1
|
Little JI, Singh PK, Zhao J, Dunn S, Matz H, Donnenberg MS. Type IV pili of Enterobacteriaceae species. EcoSal Plus 2024:eesp00032023. [PMID: 38294234 DOI: 10.1128/ecosalplus.esp-0003-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/01/2023] [Indexed: 02/01/2024]
Abstract
Type IV pili (T4Ps) are surface filaments widely distributed among bacteria and archaea. T4Ps are involved in many cellular functions and contribute to virulence in some species of bacteria. Due to the diversity of T4Ps, different properties have been observed for homologous proteins that make up T4Ps in various organisms. In this review, we highlight the essential components of T4Ps, their functions, and similarities to related systems. We emphasize the unique T4Ps of enteric pathogens within the Enterobacteriaceae family, which includes pathogenic strains of Escherichia coli and Salmonella. These include the bundle-forming pilus (BFP) of enteropathogenic E. coli (EPEC), longus (Lng) and colonization factor III (CFA/III) of enterotoxigenic E. coli (ETEC), T4P of Salmonella enterica serovar Typhi, Colonization Factor Citrobacter (CFC) of Citrobacter rodentium, T4P of Yersinia pseudotuberculosis, a ubiquitous T4P that was characterized in enterohemorrhagic E. coli (EHEC), and the R64 plasmid thin pilus. Finally, we highlight areas for further study.
Collapse
Affiliation(s)
- Janay I Little
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Pradip K Singh
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jinlei Zhao
- School of Medicine, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shakeera Dunn
- Internal Medicine Residency, Bayhealth Medical Center, Dover, Delaware, USA
| | - Hanover Matz
- Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | | |
Collapse
|
2
|
Guilvout I, Samsudin F, Huber RG, Bond PJ, Bardiaux B, Francetic O. Membrane platform protein PulF of the Klebsiella type II secretion system forms a trimeric ion channel essential for endopilus assembly and protein secretion. mBio 2024; 15:e0142323. [PMID: 38063437 PMCID: PMC10790770 DOI: 10.1128/mbio.01423-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type IV pili and type II secretion systems are members of the widespread type IV filament (T4F) superfamily of nanomachines that assemble dynamic and versatile surface fibers in archaea and bacteria. The assembly and retraction of T4 filaments with diverse surface properties and functions require the plasma membrane platform proteins of the GspF/PilC superfamily. Generally considered dimeric, platform proteins are thought to function as passive transmitters of the mechanical energy generated by the ATPase motor, to somehow promote insertion of pilin subunits into the nascent pilus fibers. Here, we generate and experimentally validate structural predictions that support the trimeric state of a platform protein PulF from a type II secretion system. The PulF trimers form selective proton or sodium channels which might energize pilus assembly using the membrane potential. The conservation of the channel sequence and structural features implies a common mechanism for all T4F assembly systems. We propose a model of the oligomeric PulF-PulE ATPase complex that provides an essential framework to investigate and understand the pilus assembly mechanism.
Collapse
Affiliation(s)
- Ingrid Guilvout
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
| | | | | | - Peter J. Bond
- Bioinformatics Institute (A-STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
| |
Collapse
|
3
|
Li Y, Santos-Moreno J, Francetic O. The periplasmic coiled coil formed by the assembly platform proteins PulL and PulM is critical for function of the Klebsiella type II secretion system. Res Microbiol 2023; 174:104075. [PMID: 37141929 DOI: 10.1016/j.resmic.2023.104075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
Bacteria use type II secretion systems (T2SS) to secrete to their surface folded proteins that confer diverse functions, from nutrient acquisition to virulence. In the Klebsiella species, T2SS-mediated secretion of pullulanase (PulA) requires assembly of a dynamic filament called the endopilus. The inner membrane assembly platform (AP) subcomplex is essential for endopilus assembly and PulA secretion. AP components PulL and PulM interact with each other through their C-terminal globular domains and transmembrane segments. Here, we investigated the roles of their periplasmic helices, predicted to form a coiled coil, in assembly and function of the PulL-PulM complex. PulL and PulM variants lacking these periplasmic helices were defective for interaction in the bacterial two-hybrid (BACTH) assay. Their functions in PulA secretion and assembly of PulG subunits into endopilus filaments were strongly reduced. Interestingly, deleting the cytoplasmic peptide of PulM nearly abolished the function of variant PulMΔN and its interaction with PulG, but not with PulL, in the BACTH assay. Nevertheless, PulL was specifically proteolyzed in the presence of the PulMΔN variant, suggesting that PulM N-terminal peptide stabilizes PulL in the cytoplasm. We discuss the implications of these results for the T2S endopilus and type IV pilus assembly mechanisms.
Collapse
Affiliation(s)
- Yuanyuan Li
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| | - Javier Santos-Moreno
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, F-75015 Paris, France.
| |
Collapse
|
4
|
Characterization of a glycan-binding complex of minor pilins completes the analysis of Streptococcus sanguinis type 4 pili subunits. Proc Natl Acad Sci U S A 2023; 120:e2216237120. [PMID: 36626560 PMCID: PMC9934059 DOI: 10.1073/pnas.2216237120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Type 4 filaments (T4F)-of which type 4 pili (T4P) are the archetype-are a superfamily of nanomachines nearly ubiquitous in prokaryotes. T4F are polymers of one major pilin, which also contain minor pilins whose roles are often poorly understood. Here, we complete the structure/function analysis of the full set of T4P pilins in the opportunistic bacterial pathogen Streptococcus sanguinis. We determined the structure of the minor pilin PilA, which is unexpectedly similar to one of the subunits of a tip-located complex of four minor pilins, widely conserved in T4F. We found that PilA interacts and dramatically stabilizes the minor pilin PilC. We determined the structure of PilC, showing that it is a modular pilin with a lectin module binding a subset of glycans prevalent in the human glycome, the host of S. sanguinis. Altogether, our findings support a model whereby the minor pilins in S. sanguinis T4P form a tip-located complex promoting adhesion to various host receptors. This has general implications for T4F.
Collapse
|
5
|
Genome Analysis of Enterobacter asburiae and Lelliottia spp. Proliferating in Oligotrophic Drinking Water Reservoirs and Lakes. Appl Environ Microbiol 2022; 88:e0047122. [PMID: 35862664 PMCID: PMC9317948 DOI: 10.1128/aem.00471-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Surface waters are one of the main sources for drinking water production, and thus microbial contamination should be as minimal as possible. However, high concentrations of coliform bacteria were detected in reservoirs and lakes used for drinking water production during summer months due to autochthonous proliferation processes. Here, we present the genomic analyses of 17 strains of Enterobacter asburiae and Lelliottia spp. proliferating in reservoirs and lakes with special focus on the hygienic relevance, antibiotic resistance, and adaptations to the oligotrophic environments. The genomes contain neither genes for the type III secretion system nor cytotoxins or hemolysins, which are considered typical virulence factors. Examination of antibiotic resistance genes revealed mainly efflux pumps and β-lactamase class C (ampC) genes. Phenotypically, single isolates of Enterobacter asburiae showed resistance to fosfomycin and ceftazidime. The genome analyses further suggest adaptations to oligotrophic and changing environmental conditions in reservoirs and lakes, e.g., genes to cope with low nitrate and phosphate levels and the ability to utilize substances released by algae, like amino acids, chitin, alginate, rhamnose, and fucose. This leads to the hypothesis that the proliferation of the coliform bacteria could occur at the end of summer due to algae die-off. IMPORTANCE Certain strains of coliform bacteria have been shown to proliferate in the oligotrophic water of drinking water reservoirs and lakes, reaching values above 104 per 100 mL. Such high concentrations challenge drinking water treatment, and occasionally the respective coliform bacteria have been detected in the treated drinking water. Thus, the question of their hygienic relevance is of high importance for water suppliers and authorities. Our genomic analyses suggest that the strains are not hygienically relevant, as typical virulence factors are absent and antibiotic resistance genes in the genomes most likely are of natural origin. Furthermore, their presence in the water is not related to fecal contamination. The proliferation in reservoirs and lakes during stable summer stratification is an autochthonic process of certain E. asburiae and Lelliottia strains that are well adapted to the surrounding oligotrophic environment.
Collapse
|
6
|
Karami Y, López-Castilla A, Ori A, Thomassin JL, Bardiaux B, Malliavin T, Izadi-Pruneyre N, Francetic O, Nilges M. Computational and biochemical analysis of type IV pilus dynamics and stability. Structure 2021; 29:1397-1409.e6. [PMID: 34520738 DOI: 10.1016/j.str.2021.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/14/2021] [Accepted: 07/20/2021] [Indexed: 11/16/2022]
Abstract
Type IV pili (T4P) are distinctive dynamic filaments at the surface of many bacteria that can rapidly extend and retract and withstand strong forces. T4P are important virulence factors in many human pathogens, including Enterohemorrhagic Escherichia coli (EHEC). The structure of the EHEC T4P has been determined by integrating nuclear magnetic resonance (NMR) and cryo-electron microscopy data. To better understand pilus assembly, stability, and function, we performed a total of 108 ms all-atom molecular dynamics simulations of wild-type and mutant T4P. Extensive characterization of the conformational landscape of T4P in different conditions of temperature, pH, and ionic strength is complemented with targeted mutagenesis and biochemical analyses. Our simulations and NMR experiments reveal a conserved set of residues defining a calcium-binding site at the interface between three pilin subunits. Calcium binding enhances T4P stability ex vivo and in vitro, supporting the role of this binding site as a potential pocket for drug design.
Collapse
Affiliation(s)
- Yasaman Karami
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Aracelys López-Castilla
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Andrea Ori
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Jenny-Lee Thomassin
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Therese Malliavin
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
| |
Collapse
|
7
|
Bird LJ, Kundu BB, Tschirhart T, Corts AD, Su L, Gralnick JA, Ajo-Franklin CM, Glaven SM. Engineering Wired Life: Synthetic Biology for Electroactive Bacteria. ACS Synth Biol 2021; 10:2808-2823. [PMID: 34637280 DOI: 10.1021/acssynbio.1c00335] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Electroactive bacteria produce or consume electrical current by moving electrons to and from extracellular acceptors and donors. This specialized process, known as extracellular electron transfer, relies on pathways composed of redox active proteins and biomolecules and has enabled technologies ranging from harvesting energy on the sea floor, to chemical sensing, to carbon capture. Harnessing and controlling extracellular electron transfer pathways using bioengineering and synthetic biology promises to heighten the limits of established technologies and open doors to new possibilities. In this review, we provide an overview of recent advancements in genetic tools for manipulating native electroactive bacteria to control extracellular electron transfer. After reviewing electron transfer pathways in natively electroactive organisms, we examine lessons learned from the introduction of extracellular electron transfer pathways into Escherichia coli. We conclude by presenting challenges to future efforts and give examples of opportunities to bioengineer microbes for electrochemical applications.
Collapse
Affiliation(s)
- Lina J. Bird
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Biki B. Kundu
- PhD Program in Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77005, United States
| | - Tanya Tschirhart
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Anna D. Corts
- Joyn Bio, Boston, Massachusetts 02210, United States
| | - Lin Su
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing 210018, People’s Republic of China
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jeffrey A. Gralnick
- Department of Plant and Microbial Biology, BioTechnology Institute, University of Minnesota, St. Paul, Minnesota 55108, United States
| | | | - Sarah M. Glaven
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, Washington, D.C. 20375, United States
| |
Collapse
|
8
|
Treuner-Lange A, Chang YW, Glatter T, Herfurth M, Lindow S, Chreifi G, Jensen GJ, Søgaard-Andersen L. PilY1 and minor pilins form a complex priming the type IVa pilus in Myxococcus xanthus. Nat Commun 2020; 11:5054. [PMID: 33028835 PMCID: PMC7541494 DOI: 10.1038/s41467-020-18803-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 09/14/2020] [Indexed: 01/05/2023] Open
Abstract
Type IVa pili are ubiquitous and versatile bacterial cell surface filaments that undergo cycles of extension, adhesion and retraction powered by the cell-envelope spanning type IVa pilus machine (T4aPM). The overall architecture of the T4aPM and the location of 10 conserved core proteins within this architecture have been elucidated. Here, using genetics, cell biology, proteomics and cryo-electron tomography, we demonstrate that the PilY1 protein and four minor pilins, which are widely conserved in T4aP systems, are essential for pilus extension in Myxococcus xanthus and form a complex that is an integral part of the T4aPM. Moreover, these proteins are part of the extended pilus. Our data support a model whereby the PilY1/minor pilin complex functions as a priming complex in T4aPM for pilus extension, a tip complex in the extended pilus for adhesion, and a cork for terminating retraction to maintain a priming complex for the next round of extension.
Collapse
Affiliation(s)
- Anke Treuner-Lange
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA, 19104, USA
| | - Timo Glatter
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Marco Herfurth
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Steffi Lindow
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany
| | - Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E California Boulevard, Pasadena, CA, 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Lotte Søgaard-Andersen
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Str. 10, 35043, Marburg, Germany.
| |
Collapse
|
9
|
Ueki T, Walker DJF, Woodard TL, Nevin KP, Nonnenmann SS, Lovley DR. An Escherichia coli Chassis for Production of Electrically Conductive Protein Nanowires. ACS Synth Biol 2020; 9:647-654. [PMID: 32125829 DOI: 10.1021/acssynbio.9b00506] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Geobacter sulfurreducens' pilin-based electrically conductive protein nanowires (e-PNs) are a revolutionary electronic material. They offer novel options for electronic sensing applications and have the remarkable ability to harvest electrical energy from atmospheric humidity. However, technical constraints limit mass cultivation and genetic manipulation of G. sulfurreducens. Therefore, we designed a strain of Escherichia coli to express e-PNs by introducing a plasmid that contained an inducible operon with E. coli genes for type IV pili biogenesis machinery and a synthetic gene designed to yield a peptide monomer that could be assembled into e-PNs. The e-PNs expressed in E. coli and harvested with a simple filtration method had the same diameter (3 nm) and conductance as e-PNs expressed in G. sulfurreducens. These results, coupled with the robustness of E. coli for mass cultivation and the extensive E. coli toolbox for genetic manipulation, greatly expand the opportunities for large-scale fabrication of novel e-PNs.
Collapse
Affiliation(s)
- Toshiyuki Ueki
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - David J. F. Walker
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Trevor L. Woodard
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Kelly P. Nevin
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Stephen S. Nonnenmann
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Department of Mechanical and Industrial Engineering, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| | - Derek R. Lovley
- Department of Microbiology, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
- Institute for Applied Life Sciences, University of Massachusetts-Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
10
|
Jacobsen T, Bardiaux B, Francetic O, Izadi-Pruneyre N, Nilges M. Structure and function of minor pilins of type IV pili. Med Microbiol Immunol 2019; 209:301-308. [PMID: 31784891 PMCID: PMC7248040 DOI: 10.1007/s00430-019-00642-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 11/14/2019] [Indexed: 02/06/2023]
Abstract
Type IV pili are versatile and highly flexible fibers formed on the surface of many Gram-negative and Gram-positive bacteria. Virulence and infection rate of several pathogenic bacteria, such as Neisseria meningitidis and Pseudomonas aeruginosa, are strongly dependent on the presence of pili as they facilitate the adhesion of the bacteria to the host cell. Disruption of the interactions between the pili and the host cells by targeting proteins involved in this interaction could, therefore, be a treatment strategy. A type IV pilus is primarily composed of multiple copies of protein subunits called major pilins. Additional proteins, called minor pilins, are present in lower abundance, but are essential for the assembly of the pilus or for its specific functions. One class of minor pilins is required to initiate the formation of pili, and may form a complex similar to that identified in the related type II secretion system. Other, species-specific minor pilins in the type IV pilus system have been shown to promote additional functions such as DNA binding, aggregation and adherence. Here, we will review the structure and the function of the minor pilins from type IV pili.
Collapse
Affiliation(s)
- Theis Jacobsen
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France.,Sorbonne Université, Complexité du Vivant, 75005, Paris, France
| | - Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France.
| |
Collapse
|
11
|
Bardiaux B, de Amorim GC, Luna Rico A, Zheng W, Guilvout I, Jollivet C, Nilges M, Egelman EH, Izadi-Pruneyre N, Francetic O. Structure and Assembly of the Enterohemorrhagic Escherichia coli Type 4 Pilus. Structure 2019; 27:1082-1093.e5. [PMID: 31056419 PMCID: PMC7003672 DOI: 10.1016/j.str.2019.03.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 02/18/2019] [Accepted: 03/25/2019] [Indexed: 12/30/2022]
Abstract
Bacterial type 4a pili are dynamic surface filaments that promote bacterial adherence, motility, and macromolecular transport. Their genes are highly conserved among enterobacteria and their expression in enterohemorrhagic Escherichia coli (EHEC) promotes adhesion to intestinal epithelia and pro-inflammatory signaling. To define the molecular basis of EHEC pilus assembly, we determined the structure of the periplasmic domain of its major subunit PpdD (PpdDp), a prototype of an enterobacterial pilin subfamily containing two disulfide bonds. The structure of PpdDp, determined by NMR, was then docked into the density envelope of purified EHEC pili obtained by cryoelectron microscopy (cryo-EM). Cryo-EM reconstruction of EHEC pili at ∼8 Å resolution revealed extremely high pilus flexibility correlating with a large extended region of the pilin stem. Systematic mutagenesis combined with functional and interaction analyses identified charged residues essential for pilus assembly. Structural information on exposed regions and interfaces between EHEC pilins is relevant for vaccine and drug discovery.
Collapse
Affiliation(s)
- Benjamin Bardiaux
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Gisele Cardoso de Amorim
- NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Areli Luna Rico
- NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Weili Zheng
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Camille Jollivet
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Michael Nilges
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22908, USA
| | - Nadia Izadi-Pruneyre
- Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, C3BI, Institut Pasteur, CNRS UMR3528, CNRS USR3756, Paris, France; NMR of Biomolecules Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France.
| |
Collapse
|
12
|
Denise R, Abby SS, Rocha EPC. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biol 2019; 17:e3000390. [PMID: 31323028 PMCID: PMC6668835 DOI: 10.1371/journal.pbio.3000390] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/31/2019] [Accepted: 07/03/2019] [Indexed: 12/21/2022] Open
Abstract
Processes of molecular innovation require tinkering and shifting in the function of existing genes. How this occurs in terms of molecular evolution at long evolutionary scales remains poorly understood. Here, we analyse the natural history of a vast group of membrane-associated molecular systems in Bacteria and Archaea-the type IV filament (TFF) superfamily-that diversified in systems involved in flagellar or twitching motility, adhesion, protein secretion, and DNA uptake. The phylogeny of the thousands of detected systems suggests they may have been present in the last universal common ancestor. From there, two lineages-a bacterial and an archaeal-diversified by multiple gene duplications, gene fissions and deletions, and accretion of novel components. Surprisingly, we find that the 'tight adherence' (Tad) systems originated from the interkingdom transfer from Archaea to Bacteria of a system resembling the 'EppA-dependent' (Epd) pilus and were associated with the acquisition of a secretin. The phylogeny and content of ancestral systems suggest that initial bacterial pili were engaged in cell motility and/or DNA uptake. In contrast, specialised protein secretion systems arose several times independently and much later in natural history. The functional diversification of the TFF superfamily was accompanied by genetic rearrangements with implications for genetic regulation and horizontal gene transfer: systems encoded in fewer loci were more frequently exchanged between taxa. This may have contributed to their rapid evolution and spread across Bacteria and Archaea. Hence, the evolutionary history of the superfamily reveals an impressive catalogue of molecular evolution mechanisms that resulted in remarkable functional innovation and specialisation from a relatively small set of components.
Collapse
Affiliation(s)
- Rémi Denise
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Sophie S. Abby
- Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble, France
| | - Eduardo P. C. Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS, UMR3525, Paris, France
| |
Collapse
|