1
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Rakonjac J, Gold VAM, León-Quezada RI, Davenport CH. Structure, Biology, and Applications of Filamentous Bacteriophages. Cold Spring Harb Protoc 2024; 2024:pdb.over107754. [PMID: 37460152 DOI: 10.1101/pdb.over107754] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
The closely related Escherichia coli Ff filamentous phages (f1, fd, and M13) have taken a fantastic journey over the past 60 years, from the urban sewerage from which they were first isolated, to their use in high-end technologies in multiple fields. Their relatively small genome size, high titers, and the virions that tolerate fusion proteins make the Ffs an ideal system for phage display. Folding of the fusions in the oxidizing environment of the E. coli periplasm makes the Ff phages a platform that allows display of eukaryotic surface and secreted proteins, including antibodies. Resistance of the Ffs to a broad range of pH and detergents facilitates affinity screening in phage display, whereas the stability of the virions at ambient temperature makes them suitable for applications in material science and nanotechnology. Among filamentous phages, only the Ffs have been used in phage display technology, because of the most advanced state of knowledge about their biology and the various tools developed for E. coli as a cloning host for them. Filamentous phages have been thought to be a rather small group, infecting mostly Gram-negative bacteria. A recent discovery of more than 10 thousand diverse filamentous phages in bacteria and archaea, however, opens a fascinating prospect for novel applications. The main aim of this review is to give detailed biological and structural information to researchers embarking on phage display projects. The secondary aim is to discuss the yet-unresolved puzzles, as well as recent developments in filamentous phage biology, from a viewpoint of their impact on current and future applications.
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Affiliation(s)
- Jasna Rakonjac
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Vicki A M Gold
- Living Systems Institute University of Exeter, Exeter, EX4 4QD, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, EX4 4QD, United Kingdom
| | - Rayén I León-Quezada
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
| | - Catherine H Davenport
- School of Natural Sciences, Massey University, Auckland 0632, New Zealand
- Nanophage Technologies Ltd., Palmerston North, Manawatu 4474, New Zealand
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2
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Geiger CJ, Wong GCL, O'Toole GA. A bacterial sense of touch: T4P retraction motor as a means of surface sensing by Pseudomonas aeruginosa PA14. J Bacteriol 2024; 206:e0044223. [PMID: 38832786 PMCID: PMC11270903 DOI: 10.1128/jb.00442-23] [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] [Indexed: 06/05/2024] Open
Abstract
Most microbial cells found in nature exist in matrix-covered, surface-attached communities known as biofilms. This mode of growth is initiated by the ability of the microbe to sense a surface on which to grow. The opportunistic pathogen Pseudomonas aeruginosa (Pa) PA14 utilizes a single polar flagellum and type 4 pili (T4P) to sense surfaces. For Pa, T4P-dependent "twitching" motility is characterized by effectively pulling the cell across a surface through a complex process of cooperative binding, pulling, and unbinding. T4P retraction is powered by hexameric ATPases. Pa cells that have engaged a surface increase production of the second messenger cyclic AMP (cAMP) over multiple generations via the Pil-Chp system. This rise in cAMP allows cells and their progeny to become better adapted for surface attachment and activates virulence pathways through the cAMP-binding transcription factor Vfr. While many studies have focused on mechanisms of T4P twitching and regulation of T4P production and function by the Pil-Chp system, the mechanism by which Pa senses and relays a surface-engagement signal to the cell is still an open question. Here we review the current state of the surface sensing literature for Pa, with a focus on T4P, and propose an integrated model of surface sensing whereby the retraction motor PilT senses and relays the signal to the Pil-Chp system via PilJ to drive cAMP production and adaptation to a surface lifestyle.
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Affiliation(s)
- C. J. Geiger
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - G. C. L. Wong
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, California, USA
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California, USA
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California, USA
| | - G. A. O'Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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3
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Pérez-Burgos M, Herfurth M, Kaczmarczyk A, Harms A, Huber K, Jenal U, Glatter T, Søgaard-Andersen L. A deterministic, c-di-GMP-dependent program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis. Nat Commun 2024; 15:6014. [PMID: 39019889 PMCID: PMC11255338 DOI: 10.1038/s41467-024-50444-4] [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: 02/18/2024] [Accepted: 07/10/2024] [Indexed: 07/19/2024] Open
Abstract
Phenotypic heterogeneity in bacteria can result from stochastic processes or deterministic programs. The deterministic programs often involve the versatile second messenger c-di-GMP, and give rise to daughter cells with different c-di-GMP levels by deploying c-di-GMP metabolizing enzymes asymmetrically during cell division. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent program that is hardwired into the cell cycle of Myxococcus xanthus to minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity is switched on during cytokinesis, resulting in a transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating phenotypically similar daughters with correct motility behaviours. Thus, our findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria can ensure the formation of dissimilar or similar daughter cells by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations.
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Affiliation(s)
- María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Marco Herfurth
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | | | - Andrea Harms
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Katrin Huber
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Urs Jenal
- Biozentrum, University of Basel, Basel, Switzerland
| | - Timo Glatter
- Core Facility for Mass Spectrometry & Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
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4
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Wang Y, Theodore M, Xing Z, Narsaria U, Yu Z, Zeng L, Zhang J. Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus. SCIENCE ADVANCES 2024; 10:eadl4450. [PMID: 38701202 PMCID: PMC11067988 DOI: 10.1126/sciadv.adl4450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Caulobacter crescentus Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in Escherichia coli, maintaining infectivity against C. crescentus, which presents promising applications, including RNA delivery and phage display.
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Affiliation(s)
- Yuhang Wang
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Matthew Theodore
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zhongliang Xing
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Utkarsh Narsaria
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Zihao Yu
- Center for Phage Technology, Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
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5
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Wielgoss S, Van Dyken JD, Velicer GJ. Mutation Rate and Effective Population Size of the Model Cooperative Bacterium Myxococcus xanthus. Genome Biol Evol 2024; 16:evae066. [PMID: 38526062 PMCID: PMC11069108 DOI: 10.1093/gbe/evae066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here, we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation accumulation experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life cycle-such as group-size reduction during fruiting-body development-or its highly structured spatial distribution have significantly influenced how these parameters have evolved.
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Affiliation(s)
- Sébastien Wielgoss
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
| | - James David Van Dyken
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Gregory J Velicer
- Department of Environmental Systems Science, Institute of Integrative Biology, ETH Zürich, 8092 Zürich, Switzerland
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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6
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Barton DL, Chang YR, Ducker W, Dobnikar J. Data-driven modelling makes quantitative predictions regarding bacteria surface motility. PLoS Comput Biol 2024; 20:e1012063. [PMID: 38743804 PMCID: PMC11125545 DOI: 10.1371/journal.pcbi.1012063] [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: 12/15/2022] [Revised: 05/24/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states.
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Affiliation(s)
- Daniel L. Barton
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yow-Ren Chang
- National Institute of Standards and Technology (NIST), 100 Bureau Dr, Gaithersburg, Maryland, United States of America
| | - William Ducker
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virgina, United States of America
| | - Jure Dobnikar
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
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7
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Treuner-Lange A, Zheng W, Viljoen A, Lindow S, Herfurth M, Dufrêne YF, Søgaard-Andersen L, Egelman EH. Tight-packing of large pilin subunits provides distinct structural and mechanical properties for the Myxococcus xanthus type IVa pilus. Proc Natl Acad Sci U S A 2024; 121:e2321989121. [PMID: 38625941 PMCID: PMC11046646 DOI: 10.1073/pnas.2321989121] [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: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 04/18/2024] Open
Abstract
Type IVa pili (T4aP) are ubiquitous cell surface filaments important for surface motility, adhesion to surfaces, DNA uptake, biofilm formation, and virulence. T4aP are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While major pilins of structurally characterized T4aP have lengths of <165 residues, the major pilin PilA of Myxococcus xanthus is unusually large with 208 residues. All major pilins have a conserved N-terminal domain and a variable C-terminal domain, and the additional residues of PilA are due to a larger C-terminal domain. We solved the structure of the M. xanthus T4aP (T4aPMx) at a resolution of 3.0 Å using cryo-EM. The T4aPMx follows the structural blueprint of other T4aP with the pilus core comprised of the interacting N-terminal α1-helices, while the globular domains decorate the T4aP surface. The atomic model of PilA built into this map shows that the large C-terminal domain has more extensive intersubunit contacts than major pilins in other T4aP. As expected from these greater contacts, the bending and axial stiffness of the T4aPMx is significantly higher than that of other T4aP and supports T4aP-dependent motility on surfaces of different stiffnesses. Notably, T4aPMx variants with interrupted intersubunit interfaces had decreased bending stiffness, pilus length, and strongly reduced motility. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4aP that expands the environmental conditions in which the T4aP system functions.
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Affiliation(s)
- Anke Treuner-Lange
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
| | - Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA22903
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-NeuveB-1348, Belgium
| | - Steffi Lindow
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
| | - Marco Herfurth
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
| | - Yves F. Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Louvain-la-NeuveB-1348, Belgium
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg35043, Germany
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA22903
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8
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Thongchol J, Yu Z, Harb L, Lin Y, Koch M, Theodore M, Narsaria U, Shaevitz J, Gitai Z, Wu Y, Zhang J, Zeng L. Removal of Pseudomonas type IV pili by a small RNA virus. Science 2024; 384:eadl0635. [PMID: 38574145 PMCID: PMC11126211 DOI: 10.1126/science.adl0635] [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: 09/29/2023] [Accepted: 02/29/2024] [Indexed: 04/06/2024]
Abstract
The retractile type IV pilus (T4P) is important for virulence of the opportunistic human pathogen Pseudomonas aeruginosa. The single-stranded RNA (ssRNA) phage PP7 binds to T4P and is brought to the cell surface through pilus retraction. Using fluorescence microscopy, we discovered that PP7 detaches T4P, which impairs cell motility and restricts the pathogen's virulence. Using cryo-electron microscopy, mutagenesis, optical trapping, and Langevin dynamics simulation, we resolved the structure of PP7, T4P, and the PP7/T4P complex and showed that T4P detachment is driven by the affinity between the phage maturation protein and its bound pilin, plus the pilus retraction force and speed, and pilus bending. Pilus detachment may be widespread among other ssRNA phages and their retractile pilus systems and offers new prospects for antibacterial prophylaxis and therapeutics.
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Affiliation(s)
- Jirapat Thongchol
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Zihao Yu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Laith Harb
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Yiruo Lin
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX 77843, USA
| | - Matthias Koch
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Matthew Theodore
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Utkarsh Narsaria
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Joshua Shaevitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA
| | - Zemer Gitai
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Yinghao Wu
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, NY 10461, USA
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
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9
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Carbo CR, Faromiki OG, Nan B. A lytic transglycosylase connects bacterial focal adhesion complexes to the peptidoglycan cell wall. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.04.588103. [PMID: 38617213 PMCID: PMC11014575 DOI: 10.1101/2024.04.04.588103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The Gram-negative bacterium Myxococcus xanthus glides on solid surfaces. Dynamic bacterial focal adhesion complexes (bFACs) convert proton motive force from the inner membrane into mechanical propulsion on the cell surface. It is unclear how the mechanical force transmits across the rigid peptidoglycan (PG) cell wall. Here we show that AgmT, a highly abundant lytic PG transglycosylase homologous to Escherichia coli MltG, couples bFACs to PG. Coprecipitation assay and single-particle microscopy reveal that the gliding motors fail to connect to PG and thus are unable to assemble into bFACs in the absence of an active AgmT. Heterologous expression of E. coli MltG restores the connection between PG and bFACs and thus rescues gliding motility in the M. xanthus cells that lack AgmT. Our results indicate that bFACs anchor to AgmT-modified PG to transmit mechanical force across the PG cell wall.
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Affiliation(s)
- Carlos Ramirez Carbo
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- The Genetics and Genomics Interdisciplinary Program, Texas A&M University, College Station, TX 77843, USA
- C. R. C and O. G. F. contribute equally to this work
| | - Olalekan G. Faromiki
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
- C. R. C and O. G. F. contribute equally to this work
| | - Beiyan Nan
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
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10
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Zhu L, Wang K, Wu X, Zheng H, Liao X. Association of specific gut microbiota with polyethylene microplastics caused gut dysbiosis and increased susceptibility to opportunistic pathogens in honeybees. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 918:170642. [PMID: 38320694 DOI: 10.1016/j.scitotenv.2024.170642] [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: 11/09/2023] [Revised: 01/31/2024] [Accepted: 01/31/2024] [Indexed: 02/13/2024]
Abstract
The emergence of microplastics as contaminants has raised concerns regarding their potential toxicity. Recent studies on microplastic pollution caused by food packaging have drawn attention to its impact on health. However, despite being used extensively in food packaging, there is little knowledge about the toxicity of polyethylene microplastics (PE-MPs). Here, we studied the toxicity of PE-MPs on the model animal honeybees using different particle sizes (1 μm, 10 μm, 100 μm in diameter). Oral exposure to 100-μm PE-MPs resulted in elevated honeybee mortality and increased their susceptibility to pathogens. This is likely due to the mechanical disruption and gut microbial dysbiosis by PE-MPs. Snodgrassella, a core functional gut bacteria, was specifically enriched on the surface of PE-MPs, which perturbs the gut microbial communities in honeybees. Furthermore, the increased mortality in challenge trials with the opportunistic pathogen Hafnia alvei for PE-MPs pre-exposed honeybees revealed a potential health risk. These findings provide fresh insights into evaluating the potential hazards associated with PE-MPs.
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Affiliation(s)
- Liya Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100085, China
| | - Kewen Wang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100085, China
| | - Xiaomeng Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100085, China.
| | - Hao Zheng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100085, China
| | - Xiaojun Liao
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100085, China
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11
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Zhao S, Zhu S, Liu S, Song G, Zhao J, Liu R, Liu H, Qu J. Quorum Sensing Enhances Direct Interspecies Electron Transfer in Anaerobic Methane Production. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:2891-2901. [PMID: 38308618 DOI: 10.1021/acs.est.3c08503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Direct interspecies electron transfer (DIET) provides an innovative way to achieve efficient methanogenesis, and this study proposes a new approach to upregulate the DIET pathway by enhancing quorum sensing (QS). Based on long-term reactor performance, QS enhancement achieved more vigorous methanogenesis with 98.7% COD removal efficiency. In the control system, methanogenesis failure occurred at the accumulated acetate of 7420 mg of COD/L and lowered pH of 6.04, and a much lower COD removal of 41.9% was observed. The more significant DIET in QS-enhancing system was supported by higher expression of conductive pili and the c-Cyts cytochrome secretion-related genes, resulting in 12.7- and 10.3-fold improvements. Moreover, QS enhancement also improved the energy production capability, with the increase of F-type and V/A-type ATPase expression by 6.3- and 4.2-fold, and this effect probably provided more energy for nanowires and c-Cyts cytochrome secretion. From the perspective of community structure, QS enhancement increased the abundance of Methanosaeta and Geobacter from 54.3 and 17.6% in the control to 63.0 and 33.8%, respectively. Furthermore, the expression of genes involved in carbon dioxide reduction and alcohol dehydrogenation increased by 0.6- and 7.1-fold, respectively. Taken together, this study indicates the positive effects of QS chemicals to stimulate DIET and advances the understanding of the DIET methanogenesis involved in environments such as anaerobic digesters and sediments.
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Affiliation(s)
- Shunan Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shaoqing Zhu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Suo Liu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ge Song
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
- Key Laboratory of Drinking Water Science and Technology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Jing Zhao
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Huijuan Liu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- Center for Water and Ecology, State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
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12
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Little JI, Singh PK, Zhao J, Dunn S, Matz H, Donnenberg MS. Type IV pili of Enterobacteriaceae species. EcoSal Plus 2024:eesp00032023. [PMID: 38294234 DOI: 10.1128/ecosalplus.esp-0003-2023] [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: 04/03/2023] [Accepted: 12/01/2023] [Indexed: 02/01/2024]
Abstract
Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the Enterobacteriaceae family, which includes pathogenic strains of Escherichia coli and Salmonella. These include the bundle-forming pilus (BFP) of enteropathogenic E. coli (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic E. coli (ETEC), T4P of Salmonella enterica serovar Typhi, Colonization Factor Citrobacter (CFC) of Citrobacter rodentium, T4P of Yersinia pseudotuberculosis, a ubiquitous T4P that was characterized in enterohemorrhagic E. coli (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.
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Affiliation(s)
- Janay I Little
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Pradip K Singh
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jinlei Zhao
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shakeera Dunn
- Internal Medicine Residency, Bayhealth Medical Center, Dover, Delaware, USA
| | - Hanover Matz
- Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
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13
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Contreras-Moreno FJ, Pérez J, Muñoz-Dorado J, Moraleda-Muñoz A, Marcos-Torres FJ. Myxococcus xanthus predation: an updated overview. Front Microbiol 2024; 15:1339696. [PMID: 38328431 PMCID: PMC10849154 DOI: 10.3389/fmicb.2024.1339696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Bacterial predators are widely distributed across a variety of natural environments. Understanding predatory interactions is of great importance since they play a defining role in shaping microbial communities in habitats such as soils. Myxococcus xanthus is a soil-dwelling bacterial predator that can prey on Gram-positive and Gram-negative bacteria and even on eukaryotic microorganisms. This model organism has been studied for many decades for its unusual lifecycle, characterized by the formation of multicellular fruiting bodies filled with myxospores. However, less is known about its predatory behavior despite being an integral part of its lifecycle. Predation in M. xanthus is a multifactorial process that involves several mechanisms working synergistically, including motility systems to efficiently track and hunt prey, and a combination of short-range and contact-dependent mechanisms to achieve prey death and feed on them. In the short-range attack, M. xanthus is best known for the collective production of secondary metabolites and hydrolytic enzymes to kill prey and degrade cellular components. On the other hand, contact-dependent killing is a cell-to-cell process that relies on Tad-like and type III secretion systems. Furthermore, recent research has revealed that metals also play an important role during predation, either by inducing oxidative stress in the prey, or by competing for essential metals. In this paper, we review the current knowledge about M. xanthus predation, focusing on the different mechanisms used to hunt, kill, and feed on its prey, considering the most recent discoveries and the transcriptomic data available.
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Affiliation(s)
| | | | | | - Aurelio Moraleda-Muñoz
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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14
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Liu X, Tachiyama S, Zhou X, Mathias RA, Bonny SQ, Khan MF, Xin Y, Roujeinikova A, Liu J, Ottemann KM. Bacterial flagella hijack type IV pili proteins to control motility. Proc Natl Acad Sci U S A 2024; 121:e2317452121. [PMID: 38236729 PMCID: PMC10823254 DOI: 10.1073/pnas.2317452121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 11/27/2023] [Indexed: 01/23/2024] Open
Abstract
Bacterial flagella and type IV pili (TFP) are surface appendages that enable motility and mechanosensing through distinct mechanisms. These structures were previously thought to have no components in common. Here, we report that TFP and some flagella share proteins PilO, PilN, and PilM, which we identified as part of the Helicobacter pylori flagellar motor. H. pylori mutants lacking PilO or PilN migrated better than wild type in semisolid agar because they continued swimming rather than aggregated into microcolonies, mimicking the TFP-regulated surface response. Like their TFP homologs, flagellar PilO/PilN heterodimers formed a peripheral cage that encircled the flagellar motor. These results indicate that PilO and PilN act similarly in flagella and TFP by differentially regulating motility and microcolony formation when bacteria encounter surfaces.
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Affiliation(s)
- Xiaolin Liu
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA95064
| | - Shoichi Tachiyama
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536
- Microbial Sciences Institute, Yale University, West Haven, CT06516
| | - Xiaotian Zhou
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Rommel A. Mathias
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC3800, Australia
| | - Sharmin Q. Bonny
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Mohammad F. Khan
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Yue Xin
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
| | - Anna Roujeinikova
- Infection and Immunity Program, Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC3800, Australia
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT06536
- Microbial Sciences Institute, Yale University, West Haven, CT06516
| | - Karen M. Ottemann
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, CA95064
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15
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Rhodes KA, Rendón MA, Ma MC, Agellon A, Johnson AC, So M. Type IV pilus retraction is required for Neisseria musculi colonization and persistence in a natural mouse model of infection. mBio 2024; 15:e0279223. [PMID: 38084997 PMCID: PMC10790696 DOI: 10.1128/mbio.02792-23] [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: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE We describe the importance of Type IV pilus retraction to colonization and persistence by a mouse commensal Neisseria, N. musculi, in its native host. Our findings have implications for the role of Tfp retraction in mediating interactions of human-adapted pathogenic and commensal Neisseria with their human host due to the relatedness of these species.
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Affiliation(s)
- Katherine A. Rhodes
- Immunobiology Department, University of Arizona College of Medicine, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - María A. Rendón
- Immunobiology Department, University of Arizona College of Medicine, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Man Cheong Ma
- Immunobiology Department, University of Arizona College of Medicine, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
| | - Al Agellon
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona, USA
| | - Andrew C.E. Johnson
- Immunobiology Department, University of Arizona College of Medicine, Tucson, Arizona, USA
| | - Magdalene So
- Immunobiology Department, University of Arizona College of Medicine, Tucson, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
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16
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Guilvout I, Samsudin F, Huber RG, Bond PJ, Bardiaux B, Francetic O. Membrane platform protein PulF of the Klebsiella type II secretion system forms a trimeric ion channel essential for endopilus assembly and protein secretion. mBio 2024; 15:e0142323. [PMID: 38063437 PMCID: PMC10790770 DOI: 10.1128/mbio.01423-23] [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: 06/05/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type IV pili and type II secretion systems are members of the widespread type IV filament (T4F) superfamily of nanomachines that assemble dynamic and versatile surface fibers in archaea and bacteria. The assembly and retraction of T4 filaments with diverse surface properties and functions require the plasma membrane platform proteins of the GspF/PilC superfamily. Generally considered dimeric, platform proteins are thought to function as passive transmitters of the mechanical energy generated by the ATPase motor, to somehow promote insertion of pilin subunits into the nascent pilus fibers. Here, we generate and experimentally validate structural predictions that support the trimeric state of a platform protein PulF from a type II secretion system. The PulF trimers form selective proton or sodium channels which might energize pilus assembly using the membrane potential. The conservation of the channel sequence and structural features implies a common mechanism for all T4F assembly systems. We propose a model of the oligomeric PulF-PulE ATPase complex that provides an essential framework to investigate and understand the pilus assembly mechanism.
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Affiliation(s)
- Ingrid Guilvout
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
| | | | | | - Peter J. Bond
- Bioinformatics Institute (A-STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
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17
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Mom J, Chouikha I, Valette O, Pieulle L, Pelicic V. Systematic functional analysis of the Com pilus in Streptococcus sanguinis: a minimalistic type 4 filament dedicated to DNA uptake in monoderm bacteria. mBio 2024; 15:e0266723. [PMID: 38095871 PMCID: PMC10790768 DOI: 10.1128/mbio.02667-23] [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: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type 4 filaments (T4F) are nanomachines ubiquitous in prokaryotes, centered on filamentous polymers of type 4 pilins. T4F are exceptionally versatile and widespread virulence factors in bacterial pathogens. The mechanisms of filament assembly and the many functions they facilitate remain poorly understood because of the complexity of T4F machineries. This hinders the development of anti-T4F drugs. The significance of our research lies in characterizing the simplest known T4F-the Com pilus that mediates DNA uptake in competent monoderm bacteria-and showing that four protein components universally conserved in T4F are sufficient for filament assembly. The Com pilus becomes a model for elucidating the mechanisms of T4F assembly.
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Affiliation(s)
- Jeremy Mom
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Iman Chouikha
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Odile Valette
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Laetitia Pieulle
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
| | - Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, Aix-Marseille Université-CNRS (UMR 7283), Institut de Microbiologie de la Méditerranée, Marseille, France
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18
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Izadi-Pruneyre N, Karami Y, Nilges M. Structure and Dynamics of Type 4a Pili and Type 2 Secretion System Endopili. Subcell Biochem 2024; 104:549-563. [PMID: 38963500 DOI: 10.1007/978-3-031-58843-3_21] [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: 07/05/2024]
Abstract
Within the highly diverse type four filament (TFF or T4F) superfamily, the machineries of type IVa pili (T4aP) and the type 2 secretion system (T2SS) in diderm bacteria exhibit a substantial sequence similarity despite divergent functions and distinct appearances: T4aP can extend micrometers beyond the outer membrane, whereas the endopili in the T2SS are restricted to the periplasm. The determination of the structure of individual components and entire filaments is crucial to understand how their structure enables them to serve different functions. However, the dynamics of these filaments poses a challenge for their high-resolution structure determination. This review presents different approaches that have been used to study the structure and dynamics of T4aP and T2SS endopili by means of integrative structural biology, cryo-electron microscopy (cryo-EM), and molecular dynamics simulations. Their conserved features and differences are presented. The non-helical stretch in the long-conserved N-terminal helix which is characteristic of all members of the TFF and the impact of calcium on structure, function, and dynamics of these filaments are discussed in detail.
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Affiliation(s)
- Nadia Izadi-Pruneyre
- Bacterial Transmembrane Systems Unit, Institut Pasteur, Université Paris Cité, CNRS UMR, Paris, France
| | - Yasaman Karami
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Institut Pasteur, Université Paris Cité, CNRS UMR, Paris, France.
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19
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Cameron TA, Margolin W. Insights into the assembly and regulation of the bacterial divisome. Nat Rev Microbiol 2024; 22:33-45. [PMID: 37524757 PMCID: PMC11102604 DOI: 10.1038/s41579-023-00942-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 08/02/2023]
Abstract
The ability to split one cell into two is fundamental to all life, and many bacteria can accomplish this feat several times per hour with high accuracy. Most bacteria call on an ancient homologue of tubulin, called FtsZ, to localize and organize the cell division machinery, the divisome, into a ring-like structure at the cell midpoint. The divisome includes numerous other proteins, often including an actin homologue (FtsA), that interact with each other at the cytoplasmic membrane. Once assembled, the protein complexes that comprise the dynamic divisome coordinate membrane constriction with synthesis of a division septum, but only after overcoming checkpoints mediated by specialized protein-protein interactions. In this Review, we summarize the most recent evidence showing how the divisome proteins of Escherichia coli assemble at the cell midpoint, interact with each other and regulate activation of septum synthesis. We also briefly discuss the potential of divisome proteins as novel antibiotic targets.
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Affiliation(s)
- Todd A Cameron
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, USA
| | - William Margolin
- Department of Microbiology and Molecular Genetics, McGovern Medical School, Houston, TX, USA.
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20
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Herfurth M, Pérez-Burgos M, Søgaard-Andersen L. The mechanism for polar localization of the type IVa pilus machine in Myxococcus xanthus. mBio 2023; 14:e0159323. [PMID: 37754549 PMCID: PMC10653833 DOI: 10.1128/mbio.01593-23] [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: 06/22/2023] [Accepted: 07/31/2023] [Indexed: 09/28/2023] Open
Abstract
IMPORTANCE Type IVa pili (T4aP) are widespread bacterial cell surface structures with important functions in motility, surface adhesion, biofilm formation, and virulence. Different bacteria have adapted different piliation patterns. To address how these patterns are established, we focused on the bipolar localization of the T4aP machine in the model organism Myxococcus xanthus by studying the localization of the PilQ secretin, the first component of this machine that assembles at the poles. Based on experiments using a combination of fluorescence microscopy, biochemistry, and computational structural analysis, we propose that PilQ, and specifically its AMIN domains, binds septal and polar peptidoglycan, thereby enabling polar Tgl localization, which then stimulates PilQ multimerization in the outer membrane. We also propose that the presence and absence of AMIN domains in T4aP secretins contribute to the different piliation patterns across bacteria.
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Affiliation(s)
- Marco Herfurth
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - María Pérez-Burgos
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lotte Søgaard-Andersen
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
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21
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Liu M, Wei G, Lai Q, Huang Z, Li M, Shao Z. Genomic and metabolic insights into the first host-associated isolate of Psychrilyobacter. Microbiol Spectr 2023; 11:e0399022. [PMID: 37754757 PMCID: PMC10580919 DOI: 10.1128/spectrum.03990-22] [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: 10/04/2022] [Accepted: 08/11/2023] [Indexed: 09/28/2023] Open
Abstract
Although gut bacteria are vital to their hosts, few studies have focused on marine animals. Psychrilyobacter is frequently related to various marine animals, but its interaction with host remains unknown due to the lack of host-associated isolate or genomic information. Here, we combined cultivation-independent and cultivation-dependent methods to uncover the potential roles of Psychrilyobacter in the host abalone. The high-throughput sequencing and literature compiling results indicated that Psychrilyobacter is widely distributed in marine and terrestrial ecosystems with both host-associated and free-living lifestyles, but with a strong niche preference in the guts of marine invertebrates, especially abalone. By in vitro enrichment that mimicked the gut inner environment, the first host-related pure culture of Psychrilyobacter was isolated from the abalone intestine. Phylogenetic, physiological, and biochemical characterizations suggested that it represents a novel species named Psychrilyobacter haliotis B1. Carbohydrate utilization experiments and genomic evidence indicated that B1 can utilize diverse host-food-related monosaccharides and disaccharides but not polysaccharides, implying its potential role in the downstream fermentation instead of the upstream food degradation in the gut. Particularly, this strain showed potential to colonize the gut and benefit the host via different strategies, such as the short-chain fatty acids generation by fermenting peptides and/or amino acids, and the putative production of diverse vitamins and antibiotics to support the host growth and antipathogenicity. To our knowledge, strain B1 represents the first host-related pure culture of Psychrilyobacter; genomic and metabolic evidence showed some beneficial characteristics of the dominant gut anaerobe to the host. IMPORTANCE Psychrilyobacter is a globally distributed bacterial genus and with an inhabiting preference for guts of marine invertebrates. Due to the difficulty of cultivation and the limited genomic information, its role in host remains largely unknown. We isolated the first host-associated Psychrilyobacter species from abalone gut and uncovered its functional potential to the host through different mechanisms. Our findings provide some insights into the understanding of host-microbe interactions on a core taxon with the marine invertebrates, and the isolate may have an application potential in the protection of marine animals.
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Affiliation(s)
- Meijia Liu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of the PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Guangshan Wei
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of the PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
| | - Qiliang Lai
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of the PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Zhaobin Huang
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of the PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
| | - Min Li
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Zongze Shao
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources of the PR China; State Key Laboratory Breeding Base of Marine Genetic Resources; Fujian Key Laboratory of Marine Genetic Resources, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Marine Sciences, Sun Yat-Sen University, Zhuhai, China
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22
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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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23
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Tassinari M, Rudzite M, Filloux A, Low HH. Assembly mechanism of a Tad secretion system secretin-pilotin complex. Nat Commun 2023; 14:5643. [PMID: 37704603 PMCID: PMC10499894 DOI: 10.1038/s41467-023-41200-1] [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: 03/13/2023] [Accepted: 08/25/2023] [Indexed: 09/15/2023] Open
Abstract
The bacterial Tight adherence Secretion System (TadSS) assembles surface pili that drive cell adherence, biofilm formation and bacterial predation. The structure and mechanism of the TadSS is mostly unknown. This includes characterisation of the outer membrane secretin through which the pilus is channelled and recruitment of its pilotin. Here we investigate RcpA and TadD lipoprotein from Pseudomonas aeruginosa. Light microscopy reveals RcpA colocalising with TadD in P. aeruginosa and when heterologously expressed in Escherichia coli. We use cryogenic electron microscopy to determine how RcpA and TadD assemble a secretin channel with C13 and C14 symmetries. Despite low sequence homology, we show that TadD shares a similar fold to the type 4 pilus system pilotin PilF. We establish that the C-terminal four residues of RcpA bind TadD - an interaction essential for secretin formation. The binding mechanism between RcpA and TadD appears distinct from known secretin-pilotin pairings in other secretion systems.
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Affiliation(s)
- Matteo Tassinari
- Department of Infectious Disease, Imperial College, London, SW7 2AZ, UK
- Human Technopole, Milan, Italy
| | - Marta Rudzite
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
| | - Alain Filloux
- Department of Life Sciences, Imperial College, London, SW7 2AZ, UK
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Harry H Low
- Department of Infectious Disease, Imperial College, London, SW7 2AZ, UK.
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24
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Saggu SK, Nath A, Kumar S. Myxobacteria: biology and bioactive secondary metabolites. Res Microbiol 2023; 174:104079. [PMID: 37169232 DOI: 10.1016/j.resmic.2023.104079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/22/2023] [Accepted: 05/04/2023] [Indexed: 05/13/2023]
Abstract
Myxobacteria are Gram-negative eubacteria and they thrive in a variety of habitats including soil rich in organic matter, rotting wood, animal dung and marine environment. Myxobacteria are a promising source of new compounds associated with diverse bioactive spectrum and unique mode of action. The genome information of myxobacteria has revealed many orphan biosynthetic pathways indicating that these bacteria can be the source of several novel natural products. In this review, we highlight the biology of myxobacteria with emphasis on their habitat, life cycle, isolation methods and enlist all the bioactive secondary metabolites purified till date and their mode of action.
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Affiliation(s)
- Sandeep Kaur Saggu
- Department of Biotechnology, Kanya Maha Vidyalaya, Jalandhar, Punjab, India - 144004.
| | - Amar Nath
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
| | - Shiv Kumar
- Guru Gobind Singh Medical College, Baba Farid University of Health Sciences, Faridkot, Punjab India 151203.
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25
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Tan ZY, Cai S, Noble AJ, Chen JK, Shi J, Gan L. Heterogeneous non-canonical nucleosomes predominate in yeast cells in situ. eLife 2023; 12:RP87672. [PMID: 37503920 PMCID: PMC10382156 DOI: 10.7554/elife.87672] [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] [Indexed: 07/29/2023] Open
Abstract
Nuclear processes depend on the organization of chromatin, whose basic units are cylinder-shaped complexes called nucleosomes. A subset of mammalian nucleosomes in situ (inside cells) resembles the canonical structure determined in vitro 25 years ago. Nucleosome structure in situ is otherwise poorly understood. Using cryo-electron tomography (cryo-ET) and 3D classification analysis of budding yeast cells, here we find that canonical nucleosomes account for less than 10% of total nucleosomes expected in situ. In a strain in which H2A-GFP is the sole source of histone H2A, class averages that resemble canonical nucleosomes both with and without GFP densities are found ex vivo (in nuclear lysates), but not in situ. These data suggest that the budding yeast intranuclear environment favors multiple non-canonical nucleosome conformations. Using the structural observations here and the results of previous genomics and biochemical studies, we propose a model in which the average budding yeast nucleosome's DNA is partially detached in situ.
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Affiliation(s)
- Zhi Yang Tan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Shujun Cai
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Alex J Noble
- National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology CenterNew YorkUnited States
| | - Jon K Chen
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Jian Shi
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
| | - Lu Gan
- Department of Biological Sciences and Center for BioImaging Sciences, National University of SingaporeSingaporeSingapore
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Treuner-Lange A, Zheng W, Viljoen A, Lindow S, Herfurth M, Dufrêne YF, Søgaard-Andersen L, Egelman EH. Large pilin subunits provide distinct structural and mechanical properties for the Myxococcus xanthus type IV pilus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.22.550172. [PMID: 37503255 PMCID: PMC10370171 DOI: 10.1101/2023.07.22.550172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Type IV pili (T4P) are ubiquitous bacterial cell surface filaments important for surface motility, adhesion to biotic and abiotic surfaces, DNA uptake, biofilm formation, and virulence. T4P are built from thousands of copies of the major pilin subunit and tipped by a complex composed of minor pilins and in some systems also the PilY1 adhesin. While the major pilins of structurally characterized T4P have lengths of up to 161 residues, the major pilin PilA of Myxococcus xanthus is unusually large with 208 residues. All major pilins have a highly conserved N-terminal domain and a highly variable C-terminal domain, and the additional residues in the M. xanthus PilA are due to a larger C-terminal domain. We solved the structure of the M. xanthus T4P (T4P Mx ) at a resolution of 3.0 Å using cryo-electron microscopy (cryo-EM). The T4P Mx follows the structural blueprint observed in other T4P with the pilus core comprised of the extensively interacting N-terminal α1-helices while the globular domains decorate the T4P surface. The atomic model of PilA built into this map shows that the large C-terminal domain has much more extensive intersubunit contacts than major pilins in other T4P. As expected from these greater contacts, the bending and axial stiffness of the T4P Mx is significantly higher than that of other T4P and supports T4P-dependent motility on surfaces of different stiffnesses. Notably, T4P Mx variants with interrupted intersubunit interfaces had decreased bending stiffness and strongly reduced motility on all surfaces. These observations support an evolutionary scenario whereby the large major pilin enables the formation of a rigid T4P that expands the environmental conditions in which the T4P system functions.
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Iruegas R, Pfefferle K, Göttig S, Averhoff B, Ebersberger I. Feature architecture aware phylogenetic profiling indicates a functional diversification of type IVa pili in the nosocomial pathogen Acinetobacter baumannii. PLoS Genet 2023; 19:e1010646. [PMID: 37498819 PMCID: PMC10374093 DOI: 10.1371/journal.pgen.1010646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/06/2023] [Indexed: 07/29/2023] Open
Abstract
The Gram-negative bacterial pathogen Acinetobacter baumannii is a major cause of hospital-acquired opportunistic infections. The increasing spread of pan-drug resistant strains makes A. baumannii top-ranking among the ESKAPE pathogens for which novel routes of treatment are urgently needed. Comparative genomics approaches have successfully identified genetic changes coinciding with the emergence of pathogenicity in Acinetobacter. Genes that are prevalent both in pathogenic and a-pathogenic Acinetobacter species were not considered ignoring that virulence factors may emerge by the modification of evolutionarily old and widespread proteins. Here, we increased the resolution of comparative genomics analyses to also include lineage-specific changes in protein feature architectures. Using type IVa pili (T4aP) as an example, we show that three pilus components, among them the pilus tip adhesin ComC, vary in their Pfam domain annotation within the genus Acinetobacter. In most pathogenic Acinetobacter isolates, ComC displays a von Willebrand Factor type A domain harboring a finger-like protrusion, and we provide experimental evidence that this finger conveys virulence-related functions in A. baumannii. All three genes are part of an evolutionary cassette, which has been replaced at least twice during A. baumannii diversification. The resulting strain-specific differences in T4aP layout suggests differences in the way how individual strains interact with their host. Our study underpins the hypothesis that A. baumannii uses T4aP for host infection as it was shown previously for other pathogens. It also indicates that many more functional complexes may exist whose precise functions have been adjusted by modifying individual components on the domain level.
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Affiliation(s)
- Ruben Iruegas
- Applied Bioinformatics Group, Inst of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Katharina Pfefferle
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stephan Göttig
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe University, Frankfurt, Germany
| | - Beate Averhoff
- Molecular Microbiology & Bioenergetics, Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Inst of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre (S-BIK-F), Frankfurt am Main, Germany
- LOEWE Centre for Translational Biodiversity Genomics (TBG), Frankfurt am Main, Germany
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28
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Kaplan M, Chang YW, Oikonomou CM, Nicolas WJ, Jewett AI, Kreida S, Dutka P, Rettberg LA, Maggi S, Jensen GJ. Bdellovibrio predation cycle characterized at nanometre-scale resolution with cryo-electron tomography. Nat Microbiol 2023; 8:1267-1279. [PMID: 37349588 PMCID: PMC11061892 DOI: 10.1038/s41564-023-01401-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/27/2023] [Indexed: 06/24/2023]
Abstract
Bdellovibrio bacteriovorus is a microbial predator that offers promise as a living antibiotic for its ability to kill Gram-negative bacteria, including human pathogens. Even after six decades of study, fundamental details of its predation cycle remain mysterious. Here we used cryo-electron tomography to comprehensively image the lifecycle of B. bacteriovorus at nanometre-scale resolution. With high-resolution images of predation in a native (hydrated, unstained) state, we discover several surprising features of the process, including macromolecular complexes involved in prey attachment/invasion and a flexible portal structure lining a hole in the prey peptidoglycan that tightly seals the prey outer membrane around the predator during entry. Unexpectedly, we find that B. bacteriovorus does not shed its flagellum during invasion, but rather resorbs it into its periplasm for degradation. Finally, following growth and division in the bdelloplast, we observe a transient and extensive ribosomal lattice on the condensed B. bacteriovorus nucleoid.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefan Kreida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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Simsek AN, Koch MD, Sanfilippo JE, Gitai Z, Gompper G, Sabass B. Type-IV pili tune an adhesion-migration trade-off during surface colonization of Pseudomonas aeruginosa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.538458. [PMID: 37215001 PMCID: PMC10197611 DOI: 10.1101/2023.05.09.538458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Bacterial pathogenicity relies on both firm surface adhesion and cell dissemination. How twitching bacteria resolve the fundamental contradiction between adhesion and migration is unknown. To address this question, we employ live-cell imaging of type-IV pili (T4P) and therewith construct a comprehensive mathematical model of Pseudomonas aeruginosa migration. The data show that only 10% to 50% of T4P bind to substrates and contribute to migration through random extension and retraction. Individual T4P do not display a measurable sensory response to surfaces, but their number increases on cellular surface contact. Attachment to surfaces is mediated, besides T4P, by passive adhesive forces acting on the cell body. Passive adhesions slow down cell migration and result in local random motion on short time scales, which is followed by directionally persistent, superdiffusive motion on longer time scales. Moreover, passive adhesions strongly enhance surface attachment under shear flow. Δ pilA mutants, which produce no T4P, robustly stick to surfaces under shear flow. In contrast, rapidly migrating Δ pilH cells, which produce an excessive number of T4P, are easily detached by shear. Wild-type cells sacrifice migration speed for robust surface attachment by maintaining a low number of active pili. The different cell strains pertain to disjunct regimes in a generic adhesion-migration trait space. Depending on the nature of the adhesion structures, adhesion and migration are either compatible or a trade-off is required for efficient bacterial surface colonization under different conditions.
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Murakami H, Sano K, Motomura K, Kuroda A, Hirota R. Assessment of horizontal gene transfer-mediated destabilization of Synechococcus elongatus PCC 7942 biocontainment system. J Biosci Bioeng 2023; 135:190-195. [PMID: 36653270 DOI: 10.1016/j.jbiosc.2022.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 01/18/2023]
Abstract
Biological containment is a biosafety strategy that prevents the dispersal of genetically modified organisms in natural ecosystems. We previously established a biocontainment system that makes bacterial growth dependent on the availability of phosphite (Pt), an ecologically rare form of phosphorus (P), by introducing Pt metabolic pathway genes and disrupting endogenous phosphate and organic phosphate transporter genes. Although this system proved highly effective, horizontal gene transfer (HGT) mediated recovery of a P transporter gene is considered as a potential pathway to abolish the Pt-dependent growth, resulting in escape from the containment. Here, we assessed the risk of HGT driven escape using the Pt-dependent cyanobacterium Synechococcus elongatus PCC 7942. Transformation experiments revealed that the Pt-dependent strain could regain phosphate transporter genes from the S. elongatus PCC 7942 wild-type genome and from the genome of the closely related strain, S. elongatus UTEX 2973. Transformed S. elongatus PCC 7942 became viable in a phosphate-containing medium. Meanwhile, transformation of the Synechocystis sp. PCC 6803 genome or environmental DNA did not yield escape strains, suggesting that only genetic material derived from phylogenetically-close species confer high risk to generate escape. Eliminating a single gene necessary for natural competence from the Pt-dependent strain reduced the escape occurrence rate. These results demonstrate that natural competence could be a potential risk to destabilize Pt-dependence, and therefore inhibiting exogenous DNA uptake would be effective for enhancing the robustness of the gene disruption-dependent biocontainment.
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Affiliation(s)
- Hiroki Murakami
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kosuke Sano
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Kei Motomura
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Unit of Biotechnology, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
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Pelicic V. Mechanism of assembly of type 4 filaments: everything you always wanted to know (but were afraid to ask). MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36947586 DOI: 10.1099/mic.0.001311] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Type 4 filaments (T4F) are a superfamily of filamentous nanomachines - virtually ubiquitous in prokaryotes and functionally versatile - of which type 4 pili (T4P) are the defining member. T4F are polymers of type 4 pilins, assembled by conserved multi-protein machineries. They have long been an important topic for research because they are key virulence factors in numerous bacterial pathogens. Our poor understanding of the molecular mechanisms of T4F assembly is a serious hindrance to the design of anti-T4F therapeutics. This review attempts to shed light on the fundamental mechanistic principles at play in T4F assembly by focusing on similarities rather than differences between several (mostly bacterial) T4F. This holistic approach, complemented by the revolutionary ability of artificial intelligence to predict protein structures, led to an intriguing mechanistic model of T4F assembly.
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Affiliation(s)
- Vladimir Pelicic
- Laboratoire de Chimie Bactérienne, UMR 7283 CNRS/Aix-Marseille Université, Institut de Microbiologie de la Méditerranée, Marseille, France
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32
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Dinet C, Mignot T. Unorthodox regulation of the MglA Ras-like GTPase controlling polarity in Myxococcus xanthus. FEBS Lett 2023; 597:850-864. [PMID: 36520515 DOI: 10.1002/1873-3468.14565] [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: 10/21/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Motile cells have developed a large array of molecular machineries to actively change their direction of movement in response to spatial cues from their environment. In this process, small GTPases act as molecular switches and work in tandem with regulators and sensors of their guanine nucleotide status (GAP, GEF, GDI and effectors) to dynamically polarize the cell and regulate its motility. In this review, we focus on Myxococcus xanthus as a model organism to elucidate the function of an atypical small Ras GTPase system in the control of directed cell motility. M. xanthus cells direct their motility by reversing their direction of movement through a mechanism involving the redirection of the motility apparatus to the opposite cell pole. The reversal frequency of moving M. xanthus cells is controlled by modular and interconnected protein networks linking the chemosensory-like frizzy (Frz) pathway - that transmits environmental signals - to the downstream Ras-like Mgl polarity control system - that comprises the Ras-like MglA GTPase protein and its regulators. Here, we discuss how variations in the GTPase interactome landscape underlie single-cell decisions and consequently, multicellular patterns.
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Affiliation(s)
- Céline Dinet
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, France
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la Méditerranée, CNRS-Aix-Marseille University, France
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Material Substrate Physical Properties Control Pseudomonas aeruginosa Biofilm Architecture. mBio 2023; 14:e0351822. [PMID: 36786569 PMCID: PMC10127718 DOI: 10.1128/mbio.03518-22] [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: 02/15/2023] Open
Abstract
In the wild, bacteria are most frequently found in the form of multicellular structures called biofilms. Biofilms grow at the surface of abiotic and living materials with wide-ranging mechanical properties. The opportunistic pathogen Pseudomonas aeruginosa forms biofilms on indwelling medical devices and on soft tissues, including burn wounds and the airway mucosa. Despite the critical role of substrates in the foundation of biofilms, we still lack a clear understanding of how material mechanics regulate their architecture and the physiology of resident bacteria. Here, we demonstrate that physical properties of hydrogel material substrates define P. aeruginosa biofilm architecture. We show that hydrogel mesh size regulates twitching motility, a surface exploration mechanism priming biofilms, ultimately controlling the organization of single cells in the multicellular community. The resulting architectural transitions increase P. aeruginosa's tolerance to colistin, a last-resort antibiotic. In addition, mechanical regulation of twitching motility affects P. aeruginosa clonal lineages, so that biofilms are more mixed on relatively denser materials. Our results thereby establish material properties as a factor that dramatically affects biofilm architecture, antibiotic efficacy, and evolution of the resident population. IMPORTANCE The biofilm lifestyle is the most widespread survival strategy in the bacterial world. Pseudomonas aeruginosa biofilms cause chronic infections and are highly recalcitrant to antimicrobials. The genetic requirements allowing P. aeruginosa to grow into biofilms are known, but not the physical stimuli that regulate their formation. Despite colonizing biological tissues, investigations of biofilms on soft materials are limited. In this work, we show that biofilms take unexpected forms when growing on soft substrates. The physical properties of the material shape P. aeruginosa biofilms by regulating surface-specific twitching motility. Physical control of biofilm morphogenesis ultimately influences the resilience of biofilms to antimicrobials, linking physical environment with tolerance to treatment. Altogether, our work established that the physical properties of a surface are a critical environmental regulator of biofilm biogenesis and evolution.
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Dazzoni R, Li Y, López-Castilla A, Brier S, Mechaly A, Cordier F, Haouz A, Nilges M, Francetic O, Bardiaux B, Izadi-Pruneyre N. Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system. Structure 2023; 31:152-165.e7. [PMID: 36586404 DOI: 10.1016/j.str.2022.12.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Revised: 10/20/2022] [Accepted: 11/29/2022] [Indexed: 12/31/2022]
Abstract
Type II secretion systems (T2SSs) allow diderm bacteria to secrete hydrolytic enzymes, adhesins, or toxins important for growth and virulence. To promote secretion of folded proteins, T2SSs assemble periplasmic filaments called pseudopili or endopili at an inner membrane subcomplex, the assembly platform (AP). Here, we combined biophysical approaches, nuclear magnetic resonance (NMR) and X-ray crystallography, to study the Klebsiella AP components PulL and PulM. We determined the structure and associations of their periplasmic domains and describe the structure of the heterodimer formed by their ferredoxin-like domains. We show how structural complementarity and plasticity favor their association during the secretion process. Cysteine scanning and crosslinking data provided additional constraints to build a structural model of the PulL-PulM assembly in the cellular context. Our structural and functional insights, together with the relative cellular abundance of its components, support the role of AP as a dynamic hub that orchestrates pilus polymerization.
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Affiliation(s)
- Régine Dazzoni
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Yuanyuan Li
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Aracelys López-Castilla
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Sébastien Brier
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Ariel Mechaly
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, 75015 Paris, France
| | - Florence Cordier
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biological NMR and HDX-MS Technological Platform, 75015 Paris, France
| | - Ahmed Haouz
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Crystallography Platform, 75015 Paris, France
| | - Michael Nilges
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Biochemistry of Macromolecular Interactions Unit, 75015 Paris, France
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, 75015 Paris.
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR3528, Structural Bioinformatics Unit, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3528, Bacterial Transmembrane Systems Unit, 75015 Paris.
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Asghar Z, Shah RA, Shatanawi W, Ali N. FENE-P fluid flow generated by self-propelling bacteria with slip effects. Comput Biol Med 2023; 153:106386. [PMID: 36587569 DOI: 10.1016/j.compbiomed.2022.106386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/27/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
It is hypothesized that gliding bacteria move by producing waves on their own surface and leave an adhesive slime trail. Slime is basically a viscoelastic slippery material. Based on these observations, we use a mathematical model (of undulating sheet) to examine the locomotion of gliding bacteria over a layer of non-Newtonian slime. The constitutive equations of FENE-P model are employed to characterize the rheological behavior of the non-Newtonian slime. Moreover, substratum beneath the slime is approximated by a multi-sinusoidal sheet. A hybrid computational technique to solve the second order DE with a system of algebraic equations is presented. The speed of organism, flow rate and energy loss at larger values of the involved parameters are simulated using bvp5c in conjunction with a modified Newton-Raphson technique (MNRT). The comparison of soft and rigid substrate, slip and no-slip boundary conditions, Newtonian and non-Newtonian slime is displayed in several figures. Streamlines pattern and velocity of the slime are also drawn for the realistic pairs of speed and flow rate and are thoroughly explained.
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Affiliation(s)
- Zeeshan Asghar
- Department of Mathematics and Sciences, College of Humanities and Sciences, Prince Sultan University, Riyadh, 11586, Saudi Arabia; NUTECH, School of Applied Sciences and Humanities, National University of Technology, Islamabad, 44000, Pakistan.
| | - Rehman Ali Shah
- Department of Mathematics and Statistics, International Islamic University, Islamabad, 44000, Pakistan
| | - Wasfi Shatanawi
- Department of Mathematics and Sciences, College of Humanities and Sciences, Prince Sultan University, Riyadh, 11586, Saudi Arabia; Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan; Department of Mathematics, Faculty of Science, The Hashemite University, P.O. Box 330127, Zarqa, 13133, Jordan.
| | - Nasir Ali
- Department of Mathematics and Statistics, International Islamic University, Islamabad, 44000, Pakistan
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Characterization of a glycan-binding complex of minor pilins completes the analysis of Streptococcus sanguinis type 4 pili subunits. Proc Natl Acad Sci U S A 2023; 120:e2216237120. [PMID: 36626560 PMCID: PMC9934059 DOI: 10.1073/pnas.2216237120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Type 4 filaments (T4F)-of which type 4 pili (T4P) are the archetype-are a superfamily of nanomachines nearly ubiquitous in prokaryotes. T4F are polymers of one major pilin, which also contain minor pilins whose roles are often poorly understood. Here, we complete the structure/function analysis of the full set of T4P pilins in the opportunistic bacterial pathogen Streptococcus sanguinis. We determined the structure of the minor pilin PilA, which is unexpectedly similar to one of the subunits of a tip-located complex of four minor pilins, widely conserved in T4F. We found that PilA interacts and dramatically stabilizes the minor pilin PilC. We determined the structure of PilC, showing that it is a modular pilin with a lectin module binding a subset of glycans prevalent in the human glycome, the host of S. sanguinis. Altogether, our findings support a model whereby the minor pilins in S. sanguinis T4P form a tip-located complex promoting adhesion to various host receptors. This has general implications for T4F.
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Bacterial Motility and Its Role in Skin and Wound Infections. Int J Mol Sci 2023; 24:ijms24021707. [PMID: 36675220 PMCID: PMC9864740 DOI: 10.3390/ijms24021707] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Skin and wound infections are serious medical problems, and the diversity of bacteria makes such infections difficult to treat. Bacteria possess many virulence factors, among which motility plays a key role in skin infections. This feature allows for movement over the skin surface and relocation into the wound. The aim of this paper is to review the type of bacterial movement and to indicate the underlying mechanisms than can serve as a target for developing or modifying antibacterial therapies applied in wound infection treatment. Five types of bacterial movement are distinguished: appendage-dependent (swimming, swarming, and twitching) and appendage-independent (gliding and sliding). All of them allow bacteria to relocate and aid bacteria during infection. Swimming motility allows bacteria to spread from 'persister cells' in biofilm microcolonies and colonise other tissues. Twitching motility enables bacteria to press through the tissues during infection, whereas sliding motility allows cocci (defined as non-motile) to migrate over surfaces. Bacteria during swarming display greater resistance to antimicrobials. Molecular motors generating the focal adhesion complexes in the bacterial cell leaflet generate a 'wave', which pushes bacterial cells lacking appendages, thereby enabling movement. Here, we present the five main types of bacterial motility, their molecular mechanisms, and examples of bacteria that utilise them. Bacterial migration mechanisms can be considered not only as a virulence factor but also as a target for antibacterial therapy.
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Lai L, Cheung YW, Martinez M, Kixmoeller K, Palao L, Steimle S, Ho MC, Black BE, Lai EM, Chang YW. In Situ Structure Determination of Bacterial Surface Nanomachines Using Cryo-Electron Tomography. Methods Mol Biol 2023; 2646:211-248. [PMID: 36842118 DOI: 10.1007/978-1-0716-3060-0_18] [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] [Indexed: 04/13/2023]
Abstract
Bacterial surface nanomachines are often refractory to structural determination in their intact form due to their extensive association with the cell envelope preventing them from being properly purified for traditional structural biology methods. Cryo-electron tomography (cryo-ET) is an emerging branch of cryo-electron microscopy that can visualize supramolecular complexes directly inside frozen-hydrated cells in 3D at nanometer resolution, therefore posing a unique capability to study the intact structures of bacterial surface nanomachines in situ and reveal their molecular association with other cellular components. Furthermore, the resolution of cryo-ET is continually improving alongside methodological advancement. Here, using the type IV pilus machine in Myxococcus xanthus as an example, we describe a step-by-step workflow for in situ structure determination including sample preparation and screening, microscope and camera tuning, tilt series acquisition, data processing and tomogram reconstruction, subtomogram averaging, and structural analysis.
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Affiliation(s)
- Longsheng Lai
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Wai Cheung
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Matthew Martinez
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kathryn Kixmoeller
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leon Palao
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Stefan Steimle
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Meng-Chiao Ho
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Ben E Black
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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Discovery of Two Inhibitors of the Type IV Pilus Assembly ATPase PilB as Potential Antivirulence Compounds. Microbiol Spectr 2022; 10:e0387722. [PMID: 36377931 PMCID: PMC9769694 DOI: 10.1128/spectrum.03877-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
With the pressing antibiotic resistance pandemic, antivirulence has been increasingly explored as an alternative strategy against bacterial infections. The bacterial type IV pilus (T4P) is a well-documented virulence factor and an attractive target for small molecules for antivirulence purposes. The PilB ATPase is essential for T4P biogenesis because it catalyzes the assembly of monomeric pilins into the polymeric pilus filament. Here, we describe the identification of two PilB inhibitors by a high-throughput screen (HTS) in vitro and their validation as effective inhibitors of T4P assembly in vivo. We used Chloracidobacterium thermophilum PilB as a model enzyme to optimize an ATPase assay for the HTS. From a library of 2,320 compounds, benserazide and levodopa, two approved drugs for Parkinson's disease, were identified and confirmed biochemically to be PilB inhibitors. We demonstrate that both compounds inhibited the T4P-dependent motility of the bacteria Myxoccocus xanthus and Acinetobacter nosocomialis. Additionally, benserazide and levodopa were shown to inhibit A. nosocomialis biofilm formation, a T4P-dependent process. Using M. xanthus as a model, we showed that both compounds inhibited T4P assembly in a dose-dependent manner. These results suggest that these two compounds are effective against the PilB protein in vivo. The potency of benserazide and levodopa as PilB inhibitors both in vitro and in vivo demonstrate potentials of the HTS and its two hits here for the development of anti-T4P chemotherapeutics. IMPORTANCE Many bacterial pathogens use their type IV pilus (T4P) to facilitate and maintain an infection in a human host. Small-molecule inhibitors of the production or assembly of the T4P are promising for the treatment and prevention of infections by these bacteria, especially in our fight against antibiotic-resistant pathogens. Here, we report the development and implementation of a method to identify anti-T4P chemicals from compound libraries by high-throughput screen. This led to the identification and validation of two T4P inhibitors both in the test tubes and in bacteria. The discovery and validation pipeline reported here as well as the confirmation of two anti-T4P inhibitors provide new venues and leads for the development of chemotherapeutics against antibiotic-resistant infections.
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CpxAR of Actinobacillus pleuropneumoniae Contributes to Heat Stress Response by Repressing Expression of Type IV Pilus Gene apfA. Microbiol Spectr 2022; 10:e0252322. [PMID: 36259970 PMCID: PMC9769684 DOI: 10.1128/spectrum.02523-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Acute pleuropneumonia in swine, caused by Actinobacillus pleuropneumoniae, is characterized by a high and sustained fever. Fever creates an adverse environment for many bacteria, leading to reduced bacterial proliferation; however, most pathogenic bacteria can tolerate higher temperatures. CpxAR is a two-component regulation system, ubiquitous among Gram-negative bacteria, which senses and responds to envelope alterations that are mostly associated with protein misfolding in the periplasm. Our previous study showed that CpxAR is necessary for the optimal growth of Actinobacillus pleuropneumoniae under heat stress. Here, we showed that mutation of the type IV pilin gene apfA rescued the growth defect of the cpxAR deletion strain under heat stress. RNA sequencing (RNA-seq) analyses revealed that 265 genes were differentially expressed in the ΔcpxAR strains grown at 42°C, including genes involved in type IV pilus biosynthesis. We also demonstrated direct binding of the CpxR protein to the promoter of the apf operon by an electrophoretic mobility shift assay and identified the binding site by a DNase I footprinting assay. In conclusion, our results revealed the important role of CpxAR in A. pleuropneumoniae resistance to heat stress by directly suppressing the expression of ApfA. IMPORTANCE Heat acts as a danger signal for pathogens, especially those infecting mammalian hosts in whom fever indicates infection. However, some bacteria have evolved exquisite mechanisms to survive under heat stress. Studying the mechanism of resistance to heat stress is crucial to understanding the pathogenesis of A. pleuropneumoniae during the acute stage of infection. Our study revealed that CpxAR plays an important role in A. pleuropneumoniae resistance to heat stress by directly suppressing expression of the type IV pilin protein ApfA.
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Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus. mBio 2022; 13:e0268822. [PMID: 36374038 PMCID: PMC9765702 DOI: 10.1128/mbio.02688-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Hydrocephalus, the leading indication for childhood neurosurgery worldwide, is particularly prevalent in low- and middle-income countries. Hydrocephalus preceded by an infection, or postinfectious hydrocephalus, accounts for up to 60% of hydrocephalus in these areas. Since many children with hydrocephalus suffer poor long-term outcomes despite surgical intervention, prevention of hydrocephalus remains paramount. Our previous studies implicated a novel bacterial pathogen, Paenibacillus thiaminolyticus, as a causal agent of neonatal sepsis and postinfectious hydrocephalus in Uganda. Here, we report the isolation of three P. thiaminolyticus strains, Mbale, Mbale2, and Mbale3, from patients with postinfectious hydrocephalus. We constructed complete genome assemblies of the clinical isolates as well as the nonpathogenic P. thiaminolyticus reference strain and performed comparative genomic and proteomic analyses to identify potential virulence factors. All three isolates carry a unique beta-lactamase gene, and two of the three isolates exhibit resistance in culture to the beta-lactam antibiotics penicillin and ampicillin. In addition, a cluster of genes carried on a mobile genetic element that encodes a putative type IV pilus operon is present in all three clinical isolates but absent in the reference strain. CRISPR-mediated deletion of the gene cluster substantially reduced the virulence of the Mbale strain in mice. Comparative proteogenomic analysis identified various additional potential virulence factors likely acquired on mobile genetic elements in the virulent strains. These results provide insight into the emergence of virulence in P. thiaminolyticus and suggest avenues for the diagnosis and treatment of this novel bacterial pathogen. IMPORTANCE Postinfectious hydrocephalus, a devastating sequela of neonatal infection, is associated with increased childhood mortality and morbidity. A novel bacterial pathogen, Paenibacillus thiaminolyticus, is highly associated with postinfectious hydrocephalus in an African cohort. Whole-genome sequencing, RNA sequencing, and proteomics of clinical isolates and a reference strain in combination with CRISPR editing identified type IV pili as a critical virulence factor for P. thiaminolyticus infection. Acquisition of a type IV pilus-encoding mobile genetic element critically contributed to converting a nonpathogenic strain of P. thiaminolyticus into a pathogen capable of causing devastating diseases. Given the widespread presence of type IV pilus in pathogens, the presence of the type IV pilus operon could serve as a diagnostic and therapeutic target in P. thiaminolyticus and related bacteria.
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Kieninger AK, Tokarz P, Janović A, Pilhofer M, Weiss GL, Maldener I. SepN is a septal junction component required for gated cell-cell communication in the filamentous cyanobacterium Nostoc. Nat Commun 2022; 13:7486. [PMID: 36470860 PMCID: PMC9722847 DOI: 10.1038/s41467-022-34946-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 11/11/2022] [Indexed: 12/09/2022] Open
Abstract
Multicellular organisms require controlled intercellular communication for their survival. Strains of the filamentous cyanobacterium Nostoc regulate cell-cell communication between sister cells via a conformational change in septal junctions. These multi-protein cell junctions consist of a septum spanning tube with a membrane-embedded plug at both ends, and a cap covering the plug on the cytoplasmic side. The identities of septal junction components are unknown, with exception of the protein FraD. Here, we identify and characterize a FraD-interacting protein, SepN, as the second component of septal junctions in Nostoc. We use cryo-electron tomography of cryo-focused ion beam-thinned cyanobacterial filaments to show that septal junctions in a sepN mutant lack a plug module and display an aberrant cap. The sepN mutant exhibits highly reduced cell-cell communication rates, as shown by fluorescence recovery after photobleaching experiments. Furthermore, the mutant is unable to gate molecule exchange through septal junctions and displays reduced filament survival after stress. Our data demonstrate the importance of controlling molecular diffusion between cells to ensure the survival of a multicellular organism.
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Affiliation(s)
- Ann-Katrin Kieninger
- grid.10392.390000 0001 2190 1447Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Piotr Tokarz
- grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Ana Janović
- grid.10392.390000 0001 2190 1447Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - Martin Pilhofer
- grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Gregor L. Weiss
- grid.5801.c0000 0001 2156 2780Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Iris Maldener
- grid.10392.390000 0001 2190 1447Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Organismic Interactions, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
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Asghar Z, Shah RA, Pasha AA, Rahman MM, Khan MWS. Controlling kinetics of self-propelled rod-like swimmers near multi sinusoidal substrate. Comput Biol Med 2022; 151:106250. [PMID: 36368110 DOI: 10.1016/j.compbiomed.2022.106250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/24/2022] [Accepted: 10/24/2022] [Indexed: 12/27/2022]
Abstract
Motility is defined as the movement of cells by some form of self-propulsion. Some organisms motile by using long flagella that quickly rotate to propel them over various surfaces (in swarming and swimming mechanism), while few motile without the aid of flagella (in twitching, sliding and gliding mechanism). Among these modes, gliding motility is adopted by a rod-shaped organism famously known as gliding bacteria. It is hypothesized that in such type of motility, organism motile under their own power by secreting a layer of slime on the substrate. In this study, an active wall is considered as a substrate and a two-dimensional wavy sheet as an organism. Slip effects are also employed in the current work. The physical properties of the slime are governed by a suitable constitutive equation of couple stress model. A sixth order BVP is obtained by utilizing lubrication assumption. For an appropriate fixed pair of flow rate and organism speed the BVP is solved by MATLAB built-in function bvp-5c. This solution is utilized in the mechanical equilibrium conditions which are obviously not satisfied yet. To satisfy these conditions, the pair of flow rate and gliding speed is refined by a root finding algorithm (modified Newton-Raphson method). By employing this numerical scheme, various figures are shown to demonstrate the effect of several associated parameters on organism speed, flow rate, energy expended by the glider, streamlines and longitudinal velocity. It is observed from the graphical results that organism speed and energy consumption is directly proportional to the couple stress parameter and slip effects.
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Affiliation(s)
- Zeeshan Asghar
- Department of Mathematics and Sciences, College of Humanities and Sciences, Prince Sultan University, Riyadh, 11586, Saudi Arabia.
| | - Rehman Ali Shah
- Department of Mathematics and Statistics, International Islamic University, Islamabad, 44000, Pakistan
| | - Amjad Ali Pasha
- Aerospace Engineering Department, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
| | - Mustafa Mutiur Rahman
- Department of Mechanical and Mechatronics Engineering, University of Waterloo, ON, N2L 3G1, Canada
| | - Muhammad Waris Saeed Khan
- Department of Mathematics and Statistics, International Islamic University, Islamabad, 44000, Pakistan
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Hughes HQ, Christman ND, Dalia TN, Ellison CK, Dalia AB. The PilT retraction ATPase promotes both extension and retraction of the MSHA type IVa pilus in Vibrio cholerae. PLoS Genet 2022; 18:e1010561. [PMID: 36542674 DOI: 10.1371/journal.pgen.1010561] [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: 06/01/2022] [Revised: 01/05/2023] [Accepted: 12/07/2022] [Indexed: 12/24/2022] Open
Abstract
Diverse bacterial species use type IVa pili (T4aP) to interact with their environments. The dynamic extension and retraction of T4aP is critical for their function, but the mechanisms that regulate this dynamic activity remain poorly understood. T4aP are typically extended via the activity of a dedicated extension motor ATPase and retracted via the action of an antagonistic retraction motor ATPase called PilT. These motors are generally functionally independent, and loss of PilT commonly results in T4aP hyperpiliation due to undeterred pilus extension. However, for the mannose-sensitive hemagglutinin (MSHA) T4aP of Vibrio cholerae, the loss of PilT unexpectedly results in a loss of surface piliation. Here, we employ a combination of genetic and cell biological approaches to dissect the underlying mechanism. Our results demonstrate that PilT is necessary for MSHA pilus extension in addition to its well-established role in promoting MSHA pilus retraction. Through a suppressor screen, we also provide genetic evidence that the MshA major pilin impacts pilus extension. Together, these findings contribute to our understanding of the factors that regulate pilus extension and describe a previously uncharacterized function for the PilT motor ATPase.
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Affiliation(s)
- Hannah Q Hughes
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Nicholas D Christman
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Triana N Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Courtney K Ellison
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, Indiana, United States of America
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Kato K, Okazaki S, Schmitt-Ulms C, Jiang K, Zhou W, Ishikawa J, Isayama Y, Adachi S, Nishizawa T, Makarova KS, Koonin EV, Abudayyeh OO, Gootenberg JS, Nishimasu H. RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease. Science 2022; 378:882-889. [PMID: 36423304 PMCID: PMC11126364 DOI: 10.1126/science.add7347] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA (tgRNA), and demonstrate that tgRNA binding induces conformational changes in Csx29. Biochemical experiments revealed tgRNA-dependent cleavage of the accessory protein Csx30 by Csx29. Reconstitution of the system in bacteria showed that Csx30 cleavage yields toxic protein fragments that cause growth arrest, which is regulated by Csx31. Csx30 binds Csx31 and the associated sigma factor RpoE (RNA polymerase, extracytoplasmic E), suggesting that Csx30-mediated RpoE inhibition modulates the cellular response to infection. We engineered the Cas7-11-Csx29-Csx30 system for programmable RNA sensing in mammalian cells. Overall, the Cas7-11-Csx29 effector is an RNA-dependent nuclease-protease.
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Affiliation(s)
- Kazuki Kato
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Sae Okazaki
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Cian Schmitt-Ulms
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Kaiyi Jiang
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Wenyuan Zhou
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Junichiro Ishikawa
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Yukari Isayama
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Shungo Adachi
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Tomohiro Nishizawa
- Graduate School of Medical Life Science, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Omar O. Abudayyeh
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jonathan S. Gootenberg
- McGovern Institute for Brain Research at MIT, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Hiroshi Nishimasu
- Structural Biology Division, Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto 600-8411, Japan
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Biofilms and Benign Colonic Diseases. Int J Mol Sci 2022; 23:ijms232214259. [PMID: 36430737 PMCID: PMC9698058 DOI: 10.3390/ijms232214259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/06/2022] [Accepted: 11/10/2022] [Indexed: 11/19/2022] Open
Abstract
The colon has a very large surface area that is covered by a dense mucus layer. The biomass in the colon includes 500-1000 bacterial species at concentrations of ~1012 colony-forming units per gram of feces. The intestinal epithelial cells and the commensal bacteria in the colon have a symbiotic relationship that results in nutritional support for the epithelial cells by the bacteria and maintenance of the optimal commensal bacterial population by colonic host defenses. Bacteria can form biofilms in the colon, but the exact frequency is uncertain because routine methods to undertake colonoscopy (i.e., bowel preparation) may dislodge these biofilms. Bacteria in biofilms represent a complex community that includes living and dead bacteria and an extracellular matrix composed of polysaccharides, proteins, DNA, and exogenous debris in the colon. The formation of biofilms occurs in benign colonic diseases, such as inflammatory bowel disease and irritable bowel syndrome. The development of a biofilm might serve as a marker for ongoing colonic inflammation. Alternatively, the development of biofilms could contribute to the pathogenesis of these disorders by providing sanctuaries for pathogenic bacteria and reducing the commensal bacterial population. Therapeutic approaches to patients with benign colonic diseases could include the elimination of biofilms and restoration of normal commensal bacteria populations. However, these studies will be extremely difficult unless investigators can develop noninvasive methods for measuring and identifying biofilms. These methods that might include the measurement of quorum sensing molecules, measurement of bile acids, and identification of bacteria uniquely associated with biofilms in the colon.
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Bautista S, Schmidt V, Guiseppi A, Mauriello EMF, Attia B, Elantak L, Mignot T, Mercier R. FrzS acts as a polar beacon to recruit SgmX, a central activator of type IV pili during Myxococcus xanthus motility. EMBO J 2022; 42:e111661. [PMID: 36345779 PMCID: PMC9811614 DOI: 10.15252/embj.2022111661] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 10/17/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022] Open
Abstract
In rod-shaped bacteria, type IV pili (Tfp) promote twitching motility by assembling and retracting at the cell pole. In Myxococcus xanthus, a bacterium that moves in highly coordinated cell groups, Tfp are activated by a polar activator protein, SgmX. However, while it is known that the Ras-like protein MglA is required for unipolar targeting, how SgmX accesses the cell pole to activate Tfp is unknown. Here, we demonstrate that a polar beacon protein, FrzS, recruits SgmX at the cell pole. We identified two main functional domains, including a Tfp-activating domain and a polar-binding domain. Within the latter, we show that the direct binding of MglA-GTP unveils a hidden motif that binds directly to the FrzS N-terminal response regulator (CheY). Structural analyses reveal that this binding occurs through a novel binding interface for response regulator domains. In conclusion, the findings unveil the protein interaction network leading to the spatial activation of Tfp at the cell pole. This tripartite system is at the root of complex collective behaviours in this predatory bacterium.
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Affiliation(s)
- Sarah Bautista
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7283)MarseilleFrance
| | - Victoria Schmidt
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7255)MarseilleFrance
| | - Annick Guiseppi
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7283)MarseilleFrance
| | - Emillia M F Mauriello
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7283)MarseilleFrance
| | - Bouchra Attia
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7255)MarseilleFrance
| | - Latifa Elantak
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7255)MarseilleFrance
| | - Tâm Mignot
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7283)MarseilleFrance
| | - Romain Mercier
- Laboratoire de Chimie Bactérienne, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS (UMR7283)MarseilleFrance
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48
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Bacteria-on-a-bead: probing the hydrodynamic interplay of dynamic cell appendages during cell separation. Commun Biol 2022; 5:1093. [PMID: 36241769 PMCID: PMC9568603 DOI: 10.1038/s42003-022-04026-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: 02/08/2022] [Accepted: 09/23/2022] [Indexed: 11/08/2022] Open
Abstract
Surface attachment of bacteria is the first step of biofilm formation and is often mediated and coordinated by the extracellular appendages, flagellum and pili. The model organism Caulobacter crescentus undergoes an asymmetric division cycle, giving rise to a motile "swarmer cell" and a sessile "stalked cell", which is attached to the surface. In the highly polarized predivisional cell, pili and flagellum, which are assembled at the pole opposite the stalk, are both activated before and during the process of cell separation. We explored the interplay of flagellum and active pili by growing predivisional cells on colloidal beads, creating a bacteria-on-a-bead system. Using this set-up, we were able to simultaneously visualize the bacterial motility and analyze the dynamics of the flagellum and pili during cell separation. The observed activities of flagellum and pili at the new cell pole of the predivisional cell result in a cooperating interplay of the appendages during approaching and attaching to a surface. Even in presence of a functioning flagellum, pili are capable of surface attachment and keeping the cell in position. Moreover, while flagellar rotation decreases the average attachment time of a single pilus, it increases the overall attachment rate of pili in a synergetic manner.
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Hughes-Games A, Davis SA, Hill DJ. Direct visualization of sequence-specific DNA binding by gonococcal type IV pili. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35920810 DOI: 10.1099/mic.0.001224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Neisseria gonorrhoeae, the causative agent of gonorrhoea, is a major burden on global healthcare systems, with an estimated ~80-90 million new global cases annually. This burden is exacerbated by increasing levels of antimicrobial resistance, which has greatly limited viable antimicrobial therapies. Decreasing gonococcal drug susceptibility has been driven largely by accumulation of chromosomal resistance determinants, which can be acquired through natural transformation, whereby DNA in the extracellular milieu is imported into cells and incorporated into the genome by homologous recombination. N. gonorrhoeae possesses a specialized system for DNA uptake, which strongly biases transformation in favour of DNA from closely related bacteria by recognizing a 10-12 bp DNA uptake sequence (DUS) motif, which is highly overrepresented in their chromosomal DNA. This process relies on numerous proteins, including the DUS-specific receptor ComP, which assemble retractile protein filaments termed type IV pili (T4P) extending from the cell surface, and one model for neisserial DNA uptake proposes that these filaments bind DNA in a DUS-dependent manner before retracting to transport DNA into the periplasm. However, conflicting evidence indicates that elongated pilus filaments may not have such a direct role in DNA binding uptake as this model suggests. Here, we quantitatively measured DNA binding to gonococcal T4P fibres by directly visualizing binding complexes with confocal fluorescence microscopy in order to confirm the sequence-specific, comP-dependent DNA binding capacity of elongated T4P fibres. This supports the idea that pilus filaments could be responsible for initially capturing DNA in the first step of sequence-specific DNA uptake.
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Affiliation(s)
- Alex Hughes-Games
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.,Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Bristol, UK.,School of Chemistry, University of Bristol, Bristol, UK
| | - Sean A Davis
- School of Chemistry, University of Bristol, Bristol, UK
| | - Darryl J Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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Revealing bacterial cell biology using cryo-electron tomography. Curr Opin Struct Biol 2022; 75:102419. [PMID: 35820259 DOI: 10.1016/j.sbi.2022.102419] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 11/21/2022]
Abstract
Visualizing macromolecules inside bacteria at a high spatial resolution has remained a challenge owing to their small size and limited resolution of optical microscopy techniques. Recent advances in cryo-electron tomography (cryo-ET) imaging methods have revealed the spatial and temporal assemblies of many macromolecules involved in different cellular processes in bacteria at a resolution of a few nanometers in their native milieu. Specifically, the application of cryo-focused ion beam (cryo-FIB) milling to thin bacterial specimens makes them amenable for high-resolution cryo-ET data collection. In this review, we highlight recent research in three emerging areas of bacterial cell biology that have benefited from the cryo-FIB-ET technology - cytoskeletal filament assembly, intracellular organelles, and multicellularity.
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