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Sobe RC, Scharf BE. The swimming defect caused by the absence of the transcriptional regulator LdtR in Sinorhizobium meliloti is restored by mutations in the motility genes motA and motS. Mol Microbiol 2024; 121:954-970. [PMID: 38458990 DOI: 10.1111/mmi.15247] [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: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/10/2024]
Abstract
The flagellar motor is a powerful macromolecular machine used to propel bacteria through various environments. We determined that flagellar motility of the alpha-proteobacterium Sinorhizobium meliloti is nearly abolished in the absence of the transcriptional regulator LdtR, known to influence peptidoglycan remodeling and stress response. LdtR does not regulate motility gene transcription. Remarkably, the motility defects of the ΔldtR mutant can be restored by secondary mutations in the motility gene motA or a previously uncharacterized gene in the flagellar regulon, which we named motS. MotS is not essential for S. meliloti motility and may serve an accessory role in flagellar motor function. Structural modeling predicts that MotS comprised an N-terminal transmembrane segment, a long-disordered region, and a conserved β-sandwich domain. The C terminus of MotS is localized in the periplasm. Genetics based substitution of MotA with MotAG12S also restored the ΔldtR motility defect. The MotAG12S variant protein features a local polarity shift at the periphery of the MotAB stator units. We propose that MotS may be required for optimal alignment of stators in wild-type flagellar motors but becomes detrimental in cells with altered peptidoglycan. Similarly, the polarity shift in stator units composed of MotB/MotAG12S might stabilize its interaction with altered peptidoglycan.
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Affiliation(s)
- Richard C Sobe
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, Virginia, USA
| | - Birgit E Scharf
- Department of Biological Sciences, Life Sciences I, Virginia Tech, Blacksburg, Virginia, USA
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2
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Singh PK, Sharma P, Afanzar O, Goldfarb MH, Maklashina E, Eisenbach M, Cecchini G, Iverson TM. CryoEM structures reveal how the bacterial flagellum rotates and switches direction. Nat Microbiol 2024; 9:1271-1281. [PMID: 38632342 PMCID: PMC11087270 DOI: 10.1038/s41564-024-01674-1] [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: 08/19/2023] [Accepted: 03/12/2024] [Indexed: 04/19/2024]
Abstract
Bacterial chemotaxis requires bidirectional flagellar rotation at different rates. Rotation is driven by a flagellar motor, which is a supercomplex containing multiple rings. Architectural uncertainty regarding the cytoplasmic C-ring, or 'switch', limits our understanding of how the motor transmits torque and direction to the flagellar rod. Here we report cryogenic electron microscopy structures for Salmonella enterica serovar typhimurium inner membrane MS-ring and C-ring in a counterclockwise pose (4.0 Å) and isolated C-ring in a clockwise pose alone (4.6 Å) and bound to a regulator (5.9 Å). Conformational differences between rotational poses include a 180° shift in FliF/FliG domains that rotates the outward-facing MotA/B binding site to inward facing. The regulator has specificity for the clockwise pose by bridging elements unique to this conformation. We used these structures to propose how the switch reverses rotation and transmits torque to the flagellum, which advances the understanding of bacterial chemotaxis and bidirectional motor rotation.
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Affiliation(s)
- Prashant K Singh
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Pankaj Sharma
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Oshri Afanzar
- Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
| | - Margo H Goldfarb
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Elena Maklashina
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - Michael Eisenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Gary Cecchini
- Molecular Biology Division, San Francisco VA Health Care System, San Francisco, CA, USA
- Department of Biochemistry & Biophysics, University of California, San Francisco, CA, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA.
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN, USA.
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3
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Wang T, Hua C, Deng X. c-di-GMP signaling in Pseudomonas syringae complex. Microbiol Res 2023; 275:127445. [PMID: 37450986 DOI: 10.1016/j.micres.2023.127445] [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: 05/30/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]
Abstract
The Pseudomonas syringae Complex is one of the model phytopathogenic bacteria for exploring plant-microbe interactions, causing devastating plant diseases and economic losses worldwide. The ubiquitous second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) plays an important role in the 'lifestyle switch' from single motile cells to biofilm formation and modulates bacterial behavior, thus influencing virulence in Pseudomonas and other bacterial species. However, less is known about the role of c-di-GMP in the P. syringae complex, in which c-di-GMP levels are controlled by diguanylate cyclases (DGCs) and phosphodiesterases (PDEs), such as Chp8, BifA and WspR. Deletion the chemotaxis receptor PscA also influences c-di-GMP levels, suggesting a cross-talk between chemotaxis and c-di-GMP pathways. Another transcription factor, FleQ, plays a dual role (positive or negative) in regulating cellulose synthesis as a c-di-GMP effector, whereas the transcription factor AmrZ regulates local c-di-GMP levels by inhibiting the DGC enzyme AdcA and the PDE enzyme MorA. Our recent research demonstrated that an increase in the c-di-GMP concentration increased biofilm development, siderophore biosynthesis and oxidative stress tolerance, while it decreased the siderophore content, bacterial motility and type III secretion system activity in P. syringae complex. These findings show that c-di-GMP intricately controls virulence in P. syringae complex, indicating that adjusting c-di-GMP levels may be a valuable tactic for defending plants against pathogens. This review highlights recent research on metabolic enzymes, regulatory mechanisms and the phenotypic consequences of c-di-GMP signaling in the P. syringae.
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Affiliation(s)
- Tingting Wang
- Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Canfeng Hua
- Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Xin Deng
- Department of Biomedicine, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China; Shenzhen Research Institute, City University of Hong Kong, Shenzhen, Hong Kong SAR, China; Tung Research Centre, City University of Hong Kong, Hong Kong SAR, China; Chengdu Research Institute, City University of Hong Kong, Chengdu, China.
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4
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Dye KJ, Salar S, Allen U, Smith W, Yang Z. Myxococcus xanthus PilB interacts with c-di-GMP and modulates motility and biofilm formation. J Bacteriol 2023; 205:e0022123. [PMID: 37695853 PMCID: PMC10521364 DOI: 10.1128/jb.00221-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
The regulation of biofilm and motile states as alternate bacterial lifestyles has been studied extensively in flagellated bacteria, where the second messenger cyclic-di-GMP (cdG) plays a crucial role. However, much less is known about the mechanisms of such regulation in motile bacteria without flagella. The bacterial type IV pilus (T4P) serves as a motility apparatus that enables Myxococcus xanthus to move on solid surfaces. PilB, the T4P assembly ATPase, is, therefore, required for T4P-dependent motility in M. xanthus. Interestingly, T4P is also involved in the regulation of exopolysaccharide as the biofilm matrix material in this bacterium. A newly discovered cdG-binding domain, MshEN, is conserved in the N-terminus of PilB (PilBN) in M. xanthus and other bacteria. This suggests that cdG may bind to PilB to control the respective outputs that regulate biofilm development and T4P-powered motility. In this study, we aimed to validate M. xanthus PilB as a cdG effector protein. We performed a systematic mutational analysis of its cdG-binding domain to investigate its relationship with motility, piliation, and biofilm formation. Excluding those resulting in low levels of PilB protein, all other substitution mutations in PilBN resulted in pilB mutants with distinct and differential phenotypes in piliation and biofilm levels in M. xanthus. This suggests that the PilBN domain plays dual roles in modulating motility and biofilm levels, and these two functions of PilB can be dependent on and independent of each other in M. xanthus. IMPORTANCE The regulation of motility and biofilm by cyclic-di-GMP in flagellated bacteria has been extensively investigated. However, our knowledge regarding this regulation in motile bacteria without flagella remains limited. Here, we aimed to address this gap by investigating a non-flagellated bacterium with motility powered by bacterial type-IV pilus (T4P). Previous studies hinted at the possibility of Myxococcus xanthus PilB, the T4P assembly ATPase, serving as a cyclic-di-GMP effector involved in regulating both motility and biofilm. Our findings strongly support the hypothesis that PilB directly interacts with cyclic-di-GMP to act as a potential switch to promote biofilm formation or T4P-dependent motility. These results shed light on the bifurcation of PilB functions and its pivotal role in coordinating biofilm formation and T4P-mediated motility.
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Affiliation(s)
- Keane J. Dye
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Safoura Salar
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Uvina Allen
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Wraylyn Smith
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Zhaomin Yang
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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5
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Xu LC, Ochetto A, Chen C, Sun D, Allcock HR, Siedlecki CA. Surfaces modified with small molecules that interfere with nucleotide signaling reduce Staphylococcus epidermidis biofilm and increase the efficacy of ciprofloxacin. Colloids Surf B Biointerfaces 2023; 227:113345. [PMID: 37196462 PMCID: PMC10355139 DOI: 10.1016/j.colsurfb.2023.113345] [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: 11/12/2022] [Revised: 03/30/2023] [Accepted: 05/11/2023] [Indexed: 05/19/2023]
Abstract
Staphylococcus epidermidis are common bacteria associated with biofilm related infections on implanted medical devices. Antibiotics are often used in combating such infections, but they may lose their efficacy in the presence of biofilms. Bacterial intracellular nucleotide second messenger signaling plays an important role in biofilm formation, and interference with the nucleotide signaling pathways provides a possible way to control biofilm formation and to increase biofilm susceptibility to antibiotic therapy. This study synthesized small molecule derivates of 4-arylazo-3,5-diamino-1 H-pyrazole (named as SP02 and SP03) and found these molecules inhibited S. epidermidis biofilm formation and induced biofilm dispersal. Analysis of bacterial nucleotide signaling molecules showed that both SP02 and SP03 significantly reduced cyclic dimeric adenosine monophosphate (c-di-AMP) levels in S. epidermidis at doses as low as 25 µM while having significant effects on multiple nucleotides signaling including cyclic dimeric guanosine monophosphate (c-di-GMP), c-di-AMP, and cyclic adenosine monophosphate (cAMP) at high doses (100 µM or greater). We then tethered these small molecules to polyurethane (PU) biomaterial surfaces and investigated biofilm formation on the modified surfaces. Results showed that the modified surfaces significantly inhibited biofilm formation during 24 h and 7-day incubations. The antibiotic ciprofloxacin was used to treat these biofilms and the efficacy of the antibiotic (2 µg/mL) was found to increase from 94.8% on unmodified PU surfaces to > 99.9% on both SP02 and SP03 modified surfaces (>3 log units). Results demonstrated the feasibility of tethering small molecules that interfere with nucleotide signaling onto polymeric biomaterial surfaces and in a way that interrupts biofilm formation and increases antibiotic efficacy for S. epidermidis infections.
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Affiliation(s)
- Li-Chong Xu
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.
| | - Alyssa Ochetto
- Department of Biological and Biomedical Sciences, Rowan University, Glassboro, NJ 08028, USA
| | - Chen Chen
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Dongxiao Sun
- Department of Pharmacology, Mass Spectrometry Core Facilities (RRID: SCR_017831), The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Harry R Allcock
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Christopher A Siedlecki
- Department of Surgery, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA; Department of Biomedical Engineering, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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Chang CP, Lagitnay RBJS, Li TR, Lai WT, Derilo RC, Chuang DY. Unleashing the Influence of cAMP Receptor Protein: The Master Switch of Bacteriocin Export in Pectobacterium carotovorum subsp. carotovorum. Int J Mol Sci 2023; 24:ijms24119752. [PMID: 37298703 DOI: 10.3390/ijms24119752] [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: 04/26/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
Pectobacterium carotovorum subsp. carotovorum (Pcc) is a Gram-negative phytopathogenic bacterium that produces carocin, a low-molecular-weight bacteriocin that can kill related strains in response to factors in the environment such as UV exposure or nutritional deficiency. The function of the catabolite activator protein (CAP), also known as the cyclic AMP receptor protein (CRP), as a regulator of carocin synthesis was examined. The crp gene was knocked out as part of the investigation, and the outcomes were assessed both in vivo and in vitro. Analysis of the DNA sequence upstream of the translation initiation site of carocin S3 revealed two putative binding sites for CRP that were confirmed using a biotinylated probe pull-down experiment. This study revealed that the deletion of crp inhibited genes involved in extracellular bacteriocin export via the flagellar type III secretion system and impacted the production of many low-molecular-weight bacteriocins. The biotinylated probe pull-down test demonstrated that when UV induction was missing, CRP preferentially attached to one of the two CAP sites while binding to both when UV induction was present. In conclusion, our research aimed to simulate the signal transduction system that controls the expression of the carocin gene in response to UV induction.
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Affiliation(s)
- Chung-Pei Chang
- Department of Anesthesiology, Show Chwan Memorial Hospital, Changhua 500, Taiwan
| | - Ruchi Briam James Sersenia Lagitnay
- College of Arts and Sciences, Bayombong Campus, Nueva Vizcaya State University, Bayombong 3700, Philippines
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Tzu-Rong Li
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Wei-Ting Lai
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
| | - Reymund Calanga Derilo
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
- College of Teacher Education, Bambang Campus, Nueva Vizcaya State University, Bambang 3702, Philippines
| | - Duen-Yau Chuang
- Department of Chemistry, National Chung Hsing University, Taichung City 400, Taiwan
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7
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Han Q, Wang SF, Qian XX, Guo L, Shi YF, He R, Yuan JH, Hou YJ, Li DF. Flagellar brake protein YcgR interacts with motor proteins MotA and FliG to regulate the flagellar rotation speed and direction. Front Microbiol 2023; 14:1159974. [PMID: 37125196 PMCID: PMC10140304 DOI: 10.3389/fmicb.2023.1159974] [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: 02/06/2023] [Accepted: 03/24/2023] [Indexed: 05/02/2023] Open
Abstract
In E. coli and related species, flagellar brake protein YcgR responds to the elevated intracellular c-di-GMP, decreases the flagellar rotation speed, causes a CCW rotation bias, and regulates bacterial swimming. Boehm et al. suggested that c-di-GMP-activated YcgR directly interacted with the motor protein MotA to curb flagellar motor output. Paul et al. proposed that YcgR disrupted the organization of the FliG C-terminal domain to bias the flagellar rotation. The target proteins are controversial, and the role of motor proteins remains unclear in flagellar rotation speed and direction regulation by YcgR. Here we assayed the motor proteins' affinity via a modified FRET biosensor and accessed the role of those key residue via bead assays. We found that YcgR could interact with both MotA and FliG, and the affinities could be enhanced upon c-di-GMP binding. Furthermore, residue D54 of YcgR-N was needed for FliG binding. The mutation of the FliG binding residue D54 or the MotA binding ones, F117 and E232, restored flagellar rotation speed in wild-type cells and cells lacking chemotaxis response regulator CheY that switched the flagellar rotation direction and decreased the CCW ratio in wild-type cells. We propose that c-di-GMP-activated YcgR regulated the flagellar rotation speed and direction via its interaction with motor proteins MotA and FliG. Our work suggest the role of YcgR-motor proteins interaction in bacterial swimming regulation.
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Affiliation(s)
- Qun Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shao-Feng Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xin-Xin Qian
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lu Guo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yi-Feng Shi
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Rui He
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Jun-Hua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Yan-Jie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Yan-Jie Hou,
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- De-Feng Li,
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Liu Z, Xu Z, Chen S, Huang J, Li T, Duan C, Zhang LH, Xu Z. CzcR Is Essential for Swimming Motility in Pseudomonas aeruginosa during Zinc Stress. Microbiol Spectr 2022; 10:e0284622. [PMID: 36416561 PMCID: PMC9769499 DOI: 10.1128/spectrum.02846-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 11/04/2022] [Indexed: 11/25/2022] Open
Abstract
Two-component system (TCS) plays a vital role in modulating target gene expression in response to the changing environments. Pseudomonas aeruginosa is a ubiquitous opportunistic pathogen that can survive under diverse stress conditions. The great adaptability of P. aeruginosa relies heavily on the abundant TCSs encoded by its genome. However, most TCSs in P. aeruginosa have not been well-characterized. CzcS/CzcR is a metal responsive TCS which displays multiple regulatory functions associated with metal hemostasis, quorum sensing activity and antibiotic resistance. In this study, we found that swimming motility of P. aeruginosa was completely abolished during zinc (Zn2+) stress when the czcR gene from the TCS CzcS/CzcR was deleted. Noticeably, CzcR was dispensable for swimming without the stress of Zn2+ excess. CzcR was shown to be activated by Zn2+ stress possibly through inducing its expression level and triggering its phosphorylation to positively regulate swimming which was abolished by Zn2+ stress in a CzcR-independent manner. Further TEM analyses and promoter activity examinations revealed that CzcR was required for the expression of genes involved in flagellar biosynthesis during Zn2+ stress. In vitro protein-DNA interaction assay showed that CzcR was capable of specifically recognizing and binding to the promoters of operons flgBCDE, flgFGHIJK, and PA1442/FliMNOPQR/flhB. Together, this study demonstrated a novel function of CzcR in regulating flagellar gene expression and motility in P. aeruginosa when the pathogen encounters Zn2+ stress conditions. IMPORTANCE The fitness of bacterial cells depends largely on their ability to sense and respond quickly to the changing environments. P. aeruginosa expresses a great number of signal sensing and transduction systems that enable the pathogen to grow and survive under diverse stress conditions and cause serious infections at different sites in many hosts. In addition to the previously characterized functions to regulate metal homeostasis, quorum sensing activity, and antibiotic resistance, here we report that CzcR is a novel regulator essential for flagellar gene expression and swimming motility in P. aeruginosa during Zn2+ stress. Since swimming motility is important for the virulence of P. aeruginosa, findings in this study might provide a new target for the treatment of P. aeruginosa infections with Zn2+-based antimicrobial agents in the future.
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Affiliation(s)
- Zhiqing Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zirui Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Shuzhen Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Jiahui Huang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Ting Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Cheng Duan
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Lian-Hui Zhang
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, People’s Republic of China
| | - Zeling Xu
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, People’s Republic of China
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9
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Chen Y, Lv M, Liang Z, Liu Z, Zhou J, Zhang L. Cyclic di-GMP modulates sessile-motile phenotypes and virulence in Dickeya oryzae via two PilZ domain receptors. MOLECULAR PLANT PATHOLOGY 2022; 23:870-884. [PMID: 35254732 PMCID: PMC9104268 DOI: 10.1111/mpp.13200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/23/2022] [Accepted: 02/08/2022] [Indexed: 05/03/2023]
Abstract
Dickeya oryzae is a bacterial pathogen causing the severe rice stem rot disease in China and other rice-growing countries. We showed recently that the universal bacterial second messenger c-di-GMP plays an important role in modulation of bacterial motility and pathogenicity, but the mechanism of regulation remains unknown. In this study, bioinformatics analysis of the D. oryzae EC1 genome led to the identification of two proteins, YcgR and BcsA, both of which contain a conserved c-di-GMP receptor domain, known as the PilZ-domain. By deleting all the genes encoding c-di-GMP-degrading enzymes in D. oryzae EC1, the resultant mutant 7ΔPDE with high c-di-GMP levels became nonmotile, formed hyperbiofilm, and lost the ability to colonize and invade rice seeds. These phenotypes were partially reversed by deletion of ycgR in the mutant 7ΔPDE, whereas deletion of bcsA only reversed the hyperbiofilm phenotype of mutant 7ΔPDE. Significantly, double deletion of ycgR and bcsA in mutant 7ΔPDE rescued its motility, biofilm formation, and virulence to levels of wild-type EC1. In vitro biochemical experiments and in vivo phenotypic assays further validated that YcgR and BcsA proteins are the receptors for c-di-GMP, which together play a critical role in regulating the c-di-GMP-associated functionality. The findings from this study fill a gap in our understanding of how c-di-GMP modulates bacterial motility and biofilm formation, and provide useful clues for further elucidation of sophisticated virulence regulatory mechanisms in this important plant pathogen.
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Affiliation(s)
- Yufan Chen
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Mingfa Lv
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Zhibin Liang
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Zhiqing Liu
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Jianuan Zhou
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
| | - Lian‐Hui Zhang
- Guangdong Laboratory for Lingnan Modern AgricultureGuangzhouChina
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research CenterSouth China Agricultural UniversityGuangzhouChina
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10
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Diguanylate Cyclase (DGC) Implicated in the Synthesis of Multiple Bacteriocins via the Flagellar-Type III Secretion System Produced by Pectobacterium carotovorum subsp. carotovorum. Int J Mol Sci 2022; 23:ijms23105649. [PMID: 35628457 PMCID: PMC9144310 DOI: 10.3390/ijms23105649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 05/09/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022] Open
Abstract
The plant pathogen Pectobacterium carotovorum subsp. carotovorum (previously Erwinia carotovora subsp. carotovora) causes soft rot and stem rot diseases in a variety of crops, including Chinese cabbage, potato, and tomato. The flagellar-type III secretion systems were used by Pcc’s virulence mechanism to export proteins or bacteriocins to the outside of the cell. DGC, a virulence factor that cyclizes c-di-GMP, a common secondary signal in physiological processes and toxin control systems of many bacteria, was discovered in Pcc’s genomic DNA. The dgc gene in Pcc was blocked using the method of homologous recombination in our study. In the in vivo setting, the results demonstrated that the dgc knockout strain does not release low molecular weight bacteriocins. The bacteriocin gene (carocin S2, carocin S3, carocin S4) and the flagellar-type III secretion system genes were also unable to be transcribed by the dgc knockout strain in the transcription experiment. We also observed that the amount of bacteriocin expressed changed when the amount of L-glutamine in the environment exceeded a particular level. These data suggested that L-glutamine influenced physiological processes in Pcc strains in some way. We hypothesized a relationship between dgc and the genes involved in Pcc LMWB external export via the flagellar-type secretion system based on these findings. In this study, the current findings led us to propose a mechanism in which DGC’s cyclic di-GMP might bind to receptor proteins and positively regulate bacteriocin transcription as well as the synthesis, mobility, and transport of toxins.
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11
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Patatin-like phospholipase CapV in Escherichia coli - morphological and physiological effects of one amino acid substitution. NPJ Biofilms Microbiomes 2022; 8:39. [PMID: 35546554 PMCID: PMC9095652 DOI: 10.1038/s41522-022-00294-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 03/22/2022] [Indexed: 11/09/2022] Open
Abstract
In rod-shaped bacteria, morphological plasticity occurs in response to stress, which blocks cell division to promote filamentation. We demonstrate here that overexpression of the patatin-like phospholipase variant CapVQ329R, but not CapV, causes pronounced sulA-independent pyridoxine-inhibited cell filamentation in the Escherichia coli K-12-derivative MG1655 associated with restriction of flagella production and swimming motility. Conserved amino acids in canonical patatin-like phospholipase A motifs, but not the nucleophilic serine, are required to mediate CapVQ329R phenotypes. Furthermore, CapVQ329R production substantially alters the lipidome and colony morphotype including rdar biofilm formation with modulation of the production of the biofilm activator CsgD, and affects additional bacterial traits such as the efficiency of phage infection and antimicrobial susceptibility. Moreover, genetically diverse commensal and pathogenic E. coli strains and Salmonella typhimurium responded with cell filamentation and modulation in colony morphotype formation to CapVQ329R expression. In conclusion, this work identifies the CapV variant CapVQ329R as a pleiotropic regulator, emphasizes a scaffold function for patatin-like phospholipases, and highlights the impact of the substitution of a single conserved amino acid for protein functionality and alteration of host physiology.
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12
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Thormann KM. Dynamic Hybrid Flagellar Motors-Fuel Switch and More. Front Microbiol 2022; 13:863804. [PMID: 35495728 PMCID: PMC9039648 DOI: 10.3389/fmicb.2022.863804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Flagellar motors are intricate rotating nanomachines that are powered by transmembrane ion gradients. The stator complexes are the powerhouses of the flagellar motor: They convert a transmembrane ion gradient, mainly of H+ or Na+, into rotation of the helical flagellar filament. They are thus essential for motor function. The number of stators synchronously engaged in the motor is surprisingly dynamic and depends on the load and the environmental concentration of the corresponding coupling ion. Thus, the rotor-stator interactions determine an important part of the properties of the motor. Numerous bacteria have been identified as possessing more than one set of stators, and some species have been demonstrated to use these different stators in various configurations to modify motor functions by dynamic in-flight swapping. Here, we review knowledge of the properties, the functions, and the evolution of these hybrid motors and discuss questions that remain unsolved.
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Affiliation(s)
- Kai M Thormann
- Fachbereich für Chemie und Biologie, Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
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13
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The Effect of the Second Messenger c-di-GMP on Bacterial Chemotaxis in Escherichia coli. Appl Environ Microbiol 2022; 88:e0037322. [PMID: 35465687 DOI: 10.1128/aem.00373-22] [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: 11/20/2022] Open
Abstract
c-di-GMP is a ubiquitous bacterial second messenger that plays a central regulatory role in diverse biological processes. c-di-GMP was known to regulate chemotaxis in multiple bacterial species, but its effect on Escherichia coli chemotaxis remained unclear. As an effector of c-di-GMP in E. coli, YcgR when bound with c-di-GMP interacts with the flagellar motor to reduce its speed and its probability of rotating clockwise (CW bias). Here, we found that a significant fraction of the c-di-GMP::YcgR dynamically exchange between the motor and the cytosol. Through fluorescent measurements, we found that there was no competitive binding between the chemotaxis response regulator CheY-P and c-di-GMP::YcgR to the motor. To test the influence of elevated c-di-GMP levels on the chemotaxis pathway, we measured the chemotactic responses of E. coli cells using a FRET assay, finding that elevated c-di-GMP levels had no effect on the upstream part of chemotaxis pathway down to the level of CheY-P concentration. This suggested that the possible effect of elevated c-di-GMP levels on chemotactic motion was through regulation of motor speed and CW bias. Using stochastic simulations of chemotactic swimming, we showed that the effects of reducing motor speed and decreasing CW bias on chemotactic drift velocity are compensating for each other, resulting in minimal effect of elevated c-di-GMP levels on E. coli chemotaxis. Therefore, elevated c-di-GMP levels promote the transition from motile to sedentary forms of bacterial life by reducing the bacterial swimming speed and CW bias, while still maintaining a nearly intact chemotaxis capability in E. coli. IMPORTANCE The ubiquitous bacterial second messenger c-di-GMP was known to regulate chemotaxis in many bacterial species, but its effect on E. coli chemotaxis was unclear. Here we studied the effect of elevated c-di-GMP levels on chemotaxis in E. coli. We found that the binding of c-di-GMP::YcgR (its effector) and the chemotaxis response regulator CheY-P to the flagellar motor are noncompetitive, and elevated c-di-GMP levels do not affect the upstream part of the chemotaxis pathway down to the level of CheY-P concentration. Elevated c-di-GMP levels exert direct effects on the flagellar motor by reducing its speed and CW bias, but the resulting effects on chemotaxis performance are compensating for each other. Our findings here showed that elevated c-di-GMP levels maintain a nearly intact chemotaxis capability when promoting the transition from motile to sedentary forms of bacterial life in E. coli.
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14
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Keegstra JM, Carrara F, Stocker R. The ecological roles of bacterial chemotaxis. Nat Rev Microbiol 2022; 20:491-504. [PMID: 35292761 DOI: 10.1038/s41579-022-00709-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
How bacterial chemotaxis is performed is much better understood than why. Traditionally, chemotaxis has been understood as a foraging strategy by which bacteria enhance their uptake of nutrients and energy, yet it has remained puzzling why certain less nutritious compounds are strong chemoattractants and vice versa. Recently, we have gained increased understanding of alternative ecological roles of chemotaxis, such as navigational guidance in colony expansion, localization of hosts or symbiotic partners and contribution to microbial diversity by the generation of spatial segregation in bacterial communities. Although bacterial chemotaxis has been observed in a wide range of environmental settings, insights into the phenomenon are mostly based on laboratory studies of model organisms. In this Review, we highlight how observing individual and collective migratory behaviour of bacteria in different settings informs the quantification of trade-offs, including between chemotaxis and growth. We argue that systematically mapping when and where bacteria are motile, in particular by transgenerational bacterial tracking in dynamic environments and in situ approaches from guts to oceans, will open the door to understanding the rich interplay between metabolism and growth and the contribution of chemotaxis to microbial life.
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Affiliation(s)
| | - Francesco Carrara
- Institute for Environmental Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Institute for Environmental Engineering, ETH Zurich, Zurich, Switzerland.
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15
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Lee CK, Schmidt WC, Webster SS, Chen JW, O'Toole GA, Wong GCL. Broadcasting of amplitude- and frequency-modulated c-di-GMP signals facilitates cooperative surface commitment in bacterial lineages. Proc Natl Acad Sci U S A 2022; 119:e2112226119. [PMID: 35064082 PMCID: PMC8795499 DOI: 10.1073/pnas.2112226119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/22/2021] [Indexed: 12/24/2022] Open
Abstract
Work on surface sensing in bacterial biofilms has focused on how cells transduce sensory input into cyclic diguanylate (c-di-GMP) signaling, low and high levels of which generally correlate with high-motility planktonic cells and low-motility biofilm cells, respectively. Using Granger causal inference methods, however, we find that single-cell c-di-GMP increases are not sufficient to imply surface commitment. Tracking entire lineages of cells from the progenitor cell onward reveals that c-di-GMP levels can exhibit increases but also undergo oscillations that can propagate across 10 to 20 generations, thereby encoding more complex instructions for community behavior. Principal component and factor analysis of lineage c-di-GMP data shows that surface commitment behavior correlates with three statistically independent composite features, which roughly correspond to mean c-di-GMP levels, c-di-GMP oscillation period, and surface motility. Surface commitment in young biofilms does not correlate to c-di-GMP increases alone but also to the emergence of high-frequency and small-amplitude modulation of elevated c-di-GMP signal along a lineage of cells. Using this framework, we dissect how increasing or decreasing signal transduction from wild-type levels, by varying the interaction strength between PilO, a component of a principal surface sensing appendage system, and SadC, a key hub diguanylate cyclase that synthesizes c-di-GMP, impacts frequency and amplitude modulation of c-di-GMP signals and cooperative surface commitment.
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Affiliation(s)
- Calvin K Lee
- Department of Bioengineering, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - William C Schmidt
- Department of Bioengineering, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - Shanice S Webster
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Jonathan W Chen
- Department of Bioengineering, University of California, Los Angeles, CA 90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
| | - George A O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH 03755
| | - Gerard C L Wong
- Department of Bioengineering, University of California, Los Angeles, CA 90095;
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095
- California NanoSystems Institute, University of California, Los Angeles, CA 90095
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16
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Homma M, Kojima S. Roles of the second messenger c‐di‐GMP in bacteria: Focusing on the topics of flagellar regulation and
Vibrio
spp. Genes Cells 2022; 27:157-172. [PMID: 35073606 PMCID: PMC9303241 DOI: 10.1111/gtc.12921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/28/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022]
Abstract
Typical second messengers include cyclic AMP (cAMP), cyclic GMP (cGMP), and inositol phosphate. In bacteria, cyclic diguanylate (c‐di‐GMP), which is not used in animals, is widely used as a second messenger for environmental responses. Initially found as a regulator of cellulose synthesis, this small molecule is known to be widely present in bacteria. A wide variety of synthesis and degradation enzymes for c‐di‐GMP exist, and the activities of effector proteins are regulated by changing the cellular c‐di‐GMP concentration in response to the environment. It has been shown well that c‐di‐GMP plays an essential role in pathogenic cycle and is involved in flagellar motility in Vibrio cholerae. In this review, we aim to explain the direct or indirect regulatory mechanisms of c‐di‐GMP in bacteria, focusing on the study of c‐di‐GMP in Vibrio spp. and in flagella, which are our research subjects.
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Affiliation(s)
- Michio Homma
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
| | - Seiji Kojima
- Division of Biological Science Graduate School of Science Nagoya University Nagoya Japan
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17
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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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18
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Holden ER, Yasir M, Turner AK, Wain J, Charles IG, Webber MA. Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli. Microb Genom 2021; 7. [PMID: 34783647 PMCID: PMC8743551 DOI: 10.1099/mgen.0.000673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Biofilms complete a life cycle where cells aggregate, grow and produce a structured community before dispersing to colonize new environments. Progression through this life cycle requires temporally controlled gene expression to maximize fitness at each stage. Previous studies have largely focused on identifying genes essential for the formation of a mature biofilm; here, we present an insight into the genes involved at different stages of biofilm formation. We used TraDIS-Xpress, a massively parallel transposon mutagenesis approach using transposon-located promoters to assay the impact of disruption or altered expression of all genes in the genome on biofilm formation. We identified 48 genes that affected the fitness of cells growing in a biofilm, including genes with known roles and those not previously implicated in biofilm formation. Regulation of type 1 fimbriae and motility were important at all time points, adhesion and motility were important for the early biofilm, whereas matrix production and purine biosynthesis were only important as the biofilm matured. We found strong temporal contributions to biofilm fitness for some genes, including some where expression changed between being beneficial or detrimental depending on the stage at which they are expressed, including dksA and dsbA. Novel genes implicated in biofilm formation included zapE and truA involved in cell division, maoP in chromosome organization, and yigZ and ykgJ of unknown function. This work provides new insights into the requirements for successful biofilm formation through the biofilm life cycle and demonstrates the importance of understanding expression and fitness through time.
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Affiliation(s)
- Emma R Holden
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - Muhammad Yasir
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - A Keith Turner
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK
| | - John Wain
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
| | - Mark A Webber
- Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk NR4 7UQ, UK.,Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, UK
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19
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Diguanylate cyclase and phosphodiesterase interact to maintain the specificity of c-di-GMP signaling in the regulation of antibiotic synthesis in Lysobacter enzymogenes. Appl Environ Microbiol 2021; 88:e0189521. [PMID: 34757823 DOI: 10.1128/aem.01895-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cyclic dimeric GMP (c-di-GMP) is a universal second messenger in bacteria. The large number of c-di-GMP-related diguanylate cyclases (DGCs), phosphodiesterases (PDEs) and effectors are responsible for the complexity and dynamics of c-di-GMP signaling. Some of these components deploy various methods to avoid undesired crosstalk to maintain signaling specificity. Synthesis of the antibiotic HSAF (Heat Stable Antifungal Factor) in Lysobacter enzymogenes is regulated by a specific c-di-GMP signaling pathway that includes a PDE LchP and a c-di-GMP effector Clp (also a transcriptional regulator). In the present study, from among 19 DGCs, we identified a diguanylate cyclase, LchD, which participates in this pathway. Subsequent investigation indicates that LchD and LchP physically interact and that the catalytic center of LchD is required for both the formation of the LchD-LchP complex and HSAF production. All the detected phenotypes support that LchD and LchP dispaly local c-di-GMP signaling to regulate HSAF biosynthesis. Although direct evidence is lacking, our investigation, which shows that the interaction between a DGC and a PDE maintains the specificity of c-di-GMP signaling, suggests the possibility of the existence of local c-di-GMP pools in bacteria. Importance Cyclic dimeric GMP (c-di-GMP) is a universal second messenger in bacteria. Signaling of c-di-GMP is complex and dynamic, and it is mediated by a large number of components, including c-di-GMP synthases (diguanylate cyclases. DGCs), c-di-GMP degrading enzymes (phosphodiesterases, PDEs), and c-di-GMP effectors. These components deploy various methods to avoid undesired crosstalk to maintain signaling specificity. In the present study, we identified a DGC that interacted with a PDE to specifically regulate antibiotic biosynthesis in L. enzymogenes. We provide direct evidence to show that the DGC and PDE form a complex, and also indirect evidence to argue that they may balance a local c-di-GMP pool to control the antibiotic production. The results represent an important finding regarding the mechanism of a pair of DGC and PDE to control the expression of specific c-di-GMP signaling pathways.
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20
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Abstract
Cyclic diguanylate (c-di-GMP) signal transduction systems provide bacteria with the ability to sense changing cell status or environmental conditions and then execute suitable physiological and social behaviors in response. In this review, we provide a comprehensive census of the stimuli and receptors that are linked to the modulation of intracellular c-di-GMP. Emerging evidence indicates that c-di-GMP networks sense light, surfaces, energy, redox potential, respiratory electron acceptors, temperature, and structurally diverse biotic and abiotic chemicals. Bioinformatic analysis of sensory domains in diguanylate cyclases and c-di-GMP-specific phosphodiesterases as well as the receptor complexes associated with them reveals that these functions are linked to a diverse repertoire of protein domain families. We describe the principles of stimulus perception learned from studying these modular sensory devices, illustrate how they are assembled in varied combinations with output domains, and summarize a system for classifying these sensor proteins based on their complexity. Biological information processing via c-di-GMP signal transduction not only is fundamental to bacterial survival in dynamic environments but also is being used to engineer gene expression circuitry and synthetic proteins with à la carte biochemical functionalities.
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21
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Wei C, Wang S, Liu P, Cheng ST, Qian G, Wang S, Fu Y, Qian W, Sun W. The PdeK-PdeR two-component system promotes unipolar localization of FimX and pilus extension in Xanthomonas oryzae pv. oryzicola. Sci Signal 2021; 14:eabi9589. [PMID: 34520229 DOI: 10.1126/scisignal.abi9589] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Chao Wei
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, and Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Shanzhi Wang
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, and Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China
| | - Pengwei Liu
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, Jilin, China
| | - Shou-Ting Cheng
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Guoliang Qian
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, Jiangsu, China
| | - Shuwei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ying Fu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wei Qian
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenxian Sun
- Department of Plant Pathology and MOA Key Laboratory of Pest Monitoring and Green Management, and Joint International Research Laboratory of Crop Molecular Breeding, Ministry of Education, China Agricultural University, Beijing 100193, China.,College of Plant Protection, Jilin Agricultural University, Changchun 130118, Jilin, China
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22
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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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23
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Abstract
Bacteria thrive both in liquids and attached to surfaces. The concentration of bacteria on surfaces is generally much higher than in the surrounding environment, offering bacteria ample opportunity for mutualistic, symbiotic, and pathogenic interactions. To efficiently populate surfaces, they have evolved mechanisms to sense mechanical or chemical cues upon contact with solid substrata. This is of particular importance for pathogens that interact with host tissue surfaces. In this review we discuss how bacteria are able to sense surfaces and how they use this information to adapt their physiology and behavior to this new environment. We first survey mechanosensing and chemosensing mechanisms and outline how specific macromolecular structures can inform bacteria about surfaces. We then discuss how mechanical cues are converted to biochemical signals to activate specific cellular processes in a defined chronological order and describe the role of two key second messengers, c-di-GMP and cAMP, in this process.
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Affiliation(s)
| | - Urs Jenal
- Biozentrum, University of Basel, CH-4056 Basel, Switzerland; ,
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24
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Özdemir C, Akçelik N, Neslihan Özdemir F, Evcili İ, Kahraman T, Gürsel İ, Akçelik M. The role of bcsE gene in the pathogenicity of Salmonella. Pathog Dis 2021; 79:6323998. [PMID: 34279609 DOI: 10.1093/femspd/ftab037] [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: 04/26/2021] [Accepted: 07/14/2021] [Indexed: 11/12/2022] Open
Abstract
The effects of the bcsE gene and BcsE protein on bacterial physiology and pathogenicity in SalmonellaTyphimurium and Salmonella Group C1 were investigated. It was observed that biofilm and pellicle formation did not occur in the bcsE gene mutants of wild-type strains. Besides, the 'rdar' (red, dry, rough) biofilm morphotype in wild-type strains changed significantly in the mutants. In terms of the bcsE gene, the swimming and swarming motility in mutant strains showed a dramatic increase compared to the wild-type strains. The Salmonella bcsE gene was cloned into Escherichia coli BL21, and the his-tagged protein produced in this strain was purified to obtain polyclonal antibodies in BALB/c mice. The antibodies were showed labeled antigen specificity to the BscE protein. As a result of immunization and systemic persistence tests carried out with BALB/c mice, BscE protein was determined to trigger high levels of humoral and cellular responses (Th1 cytokine production, IgG2a/IgG1 > 1). Systemic persistence in the liver and spleen samples decreased by 99.99% and 100% in the bcsE mutant strains. Finally, invasion abilities on HT-29 epithelial cells of wild-type strains were utterly disappeared in their bcsE gene mutant strains.
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Affiliation(s)
- Caner Özdemir
- UNAM - National Nanotechnology Research Center, Bilkent University, 06800, Ankara, Turkey
| | - Nefise Akçelik
- Biotechnology Institute, Ankara University, Ankara, Turkey
| | | | - İrem Evcili
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Tamer Kahraman
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - İhsan Gürsel
- Department of Molecular Biology and Genetics, Bilkent University, Ankara, Turkey
| | - Mustafa Akçelik
- Department of Biology, Ankara University, 06100, Ankara, Turkey
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25
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Krol E, Schäper S, Becker A. Cyclic di-GMP signaling controlling the free-living lifestyle of alpha-proteobacterial rhizobia. Biol Chem 2021; 401:1335-1348. [PMID: 32990642 DOI: 10.1515/hsz-2020-0232] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 09/14/2020] [Indexed: 12/12/2022]
Abstract
Cyclic-di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger which has been associated with a motile to sessile lifestyle switch in many bacteria. Here, we review recent insights into c-di-GMP regulated processes related to environmental adaptations in alphaproteobacterial rhizobia, which are diazotrophic bacteria capable of fixing nitrogen in symbiosis with their leguminous host plants. The review centers on Sinorhizobium meliloti, which in the recent years was intensively studied for its c-di-GMP regulatory network.
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Affiliation(s)
- Elizaveta Krol
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Simon Schäper
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, D-35032 Marburg, Germany.,Department of Biology, Philipps-Universität Marburg, D-35032 Marburg, Germany
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26
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Three PilZ Domain Proteins, PlpA, PixA, and PixB, Have Distinct Functions in Regulation of Motility and Development in Myxococcus xanthus. J Bacteriol 2021; 203:e0012621. [PMID: 33875546 PMCID: PMC8316039 DOI: 10.1128/jb.00126-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
In bacteria, the nucleotide-based second messenger bis-(3'-5')-cyclic dimeric GMP (c-di-GMP) binds to effectors to generate outputs in response to changes in the environment. In Myxococcus xanthus, c-di-GMP regulates type IV pilus-dependent motility and the starvation-induced developmental program that results in formation of spore-filled fruiting bodies; however, little is known about the effectors that bind c-di-GMP. Here, we systematically inactivated all 24 genes encoding PilZ domain-containing proteins, which are among the most common c-di-GMP effectors. We confirm that the stand-alone PilZ domain protein PlpA is important for regulation of motility independently of the Frz chemosensory system and that Pkn1, which is composed of a Ser/Thr kinase domain and a PilZ domain, is specifically important for development. Moreover, we identify two PilZ domain proteins that have distinct functions in regulating motility and development. PixB, which is composed of two PilZ domains and an acetyltransferase domain, binds c-di-GMP in vitro and regulates type IV pilus-dependent and gliding motility in a Frz-dependent manner as well as development. The acetyltransferase domain is required and sufficient for function during growth, while all three domains and c-di-GMP binding are essential for PixB function during development. PixA is a response regulator composed of a PilZ domain and a receiver domain, binds c-di-GMP in vitro, and regulates motility independently of the Frz system, likely by setting up the polarity of the two motility systems. Our results support a model whereby PlpA, PixA, and PixB act in independent pathways and have distinct functions in regulation of motility. IMPORTANCE c-di-GMP signaling controls bacterial motility in many bacterial species by binding to downstream effector proteins. Here, we identify two PilZ domain-containing proteins in Myxococcus xanthus that bind c-di-GMP. We show that PixB, which contains two PilZ domains and an acetyltransferase domain, acts in a manner that depends on the Frz chemosensory system to regulate motility via the acetyltransferase domain, while the intact protein and c-di-GMP binding are essential for PixB to support development. In contrast, PixA acts in a Frz-independent manner to regulate motility. Taking our results together with previous observations, we conclude that PilZ domain proteins and c-di-GMP act in multiple independent pathways to regulate motility and development in M. xanthus.
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A Trigger Phosphodiesterase Modulates the Global c-di-GMP Pool, Motility, and Biofilm Formation in Vibrio parahaemolyticus. J Bacteriol 2021; 203:e0004621. [PMID: 33846117 DOI: 10.1128/jb.00046-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Vibrio parahaemolyticus cells transit from free-swimming to surface adapted lifestyles, such as swarming colonies and three-dimensional biofilms. These transitions are regulated by sensory modules and regulatory networks that involve the second messenger cyclic diguanylate monophosphate (c-di-GMP). In this work, we show that a previously uncharacterized c-di-GMP phosphodiesterase (VP1881) from V. parahaemolyticus plays an important role in modulating the c-di-GMP pool. We found that the product of VP1881 promotes its own expression when the levels of c-di-GMP are low or when the phosphodiesterase (PDE) is catalytically inactive. This behavior has been observed in a class of c-di-GMP receptors called trigger phosphodiesterases, and hence we named the product of VP1881 TpdA, for trigger phosphodiesterase A. The absence of tpdA showed a negative effect on swimming motility while, its overexpression from an isopropyl-β-d-thiogalactopyranoside (IPTG)-inducible promoter showed a positive effect on both swimming and swarming motility and a negative effect on biofilm formation. Changes in TpdA abundance altered the expression of representative polar and lateral flagellar genes, as well as that of the biofilm-related gene cpsA. Our results also revealed that autoactivation of the native PtpdA promoter is sufficient to alter c-di-GMP signaling responses such as swarming and biofilm formation in V. parahaemolyticus, an observation that could have important implications in the dynamics of these social behaviors. IMPORTANCE c-di-GMP trigger phosphodiesterases (PDEs) could play a key role in controlling the heterogeneity of biofilm matrix composition, a property that endows characteristics that are potentially relevant for sustaining integrity and functionality of biofilms in a variety of natural environments. Trigger PDEs are not always easy to identify based on their sequence, and hence not many examples of these type of signaling proteins have been reported in the literature. Here, we report on the identification of a novel trigger PDE in V. parahaemolyticus and provide evidence suggesting that its autoactivation could play an important role in the progression of swarming motility and biofilm formation, multicellular behaviors that are important for the survival and dissemination of this environmental pathogen.
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Pecina A, Schwan M, Blagotinsek V, Rick T, Klüber P, Leonhard T, Bange G, Thormann KM. The Stand-Alone PilZ-Domain Protein MotL Specifically Regulates the Activity of the Secondary Lateral Flagellar System in Shewanella putrefaciens. Front Microbiol 2021; 12:668892. [PMID: 34140945 PMCID: PMC8203827 DOI: 10.3389/fmicb.2021.668892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
A number of bacterial species control the function of the flagellar motor in response to the levels of the secondary messenger c-di-GMP, which is often mediated by c-di-GMP-binding proteins that act as molecular brakes or clutches to slow the motor rotation. The gammaproteobacterium Shewanella putrefaciens possesses two distinct flagellar systems, the primary single polar flagellum and a secondary system with one to five lateral flagellar filaments. Here, we identified a protein, MotL, which specifically regulates the activity of the lateral, but not the polar, flagellar motors in response to the c-di-GMP levels. MotL only consists of a single PilZ domain binding c-di-GMP, which is crucial for its function. Deletion and overproduction analyses revealed that MotL slows down the lateral flagella at elevated levels of c-di-GMP, and may speed up the lateral flagellar-mediated movement at low c-di-GMP concentrations. In vitro interaction studies hint at an interaction of MotL with the C-ring of the lateral flagellar motors. This study shows a differential c-di-GMP-dependent regulation of the two flagellar systems in a single species, and implicates that PilZ domain-only proteins can also act as molecular regulators to control the flagella-mediated motility in bacteria.
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Affiliation(s)
- Anna Pecina
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Vitan Blagotinsek
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Tim Rick
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Patrick Klüber
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
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Biquet-Bisquert A, Labesse G, Pedaci F, Nord AL. The Dynamic Ion Motive Force Powering the Bacterial Flagellar Motor. Front Microbiol 2021; 12:659464. [PMID: 33927708 PMCID: PMC8076557 DOI: 10.3389/fmicb.2021.659464] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/02/2021] [Indexed: 11/13/2022] Open
Abstract
The bacterial flagellar motor (BFM) is a rotary molecular motor embedded in the cell membrane of numerous bacteria. It turns a flagellum which acts as a propeller, enabling bacterial motility and chemotaxis. The BFM is rotated by stator units, inner membrane protein complexes that stochastically associate to and dissociate from individual motors at a rate which depends on the mechanical and electrochemical environment. Stator units consume the ion motive force (IMF), the electrochemical gradient across the inner membrane that results from cellular respiration, converting the electrochemical energy of translocated ions into mechanical energy, imparted to the rotor. Here, we review some of the main results that form the base of our current understanding of the relationship between the IMF and the functioning of the flagellar motor. We examine a series of studies that establish a linear proportionality between IMF and motor speed, and we discuss more recent evidence that the stator units sense the IMF, altering their rates of dynamic assembly. This, in turn, raises the question of to what degree the classical dependence of motor speed on IMF is due to stator dynamics vs. the rate of ion flow through the stators. Finally, while long assumed to be static and homogeneous, there is mounting evidence that the IMF is dynamic, and that its fluctuations control important phenomena such as cell-to-cell signaling and mechanotransduction. Within the growing toolbox of single cell bacterial electrophysiology, one of the best tools to probe IMF fluctuations may, ironically, be the motor that consumes it. Perfecting our incomplete understanding of how the BFM employs the energy of ion flow will help decipher the dynamical behavior of the bacterial IMF.
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Affiliation(s)
- Anaïs Biquet-Bisquert
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Gilles Labesse
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Francesco Pedaci
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
| | - Ashley L Nord
- Centre de Biologie Structurale (CBS), INSERM, CNRS, Université Montpellier, Montpellier, France
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Hershey DM. Integrated control of surface adaptation by the bacterial flagellum. Curr Opin Microbiol 2021; 61:1-7. [PMID: 33640633 DOI: 10.1016/j.mib.2021.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/10/2021] [Accepted: 02/14/2021] [Indexed: 02/05/2023]
Abstract
Many bacteria can alternate between motile and sessile lifestyles, and wide-ranging sets of environmental stimuli regulate the transition from a free-swimming to a surface-attached state. A transenvelope machine called the flagellum, known primarily for its role in promoting cellular motility, stimulates the motile-sessile transition by detecting contact with solid substrates. Recent work has revealed a striking level of sophistication within the regulatory circuits that link flagellar function to surface colonization. I describe the current paradigm whereby the flagellum promotes the sessile state by increasing production of the second-messenger bis-(3'-5')-cyclic diguanosine monophosphate (c-di-GMP). I then highlight studies that have identified multiple routes by which the flagellum activates c-di-GMP production, calling the concept of a linear surface recognition pathway into the question. I conclude by proposing a role for the flagellum as a signaling hub that integrates environmental stimuli to coordinate a surface colonization program that occurs across a range of spatial and temporal scales.
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Affiliation(s)
- David M Hershey
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
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31
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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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32
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Morimoto YV, Minamino T. Architecture and Assembly of the Bacterial Flagellar Motor Complex. Subcell Biochem 2021; 96:297-321. [PMID: 33252734 DOI: 10.1007/978-3-030-58971-4_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
One of the central systems responsible for bacterial motility is the flagellum. The bacterial flagellum is a macromolecular protein complex that is more than five times the cell length. Flagella-driven motility is coordinated via a chemosensory signal transduction pathway, and so bacterial cells sense changes in the environment and migrate towards more desirable locations. The flagellum of Salmonella enterica serovar Typhimurium is composed of a bi-directional rotary motor, a universal joint and a helical propeller. The flagellar motor, which structurally resembles an artificial motor, is embedded within the cell envelop and spins at several hundred revolutions per second. In contrast to an artificial motor, the energy utilized for high-speed flagellar motor rotation is the inward-directed proton flow through a transmembrane proton channel of the stator unit of the flagellar motor. The flagellar motor realizes efficient chemotaxis while performing high-speed movement by an ingenious directional switching mechanism of the motor rotation. To build the universal joint and helical propeller structures outside the cell body, the flagellar motor contains its own protein transporter called a type III protein export apparatus. In this chapter we summarize the structure and assembly of the Salmonella flagellar motor complex.
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Affiliation(s)
- Yusuke V Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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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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Yuan X, Yu M, Yang CH. Innovation and Application of the Type III Secretion System Inhibitors in Plant Pathogenic Bacteria. Microorganisms 2020; 8:microorganisms8121956. [PMID: 33317075 PMCID: PMC7764658 DOI: 10.3390/microorganisms8121956] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 12/05/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Many Gram-negative pathogenic bacteria rely on a functional type III secretion system (T3SS), which injects multiple effector proteins into eukaryotic host cells, for their pathogenicity. Genetic studies conducted in different host-microbe pathosystems often revealed a sophisticated regulatory mechanism of their T3SSs, suggesting that the expression of T3SS is tightly controlled and constantly monitored by bacteria in response to the ever-changing host environment. Therefore, it is critical to understand the regulation of T3SS in pathogenic bacteria for successful disease management. This review focuses on a model plant pathogen, Dickeyadadantii, and summarizes the current knowledge of its T3SS regulation. We highlight the roles of several T3SS regulators that were recently discovered, including the transcriptional regulators: FlhDC, RpoS, and SlyA; the post-transcriptional regulators: PNPase, Hfq with its dependent sRNA ArcZ, and the RsmA/B system; and the bacterial second messenger cyclic-di-GMP (c-di-GMP). Homologs of these regulatory components have also been characterized in almost all major bacterial plant pathogens like Erwiniaamylovora, Pseudomonassyringae, Pectobacterium spp., Xanthomonas spp., and Ralstonia spp. The second half of this review shifts focus to an in-depth discussion of the innovation and development of T3SS inhibitors, small molecules that inhibit T3SSs, in the field of plant pathology. This includes T3SS inhibitors that are derived from plant phenolic compounds, plant coumarins, and salicylidene acylhydrazides. We also discuss their modes of action in bacteria and application for controlling plant diseases.
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Affiliation(s)
- Xiaochen Yuan
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA;
| | - Manda Yu
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
- Correspondence: (M.Y.); (C.-H.Y.)
| | - Ching-Hong Yang
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
- Correspondence: (M.Y.); (C.-H.Y.)
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Abstract
Dickeya zeae is the etiological agent of bacterial foot rot disease, which can cause massive economic losses in banana and rice plantations. Genome sequence analysis showed that D. zeae strain EC1 contains multiple c-di-GMP turnover genes, but their roles and regulatory mechanisms in bacterial physiology and virulence remain vague. By generating consecutive in-frame deletion mutants of the genes encoding c-di-GMP biosynthesis and degradation, respectively, we analyzed the individual and collective impacts of these c-di-GMP metabolic genes on the c-di-GMP global pool, bacterial physiology, and virulence. The significance of our study is in identifying the mechanism of c-di-GMP signaling in strain EC1 more clearly, which expands the c-di-GMP regulating patterns in Gram-negative species. The methods and experimental designs in this research will provide a valuable reference for the exploration of the complex c-di-GMP regulation mechanisms in other bacteria. Dickeya zeae is an important and aggressive bacterial phytopathogen that can cause substantial economic losses in banana and rice plantations. We previously showed that c-di-GMP signaling proteins (cyclases/phosphodiesterases) in D. zeae strain EC1 play a significant role in the bacterial sessile-to-motile transition. To determine whether there is any synergistic effect among these c-di-GMP signaling proteins, we prepared a series of mutant strains by generating consecutive in-frame deletions of the genes encoding diguanylate cyclases (which make c-di-GMP) and phosphodiesterases (which break down c-di-GMP), respectively, using EC1 as a parental strain. The results showed that the complete deletion of all the putative diguanylate cyclases resulted in significantly increased bacterial motility and abrogated biofilm formation but did not appear to affect pathogenicity and virulence factor production. In contrast, the deletion of all the c-di-GMP phosphodiesterase genes disabled motility and prevented the invasion of EC1 into rice seeds. By measuring the c-di-GMP concentrations and swimming motility of all the mutants, we propose that c-di-GMP controlled swimming behavior through a multitiered program in a c-di-GMP concentration-dependent manner, which could be described as an L-shaped regression curve. These features are quite different from those that have been shown for other bacterial species such as Salmonella and Caulobacter crescentus. Further analysis identified three c-di-GMP signaling proteins, i.e., PDE10355, DGC14945, and PDE14950, that play dominant roles in influencing the global c-di-GMP pool of strain EC1. The findings from this study highlight the complexity and plasticity of c-di-GMP regulatory circuits in different bacterial species.
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Genetic Determinants of Salmonella Resistance to the Biofilm-Inhibitory Effects of a Synthetic 4-Oxazolidinone Analog. Appl Environ Microbiol 2020; 86:AEM.01120-20. [PMID: 32769186 DOI: 10.1128/aem.01120-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Biofilms formed by Salmonella enterica are a frequent source of food supply contamination. Since biofilms are inherently resistant to disinfection, new agents capable of preventing biofilm formation are needed. Synthetic analogs of 4-oxazolidinone containing natural products have shown promise as antibiofilm compounds against Gram-positive bacteria. The purpose of our study was 2-fold: to establish the antibiofilm effects and mechanism of action of a synthetic 4-oxazolidinone analog (JJM-ox-3-70) and to establish mechanisms of resistance to this compound in Salmonella enterica serovar Typhimurium (S Typhimurium). JJM-ox-3-70 inhibited biofilm formation but had no effect on cell growth. The antibiofilm effects were linked to disruption of curli fimbriae and flagellar gene expression and alteration in swimming motility, suggesting an effect on multiple cellular processes. Using a 2-step screening approach of defined multigene and single-gene deletion mutant libraries, we identified 3 mutants that produced less biofilm in the presence of JJM-ox-3-70 than the isogenic WT, with phenotypes reversed by complementation in trans Genes responsible for S Typhimurium resistance to the compound included acrB, a component of the major drug efflux pump AcrAB-TolC, and two genes of unknown function (STM0437 and STM1292). The results of this study suggest that JJM-ox-3-70 inhibits biofilm formation by indirect inhibition of extracellular matrix production that may be linked to disruption of flagellar motility. Further work is needed to establish the role of the newly characterized genes as potential mechanisms of biofilm intrinsic antimicrobial resistance.IMPORTANCE Biofilms are resistant to killing by disinfectants and antimicrobials. S. enterica biofilms facilitate long-term host colonization and persistence in food processing environments. Synthetic analogs of 4-oxazolidinone natural products show promise as antibiofilm agents. Here, we show that a synthetic 4-oxazolidinone analog inhibits Salmonella biofilm through effects on both motility and biofilm matrix gene expression. Furthermore, we identify three genes that promote Salmonella resistance to the antibiofilm effects of the compound. This work provides insight into the mechanism of antibiofilm effects of a synthetic 4-oxazolidinone analog in Gram-negative bacteria and demonstrates new mechanisms of intrinsic antimicrobial resistance in Salmonella biofilms.
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37
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Sathyamoorthy R, Kushmaro Y, Rotem O, Matan O, Kadouri DE, Huppert A, Jurkevitch E. To hunt or to rest: prey depletion induces a novel starvation survival strategy in bacterial predators. ISME JOURNAL 2020; 15:109-123. [PMID: 32884113 DOI: 10.1038/s41396-020-00764-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/12/2020] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
The small size of bacterial cells necessitates rapid adaption to sudden environmental changes. In Bdellovibrio bacteriovorus, an obligate predator of bacteria common in oligotrophic environments, the non-replicative, highly motile attack phase (AP) cell must invade a prey to ensure replication. AP cells swim fast and respire at high rates, rapidly consuming their own contents. How the predator survives in the absence of prey is unknown. We show that starvation for prey significantly alters swimming patterns and causes exponential decay in prey-searching cells over hours, until population-wide swim-arrest. Swim-arrest is accompanied by changes in energy metabolism, enabling rapid swim-reactivation upon introduction of prey or nutrients, and a sweeping change in gene expression and gene regulation that largely differs from those of the paradigmatic stationary phase. Swim-arrest is costly as it imposes a fitness penalty in the form of delayed growth. We track the control of the swim arrest-reactivation process to cyclic-di-GMP (CdG) effectors, including two motility brakes. CRISPRi transcriptional inactivation, and in situ localization of the brakes to the cell pole, demonstrated their essential role for effective survival under prey-induced starvation. Thus, obligate predators evolved a unique CdG-controlled survival strategy, enabling them to sustain their uncommon lifestyle under fluctuating prey supply.
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Affiliation(s)
- Rajesh Sathyamoorthy
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Yuval Kushmaro
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Or Rotem
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.,Seed-x., Magshimim, Israel
| | - Ofra Matan
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Daniel E Kadouri
- Department of Oral Biology, Rutgers School of Dental Medicine, Newark, NJ, USA
| | - Amit Huppert
- Bio-statistical Unit, The Gertner Institute for Epidemiology and Health Policy Research, Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Edouard Jurkevitch
- Department of Plant Pathology and Microbiology, Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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Khan F, Tabassum N, Pham DTN, Oloketuyi SF, Kim YM. Molecules involved in motility regulation in Escherichia coli cells: a review. BIOFOULING 2020; 36:889-908. [PMID: 33028083 DOI: 10.1080/08927014.2020.1826939] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
The initial colonization of the host organism by commensal, probiotic, and pathogenic Escherichia coli strains is an important step in the development of infections and biofilms. Sensing and colonization of host cell surfaces are governed by flagellar and fimbriae/pili appendages, respectively. Biofilm formation confers great advantages on pathogenic E. coli cells such as protection against the host immune system, antimicrobial agents, and several environmental stress factors. The transition from planktonic to sessile physiological states involves several signaling cascades and factors responsible for the regulation of flagellar motility in E. coli cells. These regulatory factors have thus become important targets to control pathogenicity. Hence, attenuation of flagellar motility is considered a potential therapy against pathogenic E. coli. The present review describes signaling pathways and proteins involved in direct or indirect regulation of flagellar motility. Furthermore, application strategies for antimotility natural or synthetic compounds are discussed also.
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Affiliation(s)
- Fazlurrahman Khan
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
| | - Nazia Tabassum
- Industrial Convergence Bionix Engineering, Pukyong National University, Busan, Republic of Korea
| | - Dung Thuy Nguyen Pham
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
| | | | - Young-Mog Kim
- Institute of Food Science, Pukyong National University, Busan, Republic of Korea
- Department of Food Science and Technology, Pukyong National University, Busan, Republic of Korea
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Richter AM, Possling A, Malysheva N, Yousef KP, Herbst S, von Kleist M, Hengge R. Local c-di-GMP Signaling in the Control of Synthesis of the E. coli Biofilm Exopolysaccharide pEtN-Cellulose. J Mol Biol 2020; 432:4576-4595. [PMID: 32534064 PMCID: PMC7397504 DOI: 10.1016/j.jmb.2020.06.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 05/20/2020] [Accepted: 06/08/2020] [Indexed: 12/17/2022]
Abstract
In many bacteria, the biofilm-promoting second messenger c-di-GMP is produced and degraded by multiple diguanylate cyclases (DGC) and phosphodiesterases (PDE), respectively. High target specificity of some of these enzymes has led to theoretical concepts of "local" c-di-GMP signaling. In Escherichia coli K-12, which has 12 DGCs and 13 PDEs, a single DGC, DgcC, is specifically required for the biosynthesis of the biofilm exopolysaccharide pEtN-cellulose without affecting the cellular c-di-GMP pool, but the mechanistic basis of this target specificity has remained obscure. DGC activity of membrane-associated DgcC, which is demonstrated in vitro in nanodiscs, is shown to be necessary and sufficient to specifically activate cellulose biosynthesis in vivo. DgcC and a particular PDE, PdeK (encoded right next to the cellulose operon), directly interact with cellulose synthase subunit BcsB and with each other, thus establishing physical proximity between cellulose synthase and a local source and sink of c-di-GMP. This arrangement provides a localized, yet open source of c-di-GMP right next to cellulose synthase subunit BcsA, which needs allosteric activation by c-di-GMP. Through mathematical modeling and simulation, we demonstrate that BcsA binding from the low cytosolic c-di-GMP pool in E. coli is negligible, whereas a single c-di-GMP molecule that is produced and released in direct proximity to cellulose synthase increases the probability of c-di-GMP binding to BcsA several hundred-fold. This local c-di-GMP signaling could provide a blueprint for target-specific second messenger signaling also in other bacteria where multiple second messenger producing and degrading enzymes exist.
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Affiliation(s)
- Anja M Richter
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany; Department of Materials and the Environment, Bundesanstalt für Materialforschung und -Prüfung, 12205 Berlin, Germany
| | - Alexandra Possling
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Nadezhda Malysheva
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; MF1 Bioinformatics, Robert-Koch-Institut, 13353 Berlin, Germany
| | - Kaveh P Yousef
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany
| | - Susanne Herbst
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany
| | - Max von Kleist
- Department of Mathematics and Computer Science, Freie Universität Berlin, 14195 Berlin, Germany; MF1 Bioinformatics, Robert-Koch-Institut, 13353 Berlin, Germany
| | - Regine Hengge
- Institute of Biology/Microbiology, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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40
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Ma GL, Chandra H, Liang ZX. Taming the flagellar motor of pseudomonads with a nucleotide messenger. Environ Microbiol 2020; 22:2496-2513. [PMID: 32329141 DOI: 10.1111/1462-2920.15036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 01/11/2023]
Abstract
Pseudomonads rely on the flagellar motor to rotate a polar flagellum for swimming and swarming, and to sense surfaces for initiating the motile-to-sessile transition to adopt a surface-dwelling lifestyle. Deciphering the function and regulation of the flagellar motor is of paramount importance for understanding the behaviours of environmental and pathogenic pseudomonads. Recent studies disclosed the preeminent role played by the messenger c-di-GMP in controlling the real-time performance of the flagellar motor in pseudomonads. The studies revealed that c-di-GMP controls the dynamic exchange of flagellar stator units to regulate motor torque/speed and modulates the frequency of flagellar motor switching via the chemosensory signalling pathways. Apart from being a rotary motor, the flagellar motor is emerging as a mechanosensor that transduces surface-induced mechanical signals into an increase of cellular c-di-GMP concentration to initiate the cellular programs required for long-term colonization. Collectively, the studies generate long-awaited mechanistic insights into how c-di-GMP regulates bacterial motility and the motile-to-sessile transition. The new findings also raise the fundamental questions of how cellular c-di-GMP concentrations are dynamically coupled to flagellar output and the proton-motive force, and how c-di-GMP signalling is coordinated spatiotemporally to fine-tune flagellar response and the behaviour of pseudomonads in solutions and on surfaces.
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Affiliation(s)
- Guang-Lei Ma
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore
| | - Hartono Chandra
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore
| | - Zhao-Xun Liang
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore.,Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, 60 Nanyang Drive, S637551, Singapore
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41
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Hengge R. Linking bacterial growth, survival, and multicellularity - small signaling molecules as triggers and drivers. Curr Opin Microbiol 2020; 55:57-66. [PMID: 32244175 DOI: 10.1016/j.mib.2020.02.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 02/05/2023]
Abstract
An overarching theme of cellular regulation in bacteria arises from the trade-off between growth and stress resilience. In addition, the formation of biofilms contributes to stress survival, since these dense multicellular aggregates, in which cells are embedded in an extracellular matrix of self-produced polymers, represent a self-constructed protective and homeostatic 'niche'. As shown here for the model bacterium Escherichia coli, the inverse coordination of bacterial growth with survival and the transition to multicellularity is achieved by a highly integrated regulatory network with several sigma subunits of RNA polymerase and a small number of transcriptional hubs as central players. By conveying information about the actual (micro)environments, nucleotide second messengers such as cAMP, (p)ppGpp, and in particular c-di-GMP are the key triggers and drivers that promote either growth or stress resistance and organized multicellularity in a world of limited resources.
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Affiliation(s)
- Regine Hengge
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10115 Berlin, Germany.
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42
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Reciprocal c-di-GMP signaling: Incomplete flagellum biogenesis triggers c-di-GMP signaling pathways that promote biofilm formation. PLoS Genet 2020; 16:e1008703. [PMID: 32176702 PMCID: PMC7098655 DOI: 10.1371/journal.pgen.1008703] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 03/26/2020] [Accepted: 03/01/2020] [Indexed: 11/25/2022] Open
Abstract
The assembly status of the V. cholerae flagellum regulates biofilm formation, suggesting that the bacterium senses a lack of movement to commit to a sessile lifestyle. Motility and biofilm formation are inversely regulated by the second messenger molecule cyclic dimeric guanosine monophosphate (c-di-GMP). Therefore, we sought to define the flagellum-associated c-di-GMP-mediated signaling pathways that regulate the transition from a motile to a sessile state. Here we report that elimination of the flagellum, via loss of the FlaA flagellin, results in a flagellum-dependent biofilm regulatory (FDBR) response, which elevates cellular c-di-GMP levels, increases biofilm gene expression, and enhances biofilm formation. The strength of the FDBR response is linked with status of the flagellar stator: it can be reversed by deletion of the T ring component MotX, and reduced by mutations altering either the Na+ binding ability of the stator or the Na+ motive force. Absence of the stator also results in reduction of mannose-sensitive hemagglutinin (MSHA) pilus levels on the cell surface, suggesting interconnectivity of signal transduction pathways involved in biofilm formation. Strains lacking flagellar rotor components similarly launched an FDBR response, however this was independent of the status of assembly of the flagellar stator. We found that the FDBR response requires at least three specific diguanylate cyclases that contribute to increased c-di-GMP levels, and propose that activation of biofilm formation during this response relies on c-di-GMP-dependent activation of positive regulators of biofilm production. Together our results dissect how flagellum assembly activates c-di-GMP signaling circuits, and how V. cholerae utilizes these signals to transition from a motile to a sessile state. A key regulator of Vibrio cholerae physiology is the nucleotide-based, second messenger cyclic dimeric guanosine monophosphate (c-di-GMP). We found that the status of flagellar biosynthesis at different stages of flagellar assembly modulates c-di-GMP signaling in V. cholerae and identified diguanylate cyclases involved in this regulatory process. The effect of motility status on the cellular c-di-GMP level is partly dependent on the flagellar stator and Na+ flux through the flagellum. Finally, we showed that c-di-GMP-dependent positive regulators of biofilm formation are critical for the signaling cascade that connects motility status to biofilm formation. Our results show that in addition to c-di-GMP promoting motile to biofilm lifestyle switch, “motility status” of V. cholerae modulates c-di-GMP signaling and biofilm formation.
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43
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Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF. Structural insights into the mechanism of c-di-GMP–bound YcgR regulating flagellar motility in Escherichia coli. J Biol Chem 2020. [DOI: 10.1016/s0021-9258(17)49937-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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44
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Nord AL, Pedaci F. Mechanisms and Dynamics of the Bacterial Flagellar Motor. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1267:81-100. [PMID: 32894478 DOI: 10.1007/978-3-030-46886-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Many bacteria are able to actively propel themselves through their complex environment, in search of resources and suitable niches. The source of this propulsion is the Bacterial Flagellar Motor (BFM), a molecular complex embedded in the bacterial membrane which rotates a flagellum. In this chapter we review the known physical mechanisms at work in the motor. The BFM shows a highly dynamic behavior in its power output, its structure, and in the stoichiometry of its components. Changes in speed, rotation direction, constituent protein conformations, and the number of constituent subunits are dynamically controlled in accordance to external chemical and mechanical cues. The mechano-sensitivity of the motor is likely related to the surface-sensing ability of bacteria, relevant in the initial stage of biofilm formation.
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Affiliation(s)
- A L Nord
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France
| | - F Pedaci
- Centre de Biochimie Structurale (CBS), INSERM, CNRS, University of Montpellier, Montpellier, France.
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45
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Suchanek VM, Esteban-López M, Colin R, Besharova O, Fritz K, Sourjik V. Chemotaxis and cyclic-di-GMP signalling control surface attachment of Escherichia coli. Mol Microbiol 2019; 113:728-739. [PMID: 31793092 DOI: 10.1111/mmi.14438] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/28/2019] [Indexed: 12/18/2022]
Abstract
Attachment to surfaces is an important early step during bacterial infection and during formation of submerged biofilms. Although flagella-mediated motility is known to be important for attachment of Escherichia coli and other bacteria, implications of motility regulation by cellular signalling remain to be understood. Here, we show that motility largely promotes attachment of E. coli, including that mediated by type 1 fimbriae, by allowing cells to reach, get hydrodynamically trapped at and explore the surface. Inactivation or inhibition of the chemotaxis signalling pathway improves attachment by suppressing cell reorientations and thereby increasing surface residence times. The attachment is further enhanced by deletion of genes encoding the cyclic diguanosine monophosphate (c-di-GMP)-dependent flagellar brake YcgR or the diguanylate cyclase DgcE. Such increased attachment in absence of c-di-GMP signalling is in contrast to its commonly accepted function as a positive regulator of the sessile state. It is apparently due to the increased swimming speed of E. coli in absence of YcgR-mediated motor control, which strengthens adhesion mediated by the type 1 fimbriae. Thus, both signalling networks that regulate motility of E. coli also control its engagement with both biotic and abiotic surfaces, which has likely implications for infection and biofilm formation.
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Affiliation(s)
- Verena Maria Suchanek
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
| | - María Esteban-López
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Rémy Colin
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Olga Besharova
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Kirstin Fritz
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany
| | - Victor Sourjik
- Max Planck Institute for Terrestrial Microbiology & LOEWE Center for Synthetic Microbiology (SYNMIKRO), Marburg, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Heidelberg, Germany
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46
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Hou YJ, Yang WS, Hong Y, Zhang Y, Wang DC, Li DF. Structural insights into the mechanism of c-di-GMP-bound YcgR regulating flagellar motility in Escherichia coli. J Biol Chem 2019; 295:808-821. [PMID: 31836667 DOI: 10.1074/jbc.ra119.009739] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/29/2019] [Indexed: 01/28/2023] Open
Abstract
The motile-sessile transition is critical for bacterial survival and growth. Cyclic-di-GMP (c-di-GMP) plays a central role in controlling this transition and regulating biofilm formation via various effectors. As an effector of c-di-GMP in Escherichia coli and related species, the PilZ domain-containing protein YcgR responds to elevated c-di-GMP concentrations and acts on the flagellar motor to suppress bacterial motility in a brakelike fashion, which promotes bacterial surface attachment. To date, several target proteins within the motor, MotA, FliG, and FliM, along with different regulatory mechanisms have been reported. However, how YcgR acts on these components remains unclear. Here, we report that activated YcgR stably binds to MotA at the MotA-FliG interface and thereby regulates bacterial swimming. Biochemical and structural analyses revealed that c-di-GMP rearranges the PilZ domain configuration, resulting in the formation of a MotA-binding patch consisting of an RXXXR motif and the C-tail helix α3. Moreover, we noted that a conserved region in the YcgR-N domain, which is independent of MotA interaction, is necessary for motility regulation. On the basis of these findings, we infer that the YcgR-N domain is required for activity on other motor proteins. We propose that activated YcgR appends to MotA via its PilZ domain and thereby interrupts the MotA-FliG interaction and simultaneously interacts with other motor proteins via its YcgR-N domain to inhibit flagellar motility. Our findings suggest that the mode of interaction between YcgR and motor proteins may be shared by other PilZ family proteins.
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Affiliation(s)
- Yan-Jie Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wen-Si Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuan Hong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ying Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Da-Cheng Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - De-Feng Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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47
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Under Elevated c-di-GMP in Escherichia coli, YcgR Alters Flagellar Motor Bias and Speed Sequentially, with Additional Negative Control of the Flagellar Regulon via the Adaptor Protein RssB. J Bacteriol 2019; 202:JB.00578-19. [PMID: 31611290 DOI: 10.1128/jb.00578-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
In Escherichia coli and Salmonella, the c-di-GMP effector YcgR inhibits flagellar motility by interacting directly with the motor to alter both its bias and speed. Here, we demonstrate that in both of these bacteria, YcgR acts sequentially, altering motor bias first and then decreasing motor speed. We show that when c-di-GMP levels are high, deletion of ycgR restores wild-type motor behavior in E. coli, indicating that YcgR is the only motor effector in this bacterium. Yet, motility and chemotaxis in soft agar do not return to normal, suggesting that there is a second mechanism that inhibits motility under these conditions. In Salmonella, c-di-GMP-induced synthesis of extracellular cellulose has been reported to entrap flagella and to be responsible for the YcgR-independent motility defect. We found that this is not the case in E. coli Instead, we found through reversion analysis that deletion of rssB, which codes for a response regulator/adaptor protein that normally directs ClpXP protease to target σS for degradation, restored wild-type motility in the ycgR mutant. Our data suggest that high c-di-GMP levels may promote altered interactions between these proteins to downregulate flagellar gene expression.IMPORTANCE Flagellum-driven motility has been studied in E. coli and Salmonella for nearly half a century. Over 60 genes control flagellar assembly and function. The expression of these genes is regulated at multiple levels in response to a variety of environmental signals. Cues that elevate c-di-GMP levels, however, inhibit motility by direct binding of the effector YcgR to the flagellar motor. In this study conducted mainly in E. coli, we show that YcgR is the only effector of motor control and tease out the order of YcgR-mediated events. In addition, we find that the σS regulator protein RssB contributes to negative regulation of flagellar gene expression when c-di-GMP levels are elevated.
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48
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Schniederberend M, Williams JF, Shine E, Shen C, Jain R, Emonet T, Kazmierczak BI. Modulation of flagellar rotation in surface-attached bacteria: A pathway for rapid surface-sensing after flagellar attachment. PLoS Pathog 2019; 15:e1008149. [PMID: 31682637 PMCID: PMC6855561 DOI: 10.1371/journal.ppat.1008149] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 11/14/2019] [Accepted: 10/16/2019] [Indexed: 12/11/2022] Open
Abstract
Attachment is a necessary first step in bacterial commitment to surface-associated behaviors that include colonization, biofilm formation, and host-directed virulence. The Gram-negative opportunistic pathogen Pseudomonas aeruginosa can initially attach to surfaces via its single polar flagellum. Although many bacteria quickly detach, some become irreversibly attached and express surface-associated structures, such as Type IV pili, and behaviors, including twitching motility and biofilm initiation. P. aeruginosa that lack the GTPase FlhF assemble a randomly placed flagellum that is motile; however, we observed that these mutant bacteria show defects in biofilm formation comparable to those seen for non-motile, aflagellate bacteria. This phenotype was associated with altered behavior of ΔflhF bacteria immediately following surface-attachment. Forward and reverse genetic screens led to the discovery that FlhF interacts with FimV to control flagellar rotation at a surface, and implicated cAMP signaling in this pathway. Although cAMP controls many transcriptional programs in P. aeruginosa, known targets of this second messenger were not required to modulate flagellar rotation in surface-attached bacteria. Instead, alterations in switching behavior of the motor appeared to result from direct or indirect effects of cAMP on switch complex proteins and/or the stators associated with them.
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Affiliation(s)
- Maren Schniederberend
- Department of Medicine (Infectious Diseases), Yale University, New Haven, Connecticut, United States of America
| | - Jessica F. Williams
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Emilee Shine
- Program in Microbiology, Yale University, New Haven, Connecticut, United States of America
| | - Cong Shen
- Program in Microbiology, Yale University, New Haven, Connecticut, United States of America
| | - Ruchi Jain
- Department of Medicine (Infectious Diseases), Yale University, New Haven, Connecticut, United States of America
| | - Thierry Emonet
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Physics, Yale University, New Haven, Connecticut, United States of America
| | - Barbara I. Kazmierczak
- Department of Medicine (Infectious Diseases), Yale University, New Haven, Connecticut, United States of America
- Department of Microbial Pathogenesis, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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49
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Analysis of Brevundimonas subvibrioides Developmental Signaling Systems Reveals Inconsistencies between Phenotypes and c-di-GMP Levels. J Bacteriol 2019; 201:JB.00447-19. [PMID: 31383736 DOI: 10.1128/jb.00447-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/26/2019] [Indexed: 11/20/2022] Open
Abstract
The DivJ-DivK-PleC signaling system of Caulobacter crescentus is a signaling network that regulates polar development and the cell cycle. This system is conserved in related bacteria, including the sister genus Brevundimonas Previous studies had shown unexpected phenotypic differences between the C. crescentus divK mutant and the analogous mutant of Brevundimonas subvibrioides, but further characterization was not performed. Here, phenotypic assays analyzing motility, adhesion, and pilus production (the latter characterized by a newly discovered bacteriophage) revealed that divJ and pleC mutants have phenotypes mostly similar to their C. crescentus homologs, but divK mutants maintain largely opposite phenotypes than expected. Suppressor mutations of the B. subvibrioides divK motility defect were involved in cyclic di-GMP (c-di-GMP) signaling, including the diguanylate cyclase dgcB, and cleD which is hypothesized to affect flagellar function in a c-di-GMP dependent fashion. However, the screen did not identify the diguanylate cyclase pleD Disruption of pleD in B. subvibrioides caused no change in divK or pleC phenotypes, but did reduce adhesion and increase motility of the divJ strain. Analysis of c-di-GMP levels in these strains revealed incongruities between c-di-GMP levels and displayed phenotypes with a notable result that suppressor mutations altered phenotypes but had little impact on c-di-GMP levels in the divK background. Conversely, when c-di-GMP levels were artificially manipulated, alterations of c-di-GMP levels in the divK strain had minimal impact on phenotypes. These results suggest that DivK performs a critical function in the integration of c-di-GMP signaling into the B. subvibrioides cell cycle.IMPORTANCE Cyclic di-GMP and associated signaling proteins are widespread in bacteria, but their role in physiology is often complex and difficult to predict through genomic level analyses. In C. crescentus, c-di-GMP has been integrated into the developmental cell cycle, but there is increasing evidence that environmental factors can impact this system as well. The research presented here suggests that the integration of these signaling networks could be more complex than previously hypothesized, which could have a bearing on the larger field of c-di-GMP signaling. In addition, this work further reveals similarities and differences in a conserved regulatory network between organisms in the same taxonomic family, and the results show that gene conservation does not necessarily imply close functional conservation in genetic pathways.
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50
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Kojima S, Yoneda T, Morimoto W, Homma M. Effect of PlzD, a YcgR homologue of c-di-GMP-binding protein, on polar flagellar motility in Vibrio alginolyticus. J Biochem 2019; 166:77-88. [PMID: 30778544 DOI: 10.1093/jb/mvz014] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/14/2019] [Indexed: 01/01/2023] Open
Abstract
YcgR, a cyclic diguanylate (c-di-GMP)-binding protein expressed in Escherichia coli, brakes flagellar rotation by binding to the motor in a c-di-GMP dependent manner and has been implicated in triggering biofilm formation. Vibrio alginolyticus has a single polar flagellum and encodes YcgR homologue, PlzD. When PlzD or PlzD-GFP was highly over-produced in nutrient-poor condition, the polar flagellar motility of V. alginolyticus was reduced. This inhibitory effect is c-di-GMP independent as mutants substituting putative c-di-GMP-binding residues retain the effect. Moderate over-expression of PlzD-GFP allowed its localization at the flagellated cell pole. Truncation of the N-terminal 12 or 35 residues of PlzD abolished the inhibitory effect and polar localization, and no inhibitory effect was observed by deleting plzD or expressing an endogenous level of PlzD-GFP. Subcellular fractionation showed that PlzD, but not its N-terminally truncated variants, was precipitated when over-produced. Moreover, immunoblotting and N-terminal sequencing revealed that endogenous PlzD is synthesized from Met33. These results suggest that an N-terminal extension allows PlzD to localize at the cell pole but causes aggregation and leads to inhibition of motility. In V. alginolyticus, PlzD has a potential property to associate with the polar flagellar motor but this interaction is too weak to inhibit rotation.
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Affiliation(s)
- Seiji Kojima
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Takuro Yoneda
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Wakako Morimoto
- Department of Biological Science, School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
| | - Michio Homma
- Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya, Japan
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