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Guilvout I, Samsudin F, Huber RG, Bond PJ, Bardiaux B, Francetic O. Membrane platform protein PulF of the Klebsiella type II secretion system forms a trimeric ion channel essential for endopilus assembly and protein secretion. mBio 2024; 15:e0142323. [PMID: 38063437 PMCID: PMC10790770 DOI: 10.1128/mbio.01423-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [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: 06/05/2023] [Accepted: 10/24/2023] [Indexed: 01/17/2024] Open
Abstract
IMPORTANCE Type IV pili and type II secretion systems are members of the widespread type IV filament (T4F) superfamily of nanomachines that assemble dynamic and versatile surface fibers in archaea and bacteria. The assembly and retraction of T4 filaments with diverse surface properties and functions require the plasma membrane platform proteins of the GspF/PilC superfamily. Generally considered dimeric, platform proteins are thought to function as passive transmitters of the mechanical energy generated by the ATPase motor, to somehow promote insertion of pilin subunits into the nascent pilus fibers. Here, we generate and experimentally validate structural predictions that support the trimeric state of a platform protein PulF from a type II secretion system. The PulF trimers form selective proton or sodium channels which might energize pilus assembly using the membrane potential. The conservation of the channel sequence and structural features implies a common mechanism for all T4F assembly systems. We propose a model of the oligomeric PulF-PulE ATPase complex that provides an essential framework to investigate and understand the pilus assembly mechanism.
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Affiliation(s)
- Ingrid Guilvout
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
| | | | | | - Peter J. Bond
- Bioinformatics Institute (A-STAR), Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Structural Bioinformatics Unit, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Olivera Francetic
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Biochemistry of Macromolecular Interactions Unit, Paris, France
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Raynaud C, Sheppard D, Berry JL, Gurung I, Pelicic V. PilB from Streptococcus sanguinis is a bimodular type IV pilin with a direct role in adhesion. Proc Natl Acad Sci U S A 2021; 118:e2102092118. [PMID: 34031252 DOI: 10.1073/pnas.2102092118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Type IV pili (T4P) are functionally versatile filaments widespread in prokaryotes, composed of type IV pilins and assembled by conserved multiprotein machineries. It remains unclear how such rather simple filaments can be so versatile. Our structure/function analysis of PilB, a minor pilin of Streptococcus sanguinis T4P, offers an elegant explanation for this paradox. We show that PilB is a modular pilin with a bulky module “grafted” onto a small pilin module, which directly mediates adhesion of S. sanguinis to host cells/proteins. This evolutionary tinkering strategy appears to be prevalent in bacteria since a global analysis reveals that modular pilins are widespread and exhibit an astonishing variety of architectures. Type IV pili (T4P) are functionally versatile filamentous nanomachines, nearly ubiquitous in prokaryotes. They are predominantly polymers of one major pilin but also contain minor pilins whose functions are often poorly defined and likely to be diverse. Here, we show that the minor pilin PilB from the T4P of Streptococcus sanguinis displays an unusual bimodular three-dimensional structure with a bulky von Willebrand factor A–like (vWA) module “grafted” onto a small pilin module via a short loop. Structural modeling suggests that PilB is only compatible with a localization at the tip of T4P. By performing a detailed functional analysis, we found that 1) the vWA module contains a canonical metal ion–dependent adhesion site, preferentially binding Mg2+ and Mn2+, 2) abolishing metal binding has no impact on the structure of PilB or piliation, 3) metal binding is important for S. sanguinis T4P–mediated twitching motility and adhesion to eukaryotic cells, and 4) the vWA module shows an intrinsic binding ability to several host proteins. These findings reveal an elegant yet simple evolutionary tinkering strategy to increase T4P functional versatility by grafting a functional module onto a pilin for presentation by the filaments. This strategy appears to have been extensively used by bacteria, in which modular pilins are widespread and exhibit an astonishing variety of architectures.
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Lam T, Ellison CK, Eddington DT, Brun YV, Dalia AB, Morrison DA. Competence pili in Streptococcus pneumoniae are highly dynamic structures that retract to promote DNA uptake. Mol Microbiol 2021; 116:381-396. [PMID: 33754381 DOI: 10.1111/mmi.14718] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 01/11/2023]
Abstract
The competence pili of transformable Gram-positive species are phylogenetically related to the diverse and widespread class of extracellular filamentous organelles known as type IV pili. In Gram-negative bacteria, type IV pili act through dynamic cycles of extension and retraction to carry out diverse activities including attachment, motility, protein secretion, and DNA uptake. It remains unclear whether competence pili in Gram-positive species exhibit similar dynamic activity, and their mechanism of action for DNA uptake remains unclear. They are hypothesized to either (1) leave transient cavities in the cell wall that facilitate DNA passage, (2) form static adhesins to enrich DNA near the cell surface for subsequent uptake by membrane-embedded transporters, or (3) play an active role in translocating bound DNA via dynamic activity. Here, we use a recently described pilus labeling approach to demonstrate that competence pili in Streptococcus pneumoniae are highly dynamic structures that rapidly extend and retract from the cell surface. By labeling the principal pilus monomer, ComGC, with bulky adducts, we further demonstrate that pilus retraction is essential for natural transformation. Together, our results suggest that Gram-positive competence pili in other species may also be dynamic and retractile structures that play an active role in DNA uptake.
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Affiliation(s)
- Trinh Lam
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Courtney K Ellison
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - David T Eddington
- Department of Bioengineering, University of Illinois at Chicago, Chicago, IL, USA
| | - Yves V Brun
- Department of Biology, Indiana University, Bloomington, IN, USA.,Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, QC, Canada
| | - Ankur B Dalia
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Donald A Morrison
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL, USA
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Sheppard D, Berry JL, Denise R, Rocha EPC, Matthews S, Pelicic V. The major subunit of widespread competence pili exhibits a novel and conserved type IV pilin fold. J Biol Chem 2020; 295:6594-6604. [PMID: 32273343 PMCID: PMC7212644 DOI: 10.1074/jbc.ra120.013316] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/07/2020] [Indexed: 12/12/2022] Open
Abstract
Type IV filaments (T4F), which are helical assemblies of type IV pilins, constitute a superfamily of filamentous nanomachines virtually ubiquitous in prokaryotes that mediate a wide variety of functions. The competence (Com) pilus is a widespread T4F, mediating DNA uptake (the first step in natural transformation) in bacteria with one membrane (monoderms), an important mechanism of horizontal gene transfer. Here, we report the results of genomic, phylogenetic, and structural analyses of ComGC, the major pilin subunit of Com pili. By performing a global comparative analysis, we show that Com pili genes are virtually ubiquitous in Bacilli, a major monoderm class of Firmicutes. This also revealed that ComGC displays extensive sequence conservation, defining a monophyletic group among type IV pilins. We further report ComGC solution structures from two naturally competent human pathogens, Streptococcus sanguinis (ComGCSS) and Streptococcus pneumoniae (ComGCSP), revealing that this pilin displays extensive structural conservation. Strikingly, ComGCSS and ComGCSP exhibit a novel type IV pilin fold that is purely helical. Results from homology modeling analyses suggest that the unusual structure of ComGC is compatible with helical filament assembly. Because ComGC displays such a widespread distribution, these results have implications for hundreds of monoderm species.
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Affiliation(s)
- Devon Sheppard
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jamie-Lee Berry
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rémi Denise
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Paris 75015, France
- Sorbonne Université, Collège doctoral, Paris 75005, France
| | - Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, CNRS UMR3525, Paris 75015, France
| | - Steve Matthews
- Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
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Berry JL, Gurung I, Anonsen JH, Spielman I, Harper E, Hall AMJ, Goosens VJ, Raynaud C, Koomey M, Biais N, Matthews S, Pelicic V. Global biochemical and structural analysis of the type IV pilus from the Gram-positive bacterium Streptococcus sanguinis. J Biol Chem 2019; 294:6796-6808. [PMID: 30837269 PMCID: PMC6497953 DOI: 10.1074/jbc.ra118.006917] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 11/30/2018] [Revised: 02/27/2019] [Indexed: 11/06/2022] Open
Abstract
Type IV pili (Tfp) are functionally versatile filaments, widespread in prokaryotes, that belong to a large class of filamentous nanomachines known as type IV filaments (Tff). Although Tfp have been extensively studied in several Gram-negative pathogens where they function as key virulence factors, many aspects of their biology remain poorly understood. Here, we performed a global biochemical and structural analysis of Tfp in a recently emerged Gram-positive model, Streptococcus sanguinis In particular, we focused on the five pilins and pilin-like proteins involved in Tfp biology in S. sanguinis We found that the two major pilins, PilE1 and PilE2, (i) follow widely conserved principles for processing by the prepilin peptidase PilD and for assembly into filaments; (ii) display only one of the post-translational modifications frequently found in pilins, i.e. a methylated N terminus; (iii) are found in the same heteropolymeric filaments; and (iv) are not functionally equivalent. The 3D structure of PilE1, solved by NMR, revealed a classical pilin-fold with a highly unusual flexible C terminus. Intriguingly, PilE1 more closely resembles pseudopilins forming shorter Tff than bona fide Tfp-forming major pilins, underlining the evolutionary relatedness among different Tff. Finally, we show that S. sanguinis Tfp contain a low abundance of three additional proteins processed by PilD, the minor pilins PilA, PilB, and PilC. These findings provide the first global biochemical and structural picture of a Gram-positive Tfp and have fundamental implications for our understanding of a widespread class of filamentous nanomachines.
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Affiliation(s)
- Jamie-Lee Berry
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Ishwori Gurung
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Jan Haug Anonsen
- the Department of Biological Sciences, Proteomics and Mass Spectrometry Unit, University of Oslo, 0371 Oslo, Norway.,the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Ingrid Spielman
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Elliot Harper
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Alexander M J Hall
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vivianne J Goosens
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Claire Raynaud
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Michael Koomey
- the Department of Biological Sciences, Center for Integrative Microbial Evolution, University of Oslo, 0371 Oslo, Norway
| | - Nicolas Biais
- the Department of Biology, Brooklyn College of the City University of New York, New York, New York 11210.,The Graduate Center of the City University of New York, New York, New York 10016, and
| | - Steve Matthews
- the Centre for Structural Biology, Imperial College London, London SW7 2AZ, United Kingdom
| | - Vladimir Pelicic
- From the Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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