1
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Jeong GJ, Khan F, Tabassum N, Cho KJ, Kim YM. Marine-derived bioactive materials as antibiofilm and antivirulence agents. Trends Biotechnol 2024:S0167-7799(24)00090-8. [PMID: 38637243 DOI: 10.1016/j.tibtech.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/20/2024]
Abstract
Microbial infections are major human health issues, and, recently, the mortality rate owing to bacterial and fungal infections has been increasing. In addition to intrinsic and extrinsic antimicrobial resistance mechanisms, biofilm formation is a key adaptive resistance mechanism. Several bioactive compounds from marine organisms have been identified for use in biofilm therapy owing to their structural complexity, biocompatibility, and economic viability. In this review, we discuss recent trends in the application of marine natural compounds, marine-bioinspired nanomaterials, and marine polymer conjugates as possible therapeutic agents for controlling biofilms and virulence factors. We also comprehensively discuss the mechanisms underlying biofilm formation and inhibition of virulence factors by marine-derived materials and propose possible applications of novel and effective antibiofilm and antivirulence agents.
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Affiliation(s)
- Geum-Jae Jeong
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Fazlurrahman Khan
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea; Institute of Fisheries Science, Pukyong National University, Busan 48513, Republic of Korea.
| | - Nazia Tabassum
- Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Kyung-Jin Cho
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea
| | - Young-Mog Kim
- Department of Food Science and Technology, Pukyong National University, Busan 48513, Republic of Korea; Marine Integrated Biomedical Technology Center, The National Key Research Institutes in Universities, Pukyong National University, Busan, 48513, Republic of Korea; Research Center for Marine Integrated Bionics Technology, Pukyong National University, Busan 48513, Republic of Korea.
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2
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Granton E, Brown L, Defaye M, Moazen P, Almblad H, Randall TE, Rich JD, Geppert A, Abdullah NS, Hassanabad MF, Hiroki CH, Farias R, Nguyen AP, Schubert C, Lou Y, Andonegui G, Iftinca M, Raju D, Vargas MA, Howell PL, Füzesi T, Bains J, Kurrasch D, Harrison JJ, Altier C, Yipp BG. Biofilm exopolysaccharides alter sensory-neuron-mediated sickness during lung infection. Cell 2024; 187:1874-1888.e14. [PMID: 38518773 DOI: 10.1016/j.cell.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 01/04/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024]
Abstract
Infections of the lung cause observable sickness thought to be secondary to inflammation. Signs of sickness are crucial to alert others via behavioral-immune responses to limit contact with contagious individuals. Gram-negative bacteria produce exopolysaccharide (EPS) that provides microbial protection; however, the impact of EPS on sickness remains uncertain. Using genome-engineered Pseudomonas aeruginosa (P. aeruginosa) strains, we compared EPS-producers versus non-producers and a virulent Escherichia coli (E. coli) lung infection model in male and female mice. EPS-negative P. aeruginosa and virulent E. coli infection caused severe sickness, behavioral alterations, inflammation, and hypothermia mediated by TLR4 detection of the exposed lipopolysaccharide (LPS) in lung TRPV1+ sensory neurons. However, inflammation did not account for sickness. Stimulation of lung nociceptors induced acute stress responses in the paraventricular hypothalamic nuclei by activating corticotropin-releasing hormone neurons responsible for sickness behavior and hypothermia. Thus, EPS-producing biofilm pathogens evade initiating a lung-brain sensory neuronal response that results in sickness.
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Affiliation(s)
- Elise Granton
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Luke Brown
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Manon Defaye
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Inflammation Research Network, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Parisa Moazen
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Henrik Almblad
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Trevor E Randall
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jacquelyn D Rich
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Andrew Geppert
- Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Nasser S Abdullah
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Inflammation Research Network, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Mortaza F Hassanabad
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Carlos H Hiroki
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Raquel Farias
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Angela P Nguyen
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Courtney Schubert
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Yuefei Lou
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Graciela Andonegui
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Mircea Iftinca
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Inflammation Research Network, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deepa Raju
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mario A Vargas
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada
| | - P Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, ON, Canada; Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Tamás Füzesi
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada; Cumming School of Medicine Optogenetics Core Facility, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jaideep Bains
- Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada; Krembil Research Institute, University Health Network, Toronto, ON, Canada.
| | - Deborah Kurrasch
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada; Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - Joe Jonathan Harrison
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
| | - Christophe Altier
- Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Department of Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Inflammation Research Network, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada.
| | - Bryan G Yipp
- Department of Critical Care, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada; Calvin, Phoebe and Joan Snyder Institute for Chronic Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
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3
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Roussin-Léveillée C, Rossi CAM, Castroverde CDM, Moffett P. The plant disease triangle facing climate change: a molecular perspective. Trends Plant Sci 2024:S1360-1385(24)00060-8. [PMID: 38580544 DOI: 10.1016/j.tplants.2024.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Variations in climate conditions can dramatically affect plant health and the generation of climate-resilient crops is imperative to food security. In addition to directly affecting plants, it is predicted that more severe climate conditions will also result in greater biotic stresses. Recent studies have identified climate-sensitive molecular pathways that can result in plants being more susceptible to infection under unfavorable conditions. Here, we review how expected changes in climate will impact plant-pathogen interactions, with a focus on mechanisms regulating plant immunity and microbial virulence strategies. We highlight the complex interactions between abiotic and biotic stresses with the goal of identifying components and/or pathways that are promising targets for genetic engineering to enhance adaptation and strengthen resilience in dynamically changing environments.
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Affiliation(s)
| | - Christina A M Rossi
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, N2L 3C5, Canada
| | | | - Peter Moffett
- Centre SÈVE, Département de Biologie, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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4
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Lewis IA. Boundary flux analysis: an emerging strategy for investigating metabolic pathway activity in large cohorts. Curr Opin Biotechnol 2024; 85:103027. [PMID: 38061263 DOI: 10.1016/j.copbio.2023.103027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 11/02/2023] [Accepted: 11/15/2023] [Indexed: 02/09/2024]
Abstract
Many biological phenotypes are rooted in metabolic pathway activity rather than the concentrations of individual metabolites. Despite this, most metabolomics studies only capture steady-state metabolism - not metabolic flux. Although sophisticated metabolic flux analysis strategies have been developed, these methods are technically challenging and difficult to implement in large-cohort studies. Recently, a new boundary flux analysis (BFA) approach has emerged that captures large-scale metabolic flux phenotypes by quantifying changes in metabolite levels in the media of cultured cells. This approach is advantageous because it is relatively easy to implement yet captures complex metabolic flux phenotypes. We describe the opportunities and challenges of BFA and illustrate how it can be harnessed to investigate a wide transect of biological phenomena.
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Affiliation(s)
- Ian A Lewis
- Alberta Centre for Advanced Diagnostics, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.
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5
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Feng Q, Zhou J, Zhang L, Fu Y, Yang L. Insights into the molecular basis of c-di-GMP signalling in Pseudomonas aeruginosa. Crit Rev Microbiol 2024; 50:20-38. [PMID: 36539391 DOI: 10.1080/1040841x.2022.2154140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022]
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa can cause severe infections in immunocompromized people or cystic fibrosis (CF) patients. Because of its remarkable ability to invade the host and withstand the bacteriocidal effect of most conventional antibiotics, the infection caused by P. aeruginosa has become a major concern for human health. The switch from acute to chronic infection is governed by the second messenger bis-(3'-5')-cyclic dimeric guanosine mono-phosphate (c-di-GMP) in P. aeruginosa, and c-di-GMP is now recognized to regulate many important biological processes in pathogenesis. The c-di-GMP signalling mechanisms in P. aeruginosa have been studied extensively in the past decade, revealing complicated c-di-GMP metabolism and signalling network. In this review, the underlying mechanisms of this signalling network will be discussed, mainly focussing on how environmental cues regulate c-di-GMP signalling, protein-protein interaction mediated functional regulation, heterogeneity of c-di-GMP and cross talk between c-di-GMP signalling and other signalling systems. Understanding the molecular mechanism underlying the complex c-di-GMP signalling network would be beneficial for developing therapeutic approaches and antibacterial agents to combat the threat from P. aeruginosa.
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Affiliation(s)
- Qishun Feng
- School of Medicine, Southern University of Science and Technology, Shenzhen, PR China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, PR China
| | - Lianhui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, PR China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, PR China
| | - Yang Fu
- School of Medicine, Southern University of Science and Technology, Shenzhen, PR China
| | - Liang Yang
- School of Medicine, Southern University of Science and Technology, Shenzhen, PR China
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6
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Eilers K, Hoong Yam JK, Liu X, Goh YF, To KN, Paracuellos P, Morton R, Brizuela J, Hui Yong AM, Givskov M, Freibert SA, Bange G, Rice SA, Steinchen W, Filloux A. The dual GGDEF/EAL domain enzyme PA0285 is a Pseudomonas species housekeeping phosphodiesterase regulating early attachment and biofilm architecture. J Biol Chem 2024; 300:105659. [PMID: 38237678 PMCID: PMC10874727 DOI: 10.1016/j.jbc.2024.105659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 12/23/2023] [Accepted: 01/04/2024] [Indexed: 02/15/2024] Open
Abstract
Bacterial lifestyles depend on conditions encountered during colonization. The transition between planktonic and biofilm growth is dependent on the intracellular second messenger c-di-GMP. High c-di-GMP levels driven by diguanylate cyclases (DGCs) activity favor biofilm formation, while low levels were maintained by phosphodiesterases (PDE) encourage planktonic lifestyle. The activity of these enzymes can be modulated by stimuli-sensing domains such as Per-ARNT-Sim (PAS). In Pseudomonas aeruginosa, more than 40 PDE/DGC are involved in c-di-GMP homeostasis, including 16 dual proteins possessing both canonical DGC and PDE motifs, that is, GGDEF and EAL, respectively. It was reported that deletion of the EAL/GGDEF dual enzyme PA0285, one of five c-di-GMP-related enzymes conserved across all Pseudomonas species, impacts biofilms. PA0285 is anchored in the membrane and carries two PAS domains. Here, we confirm that its role is conserved in various P. aeruginosa strains and in Pseudomonas putida. Deletion of PA0285 impacts the early stage of colonization, and RNA-seq analysis suggests that expression of cupA fimbrial genes is involved. We demonstrate that the C-terminal portion of PA0285 encompassing the GGDEF and EAL domains binds GTP and c-di-GMP, respectively, but only exhibits PDE activity in vitro. However, both GGDEF and EAL domains are important for PA0285 PDE activity in vivo. Complementation of the PA0285 mutant strain with a copy of the gene encoding the C-terminal GGDEF/EAL portion in trans was not as effective as complementation with the full-length gene. This suggests the N-terminal transmembrane and PAS domains influence the PDE activity in vivo, through modulating the protein conformation.
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Affiliation(s)
- Kira Eilers
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Yu Fen Goh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Ka-Ning To
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Patricia Paracuellos
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Richard Morton
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Jaime Brizuela
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Denmark
| | - Sven-Andreas Freibert
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Gert Bange
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore; Microbiomes for One Systems Health and Agriculture and Food, CSIRO, Westmead, New South Wales, Australia
| | - Wieland Steinchen
- Philipps University Marburg, Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.
| | - Alain Filloux
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, United Kingdom; Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore.
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7
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Scribani Rossi C, Eckartt K, Scarchilli E, Angeli S, Price-Whelan A, Di Matteo A, Chevreuil M, Raynal B, Arcovito A, Giacon N, Fiorentino F, Rotili D, Mai A, Espinosa-Urgel M, Cutruzzolà F, Dietrich LEP, Paone A, Paiardini A, Rinaldo S. Molecular insights into RmcA-mediated c-di-GMP consumption: Linking redox potential to biofilm morphogenesis in Pseudomonas aeruginosa. Microbiol Res 2023; 277:127498. [PMID: 37776579 DOI: 10.1016/j.micres.2023.127498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 10/02/2023]
Abstract
The ability of many bacteria to form biofilms contributes to their resilience and makes infections more difficult to treat. Biofilm growth leads to the formation of internal oxygen gradients, creating hypoxic subzones where cellular reducing power accumulates, and metabolic activities can be limited. The pathogen Pseudomonas aeruginosa counteracts the redox imbalance in the hypoxic biofilm subzones by producing redox-active electron shuttles (phenazines) and by secreting extracellular matrix, leading to an increased surface area-to-volume ratio, which favors gas exchange. Matrix production is regulated by the second messenger bis-(3',5')-cyclic-dimeric-guanosine monophosphate (c-di-GMP) in response to different environmental cues. RmcA (Redox modulator of c-di-GMP) from P. aeruginosa is a multidomain phosphodiesterase (PDE) that modulates c-di-GMP levels in response to phenazine availability. RmcA can also sense the fermentable carbon source arginine via a periplasmic domain, which is linked via a transmembrane domain to four cytoplasmic Per-Arnt-Sim (PAS) domains followed by a diguanylate cyclase (DGC) and a PDE domain. The biochemical characterization of the cytoplasmic portion of RmcA reported in this work shows that the PAS domain adjacent to the catalytic domain tunes RmcA PDE activity in a redox-dependent manner, by differentially controlling protein conformation in response to FAD or FADH2. This redox-dependent mechanism likely links the redox state of phenazines (via FAD/FADH2 ratio) to matrix production as indicated by a hyperwrinkling phenotype in a macrocolony biofilm assay. This study provides insights into the role of RmcA in transducing cellular redox information into a structural response of the biofilm at the population level. Conditions of resource (i.e. oxygen and nutrient) limitation arise during chronic infection, affecting the cellular redox state and promoting antibiotic tolerance. An understanding of the molecular linkages between condition sensing and biofilm structure is therefore of crucial importance from both biological and engineering standpoints.
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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
| | - Kelly Eckartt
- Department of Biological Sciences, Columbia University, New York, USA
| | - Elisabetta Scarchilli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Simone Angeli
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | | | - Adele Di Matteo
- CNR Institute of Molecular Biology and Pathology, I-00185 Rome, Italy
| | - Maelenn Chevreuil
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Bertrand Raynal
- Plate-forme de Biophysique Moléculaire, Institut Pasteur, UMR 3528 CNRS, Paris, France
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy; Fondazione Policlinico Universitario A. Gemelli - IRCCS, Rome, Italy
| | - Noah Giacon
- Dipartimento di Scienze Biotecnologiche Di Base, Cliniche Intensivologiche e Perioperatorie Università Cattolica Del Sacro Cuore, Roma, Italy
| | - Francesco Fiorentino
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection. Estación Experimental del Zaidin, CSIC, Granada, Spain
| | - Francesca Cutruzzolà
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
| | - Lars E P Dietrich
- Department of Biological Sciences, Columbia University, New York, USA
| | - Alessio Paone
- Laboratory affiliated to Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, 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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8
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Zhang Q, Alter T, Strauch E, Hammerl JA, Schwartz K, Borowiak M, Deneke C, Fleischmann S. Genetic and Phenotypic Virulence Potential of Non-O1/Non-O139 Vibrio cholerae Isolated from German Retail Seafood. Microorganisms 2023; 11:2751. [PMID: 38004762 PMCID: PMC10672755 DOI: 10.3390/microorganisms11112751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
Non-O1 and non-O139 Vibrio cholerae (NOVC) can cause gastrointestinal infections in humans. Contaminated food, especially seafood, is an important source of human infections. In this study, the virulence potential of 63 NOVC strains isolated from retail seafood were characterized at the genotypic and phenotypic levels. Although no strain encoded the cholera toxin (CTX) and the toxin-coregulated pilus (TCP), several virulence factors, including the HlyA hemolysin, the cholix toxin ChxA, the heat-stable enterotoxin Stn, and genes coding for the type 3 and type 6 secretion systems, were detected. All strains showed hemolytic activity against human and sheep erythrocytes: 90% (n = 57) formed a strong biofilm, 52% (n = 33) were highly motile at 37 °C, and only 8% (n = 5) and 14% (n = 9) could resist ≥60% and ≥40% human serum, respectively. Biofilm formation and toxin regulation genes were also detected. cgMLST analysis demonstrated that NOVC strains from seafood cluster with clinical NOVC strains. Antimicrobial susceptibility testing (AST) results in the identification of five strains that developed non-wildtype phenotypes (medium and resistant) against the substances of the classes of beta-lactams (including penicillin, carbapenem, and cephalosporin), polymyxins, and sulphonamides. The phenotypic resistance pattern could be partially attributed to the acquired resistance determinants identified via in silico analysis. Our results showed differences in the virulence potential of the analyzed NOVC isolated from retail seafood products, which may be considered for further pathogenicity evaluation and the risk assessment of NOVC isolates in future seafood monitoring.
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Affiliation(s)
- Quantao Zhang
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Thomas Alter
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
| | - Eckhard Strauch
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Jens Andre Hammerl
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Keike Schwartz
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Maria Borowiak
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Carlus Deneke
- Department Biological Safety, German Federal Institute for Risk Assessment, Diedersdorfer Weg 1, 12277 Berlin, Germany; (E.S.); (J.A.H.)
| | - Susanne Fleischmann
- Institute of Food Safety and Food Hygiene, School of Veterinary Medicine, Freie Universität Berlin, Königsweg 69, 14163 Berlin, Germany
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9
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Yu Z, Zhang W, Yang H, Chou SH, Galperin MY, He J. Gas and light: triggers of c-di-GMP-mediated regulation. FEMS Microbiol Rev 2023; 47:fuad034. [PMID: 37339911 PMCID: PMC10505747 DOI: 10.1093/femsre/fuad034] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/01/2023] [Accepted: 06/17/2023] [Indexed: 06/22/2023] Open
Abstract
The widespread bacterial second messenger c-di-GMP is responsible for regulating many important physiological functions such as biofilm formation, motility, cell differentiation, and virulence. The synthesis and degradation of c-di-GMP in bacterial cells depend, respectively, on diguanylate cyclases and c-di-GMP-specific phosphodiesterases. Since c-di-GMP metabolic enzymes (CMEs) are often fused to sensory domains, their activities are likely controlled by environmental signals, thereby altering cellular c-di-GMP levels and regulating bacterial adaptive behaviors. Previous studies on c-di-GMP-mediated regulation mainly focused on downstream signaling pathways, including the identification of CMEs, cellular c-di-GMP receptors, and c-di-GMP-regulated processes. The mechanisms of CME regulation by upstream signaling modules received less attention, resulting in a limited understanding of the c-di-GMP regulatory networks. We review here the diversity of sensory domains related to bacterial CME regulation. We specifically discuss those domains that are capable of sensing gaseous or light signals and the mechanisms they use for regulating cellular c-di-GMP levels. It is hoped that this review would help refine the complete c-di-GMP regulatory networks and improve our understanding of bacterial behaviors in changing environments. In practical terms, this may eventually provide a way to control c-di-GMP-mediated bacterial biofilm formation and pathogenesis in general.
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Affiliation(s)
- Zhaoqing Yu
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
- Institute of Agro-Product Processing, Jiangsu Academy of Agricultural Sciences, 50 Zhongling Street, Nanjing, Jiangsu 210014, PR China
| | - Wei Zhang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - He Yang
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Shan-Ho Chou
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Jin He
- National Key Laboratory of Agricultural Microbiology and Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, 1 Shizishan Street, Wuhan, Hubei 430070, PR China
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10
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Zhang D, Yin F, Qin Q, Qiao L. Molecular responses during bacterial filamentation reveal inhibition methods of drug-resistant bacteria. Proc Natl Acad Sci U S A 2023; 120:e2301170120. [PMID: 37364094 PMCID: PMC10318954 DOI: 10.1073/pnas.2301170120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Bacterial antimicrobial resistance (AMR) is among the most significant challenges to current human society. Exposing bacteria to antibiotics can activate their self-saving responses, e.g., filamentation, leading to the development of bacterial AMR. Understanding the molecular changes during the self-saving responses can reveal new inhibition methods of drug-resistant bacteria. Herein, we used an online microfluidics mass spectrometry system for real-time characterization of metabolic changes of bacteria during filamentation under the stimulus of antibiotics. Significant pathways, e.g., nucleotide metabolism and coenzyme A biosynthesis, correlated to the filamentation of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) were identified. A cyclic dinucleotide, c-di-GMP, which is derived from nucleotide metabolism and reported closely related to bacterial resistance and tolerance, was observed significantly up-regulated during the bacterial filamentation. By using a chemical inhibitor, ebselen, to inhibit diguanylate cyclases which catalyzes the synthesis of c-di-GMP, the minimum inhibitory concentration of ceftriaxone against ESBL-E. coli was significantly decreased. This inhibitory effect was also verified with other ESBL-E. coli strains and other beta-lactam antibiotics, i.e., ampicillin. A mutant strain of ESBL-E. coli by knocking out the dgcM gene was used to demonstrate that the inhibition of the antibiotic resistance to beta-lactams by ebselen was mediated through the inhibition of the diguanylate cyclase DgcM and the modulation of c-di-GMP levels. Our study uncovers the molecular changes during bacterial filamentation and proposes a method to inhibit antibiotic-resistant bacteria by combining traditional antibiotics and chemical inhibitors against the enzymes involved in bacterial self-saving responses.
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Affiliation(s)
- Dongxue Zhang
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
| | - Fan Yin
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
| | - Qin Qin
- Changhai Hospital, The Naval Military Medical University, Shanghai200433, China
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Institutes of Biomedical Sciences, Fudan University, Shanghai200000, China
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11
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Seidel M, Skotnicka D, Glatter T, Søgaard-Andersen L. During heat stress in Myxococcus xanthus, the CdbS PilZ domain protein, in concert with two PilZ-DnaK chaperones, perturbs chromosome organization and accelerates cell death. PLoS Genet 2023; 19:e1010819. [PMID: 37339150 DOI: 10.1371/journal.pgen.1010819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023] Open
Abstract
C-di-GMP is a bacterial second messenger that regulates diverse processes in response to environmental or cellular cues. The nucleoid-associated protein (NAP) CdbA in Myxococcus xanthus binds c-di-GMP and DNA in a mutually exclusive manner in vitro. CdbA is essential for viability, and CdbA depletion causes defects in chromosome organization, leading to a block in cell division and, ultimately, cell death. Most NAPs are not essential; therefore, to explore the paradoxical cdbA essentiality, we isolated suppressor mutations that restored cell viability without CdbA. Most mutations mapped to cdbS, which encodes a stand-alone c-di-GMP binding PilZ domain protein, and caused loss-of-function of cdbS. Cells lacking CdbA and CdbS or only CdbS were fully viable and had no defects in chromosome organization. CdbA depletion caused post-transcriptional upregulation of CdbS accumulation, and this CdbS over-accumulation was sufficient to disrupt chromosome organization and cause cell death. CdbA depletion also caused increased accumulation of CsdK1 and CsdK2, two unusual PilZ-DnaK chaperones. During CdbA depletion, CsdK1 and CsdK2, in turn, enabled the increased accumulation and toxicity of CdbS, likely by stabilizing CdbS. Moreover, we demonstrate that heat stress, possibly involving an increased cellular c-di-GMP concentration, induced the CdbA/CsdK1/CsdK2/CdbS system, causing a CsdK1- and CsdK2-dependent increase in CdbS accumulation. Thereby this system accelerates heat stress-induced chromosome mis-organization and cell death. Collectively, this work describes a unique system that contributes to regulated cell death in M. xanthus and suggests a link between c-di-GMP signaling and regulated cell death in bacteria.
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Affiliation(s)
- Michael Seidel
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Dorota Skotnicka
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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12
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Razvi E, DiFrancesco BR, Wasney GA, Morrison ZA, Tam J, Auger A, Baker P, Alnabelseya N, Rich JD, Sivarajah P, Whitfield GB, Harrison JJ, Melnyk RA, Nitz M, Howell PL. Small Molecule Inhibition of an Exopolysaccharide Modification Enzyme is a Viable Strategy To Block Pseudomonas aeruginosa Pel Biofilm Formation. Microbiol Spectr 2023; 11:e0029623. [PMID: 37098898 PMCID: PMC10269871 DOI: 10.1128/spectrum.00296-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/03/2023] [Indexed: 04/27/2023] Open
Abstract
Biosynthesis of the Pel exopolysaccharide in Pseudomonas aeruginosa requires all seven genes of the pelABCDEFG operon. The periplasmic modification enzyme PelA contains a C-terminal deacetylase domain that is necessary for Pel-dependent biofilm formation. Herein, we show that extracellular Pel is not produced by a P. aeruginosa PelA deacetylase mutant. This positions PelA deacetylase activity as an attractive target to prevent Pel-dependent biofilm formation. Using a high-throughput screen (n = 69,360), we identified 56 compounds that potentially inhibit PelA esterase activity, the first enzymatic step in the deacetylase reaction. A secondary biofilm inhibition assay identified methyl 2-(2-pyridinylmethylene) hydrazinecarbodithioate (SK-017154-O) as a specific Pel-dependent biofilm inhibitor. Structure-activity relationship studies identified the thiocarbazate as a necessary functional group and that the pyridyl ring could be replaced with a phenyl substituent (compound 1). Both SK-017154-O and compound 1 inhibit Pel-dependent biofilm formation in Bacillus cereus ATCC 10987, which has a predicted extracellular PelA deacetylase in its pel operon. Michaelis-Menten kinetics determined SK-017154-O to be a noncompetitive inhibitor of PelA, while compound 1 did not directly inhibit PelA esterase activity. Cytotoxicity assays using human lung fibroblast cells showed that compound 1 is less cytotoxic than SK-017154-O. This work provides proof of concept that biofilm exopolysaccharide modification enzymes are important for biofilm formation and can serve as useful antibiofilm targets. IMPORTANCE Present in more than 500 diverse Gram-negative and 900 Gram-positive organisms, the Pel polysaccharide is one of the most phylogenetically widespread biofilm matrix determinants found to date. Partial de-N-acetylation of this α-1,4 linked N-acetylgalactosamine polymer by the carbohydrate modification enzyme PelA is required for Pel-dependent biofilm formation in Pseudomonas aeruginosa and Bacillus cereus. Given this and our observation that extracellular Pel is not produced by a P. aeruginosa PelA deactylase mutant, we developed an enzyme-based high-throughput screen and identified methyl 2-(2-pyridinylmethylene) hydrazinecarbodithioate (SK-017154-O) and its phenyl derivative as specific Pel-dependent biofilm inhibitors. Michaelis-Menten kinetics revealed SK-017154-O is a noncompetitive inhibitor and that its noncytotoxic, phenyl derivative does not directly inhibit P. aeruginosa PelA esterase activity. We provide proof of concept that exopolysaccharide modification enzymes can be targeted with small molecule inhibitors to block Pel-dependent biofilm development in both Gram-negative and Gram-positive bacteria.
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Affiliation(s)
- Erum Razvi
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | | | - Gregory A. Wasney
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Structural & Biophysical Core Facility, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - John Tam
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anick Auger
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- SPARC BioCentre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Perrin Baker
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Noor Alnabelseya
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Jacquelyn D. Rich
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Piyanka Sivarajah
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Gregory B. Whitfield
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Joe J. Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Roman A. Melnyk
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Mark Nitz
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - P. Lynne Howell
- Program in Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
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13
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Römling U, Cao LY, Bai FW. Evolution of cyclic di-GMP signalling on a short and long term time scale. Microbiology (Reading) 2023; 169:001354. [PMID: 37384391 PMCID: PMC10333796 DOI: 10.1099/mic.0.001354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 06/13/2023] [Indexed: 07/01/2023]
Abstract
Diversifying radiation of domain families within specific lineages of life indicates the importance of their functionality for the organisms. The foundation for the diversifying radiation of the cyclic di-GMP signalling network that occurred within the bacterial kingdom is most likely based in the outmost adaptability, flexibility and plasticity of the system. Integrative sensing of multiple diverse extra- and intracellular signals is made possible by the N-terminal sensory domains of the modular cyclic di-GMP turnover proteins, mutations in the protein scaffolds and subsequent signal reception by diverse receptors, which eventually rewires opposite host-associated as well as environmental life styles including parallel regulated target outputs. Natural, laboratory and microcosm derived microbial variants often with an altered multicellular biofilm behaviour as reading output demonstrated single amino acid substitutions to substantially alter catalytic activity including substrate specificity. Truncations and domain swapping of cyclic di-GMP signalling genes and horizontal gene transfer suggest rewiring of the network. Presence of cyclic di-GMP signalling genes on horizontally transferable elements in particular observed in extreme acidophilic bacteria indicates that cyclic di-GMP signalling and biofilm components are under selective pressure in these types of environments. On a short and long term evolutionary scale, within a species and in families within bacterial orders, respectively, the cyclic di-GMP signalling network can also rapidly disappear. To investigate variability of the cyclic di-GMP signalling system on various levels will give clues about evolutionary forces and discover novel physiological and metabolic pathways affected by this intriguing second messenger signalling system.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
| | - Lian-Ying Cao
- Department of Microbiology, Tumor and Cell Biology, Biomedicum, Karolinska Institutet, Stockholm, Sweden
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, PR China
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14
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Sankaewtong K, Molina JJ, Turner MS, Yamamoto R. Learning to swim efficiently in a nonuniform flow field. Phys Rev E 2023; 107:065102. [PMID: 37464629 DOI: 10.1103/physreve.107.065102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 05/16/2023] [Indexed: 07/20/2023]
Abstract
Microswimmers can acquire information on the surrounding fluid by sensing mechanical queues. They can then navigate in response to these signals. We analyze this navigation by combining deep reinforcement learning with direct numerical simulations to resolve the hydrodynamics. We study how local and nonlocal information can be used to train a swimmer to achieve particular swimming tasks in a nonuniform flow field, in particular, a zigzag shear flow. The swimming tasks are (1) learning how to swim in the vorticity direction, (2) learning how to swim in the shear-gradient direction, and (3) learning how to swim in the shear-flow direction. We find that access to laboratory frame information on the swimmer's instantaneous orientation is all that is required in order to reach the optimal policy for tasks (1) and (2). However, information on both the translational and rotational velocities seems to be required to accomplish task (3). Inspired by biological microorganisms, we also consider the case where the swimmers sense local information, i.e., surface hydrodynamic forces, together with a signal direction. This might correspond to gravity or, for microorganisms with light sensors, a light source. In this case, we show that the swimmer can reach a comparable level of performance to that of a swimmer with access to laboratory frame variables. We also analyze the role of different swimming modes, i.e., pusher, puller, and neutral.
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Affiliation(s)
| | - John J Molina
- Department of Chemical Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Matthew S Turner
- Department of Chemical Engineering, Kyoto University, Kyoto 615-8510, Japan
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Ryoichi Yamamoto
- Department of Chemical Engineering, Kyoto University, Kyoto 615-8510, Japan
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15
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Wang Z, Song L, Liu X, Shen X, Li X. Bacterial second messenger c-di-GMP: Emerging functions in stress resistance. Microbiol Res 2023; 268:127302. [PMID: 36640720 DOI: 10.1016/j.micres.2023.127302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 01/07/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
In natural environments, bacteria constantly encounter various stressful conditions, including nutrient starvation, toxic chemicals, and oxidative stress. The ability to adapt to these adverse conditions is crucial for bacterial survival. Frequently, bacteria utilize nucleotide signaling molecules such as cyclic diguanylate (c-di-GMP) to regulate their behaviors when encounter stress conditions. c-di-GMP is a ubiquitous bacterial second messenger regulating the transition between the planktonic state and biofilm state. An essential feature of biofilms is the production of extracellular matrix that covers bacterial cells and offers a physical barrier protecting the cells from environmental assaults. Beyond that, accumulating evidences have demonstrated that changes in the environment, including stress stimuli, cause the alteration of intracellular levels of c-di-GMP in bacterial cells, which is immediately sensed by a variety of downstream effectors that induce an appropriate stress response. In this review, we summarize recent research on the role of c-di-GMP signaling in bacterial responses to diverse stress conditions.
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Affiliation(s)
- Zhuo Wang
- Yuncheng Key Laboratory of Halophiles Resources Utilization, College of Life Sciences, Yuncheng University, Yuncheng, Shanxi 044000, People's Republic of China
| | - Li Song
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xiaozhen Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xihui Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xin Li
- Yuncheng Key Laboratory of Halophiles Resources Utilization, College of Life Sciences, Yuncheng University, Yuncheng, Shanxi 044000, People's Republic of China.
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16
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Liu D, Wang D, Wei Q, Zhang Y, Yu H, Ma LZ. A Library of Promoter-gfp Fusion Reporters for Studying Systematic Expression Pattern of Cyclic-di-GMP Metabolism-Related Genes in Pseudomonas aeruginosa. Appl Environ Microbiol 2023; 89:e0189122. [PMID: 36744921 DOI: 10.1128/aem.01891-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The opportunistic pathogen Pseudomonas aeruginosa is an environmental microorganism and is a model organism for biofilm research. Cyclic dimeric GMP (c-di-GMP) is a bacterial second messenger that plays critical roles in biofilm formation. P. aeruginosa contains approximately 40 genes that encode enzymes that participate in the metabolism of c-di-GMP (biosynthesis or degradation), yet it lacks tools that aid investigation of the systematic expression pattern of those genes. In this study, we constructed a promoter-gfp fusion reporter library that consists of 41 reporter plasmids. Each plasmid contains a promoter of corresponding c-di-GMP metabolism-related (CMR) genes from P. aeruginosa reference strain PAO1; thus, each promoter-gfp fusion reporter can be used to detect the promoter activity as well as the transcription of corresponding gene. The promoter activity was tested in P. aeruginosa and Escherichia coli. Among the 41 genes, the promoters of 26 genes showed activity in both P. aeruginosa and E. coli. The library was applied to determine the influence of different temperatures, growth media, and subinhibitory concentrations of antibiotics on the transcriptional profile of the 41 CMR genes in P. aeruginosa. The results showed that different growth conditions did affect the transcription of different genes, while the promoter activity of a few genes was kept at the same level under several different growth conditions. In summary, we provide a promoter-gfp fusion reporter library for systematic monitoring or study of the regulation of CMR genes in P. aeruginosa. In addition, the functional promoters can also be used as a biobrick for synthetic biology studies. IMPORTANCE The opportunistic pathogen P. aeruginosa can cause acute and chronic infections in humans, and it is one of the main pathogens in nosocomial infections. Biofilm formation is one of the most important causes for P. aeruginosa persistence in hosts and evasion of immune and antibiotic attacks. c-di-GMP is a critical second messenger to control biofilm formation. In P. aeruginosa reference strain PAO1, 41 genes are predicted to participate in the making and breaking of this dinucleotide. A major missing piece of information in this field is the systematic expression profile of those genes in response to changing environment. Toward this goal, we constructed a promoter-gfp transcriptional fusion reporter library that consists of 41 reporter plasmids, each of which contains a promoter of corresponding c-di-GMP metabolism-related genes in P. aeruginosa. This library provides a helpful tool to understand the complex regulation network related to c-di-GMP and to discover potential therapeutic targets.
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17
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Bisht K, Luecke AR, Wakeman CA. Temperature-specific adaptations and genetic requirements in a biofilm formed by Pseudomonas aeruginosa. Front Microbiol 2023; 13:1032520. [PMID: 36687584 PMCID: PMC9853522 DOI: 10.3389/fmicb.2022.1032520] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 12/07/2022] [Indexed: 01/07/2023] Open
Abstract
Pseudomonas aeruginosa is a gram-negative opportunistic pathogen often associated with nosocomial infections that are made more severe by this bacterium's ability to form robust biofilms. A biofilm is a microbial community encompassing cells embedded within an extracellular polymeric substrate (EPS) matrix that is typically secreted by the encased microbial cells. Biofilm formation is influenced by several environmental cues, and temperature fluctuations are likely to be an important stimulus in the lifecycle of P. aeruginosa as it transitions between life in aquatic or soil environments to sites of infection in the human host. Previous work has demonstrated that human body temperature can induce a shift in the biofilm EPS relative to room temperature growth, resulting in an incorporation of a filamentous phage coat protein into the biofilm EPS. In this study, we sought to identify adaptations enabling biofilm formation at room temperature or temperatures mimicking the natural environment of P. aeruginosa (23°C and 30°C) relative to temperatures mimicking life in the human host (37°C and 40°C). We identified higher biofilm: biomass ratios at lower temperatures on certain substrates, which correlated with a higher relative abundance of apparent polysaccharide EPS content. However, the known genes for EPS polysaccharide production in P. aeruginosa PA14 did not appear to be specifically important for temperature-dependent biofilm adaptation, with the pelB gene appearing to be generally important and the algD gene being generally expendable in all conditions tested. Instead, we were able to identify two previously uncharacterized hypothetical proteins (PA14_50070 and PA14_67550) specifically required for biofilm formation at 23°C and/or 30°C relative to temperatures associated with the human host. These unstudied contributors to biofilm integrity may have been previously overlooked since most P. aeruginosa biofilm studies tend to use 37°C growth temperatures. Overall, our study demonstrates that temperature shifts can have dramatic impacts on biofilm structure and highlights the importance of studying environment-specific adaptations in biofilm physiology.
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18
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Xiong R, Yan J, Mei J, Ye J, Xie J. The enhanced expression of genes encoding diguanylate cyclases under cold stress contributes to the adhesion and biofilm formation of Shewanella putrefaciens WS13. Front Nutr 2022; 9:1076932. [DOI: 10.3389/fnut.2022.1076932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 11/15/2022] [Indexed: 12/02/2022] Open
Abstract
Shewanella putrefaciens is a special spoilage bacterium of seafood during cold storage, which is easy to form biofilm and bring serious hazard to the seafood quality. Life cycle of biofilm starts after bacterial adhesion, which is essential for the formation and development of biofilm. As a ubiquitous second messenger in bacteria, c-di-GMP regulates the conversion between bacterial planktonic state and biofilm state. In this study, the adhesion and biofilm formation of S. putrefaciens WS13 under 4°C were compared to those under 30°C. Atom force microscope and scanning electron microscope were used to study the bacterial adhesion. Biofilm was analyzed by Fourier transform infrared spectroscopy, Bradford assay and phenol-sulfuric acid method. High-performance liquid chromatographic-tandem mass spectrometric and quantitative real-time PCR were applied to study c-di-GMP level and genes encoding diguanylate cyclases in cells, respectively. Results showed that the swarming mobility of S. putrefaciens WS13 was weaker under 4°C, however, the adhesive force under 4°C was 4–5 times higher than that under 30°C. Biofilm biomass, extracellular polysaccharides and extracellular proteins were 2.5 times, 3 times, and 1.6 times more than those under 30°C, respectively, but biofilm composition formed under both temperatures were similar. c-di-GMP level in S. putrefaciens WS13 under 30°C was no more than half of that in the corresponding growth stage under 4°C. Quantitative real-time PCR analysis also showed that the expression of genes encoding diguanylate cyclases were significantly enhanced under 4°C than that under 30°C. S. putrefaciens WS13 adapted to the cold stress by enhancing the expression of genes encoding diguanylate cyclases to promote bacterial adhesion and biofilm formation. This study provides a theoretical foundation for the research on the cold adaptation mechanism of specific spoilage bacteria of seafood based on c-di-GMP, and also provides a new idea to control seafood quality from the perspective of microbial molecular biology.
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Li S, Sun H, Li J, Zhao Y, Wang R, Xu L, Duan C, Li J, Wang Z, Liu Q, Wang Y, Ouyang S, Shen X, Zhang L. Autoinducer-2 and bile salts induce c-di-GMP synthesis to repress the T3SS via a T3SS chaperone. Nat Commun 2022; 13:6684. [PMID: 36335118 DOI: 10.1038/s41467-022-34607-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 10/31/2022] [Indexed: 11/07/2022] Open
Abstract
Cyclic di-GMP (c-di-GMP) transduces extracellular stimuli into intracellular responses, coordinating a plethora of important biological processes. Low levels of c-di-GMP are often associated with highly virulent behavior that depends on the type III secretion system (T3SS) effectors encoded, whereas elevated levels of c-di-GMP lead to the repression of T3SSs. However, extracellular signals that modulate c-di-GMP metabolism to control T3SSs and c-di-GMP effectors that relay environmental stimuli to changes in T3SS activity remain largely obscure. Here, we show that the quorum sensing signal autoinducer-2 (AI-2) induces c-di-GMP synthesis via a GAPES1 domain-containing diguanylate cyclase (DGC) YeaJ to repress T3SS-1 gene expression in Salmonella enterica serovar Typhimurium. YeaJ homologs capable of sensing AI-2 are present in many other species belonging to Enterobacterales. We also reveal that taurocholate and taurodeoxycholate bind to the sensory domain of the DGC YedQ to induce intracellular accumulation of c-di-GMP, thus repressing the expression of T3SS-1 genes. Further, we find that c-di-GMP negatively controls the function of T3SSs through binding to the widely conserved CesD/SycD/LcrH family of T3SS chaperones. Our results support a model in which bacteria sense changes in population density and host-derived cues to regulate c-di-GMP synthesis, thereby modulating the activity of T3SSs via a c-di-GMP-responsive T3SS chaperone.
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Kahl LJ, Eckartt KN, Morales DK, Price-Whelan A, Dietrich LEP. Light/Dark and Temperature Cycling Modulate Metabolic Electron Flow in Pseudomonas aeruginosa Biofilms. mBio 2022;:e0140722. [PMID: 35938725 DOI: 10.1128/mbio.01407-22] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sunlight drives phototrophic metabolism, which affects redox conditions and produces substrates for nonphototrophs. These environmental parameters fluctuate daily due to Earth’s rotation, and nonphototrophic organisms can therefore benefit from the ability to respond to, or even anticipate, such changes. Circadian rhythms, such as daily changes in body temperature, in host organisms can also affect local conditions for colonizing bacteria. Here, we investigated the effects of light/dark and temperature cycling on biofilms of the opportunistic pathogen Pseudomonas aeruginosa PA14. We grew biofilms in the presence of a respiratory indicator dye and found that enhanced dye reduction occurred in biofilm zones that formed during dark intervals and at lower temperatures. This pattern formation occurred with cycling of blue, red, or far-red light, and a screen of mutants representing potential sensory proteins identified two with defects in pattern formation, specifically under red light cycling. We also found that the physiological states of biofilm subzones formed under specific light and temperature conditions were retained during subsequent condition cycling. Light/dark and temperature cycling affected expression of genes involved in primary metabolic pathways and redox homeostasis, including those encoding electron transport chain components. Consistent with this, we found that cbb3-type oxidases contribute to dye reduction under light/dark cycling conditions. Together, our results indicate that cyclic changes in light exposure and temperature have lasting effects on redox metabolism in biofilms formed by a nonphototrophic, pathogenic bacterium.
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Eilers K, Kuok Hoong Yam J, Morton R, Mei Hui Yong A, Brizuela J, Hadjicharalambous C, Liu X, Givskov M, Rice SA, Filloux A. Phenotypic and integrated analysis of a comprehensive Pseudomonas aeruginosa PAO1 library of mutants lacking cyclic-di-GMP-related genes. Front Microbiol 2022; 13:949597. [PMID: 35935233 PMCID: PMC9355167 DOI: 10.3389/fmicb.2022.949597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa is a Gram-negative bacterium that is able to survive and adapt in a multitude of niches as well as thrive within many different hosts. This versatility lies within its large genome of ca. 6 Mbp and a tight control in the expression of thousands of genes. Among the regulatory mechanisms widespread in bacteria, cyclic-di-GMP signaling is one which influences all levels of control. c-di-GMP is made by diguanylate cyclases and degraded by phosphodiesterases, while the intracellular level of this molecule drives phenotypic responses. Signaling involves the modification of enzymes’ or proteins’ function upon c-di-GMP binding, including modifying the activity of regulators which in turn will impact the transcriptome. In P. aeruginosa, there are ca. 40 genes encoding putative DGCs or PDEs. The combined activity of those enzymes should reflect the overall c-di-GMP concentration, while specific phenotypic outputs could be correlated to a given set of dgc/pde. This notion of specificity has been addressed in several studies and different strains of P. aeruginosa. Here, we engineered a mutant library for the 41 individual dgc/pde genes in P. aeruginosa PAO1. In most cases, we observed a significant to slight variation in the global c-di-GMP pool of cells grown planktonically, while several mutants display a phenotypic impact on biofilm including initial attachment and maturation. If this observation of minor changes in c-di-GMP level correlating with significant phenotypic impact appears to be true, it further supports the idea of a local vs global c-di-GMP pool. In contrast, there was little to no effect on motility, which differs from previous studies. Our RNA-seq analysis indicated that all PAO1 dgc/pde genes were expressed in both planktonic and biofilm growth conditions and our work suggests that c-di-GMP networks need to be reconstructed for each strain separately and cannot be extrapolated from one to another.
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Affiliation(s)
- Kira Eilers
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Joey Kuok Hoong Yam
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Richard Morton
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Adeline Mei Hui Yong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Jaime Brizuela
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Medical Microbiology, Amsterdam UMC, Universitair Medische Centra, University of Amsterdam, Amsterdam, Netherlands
| | - Corina Hadjicharalambous
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, Zurich, Switzerland
| | - Xianghui Liu
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Michael Givskov
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, Costerton Biofilm Center, University of Copenhagen, Copenhagen, Denmark
| | - Scott A. Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Commonwealth Scientific and Industrial Research Organisation, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Melbourne, VIC, Australia
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- *Correspondence: Alain Filloux,
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22
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Bazazi P, Stone HA, Hejazi SH. Spongy all-in-liquid materials by in-situ formation of emulsions at oil-water interfaces. Nat Commun 2022; 13:4162. [PMID: 35851272 DOI: 10.1038/s41467-022-31644-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/23/2022] [Indexed: 11/17/2022] Open
Abstract
Printing a structured network of functionalized droplets in a liquid medium enables engineering collectives of living cells for functional purposes and promises enormous applications in processes ranging from energy storage to tissue engineering. Current approaches are limited to drop-by-drop printing or face limitations in reproducing the sophisticated internal features of a structured material and its interactions with the surrounding media. Here, we report a simple approach for creating stable liquid filaments of silica nanoparticle dispersions and use them as inks to print all-in-liquid materials that consist of a network of droplets. Silica nanoparticles stabilize liquid filaments at Weber numbers two orders of magnitude smaller than previously reported in liquid-liquid systems by rapidly producing a concentrated emulsion zone at the oil-water interface. We experimentally demonstrate the printed aqueous phase is emulsified in-situ; consequently, a 3D structure is achieved with flexible walls consisting of layered emulsions. The tube-like printed features have a spongy texture resembling miniaturized versions of “tube sponges” found in the oceans. A scaling analysis based on the interplay between hydrodynamics and emulsification kinetics reveals that filaments are formed when emulsions are generated and remain at the interface during the printing period. Stabilized filaments are utilized for printing liquid-based fluidic channels. All-in-liquid printing promises applications from energy storage to drug delivery and tissue engineering. Here, authors present the in-situ generation of layered emulsion in a fraction of a second at the oil-water interface forming 3D tube-like structures in a liquid medium.
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Bellotto N, Agudo-Canalejo J, Colin R, Golestanian R, Malengo G, Sourjik V. Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions, and cell growth. eLife 2022; 11:82654. [PMID: 36468683 PMCID: PMC9810338 DOI: 10.7554/elife.82654] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Inside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here, we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli. For the faster-diffusing proteins, this size dependence is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
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Affiliation(s)
- Nicola Bellotto
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | | | - Remy Colin
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-OrganizationGöttingenGermany,Rudolf Peierls Centre for Theoretical Physics, University of OxfordOxfordUnited Kingdom
| | - Gabriele Malengo
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO)MarburgGermany
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Maronde E. Cyclic Nucleotide (cNMP) Analogues: Past, Present and Future. Int J Mol Sci 2021; 22:12879. [PMID: 34884683 DOI: 10.3390/ijms222312879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 11/22/2021] [Accepted: 11/25/2021] [Indexed: 11/17/2022] Open
Abstract
Cyclic nucleotides are important second messengers involved in cellular events, and analogues of this type of molecules are promising drug candidates. Some cyclic nucleotide analogues have become standard tools for the investigation of biochemical and physiological signal transduction pathways, such as the Rp-diastereomers of adenosine and guanosine 3′,5′-cyclic monophosphorothioate, which are competitive inhibitors of cAMP- and cGMP-dependent protein kinases. Next generation analogues exhibit a higher membrane permeability, increased resistance against degradation, and improved target specificity, or are caged or photoactivatable for fast and/or targeted cellular imaging. Novel specific nucleotide analogues activating or inhibiting cyclic nucleotide-dependent ion channels, EPAC/GEF proteins, and bacterial target molecules have been developed, opening new avenues for basic and applied research. This review provides an overview of the current state of the field, what can be expected in the future and some practical considerations for the use of cyclic nucleotide analogues in biological systems.
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25
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Abstract
The intestinal microbiome influences host health, and its responsiveness to diet and disease is increasingly well studied. However, our understanding of the factors driving microbiome variation remain limited. Temperature is a core factor that controls microbial growth, but its impact on the microbiome remains to be fully explored. Although commonly assumed to be a constant 37°C, normal body temperatures vary across the animal kingdom, while individual body temperature is affected by multiple factors, including circadian rhythm, age, environmental temperature stress, and immune activation. Changes in body temperature via hypo- and hyperthermia have been shown to influence the gut microbiota in a variety of animals, with consistent effects on community diversity and stability. It is known that temperature directly modulates the growth and virulence of gastrointestinal pathogens; however, the effect of temperature on gut commensals is not well studied. Further, body temperature can influence other host factors, such as appetite and immunity, with indirect effects on the microbiome. In this minireview, we discuss the evidence linking body temperature and the intestinal microbiome and their implications for microbiome function during hypothermia, heat stress, and fever.
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Affiliation(s)
- Kelsey E. Huus
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Ruth E. Ley
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Cluster of Excellence - Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
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Randall TE, Eckartt K, Kakumanu S, Price-Whelan A, Dietrich LEP, Harrison JJ. Sensory perception in bacterial cyclic diguanylate signal transduction. J Bacteriol 2021;:JB0043321. [PMID: 34606374 DOI: 10.1128/JB.00433-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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27
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Poulin MB, Kuperman LL. Regulation of Biofilm Exopolysaccharide Production by Cyclic Di-Guanosine Monophosphate. Front Microbiol 2021; 12:730980. [PMID: 34566936 PMCID: PMC8461298 DOI: 10.3389/fmicb.2021.730980] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/09/2021] [Indexed: 11/25/2022] Open
Abstract
Many bacterial species in nature possess the ability to transition into a sessile lifestyle and aggregate into cohesive colonies, known as biofilms. Within a biofilm, bacterial cells are encapsulated within an extracellular polymeric substance (EPS) comprised of polysaccharides, proteins, nucleic acids, lipids, and other small molecules. The transition from planktonic growth to the biofilm lifecycle provides numerous benefits to bacteria, such as facilitating adherence to abiotic surfaces, evasion of a host immune system, and resistance to common antibiotics. As a result, biofilm-forming bacteria contribute to 65% of infections in humans, and substantially increase the energy and time required for treatment and recovery. Several biofilm specific exopolysaccharides, including cellulose, alginate, Pel polysaccharide, and poly-N-acetylglucosamine (PNAG), have been shown to play an important role in bacterial biofilm formation and their production is strongly correlated with pathogenicity and virulence. In many bacteria the biosynthetic machineries required for assembly of these exopolysaccharides are regulated by common signaling molecules, with the second messenger cyclic di-guanosine monophosphate (c-di-GMP) playing an especially important role in the post-translational activation of exopolysaccharide biosynthesis. Research on treatments of antibiotic-resistant and biofilm-forming bacteria through direct targeting of c-di-GMP signaling has shown promise, including peptide-based treatments that sequester intracellular c-di-GMP. In this review, we will examine the direct role c-di-GMP plays in the biosynthesis and export of biofilm exopolysaccharides with a focus on the mechanism of post-translational activation of these pathways, as well as describe novel approaches to inhibit biofilm formation through direct targeting of c-di-GMP.
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Affiliation(s)
- Myles B Poulin
- Department of Chemistry and Biochemistry, University of Maryland, College Park, College Park, MD, United States
| | - Laura L Kuperman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, College Park, MD, United States
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Kamal SM, Simpson DJ, Wang Z, Gänzle M, Römling U. Horizontal Transmission of Stress Resistance Genes Shape the Ecology of Beta- and Gamma-Proteobacteria. Front Microbiol 2021; 12:696522. [PMID: 34295324 PMCID: PMC8290217 DOI: 10.3389/fmicb.2021.696522] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 01/25/2023] Open
Abstract
The transmissible locus of stress tolerance (tLST) is found mainly in beta- and gamma-Proteobacteria and confers tolerance to elevated temperature, pressure, and chlorine. This genomic island, previously referred to as transmissible locus of protein quality control or locus of heat resistance likely originates from an environmental bacterium thriving in extreme habitats, but has been widely transmitted by lateral gene transfer. Although highly conserved, the gene content on the island is subject to evolution and gene products such as small heat shock proteins are present in several functionally distinct sequence variants. A number of these genes are xenologs of core genome genes with the gene products to widen the substrate spectrum and to be highly (complementary) expressed thus their functionality to become dominant over core genome genes. In this review, we will present current knowledge of the function of core tLST genes and discuss current knowledge on selection and counter-selection processes that favor maintenance of the tLST island, with frequent acquisition of gene products involved in cyclic di-GMP signaling, in different habitats from the environment to animals and plants, processed animal and plant products, man-made environments, and subsequently humans.
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Affiliation(s)
- Shady Mansour Kamal
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - David J Simpson
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiying Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Michael Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
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