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Green HD, Van Horn GT, Williams T, Eberly A, Morales GH, Mann R, Hauter IM, Hadjifrangiskou M, Schmitz JE. Intra-strain colony biofilm heterogeneity in uropathogenic Escherichia coli and the effect of the NlpI lipoprotein. Biofilm 2024; 8:100214. [PMID: 39184815 PMCID: PMC11344014 DOI: 10.1016/j.bioflm.2024.100214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/25/2024] [Accepted: 07/09/2024] [Indexed: 08/27/2024] Open
Abstract
Biofilm growth facilitates the interaction of uropathogenic Escherichia coli (UPEC) with the host environment. The extracellular polymeric substances (EPS) of UPEC biofilms are composed prominently of curli amyloid fiber and cellulose polysaccharide. When the organism is propagated as a colony biofilm on agar media, these macromolecules can generate pronounced macroscopic structures. Moreover, curli/cellulose associate tightly with Congo red, generating a characteristic pink-to-red staining pattern when the media is supplemented with this dye. Among different clinical isolates of UPEC, changes in the abundance of curli/cellulose can lead to diverse colony biofilm phenotypes on a strain-by-strain basis. Nevertheless, for any given isolate, these phenotypes are classically homogenous throughout the colony biofilm. Here, we report that a subset of clinical UPEC isolates display heterogenous 'peppermint' colony biofilms, with distinct pale and red subpopulations. Through isolation of these subpopulations and whole genome sequencing, we demonstrate various emergent mutations associated with the phenomenon, including within the gene encoding the outer membrane lipoprotein nlpI. Deletion of nlpI within independent strain-backgrounds increased biofilm rugosity, while its overexpression induced the peppermint phenotype. Upregulation of EPS-associated proteins and transcripts was likewise observed in the absence of nlpI. Overall, these results demonstrate that EPS elaboration in UPEC is impacted by nlpI. More broadly, this phenomenon of intra-strain colony biofilm heterogeneity may be leveraged as a tool to identify additional members within the broad collection of genes that regulate or otherwise affect biofilm formation.
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Affiliation(s)
- Hamilton D. Green
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Gerald T. Van Horn
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy Williams
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Allison Eberly
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Grace H. Morales
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Robert Mann
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Indiana M. Hauter
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Maria Hadjifrangiskou
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology & Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Jonathan E. Schmitz
- Division of Molecular Pathogenesis, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
- Vanderbilt Institute for Infection, Immunology & Inflammation, Vanderbilt University Medical Center, Nashville, TN, USA
- Center for Personalized Microbiology, Department of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
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He L, Miguel-Romero L, Patkowski JB, Alqurainy N, Rocha EPC, Costa TRD, Fillol-Salom A, Penadés JR. Tail assembly interference is a common strategy in bacterial antiviral defenses. Nat Commun 2024; 15:7539. [PMID: 39215040 PMCID: PMC11364771 DOI: 10.1038/s41467-024-51915-4] [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: 02/02/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Many bacterial immune systems recognize phage structural components to activate antiviral responses, without inhibiting the function of the phage component. These systems can be encoded in specific chromosomal loci, known as defense islands, and in mobile genetic elements such as prophages and phage-inducible chromosomal islands (PICIs). Here, we identify a family of bacterial immune systems, named Tai (for 'tail assembly inhibition'), that is prevalent in PICIs, prophages and P4-like phage satellites. Tai systems protect their bacterial host population from other phages by blocking the tail assembly step, leading to the release of tailless phages incapable of infecting new hosts. To prevent autoimmunity, some Tai-positive phages have an associated counter-defense mechanism that is expressed during the phage lytic cycle and allows for tail formation. Interestingly, the Tai defense and counter-defense genes are organized in a non-contiguous operon, enabling their coordinated expression.
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Affiliation(s)
- Lingchen He
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Laura Miguel-Romero
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Instituto de Biomedicina de Valencia (IBV), CSIC, Valencia, Spain
| | - Jonasz B Patkowski
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences & King Abdullah International Medical Research Centre, Riyadh, Saudi Arabia
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Tiago R D Costa
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Alfred Fillol-Salom
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
- School of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain.
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3
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Ojha R, Krug S, Jones P, Koestler BJ. Intact and mutated Shigella diguanylate cyclases increase c-di-GMP. J Biol Chem 2024; 300:107525. [PMID: 38960033 PMCID: PMC11327459 DOI: 10.1016/j.jbc.2024.107525] [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: 04/09/2024] [Revised: 05/31/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger cyclic di-GMP (c di-GMP) signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but five of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the four intact DGCs in a S. flexneri strain, where these four DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these four DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN, which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC pseudogenes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.
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Affiliation(s)
- Ruchi Ojha
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Stefanie Krug
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Prentiss Jones
- Department of Pathology, Western Michigan University Homer Stryker, M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Benjamin J Koestler
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA.
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4
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Ojha R, Krug S, Jones P, Koestler BJ. Intact and Degenerate Diguanylate Cyclases regulate Shigella Cyclic di-GMP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588579. [PMID: 38645013 PMCID: PMC11030455 DOI: 10.1101/2024.04.08.588579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger c-di-GMP signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but 5 of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the 4 intact DGCs in an S. flexneri strain where these 4 DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these 4 DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN , which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC genes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.
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Berk Ergun Ş, Has EG, Akçelik N, Akçelik M. Characteristics of Bacterial Biofilm Formation in Nasolacrimal Silicone Tubes Post-dacryocystorhinostomy. Cureus 2024; 16:e56112. [PMID: 38618300 PMCID: PMC11014746 DOI: 10.7759/cureus.56112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2024] [Indexed: 04/16/2024] Open
Abstract
PURPOSE To examine the biofilm formation characteristics of bacteria identified at the genus level in samples obtained from silicone tubes after dacryocystorhinostomy surgery. METHODS In the study involving consecutive patients who underwent dacryocystorhinostomy surgery at Ankara Bilkent City Hospital and whose silicone tubes were removed six months after surgery, between January 2023 and May 2023; the tubes were placed in glycerol-PBS (phosphate buffered saline) solution and cultured on descriptive selective media at the genus level. The biofilm-forming properties of the obtained isolates were examined in solid-air and liquid-air interphases. Salmonella Typhimurium ATCC SL1344 strain was used as the control bacterium. RESULTS As a result of the analysis of the samples taken from the patients, Pseudomonas spp. was identified in three of the samples, Staphylococcus spp. in five of the samples, and Streptococcus spp. in one of the samples. Among these samples, except for the bacteria identified in samples one and five, the rest were found to be strong biofilm producers. In all strong biofilm producers, the maximum biofilm production time was determined as 72 h and the incubation temperature was 37°C. The presence of cellulose and amyloid proteins in biofilm matrix structures is identified. Swimming and swarming motilities were observed in all bacterial samples. CONCLUSION Since biofilms are considered potential factors in the pathogenesis of infectious and inflammatory diseases, they are a subject that needs to be thoroughly investigated. In our study, although there were no clinical infections in any of the patients, biofilm formation was detected in the patient samples. The fact that the bacteria exhibited moderate to strong biofilm formation characteristics suggests that these microorganisms could be persistent infectious agents.
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Affiliation(s)
- Şule Berk Ergun
- Department of Ophthalmology, Ankara Bilkent City Hospital, Ankara, TUR
| | - Elif G Has
- Department of Biology, Ankara University Faculty of Science, Ankara, TUR
| | | | - Mustafa Akçelik
- Department of Biology, Ankara University Faculty of Science, Ankara, TUR
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6
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Cancino-Diaz ME, Guerrero-Barajas C, Betanzos-Cabrera G, Cancino-Diaz JC. Nucleotides as Bacterial Second Messengers. Molecules 2023; 28:7996. [PMID: 38138485 PMCID: PMC10745434 DOI: 10.3390/molecules28247996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In addition to comprising monomers of nucleic acids, nucleotides have signaling functions and act as second messengers in both prokaryotic and eukaryotic cells. The most common example is cyclic AMP (cAMP). Nucleotide signaling is a focus of great interest in bacteria. Cyclic di-AMP (c-di-AMP), cAMP, and cyclic di-GMP (c-di-GMP) participate in biological events such as bacterial growth, biofilm formation, sporulation, cell differentiation, motility, and virulence. Moreover, the cyclic-di-nucleotides (c-di-nucleotides) produced in pathogenic intracellular bacteria can affect eukaryotic host cells to allow for infection. On the other hand, non-cyclic nucleotide molecules pppGpp and ppGpp are alarmones involved in regulating the bacterial response to nutritional stress; they are also considered second messengers. These second messengers can potentially be used as therapeutic agents because of their immunological functions on eukaryotic cells. In this review, the role of c-di-nucleotides and cAMP as second messengers in different bacterial processes is addressed.
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Affiliation(s)
- Mario E. Cancino-Diaz
- Departamentos Microbiología and Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, Ciudad de México 11350, Mexico
| | - Claudia Guerrero-Barajas
- Departamento de Bioprocesos, Unidad Profesional Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Av. Acueducto, La Laguna Ticoman, Gustavo A. Madero, Ciudad de México 07340, Mexico;
| | - Gabriel Betanzos-Cabrera
- Área Académica de Nutrición y Medicina, Instituto de Ciencias de la Salud, Universidad Autónoma del Estado de Hidalgo, Carretera Pachuca-Actopan Camino a Tilcuautla s/n, Pueblo San Juan Tilcuautla, Pachuca Hidalgo 42160, Mexico;
| | - Juan C. Cancino-Diaz
- Departamentos Microbiología and Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Manuel Carpio, Plutarco Elías Calles, Miguel Hidalgo, Ciudad de México 11350, Mexico
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7
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Arredondo-Alonso S, Blundell-Hunter G, Fu Z, Gladstone RA, Fillol-Salom A, Loraine J, Cloutman-Green E, Johnsen PJ, Samuelsen Ø, Pöntinen AK, Cléon F, Chavez-Bueno S, De la Cruz MA, Ares MA, Vongsouvath M, Chmielarczyk A, Horner C, Klein N, McNally A, Reis JN, Penadés JR, Thomson NR, Corander J, Taylor PW, McCarthy AJ. Evolutionary and functional history of the Escherichia coli K1 capsule. Nat Commun 2023; 14:3294. [PMID: 37322051 PMCID: PMC10272209 DOI: 10.1038/s41467-023-39052-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage.
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Affiliation(s)
- Sergio Arredondo-Alonso
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | | | - Zuyi Fu
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Rebecca A Gladstone
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Alfred Fillol-Salom
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | | | - Elaine Cloutman-Green
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Pål J Johnsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Anna K Pöntinen
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - François Cléon
- Department of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, Tromsø, Norway
| | - Susana Chavez-Bueno
- University of Missouri Kansas City, Kansas City, USA
- Division of Infectious Diseases, Children's Mercy Hospital Kansas City, UMKC School of Medicine, Kansas City, USA
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Manivanh Vongsouvath
- Lao-Oxford-Mahosot Hospital-Wellcome Trust Research Unit (LOMWRU), Microbiology Laboratory, Mahosot Hospital, Vientiane, Lao PDR
| | - Agnieszka Chmielarczyk
- Faculty of Medicine, Chair of Microbiology, Jagiellonian University Medical College, Czysta str. 18, 31-121, Kraków, Poland
| | - Carolyne Horner
- British Society for Antimicrobial Chemotherapy, Birmingham, UK
| | - Nigel Klein
- Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Joice N Reis
- Laboratory of Pathology and Molecular Biology (LPBM), Gonçalo Moniz Research Institute, Oswaldo Cruz Foundation, Salvador, Brazil
- Faculdade de Farmácia, Universidade Federal da Bahia, Salvador, Brazil
| | - José R Penadés
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, 0317, Oslo, Norway.
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK.
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland.
| | - Peter W Taylor
- School of Pharmacy, University College London, London, UK.
| | - Alex J McCarthy
- Department of Infectious Disease, Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
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Lindberg SK, Willsey GG, Mantis NJ. Flagellar-based motility accelerates IgA-mediated agglutination of Salmonella Typhimurium at high bacterial cell densities. Front Immunol 2023; 14:1193855. [PMID: 37275888 PMCID: PMC10232770 DOI: 10.3389/fimmu.2023.1193855] [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: 03/25/2023] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Introduction Secretory IgA (SIgA) protects the intestinal epithelium from enteric pathogens such as Salmonella enterica serovar Typhimurium (STm) through a process known as immune exclusion, where invading bacteria are aggregated via antibody cross-linking, encased in mucus, and then cleared from the intestinal tract via peristalsis. At high cell densities, the STm aggregates form a tightly packed network that is reminiscent of early bacterial biofilms. However, the underlying mechanism of how SIgA mediates this transition from a motile and invasive state to an avirulent sessile state in STm is currently unknown. Methods In this report, we developed and validated a methodology known as the "snow globe" assay to enable real-time imaging and quantification of STm agglutination by the mouse monoclonal IgA Sal4. Results We observed that agglutination in the snow globe assay was dose-dependent, antigen-specific, and influenced by antibody isotype. We determined that flagellar-based motility was a prerequisite for rapid onset of agglutination, even at high cell densities where cell-cell contacts are expected to be frequent. We also investigated the roles of individual cyclic-di-GMP metabolizing enzymes previously implicated in motility and biofilm formation in Sal4 IgA-mediated agglutination. Discussion Taken together, our results demonstrate that IgA-mediated agglutination is a dynamic process influenced by bacterial motility and cell-cell collisions. We conclude that the snow globe assay is a viable platform to further decipher the molecular and genetic determinants that drive this interaction.
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Affiliation(s)
- Samantha K. Lindberg
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, United States
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Graham G. Willsey
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, United States
| | - Nicholas J. Mantis
- Department of Biomedical Sciences, University at Albany School of Public Health, Albany, NY, United States
- Division of Infectious Diseases, Wadsworth Center, New York State Department of Health, Albany, NY, United States
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Ribeiro JM, Canales J, Costas MJ, Cabezas A, Pinto RM, García-Díaz M, Martín-Cordero P, Cameselle JC. Genomic Distribution of Pro-Virulent cpdB-like Genes in Eubacteria and Comparison of the Enzyme Specificity of CpdB-like Proteins from Salmonella enterica, Escherichia coli and Streptococcus suis. Int J Mol Sci 2023; 24:ijms24044150. [PMID: 36835561 PMCID: PMC9958556 DOI: 10.3390/ijms24044150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The cpdB gene is pro-virulent in avian pathogenic Escherichia coli and in Salmonella enterica, where it encodes a periplasmic protein named CpdB. It is structurally related to cell wall-anchored proteins, CdnP and SntA, encoded by the also pro-virulent cdnP and sntA genes of Streptococcus agalactiae and Streptococcus suis, respectively. CdnP and SntA effects are due to extrabacterial hydrolysis of cyclic-di-AMP, and to complement action interference. The mechanism of CpdB pro-virulence is unknown, although the protein from non-pathogenic E. coli hydrolyzes cyclic dinucleotides. Considering that the pro-virulence of streptococcal CpdB-like proteins is mediated by c-di-AMP hydrolysis, S. enterica CpdB activity was tested as a phosphohydrolase of 3'-nucleotides, 2',3'-cyclic mononucleotides, linear and cyclic dinucleotides, and cyclic tetra- and hexanucleotides. The results help to understand cpdB pro-virulence in S. enterica and are compared with E. coli CpdB and S. suis SntA, including the activity of the latter on cyclic-tetra- and hexanucleotides reported here for the first time. On the other hand, since CpdB-like proteins are relevant to host-pathogen interactions, the presence of cpdB-like genes was probed in eubacterial taxa by TblastN analysis. The non-homogeneous genomic distribution revealed taxa with cpdB-like genes present or absent, identifying eubacteria and plasmids where they can be relevant.
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Affiliation(s)
- João Meireles Ribeiro
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain
| | - José Canales
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain
| | - María Jesús Costas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain
| | - Alicia Cabezas
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain
| | - Rosa María Pinto
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain
| | - Miguel García-Díaz
- Unidad de Aparato Digestivo, Hospital de Zafra, Área de Salud Llerena-Zafra, Servicio Extremeño de Salud, 06300 Zafra, Spain
| | - Paloma Martín-Cordero
- Servicio de Microbiología, Hospital Universitario de Badajoz, Servicio Extremeño de Salud, 06006 Badajoz, Spain
| | - José Carlos Cameselle
- Grupo de Enzimología, Departamento de Bioquímica y Biología Molecular y Genética, Facultad de Medicina y Ciencias de la Salud, Universidad de Extremadura, 06006 Badajoz, Spain
- Correspondence: ; Tel.: +34-924-289-470
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10
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Baek J, Yoon H. Cyclic di-GMP Modulates a Metabolic Flux for Carbon Utilization in Salmonella enterica Serovar Typhimurium. Microbiol Spectr 2023; 11:e0368522. [PMID: 36744926 PMCID: PMC10100716 DOI: 10.1128/spectrum.03685-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 01/16/2023] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar Typhimurium is an enteric pathogen spreading via the fecal-oral route. Transmission across humans, animals, and environmental reservoirs has forced this pathogen to rapidly respond to changing environments and adapt to new environmental conditions. Cyclic di-GMP (c-di-GMP) is a second messenger that controls the transition between planktonic and sessile lifestyles, in response to environmental cues. Our study reveals the potential of c-di-GMP to alter the carbon metabolic pathways in S. Typhimurium. Cyclic di-GMP overproduction decreased the transcription of genes that encode components of three phosphoenolpyruvate (PEP):carbohydrate phosphotransferase systems (PTSs) allocated for the uptake of glucose (PTSGlc), mannose (PTSMan), and fructose (PTSFru). PTS gene downregulation by c-di-GMP was alleviated in the absence of the three regulators, SgrS, Mlc, and Cra, suggesting their intermediary roles between c-di-GMP and PTS regulation. Moreover, Cra was found to bind to the promoters of ptsG, manX, and fruB. In contrast, c-di-GMP increased the transcription of genes important for gluconeogenesis. However, this effect of c-di-GMP in gluconeogenesis disappeared in the absence of Cra, indicating that Cra is a pivotal regulator that coordinates the carbon flux between PTS-mediated sugar uptake and gluconeogenesis, in response to cellular c-di-GMP concentrations. Since gluconeogenesis supplies precursor sugars required for extracellular polysaccharide production, Salmonella may exploit c-di-GMP as a dual-purpose signal that rewires carbon flux from glycolysis to gluconeogenesis and promotes biofilm formation using the end products of gluconeogenesis. This study sheds light on a new role for c-di-GMP in modulating carbon flux, to coordinate bacterial behavior in response to hostile environments. IMPORTANCE Cyclic di-GMP is a central signaling molecule that determines the transition between motile and nonmotile lifestyles in many bacteria. It stimulates biofilm formation at high concentrations but leads to biofilm dispersal and planktonic status at low concentrations. This study provides new insights into the role of c-di-GMP in programming carbon metabolic pathways. An increase in c-di-GMP downregulated the expression of PTS genes important for sugar uptake, while simultaneously upregulating the transcription of genes important for bacterial gluconeogenesis. The directly opposing effects of c-di-GMP on sugar metabolism were mediated by Cra (catabolite repressor/activator), a dual transcriptional regulator that modulates the direction of carbon flow. Salmonella may potentially harness c-di-GMP to promote its survival and fitness in hostile environments via the coordination of carbon metabolic pathways and the induction of biofilm formation.
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Affiliation(s)
- Jiwon Baek
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Republic of Korea
- Department of Applied Chemistry and Biological Engineering, Ajou University, Suwon, Republic of Korea
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11
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Yao Y, Xi N, Hai E, Zhang X, Guo J, Lin Z, Huang W. PA0575 (RmcA) interacts with other c-di-GMP metabolizing proteins in Pseudomonas aeruginosa PAO1. J GEN APPL MICROBIOL 2023; 68:232-241. [PMID: 35732459 DOI: 10.2323/jgam.2022.05.003] [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: 01/28/2023]
Abstract
As a central signaling molecule, c-di-GMP (bis-(3,5)-cyclic diguanosine monophosphate) is becoming the focus for research in bacteria physiology. Pseudomonas aeruginosa PAO1 genome contains highly complicated c-di-GMP metabolizing genes and a number of these proteins have been identified and investigated. Especially, a sophisticated network of these proteins is emerging. In current study, mainly through Bacteria-2-Hybrid assay, we found PA0575 (RmcA), a GGDEF-EAL dual protein, to interact with two other dual proteins of PA4601 (MorA) and PA4959 (FimX). These observations imply the intricacy of c-di-GMP metabolizing protein interactions. Our work thus provides one piece of data to increase the understandings to c-di-GMP signaling.
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Affiliation(s)
- Yanxiang Yao
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - Naren Xi
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - E Hai
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - Xiaomin Zhang
- Research Center of Medical Science and Technology, Ningxia Medical University
| | - Jiayi Guo
- Research Center of Medical Science and Technology, Ningxia Medical University
| | - Zhi Lin
- School of Life Sciences, Tianjin University
| | - Weidong Huang
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
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12
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Alqurainy N, Miguel-Romero L, Moura de Sousa J, Chen J, Rocha EPC, Fillol-Salom A, Penadés JR. A widespread family of phage-inducible chromosomal islands only steals bacteriophage tails to spread in nature. Cell Host Microbe 2023; 31:69-82.e5. [PMID: 36596306 DOI: 10.1016/j.chom.2022.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/06/2022] [Accepted: 12/01/2022] [Indexed: 01/03/2023]
Abstract
Phage satellites are genetic elements that couple their life cycle to that of helper phages they parasitize, interfering with phage packaging through the production of small capsids, where only satellites are packaged. So far, in all analyzed systems, the satellite-sized capsids are composed of phage proteins. Here, we report that a family of phage-inducible chromosomal islands (PICIs), a type of satellites, encodes all the proteins required for both the production of small-sized capsids and the exclusive packaging of the PICIs into these capsids. Therefore, this new family, named capsid-forming PICIs (cf-PICIs), only requires phage tails to generate PICI particles. Remarkably, the representative cf-PICIs are produced with no cost from their helper phages, suggesting that the relationship between these elements is not parasitic. Finally, our phylogenomic studies indicate that cf-PICIs are present both in gram-positive and gram-negative bacteria and have evolved at least three times independently to spread in nature.
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Affiliation(s)
- Nasser Alqurainy
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11426, Saudi Arabia
| | - Laura Miguel-Romero
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK
| | - Jorge Moura de Sousa
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - John Chen
- Department of Microbiology and Immunology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK; Universidad CEU Cardenal Herrera, CEU Universities, Valencia 46115, Spain.
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13
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Pavlova N, Penchovsky R. Bioinformatics and Genomic Analyses of the Suitability of Eight Riboswitches for Antibacterial Drug Targets. Antibiotics (Basel) 2022; 11:antibiotics11091177. [PMID: 36139956 PMCID: PMC9495176 DOI: 10.3390/antibiotics11091177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 11/23/2022] Open
Abstract
Antibiotic resistance (AR) is an acute problem that results in prolonged and debilitating illnesses. AR mortality worldwide is growing and causes a pressing need to research novel mechanisms of action and untested target molecules. This article presents in silico analyses of eight bacterial riboswitches for their suitability for antibacterial drug targets. Most bacterial riboswitches are located in the 5′-untranslated region of messenger RNAs, act as allosteric cis-acting gene control elements, and have not been found in humans before. Sensing metabolites, the riboswitches regulate the synthesis of vital cellular metabolites in various pathogenic bacteria. The analyses performed in this article represent a complete and informative genome-wide bioinformatics analysis of the adequacy of eight riboswitches as antibacterial drug targets in different pathogenic bacteria based on four criteria. Due to the ability of the riboswitch to control biosynthetic pathways and transport proteins of essential metabolites and the presence/absence of alternative biosynthetic pathways, we classified them into four groups based on their suitability for use as antibacterial drug targets guided by our in silico analyses. We concluded that some of them are promising targets for antibacterial drug discovery, such as the PreQ1, MoCo RNA, cyclic-di-GMP I, and cyclic-di-GMP II riboswitches.
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14
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Kharadi RR, Selbmann K, Sundin GW. A complete twelve-gene deletion null mutant reveals that cyclic di-GMP is a global regulator of phase-transition and host colonization in Erwinia amylovora. PLoS Pathog 2022; 18:e1010737. [PMID: 35914003 PMCID: PMC9371280 DOI: 10.1371/journal.ppat.1010737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/11/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is an essential bacterial second messenger that regulates biofilm formation and pathogenicity. To study the global regulatory effect of individual components of the c-di-GMP metabolic system, we deleted all 12 diguanylate cyclase (dgc) and phosphodiesterase (pde)-encoding genes in E. amylovora Ea1189 (Ea1189Δ12). Ea1189Δ12 was impaired in surface attachment due to a transcriptional dysregulation of the type IV pilus and the flagellar filament. A transcriptomic analysis of surface-exposed WT Ea1189 and Ea1189Δ12 cells indicated that genes involved in metabolism, appendage generation and global transcriptional/post-transcriptional regulation were differentially regulated in Ea1189Δ12. Biofilm formation was regulated by all 5 Dgcs, whereas type III secretion and disease development were differentially regulated by specific Dgcs. A comparative transcriptomic analysis of Ea1189Δ8 (lacks all five enzymatically active dgc and 3 pde genes) against Ea1189Δ8 expressing specific dgcs, revealed the presence of a dual modality of spatial and global regulatory frameworks in the c-di-GMP signaling network.
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Affiliation(s)
- Roshni R. Kharadi
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - Kayla Selbmann
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
| | - George W. Sundin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, United States of America
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15
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Bense S, Witte J, Preuße M, Koska M, Pezoldt L, Dröge A, Hartmann O, Müsken M, Schulze J, Fiebig T, Bähre H, Felgner S, Pich A, Häussler S. Pseudomonas aeruginosa post-translational responses to elevated c-di-GMP levels. Mol Microbiol 2022; 117:1213-1226. [PMID: 35362616 DOI: 10.1111/mmi.14902] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/22/2022] [Accepted: 03/27/2022] [Indexed: 11/29/2022]
Abstract
C-di-GMP signaling can directly influence bacterial behavior by affecting the functionality of c-di-GMP-binding proteins. In addition, c-di-GMP can exert a global effect on gene transcription or translation, e.g., via riboswitches or by binding to transcription factors. In this study, we investigated the effects of changes in intracellular c-di-GMP levels on gene expression and protein production in the opportunistic pathogen Pseudomonas aeruginosa. We induced c-di-GMP production via an ectopically introduced diguanylate cyclase and recorded the transcriptional, translational as well as proteomic profile of the cells. We demonstrate that rising levels of c-di-GMP under growth conditions otherwise characterized by low c-di-GMP levels caused a switch to a non-motile, auto-aggregative P. aeruginosa phenotype. This phenotypic switch became apparent before any c-di-GMP-dependent role on transcription, translation, or protein abundance was observed. Our results suggest that rising global c-di-GMP pools first affects the motility phenotype of P. aeruginosa by altering protein functionality and only then global gene transcription.
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Affiliation(s)
- Sarina Bense
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Julius Witte
- Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany.,Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover, Germany
| | - Matthias Preuße
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Michal Koska
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Lorena Pezoldt
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Astrid Dröge
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Oliver Hartmann
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Mathias Müsken
- Central Facility for Microscopy, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Julia Schulze
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Timm Fiebig
- Institute of Clinical Biochemistry, Hannover Medical School, Hannover, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics and Institute of Pharmacology, Hannover Medical School, Hannover, Germany. Infection Research, Hannover, Germany
| | - Sebastian Felgner
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany
| | - Andreas Pich
- Research Core Unit Proteomics and Institute for Toxicology, Hannover Medical School, Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute for Molecular Bacteriology, TWINCORE GmbH, Center of Clinical and Experimental Infection Research, a joint venture of the Hannover Medical School and the Helmholtz Center for Infection Research, Hannover, Germany.,Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark.,Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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16
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Li ML, Jiao J, Zhang B, Shi WT, Yu WH, Tian CF. Global Transcriptional Repression of Diguanylate Cyclases by MucR1 Is Essential for Sinorhizobium-Soybean Symbiosis. mBio 2021; 12:e0119221. [PMID: 34700374 PMCID: PMC8546604 DOI: 10.1128/mbio.01192-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous bacterial second messenger c-di-GMP is intensively studied in pathogens but less so in mutualistic bacteria. Here, we report a genome-wide investigation of functional diguanylate cyclases (DGCs) synthesizing c-di-GMP from two molecules of GTP in Sinorhizobium fredii CCBAU45436, a facultative microsymbiont fixing nitrogen in nodules of diverse legumes, including soybean. Among 25 proteins harboring a putative GGDEF domain catalyzing the biosynthesis of c-di-GMP, eight functional DGCs were identified by heterogenous expression in Escherichia coli in a Congo red binding assay. This screening result was further verified by in vitro enzymatic assay with purified full proteins or the GGDEF domains from representative functional and nonfunctional DGCs. In the same in vitro assay, a functional EAL domain catalyzing the degradation of c-di-GMP into pGpG was identified in a protein that has an inactive GGDEF domain but with an active phosphodiesterase (PDE) function. The identified functional DGCs generally exhibited low transcription levels in soybean nodules compared to free-living cultures, as revealed in transcriptomes. An engineered upregulation of a functional DGC in nodules led to a significant increase of c-di-GMP level and symbiotic defects, which were not observed when a functional EAL domain was upregulated at the same level. Further transcriptional analysis and gel shift assay demonstrated that these functional DGCs were all transcriptionally repressed in nodules by a global pleiotropic regulator, MucR1, that is essential in Sinorhizobium-soybean symbiosis. These findings shed novel insights onto the systematic regulation of c-di-GMP biosynthesis in mutualistic symbiosis. IMPORTANCE The ubiquitous second messenger c-di-GMP is well-known for its role in biofilm formation and host adaptation of pathogens, whereas it is less investigated in mutualistic symbioses. Here, we reveal a cocktail of eight functional diguanylate cyclases (DGCs) catalyzing the biosynthesis of c-di-GMP in a broad-host-range Sinorhizobium that can establish nitrogen-fixing nodules on soybean and many other legumes. These functional DGCs are generally transcribed at low levels in soybean nodules compared to free-living conditions. The engineered nodule-specific upregulation of DGC can elevate the c-di-GMP level and cause symbiotic defects, while the upregulation of a phosphodiesterase that quenches c-di-GMP has no detectable symbiotic defects. Moreover, eight functional DGCs located on two different replicons are all directly repressed in nodules by a global silencer, MucR1, that is essential for Sinorhizobium-soybean symbiosis. These findings represent a novel mechanism of a strategic regulation of the c-di-GMP biosynthesis arsenal in prokaryote-eukaryote interactions.
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Affiliation(s)
- Meng-Lin Li
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Tao Shi
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
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17
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Vasicek EM, O'Neal L, Parsek MR, Fitch J, White P, Gunn JS. L-Arabinose Transport and Metabolism in Salmonella Influences Biofilm Formation. Front Cell Infect Microbiol 2021; 11:698146. [PMID: 34368016 PMCID: PMC8341724 DOI: 10.3389/fcimb.2021.698146] [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: 04/20/2021] [Accepted: 06/21/2021] [Indexed: 11/28/2022] Open
Abstract
L-arabinose inducible promoters are commonly used in gene expression analysis. However, nutrient source and availability also play a role in biofilm formation; therefore, L-arabinose metabolism could impact biofilm development. In this study we examined the impact of L-arabinose on Salmonella enterica serovar Typhimurium (S. Typhimurium) biofilm formation. Using mutants impaired for the transport and metabolism of L-arabinose, we showed that L-arabinose metabolism negatively impacts S. Typhimurium biofilm formation in vitro. When L-arabinose metabolism is abrogated, biofilm formation returned to baseline levels. However, without the ability to import extracellular L-arabinose, biofilm formation significantly increased. Using RNA-Seq we identified several gene families involved in these different phenotypes including curli expression, amino acid synthesis, and L-arabinose metabolism. Several individual candidate genes were tested for their involvement in the L-arabinose-mediated biofilm phenotypes, but most played no significant role. Interestingly, in the presence of L-arabinose the diguanylate cyclase gene adrA was downregulated in wild type S. Typhimurium. Meanwhile cyaA, encoding an adenylate cyclase, was downregulated in an L-arabinose transport mutant. Using an IPTG-inducible plasmid to deplete c-di-GMP via vieA expression, we were able to abolish the increased biofilm phenotype seen in the transport mutant. However, the mechanism by which the L-arabinose import mutant forms significantly larger biofilms remains to be determined. Regardless, these data suggest that L-arabinose metabolism influences intracellular c-di-GMP levels and therefore biofilm formation. These findings are important when considering the use of an L-arabinose inducible promoter in biofilm conditions.
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Affiliation(s)
- Erin M Vasicek
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
| | - Lindsey O'Neal
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - Matthew R Parsek
- Department of Microbiology, University of Washington, Seattle, WA, United States
| | - James Fitch
- The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States.,The Institute for Genomic Medicine, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States
| | - John S Gunn
- Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital, Columbus, OH, United States.,Infectious Diseases Institute, The Ohio State University, Columbus, OH, United States.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, United States
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18
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Krol E, Schäper S, Becker A. Cyclic di-GMP signaling controlling the free-living lifestyle of alpha-proteobacterial rhizobia. Biol Chem 2021; 401:1335-1348. [PMID: 32990642 DOI: 10.1515/hsz-2020-0232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger which has been associated with a motile to sessile lifestyle switch in many bacteria. Here, we review recent insights into c-di-GMP regulated processes related to environmental adaptations in alphaproteobacterial rhizobia, which are diazotrophic bacteria capable of fixing nitrogen in symbiosis with their leguminous host plants. The review centers on Sinorhizobium meliloti, which in the recent years was intensively studied for its c-di-GMP regulatory network.
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Affiliation(s)
- Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Simon Schäper
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
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19
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Dorado‐Morales P, Martínez I, Rivero‐Buceta V, Díaz E, Bähre H, Lasa I, Solano C. Elevated c-di-GMP levels promote biofilm formation and biodesulfurization capacity of Rhodococcus erythropolis. Microb Biotechnol 2021; 14:923-937. [PMID: 33128507 PMCID: PMC8085952 DOI: 10.1111/1751-7915.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/05/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022] Open
Abstract
Bacterial biofilms provide high cell density and a superior adaptation and protection from stress conditions compared to planktonic cultures, making them a very promising approach for bioremediation. Several Rhodococcus strains can desulfurize dibenzothiophene (DBT), a major sulphur pollutant in fuels, reducing air pollution from fuel combustion. Despite multiple efforts to increase Rhodococcus biodesulfurization activity, there is still an urgent need to develop better biocatalysts. Here, we implemented a new approach that consisted in promoting Rhodococcus erythropolis biofilm formation through the heterologous expression of a diguanylate cyclase that led to the synthesis of the biofilm trigger molecule cyclic di-GMP (c-di-GMP). R. erythropolis biofilm cells displayed a significantly increased DBT desulfurization activity when compared to their planktonic counterparts. The improved biocatalyst formed a biofilm both under batch and continuous flow conditions which turns it into a promising candidate for the development of an efficient bioreactor for the removal of sulphur heterocycles present in fossil fuels.
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Affiliation(s)
- Pedro Dorado‐Morales
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| | - Igor Martínez
- Department of Systems BiologyCentro Nacional de BiotecnologíaAgencia Estatal Consejo Superior de Investigaciones CientíficasDarwin 3Madrid28049Spain
| | - Virginia Rivero‐Buceta
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones CientíficasRamiro de Maeztu 9Madrid28040Spain
| | - Eduardo Díaz
- Department of Microbial and Plant BiotechnologyCentro de Investigaciones Biológicas Margarita SalasAgencia Estatal Consejo Superior de Investigaciones CientíficasRamiro de Maeztu 9Madrid28040Spain
| | - Heike Bähre
- Research Core Unit MetabolomicsHannover Medical SchoolCarl‐Neuberg‐Straße 1Hannover30625Germany
| | - Iñigo Lasa
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
| | - Cristina Solano
- Laboratory of Microbial PathogenesisNavarrabiomed‐Universidad Pública de Navarra (UPNA)‐Complejo Hospitalario de Navarra (CHN)IdiSNAIrunlarrea 3PamplonaNavarra31008Spain
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A SNP in the Cache 1 Signaling Domain of Diguanylate Cyclase STM1987 Leads to Increased In Vivo Fitness of Invasive Salmonella Strains. Infect Immun 2021; 89:IAI.00810-20. [PMID: 33468583 DOI: 10.1128/iai.00810-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/08/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) strains are associated with gastroenteritis worldwide but are also the leading cause of bacterial bloodstream infections in sub-Saharan Africa. The invasive NTS (iNTS) strains that cause bloodstream infections differ from standard gastroenteritis-causing strains by >700 single-nucleotide polymorphisms (SNPs). These SNPs are known to alter metabolic pathways and biofilm formation and to contribute to serum resistance and are thought to signify iNTS strains becoming human adapted, similar to typhoid fever-causing Salmonella strains. Identifying SNPs that contribute to invasion or increased virulence has been more elusive. In this study, we identified a SNP in the cache 1 signaling domain of diguanylate cyclase STM1987 in the invasive Salmonella enterica serovar Typhimurium type strain D23580. This SNP was conserved in 118 other iNTS strains analyzed and was comparatively absent in global S Typhimurium isolates associated with gastroenteritis. STM1987 catalyzes the formation of bis-(3',5')-cyclic dimeric GMP (c-di-GMP) and is proposed to stimulate production of cellulose independent of the master biofilm regulator CsgD. We show that the amino acid change in STM1987 leads to a 10-fold drop in cellulose production and increased fitness in a mouse model of acute infection. Reduced cellulose production due to the SNP led to enhanced survival in both murine and human macrophage cell lines. In contrast, loss of CsgD-dependent cellulose production did not lead to any measurable change in in vivo fitness. We hypothesize that the SNP in stm1987 represents a pathoadaptive mutation for iNTS strains.
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21
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Varghese A, Ray S, Verma T, Nandi D. Multicellular String-Like Structure Formation by Salmonella Typhimurium Depends on Cellulose Production: Roles of Diguanylate Cyclases, YedQ and YfiN. Front Microbiol 2021; 11:613704. [PMID: 33381103 PMCID: PMC7769011 DOI: 10.3389/fmicb.2020.613704] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 11/24/2020] [Indexed: 11/22/2022] Open
Abstract
Bacteria face diverse stresses in the environment and, sometimes, respond by forming multi-cellular structures, e.g., biofilms. Here, we report a novel macroscopic and multi-cellular structure formed by Salmonella Typhimurium, which resembles small strings. These string-like structures, ∼1 cm long, are induced under some stress conditions: iron deprivation by 2,2-Bipyridyl or low amounts of antibiotics or ethanol in minimal media. However, cells in strings revert back to planktonic growth upon return to nutrient rich media. Compared to planktonic cells, strings are more resistant to antibiotics and oxidative stress. Also, strains lacking csgD or rpoS, which are defective in the classical rdar biofilm formation, form strings. Furthermore, some biofilm inducing conditions do not result in strings and vice-versa, demonstrating that strings are not related to classical CsgD-dependent biofilms. Cells in a string are held together by cellulose and a strain lacking bcsA, which is defective in cellulose production, does not form strings. In addition, reductive stress conditions such as dithiothreitol (DTT) or mutations in the Disulfide bonding system (DSB) also give rise to strings. The amounts of c-di-GMP are increased upon string formation and studies with single and double deletion strains of the diguanylate cyclases, yedQ (STM1987) primarily and yfiN (STM2672) partly, revealed their importance for string formation. This is the first study showcasing the ability of Salmonella to produce high amounts of cellulose in liquid culture, instead of an interface, in a CsgD-independent manner. The relevance and possible applications of strings in the production of bacterial cellulose and bioremediation are discussed.
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Affiliation(s)
- Alan Varghese
- Undergraduate program, Indian Institute of Science, Bengaluru, India
| | - Semanti Ray
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Taru Verma
- Centre for Biosystems science and engineering, Indian Institute of Science, Bengaluru, India
| | - Dipankar Nandi
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
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22
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Rodriguez-Garcia E, Zabaleta N, Gil-Farina I, Gonzalez-Aparicio M, Echeverz M, Bähre H, Solano C, Lasa I, Gonzalez-Aseguinolaza G, Hommel M. AdrA as a Potential Immunomodulatory Candidate for STING-Mediated Antiviral Therapy That Required Both Type I IFN and TNF-α Production. THE JOURNAL OF IMMUNOLOGY 2020; 206:376-385. [PMID: 33298616 DOI: 10.4049/jimmunol.2000953] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/09/2020] [Indexed: 01/12/2023]
Abstract
Several dinucleotide cyclases, including cyclic GMP-AMP synthase, and their involvement in STING-mediated immunity have been extensively studied. In this study, we tested five bacterial diguanylate cyclases from the Gram-negative bacterium Salmonella Enteritidis, identifying AdrA as the most potent inducer of a STING-mediated IFN response. AdrA wild-type (wt) or its inactive version AdrA mutant (mut) were delivered by an adenovirus (Ad) vector. Dendritic cells obtained from wt mice and infected in vitro with Ad vector containing AdrA wt, but not mut, had increased activation markers and produced large amounts of several immunostimulatory cytokines. For dendritic cells derived from STING-deficient mice, no activation was detected. The potential antiviral activity of AdrA was addressed in hepatitis B virus (HBV)-transgenic and adenovirus-associated virus (AAV)-HBV mouse models. Viremia in serum of Ad AdrA wt-treated mice was reduced significantly compared with that in Ad AdrA mut-injected mice. The viral load in the liver at sacrifice was in line with this finding. To further elucidate the molecular mechanism(s) by which AdrA confers its antiviral function, the response in mice deficient in STING or its downstream effector molecules was analyzed. wt and IFN-αR (IFNAR)-/- animals were additionally treated with anti-TNF-α (Enbrel). Interestingly, albeit less pronounced than in wt mice, in IFNAR-/- and Enbrel-treated wt mice, a reduction of serum viremia was achieved-an observation that was lost in anti-TNF-α-treated IFNAR-/- animals. No effect of AdrA wt was seen in STING-deficient animals. Thus, although STING is indispensable for the antiviral activity of AdrA, type I IFN and TNF-α are both required and act synergistically.
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Affiliation(s)
- Estefania Rodriguez-Garcia
- Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain.,Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain
| | - Nerea Zabaleta
- Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain
| | - Irene Gil-Farina
- Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain
| | - Manuela Gonzalez-Aparicio
- Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain.,Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain
| | - Maite Echeverz
- Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain.,Laboratorio Patogénesis Microbiana, Complejo Hospitalario de Navarra-Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain; and
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany
| | - Cristina Solano
- Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain.,Laboratorio Patogénesis Microbiana, Complejo Hospitalario de Navarra-Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain; and
| | - Iñigo Lasa
- Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain.,Laboratorio Patogénesis Microbiana, Complejo Hospitalario de Navarra-Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain; and
| | - Gloria Gonzalez-Aseguinolaza
- Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain; .,Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain.,Laboratorio Patogénesis Microbiana, Complejo Hospitalario de Navarra-Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain; and
| | - Mirja Hommel
- Terapia Génica y Regulación de la Expresión Génica, Centro de Investigación Médica Aplicada, Universidad de Navarra, 31008 Pamplona, Spain; .,Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain.,Laboratorio Patogénesis Microbiana, Complejo Hospitalario de Navarra-Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra, 31008 Pamplona, Spain; and
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23
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Abstract
Dickeya zeae is the etiological agent of bacterial foot rot disease, which can cause massive economic losses in banana and rice plantations. Genome sequence analysis showed that D. zeae strain EC1 contains multiple c-di-GMP turnover genes, but their roles and regulatory mechanisms in bacterial physiology and virulence remain vague. By generating consecutive in-frame deletion mutants of the genes encoding c-di-GMP biosynthesis and degradation, respectively, we analyzed the individual and collective impacts of these c-di-GMP metabolic genes on the c-di-GMP global pool, bacterial physiology, and virulence. The significance of our study is in identifying the mechanism of c-di-GMP signaling in strain EC1 more clearly, which expands the c-di-GMP regulating patterns in Gram-negative species. The methods and experimental designs in this research will provide a valuable reference for the exploration of the complex c-di-GMP regulation mechanisms in other bacteria. Dickeya zeae is an important and aggressive bacterial phytopathogen that can cause substantial economic losses in banana and rice plantations. We previously showed that c-di-GMP signaling proteins (cyclases/phosphodiesterases) in D. zeae strain EC1 play a significant role in the bacterial sessile-to-motile transition. To determine whether there is any synergistic effect among these c-di-GMP signaling proteins, we prepared a series of mutant strains by generating consecutive in-frame deletions of the genes encoding diguanylate cyclases (which make c-di-GMP) and phosphodiesterases (which break down c-di-GMP), respectively, using EC1 as a parental strain. The results showed that the complete deletion of all the putative diguanylate cyclases resulted in significantly increased bacterial motility and abrogated biofilm formation but did not appear to affect pathogenicity and virulence factor production. In contrast, the deletion of all the c-di-GMP phosphodiesterase genes disabled motility and prevented the invasion of EC1 into rice seeds. By measuring the c-di-GMP concentrations and swimming motility of all the mutants, we propose that c-di-GMP controlled swimming behavior through a multitiered program in a c-di-GMP concentration-dependent manner, which could be described as an L-shaped regression curve. These features are quite different from those that have been shown for other bacterial species such as Salmonella and Caulobacter crescentus. Further analysis identified three c-di-GMP signaling proteins, i.e., PDE10355, DGC14945, and PDE14950, that play dominant roles in influencing the global c-di-GMP pool of strain EC1. The findings from this study highlight the complexity and plasticity of c-di-GMP regulatory circuits in different bacterial species.
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24
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Liang F, Zhang B, Yang Q, Zhang Y, Zheng D, Zhang LQ, Yan Q, Wu X. Cyclic-di-GMP Regulates the Quorum-Sensing System and Biocontrol Activity of Pseudomonas fluorescens 2P24 through the RsmA and RsmE Proteins. Appl Environ Microbiol 2020; 86:e02016-20. [PMID: 33036989 PMCID: PMC7688223 DOI: 10.1128/aem.02016-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 10/04/2020] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas fluorescens 2P24 is a rhizosphere bacterium that protects many crop plants against soilborne diseases caused by phytopathogens. The PcoI/PcoR quorum-sensing (QS) system and polyketide antibiotic 2,4-diacetylphloroglucinol (2,4-DAPG) are particularly relevant to the strain's biocontrol potential. In this study, we investigated the effects of c-di-GMP on the biocontrol activity of strain 2P24. The expression of the Escherichia coli diguanylate cyclase (YedQ) and phosphodiesterase (YhjH) in P. fluorescens 2P24 significantly increased and decreased the cellular concentration of c-di-GMP, respectively. The production of the QS signals N-acyl homoserine lactones (AHLs) and 2,4-DAPG was negatively regulated by c-di-GMP in 2P24. The regulatory proteins RsmA and RsmE were positively regulated by c-di-GMP. Genomic analysis revealed that 2P24 has 23 predicted proteins that contain c-di-GMP-synthesizing or -degrading domains. Among these proteins, C0J56_12915, C0J56_13325, and C0J56_27925 contributed to the production of c-di-GMP and were also involved in the regulation of the QS signal and antibiotic 2,4-DAPG production in P. fluorescens Overexpression of C0J56_12915, C0J56_13325, and C0J56_27925 in 2P24 impaired its root colonization and biocontrol activities. Taken together, these results demonstrated that c-di-GMP played an important role in fine-tuning the biocontrol traits of P. fluorescensIMPORTANCE In various bacteria, the bacterial second messenger c-di-GMP influences a wide range of cellular processes. However, the function of c-di-GMP on biocontrol traits in the plant-beneficial rhizobacteria remains largely unclear. The present work shows that the QS system and polyketide antibiotic 2,4-DAPG production are regulated by c-di-GMP through RsmA and RsmE proteins in P. fluorescens 2P24. The diguanylate cyclases (DGCs) C0J56_12915, C0J56_13325, and C0J56_27925 are especially involved in regulating the biocontrol traits of 2P24. Our work also demonstrated a connection between the Gac/Rsm cascade and the c-di-GMP signaling pathway in P. fluorescens.
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Affiliation(s)
- Fei Liang
- College of Agriculture, Guangxi University, Nanning, China
| | - Bo Zhang
- College of Agriculture, Guangxi University, Nanning, China
| | - Qingqing Yang
- College of Agriculture, Guangxi University, Nanning, China
| | - Yang Zhang
- College of Agriculture, Guangxi University, Nanning, China
| | - Dehong Zheng
- College of Agriculture, Guangxi University, Nanning, China
| | - Li-Qun Zhang
- College of Plant Protection, China Agricultural University, Beijing, China
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana, USA
| | - Xiaogang Wu
- College of Agriculture, Guangxi University, Nanning, China
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25
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Sokaribo AS, Hansen EG, McCarthy M, Desin TS, Waldner LL, MacKenzie KD, Mutwiri G, Herman NJ, Herman DJ, Wang Y, White AP. Metabolic Activation of CsgD in the Regulation of Salmonella Biofilms. Microorganisms 2020; 8:E964. [PMID: 32604994 PMCID: PMC7409106 DOI: 10.3390/microorganisms8070964] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/09/2020] [Accepted: 06/20/2020] [Indexed: 12/31/2022] Open
Abstract
Among human food-borne pathogens, gastroenteritis-causing Salmonella strains have the most real-world impact. Like all pathogens, their success relies on efficient transmission. Biofilm formation, a specialized physiology characterized by multicellular aggregation and persistence, is proposed to play an important role in the Salmonella transmission cycle. In this manuscript, we used luciferase reporters to examine the expression of csgD, which encodes the master biofilm regulator. We observed that the CsgD-regulated biofilm system responds differently to regulatory inputs once it is activated. Notably, the CsgD system became unresponsive to repression by Cpx and H-NS in high osmolarity conditions and less responsive to the addition of amino acids. Temperature-mediated regulation of csgD on agar was altered by intracellular levels of RpoS and cyclic-di-GMP. In contrast, the addition of glucose repressed CsgD biofilms seemingly independent of other signals. Understanding the fine-tuned regulation of csgD can help us to piece together how regulation occurs in natural environments, knowing that all Salmonella strains face strong selection pressures both within and outside their hosts. Ultimately, we can use this information to better control Salmonella and develop strategies to break the transmission cycle.
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Affiliation(s)
- Akosiererem S. Sokaribo
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Elizabeth G. Hansen
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Madeline McCarthy
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
| | - Taseen S. Desin
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
- Basic Sciences Department, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - Landon L. Waldner
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Keith D. MacKenzie
- Institute for Microbial Systems and Society, Faculty of Science, University of Regina, Regina, SK S4S 0A2, Canada;
- Department of Biology, University of Regina, Regina, SK S4S 0A2, Canada
| | - George Mutwiri
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Nancy J. Herman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Dakoda J. Herman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
| | - Yejun Wang
- Department of Cell Biology and Genetics, School of Basic Medicine, Shenzhen University Health Science, Shenzhen 518060, China;
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada; (A.S.S.); (E.G.H.); (M.M.); (L.L.W.); (G.M.J.); (N.J.H.); (D.J.H.)
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada;
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26
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Cho KH, Tryon RG, Kim JH. Screening for Diguanylate Cyclase (DGC) Inhibitors Mitigating Bacterial Biofilm Formation. Front Chem 2020. [DOI: 10.3389/fchem.2020.00264 [doi link]] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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27
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Cho KH, Tryon RG, Kim JH. Screening for Diguanylate Cyclase (DGC) Inhibitors Mitigating Bacterial Biofilm Formation. Front Chem 2020; 8:264. [PMID: 32373581 PMCID: PMC7186502 DOI: 10.3389/fchem.2020.00264] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 03/18/2020] [Indexed: 01/08/2023] Open
Abstract
The majority of bacteria in the natural environment organize themselves into communal biofilms. Biofilm formation benefits bacteria conferring resistance to harmful molecules (e.g., antibiotics, disinfectants, and host immune factors) and coordinating their gene expression through quorum sensing (QS). A primary signaling molecule promoting bacterial biofilm formation is the universal second messenger cyclic di-GMP. This dinucleotide predominantly controls the gene expression of motility, adhesins, and capsule production to coordinate biofilm formation. Cyclic di-GMP is synthesized by diguanylate cyclases (DGCs) that have a GGDEF domain and is degraded by phosphodiesterases (PDEs) containing either an EAL or an HD-GYP domain. Since high cellular c-di-GMP concentrations are correlated with promoting the ability of bacteria to form biofilms, numerous research endeavors to identify chemicals capable of inhibiting the c-di-GMP synthesis activity of DGCs have been performed in order to inhibit bacterial biofilm formation. This review describes currently identified chemical inhibitors that disturb the activity of DGCs and the methods of screening and assay for their discovery.
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Affiliation(s)
- Kyu Hong Cho
- Department of Biology, Indiana State University, Terre Haute, IN, United States
| | - R Grant Tryon
- Department of Biology, Indiana State University, Terre Haute, IN, United States
| | - Jeong-Ho Kim
- Department of Biology and Chemistry, Liberty University, Lynchburg, VA, United States
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28
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Gil C, Latasa C, García-Ona E, Lázaro I, Labairu J, Echeverz M, Burgui S, García B, Lasa I, Solano C. A DIVA vaccine strain lacking RpoS and the secondary messenger c-di-GMP for protection against salmonellosis in pigs. Vet Res 2020; 51:3. [PMID: 31924274 PMCID: PMC6954585 DOI: 10.1186/s13567-019-0730-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/09/2019] [Indexed: 02/06/2023] Open
Abstract
Salmonellosis is the second most common food-borne zoonosis in the European Union, with pigs being a major reservoir of this pathogen. Salmonella control in pig production requires multiple measures amongst which vaccination may be used to reduce subclinical carriage and shedding of prevalent serovars, such as Salmonella enterica serovar Typhimurium. Live attenuated vaccine strains offer advantages in terms of enhancing cell mediated immunity and allowing inoculation by the oral route. However, main failures of these vaccines are the limited cross-protection achieved against heterologous serovars and interference with serological monitoring for infection. We have recently shown that an attenuated S. Enteritidis strain (ΔXIII) is protective against S. Typhimurium in a murine infection model. ΔXIII strain harbours 13 chromosomal deletions that make it unable to produce the sigma factor RpoS and synthesize cyclic-di-GMP (c-di-GMP). In this study, our objectives were to test the protective effects of ΔXIII strain in swine and to investigate if the use of ΔXIII permits the discrimination of vaccinated from infected pigs. Results show that oral vaccination of pre-weaned piglets with ΔXIII cross-protected against a challenge with S. Typhimurium by reducing faecal shedding and ileocaecal lymph nodes colonization, both at the time of weaning and slaughter. Vaccinated pigs showed neither faecal shedding nor tissue persistence of the vaccine strain at weaning, ensuring the absence of ΔXIII strain by the time of slaughter. Moreover, lack of the SEN4316 protein in ΔXIII strain allowed the development of a serological test that enabled the differentiation of infected from vaccinated animals (DIVA).
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Affiliation(s)
- Carmen Gil
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
| | | | - Enrique García-Ona
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
| | - Isidro Lázaro
- Instituto Navarro de Tecnologías e Infraestructuras Agroalimentarias-INTIA, 31610 Villava, Navarra Spain
| | - Javier Labairu
- Instituto Navarro de Tecnologías e Infraestructuras Agroalimentarias-INTIA, 31610 Villava, Navarra Spain
| | - Maite Echeverz
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
| | - Saioa Burgui
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
| | - Begoña García
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
| | - Cristina Solano
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Complejo Hospitalario de Navarra (CHN), IdiSNA, Irunlarrea 3, 31008 Pamplona, Navarra Spain
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29
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Fillol-Salom A, Martínez-Rubio R, Abdulrahman RF, Chen J, Davies R, Penadés JR. Phage-inducible chromosomal islands are ubiquitous within the bacterial universe. THE ISME JOURNAL 2018; 12:2114-2128. [PMID: 29875435 PMCID: PMC6092414 DOI: 10.1038/s41396-018-0156-3] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 04/20/2018] [Accepted: 05/01/2018] [Indexed: 11/15/2022]
Abstract
Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies. We suggest that the PICIs represent two or more distinct lineages, have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms or their prophage cousins. Overall, these findings represent the discovery of a universal class of mobile genetic elements.
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Affiliation(s)
- Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Roser Martínez-Rubio
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113, Moncada, Valencia, Spain
| | - Rezheen F Abdulrahman
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore
| | - Robert Davies
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
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More than Enzymes That Make or Break Cyclic Di-GMP-Local Signaling in the Interactome of GGDEF/EAL Domain Proteins of Escherichia coli. mBio 2017; 8:mBio.01639-17. [PMID: 29018125 PMCID: PMC5635695 DOI: 10.1128/mbio.01639-17] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The bacterial second messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP) ubiquitously promotes bacterial biofilm formation. Intracellular pools of c-di-GMP seem to be dynamically negotiated by diguanylate cyclases (DGCs, with GGDEF domains) and specific phosphodiesterases (PDEs, with EAL or HD-GYP domains). Most bacterial species possess multiple DGCs and PDEs, often with surprisingly distinct and specific output functions. One explanation for such specificity is "local" c-di-GMP signaling, which is believed to involve direct interactions between specific DGC/PDE pairs and c-di-GMP-binding effector/target systems. Here we present a systematic analysis of direct protein interactions among all 29 GGDEF/EAL domain proteins of Escherichia coli Since the effects of interactions depend on coexpression and stoichiometries, cellular levels of all GGDEF/EAL domain proteins were also quantified and found to vary dynamically along the growth cycle. Instead of detecting specific pairs of interacting DGCs and PDEs, we discovered a tightly interconnected protein network of a specific subset or "supermodule" of DGCs and PDEs with a coregulated core of five hyperconnected hub proteins. These include the DGC/PDE proteins representing the c-di-GMP switch that turns on biofilm matrix production in E. coli Mutants lacking these core hub proteins show drastic biofilm-related phenotypes but no changes in cellular c-di-GMP levels. Overall, our results provide the basis for a novel model of local c-di-GMP signaling in which a single strongly expressed master PDE, PdeH, dynamically eradicates global effects of several DGCs by strongly draining the global c-di-GMP pool and thereby restricting these DGCs to serving as local c-di-GMP sources that activate specific colocalized effector/target systems.IMPORTANCE c-di-GMP signaling in bacteria is believed to occur via changes in cellular c-di-GMP levels controlled by antagonistic and potentially interacting pairs of diguanylate cyclases (DGCs) and c-di-GMP phosphodiesterases (PDEs). Our systematic analysis of protein-protein interaction patterns of all 29 GGDEF/EAL domain proteins of E. coli, together with our measurements of cellular c-di-GMP levels, challenges both aspects of this current concept. Knocking out distinct DGCs and PDEs has drastic effects on E. coli biofilm formation without changing the cellular c-di-GMP level. In addition, rather than generally coming in interacting DGC/PDE pairs, a subset of DGCs and PDEs operates as central interaction hubs in a larger "supermodule," with other DGCs and PDEs behaving as "lonely players" without contacts to other c-di-GMP-related enzymes. On the basis of these data, we propose a novel concept of "local" c-di-GMP signaling in bacteria with multiple enzymes that make or break the second messenger c-di-GMP.
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31
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MacKenzie KD, Palmer MB, Köster WL, White AP. Examining the Link between Biofilm Formation and the Ability of Pathogenic Salmonella Strains to Colonize Multiple Host Species. Front Vet Sci 2017; 4:138. [PMID: 29159172 PMCID: PMC5581909 DOI: 10.3389/fvets.2017.00138] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 08/09/2017] [Indexed: 12/11/2022] Open
Abstract
Salmonella are important pathogens worldwide and a predominant number of human infections are zoonotic in nature. The ability of strains to form biofilms, which is a multicellular behavior characterized by the aggregation of cells, is predicted to be a conserved strategy for increased persistence and survival. It may also contribute to the increasing number of infections caused by ingestion of contaminated fruits and vegetables. There is a correlation between biofilm formation and the ability of strains to colonize and replicate within the intestines of multiple host species. These strains predominantly cause localized gastroenteritis infections in humans. In contrast, there are salmonellae that cause systemic, disseminated infections in a select few host species; these “invasive” strains have a narrowed host range, and most are unable to form biofilms. This includes host-restricted Salmonella serovar Typhi, which are only able to infect humans, and atypical gastroenteritis strains associated with the opportunistic infection of immunocompromised patients. From the perspective of transmission, biofilm formation is advantageous for ensuring pathogen survival in the environment. However, from an infection point of view, biofilm formation may be an anti-virulence trait. We do not know if the capacity to form biofilms prevents a strain from accessing the systemic compartments within the host or if loss of the biofilm phenotype reflects a change in a strain’s interaction with the host. In this review, we examine the connections between biofilm formation, Salmonella disease states, degrees of host adaptation, and how this might relate to different transmission patterns. A better understanding of the dynamic lifecycle of Salmonella will allow us to reduce the burden of livestock and human infections caused by these important pathogens.
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Affiliation(s)
- Keith D MacKenzie
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Melissa B Palmer
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wolfgang L Köster
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK, Canada.,Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
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32
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Bhagwat AA, Young L, Smith AD, Bhagwat M. Transcriptomic Analysis of the Swarm Motility Phenotype of Salmonella enterica Serovar Typhimurium Mutant Defective in Periplasmic Glucan Synthesis. Curr Microbiol 2017; 74:1005-1014. [PMID: 28593349 DOI: 10.1007/s00284-017-1267-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 05/14/2017] [Indexed: 12/19/2022]
Abstract
Movement of food-borne pathogens on moist surfaces enables them to migrate towards more favorable niches and facilitate their survival for extended periods of time. Salmonella enterica serovar Typhimurium mutants defective in Osmoregulated periplasmic glucans (OPG) synthesis are unable to exhibit motility on moist surfaces (swarming); however, their mobility in liquid (swim motility) remains unaffected. In order to understand the role of OPG in swarm motility, transcriptomic analysis was performed using cells growing on a moist agar surface. In opgGH deletion mutant, lack of OPG significantly altered transcription of 1039 genes out of total 4712 genes (22%). Introduction of a plasmid-borne copy of opgGH into opgGH deletion mutant restored normal expression of all but 30 genes, indicating a wide-range influence of OPG on gene expression under swarm motility condition. Major pathways that were differentially expressed in opgGH mutants were motility, virulence and invasion, and genes related to the secondary messenger molecule, cyclic di-GMP. These observations provide insights and help explain the pleiotropic nature of OPG mutants such as sub-optimal virulence and competitive organ colonization in mice, biofilm formation, and sensitivity towards detergent stress.
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Affiliation(s)
- Arvind A Bhagwat
- Environmental, Microbial, & Food Safety Laboratory, Beltsville Agriculture Research Center, USDA-ARS (USDA/ARS/EMFSL), 10300 Baltimore Ave., B173, Rm. 204, BARC-E, Beltsville, MD, 20705, USA.
| | - Lynn Young
- National Institutes of Health Library, Division of Library Services, Office of Research Services, National Institute of Health, Building 10, Bethesda, MD, 20892, USA
| | - Allen D Smith
- Diet, Genomics and Immunology Laboratory, Beltsville Human Nutrition Research Center, USDA-ARS, Beltsville, MD, 20705, USA.
| | - Medha Bhagwat
- National Institutes of Health Library, Division of Library Services, Office of Research Services, National Institute of Health, Building 10, Bethesda, MD, 20892, USA
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Bedrunka P, Graumann PL. Subcellular clustering of a putative c-di-GMP-dependent exopolysaccharide machinery affecting macro colony architecture in Bacillus subtilis. ENVIRONMENTAL MICROBIOLOGY REPORTS 2017; 9:211-222. [PMID: 27897378 DOI: 10.1111/1758-2229.12496] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 10/25/2016] [Accepted: 11/16/2016] [Indexed: 06/06/2023]
Abstract
The structure of bacterial biofilms is predominantly established through the secretion of extracellular polymeric substances (EPS). They show that Bacillus subtilis contains an operon (ydaJ-N) whose induction leads to increased Congo Red staining of biofilms and strongly altered biofilm architecture, suggesting that it mediates the production of an unknown exopolysaccharide. Supporting this idea, overproduction of YdaJKLMN leads to cell clumping during exponential growth in liquid culture, and also causes colony morphology alterations in wild type cells, as well as in a mutant background lacking the major exopolysaccharide of B. subtilis. The first gene product of the operon, YdaJ, appears to modify the overproduction effects, but is not essential for cell clumping or altered colony morphology, while the presence of the c-di-GMP receptor YdaK is required, suggesting an involvement of second messenger c-di-GMP. YdaM, YdaN and YdaK colocalize to clusters predominantly at the cell poles and are statically positioned at this subcellular site, similar to other exopolysaccharide machinery components in other bacteria. Their analysis reveals that B. subtilis contains a static subcellular assembly of an EPS machinery that affects cell aggregation and biofilm formation.
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Affiliation(s)
- Patricia Bedrunka
- LOEWE SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse, Marburg, 35043, Germany
| | - Peter L Graumann
- LOEWE SYNMIKRO, LOEWE Center for Synthetic Microbiology and Department of Chemistry, Philipps University Marburg, Hans-Meerwein Strasse, Marburg, 35043, Germany
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34
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Echeverz M, García B, Sabalza A, Valle J, Gabaldón T, Solano C, Lasa I. Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host. PLoS Genet 2017; 13:e1006816. [PMID: 28542593 PMCID: PMC5464674 DOI: 10.1371/journal.pgen.1006816] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 06/08/2017] [Accepted: 05/12/2017] [Indexed: 12/22/2022] Open
Abstract
Many bacteria build biofilm matrices using a conserved exopolysaccharide named PGA or PNAG (poly-β-1,6-N-acetyl-D-glucosamine). Interestingly, while E. coli and other members of the family Enterobacteriaceae encode the pgaABCD operon responsible for PGA synthesis, Salmonella lacks it. The evolutionary force driving this difference remains to be determined. Here, we report that Salmonella lost the pgaABCD operon after the divergence of Salmonella and Citrobacter clades, and previous to the diversification of the currently sequenced Salmonella strains. Reconstitution of the PGA machinery endows Salmonella with the capacity to produce PGA in a cyclic dimeric GMP (c-di-GMP) dependent manner. Outside the host, the PGA polysaccharide does not seem to provide any significant benefit to Salmonella: resistance against chlorine treatment, ultraviolet light irradiation, heavy metal stress and phage infection remained the same as in a strain producing cellulose, the main biofilm exopolysaccharide naturally produced by Salmonella. In contrast, PGA production proved to be deleterious to Salmonella survival inside the host, since it increased susceptibility to bile salts and oxidative stress, and hindered the capacity of S. Enteritidis to survive inside macrophages and to colonize extraintestinal organs, including the gallbladder. Altogether, our observations indicate that PGA is an antivirulence factor whose loss may have been a necessary event during Salmonella speciation to permit survival inside the host. During bacterial evolution, specific traits that optimize the organism’s fitness are selected. The production of exopolysaccharides is widespread among bacteria in which they play a protective shielding role as main constituents of biofilms. In contrast to closely related siblings, Salmonella has lost the capacity to produce the exopolysaccharide PGA. Our study reveals that Salmonella lost pga genes, and that the driving force for such a loss may have been the detrimental impact that PGA has during Salmonella invasion of internal organs where it augments the susceptibility to bile salts and oxygen radicals, reducing bacterial survival inside macrophages and rendering Salmonella avirulent. These results suggest that gene-loss has played an important role during Salmonella evolution.
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Affiliation(s)
- Maite Echeverz
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Begoña García
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Amaia Sabalza
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Jaione Valle
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Cristina Solano
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
- * E-mail: (CS); (IL)
| | - Iñigo Lasa
- Navarrabiomed-Universidad Pública de Navarra-Departamento de Salud, IDISNA, Pamplona, Spain
- * E-mail: (CS); (IL)
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Ahmad I, Cimdins A, Beske T, Römling U. Detailed analysis of c-di-GMP mediated regulation of csgD expression in Salmonella typhimurium. BMC Microbiol 2017; 17:27. [PMID: 28148244 PMCID: PMC5289004 DOI: 10.1186/s12866-017-0934-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 01/17/2017] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The secondary messenger cyclic di-GMP promotes biofilm formation by up regulating the expression of csgD, encoding the major regulator of rdar biofilm formation in Salmonella typhimurium. The GGDEF/EAL domain proteins regulate the c-di-GMP turnover. There are twenty- two GGDEF/EAL domain proteins in the genome of S. typhimurium. In this study, we dissect the role of individual GGDEF/EAL proteins for csgD expression and rdar biofilm development. RESULTS Among twelve GGDEF domains, two proteins upregulate and among fifteen EAL domains, four proteins down regulate csgD expression. We identified two additional GGDEF proteins required to promote optimal csgD expression. With the exception of the EAL domain of STM1703, solely, diguanylate cyclase and phosphodiesterase activities are required to regulate csgD mediated rdar biofilm formation. Identification of corresponding phosphodiesterases and diguanylate cyclases interacting in the csgD regulatory network indicates various levels of regulation by c-di-GMP. The phosphodiesterase STM1703 represses transcription of csgD via a distinct promoter upstream region. CONCLUSION The enzymatic activity and the protein scaffold of GGDEF/EAL domain proteins regulate csgD expression. Thereby, c-di-GMP adjusts csgD expression at multiple levels presumably using a multitude of input signals.
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Affiliation(s)
- Irfan Ahmad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Present Address: Department of Molecular Biology, Umeå University, Umeå, Sweden.,Department of Allied Health Sciences, University of Health Sciences, Lahore, Pakistan
| | - Annika Cimdins
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Timo Beske
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.,Present Address: Department of Biology, Laboratory for Microbiology, Philipps-University Marburg, Marburg, Germany
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
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36
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Murik O, Oren N, Shotland Y, Raanan H, Treves H, Kedem I, Keren N, Hagemann M, Pade N, Kaplan A. What distinguishes cyanobacteria able to revive after desiccation from those that cannot: the genome aspect. Environ Microbiol 2016; 19:535-550. [PMID: 27501380 DOI: 10.1111/1462-2920.13486] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 08/04/2016] [Indexed: 01/15/2023]
Abstract
Filamentous cyanobacteria are the main founders and primary producers in biological desert soil crusts (BSCs) and are likely equipped to cope with one of the harshest environmental conditions on earth including daily hydration/dehydration cycles, high irradiance and extreme temperatures. Here, we resolved and report on the genome sequence of Leptolyngbya ohadii, an important constituent of the BSC. Comparative genomics identified a set of genes present in desiccation-tolerant but not in dehydration-sensitive cyanobacteria. RT qPCR analyses showed that the transcript abundance of many of them is upregulated during desiccation in L. ohadii. In addition, we identified genes where the orthologs detected in desiccation-tolerant cyanobacteria differs substantially from that found in desiccation-sensitive cells. We present two examples, treS and fbpA (encoding trehalose synthase and fructose 1,6-bisphosphate aldolase respectively) where, in addition to the orthologs present in the desiccation-sensitive strains, the resistant cyanobacteria also possess genes with different predicted structures. We show that in both cases the two orthologs are transcribed during controlled dehydration of L. ohadii and discuss the genetic basis for the acclimation of cyanobacteria to the desiccation conditions in desert BSC.
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Affiliation(s)
- Omer Murik
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nadav Oren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Yoram Shotland
- Department of Chemical Engineering, Shamoon College of Engineering, Beer Sheva, 84100, Israel
| | - Hagai Raanan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Haim Treves
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Isaac Kedem
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Nir Keren
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
| | - Martin Hagemann
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, A.-Einstein-Str. 3, Rostock, D-18059, Germany
| | - Nadin Pade
- Institut für Biowissenschaften, Abteilung Pflanzenphysiologie, Universität Rostock, A.-Einstein-Str. 3, Rostock, D-18059, Germany
| | - Aaron Kaplan
- Department of Plant and Environmental Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem, 9190401, Israel
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37
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Latasa C, Echeverz M, García B, Gil C, García-Ona E, Burgui S, Casares N, Hervás-Stubbs S, Lasarte JJ, Lasa I, Solano C. Evaluation of a Salmonella Strain Lacking the Secondary Messenger C-di-GMP and RpoS as a Live Oral Vaccine. PLoS One 2016; 11:e0161216. [PMID: 27537839 PMCID: PMC4990191 DOI: 10.1371/journal.pone.0161216] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 08/02/2016] [Indexed: 01/29/2023] Open
Abstract
Salmonellosis is one of the most important bacterial zoonotic diseases transmitted through the consumption of contaminated food, with chicken and pig related products being key reservoirs of infection. Although numerous studies on animal vaccination have been performed in order to reduce Salmonella prevalence, there is still a need for an ideal vaccine. Here, with the aim of constructing a novel live attenuated Salmonella vaccine candidate, we firstly analyzed the impact of the absence of cyclic-di-GMP (c-di-GMP) in Salmonella virulence. C-di-GMP is an intracellular second messenger that controls a wide range of bacterial processes, including biofilm formation and synthesis of virulence factors, and also modulates the host innate immune response. Our results showed that a Salmonella multiple mutant in the twelve genes encoding diguanylate cyclase proteins that, as a consequence, cannot synthesize c-di-GMP, presents a moderate attenuation in a systemic murine infection model. An additional mutation of the rpoS gene resulted in a synergic attenuating effect that led to a highly attenuated strain, referred to as ΔXIII, immunogenic enough to protect mice against a lethal oral challenge of a S. Typhimurium virulent strain. ΔXIII immunogenicity relied on activation of both antibody and cell mediated immune responses characterized by the production of opsonizing antibodies and the induction of significant levels of IFN-γ, TNF-α, IL-2, IL-17 and IL-10. ΔXIII was unable to form a biofilm and did not survive under desiccation conditions, indicating that it could be easily eliminated from the environment. Moreover, ΔXIII shows DIVA features that allow differentiation of infected and vaccinated animals. Altogether, these results show ΔXIII as a safe and effective live DIVA vaccine.
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Affiliation(s)
- Cristina Latasa
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
- Recombina S. L. Mutilva, Navarra, Spain
| | - Maite Echeverz
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
| | - Begoña García
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
| | - Carmen Gil
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
| | - Enrique García-Ona
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
| | - Saioa Burgui
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
| | - Noelia Casares
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdISNA), University of Navarra, Pamplona, Spain
| | - Sandra Hervás-Stubbs
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdISNA), University of Navarra, Pamplona, Spain
| | - Juan José Lasarte
- Program of Immunology and Immunotherapy, Center for Applied Medical Research (CIMA), Instituto de Investigación Sanitaria de Navarra (IdISNA), University of Navarra, Pamplona, Spain
| | - Iñigo Lasa
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
- Navarrabiomed-Universidad Pública de Navarra, Instituto de Investigación Sanitaria de Navarra (IdISNA), Pamplona, Spain
- * E-mail: (CS); (IL)
| | - Cristina Solano
- Laboratory of Microbial Biofilms, Instituto de Agrobiotecnología (Idab), Universidad Pública de Navarra-CSIC-Gobierno de Navarra, Pamplona, Spain
- * E-mail: (CS); (IL)
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Benedetti I, de Lorenzo V, Nikel PI. Genetic programming of catalytic Pseudomonas putida biofilms for boosting biodegradation of haloalkanes. Metab Eng 2016; 33:109-118. [DOI: 10.1016/j.ymben.2015.11.004] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/02/2015] [Accepted: 11/19/2015] [Indexed: 12/18/2022]
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Diguanylate Cyclases AdrA and STM1987 Regulate Salmonella enterica Exopolysaccharide Production during Plant Colonization in an Environment-Dependent Manner. Appl Environ Microbiol 2015; 82:1237-1248. [PMID: 26655751 DOI: 10.1128/aem.03475-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 12/03/2015] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence indicates that despite exposure to harsh environmental stresses, Salmonella enterica successfully persists on plants, utilizing fresh produce as a vector to animal hosts. Among the important S. enterica plant colonization factors are those involved in biofilm formation. S. enterica biofilm formation is controlled by the signaling molecule cyclic di-GMP and represents a sessile lifestyle on surfaces that protects the bacterium from environmental factors. Thus, the transition from a motile, planktonic lifestyle to a sessile lifestyle may represent a vital step in bacterial success. This study examined the mechanisms of S. enterica plant colonization, including the role of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), the enzymes involved in cyclic di-GMP metabolism. We found that two biofilm components, cellulose and curli, are differentially required at distinct stages in root colonization and that the DGC STM1987 regulates cellulose production in this environment independent of AdrA, the DGC that controls the majority of in vitro cellulose production. In addition, we identified a new function for AdrA in the transcriptional regulation of colanic acid and demonstrated that adrA and colanic acid biosynthesis are associated with S. enterica desiccation tolerance on the leaf surface. Finally, two PDEs with known roles in motility, STM1344 and STM1697, had competitive defects in the phyllosphere, suggesting that regulation of motility is crucial for S. enterica survival in this niche. Our results indicate that specific conditions influence the contribution of individual DGCs and PDEs to bacterial success, perhaps reflective of differential responses to environmental stimuli.
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40
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Cyclic Di-GMP Regulates Multiple Cellular Functions in the Symbiotic Alphaproteobacterium Sinorhizobium meliloti. J Bacteriol 2015; 198:521-35. [PMID: 26574513 DOI: 10.1128/jb.00795-15] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2015] [Accepted: 11/09/2015] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Sinorhizobium meliloti undergoes major lifestyle changes between planktonic states, biofilm formation, and symbiosis with leguminous plant hosts. In many bacteria, the second messenger 3',5'-cyclic di-GMP (c-di-GMP, or cdG) promotes a sessile lifestyle by regulating a plethora of processes involved in biofilm formation, including motility and biosynthesis of exopolysaccharides (EPS). Here, we systematically investigated the role of cdG in S. meliloti Rm2011 encoding 22 proteins putatively associated with cdG synthesis, degradation, or binding. Single mutations in 21 of these genes did not cause evident changes in biofilm formation, motility, or EPS biosynthesis. In contrast, manipulation of cdG levels by overproducing endogenous or heterologous diguanylate cyclases (DGCs) or phosphodiesterases (PDEs) affected these processes and accumulation of N-Acyl-homoserine lactones in the culture supernatant. Specifically, individual overexpression of the S. meliloti genes pleD, SMb20523, SMb20447, SMc01464, and SMc03178 encoding putative DGCs and of SMb21517 encoding a single-domain PDE protein had an impact and resulted in increased levels of cdG. Compared to the wild type, an S. meliloti strain that did not produce detectable levels of cdG (cdG(0)) was more sensitive to acid stress. However, it was symbiotically potent, unaffected in motility, and only slightly reduced in biofilm formation. The SMc01790-SMc01796 locus, homologous to the Agrobacterium tumefaciens uppABCDEF cluster governing biosynthesis of a unipolarly localized polysaccharide, was found to be required for cdG-stimulated biofilm formation, while the single-domain PilZ protein McrA was identified as a cdG receptor protein involved in regulation of motility. IMPORTANCE We present the first systematic genome-wide investigation of the role of 3',5'-cyclic di-GMP (c-di-GMP, or cdG) in regulation of motility, biosynthesis of exopolysaccharides, biofilm formation, quorum sensing, and symbiosis in a symbiotic alpha-rhizobial species. Phenotypes of an S. meliloti strain unable to produce cdG (cdG(0)) demonstrated that this second messenger is not essential for root nodule symbiosis but may contribute to acid tolerance. Our data further suggest that enhanced levels of cdG promote sessility of S. meliloti and uncovered a single-domain PilZ protein as regulator of motility.
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Systematic Identification of Cyclic-di-GMP Binding Proteins in Vibrio cholerae Reveals a Novel Class of Cyclic-di-GMP-Binding ATPases Associated with Type II Secretion Systems. PLoS Pathog 2015; 11:e1005232. [PMID: 26506097 PMCID: PMC4624772 DOI: 10.1371/journal.ppat.1005232] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 09/25/2015] [Indexed: 11/30/2022] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule that regulates a variety of complex processes through a diverse set of c-di-GMP receptor proteins. We have utilized a systematic approach to identify c-di-GMP receptors from the pathogen Vibrio cholerae using the Differential Radial Capillary Action of Ligand Assay (DRaCALA). The DRaCALA screen identified a majority of known c-di-GMP binding proteins in V. cholerae and revealed a novel c-di-GMP binding protein, MshE (VC0405), an ATPase associated with the mannose sensitive hemagglutinin (MSHA) type IV pilus. The known c-di-GMP binding proteins identified by DRaCALA include diguanylate cyclases, phosphodiesterases, PilZ domain proteins and transcription factors VpsT and VpsR, indicating that the DRaCALA-based screen of open reading frame libraries is a feasible approach to uncover novel receptors of small molecule ligands. Since MshE lacks the canonical c-di-GMP-binding motifs, a truncation analysis was utilized to locate the c-di-GMP binding activity to the N-terminal T2SSE_N domain. Alignment of MshE homologs revealed candidate conserved residues responsible for c-di-GMP binding. Site-directed mutagenesis of these candidate residues revealed that the Arg9 residue is required for c-di-GMP binding. The ability of c-di-GMP binding to MshE to regulate MSHA dependent processes was evaluated. The R9A allele, in contrast to the wild type MshE, was unable to complement the ΔmshE mutant for the production of extracellular MshA to the cell surface, reduction in flagella swimming motility, attachment to surfaces and formation of biofilms. Testing homologs of MshE for binding to c-di-GMP identified the type II secretion ATPase of Pseudomonas aeruginosa (PA14_29490) as a c-di-GMP receptor, indicating that type II secretion and type IV pili are both regulated by c-di-GMP. Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial signaling molecule that regulates important bacterial functions, including virulence, antibiotic resistance, biofilm formation and cell division. The list of known c-di-GMP receptors is clearly incomplete. Here we utilized a systematic and unbiased biochemical approach to identify c-di-GMP receptors from the 3,812 genes of the Vibrio cholerae genome. Results from this analysis identified most known c-di-GMP receptors as well as MshE, a protein not known to interact with c-di-GMP. The c-di-GMP binding site was identified at the N-terminus of MshE and requires a conserved arginine residue in the 9th position. MshE is the ATPase that powers the secretion of the MshA pili onto the surface of the bacteria. We show that c-di-GMP binding to MshE is required for MshA export and the function of the pili in attachment and biofilm formation. ATPases responsible for related processes such as type IV pili and type II secretion were also tested for c-di-GMP binding, which identified the P. aeruginosa ATPase PA14_29490 as another c-di-GMP binding protein. These findings reveal a new class of c-di-GMP receptor and raise the possibility that c-di-GMP regulate membrane complexes through direct interaction with related type II secretion and type IV pili ATPases.
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Yuan X, Khokhani D, Wu X, Yang F, Biener G, Koestler BJ, Raicu V, He C, Waters CM, Sundin GW, Tian F, Yang CH. Cross-talk between a regulatory small RNA, cyclic-di-GMP signalling and flagellar regulator FlhDC for virulence and bacterial behaviours. Environ Microbiol 2015; 17:4745-63. [PMID: 26462993 DOI: 10.1111/1462-2920.13029] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 08/14/2015] [Accepted: 08/15/2015] [Indexed: 12/01/2022]
Abstract
Dickeya dadantii is a globally dispersed phytopathogen which causes diseases on a wide range of host plants. This pathogen utilizes the type III secretion system (T3SS) to suppress host defense responses, and secretes pectate lyase (Pel) to degrade the plant cell wall. Although the regulatory small RNA (sRNA) RsmB, cyclic diguanylate monophosphate (c-di-GMP) and flagellar regulator have been reported to affect the regulation of these two virulence factors or multiple cell behaviours such as motility and biofilm formation, the linkage between these regulatory components that coordinate the cell behaviours remain unclear. Here, we revealed a sophisticated regulatory network that connects the sRNA, c-di-GMP signalling and flagellar master regulator FlhDC. We propose multi-tiered regulatory mechanisms that link the FlhDC to the T3SS through three distinct pathways including the FlhDC-FliA-YcgR3937 pathway; the FlhDC-EcpC-RpoN-HrpL pathway; and the FlhDC-rsmB-RsmA-HrpL pathway. Among these, EcpC is the most dominant factor for FlhDC to positively regulate T3SS expression.
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Affiliation(s)
- Xiaochen Yuan
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Devanshi Khokhani
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Xiaogang Wu
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Fenghuan Yang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Gabriel Biener
- Department of Physics, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Benjamin J Koestler
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - Valerica Raicu
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA.,Department of Physics, University of Wisconsin, Milwaukee, WI, 53211, USA
| | - Chenyang He
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Christopher M Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin, Milwaukee, WI, 53211, USA
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Trampari E, Stevenson CEM, Little RH, Wilhelm T, Lawson DM, Malone JG. Bacterial rotary export ATPases are allosterically regulated by the nucleotide second messenger cyclic-di-GMP. J Biol Chem 2015; 290:24470-83. [PMID: 26265469 PMCID: PMC4591828 DOI: 10.1074/jbc.m115.661439] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 01/03/2023] Open
Abstract
The widespread second messenger molecule cyclic di-GMP (cdG) regulates the transition from motile and virulent lifestyles to sessile, biofilm-forming ones in a wide range of bacteria. Many pathogenic and commensal bacterial-host interactions are known to be controlled by cdG signaling. Although the biochemistry of cyclic dinucleotide metabolism is well understood, much remains to be discovered about the downstream signaling pathways that induce bacterial responses upon cdG binding. As part of our ongoing research into the role of cdG signaling in plant-associated Pseudomonas species, we carried out an affinity capture screen for cdG binding proteins in the model organism Pseudomonas fluorescens SBW25. The flagella export AAA+ ATPase FliI was identified as a result of this screen and subsequently shown to bind specifically to the cdG molecule, with a KD in the low micromolar range. The interaction between FliI and cdG appears to be very widespread. In addition to FliI homologs from diverse bacterial species, high affinity binding was also observed for the type III secretion system homolog HrcN and the type VI ATPase ClpB2. The addition of cdG was shown to inhibit FliI and HrcN ATPase activity in vitro. Finally, a combination of site-specific mutagenesis, mass spectrometry, and in silico analysis was used to predict that cdG binds to FliI in a pocket of highly conserved residues at the interface between two FliI subunits. Our results suggest a novel, fundamental role for cdG in controlling the function of multiple important bacterial export pathways, through direct allosteric control of export ATPase proteins.
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Affiliation(s)
| | - Clare E M Stevenson
- the Biological Chemistry Department, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | | | - Thomas Wilhelm
- the Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, United Kingdom, and
| | - David M Lawson
- the Biological Chemistry Department, John Innes Centre, Norwich NR4 7UH, United Kingdom
| | - Jacob G Malone
- From the Molecular Microbiology Department and the School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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Liang ZX. The expanding roles of c-di-GMP in the biosynthesis of exopolysaccharides and secondary metabolites. Nat Prod Rep 2015; 32:663-83. [PMID: 25666534 DOI: 10.1039/c4np00086b] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The cyclic dinucleotide c-di-GMP has emerged in the last decade as a prevalent intracellular messenger that orchestrates the transition between the motile and sessile lifestyles of many bacterial species. The motile-to-sessile transition is often associated with the formation of extracellular matrix-encased biofilm, an organized community of bacterial cells that often contributes to antibiotic resistance and host-pathogen interaction. It is increasingly clear that c-di-GMP controls motility, biofilm formation and bacterial pathogenicity partially through regulating the production of exopolysaccharides (EPS) and small-molecule secondary metabolites. This review summarizes our current understanding of the regulation of EPS biosynthesis by c-di-GMP in a diversity of bacterial species and highlights the emerging role of c-di-GMP in the biosynthesis of small-molecule secondary metabolites.
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Affiliation(s)
- Zhao-Xun Liang
- Division of Structural Biology & Biochemistry, School of Biological Sciences, Nanyang Technological University, Singapore 637551.
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Simm R, Ahmad I, Rhen M, Le Guyon S, Römling U. Regulation of biofilm formation in Salmonella enterica serovar Typhimurium. Future Microbiol 2015; 9:1261-82. [PMID: 25437188 DOI: 10.2217/fmb.14.88] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
In animals, plants and the environment, Salmonella enterica serovar Typhimurium forms the red dry and rough (rdar) biofilm characterized by extracellular matrix components curli and cellulose. With complex expression control by at least ten transcription factors, the bistably expressed orphan response regulator CsgD directs rdar morphotype development. CsgD expression is an integral part of the Hfq regulon and the complex cyclic diguanosine monophosphate signaling network partially controlled by the global RNA-binding protein CsrA. Cell wall turnover and the periplasmic redox status regulate csgD expression on a post-transcriptional level by unknown mechanisms. Furthermore, phosphorylation of CsgD is a potential inactivation and degradation signal in biofilm dissolution. Including complex incoherent feed-forward loops, regulation of biofilm formation versus motility and virulence is of recognized complexity.
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Affiliation(s)
- Roger Simm
- Department of Biochemistry, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Montebello, Oslo, Norway
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MacKenzie KD, Wang Y, Shivak DJ, Wong CS, Hoffman LJL, Lam S, Kröger C, Cameron ADS, Townsend HGG, Köster W, White AP. Bistable expression of CsgD in Salmonella enterica serovar Typhimurium connects virulence to persistence. Infect Immun 2015; 83:2312-26. [PMID: 25824832 PMCID: PMC4432751 DOI: 10.1128/iai.00137-15] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/20/2015] [Indexed: 11/20/2022] Open
Abstract
Pathogenic bacteria often need to survive in the host and the environment, and it is not well understood how cells transition between these equally challenging situations. For the human and animal pathogen Salmonella enterica serovar Typhimurium, biofilm formation is correlated with persistence outside a host, but the connection to virulence is unknown. In this study, we analyzed multicellular-aggregate and planktonic-cell subpopulations that coexist when S. Typhimurium is grown under biofilm-inducing conditions. These cell types arise due to bistable expression of CsgD, the central biofilm regulator. Despite being exposed to the same stresses, the two cell subpopulations had 1,856 genes that were differentially expressed, as determined by transcriptome sequencing (RNA-seq). Aggregated cells displayed the characteristic gene expression of biofilms, whereas planktonic cells had enhanced expression of numerous virulence genes. Increased type three secretion synthesis in planktonic cells correlated with enhanced invasion of a human intestinal cell line and significantly increased virulence in mice compared to the aggregates. However, when the same groups of cells were exposed to desiccation, the aggregates survived better, and the competitive advantage of planktonic cells was lost. We hypothesize that CsgD-based differentiation is a form of bet hedging, with single cells primed for host cell invasion and aggregated cells adapted for persistence in the environment. This allows S. Typhimurium to spread the risks of transmission and ensures a smooth transition between the host and the environment.
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Affiliation(s)
- Keith D MacKenzie
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yejun Wang
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada
| | - Dylan J Shivak
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Cynthia S Wong
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada
| | - Leia J L Hoffman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada
| | - Shirley Lam
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada
| | - Carsten Kröger
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | - Andrew D S Cameron
- Department of Biology, University of Regina, Regina, Saskatchewan, Canada
| | - Hugh G G Townsend
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Wolfgang Köster
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Aaron P White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, Saskatchewan, Canada Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Rajeev L, Luning EG, Altenburg S, Zane GM, Baidoo EEK, Catena M, Keasling JD, Wall JD, Fields MW, Mukhopadhyay A. Identification of a cyclic-di-GMP-modulating response regulator that impacts biofilm formation in a model sulfate reducing bacterium. Front Microbiol 2014; 5:382. [PMID: 25120537 PMCID: PMC4114195 DOI: 10.3389/fmicb.2014.00382] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 07/09/2014] [Indexed: 01/02/2023] Open
Abstract
We surveyed the eight putative cyclic-di-GMP-modulating response regulators (RRs) in Desulfovibrio vulgaris Hildenborough that are predicted to function via two-component signaling. Using purified proteins, we examined cyclic-di-GMP (c-di-GMP) production or turnover in vitro of all eight proteins. The two RRs containing only GGDEF domains (DVU2067, DVU0636) demonstrated c-di-GMP production activity in vitro. Of the remaining proteins, three RRs with HD-GYP domains (DVU0722, DVUA0086, and DVU2933) were confirmed to be Mn2+-dependent phosphodiesterases (PDEs) in vitro and converted c-di-GMP to its linear form, pGpG. DVU0408, containing both c-di-GMP production (GGDEF) and degradation domains (EAL), showed c-di-GMP turnover activity in vitro also with production of pGpG. No c-di-GMP related activity could be assigned to the RR DVU0330, containing a metal-dependent phosphohydrolase HD-OD domain, or to the HD-GYP domain RR, DVU1181. Studies included examining the impact of overexpressed cyclic-di-GMP-modulating RRs in the heterologous host E. coli and led to the identification of one RR, DVU0636, with increased cellulose production. Evaluation of a transposon mutant in DVU0636 indicated that the strain was impaired in biofilm formation and demonstrated an altered carbohydrate:protein ratio relative to the D. vulgaris wild type biofilms. However, grown in liquid lactate/sulfate medium, the DVU0636 transposon mutant showed no growth impairment relative to the wild-type strain. Among the eight candidates, only the transposon disruption mutant in the DVU2067 RR presented a growth defect in liquid culture. Our results indicate that, of the two diguanylate cyclases (DGCs) that function as part of two-component signaling, DVU0636 plays an important role in biofilm formation while the function of DVU2067 has pertinence in planktonic growth.
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Affiliation(s)
- Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eric G Luning
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Sara Altenburg
- Center for Biofilm Engineering, Montana State University Bozeman, MT, USA
| | - Grant M Zane
- Department of Biochemistry, University of Missouri Columbia, MO, USA
| | - Edward E K Baidoo
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Michela Catena
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jay D Keasling
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA ; Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California Berkeley, CA, USA
| | - Judy D Wall
- Department of Biochemistry, University of Missouri Columbia, MO, USA
| | - Matthew W Fields
- Center for Biofilm Engineering, Montana State University Bozeman, MT, USA ; Department of Microbiology and Immunology, Montana State University Bozeman, MT, USA
| | - Aindrila Mukhopadhyay
- Physical Biosciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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Menendez-Bravo S, Comba S, Sabatini M, Arabolaza A, Gramajo H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab Eng 2014; 24:97-106. [DOI: 10.1016/j.ymben.2014.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 04/29/2014] [Accepted: 05/05/2014] [Indexed: 01/25/2023]
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Vergara-Irigaray M, Fookes MC, Thomson NR, Tang CM. RNA-seq analysis of the influence of anaerobiosis and FNR on Shigella flexneri. BMC Genomics 2014; 15:438. [PMID: 24907032 PMCID: PMC4229854 DOI: 10.1186/1471-2164-15-438] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 05/23/2014] [Indexed: 01/03/2023] Open
Abstract
Background Shigella flexneri is an important human pathogen that has to adapt to the anaerobic environment in the gastrointestinal tract to cause dysentery. To define the influence of anaerobiosis on the virulence of Shigella, we performed deep RNA sequencing to identify transcriptomic differences that are induced by anaerobiosis and modulated by the anaerobic Fumarate and Nitrate Reduction regulator, FNR. Results We found that 528 chromosomal genes were differentially expressed in response to anaerobic conditions; of these, 228 genes were also influenced by FNR. Genes that were up-regulated in anaerobic conditions are involved in carbon transport and metabolism (e.g. ptsG, manX, murQ, cysP, cra), DNA topology and regulation (e.g. ygiP, stpA, hns), host interactions (e.g. yciD, nmpC, slyB, gapA, shf, msbB) and survival within the gastrointestinal tract (e.g. shiA, ospI, adiY, cysP). Interestingly, there was a marked effect of available oxygen on genes involved in Type III secretion system (T3SS), which is required for host cell invasion and pathogenesis. These genes, located on the large Shigella virulence plasmid, were down regulated in anaerobiosis in an FNR-dependent manner. We also confirmed anaerobic induction of csrB and csrC small RNAs in an FNR-independent manner. Conclusions Anaerobiosis promotes survival and adaption strategies of Shigella, while modulating virulence plasmid genes involved in T3SS-mediated host cell invasion. The influence of FNR on this process is more extensive than previously appreciated, although aside from the virulence plasmid, this transcriptional regulator does not govern expression of genes on other horizontally acquired sequences on the chromosome such as pathogenicity islands. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-438) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Christoph M Tang
- Sir William Dunn School of Pathology, Oxford University, Oxford, United Kingdom.
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50
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The Pseudomonas aeruginosa diguanylate cyclase GcbA, a homolog of P. fluorescens GcbA, promotes initial attachment to surfaces, but not biofilm formation, via regulation of motility. J Bacteriol 2014; 196:2827-41. [PMID: 24891445 DOI: 10.1128/jb.01628-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cyclic di-GMP is a conserved signaling molecule regulating the transitions between motile and sessile modes of growth in a variety of bacterial species. Recent evidence suggests that Pseudomonas species harbor separate intracellular pools of c-di-GMP to control different phenotypic outputs associated with motility, attachment, and biofilm formation, with multiple diguanylate cyclases (DGCs) playing distinct roles in these processes, yet little is known about the potential conservation of functional DGCs across Pseudomonas species. In the present study, we demonstrate that the P. aeruginosa homolog of the P. fluorescens DGC GcbA involved in promoting biofilm formation via regulation of swimming motility likewise synthesizes c-di-GMP to regulate surface attachment via modulation of motility, however, without affecting subsequent biofilm formation. P. aeruginosa GcbA was found to regulate flagellum-driven motility by suppressing flagellar reversal rates in a manner independent of viscosity, surface hardness, and polysaccharide production. P. fluorescens GcbA was found to be functional in P. aeruginosa and was capable of restoring phenotypes associated with inactivation of gcbA in P. aeruginosa to wild-type levels. Motility and attachment of a gcbA mutant strain could be restored to wild-type levels via overexpression of the small regulatory RNA RsmZ. Furthermore, epistasis analysis revealed that while both contribute to the regulation of initial surface attachment and flagellum-driven motility, GcbA and the phosphodiesterase DipA act within different signaling networks to regulate these processes. Our findings expand the complexity of c-di-GMP signaling in the regulation of the motile-sessile switch by providing yet another potential link to the Gac/Rsm network and suggesting that distinct c-di-GMP-modulating signaling pathways can regulate a single phenotypic output.
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