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Sharp C, Foster KR. Host control and the evolution of cooperation in host microbiomes. Nat Commun 2022; 13:3567. [PMID: 35732630 PMCID: PMC9218092 DOI: 10.1038/s41467-022-30971-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/27/2022] [Indexed: 12/14/2022] Open
Abstract
Humans, and many other species, are host to diverse symbionts. It is often suggested that the mutual benefits of host-microbe relationships can alone explain cooperative evolution. Here, we evaluate this hypothesis with evolutionary modelling. Our model predicts that mutual benefits are insufficient to drive cooperation in systems like the human microbiome, because of competition between symbionts. However, cooperation can emerge if hosts can exert control over symbionts, so long as there are constraints that limit symbiont counter evolution. We test our model with genomic data of two bacterial traits monitored by animal immune systems. In both cases, bacteria have evolved as predicted under host control, tending to lose flagella and maintain butyrate production when host-associated. Moreover, an analysis of bacteria that retain flagella supports the evolution of host control, via toll-like receptor 5, which limits symbiont counter evolution. Our work puts host control mechanisms, including the immune system, at the centre of microbiome evolution.
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Affiliation(s)
- Connor Sharp
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Kevin R Foster
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Kotov V, Lunelli M, Wald J, Kolbe M, Marlovits TC. Helical reconstruction of Salmonella and Shigella needle filaments attached to type 3 basal bodies. Biochem Biophys Rep 2021; 27:101039. [PMID: 34258394 PMCID: PMC8254080 DOI: 10.1016/j.bbrep.2021.101039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/26/2021] [Indexed: 12/02/2022] Open
Abstract
Gram-negative pathogens evolved a syringe-like nanomachine, termed type 3 secretion system, to deliver protein effectors into the cytoplasm of host cells. An essential component of this system is a long helical needle filament that protrudes from the bacterial surface and connects the cytoplasms of the bacterium and the eukaryotic cell. Previous structural research was predominantly focused on reconstituted type 3 needle filaments, which lacked the biological context. In this work we introduce a facile procedure to obtain high-resolution cryo-EM structure of needle filaments attached to the basal body of type 3 secretion systems. We validate our approach by solving the structure of Salmonella PrgI filament and demonstrate its utility by obtaining the first high-resolution cryo-EM reconstruction of Shigella MxiH filament. Our work paves the way to systematic structural characterization of attached type 3 needle filaments in the context of mutagenesis studies, protein structural evolution and drug development.
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Affiliation(s)
- Vadim Kotov
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Michele Lunelli
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- Department of Structural Infection Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Jiri Wald
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Michael Kolbe
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- Department of Structural Infection Biology, Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Chemistry, Faculty of Mathematics, Informatics and Natural Sciences, University of Hamburg, Rothenbaumchaussee 19, 20148 Hamburg, Germany
- Corresponding author. Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany.
| | - Thomas C. Marlovits
- Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany
- University Medical Centre Hamburg-Eppendorf (UKE), Martinistraße 52, 20246 Hamburg, Germany
- Deutsches Elektronen-Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
- Corresponding author. Centre for Structural Systems Biology (CSSB), Notkestraße 85, 22607 Hamburg, Germany.
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Kinosita Y, Ishida T, Yoshida M, Ito R, Morimoto YV, Goto K, Berry RM, Nishizaka T, Sowa Y. Distinct chemotactic behavior in the original Escherichia coli K-12 depending on forward-and-backward swimming, not on run-tumble movements. Sci Rep 2020; 10:15887. [PMID: 32985511 PMCID: PMC7522084 DOI: 10.1038/s41598-020-72429-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 08/27/2020] [Indexed: 11/21/2022] Open
Abstract
Most motile bacteria are propelled by rigid, helical, flagellar filaments and display distinct swimming patterns to explore their favorable environments. Escherichia coli cells have a reversible rotary motor at the base of each filament. They exhibit a run-tumble swimming pattern, driven by switching of the rotational direction, which causes polymorphic flagellar transformation. Here we report a novel swimming mode in E. coli ATCC10798, which is one of the original K-12 clones. High-speed tracking of single ATCC10798 cells showed forward and backward swimming with an average turning angle of 150°. The flagellar helicity remained right-handed with a 1.3 μm pitch and 0.14 μm helix radius, which is consistent with the feature of a curly type, regardless of motor switching; the flagella of ATCC10798 did not show polymorphic transformation. The torque and rotational switching of the motor was almost identical to the E. coli W3110 strain, which is a derivative of K-12 and a wild-type for chemotaxis. The single point mutation of N87K in FliC, one of the filament subunits, is critical to the change in flagellar morphology and swimming pattern, and lack of flagellar polymorphism. E. coli cells expressing FliC(N87K) sensed ascending a chemotactic gradient in liquid but did not spread on a semi-solid surface. Based on these results, we concluded that a flagellar polymorphism is essential for spreading in structured environments.
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Affiliation(s)
- Yoshiaki Kinosita
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan.
- Department of Physics, University of Oxford, Park load, Oxford, OX1 3PU, UK.
- Molecular Physiology Laboratory, RIKEN, Wako, Japan.
| | - Tsubasa Ishida
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan
| | - Myu Yoshida
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan
| | - Rie Ito
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan
| | - Yusuke V Morimoto
- Department of Physics and Information Technology, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Iizuka, Fukuoka, Japan
| | - Kazuki Goto
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Richard M Berry
- Department of Physics, University of Oxford, Park load, Oxford, OX1 3PU, UK
| | - Takayuki Nishizaka
- Department of Physics, Gakushuin University, 1-5-1 Mejiro, Toshima-ku, Tokyo, 171-8588, Japan
| | - Yoshiyuki Sowa
- Department of Frontier Bioscience and Research Center for Micro-Nano Technology, Hosei University, Tokyo, 184-8584, Japan.
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Burtchett T, Love C, Sarkar R, Tripp BC. A structure-function study of C-terminal residues predicted to line the export channel in Salmonella Flagellin. Biochim Biophys Acta Gen Subj 2020; 1865:129748. [PMID: 32980501 DOI: 10.1016/j.bbagen.2020.129748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/16/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND Structural studies of a Salmonella Typhimurium flagellin protein indicated that four polar or charged C-terminal amino acid residues line the inner channel of the flagellum. The hydrophilic character of these putative channel-lining residues was predicted to be essential to facilitate the transport of unfolded flagellin monomers during flagellar assembly. The structure-function relationship of these putative channel-lining residues was investigated by site-directed mutagenesis to examine effects of side chain polarity and size on flagella assembly and function. METHODS Channel-lining residue variants were generated using site-directed mutagenesis to substitute alanine and other residues to examine the effects of altered side-chain polarity on export and assembly. The export, in vivo motility function, and flagellar structure of variants was characterized by agar motility, video microscopy, immunofluorescence, and SDS-PAGE. RESULTS Alanine substitution yielded decreased motility and flagellar assembly for three of the four residues. However, alanine substitution of residue Arg 494 did not alter export, although substitution with negatively charged glutamate decreased motility and flagellar filament length. Furthermore, many of the C-terminal mutations affected flagellar filament morphology and stability, often resulting in more tightly coiled and/or more brittle flagella than the wild type. CONCLUSIONS The four channel-lining C-terminal residues may facilitate monomer protein transport but also have structural roles in determining the stability and morphology of the flagellum. GENERAL SIGNIFICANCE These results provide further insight into the complex process of bacterial flagellin export and flagellar assembly and provide evidence of previously unknown structural functions for the four putative channel-lining residues.
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Affiliation(s)
- Troy Burtchett
- Western Michigan University, Department of Biological Sciences, 1903 W. Michigan Avenue, Kalamazoo, MI 49008, USA
| | - Chloe Love
- Kalamazoo College, Department of Biology, 1200 Academy St., Kalamazoo, MI 49006, USA
| | - Reshma Sarkar
- Western Michigan University, Department of Biological Sciences, 1903 W. Michigan Avenue, Kalamazoo, MI 49008, USA
| | - Brian C Tripp
- Western Michigan University, Department of Biological Sciences, 1903 W. Michigan Avenue, Kalamazoo, MI 49008, USA.
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