Cartuja, Universidad de Granada, 18071, Granada, Spain
| | - Tino Krell
- 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
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21
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Tumewu SA, Matsui H, Yamamoto M, Noutoshi Y, Toyoda K, Ichinose Y. Identification of chemoreceptor proteins for amino acids involved in host plant infection in Pseudomonas syringae pv. tabaci 6605. Microbiol Res 2021; 253:126869. [PMID: 34597823 DOI: 10.1016/j.micres.2021.126869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/02/2021] [Accepted: 09/20/2021] [Indexed: 11/23/2022]
Abstract
Chemotaxis is crucial for Pseudomonas syringae pv. tabaci (Pta) 6605 to evoke disease in tobacco plants. Pta6605 harbors more than fifty genes for methyl-accepting chemotaxis proteins (mcp), but almost all are functionally uncharacterized. Previously we identified a dCache_1 type MCP in Pta6605 that mediates chemotaxis to γ-aminobutyric acid, called McpG. In this study, we characterized four more dCache_1 type MCPs, three of which, PscA, PscB, and PscC2, are responsible for sensing amino acids. Using a capillary chemotaxis assay, we observed that PscA, PscB, and PscC2 mutant strains had reduced chemotaxis to most amino acids, indicating that PscA and PscB mediate chemotaxis to 14 amino acids, while PscC2 has a slightly narrower ligand recognition, mediating chemotaxis to 12 amino acids. Other cellular functions were also affected in ΔpscB and ΔpscC2: swarming motility was reduced, and biofilm formation was increased. Furthermore, ΔpscB and ΔpscC2 but not ΔpscA had reduced virulence in the host tobacco plant. On the other hand, ΔpscC1 was defective in motility and did not even respond to yeast extract and was unable to cause disease. These findings supported the idea that the chemosensory pathway correlated with virulence-related phenotypes. Amino acids are abundant in tobacco apoplast; having multiple MCPs appears to support the invasion of Pta6605 into the plant.
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Affiliation(s)
- Stephany Angelia Tumewu
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Hidenori Matsui
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Mikihiro Yamamoto
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Yoshiteru Noutoshi
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Kazuhiro Toyoda
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan
| | - Yuki Ichinose
- Graduate School of Environmental and Life Science, Okayama University, Tsushima-naka 1-1-1, Kita-ku, Okayama 700-8530, Japan.
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22
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Colin R, Ni B, Laganenka L, Sourjik V. Multiple functions of flagellar motility and chemotaxis in bacterial physiology. FEMS Microbiol Rev 2021; 45:fuab038. [PMID: 34227665 PMCID: PMC8632791 DOI: 10.1093/femsre/fuab038] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 12/13/2022] Open
Abstract
Most swimming bacteria are capable of following gradients of nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one of the most-studied model systems for signal transduction and quantitative biology, and underlying molecular mechanisms are well characterized in Escherichia coli and several other model bacteria. In this review, we focus primarily on less understood aspect of bacterial chemotaxis, namely its physiological relevance for individual bacterial cells and for bacterial populations. As evident from multiple recent studies, even for the same bacterial species flagellar motility and chemotaxis might serve multiple roles, depending on the physiological and environmental conditions. Among these, finding sources of nutrients and more generally locating niches that are optimal for growth appear to be one of the major functions of bacterial chemotaxis, which could explain many chemoeffector preferences as well as flagellar gene regulation. Chemotaxis might also generally enhance efficiency of environmental colonization by motile bacteria, which involves intricate interplay between individual and collective behaviors and trade-offs between growth and motility. Finally, motility and chemotaxis play multiple roles in collective behaviors of bacteria including swarming, biofilm formation and autoaggregation, as well as in their interactions with animal and plant hosts.
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Affiliation(s)
- Remy Colin
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
| | - Bin Ni
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
- College of Resources and Environmental Science, National Academy of Agriculture Green Development, China Agricultural University, Yuanmingyuan Xilu No. 2, Beijing 100193, China
| | - Leanid Laganenka
- Institute of Microbiology, D-BIOL, ETH Zürich, Vladimir-Prelog-Weg 4, Zürich 8093, Switzerland
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & Center for Synthetic Microbiology (SYNMIKRO), Karl-von-Frisch Strasse 16, Marburg D-35043, Germany
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23
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Li Y, Liang J, Yang S, Yao J, Chen K, Yang L, Zheng W, Tian Y. Finding novel chemoreceptors that specifically sense and trigger chemotaxis toward polycyclic aromatic hydrocarbons in Novosphingobium pentaromativorans US6-1. JOURNAL OF HAZARDOUS MATERIALS 2021; 416:126246. [PMID: 34492992 DOI: 10.1016/j.jhazmat.2021.126246] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/22/2021] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Bacterial chemotaxis can improve the efficiency of aromatic compound degradation, however, knowledge of how bacteria sense high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs), is limited. Here, the chemotactic responses of Novosphingobium pentaromativorans US6-1 to 9 aromatic compounds were investigated. The results showed that US6-1 chemotactically responded to phenanthrene (PHE), pyrene (PYR), benzo[a]pyrene (BaP) and their six metabolites. Six methyl-accepting chemotaxis proteins (MCPs) were annotated from US6-1 genome, four of which contained putative ligand-binding domains (LBDs). To confirm whether these four MCPs were involved in triggering chemotaxis toward PAHs, the MCP mutants were constructed. Observations showed a loss of the chemotactic responses to benzoate, phthalate, PHE and BaP only in the mutant ∆mcp03030. Surface plasmon resonance (SPR) assays further confirmed that MCP03030LBD specifically bound phthalate, PHE, PYR and BaP, while MCP18870LBD bound only PYR. The mutant ∆mcp03030-∆mcp18870 was then constructed and was shown to have lost the chemotactic response to 5 aromatic compounds. Combined with the effects of outer membrane transporter deletion on chemotaxis and MCP deletion on the PAH degradation, our study demonstrated that the chemoreceptors MCP03030 and MCP18870 can recognize PAHs and their metabolites in the periplasm, triggering metabolism-dependent and metabolism-independent chemotaxis, and be linked with HMW-PAH biodegradation.
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Affiliation(s)
- Yuqian Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiaqing Liang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Shuyue Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Jiebin Yao
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Kai Chen
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Luxi Yang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, School of Life Sciences, Xiamen University, Xiamen 361102, China; State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
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24
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Metagenomics Assessment of Soil Fertilization on the Chemotaxis and Disease Suppressive Genes Abundance in the Maize Rhizosphere. Genes (Basel) 2021; 12:genes12040535. [PMID: 33917127 PMCID: PMC8067831 DOI: 10.3390/genes12040535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 11/19/2022] Open
Abstract
Soil fertility is a function of the level of organic and inorganic substances present in the soil, and it influences the activities of soil-borne microbes, plant growth performance and a host of other beneficial ecological functions. In this metagenomics study, we evaluated the response of maize microbial functional gene diversity involved in chemotaxis, antibiotics, siderophores, and antifungals producing genes within the rhizosphere of maize plants under compost, inorganic fertilizer, and unfertilized conditions. The results show that fertilization treatments at higher compost manure and lower inorganic fertilizer doses as well as maize plants itself in the unfertilized soil through rhizosphere effects share similar influences on the abundance of chemotaxis, siderophores, antifungal, and antibiotics synthesizing genes present in the samples, while higher doses of inorganic fertilizer and lower compost manure treatments significantly repress these genes. The implication is for a disease suppressive soil to be achieved, soil fertilization with high doses of compost manure fertilizer treatments as well as lower inorganic fertilizer should be used to enrich soil fertility and boost the abundance of chemotaxis and disease suppressive genes. Maize crops also should be planted sole or intercropped with other crops to enhance the rhizosphere effect of these plants in promoting the expression and abundance of these beneficial genes in the soil.
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Zeng Y, Charkowski AO. The Role of ATP-Binding Cassette Transporters in Bacterial Phytopathogenesis. PHYTOPATHOLOGY 2021; 111:600-610. [PMID: 33225831 DOI: 10.1094/phyto-06-20-0212-rvw] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Bacteria use selective membrane transporting strategies to support cell survival in different environments. Of the membrane transport systems, ATP-binding cassette (ABC) transporters, which utilize the energy of ATP hydrolysis to deliver substrate across the cytoplasmic membrane, are the largest and most diverse superfamily. These transporters import nutrients, export molecules, and are required for diverse cell functions, including cell division and morphology, gene regulation, surface motility, chemotaxis, and interspecies competition. Phytobacterial pathogens encode numerous ABC transporter homologs compared with related nonphytopathogens, with up to 160 transporters per genome, suggesting that plant pathogens must be able to import or respond to a greater number of molecules compared with saprophytes or animal pathogens. Despite their importance, ABC transporters have been little examined in plant pathogens. To understand bacterial phytopathogenesis and evolution, we need to understand the roles that ABC transporters play in plant-microbe interactions. In this review, we outline a multitude of roles that bacterial ABC transporters play, using both plant and animal pathogens as examples, to emphasize the importance of exploring these transporters in phytobacteriology.
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Affiliation(s)
- Yuan Zeng
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
| | - Amy O Charkowski
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO 80523
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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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Karmakar R. State of the art of bacterial chemotaxis. J Basic Microbiol 2021; 61:366-379. [PMID: 33687766 DOI: 10.1002/jobm.202000661] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/09/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
Bacterial chemotaxis is a biased movement of bacteria toward the beneficial chemical gradient or away from a toxic chemical gradient. This movement is achieved by sensing a chemical gradient by chemoreceptors. In most of the chemotaxis studies, Escherichia coli has been used as a model organism. E. coli have about 4-6 flagella on their surfaces, and the motility is achieved by rotating the flagella. Each flagellum has reversible flagellar motors at its base, which rotate the flagella in counterclockwise and clockwise directions to achieve "run" and "tumble." The chemotaxis of bacteria is regulated by a network of interacting proteins. The sensory signal is processed and transmitted to the flagellar motor by cytoplasmic proteins. Bacterial chemotaxis plays an important role in many biological processes such as biofilm formation, quorum sensing, bacterial pathogenesis, and host infection. Bacterial chemotaxis can be applied for bioremediation, horizontal gene transfer, drug delivery, or maybe some other industry in near future. This review contains an overview of bacterial chemotaxis, recent findings of the physiological importance of bacterial chemotaxis in other biological processes, and the application of bacterial chemotaxis.
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Affiliation(s)
- Richa Karmakar
- Department of Physics, University of California San Diego, La Jolla, California, USA
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28
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Molecular Mechanisms of Campylobacter Biofilm Formation and Quorum Sensing. Curr Top Microbiol Immunol 2021. [PMID: 33620656 DOI: 10.1007/978-3-030-65481-8_11] [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: 09/08/2023]
Abstract
Even though Campylobacter spp. are known to be fastidious organisms, they can survive within the natural environment. One mechanism to withstand unfavourable conditions is the formation of biofilms, a multicellular structure composed of different bacterial and other microbial species which are embedded in an extracellular matrix. High oxygen levels, low substrate concentrations and the presence of external DNA stimulate the biofilm formation by C. jejuni. These external factors trigger internal adaptation processes, e.g. via regulating the expression of genes encoding proteins required for surface structure formation, as well as motility, stress response and antimicrobial resistance. Known genes impacting biofilm formation will be summarized in this review. The formation of biofilms as well as the expression of virulence genes is often regulated in a cell density depending manner by quorum sensing, which is mediated via small signalling molecules termed autoinducers. Even though quorum sensing mechanisms of other bacteria are well understood, knowledge on the role of these mechanisms in C. jejuni biofilm formation is still scarce. The LuxS enzyme involved in generation of autoinducer-2 is present in C. jejuni, but autoinducer receptors have not been identified so far. Phenotypes of C. jejuni strains lacking a functional luxS like reduced growth, motility, oxygen stress tolerance, biofilm formation, adhesion, invasion and colonization are also summarized within this chapter. However, these phenotypes are highly variable in distinct C. jejuni strains and depend on the culture conditions applied.
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Song S, Wood TK. The Primary Physiological Roles of Autoinducer 2 in Escherichia coli Are Chemotaxis and Biofilm Formation. Microorganisms 2021; 9:microorganisms9020386. [PMID: 33672862 PMCID: PMC7918475 DOI: 10.3390/microorganisms9020386] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
Autoinducer 2 (AI-2) is a ubiquitous metabolite but, instead of acting as a "universal signal," relatively few phenotypes have been associated with it, and many scientists believe AI-2 is often a metabolic byproduct rather than a signal. Here, the aim is to present evidence that AI-2 influences both biofilm formation and motility (swarming and chemotaxis), using Escherichia coli as the model system, to establish AI-2 as a true signal with an important physiological role in this bacterium. In addition, AI-2 signaling is compared to the other primary signal of E. coli, indole, and it is shown that they have opposite effects on biofilm formation and virulence.
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Affiliation(s)
- Sooyeon Song
- Department of Animal Science, Jeonbuk National University, Jeonju-si 54896, Jeollabuk-do, Korea;
| | - Thomas K. Wood
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-7000, USA
- Correspondence:
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Sensing of autoinducer-2 by functionally distinct receptors in prokaryotes. Nat Commun 2020; 11:5371. [PMID: 33097715 PMCID: PMC7584622 DOI: 10.1038/s41467-020-19243-5] [Citation(s) in RCA: 79] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 10/01/2020] [Indexed: 12/24/2022] Open
Abstract
Autoinducer-2 (AI-2) is a quorum sensing signal that mediates communication within and between many bacterial species. However, its known receptors (LuxP and LsrB families) are not found in all the bacteria capable of responding to this signaling molecule. Here, we identify a third type of AI-2 receptor, consisting of a dCACHE domain. AI-2 binds to the dCACHE domain of chemoreceptors PctA and TlpQ of Pseudomonas aeruginosa, thus inducing chemotaxis and biofilm formation. Boron-free AI-2 is the preferred ligand for PctA and TlpQ. AI-2 also binds to the dCACHE domains of histidine kinase KinD from Bacillus subtilis and diguanylate cyclase rpHK1S-Z16 from Rhodopseudomonas palustris, enhancing their enzymatic activities. dCACHE domains (especially those belonging to a subfamily that includes the AI-2 receptors identified in the present work) are present in a large number of bacterial and archaeal proteins. Our results support the idea that AI-2 serves as a widely used signaling molecule in the coordination of cell behavior among prokaryotic species. The small molecule AI-2 acts as a quorum sensing signal, mediating communication within and between many bacterial species. Here, the authors identify a new type of AI-2 receptor, consisting of a dCACHE domain that is present in many bacterial and archaeal proteins.
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Bacterial flagellar motor as a multimodal biosensor. Methods 2020; 193:5-15. [PMID: 32640316 DOI: 10.1016/j.ymeth.2020.06.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/04/2020] [Accepted: 06/22/2020] [Indexed: 01/05/2023] Open
Abstract
Bacterial Flagellar Motor is one of nature's rare rotary molecular machines. It enables bacterial swimming and it is the key part of the bacterial chemotactic network, one of the best studied chemical signalling networks in biology, which enables bacteria to direct its movement in accordance with the chemical environment. The network can sense down to nanomolar concentrations of specific chemicals on the time scale of seconds. Motor's rotational speed is linearly proportional to the electrochemical gradients of either proton or sodium driving ions, while its direction is regulated by the chemotactic network. Recently, it has been discovered that motor is also a mechanosensor. Given these properties, we discuss the motor's potential to serve as a multifunctional biosensor and a tool for characterising and studying the external environment, the bacterial physiology itself and single molecular motor biophysics.
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Xiong Q, Liu D, Zhang H, Dong X, Zhang G, Liu Y, Zhang R. Quorum sensing signal autoinducer-2 promotes root colonization of Bacillus velezensis SQR9 by affecting biofilm formation and motility. Appl Microbiol Biotechnol 2020; 104:7177-7185. [PMID: 32621125 DOI: 10.1007/s00253-020-10713-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/07/2020] [Accepted: 06/01/2020] [Indexed: 12/29/2022]
Abstract
Root colonization of beneficial rhizobacteria is critical for their beneficial effects. Quorum sensing (QS) has been reported to affect the colonization of many plant pathogens. However, how QS signals regulate root colonization of beneficial rhizobacteria is unclear. In this study, the QS signal AI-2 synthetase-encoding gene luxS was completely deleted from the genome of the plant beneficial rhizobacterium Bacillus velezensis SQR9, and bioluminescence experiments showed that AI-2 production was blocked. Deletion of luxS reduced biofilm formation, motility, and root colonization of B. velezensis SQR9, while addition of exogenous AI-2 to the mutant restored this phenomenon. These results indicated that AI-2 positively affects the root colonization of B. velezensis SQR9. This study provided new insights for enhancing the colonization of beneficial rhizobacteria. KEY POINTS: • LuxS participated in the synthesis of the quorum sensing signal AI-2 in B. velezensis. • AI-2 enhanced motility, biofilm formation, and root colonization of B. velezensis. • AI-2 stimulated the production of γ-polyglutamic acid by B. velezensis.
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Affiliation(s)
- Qin Xiong
- 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, People's Republic of China
| | - Di 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, People's Republic of China
| | - Huihui Zhang
- Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
| | - Xiaoyan Dong
- 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, People's Republic of China
| | - Guishan Zhang
- 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, People's Republic of China.
| | - 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, People's Republic of China.
| | - Ruifu Zhang
- 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, People's Republic of China.,Jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Nanjing Agricultural University, Nanjing, 210095, People's Republic of China
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Wang S, Payne GF, Bentley WE. Quorum Sensing Communication: Molecularly Connecting Cells, Their Neighbors, and Even Devices. Annu Rev Chem Biomol Eng 2020; 11:447-468. [DOI: 10.1146/annurev-chembioeng-101519-124728] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Quorum sensing (QS) is a molecular signaling modality that mediates molecular-based cell–cell communication. Prevalent in nature, QS networks provide bacteria with a method to gather information from the environment and make decisions based on the intel. With its ability to autonomously facilitate both inter- and intraspecies gene regulation, this process can be rewired to enable autonomously actuated, but molecularly programmed, genetic control. On the one hand, novel QS-based genetic circuits endow cells with smart functions that can be used in many fields of engineering, and on the other, repurposed QS circuitry promotes communication and aids in the development of synthetic microbial consortia. Furthermore, engineered QS systems can probe and intervene in interkingdom signaling between bacteria and their hosts. Lastly, QS is demonstrated to establish conversation with abiotic materials, especially by taking advantage of biological and even electronically induced assembly processes; such QS-incorporated biohybrid devices offer innovative ways to program cell behavior and biological function.
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Affiliation(s)
- Sally Wang
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
| | - Gregory F. Payne
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
| | - William E. Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland 20850, USA
- Robert E. Fischell Institute for Biomedical Devices, University of Maryland, College Park, Maryland 20742, USA
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Miller C, Gilmore J. Detection of Quorum-Sensing Molecules for Pathogenic Molecules Using Cell-Based and Cell-Free Biosensors. Antibiotics (Basel) 2020; 9:antibiotics9050259. [PMID: 32429345 PMCID: PMC7277912 DOI: 10.3390/antibiotics9050259] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/13/2020] [Accepted: 05/14/2020] [Indexed: 11/18/2022] Open
Abstract
Since the discovery and subsequent use of penicillin, antibiotics have been used to treat most bacterial infections in the U.S. Over time, the repeated prescription of many antibiotics has given rise to many antibiotic-resistant microbes. A bacterial strain becomes resistant by horizontal gene transfer, where surviving microbes acquire genetic material or DNA fragments from adjacent bacteria that encode for resistance. In order to avoid significant bacterial resistance, novel and target therapeutics are needed. Further advancement of diagnostic technologies could be used to develop novel treatment strategies. The use of biosensors to detect quorum-sensing signaling molecules has the potential to provide timely diagnostic information toward mitigating the multidrug-resistant bacteria epidemic. Resistance and pathogenesis are controlled by quorum-sensing (QS) circuits. QS systems secrete or passively release signaling molecules when the bacterial concentration reaches a certain threshold. Signaling molecules give an early indication of virulence. Detection of these compounds in vitro or in vivo can be used to identify the onset of infection. Whole-cell and cell-free biosensors have been developed to detect quorum-sensing signaling molecules. This review will give an overview of quorum networks in the most common pathogens found in chronic and acute infections. Additionally, the current state of research surrounding the detection of quorum-sensing molecules will be reviewed. Followed by a discussion of future works toward the advancement of technologies to quantify quorum signaling molecules in chronic and acute infections.
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Yang K, Zhong Q, Qin H, Long Y, Ou H, Ye J, Qu Y. Molecular response mechanism in Escherichia coli under hexabromocyclododecane stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 708:135199. [PMID: 31780180 DOI: 10.1016/j.scitotenv.2019.135199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
The effects of hexabromocyclododecane (HBCD) on the relationship between physiological responses and metabolic networks remains unclear. To this end, cellular growth, apoptosis, reactive oxygen species, exometabolites and the proteome of Escherichia coli were investigated following exposure to 0.1 and 1 μM HBCD. The results showed that although there were no significant changes in the pH value, apoptosis and reactive oxygen species under HBCD stress, cell growth was inhibited. The metabolic network formed by glycolysis, oxidative phosphorylation, amino acids biosynthesis, membrane proteins biosynthesis, ABC transporters, glycogen storage, cell recognition, compound transport and nucleotide excision repair was disrupted. Cell chemotaxis and DNA damage repair were the effective approaches to alleviate HBCD stress. This work improves our understanding of HBCD toxicity and provides insight into the toxicological mechanism of HBCD at the molecular and network levels.
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Affiliation(s)
- Kunliang Yang
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Qiao Zhong
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Huaming Qin
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yan Long
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Huase Ou
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China
| | - Jinshao Ye
- Guangdong Key Laboratory of Environmental Pollution and Health, School of Environment, Jinan University, Guangzhou 510632, Guangdong, China.
| | - Yanfen Qu
- Zhongji Ecological Science & Technology Co., Ltd., Guangzhou 511443, Guangdong, China
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Biphasic chemotaxis of Escherichia coli to the microbiota metabolite indole. Proc Natl Acad Sci U S A 2020; 117:6114-6120. [PMID: 32123098 DOI: 10.1073/pnas.1916974117] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacterial chemotaxis to prominent microbiota metabolites such as indole is important in the formation of microbial communities in the gastrointestinal (GI) tract. However, the basis of chemotaxis to indole is poorly understood. Here, we exposed Escherichia coli to a range of indole concentrations and measured the dynamic responses of individual flagellar motors to determine the chemotaxis response. Below 1 mM indole, a repellent-only response was observed. At 1 mM indole and higher, a time-dependent inversion from a repellent to an attractant response was observed. The repellent and attractant responses were mediated by the Tsr and Tar chemoreceptors, respectively. Also, the flagellar motor itself mediated a repellent response independent of the receptors. Chemotaxis assays revealed that receptor-mediated adaptation to indole caused a bipartite response-wild-type cells were attracted to regions of high indole concentration if they had previously adapted to indole but were otherwise repelled. We propose that indole spatially segregates cells based on their state of adaptation to repel invaders while recruiting beneficial resident bacteria to growing microbial communities within the GI tract.
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Tan PY, Marcos, Liu Y. Modelling bacterial chemotaxis for indirectly binding attractants. J Theor Biol 2020; 487:110120. [PMID: 31857084 DOI: 10.1016/j.jtbi.2019.110120] [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: 07/17/2019] [Revised: 11/09/2019] [Accepted: 12/16/2019] [Indexed: 11/26/2022]
Abstract
In bacterial chemotaxis, chemoattractant molecules may bind either directly or indirectly with receptors within the cell periplasmic space. The indirect binding mechanism, which involves an intermediate periplasmic binding protein, has been reported to increase sensitivity to dilute attractant concentrations as well as range of response. Current mathematical models for bacterial chemotaxis at the population scale do not appear to take the periplasmic binding protein (BP) concentration or the indirect binding mechanics into account. We formulate an indirect binding extension to the existing Rivero equation for chemotactic velocity based on fundamental reversible enzyme kinetics. The formulated indirect binding expression accounts for the periplasmic BP concentration and the dissociation constants for binding between attractant and periplasmic BP, as well as between BP and chemoreceptor. We validate the indirect-binding model using capillary assay simulations of the chemotactic responses of E. coli to the indirectly-binding attractants maltose and AI-2. The predicted response agrees well with experimental data from a number of maltose capillary assay studies conducted in previous literature. The model is also able to achieve good agreement with AI-2 capillary assay data of one study out of two tested. The chemotactic response of E. coli towards AI-2 appears to be of higher complexity due to reports of variable periplasmic BP concentration as well as the low concentration of periplasmic BP relative to the total receptor concentration. Our current model is thus suitable for indirect binding chemotactic response systems with constant periplasmic BP concentration that is significantly larger than the total receptor concentration, such as the response of E. coli towards maltose. Further considerations may be taken into account to model the chemotactic response towards AI-2 with greater accuracy.
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Affiliation(s)
- Pei Yen Tan
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore
| | - Marcos
- School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore.
| | - Yu Liu
- Advanced Environmental Biotechnology Centre, Nanyang Environment & Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, 50 Nanyang Avenue, 639798, Singapore
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Cheng L, Min D, Liu DF, Li WW, Yu HQ. Sensing and Approaching Toxic Arsenate by Shewanella putrefaciens CN-32. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:14604-14611. [PMID: 31747260 DOI: 10.1021/acs.est.9b05890] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Although arsenic at a high concentration imposes strong selective pressure on microbes, various microbes have been found to grow in As-rich environments. So far, little is known about how microbes can sense and move toward arsenate in the environment, and the underlying molecular mechanisms have not been revealed. Here, we report the chemotaxis response toward arsenate (As(V)) by Shewanella putrefaciens CN-32, a model dissimilatory metal-reducing bacterium (DMRB), and elucidate the mechanisms. We find that S. putrefaciens CN-32 exhibits a chemotactic behavior toward As(V) and diverse electron acceptors. To sense As(V), S. putrefaciens CN-32 requires functional arsenate respiratory reductase but does not depend on its metal-reducing-like respiratory pathway. We observe that such a sense is governed by an energy taxis mechanism and mediated by several methyl-accepting chemotaxis proteins (MCPs), rather than a specific MCP. Moreover, we reveal that the chemotactic signal transduction pathway is conserved in Shewanella, and histidine kinase and flagella-mediated motility are essential for taxis toward As(V). This work reverses the conventional view about arsenic as a chemotactic inhibitor to microbes by revealing the positive chemotaxis of Shewanella to As(V).
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Orr AA, Yang J, Sule N, Chawla R, Hull KG, Zhu M, Romo D, Lele PP, Jayaraman A, Manson MD, Tamamis P. Molecular Mechanism for Attractant Signaling to DHMA by E. coli Tsr. Biophys J 2019; 118:492-504. [PMID: 31839263 DOI: 10.1016/j.bpj.2019.11.3382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/05/2019] [Accepted: 11/19/2019] [Indexed: 12/20/2022] Open
Abstract
The attractant chemotaxis response of Escherichia coli to norepinephrine requires that it be converted to 3,4-dihydroxymandelic acid (DHMA) by the monoamine oxidase TynA and the aromatic aldehyde dehydrogenase FeaB. DHMA is sensed by the serine chemoreceptor Tsr, and the attractant response requires that at least one subunit of the periplasmic domain of the Tsr homodimer (pTsr) has an intact serine-binding site. DHMA that is generated in vivo by E. coli is expected to be a racemic mixture of the (R) and (S) enantiomers, so it has been unclear whether one or both chiral forms are active. Here, we used a combination of state-of-the-art tools in molecular docking and simulations, including an in-house simulation-based docking protocol, to investigate the binding properties of (R)-DHMA and (S)-DHMA to E. coli pTsr. Our studies computationally predicted that (R)-DHMA should promote a stronger attractant response than (S)-DHMA because of a consistently greater-magnitude piston-like pushdown of the pTsr α-helix 4 toward the membrane upon binding of (R)-DHMA than upon binding of (S)-DHMA. This displacement is caused primarily by interaction of DHMA with Tsr residue Thr156, which has been shown by genetic studies to be critical for the attractant response to L-serine and DHMA. These findings led us to separate the two chiral species and test their effectiveness as chemoattractants. Both the tethered cell and motility migration coefficient assays validated the prediction that (R)-DHMA is a stronger attractant than (S)-DHMA. Our study demonstrates that refined computational docking and simulation studies combined with experiments can be used to investigate situations in which subtle differences between ligands may lead to diverse chemotactic responses.
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Affiliation(s)
- Asuka A Orr
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Jingyun Yang
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Nitesh Sule
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Ravi Chawla
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Kenneth G Hull
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Mingzhao Zhu
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Daniel Romo
- Department of Chemistry & Biochemistry and CPRIT Synthesis and Drug-Lead Discovery Laboratory, Baylor University, Waco, Texas
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Arul Jayaraman
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas
| | - Michael D Manson
- Department of Biology, Texas A&M University, College Station, Texas.
| | - Phanourios Tamamis
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas.
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Hybrid Two-Component Sensors for Identification of Bacterial Chemoreceptor Function. Appl Environ Microbiol 2019; 85:AEM.01626-19. [PMID: 31492670 DOI: 10.1128/aem.01626-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 08/31/2019] [Indexed: 12/12/2022] Open
Abstract
Soil bacteria adapt to diverse and rapidly changing environmental conditions by sensing and responding to environmental cues using a variety of sensory systems. Two-component systems are a widespread type of signal transduction system present in all three domains of life and typically are comprised of a sensor kinase and a response regulator. Many two-component systems function by regulating gene expression in response to environmental stimuli. The bacterial chemotaxis system is a modified two-component system with additional protein components and a response that, rather than regulating gene expression, involves behavioral adaptation and results in net movement toward or away from a chemical stimulus. Soil bacteria generally have 20 to 40 or more chemoreceptors encoded in their genomes. To simplify the identification of chemoeffectors (ligands) sensed by bacterial chemoreceptors, we constructed hybrid sensor proteins by fusing the sensor domains of Pseudomonas putida chemoreceptors to the signaling domains of the Escherichia coli NarX/NarQ nitrate sensors. Responses to potential attractants were monitored by β-galactosidase assays using an E. coli reporter strain in which the nitrate-responsive narG promoter was fused to lacZ Hybrid receptors constructed from PcaY, McfR, and NahY, which are chemoreceptors for aromatic acids, tricarboxylic acid cycle intermediates, and naphthalene, respectively, were sensitive and specific for detecting known attractants, and the β-galactosidase activities measured in E. coli correlated well with results of chemotaxis assays in the native P. putida strain. In addition, a screen of the hybrid receptors successfully identified new ligands for chemoreceptor proteins and resulted in the identification of six receptors that detect propionate.IMPORTANCE Relatively few of the thousands of chemoreceptors encoded in bacterial genomes have been functionally characterized. More importantly, although methyl-accepting chemotaxis proteins, the major type of chemoreceptors present in bacteria, are easily identified bioinformatically, it is not currently possible to predict what chemicals will bind to a particular chemoreceptor. Chemotaxis is known to play roles in biodegradation as well as in host-pathogen and host-symbiont interactions, but many studies are currently limited by the inability to identify relevant chemoreceptor ligands. The use of hybrid receptors and this simple E. coli reporter system allowed rapid and sensitive screening for potential chemoeffectors. The fusion site chosen for this study resulted in a high percentage of functional hybrids, indicating that it could be used to broadly test chemoreceptor responses from phylogenetically diverse samples. Considering the wide range of chemical attractants detected by soil bacteria, hybrid receptors may also be useful as sensitive biosensors.
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Fernández M, Rico-Jiménez M, Ortega Á, Daddaoua A, García García AI, Martín-Mora D, Torres NM, Tajuelo A, Matilla MA, Krell T. Determination of Ligand Profiles for Pseudomonas aeruginosa Solute Binding Proteins. Int J Mol Sci 2019; 20:ijms20205156. [PMID: 31627455 PMCID: PMC6829864 DOI: 10.3390/ijms20205156] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 01/05/2023] Open
Abstract
Solute binding proteins (SBPs) form a heterogeneous protein family that is found in all kingdoms of life. In bacteria, the ligand-loaded forms bind to transmembrane transporters providing the substrate. We present here the SBP repertoire of Pseudomonas aeruginosa PAO1 that is composed of 98 proteins. Bioinformatic predictions indicate that many of these proteins have a redundant ligand profile such as 27 SBPs for proteinogenic amino acids, 13 proteins for spermidine/putrescine, or 9 proteins for quaternary amines. To assess the precision of these bioinformatic predictions, we have purified 17 SBPs that were subsequently submitted to high-throughput ligand screening approaches followed by isothermal titration calorimetry studies, resulting in the identification of ligands for 15 of them. Experimentation revealed that PA0222 was specific for γ-aminobutyrate (GABA), DppA2 for tripeptides, DppA3 for dipeptides, CysP for thiosulphate, OpuCC for betaine, and AotJ for arginine. Furthermore, RbsB bound D-ribose and D-allose, ModA bound molybdate, tungstate, and chromate, whereas AatJ recognized aspartate and glutamate. The majority of experimentally identified ligands were found to be chemoattractants. Data show that the ligand class recognized by SPBs can be predicted with confidence using bioinformatic methods, but experimental work is necessary to identify the precise ligand profile.
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Affiliation(s)
- Matilde Fernández
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
- present address: Department of Microbiology, Faculty of Pharmacy, University of Granada, Campus de Cartuja s/n, 18071 Granada, Spain.
| | - Miriam Rico-Jiménez
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Álvaro Ortega
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Abdelali Daddaoua
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Ana Isabel García García
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Noel Mesa Torres
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Ana Tajuelo
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain.
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Distinct Chemotaxis Protein Paralogs Assemble into Chemoreceptor Signaling Arrays To Coordinate Signaling Output. mBio 2019; 10:mBio.01757-19. [PMID: 31551333 PMCID: PMC6759762 DOI: 10.1128/mbio.01757-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The assembly of chemotaxis receptors and signaling proteins into polar arrays is universal in motile chemotactic bacteria. Comparative genome analyses indicate that most motile bacteria possess multiple chemotaxis signaling systems, and experimental evidence suggests that signaling from distinct chemotaxis systems is integrated. Here, we identify one such mechanism. We show that paralogs from two chemotaxis systems assemble together into chemoreceptor arrays, forming baseplates comprised of proteins from both chemotaxis systems. These mixed arrays provide a straightforward mechanism for signal integration and coordinated response output from distinct chemotaxis systems. Given that most chemotactic bacteria encode multiple chemotaxis systems and the propensity for these systems to be laterally transferred, this mechanism may be common to ensure chemotaxis signal integration occurs. Most chemotactic motile bacteria possess multiple chemotaxis signaling systems, the functions of which are not well characterized. Chemotaxis signaling is initiated by chemoreceptors that assemble as large arrays, together with chemotaxis coupling proteins (CheW) and histidine kinase proteins (CheA), which form a baseplate with the cytoplasmic tips of receptors. These cell pole-localized arrays mediate sensing, signaling, and signal amplification during chemotaxis responses. Membrane-bound chemoreceptors with different cytoplasmic domain lengths segregate into distinct arrays. Here, we show that a bacterium, Azospirillum brasilense, which utilizes two chemotaxis signaling systems controlling distinct motility parameters, coordinates its chemotactic responses through the production of two separate membrane-bound chemoreceptor arrays by mixing paralogs within chemotaxis baseplates. The polar localization of chemoreceptors of different length classes is maintained in strains that had baseplate signaling proteins from either chemotaxis system but was lost when both systems were deleted. Chemotaxis proteins (CheA and CheW) from each of the chemotaxis signaling systems (Che1 and Che4) could physically interact with one another, and chemoreceptors from both classes present in A. brasilense could interact with Che1 and Che4 proteins. The assembly of paralogs from distinct chemotaxis pathways into baseplates provides a straightforward mechanism for coordinating signaling from distinct pathways, which we predict is not unique to this system given the propensity of chemotaxis systems for horizontal gene transfer.
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Abstract
Bacteria are often found living in aggregated multicellular communities known as biofilms. Biofilms are three-dimensional structures that confer distinct physical and biological properties to the collective of cells living within them. We used agent-based modeling to explore whether local cellular interactions were sufficient to give rise to global structural features of biofilms. Specifically, we asked whether chemorepulsion from a self-produced quorum-sensing molecule, autoinducer-2 (AI-2), was sufficient to recapitulate biofilm growth and cellular organization observed for biofilms of Helicobacter pylori, a common bacterial resident of human stomachs. To carry out this modeling, we modified an existing platform, Individual-based Dynamics of Microbial Communities Simulator (iDynoMiCS), to incorporate three-dimensional chemotaxis, planktonic cells that could join or leave the biofilm structure, and cellular production of AI-2. We simulated biofilm growth of previously characterized H. pylori strains with various AI-2 production and sensing capacities. Using biologically plausible parameters, we were able to recapitulate both the variation in biofilm mass and cellular distributions observed with these strains. Specifically, the strains that were competent to chemotax away from AI-2 produced smaller and more heterogeneously spaced biofilms, whereas the AI-2 chemotaxis-defective strains produced larger and more homogeneously spaced biofilms. The model also provided new insights into the cellular demographics contributing to the biofilm patterning of each strain. Our analysis supports the idea that cellular interactions at small spatial and temporal scales are sufficient to give rise to larger-scale emergent properties of biofilms.IMPORTANCE Most bacteria exist in aggregated, three-dimensional structures called biofilms. Although biofilms play important ecological roles in natural and engineered settings, they can also pose societal problems, for example, when they grow in plumbing systems or on medical implants. Understanding the processes that promote the growth and disassembly of biofilms could lead to better strategies to manage these structures. We had previously shown that Helicobacter pylori bacteria are repulsed by high concentrations of a self-produced molecule, AI-2, and that H. pylori mutants deficient in AI-2 sensing form larger and more homogeneously spaced biofilms. Here, we used computer simulations of biofilm formation to show that local H. pylori behavior of repulsion from high AI-2 could explain the overall architecture of H. pylori biofilms. Our findings demonstrate that it is possible to change global biofilm organization by manipulating local cell behaviors, which suggests that simple strategies targeting cells at local scales could be useful for controlling biofilms in industrial and medical settings.
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Ueda H, Stephens K, Trivisa K, Bentley WE. Bacteria Floc, but Do They Flock? Insights from Population Interaction Models of Quorum Sensing. mBio 2019; 10:e00972-19. [PMID: 31138754 PMCID: PMC6538791 DOI: 10.1128/mbio.00972-19] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 12/23/2022] Open
Abstract
Quorum sensing (QS) enables coordinated, population-wide behavior. QS-active bacteria "communicate" their number density using autoinducers which they synthesize, collect, and interpret. Tangentially, chemotactic bacteria migrate, seeking out nutrients and other molecules. It has long been hypothesized that bacterial behaviors, such as chemotaxis, were the primordial progenitors of complex behaviors of higher-order organisms. Recently, QS was linked to chemotaxis, yet the notion that these behaviors can together contribute to higher-order behaviors has not been shown. Here, we mathematically link flocking behavior, commonly observed in fish and birds, to bacterial chemotaxis and QS by constructing a phenomenological model of population-scale QS-mediated phenomena. Specifically, we recast a previously developed mathematical model of flocking and found that simulated bacterial behaviors aligned well with well-known QS behaviors. This relatively simple system of ordinary differential equations affords analytical analysis of asymptotic behavior and describes cell position and velocity, QS-mediated protein expression, and the surrounding concentrations of an autoinducer. Further, heuristic explorations of the model revealed that the emergence of "migratory" subpopulations occurs only when chemotaxis is directly linked to QS. That is, behaviors were simulated when chemotaxis was coupled to QS and when not. When coupled, the bacterial flocking model predicts the formation of two distinct groups of cells migrating at different speeds in their journey toward an attractant. This is qualitatively similar to phenomena spotted in our Escherichiacoli chemotaxis experiments as well as in analogous work observed over 50 years ago.IMPORTANCE Our modeling efforts show how cell density can affect chemotaxis; they help to explain the roots of subgroup formation in bacterial populations. Our work also reinforces the notion that bacterial mechanisms are at times exhibited in higher-order organisms.
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Affiliation(s)
- Hana Ueda
- Department of Mathematics, University of Maryland College Park, College Park, Maryland, USA
- Graduate Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland College Park, College Park, Maryland, USA
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA
| | - Kristina Stephens
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA
| | - Konstantina Trivisa
- Department of Mathematics, University of Maryland College Park, College Park, Maryland, USA
- Graduate Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland College Park, College Park, Maryland, USA
| | - William E Bentley
- Graduate Program in Applied Mathematics & Statistics, and Scientific Computation, University of Maryland College Park, College Park, Maryland, USA
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, Maryland, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, USA
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Lamb E, Trimble MJ, McCarter LL. Cell-cell communication, chemotaxis and recruitment in Vibrio parahaemolyticus. Mol Microbiol 2019; 112:99-113. [PMID: 30938898 DOI: 10.1111/mmi.14256] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/31/2019] [Indexed: 01/16/2023]
Abstract
Motile bacteria are proficient at finding optimal environments for colonization. Often, they use chemotaxis to sense nutrient availability and dangerous concentrations of toxic chemicals. For many bacteria, the repertoire of chemoreceptors is large, suggesting they possess a broad palate with respect to sensing. However, knowledge of the molecules detected by chemotaxis signal transduction systems is limited. Some bacteria, like Vibrio parahaemolyticus, are social and swarm in groups on surfaces. This marine bacterium and human pathogen secretes the S signal autoinducer, which cues degradation of intracellular c-di-GMP leading to transcription of the swarming program. Here, we report that the S signal also directs motility at a behavioral level by serving as a chemoattractant. The data demonstrate that V. parahaemolyticus senses the S signal using SscL and SscS, homologous methyl-accepting chemotaxis proteins. SscL is required by planktonic bacteria for S signal chemotaxis. SscS plays a role during swarming, and mutants lacking this chemoreceptor swarm faster and produce colonies with more deeply branched swarming fronts than the wild type or the sscL mutant. Other Vibrio species can swim toward the S signal, suggesting a recruitment role for this cell-cell communication molecule in the context of polymicrobial marine communities.
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Affiliation(s)
- Evan Lamb
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Michael J Trimble
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Linda L McCarter
- The Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, 52242, USA
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46
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Torcato IM, Kasal MR, Brito PH, Miller ST, Xavier KB. Identification of novel autoinducer-2 receptors in Clostridia reveals plasticity in the binding site of the LsrB receptor family. J Biol Chem 2019; 294:4450-4463. [PMID: 30696769 DOI: 10.1074/jbc.ra118.006938] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/26/2019] [Indexed: 12/22/2022] Open
Abstract
Autoinducer-2 (AI-2) is unique among quorum-sensing signaling molecules, as it is produced and recognized by a wide variety of bacteria and thus facilitates interspecies communication. To date, two classes of AI-2 receptors have been identified: the LuxP-type, present in the Vibrionales, and the LsrB-type, found in a number of phylogenetically distinct bacterial families. Recently, AI-2 was shown to affect the colonization levels of a variety of bacteria in the microbiome of the mouse gut, including members of the genus Clostridium, but no AI-2 receptor had been identified in this genus. Here, we identify a noncanonical, functional LsrB-type receptor in Clostridium saccharobutylicum. This novel LsrB-like receptor is the first one reported with variations in the binding-site amino acid residues that interact with AI-2. The crystal structure of the C. saccharobutylicum receptor determined at 1.35 Å resolution revealed that it binds the same form of AI-2 as the other known LsrB-type receptors, and isothermal titration calorimetry (ITC) assays showed that binding of AI-2 occurs at a submicromolar concentration. Using phylogenetic analysis, we inferred that the newly identified noncanonical LsrB receptor shares a common ancestor with known LsrB receptors and that noncanonical receptors are present in bacteria from different phyla. This led us to identify putative AI-2 receptors in bacterial species in which no receptors were known, as in bacteria belonging to the Spirochaetes and Actinobacteria phyla. Thus, this work represents a significant step toward understanding how AI-2-mediated quorum sensing influences bacterial interactions in complex biological niches.
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Affiliation(s)
- Inês M Torcato
- From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.,the Instituto de Tecnologia Química e Biológica António Xavier, Universidade NOVA de Lisboa, Avenida da República, 2780-157 Oeiras, Portugal
| | - Meghann R Kasal
- the Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, and
| | - Patrícia H Brito
- From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal.,the Chronic Disease Research Center (CEDOC), NOVA Medical School, Universidade NOVA de Lisboa, Rua Câmara Pestana, 6, 1150-082 Lisboa, Portugal
| | - Stephen T Miller
- the Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore, Pennsylvania 19081, and
| | - Karina B Xavier
- From the Instituto Gulbenkian de Ciência, Rua da Quinta Grande, 6, 2780-156 Oeiras, Portugal,
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Martín-Mora D, Fernández M, Velando F, Ortega Á, Gavira JA, Matilla MA, Krell T. Functional Annotation of Bacterial Signal Transduction Systems: Progress and Challenges. Int J Mol Sci 2018; 19:ijms19123755. [PMID: 30486299 PMCID: PMC6321045 DOI: 10.3390/ijms19123755] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 11/22/2018] [Accepted: 11/22/2018] [Indexed: 01/15/2023] Open
Abstract
Bacteria possess a large number of signal transduction systems that sense and respond to different environmental cues. Most frequently these are transcriptional regulators, two-component systems and chemosensory pathways. A major bottleneck in the field of signal transduction is the lack of information on signal molecules that modulate the activity of the large majority of these systems. We review here the progress made in the functional annotation of sensor proteins using high-throughput ligand screening approaches of purified sensor proteins or individual ligand binding domains. In these assays, the alteration in protein thermal stability following ligand binding is monitored using Differential Scanning Fluorimetry. We illustrate on several examples how the identification of the sensor protein ligand has facilitated the elucidation of the molecular mechanism of the regulatory process. We will also discuss the use of virtual ligand screening approaches to identify sensor protein ligands. Both approaches have been successfully applied to functionally annotate a significant number of bacterial sensor proteins but can also be used to study proteins from other kingdoms. The major challenge consists in the study of sensor proteins that do not recognize signal molecules directly, but that are activated by signal molecule-loaded binding proteins.
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Affiliation(s)
- David Martín-Mora
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, 18008 Granada, Spain.
| | - Matilde Fernández
- 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.
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology 'B' and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence "Campus Mare Nostrum", 30100 Murcia, Spain.
| | - José A Gavira
- Laboratorio de Estudios Cristalográficos, IACT, (CSIC-UGR), Avenida las Palmeras 4, 18100 Armilla, Spain.
| | - Miguel A Matilla
- 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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Matilla MA, Krell T. The effect of bacterial chemotaxis on host infection and pathogenicity. FEMS Microbiol Rev 2018; 42:4563582. [PMID: 29069367 DOI: 10.1093/femsre/fux052] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/19/2017] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis enables microorganisms to move according to chemical gradients. Although this process requires substantial cellular energy, it also affords key physiological benefits, including enhanced access to growth substrates. Another important implication of chemotaxis is that it also plays an important role in infection and disease, as chemotaxis signalling pathways are broadly distributed across a variety of pathogenic bacteria. Furthermore, current research indicates that chemotaxis is essential for the initial stages of infection in different human, animal and plant pathogens. This review focuses on recent findings that have identified specific bacterial chemoreceptors and corresponding chemoeffectors associated with pathogenicity. Pathogenicity-related chemoeffectors are either host and niche-specific signals or intermediates of the host general metabolism. Plant pathogens were found to contain an elevated number of chemotaxis signalling genes and functional studies demonstrate that these genes are critical for their ability to enter the host. The expanding body of knowledge of the mechanisms underlying chemotaxis in pathogens provides a foundation for the development of new therapeutic strategies capable of blocking infection and preventing disease by interfering with chemotactic signalling pathways.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - Tino Krell
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
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Thomas MA, Kleist AB, Volkman BF. Decoding the chemotactic signal. J Leukoc Biol 2018; 104:359-374. [PMID: 29873835 PMCID: PMC6099250 DOI: 10.1002/jlb.1mr0218-044] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 02/25/2018] [Indexed: 12/20/2022] Open
Abstract
From an individual bacterium to the cells that compose the human immune system, cellular chemotaxis plays a fundamental role in allowing cells to navigate, interpret, and respond to their environments. While many features of cellular chemotaxis are shared among systems as diverse as bacteria and human immune cells, the machinery that guides the migration of these model organisms varies widely. In this article, we review current literature on the diversity of chemoattractant ligands, the cell surface receptors that detect and process chemotactic gradients, and the link between signal recognition and the regulation of cellular machinery that allow for efficient directed cellular movement. These facets of cellular chemotaxis are compared among E. coli, Dictyostelium discoideum, and mammalian neutrophils to derive organizational principles by which diverse cell systems sense and respond to chemotactic gradients to initiate cellular migration.
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Affiliation(s)
- Monica A. Thomas
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Andrew B. Kleist
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Brian F. Volkman
- Department of BiochemistryMedical College of WisconsinMilwaukeeWisconsinUSA
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50
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Xavier KB. Bacterial interspecies quorum sensing in the mammalian gut microbiota [C. R. Biologies 341 (2018) https://doi.org/10.1016/j.crvi.2018.03.006]. C R Biol 2018; 341:300. [PMID: 29793840 DOI: 10.1016/j.crvi.2018.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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