1
|
Thöneböhn S, Fischer D, Kreiling V, Kemmler A, Oberheim I, Hager F, Schmid NE, Thormann KM. Identifying components of the Shewanella phage LambdaSo lysis system. J Bacteriol 2024:e0002224. [PMID: 38771038 DOI: 10.1128/jb.00022-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024] Open
Abstract
Phage-induced lysis of Gram-negative bacterial hosts usually requires a set of phage lysis proteins, a holin, an endopeptidase, and a spanin system, to disrupt each of the three cell envelope layers. Genome annotations and previous studies identified a gene region in the Shewanella oneidensis prophage LambdaSo, which comprises potential holin- and endolysin-encoding genes but lacks an obvious spanin system. By a combination of candidate approaches, mutant screening, characterization, and microscopy, we found that LambdaSo uses a pinholin/signal-anchor-release (SAR) endolysin system to induce proton leakage and degradation of the cell wall. Between the corresponding genes, we found that two extensively nested open-reading frames encode a two-component spanin module Rz/Rz1. Unexpectedly, we identified another factor strictly required for LambdaSo-induced cell lysis, the phage protein Lcc6. Lcc6 is a transmembrane protein of 65 amino acid residues with hitherto unknown function, which acts at the level of holin in the cytoplasmic membrane to allow endolysin release. Thus, LambdaSo-mediated cell lysis requires at least four protein factors (pinholin, SAR endolysin, spanin, and Lcc6). The findings further extend the known repertoire of phage proteins involved in host lysis and phage egress. IMPORTANCE Lysis of bacteria can have multiple consequences, such as the release of host DNA to foster robust biofilm. Phage-induced lysis of Gram-negative cells requires the disruption of three layers, the outer and inner membranes and the cell wall. In most cases, the lysis systems of phages infecting Gram-negative cells comprise holins to disrupt or depolarize the membrane, thereby releasing or activating endolysins, which then degrade the cell wall. This, in turn, allows the spanins to become active and fuse outer and inner membranes, completing cell envelope disruption and allowing phage egress. Here, we show that the presence of these three components may not be sufficient to allow cell lysis, implicating that also in known phages, further factors may be required.
Collapse
Affiliation(s)
- Svenja Thöneböhn
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Dorian Fischer
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Vanessa Kreiling
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Alina Kemmler
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Isabella Oberheim
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Fabian Hager
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Nicole E Schmid
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Gießen, Germany
| |
Collapse
|
2
|
Humez M, Domann E, Thormann KM, Fölsch C, Strathausen R, Vogt S, Alt V, Kühn KD. Daptomycin-Impregnated PMMA Cement against Vancomycin-Resistant Germs: Dosage, Handling, Elution, Mechanical Stability, and Effectiveness. Antibiotics (Basel) 2023; 12:1567. [PMID: 37998769 PMCID: PMC10668807 DOI: 10.3390/antibiotics12111567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 10/20/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The number of periprosthetic joint infections caused by vancomycin-resistant pathogens is increasing. Currently, no PMMA cement is commercially available to cover VRE. Daptomycin shows promising results in treating infection, offering a good safety profile and a reduced risk of developing resistance. The purpose of this in vitro study was to investigate the mechanical stability, handling properties, elution behavior, and antimicrobial effectiveness of PMMA cement loaded with three different daptomycin concentrations in comparison to commercially available antibiotic-loaded bone cement (ALBC). METHODS Mechanical properties and handling characteristics (ISO 5833, DIN 53435), HPLC elution, antimicrobial effectiveness with proliferation assay (DIN 17025), and inhibition zone testing were investigated. RESULTS All tested daptomycin concentrations met the ISO and DIN standards for mechanical strength. Loading of 40 g of PMMA cement with 0.5 g of daptomycin did not show any antimicrobial effectiveness, in contrast to 1.0 g and 1.5 g. PMMA cement with 1.5 g of daptomycin was the best in terms of elution and effectiveness, and it showed good ISO mechanical strength; ISO doughing was sticky for a little longer and setting was faster compared to the vancomycin-containing reference cement. CONCLUSION PMMA cement containing 0.5 g of gentamicin and 1.5 g of daptomycin could be a good alternative to the already established COPAL® (Wehrheim, Germany) G+V for the treatment of PJIs caused by VRE.
Collapse
Affiliation(s)
- Martina Humez
- Institute of Hygiene and Environmental Medicine, Justus-Liebig-Universität Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (E.D.); (K.M.T.)
- Heraeus Medical GmbH, Philipp-Reis-Str. 8-13, 61273 Wehrheim, Germany; (R.S.); (S.V.)
| | - Eugen Domann
- Institute of Hygiene and Environmental Medicine, Justus-Liebig-Universität Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (E.D.); (K.M.T.)
| | - Kai M. Thormann
- Institute of Hygiene and Environmental Medicine, Justus-Liebig-Universität Giessen, Schubertstrasse 81, 35392 Giessen, Germany; (E.D.); (K.M.T.)
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität Giessen, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Christian Fölsch
- Department of Orthopaedic Surgery, Justus-Liebig-University, Klinikstrasse 33, 35392 Giessen, Germany;
| | - Rainer Strathausen
- Heraeus Medical GmbH, Philipp-Reis-Str. 8-13, 61273 Wehrheim, Germany; (R.S.); (S.V.)
| | - Sebastian Vogt
- Heraeus Medical GmbH, Philipp-Reis-Str. 8-13, 61273 Wehrheim, Germany; (R.S.); (S.V.)
| | - Volker Alt
- Department of Trauma Surgery, University Medical Centre, Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Germany;
| | - Klaus-Dieter Kühn
- Department of Orthopaedics and Trauma, Medical University of Graz, Auenbruggerplatz 5, 8036 Graz, Austria
| |
Collapse
|
3
|
Chernova LS, Vishnyakov IE, Börner J, Bogachev MI, Thormann KM, Kayumov AR. The Functionality of IbpA from Acholeplasma laidlawii Is Governed by Dynamic Rearrangement of Its Globular-Fibrillar Quaternary Structure. Int J Mol Sci 2023; 24:15445. [PMID: 37895124 PMCID: PMC10607609 DOI: 10.3390/ijms242015445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/18/2023] [Accepted: 10/20/2023] [Indexed: 10/29/2023] Open
Abstract
Small heat shock proteins (sHSPs) represent a first line of stress defense in many bacteria. The primary function of these molecular chaperones involves preventing irreversible protein denaturation and aggregation. In Escherichia coli, fibrillar EcIbpA binds unfolded proteins and keeps them in a folding-competent state. Further, its structural homologue EcIbpB induces the transition of EcIbpA to globules, thereby facilitating the substrate transfer to the HSP70-HSP100 system for refolding. The phytopathogenic Acholeplasma laidlawii possesses only a single sHSP, AlIbpA. Here, we demonstrate non-trivial features of the function and regulation of the chaperone-like activity of AlIbpA according to its interaction with other components of the mycoplasma multi-chaperone network. Our results show that the efficiency of the A. laidlawii multi-chaperone system is driven with the ability of AlIbpA to form both globular and fibrillar structures, thus combining functions of both IbpA and IbpB when transferring the substrate proteins to the HSP70-HSP100 system. In contrast to EcIbpA and EcIbpB, AlIbpA appears as an sHSP, in which the competition between the N- and C-terminal domains regulates the shift of the protein quaternary structure between a fibrillar and globular form, thus representing a molecular mechanism of its functional regulation. While the C-terminus of AlIbpA is responsible for fibrils formation and substrate capture, the N-terminus seems to have a similar function to EcIbpB through facilitating further substrate protein disaggregation using HSP70. Moreover, our results indicate that prior to the final disaggregation process, AlIbpA can directly transfer the substrate to HSP100, thereby representing an alternative mechanism in the HSP interaction network.
Collapse
Affiliation(s)
- Liliya S. Chernova
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia;
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia;
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Innokentii E. Vishnyakov
- Institute of Cytology, Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia;
| | - Janek Börner
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Mikhail I. Bogachev
- Centre for Digital Telecommunication Technologies, St. Petersburg Electrotechnical University, Professora Popova 5, 197376 St. Petersburg, Russia;
| | - Kai M. Thormann
- Institute of Microbiology and Molecular Biology, Justus Liebig University, Heinrich-Buff-Ring 26, 35392 Giessen, Germany; (J.B.); (K.M.T.)
| | - Airat R. Kayumov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, Kremlevskaya 18, 420008 Kazan, Russia;
| |
Collapse
|
4
|
Kreiling V, Thormann KM. Polarity of c-di-GMP synthesis and degradation. Microlife 2023; 4:uqad014. [PMID: 37251513 PMCID: PMC10212136 DOI: 10.1093/femsml/uqad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/20/2023] [Accepted: 04/04/2023] [Indexed: 05/31/2023]
Abstract
The bacterial cell pole has long been recognized as a defined compartment for enzymatic activities that are important or even vital for the cell. Polarity of diguanylate cyclases and phosphodiesterases, enzymes that synthesize and degrade the second messenger c-di-GMP, has now been demonstrated for several bacterial systems. Here we review these polar regulatory systems and show how the asymmetry of c-di-GMP production and turnover in concert with different modes of activation and deactivation creates heterogeneity in cellular c-di-GMP levels. We highlight how this heterogeneity generates a diverse set of phenotypic identities or states and how this may benefit the cell population, and we discuss reasons why the polarity of c-di-GMP signaling is probably widespread among bacteria.
Collapse
Affiliation(s)
- Vanessa Kreiling
- Justus-Liebig-Universität, Institute of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26, 35392 Giessen, Germany
| | - Kai M Thormann
- Corresponding author. Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Heinrich-Buff-Ring 26; D-35392 Gießen, Germany. E-mail:
| |
Collapse
|
5
|
Kühn MJ, Edelmann DB, Thormann KM. Polar flagellar wrapping and lateral flagella jointly contribute to Shewanella putrefaciens environmental spreading. Environ Microbiol 2022; 24:5911-5923. [PMID: 35722744 DOI: 10.1111/1462-2920.16107] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/10/2022] [Accepted: 06/17/2022] [Indexed: 01/12/2023]
Abstract
Flagella enable bacteria to actively spread within the environment. A number of species possess two separate flagellar systems, where in most cases a primary polar flagellar system is supported by distinct secondary lateral flagella under appropriate conditions. Using functional fluorescence tagging on one of these species, Shewanella putrefaciens, as a model system, we explored how two different flagellar systems can exhibit efficient joint function. The S. putrefaciens secondary flagellar filaments are composed as a mixture of two highly homologous non-glycosylated flagellins, FlaA2 and FlaB2 . Both are solely sufficient to form a functional filament, however, full spreading motility through soft agar requires both flagellins. During swimming, lateral flagella emerge from the cell surface at angles between 30° and 50°, and only filaments located close to the cell pole may form a bundle. Upon a directional shift from forward to backward swimming initiated by the main polar flagellum, the secondary filaments flip over and thus support propulsion into either direction. Lateral flagella do not inhibit the wrapping of the polar flagellum around the cell body at high load. Accordingly, screw thread-like motility mediated by the primary flagellum and activity of lateral flagella cumulatively supports spreading through constricted environments such as polysaccharide matrices.
Collapse
Affiliation(s)
- Marco J Kühn
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany.,Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel B Edelmann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| |
Collapse
|
6
|
Schwan M, Khaledi A, Willger S, Papenfort K, Glatter T, Häußler S, Thormann KM. FlrA-independent production of flagellar proteins is required for proper flagellation in Shewanella putrefaciens. Mol Microbiol 2022; 118:670-682. [PMID: 36285560 DOI: 10.1111/mmi.14993] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 01/18/2023]
Abstract
Flagella are multiprotein complexes whose assembly and positioning require complex spatiotemporal control. Flagellar assembly is thought to be controlled by several transcriptional tiers, which are mediated through various master regulators. Here, we revisited the regulation of flagellar genes in polarly flagellated gammaproteobacteria by the regulators FlrA, RpoN (σ54 ) and FliA (σ28 ) in Shewanella putrefaciens CN-32 at the transcript and protein level. We found that a number of regulatory and structural proteins were present in the absence of the main regulators, suggesting that initiation of flagella assembly and motor activation relies on the abundance control of only a few structural key components that are required for the formation of the MS- and C-ring and the flagellar type III secretion system. We identified FlrA-independent promoters driving expression of the regulators of flagellar number and positioning, FlhF and FlhG. Reduction of the gene expression levels from these promoters resulted in the emergence of hyperflagellation. This finding indicates that basal expression is required to adjust the flagellar counter in Shewanella. This is adding a deeper layer to the regulation of flagellar synthesis and assembly.
Collapse
Affiliation(s)
- Meike Schwan
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Ariane Khaledi
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sven Willger
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kai Papenfort
- Institute for Microbiology, Friedrich Schiller University, Jena, Germany
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Mass Spectrometry and Proteomics, Marburg, Germany
| | - Susanne Häußler
- Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| |
Collapse
|
7
|
Abstract
A huge number of bacterial species are motile by flagella, which allow them to actively move toward favorable environments and away from hazardous areas and to conquer new habitats. The general perception of flagellum-mediated movement and chemotaxis is dominated by the Escherichia coli paradigm, with its peritrichous flagellation and its famous run-and-tumble navigation pattern, which has shaped the view on how bacteria swim and navigate in chemical gradients. However, a significant amount-more likely the majority-of bacterial species exhibit a (bi)polar flagellar localization pattern instead of lateral flagella. Accordingly, these species have evolved very different mechanisms for navigation and chemotaxis. Here, we review the earlier and recent findings on the various modes of motility mediated by polar flagella. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Kai M Thormann
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Gießen, Germany;
| | - Carsten Beta
- Institute of Physics and Astronomy, University of Potsdam, Potsdam, Germany;
| | - Marco J Kühn
- Institute of Bioengineering and Global Health Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland;
| |
Collapse
|
8
|
Mayer B, Schwan M, Thormann KM, Graumann PL. Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo. F1000Res 2022; 10:277. [PMID: 35707454 PMCID: PMC9178280 DOI: 10.12688/f1000research.51868.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 11/20/2022] Open
Abstract
The search for novel drugs that efficiently eliminate prokaryotic pathogens is one of the most urgent health topics of our time. Robust evaluation methods for monitoring the antibiotic stress response in prokaryotes are therefore necessary for developing respective screening strategies. Besides advantages of common
in vitro techniques, there is a growing demand for
in vivo information based on imaging techniques that allow to screen antibiotic candidates in a dynamic manner. Gathering information from imaging data in a reproducible manner, robust data processing and analysis workflows demand advanced (semi-)automation and data management to increase reproducibility. Here we demonstrate a versatile and robust semi-automated image acquisition, processing and analysis workflow to investigate bacterial cell morphology in a quantitative manner. The presented workflow, A.D.I.C.T, covers aspects of experimental setup deployment, data acquisition and handling, image processing (e.g. ROI management, data transformation into binary images, background subtraction, filtering, projections) as well as statistical evaluation of the cellular stress response (e.g. shape measurement distributions, cell shape modeling, probability density evaluation of fluorescence imaging micrographs) towards antibiotic-induced stress, obtained from time-course experiments. The imaging workflow is based on regular brightfield images combined with live-cell imaging data gathered from bacteria, in our case from recombinant
Shewanella cells, which are processed as binary images. The model organism expresses target proteins relevant for membrane-biogenesis that are functionally fused to respective fluorescent proteins. Data processing and analysis are based on customized scripts using ImageJ2/FIJI, Celltool and R packages that can be easily reproduced and adapted by users. Summing up, our approach aims at supporting life-scientists to establish their own imaging-pipeline in order to exploit their data as versatile as possible and in a reproducible manner.
Collapse
Affiliation(s)
- Benjamin Mayer
- Institute of Clinical Pharmacology, Goethe University Frankfurt Am Main, Theodor Stern Kai 7, 60590, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Hessen, 35032, Germany
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Meike Schwan
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Hessen, 35392, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Hessen, 35392, Germany
| | - Peter L. Graumann
- Department of Chemistry, Philipps Universität Marburg, Marburg, Hessen, 35032, Germany
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
| |
Collapse
|
9
|
Thormann KM. Dynamic Hybrid Flagellar Motors-Fuel Switch and More. Front Microbiol 2022; 13:863804. [PMID: 35495728 PMCID: PMC9039648 DOI: 10.3389/fmicb.2022.863804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Flagellar motors are intricate rotating nanomachines that are powered by transmembrane ion gradients. The stator complexes are the powerhouses of the flagellar motor: They convert a transmembrane ion gradient, mainly of H+ or Na+, into rotation of the helical flagellar filament. They are thus essential for motor function. The number of stators synchronously engaged in the motor is surprisingly dynamic and depends on the load and the environmental concentration of the corresponding coupling ion. Thus, the rotor-stator interactions determine an important part of the properties of the motor. Numerous bacteria have been identified as possessing more than one set of stators, and some species have been demonstrated to use these different stators in various configurations to modify motor functions by dynamic in-flight swapping. Here, we review knowledge of the properties, the functions, and the evolution of these hybrid motors and discuss questions that remain unsolved.
Collapse
Affiliation(s)
- Kai M Thormann
- Fachbereich für Chemie und Biologie, Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| |
Collapse
|
10
|
Rick T, Kreiling V, Höing A, Fiedler S, Glatter T, Steinchen W, Hochberg G, Bähre H, Seifert R, Bange G, Knauer SK, Graumann PL, Thormann KM. GGDEF domain as spatial on-switch for a phosphodiesterase by interaction with landmark protein HubP. NPJ Biofilms Microbiomes 2022; 8:35. [PMID: 35501424 PMCID: PMC9061725 DOI: 10.1038/s41522-022-00297-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractIn bacteria, the monopolar localization of enzymes and protein complexes can result in a bimodal distribution of enzyme activity between the dividing cells and heterogeneity of cellular behaviors. In Shewanella putrefaciens, the multidomain hybrid diguanylate cyclase/phosphodiesterase PdeB, which degrades the secondary messenger c-di-GMP, is located at the flagellated cell pole. Here, we show that direct interaction between the inactive diguanylate cyclase (GGDEF) domain of PdeB and the FimV domain of the polar landmark protein HubP is crucial for full function of PdeB as a phosphodiesterase. Thus, the GGDEF domain serves as a spatially controlled on-switch that effectively restricts PdeBs activity to the flagellated cell pole. PdeB regulates abundance and activity of at least two crucial surface-interaction factors, the BpfA surface-adhesion protein and the MSHA type IV pilus. The heterogeneity in c-di-GMP concentrations, generated by differences in abundance and timing of polar appearance of PdeB, orchestrates the population behavior with respect to cell-surface interaction and environmental spreading.
Collapse
|
11
|
Oña L, Giri S, Avermann N, Kreienbaum M, Thormann KM, Kost C. Obligate cross-feeding expands the metabolic niche of bacteria. Nat Ecol Evol 2021; 5:1224-1232. [PMID: 34267366 DOI: 10.1038/s41559-021-01505-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Bacteria frequently engage in obligate metabolic mutualisms with other microorganisms. However, it remains generally unclear how the resulting metabolic dependencies affect the ecological niche space accessible to the whole consortium relative to the niche space available to its constituent individuals. Here we address this issue by systematically cultivating metabolically dependent strains of different bacterial species either individually or as pairwise cocultures in a wide range of carbon sources. Our results show that obligate cross-feeding is significantly more likely to expand the metabolic niche space of interacting bacterial populations than to contract it. Moreover, niche expansion occurred predominantly between two specialist taxa and correlated positively with the phylogenetic distance between interaction partners. Together, our results demonstrate that obligate cross-feeding can significantly expand the ecological niche space of interacting bacterial genotypes, thus explaining the widespread occurrence of this type of ecological interaction in natural microbiomes.
Collapse
Affiliation(s)
- Leonardo Oña
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Samir Giri
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, Osnabrück, Germany.,Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Neele Avermann
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, Osnabrück, Germany
| | - Maximilian Kreienbaum
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Gießen, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, Osnabrück, Germany. .,Experimental Ecology and Evolution Research Group, Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany.
| |
Collapse
|
12
|
Pecina A, Schwan M, Blagotinsek V, Rick T, Klüber P, Leonhard T, Bange G, Thormann KM. Corrigendum: The Stand-Alone PilZ-Domain Protein MotL Specifically Regulates the Activity of the Secondary Lateral Flagellar System in Shewanella putrefaciens. Front Microbiol 2021; 12:726192. [PMID: 34335556 PMCID: PMC8322970 DOI: 10.3389/fmicb.2021.726192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 06/28/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Anna Pecina
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Vitan Blagotinsek
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Tim Rick
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Patrick Klüber
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| |
Collapse
|
13
|
Pecina A, Schwan M, Blagotinsek V, Rick T, Klüber P, Leonhard T, Bange G, Thormann KM. The Stand-Alone PilZ-Domain Protein MotL Specifically Regulates the Activity of the Secondary Lateral Flagellar System in Shewanella putrefaciens. Front Microbiol 2021; 12:668892. [PMID: 34140945 PMCID: PMC8203827 DOI: 10.3389/fmicb.2021.668892] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/19/2021] [Indexed: 11/13/2022] Open
Abstract
A number of bacterial species control the function of the flagellar motor in response to the levels of the secondary messenger c-di-GMP, which is often mediated by c-di-GMP-binding proteins that act as molecular brakes or clutches to slow the motor rotation. The gammaproteobacterium Shewanella putrefaciens possesses two distinct flagellar systems, the primary single polar flagellum and a secondary system with one to five lateral flagellar filaments. Here, we identified a protein, MotL, which specifically regulates the activity of the lateral, but not the polar, flagellar motors in response to the c-di-GMP levels. MotL only consists of a single PilZ domain binding c-di-GMP, which is crucial for its function. Deletion and overproduction analyses revealed that MotL slows down the lateral flagella at elevated levels of c-di-GMP, and may speed up the lateral flagellar-mediated movement at low c-di-GMP concentrations. In vitro interaction studies hint at an interaction of MotL with the C-ring of the lateral flagellar motors. This study shows a differential c-di-GMP-dependent regulation of the two flagellar systems in a single species, and implicates that PilZ domain-only proteins can also act as molecular regulators to control the flagella-mediated motility in bacteria.
Collapse
Affiliation(s)
- Anna Pecina
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Vitan Blagotinsek
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Tim Rick
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Patrick Klüber
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| | - Gert Bange
- Department of Chemistry, SYNMIKRO Research Center, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität Gießen, Giessen, Germany
| |
Collapse
|
14
|
Mayer B, Schwan M, Oviedo-Bocanegra LM, Bange G, Thormann KM, Graumann PL. Dynamics of Bacterial Signal Recognition Particle at a Single Molecule Level. Front Microbiol 2021; 12:663747. [PMID: 33995327 PMCID: PMC8120034 DOI: 10.3389/fmicb.2021.663747] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 03/18/2021] [Indexed: 11/21/2022] Open
Abstract
We have studied the localization and dynamics of bacterial Ffh, part of the SRP complex, its receptor FtsY, and of ribosomes in the Gamma-proteobacterium Shewanella putrefaciens. Using structured illumination microscopy, we show that ribosomes show a pronounced accumulation at the cell poles, whereas SRP and FtsY are distributed at distinct sites along the cell membrane, but they are not accumulated at the poles. Single molecule dynamics can be explained by assuming that all three proteins/complexes move as three distinguishable mobility fractions: a low mobility/static fraction may be engaged in translation, medium-fast diffusing fractions may be transition states, and high mobility populations likely represent freely diffusing molecules/complexes. Diffusion constants suggest that SRP and FtsY move together with slow-mobile ribosomes. Inhibition of transcription leads to loss of static molecules and reduction of medium-mobile fractions, in favor of freely diffusing subunits, while inhibition of translation appears to stall the medium mobile fractions. Depletion of FtsY leads to aggregation of Ffh, but not to loss of the medium mobile fraction, indicating that Ffh/SRP can bind to ribosomes independently from FtsY. Heat maps visualizing the three distinct diffusive populations show that while static molecules are mostly clustered at the cell membrane, diffusive molecules are localized throughout the cytosol. The medium fast populations show an intermediate pattern of preferential localization, suggesting that SRP/FtsY/ribosome transition states may form within the cytosol to finally find a translocon.
Collapse
Affiliation(s)
- Benjamin Mayer
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Meike Schwan
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Luis M. Oviedo-Bocanegra
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Peter L. Graumann
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Marburg, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Germany
| |
Collapse
|
15
|
Mayer B, Schwan M, Thormann KM, Graumann PL. Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo. F1000Res 2021; 10:277. [PMID: 35707454 PMCID: PMC9178280 DOI: 10.12688/f1000research.51868.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 11/04/2023] Open
Abstract
The search for novel drugs that efficiently eliminate prokaryotic pathogens is one of the most urgent health topics of our time. Robust evaluation methods for monitoring the antibiotic stress response in prokaryotes are therefore necessary for developing respective screening strategies. Besides advantages of common in vitro techniques, there is a growing demand for in vivo information based on imaging techniques that allow to screen antibiotic candidates in a dynamic manner. Gathering information from imaging data in a reproducible manner, robust data processing and analysis workflows demand advanced (semi-)automation and data management to increase reproducibility. Here we demonstrate a versatile and robust semi-automated image acquisition, processing and analysis workflow to investigate bacterial cell morphology in a quantitative manner. The presented workflow, A.D.I.C.T, covers aspects of experimental setup deployment, data acquisition and handling, image processing (e.g. ROI management, data transformation into binary images, background subtraction, filtering, projections) as well as statistical evaluation of the cellular stress response (e.g. shape measurement distributions, cell shape modeling, probability density evaluation of fluorescence imaging micrographs) towards antibiotic-induced stress, obtained from time-course experiments. The imaging workflow is based on regular brightfield images combined with live-cell imaging data gathered from bacteria, in our case from recombinant Shewanella cells, which are processed as binary images. The model organism expresses target proteins relevant for membrane-biogenesis that are functionally fused to respective fluorescent proteins. Data processing and analysis are based on customized scripts using ImageJ2/FIJI, Celltool and R packages that can be easily reproduced and adapted by users. Summing up, our approach aims at supporting life-scientists to establish their own imaging-pipeline in order to exploit their data as versatile as possible and in a reproducible manner.
Collapse
Affiliation(s)
- Benjamin Mayer
- Institute of Clinical Pharmacology, Goethe University Frankfurt Am Main, Theodor Stern Kai 7, 60590, Germany
- Department of Chemistry, Philipps Universität Marburg, Marburg, Hessen, 35032, Germany
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
| | - Meike Schwan
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Hessen, 35392, Germany
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Hessen, 35392, Germany
| | - Peter L. Graumann
- Department of Chemistry, Philipps Universität Marburg, Marburg, Hessen, 35032, Germany
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany
| |
Collapse
|
16
|
Hook JC, Blagotinsek V, Pané-Farré J, Mrusek D, Altegoer F, Dornes A, Schwan M, Schier L, Thormann KM, Bange G. A Proline-Rich Element in the Type III Secretion Protein FlhB Contributes to Flagellar Biogenesis in the Beta- and Gamma-Proteobacteria. Front Microbiol 2020; 11:564161. [PMID: 33384667 PMCID: PMC7771051 DOI: 10.3389/fmicb.2020.564161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 10/26/2020] [Indexed: 11/24/2022] Open
Abstract
Flagella are bacterial organelles of locomotion. Their biogenesis is highly coordinated in time and space and relies on a specialized flagellar type III secretion system (fT3SS) required for the assembly of the extracellular hook, rod, and filament parts of this complex motor device. The fT3SS protein FlhB switches secretion substrate specificity once the growing hook reaches its determined length. Here we present the crystal structure of the cytoplasmic domain of the transmembrane protein FlhB. The structure visualizes a so-far unseen proline-rich region (PRR) at the very C-terminus of the protein. Strains lacking the PRR show a decrease in flagellation as determined by hook- and filament staining, indicating a role of the PRR during assembly of the hook and filament structures. Phylogenetic analysis shows that the PRR is a primary feature of FlhB proteins of flagellated beta- and gamma-proteobacteria. Taken together, our study adds another layer of complexity and organismic diversity to the process of flagella biogenesis.
Collapse
Affiliation(s)
- John C Hook
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Vitan Blagotinsek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Jan Pané-Farré
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Devid Mrusek
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Florian Altegoer
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Anita Dornes
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Meike Schwan
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Lukas Schier
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig-Universität, Giessen, Germany
| | - Gert Bange
- SYNMIKRO Research Center, Department of Chemistry, Philipps-University Marburg, Marburg, Germany
| |
Collapse
|
17
|
Kreienbaum M, Dörrich AK, Brandt D, Schmid NE, Leonhard T, Hager F, Brenzinger S, Hahn J, Glatter T, Ruwe M, Briegel A, Kalinowski J, Thormann KM. Isolation and Characterization of Shewanella Phage Thanatos Infecting and Lysing Shewanella oneidensis and Promoting Nascent Biofilm Formation. Front Microbiol 2020; 11:573260. [PMID: 33072035 PMCID: PMC7530303 DOI: 10.3389/fmicb.2020.573260] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 08/27/2020] [Indexed: 01/21/2023] Open
Abstract
Species of the genus Shewanella are widespread in nature in various habitats, however, little is known about phages affecting Shewanella sp. Here, we report the isolation of phages from diverse freshwater environments that infect and lyse strains of Shewanella oneidensis and other Shewanella sp. Sequence analysis and microscopic imaging strongly indicate that these phages form a so far unclassified genus, now named Shewanella phage Thanatos, which can be positioned within the subfamily of Tevenvirinae (Duplodnaviria; Heunggongvirae; Uroviricota; Caudoviricetes; Caudovirales; Myoviridae; Tevenvirinae). We characterized one member of this group in more detail using S. oneidensis MR-1 as a host. Shewanella phage Thanatos-1 possesses a prolate icosahedral capsule of about 110 nm in height and 70 nm in width and a tail of about 95 nm in length. The dsDNA genome exhibits a GC content of about 34.5%, has a size of 160.6 kbp and encodes about 206 proteins (92 with an annotated putative function) and two tRNAs. Out of those 206, MS analyses identified about 155 phage proteins in PEG-precipitated samples of infected cells. Phage attachment likely requires the outer lipopolysaccharide of S. oneidensis, narrowing the phage's host range. Under the applied conditions, about 20 novel phage particles per cell were produced after a latent period of approximately 40 min, which are stable at a pH range from 4 to 12 and resist temperatures up to 55°C for at least 24 h. Addition of Thanatos to S. oneidensis results in partial dissolution of established biofilms, however, early exposure of planktonic cells to Thanatos significantly enhances biofilm formation. Taken together, we identified a novel genus of Myophages affecting S. oneidensis communities in different ways.
Collapse
Affiliation(s)
- Maximilian Kreienbaum
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Anja K Dörrich
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - David Brandt
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Nicole E Schmid
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tabea Leonhard
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Fabian Hager
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Susanne Brenzinger
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Julia Hahn
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Timo Glatter
- Facility for Mass Spectrometry and Proteomics, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Matthias Ruwe
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Ariane Briegel
- Department of Molecular Biotechnology, Institute of Biology, Leiden University, Leiden, Netherlands
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| |
Collapse
|
18
|
Nisbett LM, Binnenkade L, Bacon B, Hossain S, Kotloski NJ, Brutinel ED, Hartmann R, Drescher K, Arora DP, Muralidharan S, Thormann KM, Gralnick JA, Boon EM. NosP Signaling Modulates the NO/H-NOX-Mediated Multicomponent c-Di-GMP Network and Biofilm Formation in Shewanella oneidensis. Biochemistry 2019; 58:4827-4841. [PMID: 31682418 PMCID: PMC7290162 DOI: 10.1021/acs.biochem.9b00706] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biofilms form when bacteria aggregate in a self-secreted exopolysaccharide matrix; they are resistant to antibiotics and implicated in disease. Nitric oxide (NO) is known to mediate biofilm formation in many bacteria via ligation to H-NOX (heme-NO/oxygen binding) domains. Most NO-responsive bacteria, however, lack H-NOX domain-containing proteins. We have identified another NO-sensing protein (NosP), which is predicted to be involved in two-component signaling and biofilm regulation in many species. Here, we demonstrate that NosP participates in the previously described H-NOX/NO-responsive multicomponent c-di-GMP signaling network in Shewanella oneidensis. Strains lacking either nosP or its co-cistronic kinase nahK (previously hnoS) produce immature biofilms, while hnoX and hnoK (kinase responsive to NO/H-NOX) mutants result in wild-type biofilm architecture. We demonstrate that NosP regulates the autophosphorylation activity of NahK as well as HnoK. HnoK and NahK have been shown to regulate three response regulators (HnoB, HnoC, and HnoD) that together comprise a NO-responsive multicomponent c-di-GMP signaling network. Here, we propose that NosP/NahK adds regulation on top of H-NOX/HnoK to modulate this c-di-GMP signaling network, and ultimately biofilm formation, by governing the flux of phosphate through both HnoK and NahK. In addition, it appears that NosP and H-NOX act to counter each other in a push-pull mechanism; NosP/NahK promotes biofilm formation through inhibition of H-NOX/HnoK signaling, which itself reduces the extent of biofilm formation. Addition of NO results in a reduction of c-di-GMP and biofilm formation, primarily through disinhibition of HnoK activity.
Collapse
Affiliation(s)
- Lisa-Marie Nisbett
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Lucas Binnenkade
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Bezalel Bacon
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sajjad Hossain
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Nicholas J. Kotloski
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota 55108, United States
| | - Evan D. Brutinel
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota 55108, United States
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043 Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Renthof 6, 35032 Marburg, Germany
| | - Dhruv P. Arora
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Sandhya Muralidharan
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Kai M. Thormann
- Institute for Microbiology and Molecular Biology, Justus-Liebig-Universität Giessen, D-35392 Giessen, Germany
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, University of Minnesota—Twin Cities, St. Paul, Minnesota 55108, United States
| | - Elizabeth M. Boon
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
- Institute of Chemical Biology & Drug Discovery, Stony Brook University, Stony Brook, New York 11794-3400, United States
| |
Collapse
|
19
|
Díaz-Pascual F, Hartmann R, Lempp M, Vidakovic L, Song B, Jeckel H, Thormann KM, Yildiz FH, Dunkel J, Link H, Nadell CD, Drescher K. Breakdown of Vibrio cholerae biofilm architecture induced by antibiotics disrupts community barrier function. Nat Microbiol 2019; 4:2136-2145. [PMID: 31659297 PMCID: PMC6881181 DOI: 10.1038/s41564-019-0579-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 09/06/2019] [Indexed: 01/01/2023]
Abstract
Bacterial cells in nature are frequently exposed to changes in their chemical environment1,2. The response mechanisms of isolated cells to such stimuli have been investigated in great detail. By contrast, little is known about the emergent multicellular responses to environmental changes, such as antibiotic exposure3-7, which may hold the key to understanding the structure and functions of the most common type of bacterial communities: biofilms. Here, by monitoring all individual cells in Vibrio cholerae biofilms during exposure to antibiotics that are commonly administered for cholera infections, we found that translational inhibitors cause strong effects on cell size and shape, as well as biofilm architectural properties. We identified that single-cell-level responses result from the metabolic consequences of inhibition of protein synthesis and that the community-level responses result from an interplay of matrix composition, matrix dissociation and mechanical interactions between cells. We further observed that the antibiotic-induced changes in biofilm architecture have substantial effects on biofilm population dynamics and community assembly by enabling invasion of biofilms by bacteriophages and intruder cells of different species. These mechanistic causes and ecological consequences of biofilm exposure to antibiotics are an important step towards understanding collective bacterial responses to environmental changes, with implications for the effects of antimicrobial therapy on the ecological succession of biofilm communities.
Collapse
Affiliation(s)
| | - Raimo Hartmann
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Martin Lempp
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Lucia Vidakovic
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Boya Song
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah Jeckel
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, Gießen, Germany
| | - Fitnat H Yildiz
- Department of Microbiology and Environmental Toxicology, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Jörn Dunkel
- Department of Mathematics, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannes Link
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Synmikro Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany
| | - Carey D Nadell
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Department of Biological Sciences, Dartmouth College, Hanover, USA
| | - Knut Drescher
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
- Department of Physics, Philipps-Universität Marburg, Marburg, Germany.
- Synmikro Center for Synthetic Microbiology, Philipps-Universität Marburg, Marburg, Germany.
| |
Collapse
|
20
|
Lerch MF, Schoenfelder SMK, Marincola G, Wencker FDR, Eckart M, Förstner KU, Sharma CM, Thormann KM, Kucklick M, Engelmann S, Ziebuhr W. A non-coding RNA from the intercellular adhesion (ica) locus of Staphylococcus epidermidis controls polysaccharide intercellular adhesion (PIA)-mediated biofilm formation. Mol Microbiol 2019; 111:1571-1591. [PMID: 30873665 DOI: 10.1111/mmi.14238] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2019] [Indexed: 12/15/2022]
Abstract
Polysaccharide intercellular adhesin (PIA)-associated biofilm formation is mediated by the intercellular adhesin (ica) locus and represents a major pathomechanism of Staphylococcus epidermidis. Here, we report on a novel long non-coding (nc)RNA, named IcaZ, which is approximately 400 nucleotides in size. icaZ is located downstream of the ica repressor gene icaR and partially overlaps with the icaR 3' UTR. icaZ exclusively exists in ica-positive S. epidermidis, but not in S. aureus or other staphylococci. Inactivation of the gene completely abolishes PIA production. IcaZ is transcribed as a primary transcript from its own promoter during early- and mid-exponential growth and its transcription is induced by low temperature, ethanol and salt stress. IcaZ targets the icaR 5' UTR and hampers icaR mRNA translation, which alleviates repression of icaADBC operon transcription and results in PIA production. Interestingly, other than in S. aureus, posttranscriptional control of icaR mRNA in S. epidermidis does not involve icaR mRNA 5'/3' UTR base pairing. This suggests major structural and functional differences in icaADBC operon regulation between the two species that also involve the recruitment of ncRNAs. Together, the IcaZ ncRNA represents an unprecedented novel species-specific player involved in the control of PIA production in NBSP S. epidermidis.
Collapse
Affiliation(s)
- Maike F Lerch
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Sonja M K Schoenfelder
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Gabriella Marincola
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Freya D R Wencker
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Martin Eckart
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Konrad U Förstner
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany.,Faculty of Information Science and Communication Studies, TH Köln, Cologne, D-50678, Germany.,ZB MED-Information Centre for Life Sciences, Cologne, Germany
| | - Cynthia M Sharma
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| | - Kai M Thormann
- Institute of Microbiology and Molecular Biology, University of Gießen, Heinrich-Buff-Ring 26, Gießen, 35392, Germany
| | - Martin Kucklick
- Helmholtz Centre for Infection Research, Microbial Proteomics, Inhoffenstraße 7, Braunschweig, 38124, Germany.,Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, Braunschweig, 38106, Germany
| | - Susanne Engelmann
- Helmholtz Centre for Infection Research, Microbial Proteomics, Inhoffenstraße 7, Braunschweig, 38124, Germany.,Institute of Microbiology, Technical University Braunschweig, Spielmannstr. 7, Braunschweig, 38106, Germany
| | - Wilma Ziebuhr
- Institute of Molecular Infection Biology, University of Wuerzburg, Josef-Schneider-Str. 2, Wuerzburg, D-97080, Germany
| |
Collapse
|
21
|
Ferreira JL, Gao FZ, Rossmann FM, Nans A, Brenzinger S, Hosseini R, Wilson A, Briegel A, Thormann KM, Rosenthal PB, Beeby M. γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures. PLoS Biol 2019; 17:e3000165. [PMID: 30889173 PMCID: PMC6424402 DOI: 10.1371/journal.pbio.3000165] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 02/08/2019] [Indexed: 11/21/2022] Open
Abstract
Bacteria switch only intermittently to motile planktonic lifestyles under favorable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a switch to stationary phase, conserving energy by altering metabolism and stopping motility. About two-thirds of bacteria use flagella to swim, but how bacteria deactivate this large molecular machine remains unclear. Here, we describe the previously unreported ejection of polar motors by γ-proteobacteria. We show that these bacteria eject their flagella at the base of the flagellar hook when nutrients are depleted, leaving a relic of a former flagellar motor in the outer membrane. Subtomogram averages of the full motor and relic reveal that this is an active process, as a plug protein appears in the relic, likely to prevent leakage across their outer membrane; furthermore, we show that ejection is triggered only under nutritional depletion and is independent of the filament as a possible mechanosensor. We show that filament ejection is a widespread phenomenon demonstrated by the appearance of relic structures in diverse γ-proteobacteria including Plesiomonas shigelloides, Vibrio cholerae, Vibrio fischeri, Shewanella putrefaciens, and Pseudomonas aeruginosa. While the molecular details remain to be determined, our results demonstrate a novel mechanism for bacteria to halt costly motility when nutrients become scarce.
Collapse
Affiliation(s)
- Josie L. Ferreira
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Forson Z. Gao
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Florian M. Rossmann
- Department of Life Sciences, Imperial College London, United Kingdom
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Andrea Nans
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | | | - Rohola Hosseini
- Institute of Biology, University of Leiden, Leiden, the Netherlands
| | - Amanda Wilson
- Department of Life Sciences, Imperial College London, United Kingdom
| | - Ariane Briegel
- Institute of Biology, University of Leiden, Leiden, the Netherlands
| | - Kai M. Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Peter B. Rosenthal
- Structural Biology of Cells and Viruses Laboratory, The Francis Crick Institute, London, United Kingdom
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, United Kingdom
| |
Collapse
|
22
|
Kühn MJ, Schmidt FK, Farthing NE, Rossmann FM, Helm B, Wilson LG, Eckhardt B, Thormann KM. Spatial arrangement of several flagellins within bacterial flagella improves motility in different environments. Nat Commun 2018; 9:5369. [PMID: 30560868 PMCID: PMC6299084 DOI: 10.1038/s41467-018-07802-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 11/22/2018] [Indexed: 11/26/2022] Open
Abstract
Bacterial flagella are helical proteinaceous fibers, composed of the protein flagellin, that confer motility to many bacterial species. The genomes of about half of all flagellated species include more than one flagellin gene, for reasons mostly unknown. Here we show that two flagellins (FlaA and FlaB) are spatially arranged in the polar flagellum of Shewanella putrefaciens, with FlaA being more abundant close to the motor and FlaB in the remainder of the flagellar filament. Observations of swimming trajectories and numerical simulations demonstrate that this segmentation improves motility in a range of environmental conditions, compared to mutants with single-flagellin filaments. In particular, it facilitates screw-like motility, which enhances cellular spreading through obstructed environments. Similar mechanisms may apply to other bacterial species and may explain the maintenance of multiple flagellins to form the flagellar filament.
Collapse
Affiliation(s)
- Marco J Kühn
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Felix K Schmidt
- Fachbereich Physik und LOEWE Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, 35032, Marburg, Germany
| | - Nicola E Farthing
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK
- Department of Mathematics, University of York, Heslington, York, YO10 5DD, UK
| | - Florian M Rossmann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Bina Helm
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany
| | - Laurence G Wilson
- Department of Physics, University of York, Heslington, York, YO10 5DD, UK.
| | - Bruno Eckhardt
- Fachbereich Physik und LOEWE Zentrum für Synthetische Mikrobiologie, Philipps-Universität Marburg, 35032, Marburg, Germany.
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Gießen, 35392, Gießen, Germany.
| |
Collapse
|
23
|
Binnenkade L, Kreienbaum M, Thormann KM. Characterization of ExeM, an Extracellular Nuclease of Shewanella oneidensis MR-1. Front Microbiol 2018; 9:1761. [PMID: 30123203 PMCID: PMC6085458 DOI: 10.3389/fmicb.2018.01761] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 07/13/2018] [Indexed: 01/08/2023] Open
Abstract
Bacterial extracellular nucleases have multiple functions in processes as diverse as nutrient acquisition, natural transformation, biofilm formation, or defense against neutrophil extracellular traps (NETs). Here we explored the properties of ExeM in Shewanella oneidensis MR-1, an extracellular nuclease, which is widely conserved among species of Shewanella, Vibrio, Aeromonas, and others. In S. oneidensis, ExeM is crucial for normal biofilm formation. In vitro activity measurements on heterologously produced ExeM revealed that this enzyme is a sugar-unspecific endonuclease, which requires Ca2+ and Mg2+/Mn2+ as co-factors for full activity. ExeM was almost exclusively localized to the cytoplasmic membrane fraction, even when a putative C-terminal membrane anchor was deleted. In contrast, ExeM was not detected in medium supernatants. Based on the results we hypothesize that ExeM predominantly interacts with DNA in close proximity to the cell, e.g., to promote biofilm formation and defense against NETs, or to control uptake of DNA.
Collapse
Affiliation(s)
- Lucas Binnenkade
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Maximilian Kreienbaum
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Kai M Thormann
- Institute for Microbiology and Molecular Biology, Justus Liebig University Giessen, Giessen, Germany
| |
Collapse
|
24
|
Brenzinger S, Pecina A, Mrusek D, Mann P, Völse K, Wimmi S, Ruppert U, Becker A, Ringgaard S, Bange G, Thormann KM. ZomB is essential for flagellar motor reversals in Shewanella putrefaciens and Vibrio parahaemolyticus. Mol Microbiol 2018; 109:694-709. [PMID: 29995998 DOI: 10.1111/mmi.14070] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 01/05/2023]
Abstract
The ability of most bacterial flagellar motors to reverse the direction of rotation is crucial for efficient chemotaxis. In Escherichia coli, motor reversals are mediated by binding of phosphorylated chemotaxis protein CheY to components of the flagellar rotor, FliM and FliN, which induces a conformational switch of the flagellar C-ring. Here, we show that for Shewanella putrefaciens, Vibrio parahaemolyticus and likely a number of other species an additional transmembrane protein, ZomB, is critically required for motor reversals as mutants lacking ZomB exclusively exhibit straightforward swimming also upon full phosphorylation or overproduction of CheY. ZomB is recruited to the cell poles by and is destabilized in the absence of the polar landmark protein HubP. ZomB also co-localizes to and may thus interact with the flagellar motor. The ΔzomB phenotype was suppressed by mutations in the very C-terminal region of FliM. We propose that the flagellar motors of Shewanella, Vibrio and numerous other species harboring orthologs to ZomB are locked in counterclockwise rotation and may require interaction with ZomB to enable the conformational switch required for motor reversals. Regulation of ZomB activity or abundance may provide these species with an additional means to modulate chemotaxis efficiency.
Collapse
Affiliation(s)
- Susanne Brenzinger
- Justus-Liebig Universität, Department of Microbiology and Molecular Biology, 35392, Giessen, Germany
| | - Anna Pecina
- Justus-Liebig Universität, Department of Microbiology and Molecular Biology, 35392, Giessen, Germany
| | - Devid Mrusek
- LOEWE Center for Synthetic Microbiology (Synmikro) & Department of Chemistry, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Petra Mann
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, 35043, Marburg, Germany
| | - Kerstin Völse
- Justus-Liebig Universität, Department of Microbiology and Molecular Biology, 35392, Giessen, Germany
| | - Stephan Wimmi
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, 35043, Marburg, Germany
| | - Ulrike Ruppert
- Justus-Liebig Universität, Department of Microbiology and Molecular Biology, 35392, Giessen, Germany
| | - Anke Becker
- LOEWE Center for Synthetic Microbiology (Synmikro) & Department of Biology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Simon Ringgaard
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, 35043, Marburg, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (Synmikro) & Department of Chemistry, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Kai M Thormann
- Justus-Liebig Universität, Department of Microbiology and Molecular Biology, 35392, Giessen, Germany
| |
Collapse
|
25
|
Hintsche M, Waljor V, Großmann R, Kühn MJ, Thormann KM, Peruani F, Beta C. A polar bundle of flagella can drive bacterial swimming by pushing, pulling, or coiling around the cell body. Sci Rep 2017; 7:16771. [PMID: 29196650 PMCID: PMC5711944 DOI: 10.1038/s41598-017-16428-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 11/06/2017] [Indexed: 01/30/2023] Open
Abstract
Bacteria swim in sequences of straight runs that are interrupted by turning events. They drive their swimming locomotion with the help of rotating helical flagella. Depending on the number of flagella and their arrangement across the cell body, different run-and-turn patterns can be observed. Here, we present fluorescence microscopy recordings showing that cells of the soil bacterium Pseudomonas putida that are decorated with a polar tuft of helical flagella, can alternate between two distinct swimming patterns. On the one hand, they can undergo a classical push-pull-push cycle that is well known from monopolarly flagellated bacteria but has not been reported for species with a polar bundle of multiple flagella. Alternatively, upon leaving the pulling mode, they can enter a third slow swimming phase, where they propel themselves with their helical bundle wrapped around the cell body. A theoretical estimate based on a random-walk model shows that the spreading of a population of swimmers is strongly enhanced when cycling through a sequence of pushing, pulling, and wrapped flagellar configurations as compared to the simple push-pull-push pattern.
Collapse
Affiliation(s)
- Marius Hintsche
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam, Germany
| | - Veronika Waljor
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam, Germany
| | - Robert Großmann
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, F-06108, Nice Cedex 02, France
| | - Marco J Kühn
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Kai M Thormann
- Institut für Mikrobiologie und Molekularbiologie, Justus-Liebig-Universität Giessen, 35392, Giessen, Germany
| | - Fernando Peruani
- Université Côte d'Azur, Laboratoire J. A. Dieudonné, UMR 7351 CNRS, F-06108, Nice Cedex 02, France
| | - Carsten Beta
- University of Potsdam, Institute of Physics and Astronomy, 14476, Potsdam, Germany.
| |
Collapse
|
26
|
Brenzinger S, Dewenter L, Delalez NJ, Leicht O, Berndt V, Paulick A, Berry RM, Thanbichler M, Armitage JP, Maier B, Thormann KM. Mutations targeting the plug-domain of the Shewanella oneidensis proton-driven stator allow swimming at increased viscosity and under anaerobic conditions. Mol Microbiol 2016; 102:925-938. [PMID: 27611183 DOI: 10.1111/mmi.13499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Shewanella oneidensis MR-1 possesses two different stator units to drive flagellar rotation, the Na+ -dependent PomAB stator and the H+ -driven MotAB stator, the latter possibly acquired by lateral gene transfer. Although either stator can independently drive swimming through liquid, MotAB-driven motors cannot support efficient motility in structured environments or swimming under anaerobic conditions. Using ΔpomAB cells we isolated spontaneous mutants able to move through soft agar. We show that a mutation that alters the structure of the plug domain in MotB affects motor functions and allows cells to swim through media of increased viscosity and under anaerobic conditions. The number and exchange rates of the mutant stator around the rotor were not significantly different from wild-type stators, suggesting that the number of stators engaged is not the cause of increased swimming efficiency. The swimming speeds of planktonic mutant MotAB-driven cells was reduced, and overexpression of some of these stators caused reduced growth rates, implying that mutant stators not engaged with the rotor allow some proton leakage. The results suggest that the mutations in the MotB plug domain alter the proton interactions with the stator ion channel in a way that both increases torque output and allows swimming at decreased pmf values.
Collapse
Affiliation(s)
- Susanne Brenzinger
- Department of Microbiology and Molecular Biology at the IFZ, Justus-Liebig-Universität Gießen, Gießen, 35392, Germany.,Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany
| | - Lena Dewenter
- Department of Physics, Universität Köln, Cologne, 50674, Germany
| | | | - Oliver Leicht
- Philipps-Universität, Marburg, Germany LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany
| | - Volker Berndt
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany
| | - Anja Paulick
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, 35043, Germany
| | - Richard M Berry
- Physics Department, University of Oxford, Oxford, OX1 3QU, UK
| | - Martin Thanbichler
- Philipps-Universität, Marburg, Germany LOEWE Center for Synthetic Microbiology, Marburg, 35043, Germany.,Max-Planck-Institut für terrestrische Mikrobiologie & LOEWE Center für Synthetische Mikrobiologie, Marburg, 35043, Germany
| | | | - Berenike Maier
- Department of Physics, Universität Köln, Cologne, 50674, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology at the IFZ, Justus-Liebig-Universität Gießen, Gießen, 35392, Germany
| |
Collapse
|
27
|
Rossmann F, Brenzinger S, Knauer C, Dörrich AK, Bubendorfer S, Ruppert U, Bange G, Thormann KM. The role of FlhF and HubP as polar landmark proteins in Shewanella putrefaciens CN-32. Mol Microbiol 2015; 98:727-42. [PMID: 26235439 DOI: 10.1111/mmi.13152] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2015] [Indexed: 01/06/2023]
Abstract
Spatiotemporal regulation of cell polarity plays a role in many fundamental processes in bacteria and often relies on 'landmark' proteins which recruit the corresponding clients to their designated position. Here, we explored the localization of two multi-protein complexes, the polar flagellar motor and the chemotaxis array, in Shewanella putrefaciens CN-32. We demonstrate that polar positioning of the flagellar system, but not of the chemotaxis system, depends on the GTPase FlhF. In contrast, the chemotaxis array is recruited by a transmembrane protein which we identified as the functional ortholog of Vibrio cholerae HubP. Mediated by its periplasmic N-terminal LysM domain, SpHubP exhibits an FlhF-independent localization pattern during cell cycle similar to its Vibrio counterpart and also has a role in proper chromosome segregation. In addition, while not affecting flagellar positioning, SpHubP is crucial for normal flagellar function and is involved in type IV pili-mediated twitching motility. We hypothesize that a group of HubP/FimV homologs, characterized by a rather conserved N-terminal periplasmic section required for polar targeting and a highly variable acidic cytoplasmic part, primarily mediating recruitment of client proteins, serves as polar markers in various bacterial species with respect to different cellular functions.
Collapse
Affiliation(s)
- Florian Rossmann
- Department of Microbiology and Molecular Biology, Justus-Liebig Universität, 35392, Giessen, Germany.,Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, 35043, Marburg, Germany
| | - Susanne Brenzinger
- Department of Microbiology and Molecular Biology, Justus-Liebig Universität, 35392, Giessen, Germany.,Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, 35043, Marburg, Germany
| | - Carina Knauer
- LOEWE Center for Synthetic Microbiology (Synmikro) & Department of Chemistry, Philipps University Marburg, 35043, Marburg, Germany
| | - Anja K Dörrich
- Department of Microbiology and Molecular Biology, Justus-Liebig Universität, 35392, Giessen, Germany
| | - Sebastian Bubendorfer
- Department of Microbiology and Molecular Biology, Justus-Liebig Universität, 35392, Giessen, Germany
| | - Ulrike Ruppert
- Department of Microbiology and Molecular Biology, Justus-Liebig Universität, 35392, Giessen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (Synmikro) & Department of Chemistry, Philipps University Marburg, 35043, Marburg, Germany
| | - Kai M Thormann
- Department of Microbiology and Molecular Biology, Justus-Liebig Universität, 35392, Giessen, Germany
| |
Collapse
|
28
|
Abstract
Bacteria differ in number and location of their flagella that appear in regular patterns at the cell surface (flagellation pattern). Despite the plethora of bacterial species, only a handful of these patterns exist. The correct flagellation pattern is a prerequisite for motility, but also relates to biofilm formation and the pathogenicity of disease-causing flagellated bacteria. However, the mechanisms that maintain location and number of flagella are far from being understood. Here, we review our knowledge on mechanisms that enable bacteria to maintain their appropriate flagellation pattern. While some peritrichous flagellation patterns might occur by rather simple stochastic processes, other bacterial species appear to rely on landmark systems to define the designated flagellar position. Such landmarks are the Tip system of Caulobacter crescentus or the signal recognition particle (SRP)-GTPase FlhF and the MinD/ParA-type ATPase FlhG (synonyms: FleN, YlxH and MinD2). The latter two proteins constitute a regulatory circuit essential for diverse flagellation patterns in many Gram-positive and negative species. The interactome of FlhF/G (e.g. C-ring proteins FliM, FliN, FliY or the transcriptional regulator FleQ/FlrA) seems evolutionary adapted to meet the specific needs for a respective pattern. This variability highlights the importance of the correct flagellation pattern for motile species.
Collapse
Affiliation(s)
- Jan S Schuhmacher
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| | - Kai M Thormann
- Justus-Liebig University, Department of Microbiology and Molecular Biology, Heinrich-Buff-Ring 26-32, D-35392 Giessen, Germany
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology & Dep. of Chemistry, Philipps University Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| |
Collapse
|
29
|
Paulick A, Delalez NJ, Brenzinger S, Steel BC, Berry RM, Armitage JP, Thormann KM. Dual stator dynamics in theShewanella oneidensis MR-1 flagellar motor. Mol Microbiol 2015; 96:993-1001. [DOI: 10.1111/mmi.12984] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Anja Paulick
- Max-Planck-Institute für terrestrische Mikrobiologie; Department of Ecophysiology; 35043 Marburg Germany
| | | | - Susanne Brenzinger
- Max-Planck-Institute für terrestrische Mikrobiologie; Department of Ecophysiology; 35043 Marburg Germany
- Justus-Liebig-Universität Gießen; Department of Microbiology and Molecular Biology at the IFZ; Gießen 35392 Germany
| | | | | | | | - Kai M. Thormann
- Max-Planck-Institute für terrestrische Mikrobiologie; Department of Ecophysiology; 35043 Marburg Germany
- Justus-Liebig-Universität Gießen; Department of Microbiology and Molecular Biology at the IFZ; Gießen 35392 Germany
| |
Collapse
|
30
|
Bubendorfer S, Held S, Windel N, Paulick A, Klingl A, Thormann KM. Specificity of motor components in the dual flagellar system of Shewanella putrefaciens CN-32. Mol Microbiol 2011; 83:335-50. [PMID: 22151089 DOI: 10.1111/j.1365-2958.2011.07934.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Bacterial flagellar motors are intricate nanomachines in which the stator units and rotor component FliM may be dynamically exchanged during function. Similar to other bacterial species, the gammaproteobacterium Shewanella putrefaciens CN-32 possesses a complete secondary flagellar system along with a corresponding stator unit. Expression of the secondary system occurs during planktonic growth in complex media and leads to the formation of a subpopulation with one or more additional flagella at random positions in addition to the primary polar system. We used physiological and phenotypic characterizations of defined mutants in concert with fluorescent microscopy on labelled components of the two different systems, the stator proteins PomB and MotB, the rotor components FliM(1) and FliM(2), and the auxiliary motor components MotX and MotY, to determine localization, function and dynamics of the proteins in the flagellar motors. The results demonstrate that the polar flagellum is driven by a Na(+)-dependent FliM(1)/PomAB/MotX/MotY flagellar motor while the secondary system is rotated by a H(+)-dependent FliM(2)/MotAB motor. The components were highly specific for their corresponding motor and are unlikely to be extensively swapped or shared between the two flagellar systems under planktonic conditions. The results have implications for both specificity and dynamics of flagellar motor components.
Collapse
Affiliation(s)
- Sebastian Bubendorfer
- Department of Ecophysiology, Max-Planck-Institut für terrestrische Mikrobiologie, Marburg, Germany
| | | | | | | | | | | |
Collapse
|
31
|
Abstract
The BarA/UvrY two-component system is well conserved in species of the γ-proteobacteria and regulates numerous processes predominantly by controlling the expression of a subset of noncoding small RNAs. In this study, we identified and characterized the BarA/UvrY two-component system in the gammaproteobacterium Shewanella oneidensis MR-1. Functional interaction of sensor kinase BarA and the cognate response regulator UvrY was indicated by in vitro phosphotransfer studies. The expression of two predicted small regulatory RNAs (sRNAs), CsrB1 and CsrB2, was dependent on UvrY. Transcriptomic analysis by microarrays revealed that UvrY is a global regulator and directly or indirectly affects transcript levels of more than 200 genes in S. oneidensis. Among these are genes encoding key enzymes of central carbon metabolism such as ackA, aceAB, and pflAB. As predicted of a signal transduction pathway that controls aspects of central metabolism, mutants lacking UvrY reach a significantly higher OD than the wild type during aerobic growth on N-acetylglucosamine (NAG) while under anaerobic conditions the mutant grew more slowly. A shorter lag phase occurred with lactate as carbon source. In contrast, significant growth phenotypes were absent in complex medium. Based on these studies we hypothesize that, in S. oneidensis MR-1, the global BarA/UvrY/Csr regulatory pathway is involved in central carbon metabolism processes.
Collapse
Affiliation(s)
- Lucas Binnenkade
- Department of Ecophysiology, Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| | - Jürgen Lassak
- Department of Ecophysiology, Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| | - Kai M. Thormann
- Department of Ecophysiology, Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
- * E-mail:
| |
Collapse
|
32
|
Abstract
Background Biofilm formation has been studied in much detail for a variety of bacterial species, as it plays a major role in the pathogenicity of bacteria. However, only limited information is available for the development of archaeal communities that are frequently found in many natural environments. Methodology We have analyzed biofilm formation in three closely related hyperthermophilic crenarchaeotes: Sulfolobus acidocaldarius, S. solfataricus and S. tokodaii. We established a microtitre plate assay adapted to high temperatures to determine how pH and temperature influence biofilm formation in these organisms. Biofilm analysis by confocal laser scanning microscopy demonstrated that the three strains form very different communities ranging from simple carpet-like structures in S. solfataricus to high density tower-like structures in S. acidocaldarius in static systems. Lectin staining indicated that all three strains produced extracellular polysaccharides containing glucose, galactose, mannose and N-acetylglucosamine once biofilm formation was initiated. While flagella mutants had no phenotype in two days old static biofilms of S. solfataricus, a UV-induced pili deletion mutant showed decreased attachment of cells. Conclusion The study gives first insights into formation and development of crenarchaeal biofilms in extreme environments.
Collapse
Affiliation(s)
- Andrea Koerdt
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Julia Gödeke
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jürgen Berger
- Electron Microscopy, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Kai M. Thormann
- Department of Ecophysiology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Sonja-Verena Albers
- Molecular Biology of Archaea, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- * E-mail:
| |
Collapse
|
33
|
Abstract
Many bacteria are motile by means of flagella, semi-rigid helical filaments rotated at the filament's base and energized by proton or sodium-ion gradients. Torque is created between the two major components of the flagellar motor: the rotating switch complex and the cell-wall-associated stators, which are arranged in a dynamic ring-like structure. Being motile provides a survival advantage to many bacteria, and thus the flagellar motor should work optimally under a wide range of environmental conditions. Recent studies have demonstrated that numerous species possess a single flagellar system but have two or more individual stator systems that contribute differentially to flagellar rotation. This review describes recent findings on rotor–stator interactions, on the role of different stators, and on how stator selection could be regulated. An emerging model suggests that bacterial flagellar motors are dynamic and can be tuned by stator swapping in response to different environmental conditions.
Collapse
Affiliation(s)
- Kai M. Thormann
- Department of Ecophysiology, Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| | - Anja Paulick
- Department of Ecophysiology, Max-Planck-Institut für Terrestrische Mikrobiologie, Marburg, Germany
| |
Collapse
|
34
|
Paulick A, Koerdt A, Lassak J, Huntley S, Wilms I, Narberhaus F, Thormann KM. Two different stator systems drive a single polar flagellum inShewanella oneidensisMR-1. Mol Microbiol 2009; 71:836-50. [DOI: 10.1111/j.1365-2958.2008.06570.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
35
|
Thormann KM, Duttler S, Saville RM, Hyodo M, Shukla S, Hayakawa Y, Spormann AM. Control of formation and cellular detachment from Shewanella oneidensis MR-1 biofilms by cyclic di-GMP. J Bacteriol 2006; 188:2681-91. [PMID: 16547056 PMCID: PMC1428383 DOI: 10.1128/jb.188.7.2681-2691.2006] [Citation(s) in RCA: 168] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Stability and resilience against environmental perturbations are critical properties of medical and environmental biofilms and pose important targets for their control. Biofilm stability is determined by two mutually exclusive processes: attachment of cells to and detachment from the biofilm matrix. Using Shewanella oneidensis MR-1, an environmentally versatile, Fe(III) and Mn(IV) mineral-reducing microorganism, we identified mxdABCD as a new set of genes essential for formation of a three-dimensional biofilm. Molecular analysis revealed that mxdA encodes a cyclic bis(3',5')guanylic acid (cyclic di-GMP)-forming enzyme with an unusual GGDEF motif, i.e., NVDEF, which is essential for its function. mxdB encodes a putative membrane-associated glycosyl transferase. Both genes are essential for matrix attachment. The attachment-deficient phenotype of a DeltamxdA mutant was rescued by ectopic expression of VCA0956, encoding another diguanylate cyclase. Interestingly, a rapid cellular detachment from the biofilm occurred upon induction of yhjH, a gene encoding an enzyme that has been shown to have phosphodiesterase activity. In this way, it was possible to bypass the previously identified sudden depletion of molecular oxygen as an environmental trigger to induce biofilm dissolution. We propose a model for c-di-GMP as a key intracellular regulator for controlling biofilm stability by shifting the state of a biofilm cell between attachment and detachment in a concentration-dependent manner.
Collapse
Affiliation(s)
- Kai M Thormann
- Department of Civil Engineering, James H. Clark Center for Biomedical Engineering and Science, Stanford University, Stanford, CA 94305-5429, USA
| | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Active detachment of cells from microbial biofilms is a critical yet poorly understood step in biofilm development. We discovered that detachment of cells from biofilms of Shewanella oneidensis MR-1 can be induced by arresting the medium flow in a hydrodynamic biofilm system. Induction of detachment was rapid, and substantial biofilm dispersal started as soon as 5 min after the stop of flow. We developed a confocal laser scanning microscopy-based assay to quantify detachment. The extent of biomass loss was found to be dependent on the time interval of flow stop and on the thickness of the biofilm. Up to 80% of the biomass of 16-h-old biofilms could be induced to detach. High-resolution microscopy studies revealed that detachment was associated with an overall loosening of the biofilm structure and a release of individual cells or small cell clusters. Swimming motility was not required for detachment. Although the loosening of cells from the biofilm structure was observed evenly throughout thin biofilms, the most pronounced detachment in thicker biofilms occurred in regions exposed to the flow of medium, suggesting a metabolic control of detachability. Deconvolution of the factors associated with the stop of medium flow revealed that a sudden decrease in oxygen tension is the predominant trigger for initiating detachment of individual cells. In contrast, carbon limitation did not trigger any substantial detachment, suggesting a physiological link between oxygen sensing or metabolism and detachment. In-frame deletions were introduced into genes encoding the known and putative global transcriptional regulators ArcA, CRP, and EtrA (FNR), which respond to changes in oxygen tension in S. oneidensis MR-1. Biofilms of null mutants in arcA and crp were severely impacted in the stop-of-flow-induced detachment response, suggesting a role for these genes in regulation of detachment. In contrast, an DeltaetrA mutant displayed a variable detachment phenotype. From this genetic evidence we conclude that detachment is a biologically controlled process and that a rapid change in oxygen concentration is a critical factor in detachment and, consequently, in dispersal of S. oneidensis cells from biofilms. Similar mechanisms might also operate in other bacteria.
Collapse
Affiliation(s)
- Kai M Thormann
- Department of Civil and Environmental Engineering, James H. Clark Center, E250, Stanford University, Stanford, CA 94305-5429, USA
| | | | | | | |
Collapse
|
37
|
Abstract
Shewanella oneidensis MR-1 is a facultative Fe(III)- and Mn(IV)-reducing microorganism and serves as a model for studying microbially induced dissolution of Fe or Mn oxide minerals as well as biogeochemical cycles. In soil and sediment environments, S. oneidensis biofilms form on mineral surfaces and are critical for mediating the metabolic interaction between this microbe and insoluble metal oxide phases. In order to develop an understanding of the molecular basis of biofilm formation, we investigated S. oneidensis biofilms developing on glass surfaces in a hydrodynamic flow chamber system. After initial attachment, growth of microcolonies and lateral spreading of biofilm cells on the surface occurred simultaneously within the first 24 h. Once surface coverage was almost complete, biofilm development proceeded with extensive vertical growth, resulting in formation of towering structures giving rise to pronounced three-dimensional architecture. Biofilm development was found to be dependent on the nutrient conditions, suggesting a metabolic control. In global transposon mutagenesis, 173 insertion mutants out of 15,000 mutants screened were identified carrying defects in initial attachment and/or early stages in biofilm formation. Seventy-one of those mutants exhibited a nonswimming phenotype, suggesting a role of swimming motility or motility elements in biofilm formation. Disruption mutations in motility genes (flhB, fliK, and pomA), however, did not affect initial attachment but affected progression of biofilm development into pronounced three-dimensional architecture. In contrast, mutants defective in mannose-sensitive hemagglutinin type IV pilus biosynthesis and in pilus retraction (pilT) showed severe defects in adhesion to abiotic surfaces and biofilm formation, respectively. The results provide a basis for understanding microbe-mineral interactions in natural environments.
Collapse
Affiliation(s)
- Kai M Thormann
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA 94305-5429, USA
| | | | | | | | | |
Collapse
|