1
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Wang K, Li W, Cui H, Qin S. Phylogenetic distribution and characterization of conserved C-di-GMP metabolizing proteins in filamentous cyanobacterium Arthrospira. Gene 2024; 927:148643. [PMID: 38844269 DOI: 10.1016/j.gene.2024.148643] [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: 01/22/2024] [Revised: 04/18/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Cyclic diguanosine monophosphate (c-di-GMP) is a second messenger in bacteria that regulates multiple biological functions, including biofilm formation, virulence, and intercellular communication. However, c-di-GMP signaling is virtually unknown in economically important filamentous cyanobacteria, Arthrospira. In this study, we predicted 31 genes encoding GGDEF-domain proteins from A. platensis NIES39 as potential diguanylate cyclases (DGCs). Phylogenetic distribution analysis showed five genes (RS09460, RS04865, RS26155, M01840, and E02220) with highly conserved distribution across 25 Arthrospira strains. Adc1 encoded by RS09460 was further characterized as a typical DGC. By establishing the genetic transformation system of Arthrospira, we demonstrated that the overexpression of Adc1 promoted the production of extracellular polymeric substances (EPS), which in turn caused the aggregation of filaments. We also confirmed that RS04865 and RS26155 may encode active DGCs, while enzymatic activity assays showed that proteins encoded by M01840 and E02220 have phosphodiesterase (PDE) activity. Meta-analysis revealed that the expression profiles of RS09460 and RS04865 were unaffected under 31 conditions, suggesting that they may function as conserved genes in maintaining the basal level of c-di-GMP in Arthrospira. In summary, this report will provide the basis for further studies of c-di-GMP signal in Arthrospira.
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Affiliation(s)
- Kang Wang
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wenjun Li
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Hongli Cui
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Song Qin
- Key Laboratory of Coastal Biology and Biological Resource Utilization, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
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2
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Rico-Jiménez M, Udaondo Z, Krell T, Matilla MA. Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica. mSystems 2024; 9:e0016524. [PMID: 38837409 PMCID: PMC11264596 DOI: 10.1128/msystems.00165-24] [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: 02/02/2024] [Accepted: 04/26/2024] [Indexed: 06/07/2024] Open
Abstract
The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria. IMPORTANCE Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.
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Affiliation(s)
- Miriam Rico-Jiménez
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Zulema Udaondo
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, Arkansas, Spain
| | - Tino Krell
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Miguel A. Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
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3
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Lai LY, Satishkumar N, Cardozo S, Hemmadi V, Marques LB, Huang L, Filipe SR, Pinho MG, Chambers HF, Chatterjee SS. Altered PBP4 and GdpP functions synergistically mediate MRSA-like high-level, broad-spectrum β-lactam resistance in Staphylococcus aureus. mBio 2024; 15:e0288923. [PMID: 38530033 PMCID: PMC11077961 DOI: 10.1128/mbio.02889-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/04/2024] [Indexed: 03/27/2024] Open
Abstract
Infections caused by Staphylococcus aureus are a leading cause of mortality worldwide. S. aureus infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are particularly difficult to treat due to their resistance to next-generation β-lactams (NGBs) such as methicillin, nafcillin, and oxacillin. Resistance to NGBs, which is alternatively known as broad-spectrum β-lactam resistance, is classically mediated by PBP2a, a penicillin-binding protein encoded by mecA (or mecC) in MRSA. Thus, presence of mec genes among S. aureus spp. serves as the predictor of resistance to NGBs and facilitates determination of the proper therapeutic strategy for a staphylococcal infection. Although far less appreciated, mecA-deficient S. aureus strains can also exhibit NGB resistance. These strains, which are collectively termed as methicillin-resistant lacking mec (MRLM), are currently being identified in increasing numbers among natural resistant isolates of S. aureus. The mechanism/s through which MRLMs produce resistance to NGBs remains unknown. In this study, we demonstrate that mutations that alter PBP4 and GdpP functions, which are often present among MRLMs, can synergistically mediate resistance to NGBs. Furthermore, our results unravel that this novel mechanism potentially enables MRLMs to produce resistance toward NGBs at levels comparable to those of MRSAs. Our study provides a fresh new perspective about alternative mechanisms of NGB resistance, challenging our current overall understanding of high-level, broad-spectrum β-lactam resistance in S. aureus. It thus suggests reconsideration of the current approach toward diagnosis and treatment of β-lactam-resistant S. aureus infections. IMPORTANCE In Staphylococcus aureus, high-level, broad-spectrum resistance to β-lactams such as methicillin, also referred to as methicillin resistance, is largely attributed to mecA. This study demonstrates that S. aureus strains that lack mecA but contain mutations that functionally alter PBP4 and GdpP can also mediate high-level, broad-spectrum resistance to β-lactams. Resistance brought about by the synergistic action of functionally altered PBP4 and GdpP was phenotypically comparable to that displayed by mecA, as seen by increased bacterial survival in the presence of β-lactams. An analysis of mutations detected in naturally isolated strains of S. aureus revealed that a significant proportion of them had similar pbp4 and GGDEF domain protein containing phosphodiesterase (gdpP) mutations, making this study clinically significant. This study not only identifies important players of non-classical mechanisms of β-lactam resistance but also indicates reconsideration of current clinical diagnosis and treatment protocols of S. aureus infections.
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Affiliation(s)
- Li-Yin Lai
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Sasha Cardozo
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Vijay Hemmadi
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
| | - Leonor B. Marques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Liusheng Huang
- Department of Clinical Pharmacy, Drug Research Unit, University of California, San Francisco, California, USA
| | - Sergio R. Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Mariana G. Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Henry F. Chambers
- Division of Infectious Diseases, School of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Som S. Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, Baltimore, Maryland, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, Maryland, USA
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4
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Lai LY, Satishkumar N, Cardozo S, Hemmadi V, Marques LB, Huang L, Filipe SR, Pinho MG, Chambers HF, Chatterjee SS. Altered PBP4 and GdpP functions synergistically mediate MRSA-like high-level, broad-spectrum β-lactam resistance in Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.564222. [PMID: 37961375 PMCID: PMC10634853 DOI: 10.1101/2023.10.26.564222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Infections caused by Staphylococcus aureus are a leading cause of mortality worldwide. S. aureus infections caused by Methicillin-Resistant Staphylococcus aureus (MRSA) are particularly difficult to treat due to their resistance to Next Generation β-lactams (NGB) such as Methicillin, Nafcillin, Oxacillin etc. Resistance to NGBs, which is alternatively known as broad-spectrum β-lactam resistance is classically mediated by PBP2a, a Penicillin-Binding Protein encoded by mecA (or mecC) in MRSA. Thus, presence of mec genes among S. aureus serves as the predictor of resistance to NGBs and facilitates determination of the proper therapeutic strategy for a staphylococcal infection. Although far less appreciated, mecA deficient S. aureus strains can also exhibit NGB resistance. These strains, which are collectively termed as Methicillin-Resistant Lacking mec (MRLM) are currently being identified in increasing numbers among natural resistant isolates of S. aureus. The mechanism/s through which MRLMs produce resistance to NGBs remains unknown. In this study, we demonstrate that mutations that alter PBP4 and GdpP functions, which are often present among MRLMs can synergistically mediate resistance to NGBs. Furthermore, our results unravel that this novel mechanism potentially enables MRLMs to produce resistance towards NGBs at levels comparable to that of MRSAs. Our study, provides a fresh new perspective about alternative mechanisms of NGBs resistance, challenging our current overall understanding of high-level, broad-spectrum β-lactam resistance in S. aureus. It thus suggests reconsideration of the current approach towards diagnosis and treatment of β-lactam resistant S. aureus infections.
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Affiliation(s)
- Li-Yin Lai
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Nidhi Satishkumar
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Sasha Cardozo
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Vijay Hemmadi
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
| | - Leonor B. Marques
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Liusheng Huang
- Drug Research Unit, Department of Clinical Pharmacy, University of California, San Francisco, San Francisco, CA, USA
| | - Sergio R. Filipe
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Caparica, Portugal
| | - Mariana G. Pinho
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Henry F. Chambers
- Division of Infectious Diseases, School of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Som S. Chatterjee
- Department of Microbial Pathogenesis, School of Dentistry, University of Maryland Baltimore, USA
- Institute of Marine and Environmental Technology (IMET), Baltimore, USA
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5
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Patterson DC, Weinert EE. Spectrophotometric Method for the Quantification and Kinetic Evaluation of In Vitro c-di-GMP Hydrolysis in the Presence and Absence of Oxygen. Methods Mol Biol 2023; 2648:87-98. [PMID: 37039987 DOI: 10.1007/978-1-0716-3080-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
A spectrophotometric method to measure hydrolysis of the bacterial second messenger cyclic dimeric guanosine monophosphate is described for characterization of enzymes under aerobic and anaerobic conditions. The method allows for obtaining all necessary data to calculate KM and kcat from reactions within a single 96-well plate that can be measured using a standard plate reader. The spectrophotometric assay has been used to measure the rates and obtain Michaelis-Menten parameters for the c-di-GMP phosphodiesterase DcpG with the sensor domain in various ligation states.
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Affiliation(s)
- Dayna C Patterson
- Department of Chemistry, Penn State University, University Park, PA, USA
| | - Emily E Weinert
- Department of Chemistry, Penn State University, University Park, PA, USA.
- Department of Biochemistry & Molecular Biology, Penn State University, University Park, PA, USA.
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6
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The BDSF quorum sensing receptor RpfR regulates Bep exopolysaccharide synthesis in Burkholderia cenocepacia via interaction with the transcriptional regulator BerB. NPJ Biofilms Microbiomes 2022; 8:93. [DOI: 10.1038/s41522-022-00356-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/07/2022] [Indexed: 11/24/2022] Open
Abstract
AbstractThe polysaccharide Bep is essential for in vitro biofilm formation of the opportunistic pathogen Burkholderia cenocepacia. We found that the Burkholderia diffusible signaling factor (BDSF) quorum sensing receptor RpfR is a negative regulator of the bep gene cluster in B. cenocepacia. An rpfR mutant formed wrinkled colonies, whereas additional mutations in the bep genes or known bep regulators like berA and berB restored the wild-type smooth colony morphology. We found that there is a good correlation between intracellular c-di-GMP levels and bep expression when the c-di-GMP level is increased or decreased through ectopic expression of a diguanylate cyclase or a c-di-GMP phosphodiesterase, respectively. However, when the intracellular c-di-GMP level is changed by site directed mutagenesis of the EAL or GGDEF domain of RpfR there is no correlation between intracellular c-di-GMP levels and bep expression. Except for rpfR, deletion mutants of all 25 c-di-GMP phosphodiesterase and diguanylate cyclase genes encoded by B. cenocepacia showed no change to berA and bep gene expression. Moreover, bacterial two-hybrid assays provided evidence that RpfR and BerB physically interact and give specificity to the regulation of the bep genes. We suggest a model where RpfR binds BerB at low c-di-GMP levels to sequester this RpoN-dependent activator to an RpfR/RpfF complex. If the c-di-GMP levels rise, possibly by the enzymatic action of RpfR, BerB binds c-di-GMP and is released from the RpfR/RpfF complex and associates with RpoN to activate transcription of berA, and the BerA protein subsequently activates transcription of the bep genes.
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7
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Mukkayyan N, Poon R, Sander PN, Lai LY, Zubair-Nizami Z, Hammond MC, Chatterjee SS. In Vivo Detection of Cyclic-di-AMP in Staphylococcus aureus. ACS OMEGA 2022; 7:32749-32753. [PMID: 36120079 PMCID: PMC9476191 DOI: 10.1021/acsomega.2c04538] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
Cyclic-di-AMP (CDA) is a signaling molecule that controls various cellular functions including antibiotic tolerance and osmoregulation in Staphylococcus aureus (S. aureus). In this study, we developed a novel biosensor (bsuO P6-4) for in vivo detection of CDA in S. aureus. The fluorescent biosensor is based on a natural CDA riboswitch from Bacillus subtilis connected at its P6 stem to the dye-binding aptamer Spinach. Our study showed that bsuO P6-4 could detect a wide concentration range of CDA in both laboratory and clinical strains, making it suitable for use in both basic and clinical research applications.
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Affiliation(s)
- Nagaraja Mukkayyan
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Raymond Poon
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Philipp N. Sander
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
| | - Li-Yin Lai
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Zahra Zubair-Nizami
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
| | - Ming C. Hammond
- Department
of Chemistry, University of California, Berkeley, California 94720, United States
- Department
of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Som S. Chatterjee
- Department
of Microbial Pathogenesis, School of Dentistry, University of Maryland, Baltimore, Maryland 21202, United States
- Institute
of Marine and Environmental Technology, Baltimore, Maryland 21202, United States
- University
of Maryland Center for Environmental Science, Baltimore, Maryland 21202, United States
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8
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Oberkampf M, Hamiot A, Altamirano-Silva P, Bellés-Sancho P, Tremblay YDN, DiBenedetto N, Seifert R, Soutourina O, Bry L, Dupuy B, Peltier J. c-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by Clostridioides difficile. Sci Signal 2022; 15:eabn8171. [PMID: 36067333 PMCID: PMC9831359 DOI: 10.1126/scisignal.abn8171] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To colonize the host and cause disease, the human enteropathogen Clostridioides difficile must sense, respond, and adapt to the harsh environment of the gastrointestinal tract. We showed that the production and degradation of cyclic diadenosine monophosphate (c-di-AMP) were necessary during different phases of C. difficile growth, environmental adaptation, and infection. The production of this nucleotide second messenger was essential for growth because it controlled the uptake of potassium and also contributed to biofilm formation and cell wall homeostasis, whereas its degradation was required for osmotolerance and resistance to detergents and bile salts. The c-di-AMP binding transcription factor BusR repressed the expression of genes encoding the compatible solute transporter BusAA-AB. Compared with the parental strain, a mutant lacking BusR was more resistant to hyperosmotic and bile salt stresses, whereas a mutant lacking BusAA was more susceptible. A short exposure of C. difficile cells to bile salts decreased intracellular c-di-AMP concentrations, suggesting that changes in membrane properties induce alterations in the intracellular c-di-AMP concentration. A C. difficile strain that could not degrade c-di-AMP failed to persist in a mouse gut colonization model as long as the wild-type strain did. Thus, the production and degradation of c-di-AMP in C. difficile have pleiotropic effects, including the control of osmolyte uptake to confer osmotolerance and bile salt resistance, and its degradation is important for host colonization.
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Affiliation(s)
- Marine Oberkampf
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Audrey Hamiot
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Pamela Altamirano-Silva
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Paula Bellés-Sancho
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Yannick D. N. Tremblay
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Nicholas DiBenedetto
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Roland Seifert
- Institute of Pharmacology and Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Bruno Dupuy
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - Johann Peltier
- Institut Pasteur, Université Paris Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
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9
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Quantification of cyclic AMP and cyclic GMP levels in Krebs-Henseleit solution by LC-MS/MS: application in washed platelet aggregation samples. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1211:123472. [DOI: 10.1016/j.jchromb.2022.123472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/29/2022]
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10
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Thomson M, Liu Y, Nunta K, Cheyne A, Fernandes N, Williams R, Garza-Garcia A, Larrouy-Maumus G. Expression of a novel mycobacterial phosphodiesterase successfully lowers cAMP levels resulting in reduced tolerance to cell wall-targeting antimicrobials. J Biol Chem 2022; 298:102151. [PMID: 35718063 PMCID: PMC9293780 DOI: 10.1016/j.jbc.2022.102151] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/09/2023] Open
Abstract
cAMP and antimicrobial susceptibility in mycobacteriaAntimicrobial tolerance, the ability to survive exposure to antimicrobials via transient nonspecific means, promotes the development of antimicrobial resistance (AMR). The study of the molecular mechanisms that result in antimicrobial tolerance is therefore essential for the understanding of AMR. In gram-negative bacteria, the second messenger molecule 3'',5''-cAMP has been previously shown to be involved in AMR. In mycobacteria, however, the role of cAMP in antimicrobial tolerance has been difficult to probe due to its particular complexity. In order to address this difficulty, here, through unbiased biochemical approaches consisting in the fractionation of clear protein lysate from a mycobacterial strain deleted for the known cAMP phosphodiesterase (Rv0805c) combined with mass spectrometry techniques, we identified a novel cyclic nucleotide-degrading phosphodiesterase enzyme (Rv1339) and developed a system to significantly decrease intracellular cAMP levels through plasmid expression of Rv1339 using the constitutive expression system, pVV16. In Mycobacterium smegmatis mc2155, we demonstrate that recombinant expression of Rv1339 reduced cAMP levels threefold and resulted in altered gene expression, impaired bioenergetics, and a disruption in peptidoglycan biosynthesis leading to decreased tolerance to antimicrobials that target cell wall synthesis such as ethambutol, D-cycloserine, and vancomycin. This work increases our understanding of the role of cAMP in mycobacterial antimicrobial tolerance, and our observations suggest that nucleotide signaling may represent a new target for the development of antimicrobial therapies.
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Affiliation(s)
- Michael Thomson
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Yi Liu
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Kanokkan Nunta
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Ashleigh Cheyne
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom
| | - Nadia Fernandes
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | - Richard Williams
- Imperial BRC Genomics Facility, Imperial College London, London, United Kingdom
| | | | - Gerald Larrouy-Maumus
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Faculty of Natural Sciences, Imperial College London, London, United Kingdom,For correspondence: Gerald Larrouy-Maumus
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11
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Ning H, Liang X, Xie Y, Bai L, Zhang W, Wang L, Kang J, Lu Y, Ma Y, Bai G, Bai Y. c-di-AMP Accumulation Regulates Growth, Metabolism, and Immunogenicity of Mycobacterium smegmatis. Front Microbiol 2022; 13:865045. [PMID: 35685938 PMCID: PMC9171234 DOI: 10.3389/fmicb.2022.865045] [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: 01/29/2022] [Accepted: 04/14/2022] [Indexed: 11/13/2022] Open
Abstract
Cyclic dimeric adenosine monophosphate (c-di-AMP) is a ubiquitous second messenger of bacteria involved in diverse physiological processes as well as host immune responses. MSMEG_2630 is a c-di-AMP phosphodiesterase (cnpB) of Mycobacterium smegmatis, which is homologous to Mycobacterium tuberculosis Rv2837c. In this study, cnpB-deleted (ΔcnpB), -complemented (ΔcnpB::C), and -overexpressed (ΔcnpB::O) strains of M. smegmatis were constructed to investigate the role of c-di-AMP in regulating mycobacterial physiology and immunogenicity. This study provides more precise evidence that elevated c-di-AMP level resulted in smaller colonies, shorter bacteria length, impaired growth, and inhibition of potassium transporter in M. smegmatis. This is the first study to report that elevated c-di-AMP level could inhibit biofilm formation and induce porphyrin accumulation in M. smegmatis by regulating associated gene expressions, which may have effects on drug resistance and virulence of mycobacterium. Moreover, the cnpB-deleted strain with an elevated c-di-AMP level could induce enhanced Th1 immune responses after M. tuberculosis infection. Further, the pathological changes and the bacteria burden in ΔcnpB group were comparable with the wild-type M. smegmatis group against M. tuberculosis venous infection in the mouse model. Our findings enhanced the understanding of the physiological role of c-di-AMP in mycobacterium, and M. smegmatis cnpB-deleted strain with elevated c-di-AMP level showed the potential for a vaccine against tuberculosis.
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Affiliation(s)
- Huanhuan Ning
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
| | - Xuan Liang
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
- College of Life Sciences, Northwest University, Xi’an, China
| | - Yanling Xie
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
- School of Life Sciences, Yan’an University, Yan’an, China
| | - Lu Bai
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
- School of Life Sciences, Yan’an University, Yan’an, China
| | - Wei Zhang
- Department of Pediatrics, Tangdu Hospital, Air Force Medical University, Xi’an, China
| | - Lifei Wang
- Graduate School, Chang’an University, Xi’an, China
| | - Jian Kang
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
| | - Yanzhi Lu
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
| | - Yanling Ma
- College of Life Sciences, Northwest University, Xi’an, China
| | - Guangchun Bai
- Department of Immunology and Microbial Disease, Albany Medical College, Albany, NY, United States
- *Correspondence: Guangchun Bai,
| | - Yinlan Bai
- Department of Microbiology and Pathogen Biology, Air Force Medical University, Xi’an, China
- Yinlan Bai,
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12
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Patatin-like phospholipase CapV in Escherichia coli - morphological and physiological effects of one amino acid substitution. NPJ Biofilms Microbiomes 2022; 8:39. [PMID: 35546554 PMCID: PMC9095652 DOI: 10.1038/s41522-022-00294-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
In rod-shaped bacteria, morphological plasticity occurs in response to stress, which blocks cell division to promote filamentation. We demonstrate here that overexpression of the patatin-like phospholipase variant CapVQ329R, but not CapV, causes pronounced sulA-independent pyridoxine-inhibited cell filamentation in the Escherichia coli K-12-derivative MG1655 associated with restriction of flagella production and swimming motility. Conserved amino acids in canonical patatin-like phospholipase A motifs, but not the nucleophilic serine, are required to mediate CapVQ329R phenotypes. Furthermore, CapVQ329R production substantially alters the lipidome and colony morphotype including rdar biofilm formation with modulation of the production of the biofilm activator CsgD, and affects additional bacterial traits such as the efficiency of phage infection and antimicrobial susceptibility. Moreover, genetically diverse commensal and pathogenic E. coli strains and Salmonella typhimurium responded with cell filamentation and modulation in colony morphotype formation to CapVQ329R expression. In conclusion, this work identifies the CapV variant CapVQ329R as a pleiotropic regulator, emphasizes a scaffold function for patatin-like phospholipases, and highlights the impact of the substitution of a single conserved amino acid for protein functionality and alteration of host physiology.
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13
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Nakane D, Enomoto G, Bähre H, Hirose Y, Wilde A, Nishizaka T. Thermosynechococcus switches the direction of phototaxis by a c-di-GMP-dependent process with high spatial resolution. eLife 2022; 11:73405. [PMID: 35535498 PMCID: PMC9090330 DOI: 10.7554/elife.73405] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Many cyanobacteria, which use light as an energy source via photosynthesis, show directional movement towards or away from a light source. However, the molecular and cell biological mechanisms for switching the direction of movement remain unclear. Here, we visualized type IV pilus-dependent cell movement in the rod-shaped thermophilic cyanobacterium Thermosynechococcus vulcanus using optical microscopy at physiological temperature and light conditions. Positive and negative phototaxis were controlled on a short time scale of 1 min. The cells smoothly moved over solid surfaces towards green light, but the direction was switched to backward movement when we applied additional blue light illumination. The switching was mediated by three photoreceptors, SesA, SesB, and SesC, which have cyanobacteriochrome photosensory domains and synthesis/degradation activity of the bacterial second messenger cyclic dimeric GMP (c-di-GMP). Our results suggest that the decision-making process for directional switching in phototaxis involves light-dependent changes in the cellular concentration of c-di-GMP. Direct visualization of type IV pilus filaments revealed that rod-shaped cells can move perpendicular to the light vector, indicating that the polarity can be controlled not only by pole-to-pole regulation but also within-a-pole regulation. This study provides insights into previously undescribed rapid bacterial polarity regulation via second messenger signalling with high spatial resolution.
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Affiliation(s)
- Daisuke Nakane
- Department of Engineering Science, Graduate School of Informatics and Engineering, The University of Electro-Communications, Tokyo, Japan
| | - Gen Enomoto
- Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, Toyohashi, Japan
| | - Annegret Wilde
- Institute of Biology III, University of Freiburg, Freiburg, Germany.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
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14
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Gao Y, Xu Y, Li Y, Chen K, Wu X, Liu Y, Feng X, Kong D, Ning X. The First FRET-Based RNA Aptamer NanoKit for Sensitively and Specifically Detecting c-di-GMP. NANO LETTERS 2022; 22:716-725. [PMID: 34994567 DOI: 10.1021/acs.nanolett.1c03970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An effective method to identify c-di-GMP may significantly facilitate the exploration of its signaling pathways and bacterial pathogenesis. Herein, we have developed the first conjugated polymer-amplified RNA aptamer NanoKit with a unique core-shell-shell architecture, which combines the advantages of high selectivity of RNA aptamers and high sensitivity of strong fluorescence resonance energy transfer (FRET) effect, for precisely detecting c-di-GMP. We identified that NanoKit could selectively detect c-di-GMP with a low detection limit of 50 pM. Importantly, NanoKit could identify bacterial species and physiological states, such as planktonic, biofilm, and even antibiotic-resistance, on the basis of their different c-di-GMP expression patterns. Particularly, NanoKit could distinguish bacterial infection and inflammation and identify Pseudomonas aeruginosa associated pneumonia and sepsis, thereby guiding treatment choice and monitoring antibiotic effects. Therefore, NanoKit provides a promising strategy to rapidly identify c-di-GMP and its associated diseases and may benefit for pathophoresis management.
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Affiliation(s)
- Ya Gao
- National Laboratory of Solid State Microstructures, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
| | - Yurui Xu
- National Laboratory of Solid State Microstructures, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
| | - Yanyan Li
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210093, China
| | - Kerong Chen
- National Laboratory of Solid State Microstructures, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
| | - Xiaotong Wu
- National Laboratory of Solid State Microstructures, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
| | - Yuhang Liu
- National Laboratory of Solid State Microstructures, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
| | - Xuli Feng
- School of Pharmaceutical Sciences and Innovative Drug Research Center, Chongqing University, Chongqing 401331, China
| | - Desheng Kong
- College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, State Key Laboratory of Analytical Chemistry for Life Science, Nanjing University, Nanjing 210093, China
| | - Xinghai Ning
- National Laboratory of Solid State Microstructures, Collaborative Innovation Center of Advanced Microstructures, Chemistry and Biomedicine Innovation Center, College of Engineering and Applied Sciences, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing 210093, China
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15
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Loss of GdpP function in Staphylococcus aureus leads to β-lactam tolerance and enhanced evolution of β-lactam resistance. Antimicrob Agents Chemother 2021; 66:e0143121. [PMID: 34843389 DOI: 10.1128/aac.01431-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections caused by Staphylococcus aureus are a leading cause of mortality. Treating infections caused by S. aureus is difficult due to resistance against most traditional antibiotics, including β-lactams. We previously reported the presence of mutations in gdpP among S. aureus strains that were obtained by serial passaging in β-lactam drugs. Similar mutations have recently been reported in natural S. aureus isolates that are either non-susceptible or resistant to β-lactam antibiotics. gdpP codes for a phosphodiesterase that cleaves cyclic-di-AMP (CDA), a newly discovered second messenger. In this study, we sought to identify the role of gdpP in β-lactam resistance in S. aureus. Our results showed that gdpP associated mutations caused loss of phosphodiesterase function, leading to increased CDA accumulation in the bacterial cytosol. Deletion of gdpP led to an enhanced ability of the bacteria to withstand a β-lactam challenge (two to three log increase in bacterial colony forming units) by promoting tolerance without enhancing MICs of β-lactam antibiotics. Our results demonstrated that increased drug tolerance due to loss of GdpP function can provide a selective advantage in acquisition of high-level β-lactam resistance. Loss of GdpP function thus increases tolerance to β-lactams that can lead to its therapy failure and can permit β-lactam resistance to occur more readily.
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16
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Annibal A, Ripa R, Ballhysa E, Latza C, Hochhard N, Antebi A. Mass spectrometric characterization of cyclic dinucleotides (CDNs) in vivo. Anal Bioanal Chem 2021; 413:6457-6468. [PMID: 34476522 PMCID: PMC8412381 DOI: 10.1007/s00216-021-03628-6] [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: 06/01/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 12/03/2022]
Abstract
Cyclic dinucleotides (CDNs) are key secondary messenger molecules produced by cyclic dinucleotide synthases that trigger various cellular signaling cascades from bacteria to vertebrates. In mammals, cyclic GMP-AMP synthase (cGAS) has been shown to bind to intracellular DNA and catalyze the production of the dinucleotide 2′3′ cGAMP, which signals downstream effectors to regulate immune function, interferon signaling, and the antiviral response. Despite the importance of CDNs, sensitive and accurate methods to measure their levels in vivo are lacking. Here, we report a novel LC-MS/MS method to quantify CDNs in vivo. We characterized the mass spectrometric behavior of four different biologically relevant CDNs (c-di-AMP, c-di-GMP, 3′3′ cGAMP, 2′3′ cGAMP) and provided a means of visually representing fragmentation resulting from collision-induced dissociation at different energies using collision energy breakdown graphs. We then validated the method and quantified CDNs in two in vivo systems, the bacteria Escherichia coli OP50 and the killifish Nothobranchius furzeri. We found that optimization of LC-MS/MS parameters is crucial to sensitivity and accuracy. These technical advances should help illuminate physiological and pathological roles of these CDNs in in vivo settings. Graphical abstract ![]()
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Affiliation(s)
- Andrea Annibal
- Max Planck Institute for Biology of Ageing, Cologne, Germany.
| | - Roberto Ripa
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Eugen Ballhysa
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Christian Latza
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Nadine Hochhard
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Adam Antebi
- Max Planck Institute for Biology of Ageing, Cologne, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.
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17
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Oeser S, Wallner T, Schuergers N, Bučinská L, Sivabalasarma S, Bähre H, Albers SV, Wilde A. Minor pilins are involved in motility and natural competence in the cyanobacterium Synechocystis sp. PCC 6803. Mol Microbiol 2021; 116:743-765. [PMID: 34115422 DOI: 10.1111/mmi.14768] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 06/04/2021] [Accepted: 06/05/2021] [Indexed: 11/28/2022]
Abstract
Cyanobacteria synthesize type IV pili, which are known to be essential for motility, adhesion and natural competence. They consist of long flexible fibers that are primarily composed of the major pilin PilA1 in Synechocystis sp. PCC 6803. In addition, Synechocystis encodes less abundant pilin-like proteins, which are known as minor pilins. In this study, we show that the minor pilin PilA5 is essential for natural transformation but is dispensable for motility and flocculation. In contrast, a set of minor pilins encoded by the pilA9-slr2019 transcriptional unit are necessary for motility but are dispensable for natural transformation. Neither pilA5-pilA6 nor pilA9-slr2019 are essential for pilus assembly as mutant strains showed type IV pili on the cell surface. Three further gene products with similarity to PilX-like minor pilins have a function in flocculation of Synechocystis. The results of our study indicate that different minor pilins facilitate distinct pilus functions. Further, our microarray analysis demonstrated that the transcription levels of the minor pilin genes change in response to surface contact. A total of 122 genes were determined to have altered transcription between planktonic and surface growth, including several plasmid genes which are involved exopolysaccharide synthesis and the formation of bloom-like aggregates.
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Affiliation(s)
- Sabrina Oeser
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Thomas Wallner
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Nils Schuergers
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Lenka Bučinská
- Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Trebon, Czech Republic
| | - Shamphavi Sivabalasarma
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Heike Bähre
- Research Core Unit Metabolomics, Medical School Hannover, Hannover, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Institute of Biology II, University of Freiburg, Freiburg, Germany.,Spemann Graduate School of Biology and Medicine, University of Freiburg, Freiburg, Germany
| | - Annegret Wilde
- Molecular Genetics, Institute of Biology III, University of Freiburg, Freiburg, Germany
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18
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Ruksakiet K, Stercz B, Tóth G, Jaikumpun P, Gróf I, Tengölics R, Lohinai ZM, Horváth P, Deli MA, Steward MC, Dobay O, Zsembery Á. Bicarbonate Evokes Reciprocal Changes in Intracellular Cyclic di-GMP and Cyclic AMP Levels in Pseudomonas aeruginosa. BIOLOGY 2021; 10:biology10060519. [PMID: 34200909 PMCID: PMC8230467 DOI: 10.3390/biology10060519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 11/23/2022]
Abstract
The formation of Pseudomonas aeruginosa biofilms in cystic fibrosis (CF) is one of the most common causes of morbidity and mortality in CF patients. Cyclic di-GMP and cyclic AMP are second messengers regulating the bacterial lifestyle transition in response to environmental signals. We aimed to investigate the effects of extracellular pH and bicarbonate on intracellular c-di-GMP and cAMP levels, and on biofilm formation. P. aeruginosa was inoculated in a brain−heart infusion medium supplemented with 25 and 50 mM NaCl in ambient air (pH adjusted to 7.4 and 7.7 respectively), or with 25 and 50 mM NaHCO3 in 5% CO2 (pH 7.4 and 7.7). After 16 h incubation, c-di-GMP and cAMP were extracted and their concentrations determined. Biofilm formation was investigated using an xCelligence real-time cell analyzer and by crystal violet assay. Our results show that HCO3− exposure decreased c-di-GMP and increased cAMP levels in a dose-dependent manner. Biofilm formation was also reduced after 48 h exposure to HCO3−. The reciprocal changes in second messenger concentrations were not influenced by changes in medium pH or osmolality. These findings indicate that HCO3− per se modulates the levels of c-di-GMP and cAMP, thereby inhibiting biofilm formation and promoting the planktonic lifestyle of the bacteria.
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Affiliation(s)
- Kasidid Ruksakiet
- Department of Oral Biology, Semmelweis University, H-1089 Budapest, Hungary; (K.R.); (P.J.); (M.C.S.)
- Department of Conservative Dentistry, Semmelweis University, H-1085 Budapest, Hungary;
| | - Balázs Stercz
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, H-1089 Budapest, Hungary; (B.S.); (O.D.)
| | - Gergő Tóth
- Department of Pharmaceutical Chemistry, Semmelweis University, H-1092 Budapest, Hungary; (G.T.); (P.H.)
| | - Pongsiri Jaikumpun
- Department of Oral Biology, Semmelweis University, H-1089 Budapest, Hungary; (K.R.); (P.J.); (M.C.S.)
| | - Ilona Gróf
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (I.G.); (M.A.D.)
| | - Roland Tengölics
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary;
- HCEMM-BRC Metabolic Systems Biology Laboratory, H-6726 Szeged, Hungary
| | - Zsolt M. Lohinai
- Department of Conservative Dentistry, Semmelweis University, H-1085 Budapest, Hungary;
| | - Péter Horváth
- Department of Pharmaceutical Chemistry, Semmelweis University, H-1092 Budapest, Hungary; (G.T.); (P.H.)
| | - Mária A. Deli
- Institute of Biophysics, Biological Research Centre, H-6726 Szeged, Hungary; (I.G.); (M.A.D.)
| | - Martin C. Steward
- Department of Oral Biology, Semmelweis University, H-1089 Budapest, Hungary; (K.R.); (P.J.); (M.C.S.)
- School of Medical Sciences, University of Manchester, Manchester M13 9PL, UK
| | - Orsolya Dobay
- Institute of Medical Microbiology, Faculty of Medicine, Semmelweis University, H-1089 Budapest, Hungary; (B.S.); (O.D.)
| | - Ákos Zsembery
- Department of Oral Biology, Semmelweis University, H-1089 Budapest, Hungary; (K.R.); (P.J.); (M.C.S.)
- Correspondence:
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19
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Liu Y, Lee C, Li F, Trček J, Bähre H, Guo RT, Chen CC, Chernobrovkin A, Zubarev R, Römling U. A Cyclic di-GMP Network Is Present in Gram-Positive Streptococcus and Gram-Negative Proteus Species. ACS Infect Dis 2020; 6:2672-2687. [PMID: 32786278 PMCID: PMC7551669 DOI: 10.1021/acsinfecdis.0c00314] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 01/16/2023]
Abstract
The ubiquitous cyclic di-GMP (c-di-GMP) network is highly redundant with numerous GGDEF domain proteins as diguanylate cyclases and EAL domain proteins as c-di-GMP specific phosphodiesterases comprising those domains as two of the most abundant bacterial domain superfamilies. One hallmark of the c-di-GMP network is its exalted plasticity as c-di-GMP turnover proteins can rapidly vanish from species within a genus and possess an above average transmissibility. To address the evolutionary forces of c-di-GMP turnover protein maintenance, conservation, and diversity, we investigated a Gram-positive and a Gram-negative species, which preserved only one single clearly identifiable GGDEF domain protein. Species of the family Morganellaceae of the order Enterobacterales exceptionally show disappearance of the c-di-GMP signaling network, but Proteus spp. still retained one diguanylate cyclase. As another example, in species of the bovis, pyogenes, and salivarius subgroups as well as Streptococcus suis and Streptococcus henryi of the genus Streptococcus, one candidate diguanylate cyclase was frequently identified. We demonstrate that both proteins encompass PAS (Per-ARNT-Sim)-GGDEF domains, possess diguanylate cyclase catalytic activity, and are suggested to signal via a PilZ receptor domain at the C-terminus of type 2 glycosyltransferase constituting BcsA cellulose synthases and a cellulose synthase-like protein CelA, respectively. Preservation of the ancient link between production of cellulose(-like) exopolysaccharides and c-di-GMP signaling indicates that this functionality is even of high ecological importance upon maintenance of the last remnants of a c-di-GMP signaling network in some of today's free-living bacteria.
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Affiliation(s)
- Ying Liu
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Changhan Lee
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Fengyang Li
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Janja Trček
- Faculty
of Natural Sciences and Mathematics, Department of Biology, University
of Maribor, 2000 Maribor, Slovenia
| | - Heike Bähre
- Research
Core Unit Metabolomics, Hannover Medical
School, D-30625 Hannover, Germany
| | - Rey-Ting Guo
- State
Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative
Innovation Center for Green Transformation of Bio-Resources, Hubei
Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Chun-Chi Chen
- State
Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative
Innovation Center for Green Transformation of Bio-Resources, Hubei
Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, 430062, P.R. China
| | - Alexey Chernobrovkin
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Roman Zubarev
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
- Department
of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
| | - Ute Römling
- Department
of Microbiology, Tumor and Cell Biology and Department of Medical Biochemistry
and Biophysics, Biomedicum, Karolinska Institutet, SE-171 77 Stockholm, Sweden
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20
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Rørvik GH, Liskiewicz KA, Kryuchkov F, Naemi AO, Aasheim HC, Petersen FC, Küntziger TM, Simm R. Cyclic Di-adenosine Monophosphate Regulates Metabolism and Growth in the Oral Commensal Streptococcus mitis. Microorganisms 2020; 8:microorganisms8091269. [PMID: 32825526 PMCID: PMC7570391 DOI: 10.3390/microorganisms8091269] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 01/15/2023] Open
Abstract
Cyclic di-adenosine monophosphate (c-di-AMP) has emerged as an important bacterial signaling molecule that functions both as an intracellular second messenger in bacterial cells and an extracellular ligand involved in bacteria-host cross-talk. In this study, we identify and characterize proteins involved in controlling the c-di-AMP concentration in the oral commensal and opportunistic pathogen Streptococcusmitis (S. mitis). We identified three known types of c-di-AMP turnover proteins in the genome of S. mitis CCUG31611: a CdaA-type diadenylate cyclase as well as GdpP-, and DhhP-type phosphodiesterases. Biochemical analyses of purified proteins demonstrated that CdaA synthesizes c-di-AMP from ATP whereas both phosphodiesterases can utilize c-di-AMP as well as the intermediary metabolite of c-di-AMP hydrolysis 5'-phosphadenylyl-adenosine (pApA) as substrate to generate AMP, albeit at different catalytic efficiency. Using deletion mutants of each of the genes encoding c-di-AMP turnover proteins, we show by high resolution MS/MS that the intracellular concentration of c-di-AMP is increased in deletion mutants of the phosphodiesterases and non-detectable in the cdaA-mutant. We also detected pApA in mutants of the DhhP-type phosphodiesterase. Low and high levels of c-di-AMP were associated with longer and shorter chains of S. mitis, respectively indicating a role in regulation of cell division. The deletion mutant of the DhhP-type phosphodiesterase displayed slow growth and reduced rate of glucose metabolism.
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Affiliation(s)
- Gro Herredsvela Rørvik
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Krystyna Anna Liskiewicz
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Fedor Kryuchkov
- Norwegian Veterinary Institute, Pb 750 Sentrum, 0106 Oslo, Norway;
| | - Ali-Oddin Naemi
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Hans-Christian Aasheim
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Fernanda C. Petersen
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Thomas M. Küntziger
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
| | - Roger Simm
- Institute of Oral Biology, University of Oslo, 0316 Oslo, Norway; (G.H.R.); (K.A.L.); (A.-O.N.); (H.-C.A.); (F.C.P.); (T.M.K.)
- Correspondence:
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21
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The zoonotic pathogen Leptospira interrogans mitigates environmental stress through cyclic-di-GMP-controlled biofilm production. NPJ Biofilms Microbiomes 2020; 6:24. [PMID: 32532998 PMCID: PMC7293261 DOI: 10.1038/s41522-020-0134-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/14/2020] [Indexed: 12/24/2022] Open
Abstract
The zoonotic bacterium Leptospira interrogans is the aetiological agent of leptospirosis, a re-emerging infectious disease that is a growing public health concern. Most human cases of leptospirosis result from environmental infection. Biofilm formation and its contribution to the persistence of virulent leptospires in the environment or in the host have scarcely been addressed. Here, we examined spatial and time-domain changes in biofilm production by L. interrogans. Our observations showed that biofilm formation in L. interrogans is a highly dynamic process and leads to a polarized architecture. We notably found that the biofilm matrix is composed of extracellular DNA, which enhances the biofilm's cohesiveness. By studying L. interrogans mutants with defective diguanylate cyclase and phosphodiesterase genes, we show that biofilm production is regulated by intracellular levels of bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) and underpins the bacterium's ability to withstand a wide variety of simulated environmental stresses. Our present results show how the c-di-GMP pathway regulates biofilm formation by L. interrogans, provide insights into the environmental persistence of L. interrogans and, more generally, highlight leptospirosis as an environment-borne threat to human health.
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Petchiappan A, Naik SY, Chatterji D. Tracking the homeostasis of second messenger cyclic-di-GMP in bacteria. Biophys Rev 2020; 12:719-730. [PMID: 32060735 PMCID: PMC7311556 DOI: 10.1007/s12551-020-00636-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 02/05/2020] [Indexed: 01/09/2023] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is an important second messenger in bacteria which regulates the bacterial transition from motile to sessile phase and also plays a major role in processes such as cell division, exopolysaccharide synthesis, and biofilm formation. Due to its crucial role in dictating the bacterial phenotype, the synthesis and hydrolysis of c-di-GMP is tightly regulated via multiple mechanisms. Perturbing the c-di-GMP homeostasis affects bacterial growth and survival, so it is necessary to understand the underlying mechanisms related to c-di-GMP metabolism. Most techniques used for estimating the c-di-GMP concentration lack single-cell resolution and do not provide information about any heterogeneous distribution of c-di-GMP inside cells. In this review, we briefly discuss how the activity of c-di-GMP metabolising enzymes, particularly bifunctional proteins, is modulated to maintain c-di-GMP homeostasis. We further highlight how fluorescence-based methods aid in understanding the spatiotemporal regulation of c-di-GMP signalling. Finally, we discuss the blind spots in our understanding of second messenger signalling and outline how they can be addressed in the future.
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Affiliation(s)
| | - Sujay Y Naik
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Dipankar Chatterji
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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23
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Kosmacz M, Sokołowska EM, Bouzaa S, Skirycz A. Towards a functional understanding of the plant metabolome. CURRENT OPINION IN PLANT BIOLOGY 2020; 55:47-51. [PMID: 32224339 DOI: 10.1016/j.pbi.2020.02.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 01/22/2020] [Accepted: 02/14/2020] [Indexed: 05/24/2023]
Abstract
Plants are true organic chemists-the chemical diversity of plant metabolomes goes hand in hand with functional diversity. New, often unexpected roles are being reported for both evolutionarily conserved and well-characterised central metabolites such as amino acids, nucleotides, and sugars, and for specialized/secondary metabolites such as carotenoids, glucosinolates, and terpenoids. Our review aims to highlight recent studies reporting novel roles of metabolites and to emphasize the importance of cell-wide identification of metabolite-protein complexes for the comprehensive, functional understanding of the plant metabolome.
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Affiliation(s)
- Monika Kosmacz
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Ewelina Maria Sokołowska
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Saad Bouzaa
- Laboratory of Genetic Resources and Biotechnology, Higher National Agronomic School (ENSA), Algiers, Algeria
| | - Aleksandra Skirycz
- Department of Molecular Physiology, Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam, Germany.
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24
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Dippel AB, Anderson WA, Park JH, Yildiz FH, Hammond MC. Development of Ratiometric Bioluminescent Sensors for in Vivo Detection of Bacterial Signaling. ACS Chem Biol 2020; 15:904-914. [PMID: 32186367 DOI: 10.1021/acschembio.9b00800] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Second messenger signaling networks allow cells to sense and adapt to changing environmental conditions. In bacteria, the nearly ubiquitous second messenger molecule cyclic di-GMP coordinates diverse processes such as motility, biofilm formation, and virulence. In bacterial pathogens, these signaling networks allow the bacteria to survive changing environmental conditions that are experienced during infection of a mammalian host. While studies have examined the effects of cyclic di-GMP levels on virulence in these pathogens, it has not been possible to visualize cyclic di-GMP levels in real time during the stages of host infection. Toward this goal, we generate the first ratiometric, chemiluminescent biosensor scaffold that selectively responds to c-di-GMP. By engineering the biosensor scaffold, a suite of Venus-YcgR-NLuc (VYN) biosensors is generated that provide extremely high sensitivity (KD < 300 pM) and large changes in the bioluminescence resonance energy transfer (BRET) signal (up to 109%). As a proof-of-concept that VYN biosensors can image cyclic di-GMP in tissues, we show that the VYN biosensors function in the context of a tissue phantom model, with only ∼103-104 biosensor-expressing E. coli cells required for the measurement. Furthermore, we utilize the biosensor in vitro to assess changes in cyclic di-GMP in V. cholerae grown with different inputs found in the host environment. The VYN sensors developed here can serve as robust in vitro diagnostic tools for high throughput screening, as well as genetically encodable tools for monitoring the dynamics of c-di-GMP in live cells, and lay the groundwork for live cell imaging of c-di-GMP dynamics in bacteria within tissues and other complex environments.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Wyatt A. Anderson
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
| | - Jin Hwan Park
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Fitnat H. Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, California 95064, United States
| | - Ming C. Hammond
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, United States
- Department of Chemistry and Henry Eyring Center for Cell and Genome Sciences, University of Utah, Salt Lake City, Utah 84112, United States
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25
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Wallner T, Pedroza L, Voigt K, Kaever V, Wilde A. The cyanobacterial phytochrome 2 regulates the expression of motility-related genes through the second messenger cyclic di-GMP. Photochem Photobiol Sci 2020; 19:631-643. [PMID: 32255440 DOI: 10.1039/c9pp00489k] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The cyanobacterial phytochrome Cph2 is a light-dependent diguanylate cyclase of the cyanobacterium Synechocystis 6803. Under blue light, Cph2-dependent increase in the cellular c-di-GMP concentration leads to inhibition of surface motility and enhanced flocculation of cells in liquid culture. However, the targets of second messenger signalling in this cyanobacterium and its mechanism of action remained unclear. Here, we determined the cellular concentrations of cAMP and c-di-GMP in wild-type and Δcph2 cells after exposure to blue and green light. Inactivation of cph2 completely abolished the blue-light dependent increase in c-di-GMP content. Therefore, a microarray analysis with blue-light grown wild-type and Δcph2 mutant cells was used to identify c-di-GMP dependent alterations in transcript accumulation. The increase in the c-di-GMP content alters expression of genes encoding putative cell appendages, minor pilins and components of chemotaxis systems. The mRNA encoding the minor pilins pilA5-pilA6 was negatively affected by high c-di-GMP content under blue light, whereas the minor pilin encoding operon pilA9-slr2019 accumulates under these conditions, suggesting opposing functions of the respective gene sets. Artificial overproduction of c-di-GMP leads to similar changes in minor pilin gene expression and supports previous findings that c-di-GMP is important for flocculation via the function of minor pilins. Mutational and gene expression analysis further suggest that SyCRP2, a CRP-like transcription factor, is involved in regulation of minor pilin and putative chaperone usher pili gene expression.
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Affiliation(s)
- Thomas Wallner
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany.
| | - Laura Pedroza
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Karsten Voigt
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Annegret Wilde
- Molecular Genetics of Prokaryotes, Institute of Biology III, University of Freiburg, Freiburg, Germany
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26
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Maity C, Ghosh D, Guha S. Assays for Intracellular Cyclic Adenosine Monophosphate (cAMP) and Lysosomal Acidification. Methods Mol Biol 2020; 1996:161-178. [PMID: 31127555 DOI: 10.1007/978-1-4939-9488-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cyclic adenosine monophosphate (3',5'-cAMP) is a multifunctional second messenger which controls extremely diverse and physiologically important biochemical pathways. Among its myriad roles, 3',5'-cAMP functions as an intracellular regulator of lysosomal pH, which is essential for the activity of acidic lysosomal enzymes. Defects in lysosomal acidification are attributed to many diseases like macular degeneration, Parkinson's, Alzheimer's, and cystic fibrosis. Strategic re-acidification of defective lysosomes by pharmacological increase of intracellular cAMP offers exciting therapeutic potential in these diseases. Modular assays for accurate assessment of intracellular cAMP and lysosomal pH are a critical component of this research. We describe label-free targeted metabolomics for quantitating intracellular cAMP and integrated assays for measuring lysosomal pH. These hybrid assays offer fast, unbiased information on intracellular cAMP concentrations and lysosomal pH that can be applied to many cell types and putative drug screening strategies.
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Affiliation(s)
- Chiranjit Maity
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Dipankar Ghosh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Sonia Guha
- Stein Eye Institute, University of California Los Angeles, Los Angeles, CA, USA.
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27
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Nisbett LM, Binnenkade L, Bacon B, Hossain S, Kotloski NJ, Brutinel ED, Hartmann R, Drescher K, Arora DP, Muralidharan S, Thormann KM, Gralnick JA, Boon EM. NosP Signaling Modulates the NO/H-NOX-Mediated Multicomponent c-Di-GMP Network and Biofilm Formation in Shewanella oneidensis. Biochemistry 2019; 58:4827-4841. [PMID: 31682418 PMCID: PMC7290162 DOI: 10.1021/acs.biochem.9b00706] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biofilms form when bacteria aggregate in a self-secreted exopolysaccharide matrix; they are resistant to antibiotics and implicated in disease. Nitric oxide (NO) is known to mediate biofilm formation in many bacteria via ligation to H-NOX (heme-NO/oxygen binding) domains. Most NO-responsive bacteria, however, lack H-NOX domain-containing proteins. We have identified another NO-sensing protein (NosP), which is predicted to be involved in two-component signaling and biofilm regulation in many species. Here, we demonstrate that NosP participates in the previously described H-NOX/NO-responsive multicomponent c-di-GMP signaling network in Shewanella oneidensis. Strains lacking either nosP or its co-cistronic kinase nahK (previously hnoS) produce immature biofilms, while hnoX and hnoK (kinase responsive to NO/H-NOX) mutants result in wild-type biofilm architecture. We demonstrate that NosP regulates the autophosphorylation activity of NahK as well as HnoK. HnoK and NahK have been shown to regulate three response regulators (HnoB, HnoC, and HnoD) that together comprise a NO-responsive multicomponent c-di-GMP signaling network. Here, we propose that NosP/NahK adds regulation on top of H-NOX/HnoK to modulate this c-di-GMP signaling network, and ultimately biofilm formation, by governing the flux of phosphate through both HnoK and NahK. In addition, it appears that NosP and H-NOX act to counter each other in a push-pull mechanism; NosP/NahK promotes biofilm formation through inhibition of H-NOX/HnoK signaling, which itself reduces the extent of biofilm formation. Addition of NO results in a reduction of c-di-GMP and biofilm formation, primarily through disinhibition of HnoK activity.
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Affiliation(s)
- Lisa-Marie Nisbett
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lucas Binnenkade
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Bezalel Bacon
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sajjad Hossain
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Nicholas J. Kotloski
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota 55108, United States
| | - Evan D. Brutinel
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota 55108, United States
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
| | - Dhruv P. Arora
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sandhya Muralidharan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Kai M. Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota 55108, United States
| | - Elizabeth M. Boon
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
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28
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Wright TA, Jiang L, Park JJ, Anderson WA, Chen G, Hallberg ZF, Nan B, Hammond MC. Second messengers and divergent HD-GYP phosphodiesterases regulate 3',3'-cGAMP signaling. Mol Microbiol 2019; 113:222-236. [PMID: 31665539 DOI: 10.1111/mmi.14412] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2019] [Indexed: 12/16/2022]
Abstract
3',3'-cyclic GMP-AMP (cGAMP) is the third cyclic dinucleotide (CDN) to be discovered in bacteria. No activators of cGAMP signaling have yet been identified, and the signaling pathways for cGAMP have been inferred to display a narrow distribution based upon the characterized synthases, DncV and Hypr GGDEFs. Here, we report that the ubiquitous second messenger cyclic AMP (cAMP) is an activator of the Hypr GGDEF enzyme GacB from Myxococcus xanthus. Furthermore, we show that GacB is inhibited directly by cyclic di-GMP, which provides evidence for cross-regulation between different CDN pathways. Finally, we reveal that the HD-GYP enzyme PmxA is a cGAMP-specific phosphodiesterase (GAP) that promotes resistance to osmotic stress in M. xanthus. A signature amino acid change in PmxA was found to reprogram substrate specificity and was applied to predict the presence of non-canonical HD-GYP phosphodiesterases in many bacterial species, including phyla previously not known to utilize cGAMP signaling.
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Affiliation(s)
- Todd A Wright
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, 84112, USA
| | - Lucy Jiang
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - James J Park
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Wyatt A Anderson
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA.,Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, 84112, USA
| | - Ge Chen
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Zachary F Hallberg
- Department of Chemistry, University of California, Berkeley, CA, 94720, USA
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Ming C Hammond
- Department of Chemistry and Henry Eyring Center for Cell and Genome Science, University of Utah, Salt Lake City, UT, 84112, USA
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29
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Nicholls TJ, Spåhr H, Jiang S, Siira SJ, Koolmeister C, Sharma S, Kauppila JHK, Jiang M, Kaever V, Rackham O, Chabes A, Falkenberg M, Filipovska A, Larsson NG, Gustafsson CM. Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria. Mol Cell 2019; 76:784-796.e6. [PMID: 31588022 PMCID: PMC6900737 DOI: 10.1016/j.molcel.2019.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 07/12/2019] [Accepted: 09/04/2019] [Indexed: 12/12/2022]
Abstract
Oligoribonucleases are conserved enzymes that degrade short RNA molecules of up to 5 nt in length and are assumed to constitute the final stage of RNA turnover. Here we demonstrate that REXO2 is a specialized dinucleotide-degrading enzyme that shows no preference between RNA and DNA dinucleotide substrates. A heart- and skeletal-muscle-specific knockout mouse displays elevated dinucleotide levels and alterations in gene expression patterns indicative of aberrant dinucleotide-primed transcription initiation. We find that dinucleotides act as potent stimulators of mitochondrial transcription initiation in vitro. Our data demonstrate that increased levels of dinucleotides can be used to initiate transcription, leading to an increase in transcription levels from both mitochondrial promoters and other, nonspecific sequence elements in mitochondrial DNA. Efficient RNA turnover by REXO2 is thus required to maintain promoter specificity and proper regulation of transcription in mammalian mitochondria.
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Affiliation(s)
- Thomas J Nicholls
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Henrik Spåhr
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany; Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Shan Jiang
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Stefan J Siira
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; Centre for Medical Research, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Camilla Koolmeister
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Johanna H K Kauppila
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Min Jiang
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, 50931 Cologne, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, 30625 Hannover, Germany
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, WA 6102, Australia; Curtin Health Innovation Research Institute, Curtin University, Bentley, WA 6102, Australia
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå 901 87, Sweden
| | - Maria Falkenberg
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, WA 6009, Australia; School of Molecular Sciences, The University of Western Australia, Nedlands, WA, Australia
| | - Nils-Göran Larsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 17177, Sweden; Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm 17177, Sweden.
| | - Claes M Gustafsson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, PO Box 440, Gothenburg 405 30, Sweden.
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30
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Analysis of Brevundimonas subvibrioides Developmental Signaling Systems Reveals Inconsistencies between Phenotypes and c-di-GMP Levels. J Bacteriol 2019; 201:JB.00447-19. [PMID: 31383736 DOI: 10.1128/jb.00447-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/26/2019] [Indexed: 11/20/2022] Open
Abstract
The DivJ-DivK-PleC signaling system of Caulobacter crescentus is a signaling network that regulates polar development and the cell cycle. This system is conserved in related bacteria, including the sister genus Brevundimonas Previous studies had shown unexpected phenotypic differences between the C. crescentus divK mutant and the analogous mutant of Brevundimonas subvibrioides, but further characterization was not performed. Here, phenotypic assays analyzing motility, adhesion, and pilus production (the latter characterized by a newly discovered bacteriophage) revealed that divJ and pleC mutants have phenotypes mostly similar to their C. crescentus homologs, but divK mutants maintain largely opposite phenotypes than expected. Suppressor mutations of the B. subvibrioides divK motility defect were involved in cyclic di-GMP (c-di-GMP) signaling, including the diguanylate cyclase dgcB, and cleD which is hypothesized to affect flagellar function in a c-di-GMP dependent fashion. However, the screen did not identify the diguanylate cyclase pleD Disruption of pleD in B. subvibrioides caused no change in divK or pleC phenotypes, but did reduce adhesion and increase motility of the divJ strain. Analysis of c-di-GMP levels in these strains revealed incongruities between c-di-GMP levels and displayed phenotypes with a notable result that suppressor mutations altered phenotypes but had little impact on c-di-GMP levels in the divK background. Conversely, when c-di-GMP levels were artificially manipulated, alterations of c-di-GMP levels in the divK strain had minimal impact on phenotypes. These results suggest that DivK performs a critical function in the integration of c-di-GMP signaling into the B. subvibrioides cell cycle.IMPORTANCE Cyclic di-GMP and associated signaling proteins are widespread in bacteria, but their role in physiology is often complex and difficult to predict through genomic level analyses. In C. crescentus, c-di-GMP has been integrated into the developmental cell cycle, but there is increasing evidence that environmental factors can impact this system as well. The research presented here suggests that the integration of these signaling networks could be more complex than previously hypothesized, which could have a bearing on the larger field of c-di-GMP signaling. In addition, this work further reveals similarities and differences in a conserved regulatory network between organisms in the same taxonomic family, and the results show that gene conservation does not necessarily imply close functional conservation in genetic pathways.
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31
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Baena I, Pérez-Mendoza D, Sauviac L, Francesch K, Martín M, Rivilla R, Bonilla I, Bruand C, Sanjuán J, Lloret J. A partner-switching system controls activation of mixed-linkage β-glucan synthesis by c-di-GMP in Sinorhizobium meliloti. Environ Microbiol 2019; 21:3379-3391. [PMID: 30963697 DOI: 10.1111/1462-2920.14624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/06/2019] [Indexed: 11/29/2022]
Abstract
Sinorhizobium meliloti synthesizes a linear mixed-linkage (1 → 3)(1 → 4)-β-d-glucan (ML β-glucan, MLG) in response to high levels of cyclic diguanylate (c-di-GMP). Two proteins BgsA and BgsB are required for MLG synthesis, BgsA being the glucan synthase which is activated upon c-di-GMP binding to its C-terminal domain. Here we report that the product of bgrR (SMb20447) is a diguanylate cyclase (DGC) that provides c-di-GMP for the synthesis of MLG by BgsA. bgrR is the first gene of a hexacistronic bgrRSTUWV operon, likely encoding a partner-switching regulatory network where BgrR is the final target. Using different approaches, we have determined that the products of genes bgrU (containing a putative PP2C serine phosphatase domain) and bgrW (with predicted kinase effector domain), modulate the phosphorylation status and the activity of the STAS domain protein BgrV. We propose that unphosphorylated BgrV inhibits BgrR DGC activity, perhaps through direct protein-protein interactions as established for other partner switchers. A bgrRSTUWV operon coexists with MLG structural bgsBA genes in many rhizobial genomes but is also present in some MLG non-producers, suggesting a role of this partner-switching system in other processes besides MLG biosynthesis.
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Affiliation(s)
- Irene Baena
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Pérez-Mendoza
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Laurent Sauviac
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Kevin Francesch
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ildefonso Bonilla
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Claude Bruand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Juan Sanjuán
- Departamento de Microbiología del Suelo y Sistemas Simbióticos, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Granada, Spain
| | - Javier Lloret
- Departamento de Biología, Universidad Autónoma de Madrid, Madrid, Spain
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Hallberg ZF, Chan CH, Wright TA, Kranzusch PJ, Doxzen KW, Park JJ, Bond DR, Hammond MC. Structure and mechanism of a Hypr GGDEF enzyme that activates cGAMP signaling to control extracellular metal respiration. eLife 2019; 8:43959. [PMID: 30964001 PMCID: PMC6456294 DOI: 10.7554/elife.43959] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/12/2019] [Indexed: 12/16/2022] Open
Abstract
A newfound signaling pathway employs a GGDEF enzyme with unique activity compared to the majority of homologs associated with bacterial cyclic di-GMP signaling. This system provides a rare opportunity to study how signaling proteins natively gain distinct function. Using genetic knockouts, riboswitch reporters, and RNA-Seq, we show that GacA, the Hypr GGDEF in Geobacter sulfurreducens, specifically regulates cyclic GMP-AMP (3′,3′-cGAMP) levels in vivo to stimulate gene expression associated with metal reduction separate from electricity production. To reconcile these in vivo findings with prior in vitro results that showed GacA was promiscuous, we developed a full kinetic model combining experimental data and mathematical modeling to reveal mechanisms that contribute to in vivo specificity. A 1.4 Å-resolution crystal structure of the Geobacter Hypr GGDEF domain was determined to understand the molecular basis for those mechanisms, including key cross-dimer interactions. Together these results demonstrate that specific signaling can result from a promiscuous enzyme. Microscopic organisms known as bacteria are found in virtually every environment on the planet. One reason bacteria are so successful is that they are able to form communities known as biofilms on surfaces in animals and other living things, as well as on rocks and other features in the environment. These biofilms protect the bacteria from fluctuations in the environment and toxins. For over 30 years, a class of enzymes called the GGDEF enzymes were thought to make a single signal known as cyclic di-GMP that regulates the formation of biofilms. However, in 2016, a team of researchers reported that some GGDEF enzymes, including one from a bacterium called Geobacter sulfurreducens, were also able to produce two other signals known as cGAMP and cyclic di-AMP. The experiments involved making the enzymes and testing their activity outside the cell. Therefore, it remained unclear whether these enzymes (dubbed ‘Hypr’ GGDEF enzymes) actually produce all three signals inside cells and play a role in forming bacterial biofilms. G. sulfurreducens is unusual because it is able to grow on metallic minerals or electrodes to generate electrical energy. As part of a community of microorganisms, they help break down pollutants in contaminated areas and can generate electricity from wastewater. Now, Hallberg, Chan et al. – including many of the researchers involved in the 2016 work – combined several experimental and mathematical approaches to study the Hypr GGDEF enzymes in G. sulfurreducens. The experiments show that the Hypr GGDEF enzymes produced cGAMP, but not the other two signals, inside the cells. This cGAMP regulated the ability of G. sulfurreducens to grow by extracting electrical energy from the metallic minerals, which appears to be a new, biofilm-less lifestyle. Further experiments revealed how Hypr GGDEF enzymes have evolved to preferentially make cGAMP over the other two signals. Together, these findings demonstrate that enzymes with the ability to make several different signals, are capable of generating specific responses in bacterial cells. By understanding how bacteria make decisions, it may be possible to change their behaviors. The findings of Hallberg, Chan et al. help to identify the signaling pathways involved in this decision-making and provide new tools to study them in the future.
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Affiliation(s)
- Zachary F Hallberg
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Chi Ho Chan
- Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, Minnesota, United States
| | - Todd A Wright
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Philip J Kranzusch
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, United States.,Parker Institute for Cancer Immunotherapy at Dana-Farber Cancer Institute, Boston, United States
| | - Kevin W Doxzen
- Biophysics Graduate Group, University of California, Berkeley, Berkeley, United States
| | - James J Park
- Department of Chemistry, University of California, Berkeley, Berkeley, United States
| | - Daniel R Bond
- Department of Plant and Microbial Biology and BioTechnology Institute, University of Minnesota, Minnesota, United States
| | - Ming C Hammond
- Department of Chemistry, University of California, Berkeley, Berkeley, United States.,Department of Molecular & Cell Biology, University of California, Berkeley, Berkeley, United States.,Department of Chemistry, University of Utah, Salt Lake City, United States
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33
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DncV Synthesizes Cyclic GMP-AMP and Regulates Biofilm Formation and Motility in Escherichia coli ECOR31. mBio 2019; 10:mBio.02492-18. [PMID: 30837338 PMCID: PMC6401482 DOI: 10.1128/mbio.02492-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The ability of bacteria to sense and respond to environmental signals is critical for survival. Bacteria use cyclic dinucleotides as second messengers to regulate a number of physiological processes, such as the fundamental life style transition between motility and sessility (biofilm formation). cGAMP, which is synthesized by a dinucleotide cyclase called DncV, is a newly discovered second messenger involved in virulence and chemotaxis in the Vibrio cholerae biovar El Tor causing the current 7th cholera pandemic. However, to what extent cGAMP exists and participates in physiological processes in other bacteria is still unknown. In this study, we found an elevated cGAMP level to possibly regulate biofilm formation and motility in the animal commensal E. coli strain ECOR31. Thus, we detected a novel role for cGAMP signaling in regulation of physiological processes other than those previously reported in proteobacterial species. Cyclic dinucleotides (cDNs) act as intracellular second messengers, modulating bacterial physiology to regulate the fundamental life style transition between motility and sessility commonly known as biofilm formation. Cyclic GMP-AMP (cGAMP), synthesized by the dinucleotide cyclase DncV, is a newly discovered cDN second messenger involved in virulence and chemotaxis in Vibrio cholerae O1 biovar El Tor. Here we report a novel role for horizontally transferred DncV in cGAMP production and regulation of biofilm formation and motility in the animal commensal strain Escherichia coli ECOR31. ECOR31 expresses a semiconstitutive temperature-independent rdar (red, dry, and rough) morphotype on Congo red agar plates characterized by the extracellular matrix components cellulose and curli fimbriae which requires activation by the major biofilm regulator CsgD and cyclic di-GMP signaling. In contrast, C-terminal His-tagged DncV negatively regulates the rdar biofilm morphotype and cell aggregation via downregulation of csgD mRNA steady-state level. Furthermore, DncV sequentially promotes and inhibits adhesion to the abiotic surface after 24 h and 48 h of growth, respectively. DncV also suppresses swimming and swarming motility posttranscriptional of the class 1 flagellum regulon gene flhD. Purified DncV produced different cDNs, cyclic di-GMP, cyclic di-AMP, an unknown product(s), and the dominant species 3′3′-cGAMP. In vivo, only the 3′3′-cGAMP concentration was elevated upon short-term overexpression of dncV, making this work a first report on cGAMP production in E. coli. Regulation of rdar biofilm formation and motility upon overexpression of untagged DncV in combination with three adjacent cotransferred gene products suggests a novel temperature-dependent cGAMP signaling module in E. coli ECOR31.
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Zhang Y, Sass A, Van Acker H, Wille J, Verhasselt B, Van Nieuwerburgh F, Kaever V, Crabbé A, Coenye T. Coumarin Reduces Virulence and Biofilm Formation in Pseudomonas aeruginosa by Affecting Quorum Sensing, Type III Secretion and C-di-GMP Levels. Front Microbiol 2018; 9:1952. [PMID: 30186266 PMCID: PMC6110822 DOI: 10.3389/fmicb.2018.01952] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 08/02/2018] [Indexed: 01/09/2023] Open
Abstract
As one of the major pathogens in wound infections, Pseudomonas aeruginosa produces several virulence factors and forms biofilms; these processes are under the regulation of various quorum sensing (QS) systems. Therefore, QS has been regarded as a promising target to treat P. aeruginosa infections. In the present study, we evaluated the effect of the plant-derived QS inhibitor coumarin on P. aeruginosa biofilms and virulence. Coumarin inhibited QS in the P. aeruginosa QSIS2 biosensor strain, reduced protease and pyocyanin production, and inhibited biofilm formation in microtiter plates in different P. aeruginosa strains. The effects of coumarin in inhibiting biofilm formation in an in vitro wound model and reducing P. aeruginosa virulence in the Lucilia sericata infection model were strain-dependent. Transcriptome analysis revealed that several key genes involved in the las, rhl, Pseudomonas quinolone signal (PQS), and integrated QS (IQS) systems were downregulated in coumarin-treated biofilms of P. aeruginosa PAO1. Coumarin also changed the expression of genes related to type III secretion and cyclic diguanylate (c-di-GMP) metabolism. The cellular c-di-GMP level of P. aeruginosa PAO1 and recent clinical P. aeruginosa strains was significantly reduced by coumarin. These results provide new evidence for the possible application of coumarin as an anti-biofilm and anti-virulence agent against P. aeruginosa in wound infections.
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Affiliation(s)
- Yunhui Zhang
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Andrea Sass
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Heleen Van Acker
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Jasper Wille
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Bruno Verhasselt
- Department of Medical Microbiology, Ghent University Hospital, Ghent, Belgium
| | | | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Hanover, Germany
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology, Ghent University, Ghent, Belgium
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35
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Schäper S, Yau HCL, Krol E, Skotnicka D, Heimerl T, Gray J, Kaever V, Søgaard-Andersen L, Vollmer W, Becker A. Seven-transmembrane receptor protein RgsP and cell wall-binding protein RgsM promote unipolar growth in Rhizobiales. PLoS Genet 2018; 14:e1007594. [PMID: 30102748 PMCID: PMC6107284 DOI: 10.1371/journal.pgen.1007594] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 08/23/2018] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Members of the Rhizobiales (class of α-proteobacteria) display zonal peptidoglycan cell wall growth at one cell pole, contrasting with the dispersed mode of cell wall growth along the sidewalls of many other rod-shaped bacteria. Here we show that the seven-transmembrane receptor (7TMR) protein RgsP (SMc00074), together with the putative membrane-anchored peptidoglycan metallopeptidase RgsM (SMc02432), have key roles in unipolar peptidoglycan formation during growth and at mid-cell during cell division in Sinorhizobium meliloti. RgsP is composed of a periplasmic globular 7TMR-DISMED2 domain, a membrane-spanning region, and cytoplasmic PAS, GGDEF and EAL domains. The EAL domain confers phosphodiesterase activity towards the second messenger cyclic di-GMP, a key regulatory player in the transition between bacterial lifestyles. RgsP and RgsM localize to sites of zonal cell wall synthesis at the new cell pole and cell divison site, suggesting a role in cell wall biogenesis. The two proteins are essential for cell wall biogenesis and cell growth. Cells depleted of RgsP or RgsM had an altered muropeptide composition and RgsM binds to peptidoglycan. RgsP and RgsM orthologs are functional when interchanged between α-rhizobial species pointing to a conserved mechanism for cell wall biogenesis/remodeling within the Rhizobiales. Overall, our findings suggest that RgsP and RgsM contribute to the regulation of unipolar cell wall biogenesis in α-rhizobia.
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Affiliation(s)
- Simon Schäper
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Hamish C. L. Yau
- Center for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Elizaveta Krol
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Dorota Skotnicka
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Heimerl
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Joe Gray
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Waldemar Vollmer
- Center for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- Faculty of Biology, Philipps-Universität Marburg, Marburg, Germany
- * E-mail:
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36
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Bähre H, Kaever V. Identification and Quantification of Cyclic Di-Guanosine Monophosphate and Its Linear Metabolites by Reversed-Phase LC-MS/MS. Methods Mol Biol 2018; 1657:45-58. [PMID: 28889285 DOI: 10.1007/978-1-4939-7240-1_5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyclic dinucleotides such as bis-(3',5')-cyclic dimeric guanosine monophosphate (3',3'-c-di-GMP) represent an important class of second messengers in bacteria and are involved in numerous (patho)physiological settings. Here, we describe a sensitive and specific quantification method for 3',3'-c-di-GMP by HPLC-coupled tandem mass spectrometry (LC-MS/MS). Additionally, linear 3',3'-c-di-GMP metabolites, i.e., 5'-phosphoguanylyl-3',5'-guanosine (pGpG) and 5'-guanosine monophosphate (5'-GMP), as well as cyclic guanosine monophosphate (3',5'-cGMP) and 3',3' c-di-GMP analogues (2',3'-c-di-GMP and 2',2'-c-di-GMP) can be simultaneously determined by this method.
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Affiliation(s)
- Heike Bähre
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Institute of Pharmacology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
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37
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Petrova OE, Sauer K. High-Performance Liquid Chromatography (HPLC)-Based Detection and Quantitation of Cellular c-di-GMP. Methods Mol Biol 2018; 1657:33-43. [PMID: 28889284 DOI: 10.1007/978-1-4939-7240-1_4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The modulation of c-di-GMP levels plays a vital role in the regulation of various processes in a wide array of bacterial species. Thus, investigation of c-di-GMP regulation requires reliable methods for the assessment of c-di-GMP levels and turnover. Reversed-phase high-performance liquid chromatography (RP-HPLC) analysis has become a commonly used approach to accomplish these goals. The following describes the extraction and HPLC-based detection and quantification of c-di-GMP from Pseudomonas aeruginosa samples, a procedure that is amenable to modifications for the analysis of c-di-GMP in other bacterial species.
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Affiliation(s)
- Olga E Petrova
- Department of Biological Sciences, Binghamton Biofilm Research Center (BBRC), Binghamton University, 2401 ITC Building, 85 Murray Hill Road, Binghamton, NY, 13902, USA.
| | - Karin Sauer
- Department of Biological Sciences, Binghamton Biofilm Research Center (BBRC), Binghamton University, 2401 ITC Building, 85 Murray Hill Road, Binghamton, NY, 13902, USA
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38
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Abstract
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important signaling molecule for community behavior control, cell morphogenesis, and virulence in bacteria. In addition to protein effectors, this second messenger binds RNA molecules that act as riboswitches to control target gene expression. In this chapter, we describe a method for experimental validation of the functionality of c-di-GMP-responsive riboswitches and the analysis of c-di-GMP control of target gene expression by qRT-PCR and Northern blot. This procedure can be used for the studies of in silico-predicted riboswitch candidates, as well as a targeted experimental approach for exploring the data from next-generation sequencing. The examples on the analysis of type I and type II c-di-GMP-responsive riboswitches in Clostridium difficile are provided to illustrate the application of the method.
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Affiliation(s)
- Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr Roux, 75724, Paris Cedex 15, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 25 rue du Dr Roux, 75724, Paris Cedex 15, France. .,Université Paris Diderot, Sorbonne Paris Cité, 25 rue du Dr Roux, 75724, Paris Cedex 15, France. .,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette Cedex, France.
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39
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Gründling A, Lee VT. Old concepts, new molecules and current approaches applied to the bacterial nucleotide signalling field. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0503. [PMID: 27672152 PMCID: PMC5052745 DOI: 10.1098/rstb.2015.0503] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2016] [Indexed: 12/25/2022] Open
Abstract
Signalling nucleotides are key molecules that help bacteria to rapidly coordinate cellular pathways and adapt to changes in their environment. During the past 10 years, the nucleotide signalling field has seen much excitement, as several new signalling nucleotides have been discovered in both eukaryotic and bacterial cells. The fields have since advanced quickly, aided by the development of important tools such as the synthesis of modified nucleotides, which, combined with sensitive mass spectrometry methods, allowed for the rapid identification of specific receptor proteins along with other novel genome-wide screening methods. In this review, we describe the principle concepts of nucleotide signalling networks and summarize the recent work that led to the discovery of the novel signalling nucleotides. We also highlight current approaches applied to the research in the field as well as resources and methodological advances aiding in a rapid identification of nucleotide-specific receptor proteins. This article is part of the themed issue ‘The new bacteriology’.
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Affiliation(s)
- Angelika Gründling
- Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Vincent T Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, MD 20742, USA
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40
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Angerer V, Schwenk P, Wallner T, Kaever V, Hiltbrunner A, Wilde A. The protein Slr1143 is an active diguanylate cyclase in Synechocystis sp. PCC 6803 and interacts with the photoreceptor Cph2. Microbiology (Reading) 2017. [DOI: 10.1099/mic.0.000475] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Veronika Angerer
- Institute for Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Philipp Schwenk
- Institute for Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Wallner
- Institute for Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, 30623 Hannover, Germany
| | - Andreas Hiltbrunner
- Institute for Biology II, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Annegret Wilde
- Institute for Biology III, Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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41
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Schmid N, Suppiger A, Steiner E, Pessi G, Kaever V, Fazli M, Tolker-Nielsen T, Jenal U, Eberl L. High intracellular c-di-GMP levels antagonize quorum sensing and virulence gene expression in Burkholderia cenocepacia H111. MICROBIOLOGY-SGM 2017; 163:754-764. [PMID: 28463102 DOI: 10.1099/mic.0.000452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The opportunistic human pathogen Burkholderia cenocepacia H111 uses two chemically distinct signal molecules for controlling gene expression in a cell density-dependent manner: N-acyl-homoserine lactones (AHLs) and cis-2-dodecenoic acid (BDSF). Binding of BDSF to its cognate receptor RpfR lowers the intracellular c-di-GMP level, which in turn leads to differential expression of target genes. In this study we analysed the transcriptional profile of B. cenocepacia H111 upon artificially altering the cellular c-di-GMP level. One hundred and eleven genes were shown to be differentially expressed, 96 of which were downregulated at a high c-di-GMP concentration. Our analysis revealed that the BDSF, AHL and c-di-GMP regulons overlap for the regulation of 24 genes and that a high c-di-GMP level suppresses expression of AHL-regulated genes. Phenotypic analyses confirmed changes in the expression of virulence factors, the production of AHL signal molecules and the biosynthesis of different biofilm matrix components upon altered c-di-GMP levels. We also demonstrate that the intracellular c-di-GMP level determines the virulence of B. cenocepacia to Caenorhabditis elegans and Galleria mellonella.
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Affiliation(s)
- Nadine Schmid
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Angela Suppiger
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Elisabeth Steiner
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Gabriella Pessi
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Mustafa Fazli
- Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Urs Jenal
- Focal Area of Infection Biology, Biozentrum, University of Basel, Basel, Switzerland
| | - Leo Eberl
- Institute of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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42
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Abstract
Cyclic dinucleotides (CDNs) are highly versatile signalling molecules that control various important biological processes in bacteria. The best-studied example is cyclic di-GMP (c-di-GMP). Known since the late 1980s, it is now recognized as a near-ubiquitous second messenger that coordinates diverse aspects of bacterial growth and behaviour, including motility, virulence, biofilm formation and cell cycle progression. In this Review, we discuss important new insights that have been gained into the molecular principles of c-di-GMP synthesis and degradation, which are mediated by diguanylate cyclases and c-di-GMP-specific phosphodiesterases, respectively, and the cellular functions that are exerted by c-di-GMP-binding effectors and their diverse targets. Finally, we provide a short overview of the signalling versatility of other CDNs, including c-di-AMP and cGMP-AMP (cGAMP).
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43
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Bowman L, Zeden MS, Schuster CF, Kaever V, Gründling A. New Insights into the Cyclic Di-adenosine Monophosphate (c-di-AMP) Degradation Pathway and the Requirement of the Cyclic Dinucleotide for Acid Stress Resistance in Staphylococcus aureus. J Biol Chem 2016; 291:26970-26986. [PMID: 27834680 PMCID: PMC5207132 DOI: 10.1074/jbc.m116.747709] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 11/09/2016] [Indexed: 12/02/2022] Open
Abstract
Nucleotide signaling networks are key to facilitate alterations in gene expression, protein function, and enzyme activity in response to diverse stimuli. Cyclic di-adenosine monophosphate (c-di-AMP) is an important secondary messenger molecule produced by the human pathogen Staphylococcus aureus and is involved in regulating a number of physiological processes including potassium transport. S. aureus must ensure tight control over its cellular levels as both high levels of the dinucleotide and its absence result in a number of detrimental phenotypes. Here we show that in addition to the membrane-bound Asp-His-His and Asp-His-His-associated (DHH/DHHA1) domain-containing phosphodiesterase (PDE) GdpP, S. aureus produces a second cytoplasmic DHH/DHHA1 PDE Pde2. Although capable of hydrolyzing c-di-AMP, Pde2 preferentially converts linear 5'-phosphadenylyl-adenosine (pApA) to AMP. Using a pde2 mutant strain, pApA was detected for the first time in S. aureus, leading us to speculate that this dinucleotide may have a regulatory role under certain conditions. Moreover, pApA is involved in a feedback inhibition loop that limits GdpP-dependent c-di-AMP hydrolysis. Another protein linked to the regulation of c-di-AMP levels in bacteria is the predicted regulator protein YbbR. Here, it is shown that a ybbR mutant S. aureus strain has increased acid sensitivity that can be bypassed by the acquisition of mutations in a number of genes, including the gene coding for the diadenylate cyclase DacA. We further show that c-di-AMP levels are slightly elevated in the ybbR suppressor strains tested as compared with the wild-type strain. With this, we not only identified a new role for YbbR in acid stress resistance in S. aureus but also provide further insight into how c-di-AMP levels impact acid tolerance in this organism.
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Affiliation(s)
- Lisa Bowman
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
| | - Merve S Zeden
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
| | - Christopher F Schuster
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
| | - Volkhard Kaever
- the Research Core Unit Metabolomics, Hannover Medical School, Hannover D-306625, Germany
| | - Angelika Gründling
- From the Section of Microbiology and Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom and
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Bose D, Su Y, Marcus A, Raulet DH, Hammond MC. An RNA-Based Fluorescent Biosensor for High-Throughput Analysis of the cGAS-cGAMP-STING Pathway. Cell Chem Biol 2016; 23:1539-1549. [PMID: 27889408 DOI: 10.1016/j.chembiol.2016.10.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/02/2016] [Accepted: 10/25/2016] [Indexed: 12/15/2022]
Abstract
In mammalian cells, the second messenger (2'-5',3'-5') cyclic guanosine monophosphate-adenosine monophosphate (2',3'-cGAMP), is produced by the cytosolic DNA sensor cGAMP synthase (cGAS), and subsequently bound by the stimulator of interferon genes (STING) to trigger interferon response. Thus, the cGAS-cGAMP-STING pathway plays a critical role in pathogen detection, as well as pathophysiological conditions including cancer and autoimmune disorders. However, studying and targeting this immune signaling pathway has been challenging due to the absence of tools for high-throughput analysis. We have engineered an RNA-based fluorescent biosensor that responds to 2',3'-cGAMP. The resulting "mix-and-go" cGAS activity assay shows excellent statistical reliability as a high-throughput screening (HTS) assay and distinguishes between direct and indirect cGAS inhibitors. Furthermore, the biosensor enables quantitation of 2',3'-cGAMP in mammalian cell lysates. We envision this biosensor-based assay as a resource to study the cGAS-cGAMP-STING pathway in the context of infectious diseases, cancer immunotherapy, and autoimmune diseases.
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Affiliation(s)
- Debojit Bose
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Yichi Su
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Assaf Marcus
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David H Raulet
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ming C Hammond
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.
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Evidence for Escherichia coli Diguanylate Cyclase DgcZ Interlinking Surface Sensing and Adhesion via Multiple Regulatory Routes. J Bacteriol 2016; 198:2524-35. [PMID: 27402625 DOI: 10.1128/jb.00320-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2016] [Accepted: 07/01/2016] [Indexed: 12/12/2022] Open
Abstract
UNLABELLED DgcZ is the main cyclic dimeric GMP (c-di-GMP)-producing diguanylate cyclase (DGC) controlling biosynthesis of the exopolysaccharide poly-β-1,6-N-acetylglucosamine (poly-GlcNAc or PGA), which is essential for surface attachment of Escherichia coli Although the complex regulation of DgcZ has previously been investigated, its primary role and the physiological conditions under which the protein is active are not fully understood. Transcription of dgcZ is regulated by the two-component system CpxAR activated by the lipoprotein NlpE in response to surface sensing. Here, we show that the negative effect of a cpxR mutation and the positive effect of nlpE overexpression on biofilm formation both depend on DgcZ. Coimmunoprecipitation data suggest several potential interaction partners of DgcZ. Interaction with FrdB, a subunit of the fumarate reductase complex (FRD) involved in anaerobic respiration and in control of flagellum assembly, was further supported by a bacterial-two-hybrid assay. Furthermore, the FRD complex was required for the increase in DgcZ-mediated biofilm formation upon induction of oxidative stress by addition of paraquat. A DgcZ-mVENUS fusion protein was found to localize at one bacterial cell pole in response to alkaline pH and carbon starvation. Based on our data and previous knowledge, an integrative role of DgcZ in regulation of surface attachment is proposed. We speculate that both DgcZ-stimulated PGA biosynthesis and interaction of DgcZ with the FRD complex contribute to impeding bacterial escape from the surface. IMPORTANCE Bacterial cells can grow by clonal expansion to surface-associated biofilms that are ubiquitous in the environment but also constitute a pervasive problem related to bacterial infections. Cyclic dimeric GMP (c-di-GMP) is a widespread bacterial second messenger involved in regulation of motility and biofilm formation, and plays a primary role in bacterial surface attachment. E. coli possesses a plethora of c-di-GMP-producing diguanylate cyclases, including DgcZ. Our study expands the knowledge on the role of DgcZ in regulation of surface attachment and suggests that it interconnects surface sensing and adhesion via multiple routes.
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46
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Groizeleau J, Rybtke M, Andersen JB, Berthelsen J, Liu Y, Yang L, Nielsen TE, Kaever V, Givskov M, Tolker-Nielsen T. The anti-cancerous drug doxorubicin decreases the c-di-GMP content in Pseudomonas aeruginosa but promotes biofilm formation. MICROBIOLOGY-SGM 2016; 162:1797-1807. [PMID: 27526691 DOI: 10.1099/mic.0.000354] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Current antibiotic treatments are insufficient in eradicating bacterial biofilms, which represent the primary cause of chronic bacterial infections. Thus, there is an urgent need for new strategies to eradicate biofilm infections. The second messenger c-di-GMP is a positive regulator of biofilm formation in many clinically relevant bacteria. It is hypothesized that drugs lowering the intracellular level of c-di-GMP will force biofilm bacteria into a more treatable planktonic lifestyle. To identify compounds capable of lowering c-di-GMP levels in Pseudomonas aeruginosa, we screened 5000 compounds for their potential c-di-GMP-lowering effect using a recently developed c-di-GMP biosensor strain. Our screen identified the anti-cancerous drug doxorubicin as a potent c-di-GMP inhibitor. In addition, the drug decreased the transcription of many biofilm-related genes. However, despite its effect on the c-di-GMP content in P. aeruginosa, doxorubicin was unable to inhibit biofilm formation or disperse established biofilms. On the contrary, the drug was found to promote P. aeruginosa biofilm formation, possibly through release of extracellular DNA from a subpopulation of killed bacteria. Our findings emphasize that lowering of the c-di-GMP content in bacteria might not be sufficient to mediate biofilm inhibition or dispersal.
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Affiliation(s)
- Julie Groizeleau
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Bo Andersen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Berthelsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Yang Liu
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Liang Yang
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Thomas E Nielsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Volkhard Kaever
- Research Core Unit Metabolomics, Hannover Medical School, Hannover, Germany
| | - Michael Givskov
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Tim Tolker-Nielsen
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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47
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Cyclic di-GMP contributes to adaption and virulence of Bacillus thuringiensis through a riboswitch-regulated collagen adhesion protein. Sci Rep 2016; 6:28807. [PMID: 27381437 PMCID: PMC4933901 DOI: 10.1038/srep28807] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/10/2016] [Indexed: 02/06/2023] Open
Abstract
Cyclic di-GMP is a ubiquitous second messenger that regulates diverse cellular processes in bacteria by binding to various protein or riboswitch effectors. In Bacillus thuringiensis BMB171, a c-di-GMP riboswitch termed Bc2 RNA resides in the 5'-untranslated region (5'-UTR) of an mRNA that encodes a collagen adhesion protein (Cap). The expression of cap was strongly repressed in parent strain BMB171 because of the presence of Bc2 RNA but was significantly promoted in the Bc2 RNA markerless deletion mutant. Bc2 RNA acts as a genetic "on" switch, which forms an anti-terminator structure to promote cap read-through transcription upon c-di-GMP binding. As a result, cap transcription was de-repressed under high c-di-GMP levels. Therefore, Bc2 RNA regulates cap expression using a repression/de-repression model. Bc2 RNA-regulated Cap was also found to be tightly associated with motility, aggregation, exopolysaccharide secretion, biofilm formation, and virulence of B. thuringiensis BMB171 against its host insect Helicoverpa armigera.
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48
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The DSF type quorum sensing signalling system RpfF/R regulates diverse phenotypes in the opportunistic pathogen Cronobacter. Sci Rep 2016; 6:18753. [PMID: 26725701 PMCID: PMC4698668 DOI: 10.1038/srep18753] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/25/2015] [Indexed: 12/11/2022] Open
Abstract
Several bacterial pathogens produce diffusible signal factor (DSF)-type quorum sensing (QS) signals to control biofilm formation and virulence. Previous work showed that in Burkholderia cenocepacia the RpfFBc/RpfR system is involved in sensing and responding to DSF signals and that this signal/sensor gene pair is highly conserved in several bacterial species including Cronobacter spp. Here we show that C. turicensis LMG 23827T possesses a functional RpfF/R system that is involved in the regulation of various phenotypes, including colony morphology, biofilm formation and swarming motility. In vivo experiments using the zebrafish embryo model revealed a role of this regulatory system in virulence of this opportunistic pathogen. We provide evidence that the RpfF/R system modulates the intracellular c-di-GMP level of the organism, an effect that may underpin the alteration in phenotype and thus the regulated phenotypes may be a consequence thereof. This first report on an RpfF/R-type QS system of an organism outside the genus Burkholderia revealed that both the underlying molecular mechanisms as well as the regulated functions show a high degree of conservation.
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49
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He Q, Wang F, Liu S, Zhu D, Cong H, Gao F, Li B, Wang H, Lin Z, Liao J, Gu L. Structural and Biochemical Insight into the Mechanism of Rv2837c from Mycobacterium tuberculosis as a c-di-NMP Phosphodiesterase. J Biol Chem 2015; 291:3668-81. [PMID: 26668313 DOI: 10.1074/jbc.m115.699801] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 12/18/2022] Open
Abstract
The intracellular infections of Mycobacterium tuberculosis, which is the causative agent of tuberculosis, are regulated by many cyclic dinucleotide signaling. Rv2837c from M. tuberculosis is a soluble, stand-alone DHH-DHHA1 domain phosphodiesterase that down-regulates c-di-AMP through catalytic degradation and plays an important role in M. tuberculosis infections. Here, we report the crystal structure of Rv2837c (2.0 Å), and its complex with hydrolysis intermediate 5'-pApA (2.35 Å). Our structures indicate that both DHH and DHHA1 domains are essential for c-di-AMP degradation. Further structural analysis shows that Rv2837c does not distinguish adenine from guanine, which explains why Rv2837c hydrolyzes all linear dinucleotides with almost the same efficiency. We observed that Rv2837c degraded other c-di-NMPs at a lower rate than it did on c-di-AMP. Nevertheless, our data also showed that Rv2837c significantly decreases concentrations of both c-di-AMP and c-di-GMP in vivo. Our results suggest that beside its major role in c-di-AMP degradation Rv2837c could also regulate c-di-GMP signaling pathways in bacterial cell.
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Affiliation(s)
- Qing He
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Feng Wang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Shiheng Liu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Deyu Zhu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Hengjiang Cong
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Fei Gao
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Bingqing Li
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Hongwei Wang
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China
| | - Zong Lin
- the Department of Biotechnology and Biomedicine, Yangtze Delta Region Institute of Tsinghua University, Jiaxing, Zhejiang 314006, China, and
| | - Jun Liao
- the School of Life Science and Technology, ShanghaiTech University, Shanghai 200031, China
| | - Lichuan Gu
- From the State Key Laboratory of Microbial Technology, School of Life Sciences, Shandong University, Jinan, Shandong, 250100, China,
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50
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Cheng X, Zheng X, Zhou X, Zeng J, Ren Z, Xu X, Cheng L, Li M, Li J, Li Y. Regulation of oxidative response and extracellular polysaccharide synthesis by a diadenylate cyclase in Streptococcus mutans. Environ Microbiol 2015; 18:904-22. [PMID: 26548332 DOI: 10.1111/1462-2920.13123] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/29/2015] [Accepted: 11/01/2015] [Indexed: 02/05/2023]
Abstract
Cyclic diadenosine monophosphate (c-di-AMP) has been implicated in the control of many important bacterial activities. However, the function of this molecule in Streptococcus mutans, the primary aetiological agent of human dental caries, is unknown. In this study, we identified and characterized a diadenylate cyclase, named CdaA, in S. mutans. Furthermore, we showed that in-frame deletion of the cdaA gene in S. mutans causes decreased c-di-AMP levels, increased sensitivity to hydrogen peroxide and increased production of extracellular polysaccharides. Global gene expression profiling revealed that more than 200 genes were significantly upregulated or downregulated (> 2.0-fold) in the cdaA mutant. Interestingly, genes with increased or decreased expression were clustered in cellular polysaccharide biosynthetic processes and oxidoreductase activity respectively. Notably, the expression of several genomic islands, such as GTF-B/C, TnSmu, CRISPR1-Cas and CRISPR2-Cas, was found to be altered in the cdaA mutant, indicating a possible link between these genomic islands and c-di-AMP signalling. Collectively, the results reported here show that CdaA is an important global modulator in S. mutans and is required for optimal growth and environmental adaption. This report also paves the way to unveil further the roles of c-di-AMP signalling networks in the biology and pathogenicity of S. mutans.
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Affiliation(s)
- Xingqun Cheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Zheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xuedong Zhou
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jumei Zeng
- Department of Infectious Diseases, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | - Zhi Ren
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Xin Xu
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lei Cheng
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Mingyun Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Jiyao Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuqing Li
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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