1
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Ojha R, Krug S, Jones P, Koestler BJ. Intact and mutated Shigella diguanylate cyclases increase c-di-GMP. J Biol Chem 2024; 300:107525. [PMID: 38960033 DOI: 10.1016/j.jbc.2024.107525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/31/2024] [Accepted: 06/21/2024] [Indexed: 07/05/2024] Open
Abstract
The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger cyclic di-GMP (c di-GMP) signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but five of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the four intact DGCs in a S. flexneri strain, where these four DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these four DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN, which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC pseudogenes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.
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Affiliation(s)
- Ruchi Ojha
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA
| | - Stefanie Krug
- Department of Microbiology, University of Washington, Seattle, Washington, USA
| | - Prentiss Jones
- Department of Pathology, Western Michigan University Homer Stryker, M.D. School of Medicine, Kalamazoo, Michigan, USA
| | - Benjamin J Koestler
- Department of Biological Sciences, Western Michigan University, Kalamazoo, Michigan, USA.
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2
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Jusufovic N, Krusenstjerna AC, Savage CR, Saylor TC, Brissette CA, Zückert WR, Schlax PJ, Motaleb MA, Stevenson B. Borrelia burgdorferi PlzA is a cyclic-di-GMP dependent DNA and RNA binding protein. Mol Microbiol 2024; 121:1039-1062. [PMID: 38527857 DOI: 10.1111/mmi.15254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 03/05/2024] [Accepted: 03/13/2024] [Indexed: 03/27/2024]
Abstract
The PilZ domain-containing protein, PlzA, is the only known cyclic di-GMP binding protein encoded by all Lyme disease spirochetes. PlzA has been implicated in the regulation of many borrelial processes, but the effector mechanism of PlzA was not previously known. Here, we report that PlzA can bind DNA and RNA and that nucleic acid binding requires c-di-GMP, with the affinity of PlzA for nucleic acids increasing as concentrations of c-di-GMP were increased. A mutant PlzA that is incapable of binding c-di-GMP did not bind to any tested nucleic acids. We also determined that PlzA interacts predominantly with the major groove of DNA and that sequence length and G-C content play a role in DNA binding affinity. PlzA is a dual-domain protein with a PilZ-like N-terminal domain linked to a canonical C-terminal PilZ domain. Dissection of the domains demonstrated that the separated N-terminal domain bound nucleic acids independently of c-di-GMP. The C-terminal domain, which includes the c-di-GMP binding motifs, did not bind nucleic acids under any tested conditions. Our data are supported by computational docking, which predicts that c-di-GMP binding at the C-terminal domain stabilizes the overall protein structure and facilitates PlzA-DNA interactions via residues in the N-terminal domain. Based on our data, we propose that levels of c-di-GMP during the various stages of the enzootic life cycle direct PlzA binding to regulatory targets.
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Affiliation(s)
- Nerina Jusufovic
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Andrew C Krusenstjerna
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Christina R Savage
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Timothy C Saylor
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
| | - Catherine A Brissette
- Department of Biomedical Sciences, University of North Dakota, School of Medicine and Health Sciences, Grand Forks, North Dakota, USA
| | - Wolfram R Zückert
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas School of Medicine, Kansas City, Kansas, USA
| | - Paula J Schlax
- Department of Chemistry and Biochemistry, Bates College, Lewiston, Maine, USA
| | - Md A Motaleb
- Department of Microbiology and Immunology, Brody School of Medicine, East Carolina University, Greenville, North Carolina, USA
| | - Brian Stevenson
- Microbiology, Immunology and Molecular Genetics, University of Kentucky College of Medicine, University of Kentucky, Lexington, Kentucky, USA
- Department of Entomology, University of Kentucky, Lexington, Kentucky, USA
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3
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Ojha R, Krug S, Jones P, Koestler BJ. Intact and Degenerate Diguanylate Cyclases regulate Shigella Cyclic di-GMP. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.08.588579. [PMID: 38645013 PMCID: PMC11030455 DOI: 10.1101/2024.04.08.588579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The intracellular human pathogen Shigella invades the colonic epithelium to cause disease. Prior to invasion, this bacterium navigates through different environments within the human body, including the stomach and the small intestine. To adapt to changing environments, Shigella uses the bacterial second messenger c-di-GMP signaling system, synthesized by diguanylate cyclases (DGCs) encoding GGDEF domains. Shigella flexneri encodes a total of 9 GGDEF or GGDEF-EAL domain enzymes in its genome, but 5 of these genes have acquired mutations that presumably inactivated the c-di-GMP synthesis activity of these enzymes. In this study, we examined individual S. flexneri DGCs for their role in c-di-GMP synthesis and pathogenesis. We individually expressed each of the 4 intact DGCs in an S. flexneri strain where these 4 DGCs had been deleted (Δ4DGC). We found that the 4 S. flexneri intact DGCs synthesize c-di-GMP at different levels in vitro and during infection of tissue-cultured cells. We also found that dgcF and dgcI expression significantly reduces invasion and plaque formation, and dgcF expression increases acid sensitivity, and that these phenotypes did not correspond with measured c-di-GMP levels. However, deletion of these 4 DGCs did not eliminate S. flexneri c-di-GMP, and we found that dgcE, dgcQ, and dgcN , which all have nonsense mutations prior to the GGDEF domain, still produce c-di-GMP. These S. flexneri degenerate DGC genes are expressed as multiple proteins, consistent with multiple start codons within the gene. We propose that both intact and degenerate DGCs contribute to S. flexneri c-di-GMP signaling.
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4
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Liu C, Shi R, Jensen MS, Zhu J, Liu J, Liu X, Sun D, Liu W. The global regulation of c-di-GMP and cAMP in bacteria. MLIFE 2024; 3:42-56. [PMID: 38827514 PMCID: PMC11139211 DOI: 10.1002/mlf2.12104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/16/2023] [Accepted: 10/09/2023] [Indexed: 06/04/2024]
Abstract
Nucleotide second messengers are highly versatile signaling molecules that regulate a variety of key biological processes in bacteria. The best-studied examples are cyclic AMP (cAMP) and bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP), which both act as global regulators. Global regulatory frameworks of c-di-GMP and cAMP in bacteria show several parallels but also significant variances. In this review, we illustrate the global regulatory models of the two nucleotide second messengers, compare the different regulatory frameworks between c-di-GMP and cAMP, and discuss the mechanisms and physiological significance of cross-regulation between c-di-GMP and cAMP. c-di-GMP responds to numerous signals dependent on a great number of metabolic enzymes, and it regulates various signal transduction pathways through its huge number of effectors with varying activities. In contrast, due to the limited quantity, the cAMP metabolic enzymes and its major effector are regulated at different levels by diverse signals. cAMP performs its global regulatory function primarily by controlling the transcription of a large number of genes via cAMP receptor protein (CRP) in most bacteria. This review can help us understand how bacteria use the two typical nucleotide second messengers to effectively coordinate and integrate various physiological processes, providing theoretical guidelines for future research.
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Affiliation(s)
- Cong Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Rui Shi
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Marcus S. Jensen
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jingrong Zhu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Jiawen Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Xiaobo Liu
- Key Laboratory of Metabolic Engineering and Biosynthesis Technology, Ministry of Industry and Information TechnologyNanjing University of Science and TechnologyNanjingChina
| | - Di Sun
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
| | - Weijie Liu
- Jiangsu Key Laboratory of Phylogenomics & Comparative Genomics, School of Life SciencesJiangsu Normal UniversityXuzhouChina
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5
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Zhan X, Zhang K, Wang C, Fan Q, Tang X, Zhang X, Wang K, Fu Y, Liang H. A c-di-GMP signaling module controls responses to iron in Pseudomonas aeruginosa. Nat Commun 2024; 15:1860. [PMID: 38424057 PMCID: PMC10904736 DOI: 10.1038/s41467-024-46149-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024] Open
Abstract
Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a bacterial second messenger that modulates various processes including biofilm formation, motility, and host-microbe symbiosis. Numerous studies have conducted comprehensive analysis of c-di-GMP. However, the mechanisms by which certain environmental signals such as iron control intracellular c-di-GMP levels are unclear. Here, we show that iron regulates c-di-GMP levels in Pseudomonas aeruginosa by modulating the interaction between an iron-sensing protein, IsmP, and a diguanylate cyclase, ImcA. Binding of iron to the CHASE4 domain of IsmP inhibits the IsmP-ImcA interaction, which leads to increased c-di-GMP synthesis by ImcA, thus promoting biofilm formation and reducing bacterial motility. Structural characterization of the apo-CHASE4 domain and its binding to iron allows us to pinpoint residues defining its specificity. In addition, the cryo-electron microscopy structure of ImcA in complex with a c-di-GMP analog (GMPCPP) suggests a unique conformation in which the compound binds to the catalytic pockets and to the membrane-proximal side located at the cytoplasm. Thus, our results indicate that a CHASE4 domain directly senses iron and modulates the crosstalk between c-di-GMP metabolic enzymes.
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Affiliation(s)
- Xueliang Zhan
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Kuo Zhang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Chenchen Wang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Qiao Fan
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Xiujia Tang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xi Zhang
- College of Life Sciences, Northwest University, Xi'an, ShaanXi, China
| | - Ke Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yang Fu
- College of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Haihua Liang
- College of Medicine, Southern University of Science and Technology, Shenzhen, China.
- University Laboratory of Metabolism and Health of Guangdong, Southern University of Science and Technology, Shenzhen, China.
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6
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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] [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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7
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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] [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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8
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Santoro S, Bertoni G, Ferrara S. Fluorescence-based Evaluation of Cyclic di-GMP Levels in Pseudomonas aeruginosa. Methods Mol Biol 2024; 2721:45-54. [PMID: 37819514 DOI: 10.1007/978-1-0716-3473-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The ability of Pseudomonas aeruginosa to establish chronic infections is associated with an effective switch from a motile to a sessile lifestyle. This proficiency is controlled by intracellular levels of the second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP). Targeting the c-di-GMP network could be a strategy to interfere with P. aeruginosa pathogenicity. Therefore, the development of tools to profile c-di-GMP intracellular levels is crucial. Here, we describe a protocol for the in vivo measurement of c-di-GMP levels in P. aeruginosa.
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Affiliation(s)
- Silvia Santoro
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
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9
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Römling U. Cyclic di-GMP signaling-Where did you come from and where will you go? Mol Microbiol 2023; 120:564-574. [PMID: 37427497 DOI: 10.1111/mmi.15119] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/17/2023] [Accepted: 06/22/2023] [Indexed: 07/11/2023]
Abstract
Microbes including bacteria are required to respond to their often continuously changing ecological niches in order to survive. While many signaling molecules are produced as seemingly circumstantial byproducts of common biochemical reactions, there are a few second messenger signaling systems such as the ubiquitous cyclic di-GMP second messenger system that arise through the synthesis of dedicated multidomain enzymes triggered by multiple diverse external and internal signals. Being one of the most numerous and widespread signaling system in bacteria, cyclic di-GMP signaling contributes to adjust physiological and metabolic responses in all available ecological niches. Those niches range from deep-sea and hydrothermal springs to the intracellular environment in human immune cells such as macrophages. This outmost adaptability is possible by the modularity of the cyclic di-GMP turnover proteins which enables coupling of enzymatic activity to the diversity of sensory domains and the flexibility in cyclic di-GMP binding sites. Nevertheless, commonly regulated fundamental microbial behavior include biofilm formation, motility, and acute and chronic virulence. The dedicated domains carrying out the enzymatic activity indicate an early evolutionary origin and diversification of "bona fide" second messengers such as cyclic di-GMP which is estimated to have been present in the last universal common ancestor of archaea and bacteria and maintained in the bacterial kingdom until today. This perspective article addresses aspects of our current view on the cyclic di-GMP signaling system and points to knowledge gaps that still await answers.
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Affiliation(s)
- Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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10
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Gong XX, Zeng YH, Chen HM, Zhang N, Han Y, Long H, Xie ZY. Bioinformatic and functional characterization of cyclic-di-GMP metabolic proteins in Vibrio alginolyticus unveils key diguanylate cyclases controlling multiple biofilm-associated phenotypes. Front Microbiol 2023; 14:1258415. [PMID: 37808288 PMCID: PMC10552763 DOI: 10.3389/fmicb.2023.1258415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/05/2023] [Indexed: 10/10/2023] Open
Abstract
The biofilm lifestyle is critical for bacterial survival and proliferation in the fluctuating marine environment. Cyclic diguanylate (c-di-GMP) is a key second messenger during bacterial adaptation to various environmental signals, which has been identified as a master regulator of biofilm formation. However, little is known about whether and how c-di-GMP signaling regulates biofilm formation in Vibrio alginolyticus, a globally dominant marine pathogen. Here, a large set of 63 proteins were predicted to participate in c-di-GMP metabolism (biosynthesis or degradation) in a pathogenic V. alginolyticus strain HN08155. Guided by protein homology, conserved domains and gene context information, a representative subset of 22 c-di-GMP metabolic proteins were selected to determine which ones affect biofilm-associated phenotypes. By comparing phenotypic differences between the wild-type and mutants or overexpression strains, we found that 22 c-di-GMP metabolic proteins can separately regulate different phenotypic outputs in V. alginolyticus. The results indicated that overexpression of four c-di-GMP metabolic proteins, including VA0356, VA1591 (CdgM), VA4033 (DgcB) and VA0088, strongly enhanced rugose colony morphotypes and strengthened Congo Red (CR) binding capacity, both of which are indicators of biofilm matrix overproduction. Furthermore, rugose enhanced colonies were accompanied by increased transcript levels of extracellular polysaccharide (EPS) biosynthesis genes and decreased expression of flagellar synthesis genes compared to smooth colonies (WTpBAD control), as demonstrated by overexpression strains WTp4033 and ∆VA4033p4033. Overall, the high abundance of c-di-GMP metabolic proteins in V. alginolyticus suggests that c-di-GMP signaling and regulatory system could play a key role in its response and adaptation to the ever-changing marine environment. This work provides a robust foundation for the study of the molecular mechanisms of c-di-GMP in the biofilm formation of V. alginolyticus.
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Affiliation(s)
- Xiao-Xiao Gong
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan, China
- College of Marine Sciences, Hainan University, Haikou, Hainan, China
| | - Yan-Hua Zeng
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
| | - Hai-Min Chen
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan, China
- College of Marine Sciences, Hainan University, Haikou, Hainan, China
| | - Na Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan, China
- College of Marine Sciences, Hainan University, Haikou, Hainan, China
| | - Yue Han
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan, China
- College of Marine Sciences, Hainan University, Haikou, Hainan, China
| | - Hao Long
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
| | - Zhen-Yu Xie
- State Key Laboratory of Marine Resource Utilization in the South China Sea, Hainan University, Haikou, Hainan, China
- Hainan Provincial Key Laboratory for Tropical Hydrobiology and Biotechnology, Hainan University, Haikou, Hainan, China
- College of Marine Sciences, Hainan University, Haikou, Hainan, China
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11
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Cimdins-Ahne A, Naemi AO, Li F, Simm R, Römling U. Characterisation of Variants of Cyclic di-GMP Turnover Proteins Associated with Semi-Constitutive rdar Morphotype Expression in Commensal and Uropathogenic Escherichia coli Strains. Microorganisms 2023; 11:2048. [PMID: 37630608 PMCID: PMC10459773 DOI: 10.3390/microorganisms11082048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Expression of rdar (red, dry, and rough) colony morphology-based biofilm formation in Escherichia coli is highly variable. To investigate the molecular mechanisms of semi-constitutive rdar morphotype formation, we compared their cyclic di-GMP turnover protein content and variability to the highly regulated, temperature-dependent morphotype of the historical and modern ST10 isolates E. coli MG1655 and Fec10, respectively. Subsequently, we assessed the effects of cyclic di-GMP turnover protein variants of the EAL phosphodiesterases YcgG and YjcC and the horizontally transferred diguanylate cyclase DgcX on biofilm formation and motility. The two YcgG variants with truncations of the N-terminal CSS signaling domain were oppositely effective in targeting downregulation of rdar biofilm formation compared to the full-length reference protein. Expression of the C-terminal truncated variants YjcCFec67 and YjcCTob1 showed highly diminished apparent phosphodiesterase activity compared to the reference YjcCMG1655. For YjcCFec101, substitution of the C-terminus led to an apparently inactive enzyme. Overexpression of the diguanylate cyclase DgcX contributed to upregulation of cellulose biosynthesis but not to elevated expression of the major biofilm regulator csgD in the "classical" rdar-expressing commensal strain E. coli Fec10. Thus, the c-di-GMP regulating network is highly complex with protein variants displaying substantially different apparent enzymatic activities.
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Affiliation(s)
- Annika Cimdins-Ahne
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; (A.C.-A.); (F.L.)
| | - Ali-Oddin Naemi
- Institute of Oral Biology, University of Oslo, 0313 Oslo, Norway; (A.-O.N.); (R.S.)
| | - Fengyang Li
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; (A.C.-A.); (F.L.)
| | - Roger Simm
- Institute of Oral Biology, University of Oslo, 0313 Oslo, Norway; (A.-O.N.); (R.S.)
- Norwegian Veterinary Institute, 0106 Oslo, Norway
| | - Ute Römling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 171 77 Stockholm, Sweden; (A.C.-A.); (F.L.)
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12
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Vide U, Kasapović D, Fuchs M, Heimböck MP, Totaro MG, Zenzmaier E, Winkler A. Illuminating the inner workings of a natural protein switch: Blue-light sensing in LOV-activated diguanylate cyclases. SCIENCE ADVANCES 2023; 9:eadh4721. [PMID: 37531459 PMCID: PMC10396304 DOI: 10.1126/sciadv.adh4721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/28/2023] [Indexed: 08/04/2023]
Abstract
Regulatory proteins play a crucial role in adaptation to environmental cues. Especially for lifestyle transitions, such as cell proliferation or apoptosis, switch-like characteristics are desirable. While nature frequently uses regulatory circuits to amplify or dampen signals, stand-alone protein switches are interesting for applications like biosensors, diagnostic tools, or optogenetics. However, such stand-alone systems frequently feature limited dynamic and operational ranges and suffer from slow response times. Here, we characterize a LOV-activated diguanylate cyclase (LadC) that offers precise temporal and spatial control of enzymatic activity with an exceptionally high dynamic range over four orders of magnitude. To establish this pronounced activation, the enzyme exhibits a two-stage activation process in which its activity is inhibited in the dark by caging its effector domains and stimulated upon illumination by the formation of an extended coiled-coil. These switch-like characteristics of the LadC system can be used to develop new optogenetic tools with tight regulation.
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Affiliation(s)
- Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Dženita Kasapović
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Maximilian Fuchs
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Martin P. Heimböck
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Massimo G. Totaro
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Elfriede Zenzmaier
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- BioTechMed-Graz, Mozartgasse 12/II, 8010 Graz, Austria
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13
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Liu F, Wang F, Yuan Y, Li X, Zhong X, Yang M. Quorum sensing signal synthases enhance Vibrio parahaemolyticus swarming motility. Mol Microbiol 2023; 120:241-257. [PMID: 37330634 DOI: 10.1111/mmi.15113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 05/30/2023] [Accepted: 06/08/2023] [Indexed: 06/19/2023]
Abstract
Vibrio parahaemolyticus is a significant food-borne pathogen that is found in diverse aquatic habitats. Quorum sensing (QS), a signaling system for cell-cell communication, plays an important role in V. parahaemolyticus persistence. We characterized the function of three V. parahaemolyticus QS signal synthases, CqsAvp , LuxMvp , and LuxSvp , and show that they are essential to activate QS and regulate swarming. We found that CqsAvp , LuxMvp , and LuxSvp activate a QS bioluminescence reporter through OpaR. However, V. parahaemolyticus exhibits swarming defects in the absence of CqsAvp , LuxMvp , and LuxSvp , but not OpaR. The swarming defect of this synthase mutant (termed Δ3AI) was recovered by overexpressing either LuxOvp D47A , a mimic of dephosphorylated LuxOvp mutant, or the scrABC operon. CqsAvp , LuxMvp , and LuxSvp inhibit lateral flagellar (laf) gene expression by inhibiting the phosphorylation of LuxOvp and the expression of scrABC. Phosphorylated LuxOvp enhances laf gene expression in a mechanism that involves modulating c-di-GMP levels. However, enhancing swarming requires phosphorylated and dephosphorylated LuxOvp which is regulated by the QS signals that are synthesized by CqsAvp , LuxMvp , and LuxSvp . The data presented here suggest an important strategy of swarming regulation by the integration of QS and c-di-GMP signaling pathways in V. parahaemolyticus.
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Affiliation(s)
- Fuwen Liu
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Fei Wang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Yixuan Yuan
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Xiaoran Li
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Xiaojun Zhong
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
| | - Menghua Yang
- Key Laboratory of Applied Technology on Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Laboratory for Animal Health Inspection & Internet Technology, College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A & F University, Hangzhou, China
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14
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Gür M, Erdmann J, Will A, Liang Z, Andersen JB, Tolker-Nielsen T, Häussler S. Challenges in using transcriptome data to study the c-di-GMP signaling network in Pseudomonas aeruginosa clinical isolates. FEMS MICROBES 2023; 4:xtad012. [PMID: 37564278 PMCID: PMC10411656 DOI: 10.1093/femsmc/xtad012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/31/2023] [Accepted: 07/17/2023] [Indexed: 08/12/2023] Open
Abstract
In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding DGCs. This approach might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, while we demonstrate that the selection of subgroups of clinical isolates with high versus low expression of sigma factor encoding genes served the identification of their downstream regulons, we were unable to confirm the predicted DGC regulons, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon prolonged cultivation of clinical P. aeruginosa isolates.
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Affiliation(s)
- Melisa Gür
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Strasse 7, 30265 Hannover, Germany
| | - Jelena Erdmann
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Strasse 7, 30265 Hannover, Germany
| | - Anke Will
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Strasse 7, 30265 Hannover, Germany
| | - Ziwei Liang
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B 24.1, 2100 Copenhagen, Denmark
| | - Jens Bo Andersen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B 24.1, 2100 Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B 24.1, 2100 Copenhagen, Denmark
| | - Susanne Häussler
- Institute for Molecular Bacteriology, TWINCORE, Centre for Experimental and Clinical Infection Research, Feodor-Lynen-Strasse 7, 30265 Hannover, Germany
- Department of Molecular Bacteriology, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124 Braunschweig, Germany
- Department of Clinical Microbiology, Copenhagen University Hospital – Rigshospitalet, Ole Maaloes Vej 26, 2100 Copenhagen, Denmark
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15
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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] [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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16
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Scherhag A, Räschle M, Unbehend N, Venn B, Glueck D, Mühlhaus T, Keller S, Pérez Patallo E, Zehner S, Frankenberg-Dinkel N. Characterization of a soluble library of the Pseudomonas aeruginosa PAO1 membrane proteome with emphasis on c-di-GMP turnover enzymes. MICROLIFE 2023; 4:uqad028. [PMID: 37441524 PMCID: PMC10335732 DOI: 10.1093/femsml/uqad028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 04/28/2023] [Accepted: 05/30/2023] [Indexed: 07/15/2023]
Abstract
Studies of protein-protein interactions in membranes are very important to fully understand the biological function of a cell. The extraction of proteins from the native membrane environment is a critical step in the preparation of membrane proteins that might affect the stability of protein complexes. In this work, we used the amphiphilic diisobutylene/maleic acid copolymer to extract the membrane proteome of the opportunistic pathogen Pseudomonas aeruginosa, thereby creating a soluble membrane-protein library within a native-like lipid-bilayer environment. Size fractionation of nanodisc-embedded proteins and subsequent mass spectrometry enabled the identification of 3358 proteins. The native membrane-protein library showed a very good overall coverage compared to previous proteome data. The pattern of size fractionation indicated that protein complexes were preserved in the library. More than 20 previously described complexes, e.g. the SecYEG and Pili complexes, were identified and analyzed for coelution. Although the mass-spectrometric dataset alone did not reveal new protein complexes, combining pulldown assays with mass spectrometry was successful in identifying new protein interactions in the native membrane-protein library. Thus, we identified several candidate proteins for interactions with the membrane phosphodiesterase NbdA, a member of the c-di-GMP network. We confirmed the candidate proteins CzcR, PA4200, SadC, and PilB as novel interaction partners of NbdA using the bacterial adenylate cyclase two-hybrid assay. Taken together, this work demonstrates the usefulness of the native membrane-protein library of P. aeruginosa for the investigation of protein interactions and membrane-protein complexes. Data are available via ProteomeXchange with identifiers PXD039702 and PXD039700.
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Affiliation(s)
- Anna Scherhag
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Markus Räschle
- Department of Molecular Genetics, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Niklas Unbehend
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Benedikt Venn
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - David Glueck
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Timo Mühlhaus
- Department of Computational Systems Biology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | - Sandro Keller
- Department of Biophysics, Institute of Molecular Biosciences (IMB), NAWI Graz, University of Graz, Graz 8010, Austria
- Department of Field of Excellence BioHealth, University of Graz, Graz 8010, Austria
- BioTechMed-Graz, Graz 8010, Austria
| | - Eugenio Pérez Patallo
- Department of Microbiology, RPTU Kaiserslautern-Landau, Kaiserslautern 67655, Germany
| | | | - Nicole Frankenberg-Dinkel
- Corresponding author. RPTU Kaiserslautern-Landau, Microbiology, Kaiserslautern 67655, Germany. E-mail:
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17
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Lamprecht O, Ratnikava M, Jacek P, Kaganovitch E, Buettner N, Fritz K, Biazruchka I, Köhler R, Pietsch J, Sourjik V. Regulation by cyclic di-GMP attenuates dynamics and enhances robustness of bimodal curli gene activation in Escherichia coli. PLoS Genet 2023; 19:e1010750. [PMID: 37186613 DOI: 10.1371/journal.pgen.1010750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 05/25/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Curli amyloid fibers are a major constituent of the extracellular biofilm matrix formed by bacteria of the Enterobacteriaceae family. Within Escherichia coli biofilms, curli gene expression is limited to a subpopulation of bacteria, leading to heterogeneity of extracellular matrix synthesis. Here we show that bimodal activation of curli gene expression also occurs in well-mixed planktonic cultures of E. coli, resulting in all-or-none stochastic differentiation into distinct subpopulations of curli-positive and curli-negative cells at the entry into the stationary phase of growth. Stochastic curli activation in individual E. coli cells could further be observed during continuous growth in a conditioned medium in a microfluidic device, which further revealed that the curli-positive state is only metastable. In agreement with previous reports, regulation of curli gene expression by the second messenger c-di-GMP via two pairs of diguanylate cyclase and phosphodiesterase enzymes, DgcE/PdeH and DgcM/PdeR, modulates the fraction of curli-positive cells. Unexpectedly, removal of this regulatory network does not abolish the bimodality of curli gene expression, although it affects dynamics of activation and increases heterogeneity of expression levels among individual cells. Moreover, the fraction of curli-positive cells within an E. coli population shows stronger dependence on growth conditions in the absence of regulation by DgcE/PdeH and DgcM/PdeR pairs. We thus conclude that, while not required for the emergence of bimodal curli gene expression in E. coli, this c-di-GMP regulatory network attenuates the frequency and dynamics of gene activation and increases its robustness to cellular heterogeneity and environmental variation.
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Affiliation(s)
- Olga Lamprecht
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Maryia Ratnikava
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Paulina Jacek
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Eugen Kaganovitch
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Nina Buettner
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Kirstin Fritz
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Ina Biazruchka
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Robin Köhler
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Julian Pietsch
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology and Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
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18
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Junkermeier EH, Hengge R. Local signaling enhances output specificity of bacterial c-di-GMP signaling networks. MICROLIFE 2023; 4:uqad026. [PMID: 37251514 PMCID: PMC10211494 DOI: 10.1093/femsml/uqad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
For many years the surprising multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins has intrigued researchers studying bacterial second messengers. How can several signaling pathways act in parallel to produce specific outputs despite relying on the same diffusible second messenger maintained at a certain global cellular concentration? Such high specificity and flexibility arise from combining modes of local and global c-di-GMP signaling in complex signaling networks. Local c-di-GMP signaling can be experimentally shown by three criteria being met: (i) highly specific knockout phenotypes for particular c-di-GMP-related enzymes, (ii) actual cellular c-di-GMP levels that remain unchanged by such mutations and/or below the Kd's of the relevant c-di-GMP-binding effectors, and (iii) direct interactions between the signaling proteins involved. Here, we discuss the rationale behind these criteria and present well-studied examples of local c-di-GMP signaling in Escherichia coli and Pseudomonas. Relatively simple systems just colocalize a local source and/or a local sink for c-di-GMP, i.e. a diguanylate cyclase (DGC) and/or a specific phosphodiesterase (PDE), respectively, with a c-di-GMP-binding effector/target system. More complex systems also make use of regulatory protein interactions, e.g. when a "trigger PDE" responds to locally provided c-di-GMP, and thereby serves as a c-di-GMP-sensing effector that directly controls a target's activity, or when a c-di-GMP-binding effector recruits and directly activates its own "private" DGC. Finally, we provide an outlook into how cells can combine local and global signaling modes of c-di-GMP and possibly integrate those into other signaling nucleotides networks.
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Affiliation(s)
- Eike H Junkermeier
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany
| | - Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
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19
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Hwang Y, Harshey RM. A Second Role for the Second Messenger Cyclic-di-GMP in E. coli: Arresting Cell Growth by Altering Metabolic Flow. mBio 2023; 14:e0061923. [PMID: 37036337 PMCID: PMC10127611 DOI: 10.1128/mbio.00619-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/11/2023] Open
Abstract
c-di-GMP primarily controls motile to sessile transitions in bacteria. Diguanylate cyclases (DGCs) catalyze the synthesis of c-di-GMP from two GTP molecules. Typically, bacteria encode multiple DGCs that are activated by specific environmental signals. Their catalytic activity is modulated by c-di-GMP binding to autoinhibitory sites (I-sites). YfiN is a conserved inner membrane DGC that lacks these sites. Instead, YfiN activity is directly repressed by periplasmic YfiR, which is inactivated by redox stress. In Escherichia coli, an additional envelope stress causes YfiN to relocate to the mid-cell to inhibit cell division by interacting with the division machinery. Here, we report a third activity for YfiN in E. coli, where cell growth is inhibited without YfiN relocating to the division site. This action of YfiN is only observed when the bacteria are cultured on gluconeogenic carbon sources, and is dependent on absence of the autoinhibitory sites. Restoration of I-site function relieves the growth-arrest phenotype, and disabling this function in a heterologous DGC causes acquisition of this phenotype. Arrested cells are tolerant to a wide range of antibiotics. We show that the likely cause of growth arrest is depletion of cellular GTP from run-away synthesis of c-di-GMP, explaining the dependence of growth arrest on gluconeogenic carbon sources that exhaust more GTP during production of glucose. This is the first report of c-di-GMP-mediated growth arrest by altering metabolic flow. IMPORTANCE The c-di-GMP signaling network in bacteria not only controls a variety of cellular processes such as motility, biofilms, cell development, and virulence, but does so by a dizzying array of mechanisms. The DGC YfiN singularly represents the versatility of this network in that it not only inhibits motility and promotes biofilms, but also arrests growth in Escherichia coli by relocating to the mid-cell and blocking cell division. The work described here reveals that YfiN arrests growth by yet another mechanism in E. coli, changing metabolic flow. This function of YfiN, or of DGCs without autoinhibitory I-sites, may contribute to antibiotic tolerant persisters in relevant niches such as the gut where gluconeogenic sugars are found.
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Affiliation(s)
- YuneSahng Hwang
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, Texas, USA
| | - Rasika M. Harshey
- Department of Molecular Biosciences and LaMontagne Center for Infectious Diseases, University of Texas at Austin, Austin, Texas, USA
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20
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Hengge R, Pruteanu M, Stülke J, Tschowri N, Turgay K. Recent advances and perspectives in nucleotide second messenger signaling in bacteria. MICROLIFE 2023; 4:uqad015. [PMID: 37223732 PMCID: PMC10118264 DOI: 10.1093/femsml/uqad015] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/28/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023]
Abstract
Nucleotide second messengers act as intracellular 'secondary' signals that represent environmental or cellular cues, i.e. the 'primary' signals. As such, they are linking sensory input with regulatory output in all living cells. The amazing physiological versatility, the mechanistic diversity of second messenger synthesis, degradation, and action as well as the high level of integration of second messenger pathways and networks in prokaryotes has only recently become apparent. In these networks, specific second messengers play conserved general roles. Thus, (p)ppGpp coordinates growth and survival in response to nutrient availability and various stresses, while c-di-GMP is the nucleotide signaling molecule to orchestrate bacterial adhesion and multicellularity. c-di-AMP links osmotic balance and metabolism and that it does so even in Archaea may suggest a very early evolutionary origin of second messenger signaling. Many of the enzymes that make or break second messengers show complex sensory domain architectures, which allow multisignal integration. The multiplicity of c-di-GMP-related enzymes in many species has led to the discovery that bacterial cells are even able to use the same freely diffusible second messenger in local signaling pathways that can act in parallel without cross-talking. On the other hand, signaling pathways operating with different nucleotides can intersect in elaborate signaling networks. Apart from the small number of common signaling nucleotides that bacteria use for controlling their cellular "business," diverse nucleotides were recently found to play very specific roles in phage defense. Furthermore, these systems represent the phylogenetic ancestors of cyclic nucleotide-activated immune signaling in eukaryotes.
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Affiliation(s)
- Regine Hengge
- Corresponding author. Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Philippstr. 13 – Haus 22, 10115 Berlin, Germany. Tel: +49-30-2093-49686; Fax: +49-30-2093-49682; E-mail:
| | | | - Jörg Stülke
- Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August-Universität Göttingen, 37077 Göttingen, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
| | - Kürşad Turgay
- Institute of Microbiology, Leibniz-Universität Hannover, 30419 Hannover, Germany
- Max Planck Unit for the Science of Pathogens, 10115 Berlin, Germany
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Ximinies AD, Dou Y, Mishra A, Zhang K, Deivanayagam C, Wang C, Fletcher HM. The Oxidative Stress-Induced Hypothetical Protein PG_0686 in Porphyromonas gingivalis W83 Is a Novel Diguanylate Cyclase. Microbiol Spectr 2023; 11:e0441122. [PMID: 36719196 PMCID: PMC10101095 DOI: 10.1128/spectrum.04411-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/06/2023] [Indexed: 02/01/2023] Open
Abstract
The survival/adaptation of Porphyromonas gingivalis to the inflammatory environment of the periodontal pocket requires an ability to overcome oxidative stress. Several functional classes of genes, depending on the severity and duration of the exposure, were induced in P. gingivalis under H2O2-induced oxidative stress. The PG_0686 gene was highly upregulated under prolonged oxidative stress. PG_0686, annotated as a hypothetical protein of unknown function, is a 60 kDa protein that carries several domains including hemerythrin, PAS10, and domain of unknown function (DUF)-1858. Although PG_0686 showed some relatedness to several diguanylate cyclases (DGCs), it is missing the classical conserved, active site sequence motif (GGD[/E]EF), commonly observed in other bacteria. PG_0686-related proteins are observed in other anaerobic bacterial species. The isogenic mutant P. gingivalis FLL361 (ΔPG_0686::ermF) showed increased sensitivity to H2O2, and decreased gingipain activity compared to the parental strain. Transcriptome analysis of P. gingivalis FLL361 showed the dysregulation of several gene clusters/operons, known oxidative stress resistance genes, and transcriptional regulators, including PG_2212, CdhR and PG_1181 that were upregulated under normal anaerobic conditions. The intracellular level of c-di-GMP in P. gingivalis FLL361 was significantly decreased compared to the parental strain. The purified recombinant PG_0686 (rPG_0686) protein catalyzed the formation of c-di-GMP from GTP. Collectively, our data suggest a global regulatory property for PG_0686 that may be part of an unconventional second messenger signaling system in P. gingivalis. Moreover, it may coordinately regulate a pathway(s) vital for protection against environmental stress, and is significant in the pathogenicity of P. gingivalis and other anaerobes. IMPORTANCE Porphyromonas gingivalis is an important etiological agent in periodontitis and other systemic diseases. There is still a gap in our understanding of the mechanisms that P. gingivalis uses to survive the inflammatory microenvironment of the periodontal pocket. The hypothetical PG_0686 gene was highly upregulated under prolonged oxidative stress. Although the tertiary structure of PG_0686 showed little relatedness to previously characterized diguanylate cyclases (DGCs), and does not contain the conserved GGD(/E)EF catalytic domain motif sequence, an ability to catalyze the formation of c-di-GMP from GTP is demonstrated. The second messenger pathway for c-di-GMP was previously predicted to be absent in P. gingivalis. PG_0686 paralogs are identified in other anaerobic bacteria. Thus, PG_0686 may represent a novel class of DGCs, which is yet to be characterized. In conclusion, we have shown, for the first time, evidence for the presence of c-di-GMP signaling with environmental stress protective function in P. gingivalis.
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Affiliation(s)
- Alexia D. Ximinies
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Yuetan Dou
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Arunima Mishra
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Kangling Zhang
- Department of Pharmacology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Champion Deivanayagam
- Department of Biochemistry and Molecular Genetics, University of Alabama, Birmingham, Alabama, USA
| | - Charles Wang
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
| | - Hansel M. Fletcher
- Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California, USA
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22
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Yao Y, Xi N, Hai E, Zhang X, Guo J, Lin Z, Huang W. PA0575 (RmcA) interacts with other c-di-GMP metabolizing proteins in Pseudomonas aeruginosa PAO1. J GEN APPL MICROBIOL 2023; 68:232-241. [PMID: 35732459 DOI: 10.2323/jgam.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
As a central signaling molecule, c-di-GMP (bis-(3,5)-cyclic diguanosine monophosphate) is becoming the focus for research in bacteria physiology. Pseudomonas aeruginosa PAO1 genome contains highly complicated c-di-GMP metabolizing genes and a number of these proteins have been identified and investigated. Especially, a sophisticated network of these proteins is emerging. In current study, mainly through Bacteria-2-Hybrid assay, we found PA0575 (RmcA), a GGDEF-EAL dual protein, to interact with two other dual proteins of PA4601 (MorA) and PA4959 (FimX). These observations imply the intricacy of c-di-GMP metabolizing protein interactions. Our work thus provides one piece of data to increase the understandings to c-di-GMP signaling.
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Affiliation(s)
- Yanxiang Yao
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - Naren Xi
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - E Hai
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
| | - Xiaomin Zhang
- Research Center of Medical Science and Technology, Ningxia Medical University
| | - Jiayi Guo
- Research Center of Medical Science and Technology, Ningxia Medical University
| | - Zhi Lin
- School of Life Sciences, Tianjin University
| | - Weidong Huang
- School of Basic Medicine, Department of Biochemistry and Molecular Biology, Ningxia Medical University
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23
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Gong H, Jiang W, Yang Y, Zhang Y, Chen X, Li W, Yang P, Wang Z, Wang Q, Li Y. Cyclic di-GMP regulates bacterial colonization and further biocontrol efficacy of Bacillus velezensis against apple ring rot disease via its potential receptor YdaK. Front Microbiol 2022; 13:1034168. [PMID: 36590391 PMCID: PMC9800504 DOI: 10.3389/fmicb.2022.1034168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/02/2022] [Indexed: 12/23/2022] Open
Abstract
Bacillus species are among the most investigated beneficial bacteria and widely used in agricultural systems as biological control agents. Its biocontrol efficacy is controlled by diverse regulators. Cyclic diguanylate (c-di-GMP) is a nearly universal second messenger in bacteria and modulates various important physiological processes, including motility, biofilm formation, antifungal antibiotic production and host colonization. However, the impact of c-di-GMP on biocontrol efficacy of beneficial bacteria is unknown. Bacillus velezensis PG12 is an effective biocontrol strain against apple ring rot disease caused by Botryosphaeria dothidea. In this study, the contribution of c-di-GMP to biocontrol efficacy of B. velezensis PG12 was investigated. Deletion of single gene encoding diguanylate cyclase or phosphodiesterase did not affect its biocontrol efficacy against apple ring rot. However, artificial modulation of c-di-GMP level in the cells leads to a significant change of biocontrol efficacy, suggesting that c-di-GMP positively regulates biocontrol efficacy of B. velezensis PG12 against apple ring rot disease. More evidences indicate that c-di-GMP does not affect the antagonistic activity of B. velezensis PG12 against B. dothidea in vitro and in vivo, but positively regulates biofilm formation of B. velezensis PG12 and its colonization on apple fruits. Importantly, deletion of ydaK could rescue the inhibition of biofilm formation, bacterial colonization and biocontrol efficacy caused by low c-di-GMP level, indicating that YdaK is the potential c-di-GMP receptor to regulate biofilm formation, colonization and effective biological control. However, YdaK did not affect the antagonistic activity of B. velezensis PG12 against B. dothidea. Based on these findings, we propose that c-di-GMP regulates biofilm formation, subsequently the bacterial colonization on apple fruits and thus biocontrol efficacy of B. velezensis through its receptor YdaK. This is the first report showing that c-di-GMP plays a role in biocontrol efficacy of beneficial bacteria.
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Affiliation(s)
- Huiling Gong
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wenxiao Jiang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yang Yang
- Chongqing Key Laboratory of Plant Disease Biology, College of Plant Protection, Southwest University, Chongqing, China
| | - Yue Zhang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xufei Chen
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Wei Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Panlei Yang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Zhenshuo Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Qi Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Yan Li
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China,*Correspondence: Yan Li,
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The Wsp chemosensory system modulates c-di-GMP-dependent biofilm formation by integrating DSF quorum sensing through the WspR-RpfG complex in Lysobacter. NPJ Biofilms Microbiomes 2022; 8:97. [PMID: 36526637 PMCID: PMC9758175 DOI: 10.1038/s41522-022-00365-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 12/06/2022] [Indexed: 12/23/2022] Open
Abstract
The ubiquitous Wsp (wrinkly spreader phenotype) chemosensory system and DSF (diffusible signal factor) quorum sensing are two important chemically associated signaling systems that mediate bacterial communications between the host and environment. Although these two systems individually control biofilm formation in pathogenic bacteria via the ubiquitous second messenger c-di-GMP, their crosstalk mechanisms remain elusive. Here we present a scenario from the plant-beneficial and antifungal bacterium Lysobacter enzymogenes OH11, where biofilm formation favors the colonization of this bacterium in fungal hyphae. We found that the Wsp system regulated biofilm formation via WspR-mediated c-di-GMP signaling, whereas DSF system did not depend on the enzymatic activity of RpfG to regulate biofilm formation. We further found that WspR, a diguanylate cyclase (DGC) responsible for c-di-GMP synthesis, could directly bind to one of the DSF signaling components, RpfG, an active phosphodiesterase (PDE) responsible for c-di-GMP degradation. Thus, the WspR-RpfG complex represents a previously undiscovered molecular linker connecting the Wsp and DSF systems. Mechanistically, RpfG could function as an adaptor protein to bind and inhibit the DGC activity of unphosphorylated WspR independent of its PDE activity. Phosphorylation of WspR impaired its binding affinity to RpfG and also blocked the ability of RpfG to act as an adaptor protein, which enabled the Wsp system to regulate biofilm formation in a c-di-GMP-dependent manner by dynamically integrating the DSF system. Our findings demonstrated a previously uncharacterized mechanism of crosstalk between Wsp and DSF systems in plant-beneficial and antifungal bacteria.
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25
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Alonso-Reyes DG, Galván FS, Irazoqui JM, Amadio A, Tschoeke D, Thompson F, Albarracín VH, Farias ME. Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites. MICROBIAL ECOLOGY 2022:10.1007/s00248-022-02112-7. [PMID: 36161499 DOI: 10.1007/s00248-022-02112-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.
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Affiliation(s)
- Daniel Gonzalo Alonso-Reyes
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
| | - Fátima Silvina Galván
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina
| | - José Matías Irazoqui
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Ariel Amadio
- Instituto de Investigación de La Cadena Láctea (INTA-CONICET), Rafaela, Argentina
| | - Diogo Tschoeke
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and Coppe, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Virginia Helena Albarracín
- Laboratorio de Microbiología Ultraestructural Y Molecular, Centro Integral de Microscopía Electrónica (CIME,), CONICET-Universidad Nacional de Tucumán, Camino de Sirga s/n, Finca El Manantial, Yerba Buena (4107), San Miguel de Tucumán, Tucumán, Argentina.
- Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, Tucumán, Argentina.
| | - María Eugenia Farias
- Laboratorio de Investigaciones Microbiológicas de Lagunas Andinas (LIMLA), Planta Piloto de Procesos Industriales y Microbiológicos (PROIMI), CCT, CONICET, Tucumán, Argentina
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26
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A complete twelve-gene deletion null mutant reveals that cyclic di-GMP is a global regulator of phase-transition and host colonization in Erwinia amylovora. PLoS Pathog 2022; 18:e1010737. [PMID: 35914003 PMCID: PMC9371280 DOI: 10.1371/journal.ppat.1010737] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/11/2022] [Accepted: 07/11/2022] [Indexed: 11/19/2022] Open
Abstract
Cyclic-di-GMP (c-di-GMP) is an essential bacterial second messenger that regulates biofilm formation and pathogenicity. To study the global regulatory effect of individual components of the c-di-GMP metabolic system, we deleted all 12 diguanylate cyclase (dgc) and phosphodiesterase (pde)-encoding genes in E. amylovora Ea1189 (Ea1189Δ12). Ea1189Δ12 was impaired in surface attachment due to a transcriptional dysregulation of the type IV pilus and the flagellar filament. A transcriptomic analysis of surface-exposed WT Ea1189 and Ea1189Δ12 cells indicated that genes involved in metabolism, appendage generation and global transcriptional/post-transcriptional regulation were differentially regulated in Ea1189Δ12. Biofilm formation was regulated by all 5 Dgcs, whereas type III secretion and disease development were differentially regulated by specific Dgcs. A comparative transcriptomic analysis of Ea1189Δ8 (lacks all five enzymatically active dgc and 3 pde genes) against Ea1189Δ8 expressing specific dgcs, revealed the presence of a dual modality of spatial and global regulatory frameworks in the c-di-GMP signaling network.
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27
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation. mSystems 2022; 7:e0151821. [PMID: 35311563 PMCID: PMC9040814 DOI: 10.1128/msystems.01518-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Shewanella spp. play important ecological and biogeochemical roles, due in part to their versatile metabolism and swift integration of stimuli. While Shewanella spp. are primarily considered environmental microbes, Shewanella algae is increasingly recognized as an occasional human pathogen. S. algae shares the broad metabolic and respiratory repertoire of Shewanella spp. and thrives in similar ecological niches. In S. algae, nitrate and dimethyl sulfoxide (DMSO) respiration promote biofilm formation strain specifically, with potential implication of taxis and cyclic diguanosine monophosphate (c-di-GMP) signaling. Signal transduction systems in S. algae have not been investigated. To fill these knowledge gaps, we provide here an inventory of the c-di-GMP turnover proteome and chemosensory networks of the type strain S. algae CECT 5071 and compare them with those of 41 whole-genome-sequenced clinical and environmental S. algae isolates. Besides comparative analysis of genetic content and identification of laterally transferred genes, the occurrence and topology of c-di-GMP turnover proteins and chemoreceptors were analyzed. We found S. algae strains to encode 61 to 67 c-di-GMP turnover proteins and 28 to 31 chemoreceptors, placing S. algae near the top in terms of these signaling capacities per Mbp of genome. Most c-di-GMP turnover proteins were predicted to be catalytically active; we describe in them six novel N-terminal sensory domains that appear to control their catalytic activity. Overall, our work defines the c-di-GMP and chemosensory signal transduction pathways in S. algae, contributing to a better understanding of its ecophysiology and establishing S. algae as an auspicious model for the analysis of metabolic and signaling pathways within the genus Shewanella. IMPORTANCEShewanella spp. are widespread aquatic bacteria that include the well-studied freshwater model strain Shewanella oneidensis MR-1. In contrast, the physiology of the marine and occasionally pathogenic species Shewanella algae is poorly understood. Chemosensory and c-di-GMP signal transduction systems integrate environmental stimuli to modulate gene expression, including the switch from a planktonic to sessile lifestyle and pathogenicity. Here, we systematically dissect the c-di-GMP proteome and chemosensory pathways of the type strain S. algae CECT 5071 and 41 additional S. algae isolates. We provide insights into the activity and function of these proteins, including a description of six novel sensory domains. Our work will enable future analyses of the complex, intertwined c-di-GMP metabolism and chemotaxis networks of S. algae and their ecophysiological role.
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Liu C, Sun D, Liu J, Chen Y, Zhou X, Ru Y, Zhu J, Liu W. cAMP and c-di-GMP synergistically support biofilm maintenance through the direct interaction of their effectors. Nat Commun 2022; 13:1493. [PMID: 35315431 PMCID: PMC8938473 DOI: 10.1038/s41467-022-29240-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 03/07/2022] [Indexed: 01/12/2023] Open
Abstract
Nucleotide second messengers, such as cAMP and c-di-GMP, regulate many physiological processes in bacteria, including biofilm formation. There is evidence of cross-talk between pathways mediated by c-di-GMP and those mediated by the cAMP receptor protein (CRP), but the mechanisms are often unclear. Here, we show that cAMP-CRP modulates biofilm maintenance in Shewanella putrefaciens not only via its known effects on gene transcription, but also through direct interaction with a putative c-di-GMP effector on the inner membrane, BpfD. Binding of cAMP-CRP to BpfD enhances the known interaction of BpfD with protease BpfG, which prevents proteolytic processing and release of a cell surface-associated adhesin, BpfA, thus contributing to biofilm maintenance. Our results provide evidence of cross-talk between cAMP and c-di-GMP pathways through direct interaction of their effectors, and indicate that cAMP-CRP can play regulatory roles at the post-translational level. Nucleotide second messengers, such as cAMP and c-di-GMP, regulate many physiological processes in bacteria, including biofilm formation. Here, the authors provide evidence of cross-talk between cAMP and c-di-GMP pathways through direct interaction of their effectors, showing that the cAMP receptor protein (CRP) can play regulatory roles at the post-translational level.
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29
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Duggal Y, Kurasz JE, Fontaine BM, Marotta NJ, Chauhan SS, Karls AC, Weinert EE. Cellular Effects of 2',3'-Cyclic Nucleotide Monophosphates in Gram-Negative Bacteria. J Bacteriol 2022; 204:e0020821. [PMID: 34662237 PMCID: PMC8765455 DOI: 10.1128/jb.00208-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 10/06/2021] [Indexed: 12/13/2022] Open
Abstract
Organismal adaptations to environmental stimuli are governed by intracellular signaling molecules such as nucleotide second messengers. Recent studies have identified functional roles for the noncanonical 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) in both eukaryotes and prokaryotes. In Escherichia coli, 2',3'-cNMPs are produced by RNase I-catalyzed RNA degradation, and these cyclic nucleotides modulate biofilm formation through unknown mechanisms. The present work dissects cellular processes in E. coli and Salmonella enterica serovar Typhimurium that are modulated by 2',3'-cNMPs through the development of cell-permeable 2',3'-cNMP analogs and a 2',3'-cyclic nucleotide phosphodiesterase. Utilization of these chemical and enzymatic tools, in conjunction with phenotypic and transcriptomic investigations, identified pathways regulated by 2',3'-cNMPs, including flagellar motility and biofilm formation, and by oligoribonucleotides with 3'-terminal 2',3'-cyclic phosphates, including responses to cellular stress. Furthermore, interrogation of metabolomic and organismal databases has identified 2',3'-cNMPs in numerous organisms and homologs of the E. coli metabolic proteins that are involved in key eukaryotic pathways. Thus, the present work provides key insights into the roles of these understudied facets of nucleotide metabolism and signaling in prokaryotic physiology and suggest broad roles for 2',3'-cNMPs among bacteria and eukaryotes. IMPORTANCE Bacteria adapt to environmental challenges by producing intracellular signaling molecules that control downstream pathways and alter cellular processes for survival. Nucleotide second messengers serve to transduce extracellular signals and regulate a wide array of intracellular pathways. Recently, 2',3'-cyclic nucleotide monophosphates (2',3'-cNMPs) were identified as contributing to the regulation of cellular pathways in eukaryotes and prokaryotes. In this study, we define previously unknown cell processes that are affected by fluctuating 2',3'-cNMP levels or RNA oligomers with 2',3'-cyclic phosphate termini in E. coli and Salmonella Typhimurium, providing a framework for studying novel signaling networks in prokaryotes. Furthermore, we utilize metabolomics databases to identify additional prokaryotic and eukaryotic species that generate 2',3'-cNMPs as a resource for future studies.
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Affiliation(s)
- Yashasvika Duggal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | | | | | - Nick J. Marotta
- Molecular, Cellular and Integrative Biosciences Program, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Shikha S. Chauhan
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Anna C. Karls
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Emily E. Weinert
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
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Cutruzzolà F, Paiardini A, Scribani Rossi C, Spizzichino S, Paone A, Giardina G, Rinaldo S. A conserved scaffold with heterogeneous metal ion binding site: the multifaceted example of HD-GYP proteins. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214228] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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31
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Park S, Sauer K. Controlling Biofilm Development Through Cyclic di-GMP Signaling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1386:69-94. [PMID: 36258069 PMCID: PMC9891824 DOI: 10.1007/978-3-031-08491-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The cyclic di-GMP (c-di-GMP) second messenger represents a signaling system that regulates many bacterial behaviors and is of key importance for driving the lifestyle switch between motile loner cells and biofilm formers. This review provides an up-to-date summary of c-di-GMP pathways connected to biofilm formation by the opportunistic pathogen P. aeruginosa. Emphasis will be on the timing of c-di-GMP production over the course of biofilm formation, to highlight non-uniform and hierarchical increases in c-di-GMP levels, as well as biofilm growth conditions that do not conform with our current model of c-di-GMP.
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Affiliation(s)
- Soyoung Park
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA
- Binghamton Biofilm Research Center (BBRC), Binghamton University, Binghamton, NY, USA
| | - Karin Sauer
- Department of Biological Sciences, Binghamton University, Binghamton, NY, USA.
- Binghamton Biofilm Research Center (BBRC), Binghamton University, Binghamton, NY, USA.
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Cox CA, Bogacz M, El Abbar FM, Browning DD, Hsueh BY, Waters CM, Lee VT, Thompson SA. The Campylobacter jejuni Response Regulator and Cyclic-Di-GMP Binding CbrR Is a Novel Regulator of Flagellar Motility. Microorganisms 2021; 10:microorganisms10010086. [PMID: 35056537 PMCID: PMC8779298 DOI: 10.3390/microorganisms10010086] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/19/2021] [Accepted: 12/29/2021] [Indexed: 01/03/2023] Open
Abstract
A leading cause of bacterial gastroenteritis, Campylobacter jejuni is also associated with broad sequelae, including extragastrointestinal conditions such as reactive arthritis and Guillain-Barré Syndrome (GBS). CbrR is a C. jejuni response regulator that is annotated as a diguanylate cyclase (DGC), an enzyme that catalyzes the synthesis of c-di-GMP, a universal bacterial second messenger, from GTP. In C. jejuni DRH212, we constructed an unmarked deletion mutant, cbrR-, and complemented mutant, cbrR+. Motility assays indicated a hyper-motile phenotype associated with cbrR-, whereas motility was deficient in cbrR+. The overexpression of CbrR in cbrR+ was accompanied by a reduction in expression of FlaA, the major flagellin. Biofilm assays and scanning electron microscopy demonstrated similarities between DRH212 and cbrR-; however, cbrR+ was unable to form significant biofilms. Transmission electron microscopy showed similar cell morphology between the three strains; however, cbrR+ cells lacked flagella. Differential radial capillary action of ligand assays (DRaCALA) showed that CbrR binds GTP and c-di-GMP. Liquid chromatography tandem mass spectrometry detected low levels of c-di-GMP in C. jejuni and in E. coli expressing CbrR. CbrR is therefore a negative regulator of FlaA expression and motility, a critical virulence factor in C. jejuni pathogenesis.
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Affiliation(s)
- Claudia A. Cox
- Department of Medicine, Division of Infectious Diseases, Augusta University, Augusta, GA 30912, USA; (C.A.C.); (M.B.); (F.M.E.A.)
| | - Marek Bogacz
- Department of Medicine, Division of Infectious Diseases, Augusta University, Augusta, GA 30912, USA; (C.A.C.); (M.B.); (F.M.E.A.)
| | - Faiha M. El Abbar
- Department of Medicine, Division of Infectious Diseases, Augusta University, Augusta, GA 30912, USA; (C.A.C.); (M.B.); (F.M.E.A.)
| | - Darren D. Browning
- Department of Biochemistry and Molecular Biology, Augusta University, Augusta, GA 30912, USA;
| | - Brian Y. Hsueh
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (B.Y.H.); (C.M.W.)
| | - Chris M. Waters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; (B.Y.H.); (C.M.W.)
| | - Vincent T. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742, USA;
| | - Stuart A. Thompson
- Department of Medicine, Division of Infectious Diseases, Augusta University, Augusta, GA 30912, USA; (C.A.C.); (M.B.); (F.M.E.A.)
- Correspondence:
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33
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Halte M, Wörmann ME, Bogisch M, Erhardt M, Tschowri N. BldD-based bimolecular fluorescence complementation for in vivo detection of the second messenger cyclic di-GMP. Mol Microbiol 2021; 117:705-713. [PMID: 34961989 DOI: 10.1111/mmi.14876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/21/2021] [Accepted: 12/23/2021] [Indexed: 11/27/2022]
Abstract
The widespread bacterial second messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP) is an important regulator of biofilm formation, virulence and cell differentiation. C-di-GMP-specific biosensors that allow detection and visualization of c-di-GMP levels in living cells are key to our understanding of how c-di-GMP fluctuations drive cellular responses. Here, we describe a novel c-di-GMP biosensor, CensYBL, that is based on c-di-GMP-induced dimerization of the effector protein BldD from Streptomyces resulting in bimolecular fluorescence complementation of split-YPet fusion proteins. As a proof-of-principle, we demonstrate that CensYBL is functional in detecting fluctuations in intracellular c-di-GMP levels in the Gram-negative model bacteria Escherichia coli and Salmonella enterica serovar Typhimurium. Using deletion mutants of c-di-GMP diguanylate cyclases and phosphodiesterases, we show that c-di-GMP dependent dimerization of CBldD-YPet results in fluorescence complementation reflecting intracellular c-di-GMP levels. Overall, we demonstrate that the CensYBL biosensor is a user-friendly and versatile tool that allows to investigate c-di-GMP variations using single-cell and population-wide experimental set-ups.
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Affiliation(s)
- Manuel Halte
- Institute for Biology / Bacterial Physiology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Mirka E Wörmann
- Institute for Biology / Microbiology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Maxim Bogisch
- Institute for Biology / Microbiology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany
| | - Marc Erhardt
- Institute for Biology / Bacterial Physiology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.,Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Natalia Tschowri
- Institute of Microbiology, Leibniz Universität Hannover, 30419, Hannover, Germany
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34
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A Novel Locally c-di-GMP-Controlled Exopolysaccharide Synthase Required for Bacteriophage N4 Infection of Escherichia coli. mBio 2021; 12:e0324921. [PMID: 34903052 PMCID: PMC8669469 DOI: 10.1128/mbio.03249-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A major target of c-di-GMP signaling is the production of biofilm-associated extracellular polymeric substances (EPS), which in Escherichia coli K-12 include amyloid curli fibers, phosphoethanolamine-modified cellulose, and poly-N-acetylglucosamine. However, the characterized c-di-GMP-binding effector systems are largely outnumbered by the 12 diguanylate cyclases (DGCs) and 13 phosphodiesterases (PDEs), which synthetize and degrade c-di-GMP, respectively. E. coli possesses a single protein with a potentially c-di-GMP-binding MshEN domain, NfrB, which-together with the outer membrane protein NfrA-is known to serve as a receptor system for phage N4. Here, we show that NfrB not only binds c-di-GMP with high affinity but, as a novel c-di-GMP-controlled glycosyltransferase, synthesizes a secreted EPS, which can impede motility and is required as an initial receptor for phage N4 infection. In addition, a systematic screening of the 12 DGCs of E. coli K-12 revealed that specifically DgcJ is required for the infection with phage N4 and interacts directly with NfrB. This is in line with local signaling models, where specific DGCs and/or PDEs form protein complexes with particular c-di-GMP effector/target systems. Our findings thus provide further evidence that intracellular signaling pathways, which all use the same diffusible second messenger, can act in parallel in a highly specific manner. IMPORTANCE Key findings in model organisms led to the concept of "local" signaling, challenging the dogma of a gradually increasing global intracellular c-di-GMP concentration driving the motile-sessile transition in bacteria. In our current model, bacteria dynamically combine both global and local signaling modes, in which specific DGCs and/or PDEs team up with effector/target systems in multiprotein complexes. The present study highlights a novel example of how specificity in c-di-GMP signaling can be achieved by showing NfrB as a novel c-di-GMP binding effector in E. coli, which is controlled in a local manner specifically by DgcJ. We further show that NfrB (which was initially found as a part of a receptor system for phage N4) is involved in the production of a novel exopolysaccharide. Finally, our data shine new light on host interaction of phage N4, which uses this exopolysaccharide as an initial receptor for adsorption.
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35
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Sequence conservation, domain architectures, and phylogenetic distribution of the HD-GYP type c-di-GMP phosphodiesterases. J Bacteriol 2021; 204:e0056121. [PMID: 34928179 DOI: 10.1128/jb.00561-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The HD-GYP domain, named after two of its conserved sequence motifs, was first described in 1999 as a specialized version of the widespread HD phosphohydrolase domain that had additional highly conserved amino acid residues. Domain associations of HD-GYP indicated its involvement in bacterial signal transduction and distribution patterns of this domain suggested that it could serve as a hydrolase of the bacterial second messenger c-di-GMP, in addition to or instead of the EAL domain. Subsequent studies confirmed the ability of various HD-GYP domains to hydrolyze c-di-GMP to linear pGpG and/or GMP. Certain HD-GYP-containing proteins hydrolyze another second messenger, cGAMP, and some HD-GYP domains participate in regulatory protein-protein interactions. The recently solved structures of HD-GYP domains from four distinct organisms clarified the mechanisms of c-di-GMP binding and metal-assisted hydrolysis. However, the HD-GYP domain is poorly represented in public domain databases, which causes certain confusion about its phylogenetic distribution, functions, and domain architectures. Here, we present a refined sequence model for the HD-GYP domain and describe the roles of its most conserved residues in metal and/or substrate binding. We also calculate the numbers of HD-GYPs encoded in various genomes and list the most common domain combinations involving HD-GYP, such as the RpfG (REC-HD-GYP), Bd1817 (DUF3391- HD-GYP), and PmGH (GAF-HD-GYP) protein families. We also provide the descriptions of six HD-GYP-associated domains, including four novel integral membrane sensor domains. This work is expected to stimulate studies of diverse HD-GYP-containing proteins, their N-terminal sensor domains and the signals to which they respond. IMPORTANCE The HD-GYP domain forms class II of c-di-GMP phosphodiesterases that control the cellular levels of the universal bacterial second messenger c-di-GMP and therefore affect flagellar and/or twitching motility, cell development, biofilm formation, and, often, virulence. Despite more than 20 years of research, HD-GYP domains are insufficiently characterized; they are often confused with 'classical' HD domains that are involved in various housekeeping activities and may participate in signaling, hydrolyzing (p)ppGpp and c-di-AMP. This work provides an updated description of the HD-GYP domain, including its sequence conservation, phylogenetic distribution, domain architectures, and the most widespread HD-GYP-containing protein families. This work shows that HD-GYP domains are widespread in many environmental bacteria and are predominant c-di-GMP hydrolases in many lineages, including clostridia and deltaproteobacteria.
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36
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Abstract
Shigella flexneri is an intracellular human pathogen that invades colonic cells and causes bloody diarrhea. S. flexneri evolved from commensal Escherichia coli, and genome comparisons reveal that S. flexneri has lost approximately 20% of its genes through the process of pathoadaptation, including a disproportionate number of genes associated with the turnover of the nucleotide-based second messenger cyclic di-GMP (c-di-GMP); however, the remaining c-di-GMP turnover enzymes are highly conserved. c-di-GMP regulates many behavioral changes in other bacteria in response to changing environmental conditions, including biofilm formation, but this signaling system has not been examined in S. flexneri. In this study, we expressed VCA0956, a constitutively active c-di-GMP synthesizing diguanylate cyclase (DGC) from Vibrio cholerae, in S. flexneri to determine if virulence phenotypes were regulated by c-di-GMP. We found that expressing VCA0956 in S. flexneri increased c-di-GMP levels, and this corresponds with increased biofilm formation and reduced acid resistance, host cell invasion, and plaque size. We examined the impact of VCA0956 expression on the S. flexneri transcriptome and found that genes related to acid resistance were repressed, and this corresponded with decreased survival to acid shock. We also found that individual S. flexneri DGC mutants exhibit reduced biofilm formation and reduced host cell invasion and plaque size, as well as increased resistance to acid shock. This study highlights the importance of c-di-GMP signaling in regulating S. flexneri virulence phenotypes. IMPORTANCE The intracellular human pathogen Shigella causes dysentery, resulting in as many as one million deaths per year. Currently, there is no approved vaccine for the prevention of shigellosis, and the incidence of antimicrobial resistance among Shigella species is on the rise. Here, we explored how the widely conserved c-di-GMP bacterial signaling system alters Shigella behaviors associated with pathogenesis. We found that expressing or removing enzymes associated with c-di-GMP synthesis results in changes in Shigella's ability to form biofilms, invade host cells, form lesions in host cell monolayers, and resist acid stress.
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Li ML, Jiao J, Zhang B, Shi WT, Yu WH, Tian CF. Global Transcriptional Repression of Diguanylate Cyclases by MucR1 Is Essential for Sinorhizobium-Soybean Symbiosis. mBio 2021; 12:e0119221. [PMID: 34700374 PMCID: PMC8546604 DOI: 10.1128/mbio.01192-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/22/2021] [Indexed: 11/20/2022] Open
Abstract
The ubiquitous bacterial second messenger c-di-GMP is intensively studied in pathogens but less so in mutualistic bacteria. Here, we report a genome-wide investigation of functional diguanylate cyclases (DGCs) synthesizing c-di-GMP from two molecules of GTP in Sinorhizobium fredii CCBAU45436, a facultative microsymbiont fixing nitrogen in nodules of diverse legumes, including soybean. Among 25 proteins harboring a putative GGDEF domain catalyzing the biosynthesis of c-di-GMP, eight functional DGCs were identified by heterogenous expression in Escherichia coli in a Congo red binding assay. This screening result was further verified by in vitro enzymatic assay with purified full proteins or the GGDEF domains from representative functional and nonfunctional DGCs. In the same in vitro assay, a functional EAL domain catalyzing the degradation of c-di-GMP into pGpG was identified in a protein that has an inactive GGDEF domain but with an active phosphodiesterase (PDE) function. The identified functional DGCs generally exhibited low transcription levels in soybean nodules compared to free-living cultures, as revealed in transcriptomes. An engineered upregulation of a functional DGC in nodules led to a significant increase of c-di-GMP level and symbiotic defects, which were not observed when a functional EAL domain was upregulated at the same level. Further transcriptional analysis and gel shift assay demonstrated that these functional DGCs were all transcriptionally repressed in nodules by a global pleiotropic regulator, MucR1, that is essential in Sinorhizobium-soybean symbiosis. These findings shed novel insights onto the systematic regulation of c-di-GMP biosynthesis in mutualistic symbiosis. IMPORTANCE The ubiquitous second messenger c-di-GMP is well-known for its role in biofilm formation and host adaptation of pathogens, whereas it is less investigated in mutualistic symbioses. Here, we reveal a cocktail of eight functional diguanylate cyclases (DGCs) catalyzing the biosynthesis of c-di-GMP in a broad-host-range Sinorhizobium that can establish nitrogen-fixing nodules on soybean and many other legumes. These functional DGCs are generally transcribed at low levels in soybean nodules compared to free-living conditions. The engineered nodule-specific upregulation of DGC can elevate the c-di-GMP level and cause symbiotic defects, while the upregulation of a phosphodiesterase that quenches c-di-GMP has no detectable symbiotic defects. Moreover, eight functional DGCs located on two different replicons are all directly repressed in nodules by a global silencer, MucR1, that is essential for Sinorhizobium-soybean symbiosis. These findings represent a novel mechanism of a strategic regulation of the c-di-GMP biosynthesis arsenal in prokaryote-eukaryote interactions.
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Affiliation(s)
- Meng-Lin Li
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jian Jiao
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Biliang Zhang
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Tao Shi
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wen-Hao Yu
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chang-Fu Tian
- State Key Laboratory of Agrobiotechnology, MOA Key Laboratory of Soil Microbiology, and Rhizobium Research Center, College of Biological Sciences, China Agricultural University, Beijing, China
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38
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Abidi W, Torres-Sánchez L, Siroy A, Krasteva PV. Weaving of bacterial cellulose by the Bcs secretion systems. FEMS Microbiol Rev 2021; 46:6388354. [PMID: 34634120 PMCID: PMC8892547 DOI: 10.1093/femsre/fuab051] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 10/08/2021] [Indexed: 12/13/2022] Open
Abstract
Cellulose is the most abundant biological compound on Earth and while it is the predominant building constituent of plants, it is also a key extracellular matrix component in many diverse bacterial species. While bacterial cellulose was first described in the 19th century, it was not until this last decade that a string of structural works provided insights into how the cellulose synthase BcsA, assisted by its inner-membrane partner BcsB, senses c-di-GMP to simultaneously polymerize its substrate and extrude the nascent polysaccharide across the inner bacterial membrane. It is now established that bacterial cellulose can be produced by several distinct types of cellulose secretion systems and that in addition to BcsAB, they can feature multiple accessory subunits, often indispensable for polysaccharide production. Importantly, the last years mark significant progress in our understanding not only of cellulose polymerization per se but also of the bigger picture of bacterial signaling, secretion system assembly, biofilm formation and host tissue colonization, as well as of structural and functional parallels of this dominant biosynthetic process between the bacterial and eukaryotic domains of life. Here, we review current mechanistic knowledge on bacterial cellulose secretion with focus on the structure, assembly and cooperativity of Bcs secretion system components.
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Affiliation(s)
- Wiem Abidi
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.,École doctorale 'Innovation thérapeutique: du fundamental à l'appliqué' (ITFA), Université Paris-Saclay, 92296, Chatenay-Malabry, France
| | - Lucía Torres-Sánchez
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France.,École doctorale 'Innovation thérapeutique: du fundamental à l'appliqué' (ITFA), Université Paris-Saclay, 92296, Chatenay-Malabry, France
| | - Axel Siroy
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
| | - Petya Violinova Krasteva
- 'Structural Biology of Biofilms' group, European Institute of Chemistry and Biology (IECB), F-33600 Pessac, France.,Université de Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, F-33600 Pessac, France
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39
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Serra DO, Hengge R. Bacterial Multicellularity: The Biology of Escherichia coli Building Large-Scale Biofilm Communities. Annu Rev Microbiol 2021; 75:269-290. [PMID: 34343018 DOI: 10.1146/annurev-micro-031921-055801] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Biofilms are a widespread multicellular form of bacterial life. The spatial structure and emergent properties of these communities depend on a polymeric extracellular matrix architecture that is orders of magnitude larger than the cells that build it. Using as a model the wrinkly macrocolony biofilms of Escherichia coli, which contain amyloid curli fibers and phosphoethanolamine (pEtN)-modified cellulose as matrix components, we summarize here the structure, building, and function of this large-scale matrix architecture. Based on different sigma and other transcription factors as well as second messengers, the underlying regulatory network reflects the fundamental trade-off between growth and survival. It controls matrix production spatially in response to long-range chemical gradients, but it also generates distinct patterns of short-range matrix heterogeneity that are crucial for tissue-like elasticity and macroscopic morphogenesis. Overall, these biofilms confer protection and a potential for homeostasis, thereby reducing maintenance energy, which makes multicellularity an emergent property of life itself. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Diego O Serra
- Instituto de Biología Molecular y Celular de Rosario (IBR), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Rosario (UNR), 2000 Rosario, Argentina
| | - Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
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40
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Andersen JB, Hultqvist LD, Jansen CU, Jakobsen TH, Nilsson M, Rybtke M, Uhd J, Fritz BG, Seifert R, Berthelsen J, Nielsen TE, Qvortrup K, Givskov M, Tolker-Nielsen T. Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms. NPJ Biofilms Microbiomes 2021; 7:59. [PMID: 34244523 PMCID: PMC8271024 DOI: 10.1038/s41522-021-00225-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022] Open
Abstract
Microbial biofilms are involved in a number of infections that cannot be cured, as microbes in biofilms resist host immune defenses and antibiotic therapies. With no strict biofilm-antibiotic in the current pipelines, there is an unmet need for drug candidates that enable the current antibiotics to eradicate bacteria in biofilms. We used high-throughput screening to identify chemical compounds that reduce the intracellular c-di-GMP content in Pseudomonas aeruginosa. This led to the identification of a small molecule that efficiently depletes P. aeruginosa for c-di-GMP, inhibits biofilm formation, and disperses established biofilm. A combination of our lead compound with standard of care antibiotics showed improved eradication of an implant-associated infection established in mice. Genetic analyses provided evidence that the anti-biofilm compound stimulates the activity of the c-di-GMP phosphodiesterase BifA in P. aeruginosa. Our work constitutes a proof of concept for c-di-GMP phosphodiesterase-activating drugs administered in combination with antibiotics as a viable treatment strategy for otherwise recalcitrant infections.
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Affiliation(s)
- Jens Bo Andersen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Louise Dahl Hultqvist
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Tim Holm Jakobsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Nilsson
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Uhd
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Blaine Gabriel Fritz
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Roland Seifert
- Institute of Pharmacology and Research Core Unit Metabolomics, Hannover Medical School Carl-Neuberg-Straße 1, Hannover, Germany
| | - Jens Berthelsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Eiland Nielsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Katrine Qvortrup
- Department of Chemistry, Technical University of Denmark, Lyngby, Denmark
| | - Michael Givskov
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center. Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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41
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Ishikawa K, Chubachi C, Tochigi S, Hoshi N, Kojima S, Hyodo M, Hayakawa Y, Furuta T, Kera K, Uozumi N. Functional characterization of multiple PAS domain-containing diguanylate cyclases in Synechocystis sp. PCC 6803. MICROBIOLOGY-SGM 2021; 166:659-668. [PMID: 32478657 DOI: 10.1099/mic.0.000929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a second messenger known to control a variety of bacterial processes. The model cyanobacterium, Synechocystis sp. PCC 6803, has a score of genes encoding putative enzymes for c-di-GMP synthesis and degradation. However, most of them have not been functionally characterized. Here, we chose four genes in Synechocystis (dgcA-dgcD), which encode proteins with a GGDEF, diguanylate cyclase (DGC) catalytic domain and multiple Per-ARNT-Sim (PAS) conserved regulatory motifs, for detailed analysis. Purified DgcA, DgcB and DgcC were able to catalyze synthesis of c-di-GMP from two GTPs in vitro. DgcA had the highest activity, compared with DgcB and DgcC. DgcD did not show detectable activity. DgcA activity was specific for GTP and stimulated by the divalent cations, magnesium or manganese. Full activity of DgcA required the presence of the multiple PAS domains, probably because of their role in protein dimerization or stability. Synechocystis mutants carrying single deletions of dgcA-dgcD were not affected in their growth rate or biofilm production during salt stress, suggesting that there was functional redundancy in vivo. In contrast, overexpression of dgcA resulted in increased biofilm formation in the absence of salt stress. In this study, we characterize the enzymatic and physiological function of DgcA-DgcD, and propose that the PAS domains in DgcA function in maintaining the enzyme in its active form.
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Affiliation(s)
- Ko Ishikawa
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Chihiro Chubachi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Saeko Tochigi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Naomi Hoshi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Seiji Kojima
- Panasonic corporation, Technology Innovation Division, Hikaridai 3-4, Seika-cho, Soraku-gun, Kyoto 619-0237, Japan
| | - Mamoru Hyodo
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Toyota 470-0392, Japan
| | - Yoshihiro Hayakawa
- Department of Applied Chemistry, Faculty of Engineering, Aichi Institute of Technology, Toyota 470-0392, Japan
| | - Tadaomi Furuta
- School of Life Science and Technology, Tokyo Institute of Technology, B-62 4259, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Kota Kera
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
| | - Nobuyuki Uozumi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Aobayama 6-6-07, Sendai 980-8579, Japan
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Identification of a Diguanylate Cyclase That Facilitates Biofilm Formation on Electrodes by Shewanella oneidensis MR-1. Appl Environ Microbiol 2021; 87:AEM.00201-21. [PMID: 33637573 DOI: 10.1128/aem.00201-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 12/29/2022] Open
Abstract
In many bacteria, cyclic diguanosine monophosphate (c-di-GMP), synthesized by diguanylate cyclase (DGC), serves as a second messenger involved in the regulation of biofilm formation. Although studies have suggested that c-di-GMP also regulates the formation of electrochemically active biofilms (EABFs) by Shewanella oneidensis MR-1, DGCs involved in this process remained to be identified. Here, we report that the SO_1646 gene, hereafter named dgcS, is upregulated under medium flow conditions in electrochemical flow cells (EFCs), and its product (DgcS) functions as a major DGC in MR-1. In vitro assays demonstrated that purified DgcS catalyzed the synthesis of c-di-GMP from GTP. Comparisons of intracellular c-di-GMP levels in the wild-type strain and a dgcS deletion mutant (ΔdgcS mutant) showed that production of c-di-GMP was markedly reduced in the ΔdgcS mutant when cells were grown in batch cultures and on electrodes in EFCs. Cultivation of the ΔdgcS mutant in EFCs also revealed that the loss of DgcS resulted in impaired biofilm formation and decreased current generation. These findings demonstrate that MR-1 uses DgcS to synthesize c-di-GMP under medium flow conditions, thereby activating biofilm formation on electrodes.IMPORTANCE Bioelectrochemical systems (BESs) have attracted wide attention owing to their utility in sustainable biotechnology processes, such as microbial fuel cells and electrofermentation systems. In BESs, electrochemically active bacteria (EAB) form biofilms on electrode surfaces, thereby serving as effective catalysts for the interconversion between chemical and electric energy. It is therefore important to understand mechanisms for the formation of biofilm by EAB grown on electrodes. Here, we show that a model EAB, S. oneidensis MR-1, expresses DgcS as a major DGC, thereby activating the formation of biofilms on electrodes via c-di-GMP-dependent signal transduction cascades. The findings presented herein provide the molecular basis for improving electrochemical interactions between EAB and electrodes in BESs. The results also offer molecular insights into how Shewanella regulates biofilm formation on solid surfaces in the natural environment.
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Grekov I, Thöming JG, Kordes A, Häussler S. Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions. THE ISME JOURNAL 2021; 15:1165-1177. [PMID: 33273720 PMCID: PMC8115180 DOI: 10.1038/s41396-020-00841-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 11/04/2020] [Accepted: 11/11/2020] [Indexed: 01/29/2023]
Abstract
Identifying genetic factors that contribute to the evolution of adaptive phenotypes in pathogenic bacteria is key to understanding the establishment of infectious diseases. In this study, we performed mutation accumulation experiments to record the frequency of mutations and their effect on fitness in hypermutator strains of the environmental bacterium Pseudomonas aeruginosa in comparison to the host-niche-adapted Salmonella enterica. We demonstrate that P. aeruginosa, but not S. enterica, hypermutators evolve toward higher fitness under planktonic conditions. Adaptation to increased growth performance was accompanied by a reversible perturbing of the local genetic context of membrane and cell wall biosynthesis genes. Furthermore, we observed a fine-tuning of complex regulatory circuits involving multiple di-guanylate modulating enzymes that regulate the transition between fast growing planktonic and sessile biofilm-associated lifestyles. The redundancy and local specificity of the di-guanylate signaling pathways seem to allow a convergent shift toward increased growth performance across niche-adapted clonal P. aeruginosa lineages, which is accompanied by a pronounced heterogeneity of their motility, virulence, and biofilm phenotypes.
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Affiliation(s)
- Igor Grekov
- grid.7490.a0000 0001 2238 295XDepartment of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany ,grid.475435.4Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Janne Gesine Thöming
- grid.452370.70000 0004 0408 1805Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany ,grid.475435.4Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Adrian Kordes
- grid.452370.70000 0004 0408 1805Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany ,grid.10423.340000 0000 9529 9877Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Susanne Häussler
- grid.7490.a0000 0001 2238 295XDepartment of Molecular Bacteriology, Helmholtz Centre for Infection Research, Braunschweig, Germany ,grid.452370.70000 0004 0408 1805Institute of Molecular Bacteriology, TWINCORE Centre for Experimental and Clinical Infection Research, Hannover, Germany ,grid.475435.4Department of Clinical Microbiology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.10423.340000 0000 9529 9877Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
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Induction of Native c-di-GMP Phosphodiesterases Leads to Dispersal of Pseudomonas aeruginosa Biofilms. Antimicrob Agents Chemother 2021; 65:AAC.02431-20. [PMID: 33495218 DOI: 10.1128/aac.02431-20] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 01/15/2021] [Indexed: 01/07/2023] Open
Abstract
A decade of research has shown that the molecule c-di-GMP functions as a central second messenger in many bacteria. A high level of c-di-GMP is associated with biofilm formation, whereas a low level of c-di-GMP is associated with a planktonic single-cell bacterial lifestyle. c-di-GMP is formed by diguanylate cyclases and is degraded by specific phosphodiesterases. We previously presented evidence that the ectopic expression of the Escherichia coli phosphodiesterase YhjH in Pseudomonas aeruginosa results in biofilm dispersal. More recently, however, evidence has been presented that the induction of native c-di-GMP phosphodiesterases does not lead to a dispersal of P. aeruginosa biofilms. The latter result may discourage attempts to use c-di-GMP signaling as a target for the development of antibiofilm drugs. However, here, we demonstrate that the induction of the P. aeruginosa c-di-GMP phosphodiesterases PA2133 and BifA indeed results in the dispersal of P. aeruginosa biofilms in both a microtiter tray biofilm assay and a flow cell biofilm system.
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A SNP in the Cache 1 Signaling Domain of Diguanylate Cyclase STM1987 Leads to Increased In Vivo Fitness of Invasive Salmonella Strains. Infect Immun 2021; 89:IAI.00810-20. [PMID: 33468583 DOI: 10.1128/iai.00810-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 01/11/2021] [Indexed: 02/08/2023] Open
Abstract
Nontyphoidal Salmonella (NTS) strains are associated with gastroenteritis worldwide but are also the leading cause of bacterial bloodstream infections in sub-Saharan Africa. The invasive NTS (iNTS) strains that cause bloodstream infections differ from standard gastroenteritis-causing strains by >700 single-nucleotide polymorphisms (SNPs). These SNPs are known to alter metabolic pathways and biofilm formation and to contribute to serum resistance and are thought to signify iNTS strains becoming human adapted, similar to typhoid fever-causing Salmonella strains. Identifying SNPs that contribute to invasion or increased virulence has been more elusive. In this study, we identified a SNP in the cache 1 signaling domain of diguanylate cyclase STM1987 in the invasive Salmonella enterica serovar Typhimurium type strain D23580. This SNP was conserved in 118 other iNTS strains analyzed and was comparatively absent in global S Typhimurium isolates associated with gastroenteritis. STM1987 catalyzes the formation of bis-(3',5')-cyclic dimeric GMP (c-di-GMP) and is proposed to stimulate production of cellulose independent of the master biofilm regulator CsgD. We show that the amino acid change in STM1987 leads to a 10-fold drop in cellulose production and increased fitness in a mouse model of acute infection. Reduced cellulose production due to the SNP led to enhanced survival in both murine and human macrophage cell lines. In contrast, loss of CsgD-dependent cellulose production did not lead to any measurable change in in vivo fitness. We hypothesize that the SNP in stm1987 represents a pathoadaptive mutation for iNTS strains.
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Alkaline pH Increases Swimming Speed and Facilitates Mucus Penetration for Vibrio cholerae. J Bacteriol 2021; 203:JB.00607-20. [PMID: 33468594 PMCID: PMC8088521 DOI: 10.1128/jb.00607-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/05/2021] [Indexed: 01/05/2023] Open
Abstract
The diarrheal disease cholera is still a burden for populations in developing countries with poor sanitation. To develop effective vaccines and prevention strategies against Vibrio cholerae, we must understand the initial steps of infection leading to the colonization of the small intestine. Intestinal mucus is the first line of defense against intestinal pathogens. It acts as a physical barrier between epithelial tissues and the lumen that enteropathogens must overcome to establish a successful infection. We investigated the motile behavior of two Vibrio cholerae strains (El Tor C6706 and Classical O395) in mucus using single-cell tracking in unprocessed porcine intestinal mucus. We determined that V. cholerae can penetrate mucus using flagellar motility and that alkaline pH increases swimming speed and, consequently, improves mucus penetration. Microrheological measurements indicate that changes in pH between 6 and 8 (the physiological range for the human small intestine) had little effect on the viscoelastic properties of mucus. Finally, we determined that acidic pH promotes surface attachment by activating the mannose-sensitive hemagglutinin (MshA) pilus in V. cholerae El Tor C6706 without a measurable change in the total cellular concentration of the secondary messenger cyclic dimeric GMP (c-di-GMP). Overall, our results support the hypothesis that pH is an important factor affecting the motile behavior of V. cholerae and its ability to penetrate mucus. Therefore, changes in pH along the human small intestine may play a role in determining the preferred site for V. cholerae during infection. IMPORTANCE The diarrheal disease cholera is still a burden for populations in developing countries with poor sanitation. To develop effective vaccines and prevention strategies against Vibrio cholerae, we must understand the initial steps of infection leading to the colonization of the small intestine. To infect the host and deliver the cholera toxin, V. cholerae has to penetrate the mucus layer protecting the intestinal tissues. However, the interaction of V. cholerae with intestinal mucus has not been extensively investigated. In this report, we demonstrated using single-cell tracking that V. cholerae can penetrate intestinal mucus using flagellar motility. In addition, we observed that alkaline pH improves the ability of V. cholerae to penetrate mucus. This finding has important implications for understanding the dynamics of infection, because pH varies significantly along the small intestine, between individuals, and between species. Blocking mucus penetration by interfering with flagellar motility in V. cholerae, reinforcing the mucosa, controlling intestinal pH, or manipulating the intestinal microbiome will offer new strategies to fight cholera.
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Hengge R. High-Specificity Local and Global c-di-GMP Signaling. Trends Microbiol 2021; 29:993-1003. [PMID: 33640237 DOI: 10.1016/j.tim.2021.02.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/31/2021] [Accepted: 02/01/2021] [Indexed: 11/26/2022]
Abstract
The striking multiplicity, signal input diversity, and output specificity of c-di-GMP signaling proteins in many bacteria has brought second messenger signaling back onto the agenda of contemporary microbiology. How can several signaling pathways act in parallel in a specific manner if all of them use the same diffusible second messenger present at a certain global cellular concentration? Recent research has now shown that bacteria achieve this by flexibly combining modes of local and global c-di-GMP signaling in complex signaling networks. Three criteria have to be met to define local c-di-GMP signaling: specific knockout phenotypes, direct interactions between proteins involved, and actual cellular c-di-GMP levels remaining below the Kd of effectors. Adaptive changes in signaling network architecture can further enhance signaling flexibility.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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Loss of cell wall integrity genes cpxA and mrcB causes flocculation in Escherichia coli. Biochem J 2021; 478:41-59. [PMID: 33196080 DOI: 10.1042/bcj20200723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 11/17/2022]
Abstract
Flocculation has been recognized for hundreds of years as an important phenomenon in brewing and wastewater treatment. However, the underlying molecular mechanisms remain elusive. The lack of a distinct phenotype to differentiate between slow-growing mutants and floc-forming mutants prevents the isolation of floc-related gene by conventional mutant screening. To overcome this, we performed a two-step Escherichia coli mutant screen. The initial screen of E. coli for mutants conferring floc production during high salt treatment yielded a mutant containing point mutations in 61 genes. The following screen of the corresponding single-gene mutants identified two genes, mrcB, encoding a peptidoglycan-synthesizing enzyme and cpxA, encoding a histidine kinase of a two-component signal transduction system that contributed to salt tolerance and flocculation prevention. Both single mutants formed flocs during high salt shock, these flocs contained cytosolic proteins. ΔcpxA exhibited decreased growth with increasing floc production and addition of magnesium to ΔcpxA suppressed floc production effectively. In contrast, the growth of ΔmrcB was inconsistent under high salt conditions. In both strains, flocculation was accompanied by the release of membrane vesicles containing inner and outer membrane proteins. Of 25 histidine kinase mutants tested, ΔcpxA produced the highest amount of proteins in floc. Expression of cpxP was up-regulated by high salt in ΔcpxA, suggesting that high salinity and activation of CpxR might promote floc formation. The finding that ΔmrcB or ΔcpxA conferred floc production indicates that cell envelope stress triggered by unfavorable environmental conditions cause the initiation of flocculation in E. coli.
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Yilmaz C, Rangarajan AA, Schnetz K. The transcription regulator and c-di-GMP phosphodiesterase PdeL represses motility in Escherichia coli. J Bacteriol 2020; 203:JB.00427-20. [PMID: 33318048 PMCID: PMC8095459 DOI: 10.1128/jb.00427-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/09/2020] [Indexed: 12/16/2022] Open
Abstract
PdeL is a transcription regulator and catalytically active c-di-GMP phosphodiesterases (PDE) in Escherichia coli PdeL has been shown to be a transcription autoregulator, while no other target genes have been identified so far. Here, we show that PdeL represses transcription of the flagella class II operon, fliFGHIJK, and activates sslE encoding an extracellular anchored metalloprotease, among additional loci. DNA-binding studies and expression analyses using plasmidic reporters suggest that regulation of the fliF and sslE promoters by PdeL is direct. Transcription repression of the fliFGHIJK operon, encoding protein required for assembly of the flagellar basal body, results in inhibition of motility on soft agar plates and reduction of flagella assembly, as shown by fluorescence staining of the flagella hook protein FlgE. PdeL-mediated repression of motility is independent of its phosphodiesterase activity. Thus, in motility control the transcription regulator function of PdeL reducing the number of assembled flagella is apparently epistatic to its phosphodiesterase function, which can indirectly promote the activity of the flagellar motor by lowering the c-di-GMP concentration.Bacteria adopt different lifestyles depending on their environment and physiological condition. In Escherichia coli and other enteric bacteria the transition between the motile and the sessile state is controlled at multiple levels from the regulation of gene expression to the modulation of various processes by the second messenger c-di-GMP as signaling molecule. The significance of our research is in identifying PdeL, a protein of dual function that hydrolyzes c-di-GMP and that regulates transcription of genes, as a repressor of Flagella gene expression and an inhibitor of motility, which adds an additional regulatory switch to the control of motility.
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Affiliation(s)
- Cihan Yilmaz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
| | | | - Karin Schnetz
- Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674 Cologne, Germany
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Koul V, Srivastava D, Singh PP, Kochar M. Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions. BMC Genomics 2020; 21:821. [PMID: 33228533 PMCID: PMC7685610 DOI: 10.1186/s12864-020-07212-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 11/05/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are non-coding RNAs known to regulate various biological functions such as stress adaptation, metabolism, virulence as well as pathogenicity across a wide range of bacteria, mainly by controlling mRNA stabilization or regulating translation. Identification and functional characterization of sRNAs has been carried out in various plant growth-promoting bacteria and they have been shown to help the cells cope up with environmental stress. No study has been carried out to uncover these regulatory molecules in the diazotrophic alpha-proteobacterium Azospirillum brasilense Sp245 to date. RESULTS Expression-based sRNA identification (RNA-seq) revealed the first list of ~ 468 sRNA candidate genes in A. brasilense Sp245 that were differentially expressed in nitrogen starvation versus non-starved conditions. In parallel, in silico tools also identified 2 of the above as candidate sRNAs. Altogether, putative candidates were stringently curated from RNA-seq data based on known sRNA parameters (size, location, secondary structure, and abundance). In total, ~ 59 significantly expressed sRNAs were identified in this study of which 53 are potentially novel sRNAs as they have no Rfam and BSRD homologs. Sixteen sRNAs were randomly selected and validated for differential expression, which largely was found to be in congruence with the RNA-seq data. CONCLUSIONS Differential expression of 468 A. brasilense sRNAs was indicated by RNA-seq data, a subset of which was confirmed by expression analysis. Four of the significantly expressed sRNAs were not observed in nitrogen starvation while 16 sRNAs were found to be exclusively expressed in nitrogen depletion. Putative candidate sRNAs identified have potential mRNA targets primarily involved in stress (abiotic and biotic) adaptability; regulation of bacterial cellular, biological and molecular pathways such as nitrogen fixation, polyhydroxybutyrate synthesis, chemotaxis, biofilm formation and transcriptional regulation. In addition to directly influencing bacteria, some of these sRNAs also have targets influencing plant-microbe interactions through adhesion of bacteria to plant roots directly, suppressing host response, inducing plant defence and signalling.
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Affiliation(s)
- Vatsala Koul
- The Energy and Resources Institute, Darbari Seth Block, India Habitat Centre, Lodhi Road, New Delhi, 110003, India
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Divya Srivastava
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India
| | - Pushplata Prasad Singh
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
| | - Mandira Kochar
- TERI Deakin Nanobiotechnology Centre, Sustainable Agriculture Division, The Energy and Resources Institute, Gurugram-Faridabad Road, Gwal Pahari, Haryana, 122003, India.
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