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Johnson GE, Fei C, Wingreen NS, Bassler BL. Single-cell gene-expression measurements in Vibrio cholerae biofilms reveal spatiotemporal patterns underlying development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603784. [PMID: 39071398 PMCID: PMC11275835 DOI: 10.1101/2024.07.17.603784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Bacteria commonly exist in multicellular, surface-attached communities called biofilms. Biofilms are central to ecology, medicine, and industry. The Vibrio cholerae pathogen forms biofilms from single founder cells that, via cell division, mature into three-dimensional structures with distinct, yet reproducible, regional architectures. To define mechanisms underlying biofilm developmental transitions, we establish a single-molecule fluorescence in situ hybridization (smFISH) approach that enables accurate quantitation of spatiotemporal gene-expression patterns in biofilms at individual-cell resolution. smFISH analyses of V. cholerae biofilm regulatory and structural genes demonstrate that, as biofilms mature, matrix gene expression decreases, and simultaneously, a pattern emerges in which matrix gene expression is largely confined to peripheral biofilm cells. Both quorum sensing and c-di-GMP-signaling are required to generate the proper temporal pattern of matrix gene expression, while c-di-GMP-signaling sets the regional expression pattern without input from quorum sensing. The smFISH strategy provides insight into mechanisms conferring particular fates to individual biofilm cells.
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Scribani Rossi C, Parisi G, Paiardini A, Rinaldo S. Exploring Innovative Approaches to Isolate a One-Component c-di-GMP Transducer: A Pilot Study. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023. [PMID: 37608242 DOI: 10.1007/5584_2023_787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Environmental nutrients control bacterial biofilm homeostasis, by regulating the intracellular levels of c-di-GMP. One component transducers can sense different classes of small molecules through a periplasmic domain; the nutrient recognition triggers the subsequent regulation of the downstream cytosolic diguanylate cyclase (GGDEF) or phosphodiesterase (EAL) domains, via transmembrane helix(ces), to finally change c-di-GMP levels.Protein studies on such transducers have been mainly carried out on isolated domains due to the presence of the transmembrane portion. Nevertheless, the cleavage of GGDEF and EAL-containing proteins could be detrimental since both tertiary and quaternary structures could be allosterically controlled; to by-pass this limitation, studies on the corresponding full-length proteins are highly desired.We have in silico selected a GGDEF-EAL transducer from Dyella thiooxydans (ann. A0A160N0B7), whose periplasmic binding domain was predicted to bind to arginine, a nutrient often associated with chronic infections and biofilm. This protein has been used as an in vitro tool for the identification of the best approach for its isolation, including (i) protein engineering to produce a water-soluble version via QTY (Glutamine, Threonine, and Tyrosine) code or (ii) nanodiscs assembly. The results on this "prototype" may represent the proof-of-concept for future isolation of other transmembrane proteins sharing the same architecture, including more complex nutrient-based transducers controlling c-di-GMP levels.
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Affiliation(s)
- Chiara Scribani Rossi
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuroscience, Istituto Italiano di Tecnologia, Rome, Italy
| | - Alessandro Paiardini
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti - Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.
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Nutrient Sensing and Biofilm Modulation: The Example of L-arginine in Pseudomonas. Int J Mol Sci 2022; 23:ijms23084386. [PMID: 35457206 PMCID: PMC9028604 DOI: 10.3390/ijms23084386] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 12/01/2022] Open
Abstract
Bacterial biofilm represents a multicellular community embedded within an extracellular matrix attached to a surface. This lifestyle confers to bacterial cells protection against hostile environments, such as antibiotic treatment and host immune response in case of infections. The Pseudomonas genus is characterised by species producing strong biofilms difficult to be eradicated and by an extraordinary metabolic versatility which may support energy and carbon/nitrogen assimilation under multiple environmental conditions. Nutrient availability can be perceived by a Pseudomonas biofilm which, in turn, readapts its metabolism to finally tune its own formation and dispersion. A growing number of papers is now focusing on the mechanism of nutrient perception as a possible strategy to weaken the biofilm barrier by environmental cues. One of the most important nutrients is amino acid L-arginine, a crucial metabolite sustaining bacterial growth both as a carbon and a nitrogen source. Under low-oxygen conditions, L-arginine may also serve for ATP production, thus allowing bacteria to survive in anaerobic environments. L-arginine has been associated with biofilms, virulence, and antibiotic resistance. L-arginine is also a key precursor of regulatory molecules such as polyamines, whose involvement in biofilm homeostasis is reported. Given the biomedical and biotechnological relevance of biofilm control, the state of the art on the effects mediated by the L-arginine nutrient on biofilm modulation is presented, with a special focus on the Pseudomonas biofilm. Possible biotechnological and biomedical applications are also discussed.
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Zhang J, Hu L, Zhang H, He Z. Cyclic
di‐GMP
triggers the hypoxic adaptation of
Mycobacterium bovis
through a metabolic switching regulator
ArgR. Environ Microbiol 2022; 24:4382-4400. [DOI: 10.1111/1462-2920.15987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Jiaxun Zhang
- College of Life Science and Technology Huazhong Agricultural University Wuhan 430070 China
| | - Lihua Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and Technology Guangxi University Nanning 530004 China
| | - Hua Zhang
- College of Life Science and Technology Huazhong Agricultural University Wuhan 430070 China
| | - Zheng‐Guo He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐bioresources, College of Life Science and Technology Guangxi University Nanning 530004 China
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Bridges AA, Prentice JA, Fei C, Wingreen NS, Bassler BL. Quantitative input-output dynamics of a c-di-GMP signal transduction cascade in Vibrio cholerae. PLoS Biol 2022; 20:e3001585. [PMID: 35302986 PMCID: PMC8967002 DOI: 10.1371/journal.pbio.3001585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/30/2022] [Accepted: 02/25/2022] [Indexed: 12/13/2022] Open
Abstract
Bacterial biofilms are multicellular communities that collectively overcome environmental threats and clinical treatments. To regulate the biofilm lifecycle, bacteria commonly transduce sensory information via the second messenger molecule cyclic diguanylate (c-di-GMP). Using experimental and modeling approaches, we quantitatively capture c-di-GMP signal transmission via the bifunctional polyamine receptor NspS-MbaA, from ligand binding to output, in the pathogen Vibrio cholerae. Upon binding of norspermidine or spermidine, NspS-MbaA synthesizes or degrades c-di-GMP, respectively, which, in turn, drives alterations specifically to biofilm gene expression. A long-standing question is how output specificity is achieved via c-di-GMP, a diffusible molecule that regulates dozens of effectors. We show that NspS-MbaA signals locally to specific effectors, sensitizing V. cholerae to polyamines. However, local signaling is not required for specificity, as changes to global cytoplasmic c-di-GMP levels can selectively regulate biofilm genes. This work establishes the input-output dynamics underlying c-di-GMP signaling, which could be useful for developing bacterial manipulation strategies.
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Affiliation(s)
- Andrew A. Bridges
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Jojo A. Prentice
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
| | - Chenyi Fei
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Ned S. Wingreen
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- * E-mail: (NSW); (BLB)
| | - Bonnie L. Bassler
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, United States of America
- The Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
- * E-mail: (NSW); (BLB)
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Biswas S, Chouhan OP, Bandekar D. Diguanylate Cyclases in Vibrio cholerae: Essential Regulators of Lifestyle Switching. Front Cell Infect Microbiol 2020; 10:582947. [PMID: 33194821 PMCID: PMC7642852 DOI: 10.3389/fcimb.2020.582947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 09/14/2020] [Indexed: 01/04/2023] Open
Abstract
Biofilm formation in Vibrio cholerae empowers the bacteria to lead a dual lifestyle and enhances its infectivity. While the formation and dispersal of the biofilm involves multiple components—both proteinaceous and non-proteinaceous, the key to the regulatory control lies with the ubiquitous secondary signaling molecule, cyclic-di-GMP (c-di-GMP). A number of different cellular components may interact with c-di-GMP, but the onus of synthesis of this molecule lies with a class of enzymes known as diguanylate cyclases (DGCs). DGC activity is generally associated with proteins possessing a GGDEF domain, ubiquitously present across all bacterial systems. V. cholerae is also endowed with multiple DGCs and information about some of them have been pouring in over the past decade. This review summarizes the DGCs confirmed till date in V. cholerae, and emphasizes the importance of DGCs and their product, c-di-GMP in the virulence and lifecycle of the bacteria.
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Affiliation(s)
- Sumit Biswas
- ViStA Lab, Department of Biological Sciences, Birla Institute of Technology and Sciences (BITS), Pilani-KK Birla Goa Campus, Goa, India
| | - Om Prakash Chouhan
- ViStA Lab, Department of Biological Sciences, Birla Institute of Technology and Sciences (BITS), Pilani-KK Birla Goa Campus, Goa, India
| | - Divya Bandekar
- ViStA Lab, Department of Biological Sciences, Birla Institute of Technology and Sciences (BITS), Pilani-KK Birla Goa Campus, Goa, India
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Rinaldo S, Giardina G, Mantoni F, Paone A, Cutruzzolà F. Beyond nitrogen metabolism: nitric oxide, cyclic-di-GMP and bacterial biofilms. FEMS Microbiol Lett 2019; 365:4834012. [PMID: 29401255 DOI: 10.1093/femsle/fny029] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
The nitrogen cycle pathways are responsible for the circulation of inorganic and organic N-containing molecules in nature. Among these pathways, those involving amino acids, N-oxides and in particular nitric oxide (NO) play strategic roles in the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond their role in the N-cycle, amino acids and NO are also signalling molecules able to influence group behaviour in microorganisms and cell-cell communication in multicellular organisms, including humans. In this minireview, we summarise the role of these compounds in the homeostasis of the bacterial communities called biofilms, commonly found in environmental, industrial and medical settings. Biofilms are difficult to eradicate since they are highly resistant to antimicrobials and to the host immune system. We highlight the effect of amino acids such as glutamate, glutamine and arginine and of NO on the signalling pathways involved in the metabolism of 3',5'-cyclic diguanylic acid (c-di-GMP), a master regulator of motility, attachment and group behaviour in bacteria. The study of the metabolic routes involving these N-containing compounds represents an attractive topic to identify targets for biofilm control in both natural and medical settings.
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Affiliation(s)
- Serena Rinaldo
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Giorgio Giardina
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Federico Mantoni
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
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Paiardini A, Mantoni F, Giardina G, Paone A, Janson G, Leoni L, Rampioni G, Cutruzzolà F, Rinaldo S. A novel bacterial l-arginine sensor controlling c-di-GMP levels in Pseudomonas aeruginosa. Proteins 2018; 86:1088-1096. [PMID: 30040157 DOI: 10.1002/prot.25587] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 01/16/2023]
Abstract
Nutrients such as amino acids play key roles in shaping the metabolism of microorganisms in natural environments and in host-pathogen interactions. Beyond taking part to cellular metabolism and to protein synthesis, amino acids are also signaling molecules able to influence group behavior in microorganisms, such as biofilm formation. This lifestyle switch involves complex metabolic reprogramming controlled by local variation of the second messenger 3', 5'-cyclic diguanylic acid (c-di-GMP). The intracellular levels of this dinucleotide are finely tuned by the opposite activity of dedicated diguanylate cyclases (GGDEF signature) and phosphodiesterases (EAL and HD-GYP signatures), which are usually allosterically controlled by a plethora of environmental and metabolic clues. Among the genes putatively involved in controlling c-di-GMP levels in P. aeruginosa, we found that the multidomain transmembrane protein PA0575, bearing the tandem signature GGDEF-EAL, is an l-arginine sensor able to hydrolyse c-di-GMP. Here, we investigate the basis of arginine recognition by integrating bioinformatics, molecular biophysics and microbiology. Although the role of nutrients such as l-arginine in controlling the cellular fate in P. aeruginosa (including biofilm, pathogenicity and virulence) is already well established, we identified the first l-arginine sensor able to link environment sensing, c-di-GMP signaling and biofilm formation in this bacterium.
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Affiliation(s)
- A Paiardini
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - F Mantoni
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - G Giardina
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - A Paone
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy
| | - G Janson
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy
| | - L Leoni
- Department of Science, University Roma Tre (I), Roma, Italy
| | - G Rampioni
- Department of Science, University Roma Tre (I), Roma, Italy
| | - F Cutruzzolà
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
| | - S Rinaldo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome (I), Roma, Italy.,Istituto Pasteur Italia-Fondazione Cenci Bolognetti, Roma, Italy
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