1
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Johnson S, Deme JC, Furlong EJ, Caesar JJE, Chevance FFV, Hughes KT, Lea SM. Structural basis of directional switching by the bacterial flagellum. Nat Microbiol 2024; 9:1282-1292. [PMID: 38459206 DOI: 10.1038/s41564-024-01630-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 02/01/2024] [Indexed: 03/10/2024]
Abstract
The bacterial flagellum is a macromolecular protein complex that harvests energy from uni-directional ion flow across the inner membrane to power bacterial swimming via rotation of the flagellar filament. Rotation is bi-directional, with binding of a cytoplasmic chemotactic response regulator controlling reversal, though the structural and mechanistic bases for rotational switching are not well understood. Here we present cryoelectron microscopy structures of intact Salmonella flagellar basal bodies (3.2-5.5 Å), including the cytoplasmic C-ring complexes required for power transmission, in both counter-clockwise and clockwise rotational conformations. These reveal 180° movements of both the N- and C-terminal domains of the FliG protein, which, when combined with a high-resolution cryoelectron microscopy structure of the MotA5B2 stator, show that the stator shifts from the outside to the inside of the C-ring. This enables rotational switching and reveals how uni-directional ion flow across the inner membrane is used to accomplish bi-directional rotation of the flagellum.
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Affiliation(s)
- Steven Johnson
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
| | - Justin C Deme
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA
| | - Emily J Furlong
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Division of Biomedical Science and Biochemistry, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Joseph J E Caesar
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
- Central Oxford Structural Molecular Imaging Centre, University of Oxford, Oxford, UK
| | | | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT, USA
| | - Susan M Lea
- Center for Structural Biology, CCR, NCI, Frederick, MD, USA.
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2
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Mukhopadhyay S, Bishayi R, Shaji A, Lee AH, Gupta R, Mohajeri M, Katiyar A, McKee B, Schmitz IR, Shin R, Lele TP, Lele PP. Dynamic Adaptation in Extant Porins Facilitates Antibiotic Tolerance in Energetic Escherichia coli. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583920. [PMID: 38496420 PMCID: PMC10942424 DOI: 10.1101/2024.03.07.583920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Bacteria can tolerate antibiotics despite lacking the genetic components for resistance. The prevailing notion is that tolerance results from depleted cellular energy or cell dormancy. In contrast to this view, many cells in the tolerant population of Escherichia coli can exhibit motility - a phenomenon that requires cellular energy, specifically, the proton-motive force (PMF). As these motile-tolerant cells are challenging to isolate from the heterogeneous tolerant population, their survival mechanism is unknown. Here, we discovered that motile bacteria segregate themselves from the tolerant population under micro-confinement, owing to their unique ability to penetrate micron-sized channels. Single-cell measurements on the motile-tolerant population showed that the cells retained a high PMF, but they did not survive through active efflux alone. By utilizing growth assays, single-cell fluorescence studies, and chemotaxis assays, we showed that the cells survived by dynamically inhibiting the function of existing porins in the outer membrane. A drug transport model for porin-mediated intake and efflux pump-mediated expulsion suggested that energetic tolerant cells withstand antibiotics by constricting their porins. The novel porin adaptation we have uncovered is independent of gene expression changes and may involve electrostatic modifications within individual porins to prevent extracellular ligand entry.
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3
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Rachwalski K, Tu MM, Madden SJ, French S, Hansen DM, Brown ED. A mobile CRISPRi collection enables genetic interaction studies for the essential genes of Escherichia coli. CELL REPORTS METHODS 2024; 4:100693. [PMID: 38262349 PMCID: PMC10832289 DOI: 10.1016/j.crmeth.2023.100693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/27/2023] [Accepted: 12/22/2023] [Indexed: 01/25/2024]
Abstract
Advances in gene editing, in particular CRISPR interference (CRISPRi), have enabled depletion of essential cellular machinery to study the downstream effects on bacterial physiology. Here, we describe the construction of an ordered E. coli CRISPRi collection, designed to knock down the expression of 356 essential genes with the induction of a catalytically inactive Cas9, harbored on the conjugative plasmid pFD152. This mobile CRISPRi library can be conjugated into other ordered genetic libraries to assess combined effects of essential gene knockdowns with non-essential gene deletions. As proof of concept, we probed cell envelope synthesis with two complementary crosses: (1) an Lpp deletion into every CRISPRi knockdown strain and (2) the lolA knockdown plasmid into the Keio collection. These experiments revealed a number of notable genetic interactions for the essential phenotype probed and, in particular, showed suppressing interactions for the loci in question.
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Affiliation(s)
- Kenneth Rachwalski
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Megan M Tu
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Sean J Madden
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Shawn French
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Drew M Hansen
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, ON L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON L8S 4L8, Canada.
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4
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Zhang H, Zhao Z, Guan W, Zhong Y, Wang Y, Zhou Q, Liu F, Luo Q, Liu J, Ni J, He N, Guo D, Li L, Xing Q. Nano-Selenium inhibited antibiotic resistance genes and virulence factors by suppressing bacterial selenocompound metabolism and chemotaxis pathways in animal manure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 263:115277. [PMID: 37499390 DOI: 10.1016/j.ecoenv.2023.115277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023]
Abstract
Numerous antibiotic resistance genes (ARGs) and virulence factors (VFs) found in animal manure pose significant risks to human health. However, the effects of graphene sodium selenite (GSSe), a novel chemical nano-Selenium, and biological nano-Selenium (BNSSe), a new bioaugmentation nano-Se, on bacterial Se metabolism, chemotaxis, ARGs, and VFs in animal manure remain unknown. In this study, we investigated the effects of GSSe and BNSSe on ARGs and VFs expression in broiler manure using high-throughput sequencing. Results showed that BNSSe reduced Se pressure during anaerobic fermentation by inhibiting bacterial selenocompound metabolism pathways, thereby lowering manure Selenium pollution. Additionally, the expression levels of ARGs and VFs were lower in the BNSSe group compared to the Sodium Selenite and GSSe groups, as BNSSe inhibited bacterial chemotaxis pathways. Co-occurrence network analysis identified ARGs and VFs within the following phyla Bacteroidetes (genera Butyricimonas, Odoribacter, Paraprevotella, and Rikenella), Firmicutes (genera Lactobacillus, Candidatus_Borkfalkia, Merdimonas, Oscillibacter, Intestinimonas, and Megamonas), and Proteobacteria (genera Desulfovibrio). The expression and abundance of ARGs and VFs genes were found to be associated with ARGs-VFs coexistence. Moreover, BNSSe disruption of bacterial selenocompound metabolism and chemotaxis pathways resulted in less frequent transfer of ARGs and VFs. These findings indicate that BNSSe can reduce ARGs and VFs expression in animal manure by suppressing bacterial selenocompound metabolism and chemotaxis pathways.
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Affiliation(s)
- Haibo Zhang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Zhigang Zhao
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Weikun Guan
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yuhong Zhong
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Yang Wang
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qilong Zhou
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Fuyu Liu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Qi Luo
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Junyi Liu
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Jian Ni
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Ning He
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Dongsheng Guo
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China
| | - Lizhi Li
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China.
| | - Qingfeng Xing
- College of Life Science and Resources and Environment, Yichun University, Yi Chun 336000, China.
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Zhao S, Nan Y, Yao R, Wang L, Zeng X, Aadil RM, Shabbir MA. Antibacterial Activity and Transcriptomic Analysis of Hesperetin against Alicyclobacillus acidoterrestris Vegetative Cells. Foods 2023; 12:3276. [PMID: 37685209 PMCID: PMC10487046 DOI: 10.3390/foods12173276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/16/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
The aim of this research was to investigate the antimicrobial characteristics and mechanism of hesperetin against Alicyclobacillus acidoterrestris vegetative cells. The results presented show that hesperetin had effective antimicrobial activity on Alicyclobacillus acidoterrestris vegetative cells, minimum inhibition concentration (MIC) of 0.0625 g/L, and minimum bacterial concentration (MBC) greater than 2 g/L. Moreover, treatment of hesperetin caused significant damage to cell integrity, preventing the growth of Alicyclobacillus acidoterrestris vegetative cells, enhancing the leakage of nucleic acid and proteins, and destroying the vegetative cell morphology. To further investigate the mechanism, transcriptomic analysis was carried out, and 3056 differentially expressed genes (DEGs) were detected. Gene ontology (GO) enrichment analysis revealed that hesperetin inhibits Alicyclobacillus acidoterrestris by affecting the intracellular nitrogen metabolism and amino acid metabolism. The Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis explained that hesperetin was also able to prevent the growth of Alicyclobacillus acidoterrestris by affecting the processes of nutrient transport, energy metabolism, and flagella motility. These results provide new insights into the antimicrobial effects and mechanism of hesperetin against Alicyclobacillus acidoterrestris, which provides a new method for inactive Alicyclobacillus acidoterrestris in the juice industry.
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Affiliation(s)
- Siqi Zhao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
| | - Yanzi Nan
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
| | - Runyu Yao
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
| | - Langhong Wang
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
- School of Food Science and Engineering, Guangdong Provincial Key Laboratory of Intelligent Food Manufacturing, Foshan University, Foshan 528225, China
| | - Xinan Zeng
- School of Food Science and Engineering, South China University of Technology, Guangzhou 510641, China; (S.Z.); (Y.N.); (R.Y.); (L.W.)
- School of Food Science and Engineering, Guangdong Provincial Key Laboratory of Intelligent Food Manufacturing, Foshan University, Foshan 528225, China
| | - Rana Muhammad Aadil
- National Institute of Food Science and Technology, University of Agriculture, Faisalabad 38000, Pakistan; (R.M.A.); (M.A.S.)
| | - Muhammad Asim Shabbir
- National Institute of Food Science and Technology, University of Agriculture, Faisalabad 38000, Pakistan; (R.M.A.); (M.A.S.)
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6
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Abdulkadieva MM, Sysolyatina EV, Vasilieva EV, Litvinenko VV, Kalinin EV, Zhukhovitsky VG, Shevlyagina NV, Andreevskaya SG, Stanishevskyi YM, Vasiliev MM, Petrov OF, Ermolaeva SA. Motility provides specific adhesion patterns and improves Listeria monocytogenes invasion into human HEp-2 cells. PLoS One 2023; 18:e0290842. [PMID: 37651463 PMCID: PMC10470941 DOI: 10.1371/journal.pone.0290842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 08/17/2023] [Indexed: 09/02/2023] Open
Abstract
Listeria monocytogenes is motile at 22°C and non-motile at 37°C. In contrast, expression of L. monocytogenes virulence factors is low at 22°C and up-regulated at 37°C. Here, we studied a character of L. monocytogenes near surface swimming (NSS) motility and its effects on adhesion patterns and invasion into epithelial cells. L. monocytogenes and its saprophytic counterpart L. innocua both grown at 22°C showed similar NSS characteristics including individual velocities, trajectory lengths, residence times, and an asymmetric distribution of velocity directions. Similar NSS patterns correlated with similar adhesion patterns. Motile bacteria, including both pathogenic and saprophytic species, showed a preference for adhering to the periphery of epithelial HEp-2 cells. In contrast, non-motile bacteria were evenly distributed across the cell surface, including areas over the nucleus. However, the uneven distribution of motile bacteria did not enhance the invasion into HEp-2 cells unless virulence factor production was up-regulated by the transient shift of the culture to 37°C. Motile L. monocytogenes grown overnight at 22°C and then shifted to 37°C for 2 h expressed invasion factors at the same level and invaded human cells up to five times more efficiently comparatively with non-motile bacteria grown overnight at 37°C. Taken together, obtained results demonstrated that (i) NSS motility and correspondent peripheral location over the cell surface did not depend on L. monocytogenes virulence traits; (ii) motility improved L. monocytogenes invasion into human HEp-2 cells within a few hours after the transition from the ambient temperature to the human body temperature.
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Affiliation(s)
- Mariam M. Abdulkadieva
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
- Institute of Biochemical Technology and Nanotechnology, People’s Friendship University RUDN, Moscow, Russia
| | - Elena V. Sysolyatina
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
| | - Elena V. Vasilieva
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Veronika V. Litvinenko
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Egor V. Kalinin
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Institute of Biochemical Technology and Nanotechnology, People’s Friendship University RUDN, Moscow, Russia
| | - Vladimir G. Zhukhovitsky
- Department of Bacterial Infections, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
- Russian Medical Academy of Continuing Professional Education (RMANPO), Ministry of Public Health, Moscow, Russia
| | - Natalia V. Shevlyagina
- Department of Bacterial Infections, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
| | - Svetlana G. Andreevskaya
- Department of Bacterial Infections, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
| | - Yaroslav M. Stanishevskyi
- Institute of Biochemical Technology and Nanotechnology, People’s Friendship University RUDN, Moscow, Russia
| | - Mikhail M. Vasiliev
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Oleg F. Petrov
- Department of Dusty Plasmas, Joint Institute of High Temperatures RAS, Moscow, Russia
| | - Svetlana A. Ermolaeva
- Department of Infections with Natural Foci, Gamaleya National Research Centre of Epidemiology and Microbiology, Moscow, Russia
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7
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Hu H, Popp PF, Santiveri M, Roa-Eguiara A, Yan Y, Martin FJO, Liu Z, Wadhwa N, Wang Y, Erhardt M, Taylor NMI. Ion selectivity and rotor coupling of the Vibrio flagellar sodium-driven stator unit. Nat Commun 2023; 14:4411. [PMID: 37500658 PMCID: PMC10374538 DOI: 10.1038/s41467-023-39899-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 07/04/2023] [Indexed: 07/29/2023] Open
Abstract
Bacteria swim using a flagellar motor that is powered by stator units. Vibrio spp. are highly motile bacteria responsible for various human diseases, the polar flagella of which are exclusively driven by sodium-dependent stator units (PomAB). However, how ion selectivity is attained, how ion transport triggers the directional rotation of the stator unit, and how the stator unit is incorporated into the flagellar rotor remained largely unclear. Here, we have determined by cryo-electron microscopy the structure of Vibrio PomAB. The electrostatic potential map uncovers sodium binding sites, which together with functional experiments and molecular dynamics simulations, reveal a mechanism for ion translocation and selectivity. Bulky hydrophobic residues from PomA prime PomA for clockwise rotation. We propose that a dynamic helical motif in PomA regulates the distance between PomA subunit cytoplasmic domains, stator unit activation, and torque transmission. Together, our study provides mechanistic insights for understanding ion selectivity and rotor incorporation of the stator unit of the bacterial flagellum.
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Affiliation(s)
- Haidai Hu
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Philipp F Popp
- Institute for Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
| | - Mònica Santiveri
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Aritz Roa-Eguiara
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Yumeng Yan
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Freddie J O Martin
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Zheyi Liu
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China
| | - Navish Wadhwa
- Department of Physics, Arizona State University, Tempe, AZ, 85287, USA
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ, 85287, USA
| | - Yong Wang
- College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
- The Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining, 314400, China
| | - Marc Erhardt
- Institute for Biology/Molecular Microbiology, Humboldt-Universität zu Berlin, Philippstr. 13, 10115, Berlin, Germany
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | - Nicholas M I Taylor
- Structural Biology of Molecular Machines Group, Protein Structure & Function Program, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
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8
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Sheng Q, Liu A, Yang P, Chen Z, Wang P, Sun H, Li C, McMinn A, Chen Y, Zhang Y, Su H, Chen X, Zhang Y. The FilZ Protein Contains a Single PilZ Domain and Facilitates the Swarming Motility of Pseudoalteromonas sp. SM9913. Microorganisms 2023; 11:1566. [PMID: 37375068 DOI: 10.3390/microorganisms11061566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Swarming regulation is complicated in flagellated bacteria, especially those possessing dual flagellar systems. It remains unclear whether and how the movement of the constitutive polar flagellum is regulated during swarming motility of these bacteria. Here, we report the downregulation of polar flagellar motility by the c-di-GMP effector FilZ in the marine sedimentary bacterium Pseudoalteromonas sp. SM9913. Strain SM9913 possesses two flagellar systems, and filZ is located in the lateral flagellar gene cluster. The function of FilZ is negatively controlled by intracellular c-di-GMP. Swarming in strain SM9913 consists of three periods. Deletion and overexpression of filZ revealed that, during the period when strain SM9913 expands quickly, FilZ facilitates swarming. In vitro pull-down and bacterial two-hybrid assays suggested that, in the absence of c-di-GMP, FilZ interacts with the CheW homolog A2230, which may be involved in the chemotactic signal transduction pathway to the polar flagellar motor protein FliMp, to interfere with polar flagellar motility. When bound to c-di-GMP, FilZ loses its ability to interact with A2230. Bioinformatic investigation indicated that filZ-like genes are present in many bacteria with dual flagellar systems. Our findings demonstrate a novel mode of regulation of bacterial swarming motility.
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Affiliation(s)
- Qi Sheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Ang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Peiling Yang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Zhuowei Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Peng Wang
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Haining Sun
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Chunyang Li
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Andrew McMinn
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS 7005, Australia
| | - Yin Chen
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Yuzhong Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Ocean University of China, Qingdao 266100, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Hainan Su
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
| | - Xiulan Chen
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Yuqiang Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China
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9
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Morimoto YV, Minamino T. Measurements of the Ion Channel Activity of the Transmembrane Stator Complex in the Bacterial Flagellar Motor. Methods Mol Biol 2023; 2646:83-94. [PMID: 36842108 DOI: 10.1007/978-1-0716-3060-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
The bacterial flagellum is driven by a rotational motor located at the base of the flagellum. The stator unit complex conducts cations such as protons (H+) and sodium ions (Na+) along the electrochemical potential across the cytoplasmic membrane and interacts with the rotor to generate the rotational force. Escherichia coli and Salmonella have the H+-type stator complex, which serves as a transmembrane H+ channel that couples H+ flow through an ion channel to torque generation whereas Vibrio and some Bacillus species have the Na+-type stator complex. In this chapter, we describe how to measure the ion conductivity of the transmembrane stator complex over-expressed in E. coli cells using fluorescent indicators. Intensity measurements of fluorescent indicators using either a fluorescence spectrophotometer or microscope allow quantitative detection of changes in the intracellular ion concentrations due to the ion channel activity of the transmembrane protein 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, Iizuka, Fukuoka, Japan.
- Japan Science and Technology Agency, PRESTO, Kawaguchi, Saitama, Japan.
| | - Tohru Minamino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
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10
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Terashima H, Homma M, Kojima S. Site-Directed Cross-Linking Between Bacterial Flagellar Motor Proteins In Vivo. Methods Mol Biol 2023; 2646:71-82. [PMID: 36842107 DOI: 10.1007/978-1-0716-3060-0_7] [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: 02/27/2023]
Abstract
The bacterial flagellum employs a rotary motor embedded on the cell surface. The motor consists of the stator and rotor elements and is driven by ion influx (typically H+ or Na+) through an ion channel of the stator. Ion influx induces conformational changes in the stator, followed by changes in the interactions between the stator and rotor. The driving force to rotate the flagellum is thought to be generated by changing the stator-rotor interactions. In this chapter, we describe two methods for investigating the interactions between the stator and rotor: site-directed in vivo photo-crosslinking and site-directed in vivo cysteine disulfide crosslinking.
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Affiliation(s)
- Hiroyuki Terashima
- Department of Bacteriology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan.
| | - 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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11
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Gupta R, Yuan J, Lele PP. Bacterial Proprioception: Can a Bacterium Sense Its Movement? Front Microbiol 2022; 13:928408. [PMID: 35875555 PMCID: PMC9302961 DOI: 10.3389/fmicb.2022.928408] [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: 04/25/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
The evolution of the bacterial flagellum gave rise to motility and repurposing of a signaling network, now termed the chemotaxis network, enabled biasing of cell movements. This made it possible for the bacterium to seek out favorable chemical environments. To enable chemotaxis, the chemotaxis network sensitively detects extracellular chemical stimuli and appropriately modulates flagellar functions. Additionally, the flagellar motor itself is capable of detecting mechanical stimuli and adapts its structure and function in response, likely triggering a transition from planktonic to surface-associated lifestyles. Recent work has shown a link between the flagellar motor's response to mechanical stimuli and the chemotactic output. Here, we elaborate on this link and discuss how it likely helps the cell sense and adapt to changes in its swimming speeds in different environments. We discuss the mechanism whereby the motor precisely tunes its chemotaxis output under different mechanical loads, analogous to proprioception in higher order organisms. We speculate on the roles bacterial proprioception might play in a variety of phenomena including the transition to surface-associated lifestyles such as swarming and biofilms.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei, China
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX, United States
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12
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Guo S, Liu J. The Bacterial Flagellar Motor: Insights Into Torque Generation, Rotational Switching, and Mechanosensing. Front Microbiol 2022; 13:911114. [PMID: 35711788 PMCID: PMC9195833 DOI: 10.3389/fmicb.2022.911114] [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: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 11/18/2022] Open
Abstract
The flagellar motor is a bidirectional rotary nanomachine used by many bacteria to sense and move through environments of varying complexity. The bidirectional rotation of the motor is governed by interactions between the inner membrane-associated stator units and the C-ring in the cytoplasm. In this review, we take a structural biology perspective to discuss the distinct conformations of the stator complex and the C-ring that regulate bacterial motility by switching rotational direction between the clockwise (CW) and counterclockwise (CCW) senses. We further contextualize recent in situ structural insights into the modulation of the stator units by accessory proteins, such as FliL, to generate full torque. The dynamic structural remodeling of the C-ring and stator complexes as well as their association with signaling and accessory molecules provide a mechanistic basis for how bacteria adjust motility to sense, move through, and survive in specific niches both outside and within host cells and tissues.
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Affiliation(s)
- Shuaiqi Guo
- Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, United States
| | - Jun Liu
- Microbial Sciences Institute, Yale University, West Haven, CT, United States.,Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, United States
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13
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Homma M, Kojima S. The Periplasmic Domain of the Ion-Conducting Stator of Bacterial Flagella Regulates Force Generation. Front Microbiol 2022; 13:869187. [PMID: 35572622 PMCID: PMC9093738 DOI: 10.3389/fmicb.2022.869187] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/24/2022] [Indexed: 11/23/2022] Open
Abstract
The bacterial flagellar stator is a unique ion-conducting membrane protein complex composed of two kinds of proteins, the A subunit and the B subunit. The stator couples the ion-motive force across the membrane into rotational force. The stator becomes active only when it is incorporated into the flagellar motor. The periplasmic region of the B subunit positions the stator by using the peptidoglycan-binding (PGB) motif in its periplasmic C-terminal domain to attach to the cell wall. Functional studies based on the crystal structures of the C-terminal domain of the B subunit (MotBC or PomBC) reveal that a dramatic conformational change in a characteristic α-helix allows the stator to conduct ions efficiently and bind to the PG layer. The plug and the following linker region between the transmembrane (TM) and PG-binding domains of the B subunit function in regulating the ion conductance. In Vibrio spp., the transmembrane protein FliL and the periplasmic MotX and MotY proteins also contribute to the motor function. In this review, we describe the functional and structural changes which the stator units undergo to regulate the activity of the stator to drive flagellar rotation.
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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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14
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Yang Y, Yue C, Zhang C, Yuan J. Chemotactic response of Escherichia coli to polymer solutions. Phys Biol 2022; 19. [PMID: 35545074 DOI: 10.1088/1478-3975/ac6eb1] [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: 12/17/2021] [Accepted: 05/11/2022] [Indexed: 11/12/2022]
Abstract
Polymers are important components of the complex fluid environment for microorganisms. The mechanical effects on bacterial motile behavior due to the viscous or viscoelastic properties of polymers were extensively studied, whereas possible chemical effects on bacterial motility through bacterial chemoreception of the polymers were unclear. Here we studied the chemotactic response of Escherichia coli to polymeric solutions by combining the bead assay and FRET measurements. We found that the wild-type E. coli strain exhibited an attractant response to widely used polymers such as Ficoll 400, PEG 20000 and PVP 360000, and the response amplitude from chemoreception was much larger than that from the load-dependence of motor switching due to viscosity change. The chemotactic response depended on the type of receptors and the chain length of the polymers. Our findings here provided novel ingredients for further studies of bacterial motile behavior in complex fluids.
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Affiliation(s)
- Yue Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, 96 Jinzhai Rd, Hefei, Anhui, 230026, CHINA
| | - Caijuan Yue
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, 96 Jinzhai Rd, Hefei, Anhui, 230026, CHINA
| | - Chi Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, 96 Jinzhai Rd, Hefei, Anhui, 230026, CHINA
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, 96 Jinzhai Rd, Hefei, Anhui, 230026, CHINA
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15
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Geng R, Cheng L, Cao C, Liu Z, Liu D, Xiao Z, Wu X, Huang Z, Feng Q, Luo C, Chen Z, Zhang Z, Jiang C, Ren M, Yang A. Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification. Front Microbiol 2022; 13:854792. [PMID: 35602040 PMCID: PMC9121018 DOI: 10.3389/fmicb.2022.854792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 04/22/2022] [Indexed: 11/23/2022] Open
Abstract
Ralstonia solanacearum species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from Burkholderiales and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.
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Affiliation(s)
- Ruimei Geng
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Lirui Cheng
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Changdai Cao
- Shandong Rizhao Tobacco Company Ltd., Rizhao, China
| | - Zhengwen Liu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dan Liu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhiliang Xiao
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Xiuming Wu
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhenrui Huang
- Key Laboratory of Crop Genetic Improvement, Engineering and Technology Research Center for Tobacco Breeding and Comprehensive Utilization of Guangdong, Crops Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Quanfu Feng
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Chenggang Luo
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhiqiang Chen
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Zhenchen Zhang
- Key Laboratory of Crop Genetic Improvement, Engineering and Technology Research Center for Tobacco Breeding and Comprehensive Utilization of Guangdong, Crops Research Institute of Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Caihong Jiang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Min Ren
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- *Correspondence: Min Ren,
| | - Aiguo Yang
- Key Laboratory for Tobacco Gene Resources, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, China
- Aiguo Yang,
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16
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Gupta R, Rhee KY, Beagle SD, Chawla R, Perdomo N, Lockless SW, Lele PP. Indole modulates cooperative protein-protein interactions in the flagellar motor. PNAS NEXUS 2022; 1. [PMID: 35719892 PMCID: PMC9205328 DOI: 10.1093/pnasnexus/pgac035] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Indole is a major component of the bacterial exometabolome, and the mechanisms for its wide-ranging effects on bacterial physiology are biomedically significant, although they remain poorly understood. Here, we determined how indole modulates the functions of a widely conserved motility apparatus, the bacterial flagellum. Our experiments in Escherichia coli revealed that indole influences the rotation rates and reversals in the flagellum’s direction of rotation via multiple mechanisms. At concentrations higher than 1 mM, indole decreased the membrane potential to dissipate the power available for the rotation of the motor that operates the flagellum. Below 1 mM, indole did not dissipate the membrane potential. Instead, experiments and modeling indicated that indole weakens cooperative protein interactions within the flagellar complexes to inhibit motility. The metabolite also induced reversals in the rotational direction of the motor to promote a weak chemotactic response, even when the chemotaxis response regulator, CheY, was lacking. Experiments further revealed that indole does not require the transporter Mtr to cross the membrane and influence motor functions. Based on these findings, we propose that indole modulates intra- and inter-protein interactions in the cell to influence several physiological functions.
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Affiliation(s)
- Rachit Gupta
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Kathy Y Rhee
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Sarah D Beagle
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Ravi Chawla
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA 92037, USA
| | - Nicolas Perdomo
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
| | - Steve W Lockless
- Department of Biology, Texas A&M University, College Station, TX 77843-3258, USA
| | - Pushkar P Lele
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843-3122, USA
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17
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Abstract
SignificanceHow flagella sense complex environments and control bacterial motility remain fascinating questions. Here, we deploy cryo-electron tomography to determine in situ structures of the flagellar motor in wild-type and mutant cells of Borrelia burgdorferi, revealing that three flagellar proteins (FliL, MotA, and MotB) form a unique supramolecular complex in situ. Importantly, FliL not only enhances motor function by forming a ring around the stator complex MotA/MotB in its extended, active conformation but also facilitates assembly of the stator complex around the motor. Our in situ data provide insights into how cooperative remodeling of the FliL-stator supramolecular complex helps regulate the collective ion flux and establishes the optimal function of the flagellar motor to guide bacterial motility in various environments.
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18
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Mutations in the stator protein PomA affect switching of rotational direction in bacterial flagellar motor. Sci Rep 2022; 12:2979. [PMID: 35194097 PMCID: PMC8863984 DOI: 10.1038/s41598-022-06947-5] [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: 09/17/2021] [Accepted: 02/03/2022] [Indexed: 12/03/2022] Open
Abstract
The flagellar motor rotates bi-directionally in counter-clockwise (CCW) and clockwise (CW) directions. The motor consists of a stator and a rotor. Recent structural studies have revealed that the stator is composed of a pentameric ring of A subunits and a dimer axis of B subunits. Highly conserved charged and neighboring residues of the A subunit interacts with the rotor, generating torque through a gear-like mechanism. The rotational direction is controlled by chemotaxis signaling transmitted to the rotor, with less evidence for the stator being involved. In this study, we report novel mutations that affect the switching of the rotational direction at the putative interaction site of the stator to generate rotational force. Our results highlight an aspect of flagellar motor function that appropriate switching of the interaction states between the stator and rotor is critical for controlling the rotational direction.
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