1
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Gahlot DK, Taheri N, MacIntyre S. Diversity in Genetic Regulation of Bacterial Fimbriae Assembled by the Chaperone Usher Pathway. Int J Mol Sci 2022; 24:ijms24010161. [PMID: 36613605 PMCID: PMC9820224 DOI: 10.3390/ijms24010161] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 12/24/2022] Open
Abstract
Bacteria express different types of hair-like proteinaceous appendages on their cell surface known as pili or fimbriae. These filamentous structures are primarily involved in the adherence of bacteria to both abiotic and biotic surfaces for biofilm formation and/or virulence of non-pathogenic and pathogenic bacteria. In pathogenic bacteria, especially Gram-negative bacteria, fimbriae play a key role in bacteria-host interactions which are critical for bacterial invasion and infection. Fimbriae assembled by the Chaperone Usher pathway (CUP) are widespread within the Enterobacteriaceae, and their expression is tightly regulated by specific environmental stimuli. Genes essential for expression of CUP fimbriae are organised in small blocks/clusters, which are often located in proximity to other virulence genes on a pathogenicity island. Since these surface appendages play a crucial role in bacterial virulence, they have potential to be harnessed in vaccine development. This review covers the regulation of expression of CUP-assembled fimbriae in Gram-negative bacteria and uses selected examples to demonstrate both dedicated and global regulatory mechanisms.
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Affiliation(s)
- Dharmender K. Gahlot
- School of Biological Sciences, University of Reading, Reading RG6 6EX, UK
- Department of Molecular Biology, Umeå University, 901 87 Umeå, Sweden
- Umeå Centre for Microbial Research (UCMR), Umeå University, 901 87 Umeå, Sweden
- Correspondence: (D.K.G.); (S.M.)
| | - Nayyer Taheri
- APC Microbiome Institute, University College Cork, T12 K8AF Cork, Ireland
| | - Sheila MacIntyre
- School of Biological Sciences, University of Reading, Reading RG6 6EX, UK
- Correspondence: (D.K.G.); (S.M.)
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2
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Shanmugasundarasamy T, Karaiyagowder Govindarajan D, Kandaswamy K. A review on pilus assembly mechanisms in Gram-positive and Gram-negative bacteria. Cell Surf 2022; 8:100077. [PMID: 35493982 PMCID: PMC9046445 DOI: 10.1016/j.tcsw.2022.100077] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/08/2022] [Accepted: 04/18/2022] [Indexed: 12/17/2022] Open
Abstract
The surface of Gram-positive and Gram-negative bacteria contains long hair-like proteinaceous protrusion known as pili or fimbriae. Historically, pilin proteins were considered to play a major role in the transfer of genetic material during bacterial conjugation. Recent findings however elucidate their importance in virulence, biofilm formation, phage transduction, and motility. Therefore, it is crucial to gain mechanistic insights on the subcellular assembly of pili and the localization patterns of their subunit proteins (major and minor pilins) that aid the macromolecular pilus assembly at the bacterial surface. In this article, we review the current knowledge of pilus assembly mechanisms in a wide range of Gram-positive and Gram-negative bacteria, including subcellular localization patterns of a few pilin subunit proteins and their role in virulence and pathogenesis.
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Pakharukova N, Malmi H, Tuittila M, Dahlberg T, Ghosal D, Chang YW, Myint SL, Paavilainen S, Knight SD, Lamminmäki U, Uhlin BE, Andersson M, Jensen G, Zavialov AV. Archaic chaperone-usher pili self-secrete into superelastic zigzag springs. Nature 2022; 609:335-340. [PMID: 35853476 PMCID: PMC9452303 DOI: 10.1038/s41586-022-05095-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 07/08/2022] [Indexed: 11/23/2022]
Abstract
Adhesive pili assembled through the chaperone-usher pathway are hair-like appendages that mediate host tissue colonization and biofilm formation of Gram-negative bacteria1-3. Archaic chaperone-usher pathway pili, the most diverse and widespread chaperone-usher pathway adhesins, are promising vaccine and drug targets owing to their prevalence in the most troublesome multidrug-resistant pathogens1,4,5. However, their architecture and assembly-secretion process remain unknown. Here, we present the cryo-electron microscopy structure of the prototypical archaic Csu pilus that mediates biofilm formation of Acinetobacter baumannii-a notorious multidrug-resistant nosocomial pathogen. In contrast to the thick helical tubes of the classical type 1 and P pili, archaic pili assemble into an ultrathin zigzag architecture secured by an elegant clinch mechanism. The molecular clinch provides the pilus with high mechanical stability as well as superelasticity, a property observed for the first time, to our knowledge, in biomolecules, while enabling a more economical and faster pilus production. Furthermore, we demonstrate that clinch formation at the cell surface drives pilus secretion through the outer membrane. These findings suggest that clinch-formation inhibitors might represent a new strategy to fight multidrug-resistant bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Henri Malmi
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Minna Tuittila
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Tobias Dahlberg
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, Victoria, Australia
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Si Lhyam Myint
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Sari Paavilainen
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland
| | - Stefan David Knight
- Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Urpo Lamminmäki
- Department of Life Technologies, University of Turku, Turku, Finland
| | - Bernt Eric Uhlin
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Magnus Andersson
- Department of Physics, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Grant Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Anton V Zavialov
- Joint Biotechnology Laboratory, MediCity, Faculty of Medicine, University of Turku, Turku, Finland.
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4
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Optimised Heterologous Expression and Functional Analysis of the Yersinia pestis F1-Capsular Antigen Regulator Caf1R. Int J Mol Sci 2021; 22:ijms22189805. [PMID: 34575967 PMCID: PMC8470410 DOI: 10.3390/ijms22189805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 12/14/2022] Open
Abstract
The bacterial pathogen, Yersinia pestis, has caused three historic pandemics and continues to cause small outbreaks worldwide. During infection, Y. pestis assembles a capsule-like protective coat of thin fibres of Caf1 subunits. This F1 capsular antigen has attracted much attention due to its clinical value in plague diagnostics and anti-plague vaccine development. Expression of F1 is tightly regulated by a transcriptional activator, Caf1R, of the AraC/XylS family, proteins notoriously prone to aggregation. Here, we have optimised the recombinant expression of soluble Caf1R. Expression from the native and synthetic codon-optimised caf1R cloned in three different expression plasmids was examined in a library of E. coli host strains. The functionality of His-tagged Caf1R was demonstrated in vivo, but insolubility was a problem with overproduction. High levels of soluble MBP-Caf1R were produced from codon optimised caf1R. Transcriptional-lacZ reporter fusions defined the PM promoter and Caf1R binding site responsible for transcription of the cafMA1 operon. Use of the identified Caf1R binding caf DNA sequence in an electrophoretic mobility shift assay (EMSA) confirmed correct folding and functionality of the Caf1R DNA-binding domain in recombinant MBP-Caf1R. Availability of functional recombinant Caf1R will be a valuable tool to elucidate control of expression of F1 and Caf1R-regulated pathophysiology of Y. pestis.
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5
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Pandey NK, Verma G, Kushwaha GS, Suar M, Bhavesh NS. Crystal structure of the usher chaperone YadV reveals a monomer with the proline lock in closed conformation suggestive of an intermediate state. FEBS Lett 2020; 594:3057-3066. [DOI: 10.1002/1873-3468.13883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/15/2020] [Accepted: 07/02/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Nishant Kumar Pandey
- Transcription Regulation Group International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi India
- School of Biotechnology Kalinga Institute of Industrial Technology (KIIT), (Deemed to be University) Bhubaneswar India
| | - Garima Verma
- Transcription Regulation Group International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi India
| | - Gajraj Singh Kushwaha
- Transcription Regulation Group International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi India
| | - Mrutyunjay Suar
- School of Biotechnology Kalinga Institute of Industrial Technology (KIIT), (Deemed to be University) Bhubaneswar India
| | - Neel Sarovar Bhavesh
- Transcription Regulation Group International Centre for Genetic Engineering and Biotechnology (ICGEB) New Delhi India
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Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs). Folia Microbiol (Praha) 2019; 65:45-65. [DOI: 10.1007/s12223-019-00719-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 05/20/2019] [Indexed: 12/17/2022]
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7
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Pakharukova N, McKenna S, Tuittila M, Paavilainen S, Malmi H, Xu Y, Parilova O, Matthews S, Zavialov AV. Archaic and alternative chaperones preserve pilin folding energy by providing incomplete structural information. J Biol Chem 2018; 293:17070-17080. [PMID: 30228191 DOI: 10.1074/jbc.ra118.004170] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 09/14/2018] [Indexed: 11/06/2022] Open
Abstract
Adhesive pili are external component of fibrous adhesive organelles and help bacteria attach to biotic or abiotic surfaces. The biogenesis of adhesive pili via the chaperone-usher pathway (CUP) is independent of external energy sources. In the classical CUP, chaperones transport assembly-competent pilins in a folded but expanded conformation. During donor-strand exchange, pilins subsequently collapse, producing a tightly packed hydrophobic core and releasing the necessary free energy to drive fiber formation. Here, we show that pilus biogenesis in non-classical, archaic, and alternative CUPs uses a different source of conformational energy. High-resolution structures of the archaic Csu-pili system from Acinetobacter baumannii revealed that non-classical chaperones employ a short donor strand motif that is insufficient to fully complement the pilin fold. This results in chaperone-bound pilins being trapped in a substantially unfolded intermediate. The exchange of this short motif with the longer donor strand from adjacent pilin provides the full steric information essential for folding, and thereby induces a large unfolded-to-folded conformational transition to drive assembly. Our findings may inform the development of anti-adhesion drugs (pilicides) to combat bacterial infections.
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Affiliation(s)
- Natalia Pakharukova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sophie McKenna
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Minna Tuittila
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Sari Paavilainen
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Henri Malmi
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Yingqi Xu
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Olena Parilova
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
| | - Steve Matthews
- the Department of Life Sciences, Imperial College London, South Kensington Campus, London SW72AZ, United Kingdom
| | - Anton V Zavialov
- From the Department of Chemistry, University of Turku, Joint Biotechnology Laboratory (JBL), Arcanum, Vatselankatu 2, Turku FIN-20500, Finland and
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8
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Lee JY, Miller DP, Wu L, Casella CR, Hasegawa Y, Lamont RJ. Maturation of the Mfa1 Fimbriae in the Oral Pathogen Porphyromonas gingivalis. Front Cell Infect Microbiol 2018; 8:137. [PMID: 29868494 PMCID: PMC5954841 DOI: 10.3389/fcimb.2018.00137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/18/2018] [Indexed: 12/17/2022] Open
Abstract
The Mfa1 fimbriae of the periodontal pathogen Porphyromonas gingivalis are involved in adhesion, including binding to synergistic species in oral biofilms. Mfa1 fimbriae are comprised of 5 proteins: the structural component Mfa1, the anchor Mfa2, and Mfa3-5 which constitute the fimbrial tip complex. Interactions among the Mfa proteins and the polymerization mechanism for Mfa1 are poorly understood. Here we show that Mfa3 can bind to Mfa1, 2, 4, and 5 in vitro, and may function as an adaptor protein interlinking other fimbrial subunits. Polymerization of Mfa1 is independent of Mfa3-5 and requires proteolytic processing mediated by the RgpA/B arginine gingipains of P. gingivalis. Both the N- and C- terminal regions of Mfa1 are necessary for polymerization; however, potential β-strand disrupting amino acid substitutions in these regions do not impair Mfa1 polymerization. In contrast, substitution of hydrophobic amino acids with charged residues in either the N- or C- terminal domains yielded Mfa1 proteins that failed to polymerize. Collectively, these results indicate that Mfa3 serves as an adaptor protein between Mfa1 and other accessory fimbrial proteins. Mfa1 fimbrial polymerization is dependent on hydrophobicity in both the N- and C-terminal regions, indicative of an assembly mechanism involving the terminal regions forming a hydrophobic binding interface between Mfa1 subunits.
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Affiliation(s)
- Jae Y Lee
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, United States
| | - Daniel P Miller
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, United States
| | - Leng Wu
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, United States
| | - Carolyn R Casella
- Department of Microbiology and Immunology, University of Louisville, Louisville, KY, United States
| | - Yoshiaki Hasegawa
- Department of Microbiology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Richard J Lamont
- Department of Oral Immunology and Infectious Diseases, University of Louisville, Louisville, KY, United States
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9
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Werneburg GT, Thanassi DG. Pili Assembled by the Chaperone/Usher Pathway in Escherichia coli and Salmonella. EcoSal Plus 2018; 8:10.1128/ecosalplus.ESP-0007-2017. [PMID: 29536829 PMCID: PMC5940347 DOI: 10.1128/ecosalplus.esp-0007-2017] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 12/12/2022]
Abstract
Gram-negative bacteria assemble a variety of surface structures, including the hair-like organelles known as pili or fimbriae. Pili typically function in adhesion and mediate interactions with various surfaces, with other bacteria, and with other types of cells such as host cells. The chaperone/usher (CU) pathway assembles a widespread class of adhesive and virulence-associated pili. Pilus biogenesis by the CU pathway requires a dedicated periplasmic chaperone and integral outer membrane protein termed the usher, which forms a multifunctional assembly and secretion platform. This review addresses the molecular and biochemical aspects of the CU pathway in detail, focusing on the type 1 and P pili expressed by uropathogenic Escherichia coli as model systems. We provide an overview of representative CU pili expressed by E. coli and Salmonella, and conclude with a discussion of potential approaches to develop antivirulence therapeutics that interfere with pilus assembly or function.
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Affiliation(s)
- Glenn T. Werneburg
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
- Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA
| | - David G. Thanassi
- Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY, USA
- Center for Infectious Diseases, Stony Brook University, Stony Brook, NY, USA
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10
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Högbom M, Ihalin R. Functional and structural characteristics of bacterial proteins that bind host cytokines. Virulence 2017; 8:1592-1601. [PMID: 28783440 PMCID: PMC5810482 DOI: 10.1080/21505594.2017.1363140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Several human pathogens bind and respond to host cytokines, which can be considered a virulence mechanism that communicates defensive actions of the host to the pathogen. This review summarizes the current knowledge of bacterial cytokine-binding proteins, with a particular focus on their functional and structural characteristics. Many bacterial cytokine-binding proteins function in the development of infection and inflammation and mediate adhesion to host cells, suggesting multiple roles in pathogen-host interactions. The regions of the bacterial proteins that interact with host cytokines can display structural similarities to other proteins involved in cytokine signaling. However, there appears to be no central shared structural themes for bacterial cytokine-binding proteins, and they appear to possess structures that are different from the cytokine receptors of the host. Atomic-level information regarding receptor-cytokine interactions is needed to be able to disrupt these interactions and to elucidate the specific consequences of cytokine binding in a pathogen and host.
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Affiliation(s)
- Martin Högbom
- a Department of Biochemistry and Biophysics , Stockholm University , Stockholm , Sweden
| | - Riikka Ihalin
- b Department of Biochemistry , University of Turku , Turku , Finland
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11
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Pakharukova N, Tuittila M, Paavilainen S, Zavialov A. Methylation, crystallization and SAD phasing of the Csu pilus CsuC-CsuE chaperone-adhesin subunit pre-assembly complex from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2017; 73:450-454. [PMID: 28777087 PMCID: PMC5544001 DOI: 10.1107/s2053230x17009566] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/27/2017] [Indexed: 11/10/2022] Open
Abstract
Acinetobacter baumannii is one of the most difficult Gram-negative bacteria to control and treat. This pathogen forms biofilms on hospital surfaces and medical devices using Csu pili assembled via the archaic chaperone-usher pathway. To uncover the mechanism of bacterial attachment to abiotic surfaces, it was aimed to determine the crystal structure of the pilus tip adhesin CsuE. The CsuC-CsuE chaperone-subunit pre-assembly complex was purified from the periplasm of Escherichia coli overexpressing CsuC and CsuE. Despite the high purity of the complex, no crystals could be obtained. This challenge was solved by the methylation of lysine residues. The complex was crystallized in 0.1 M bis-tris pH 5.5, 17% PEG 3350 using the hanging-drop vapour-diffusion method. The crystals diffracted to a resolution of 2.31 Å and belonged to the triclinic space group P1, with unit-cell parameters a = 53.84, b = 63.85, c = 89.25 Å, α = 74.65, β = 79.65, γ = 69.07°. Initial phases were derived from a single anomalous diffraction experiment using a selenomethionine derivative.
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Affiliation(s)
- Natalia Pakharukova
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Minna Tuittila
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Sari Paavilainen
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Anton Zavialov
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
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12
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Pakharukova N, Garnett JA, Tuittila M, Paavilainen S, Diallo M, Xu Y, Matthews SJ, Zavialov AV. Structural Insight into Archaic and Alternative Chaperone-Usher Pathways Reveals a Novel Mechanism of Pilus Biogenesis. PLoS Pathog 2015; 11:e1005269. [PMID: 26587649 PMCID: PMC4654587 DOI: 10.1371/journal.ppat.1005269] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 10/22/2015] [Indexed: 11/18/2022] Open
Abstract
Gram-negative pathogens express fibrous adhesive organelles that mediate targeting to sites of infection. The major class of these organelles is assembled via the classical, alternative and archaic chaperone-usher pathways. Although non-classical systems share a wider phylogenetic distribution and are associated with a range of diseases, little is known about their assembly mechanisms. Here we report atomic-resolution insight into the structure and biogenesis of Acinetobacter baumannii Csu and Escherichia coli ECP biofilm-mediating pili. We show that the two non-classical systems are structurally related, but their assembly mechanism is strikingly different from the classical assembly pathway. Non-classical chaperones, unlike their classical counterparts, maintain subunits in a substantially disordered conformational state, akin to a molten globule. This is achieved by a unique binding mechanism involving the register-shifted donor strand complementation and a different subunit carboxylate anchor. The subunit lacks the classical pre-folded initiation site for donor strand exchange, suggesting that recognition of its exposed hydrophobic core starts the assembly process and provides fresh inspiration for the design of inhibitors targeting chaperone-usher systems.
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Affiliation(s)
- Natalia Pakharukova
- Department of Chemistry, University of Turku, Turku, JBL, Arcanum, Turku, Finland
| | - James A. Garnett
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Minna Tuittila
- Department of Chemistry, University of Turku, Turku, JBL, Arcanum, Turku, Finland
| | - Sari Paavilainen
- Department of Chemistry, University of Turku, Turku, JBL, Arcanum, Turku, Finland
| | - Mamou Diallo
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Yingqi Xu
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Steve J. Matthews
- Centre for Structural Biology, Department of Life Sciences, Imperial College London, South Kensington, London, United Kingdom
| | - Anton V. Zavialov
- Department of Chemistry, University of Turku, Turku, JBL, Arcanum, Turku, Finland
- * E-mail:
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13
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Chahales P, Thanassi DG. Structure, Function, and Assembly of Adhesive Organelles by Uropathogenic Bacteria. Microbiol Spectr 2015; 3:10.1128/microbiolspec.UTI-0018-2013. [PMID: 26542038 PMCID: PMC4638162 DOI: 10.1128/microbiolspec.uti-0018-2013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 01/02/2023] Open
Abstract
Bacteria assemble a wide range of adhesive proteins, termed adhesins, to mediate binding to receptors and colonization of surfaces. For pathogenic bacteria, adhesins are critical for early stages of infection, allowing the bacteria to initiate contact with host cells, colonize different tissues, and establish a foothold within the host. The adhesins expressed by a pathogen are also critical for bacterial-bacterial interactions and the formation of bacterial communities, including biofilms. The ability to adhere to host tissues is particularly important for bacteria that colonize sites such as the urinary tract, where the flow of urine functions to maintain sterility by washing away non-adherent pathogens. Adhesins vary from monomeric proteins that are directly anchored to the bacterial surface to polymeric, hair-like fibers that extend out from the cell surface. These latter fibers are termed pili or fimbriae, and were among the first identified virulence factors of uropathogenic Escherichia coli. Studies since then have identified a range of both pilus and non-pilus adhesins that contribute to bacterial colonization of the urinary tract, and have revealed molecular details of the structures, assembly pathways, and functions of these adhesive organelles. In this review, we describe the different types of adhesins expressed by both Gram-negative and Gram-positive uropathogens, what is known about their structures, how they are assembled on the bacterial surface, and the functions of specific adhesins in the pathogenesis of urinary tract infections.
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Affiliation(s)
- Peter Chahales
- Center for Infectious Diseases and Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794
| | - David G Thanassi
- Center for Infectious Diseases and Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794
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14
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Pakharukova N, Tuittila M, Paavilainen S, Zavialov A. Crystallization and preliminary X-ray diffraction analysis of the Csu pili CsuC-CsuA/B chaperone-major subunit pre-assembly complex from Acinetobacter baumannii. Acta Crystallogr F Struct Biol Commun 2015; 71:770-4. [PMID: 26057810 PMCID: PMC4461345 DOI: 10.1107/s2053230x15007955] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/21/2015] [Indexed: 11/10/2022] Open
Abstract
The attachment of many Gram-negative pathogens to biotic and abiotic surfaces is mediated by fimbrial adhesins, which are assembled via the classical, alternative and archaic chaperone-usher (CU) pathways. The archaic CU fimbrial adhesins have the widest phylogenetic distribution, yet very little is known about their structure and mechanism of assembly. To elucidate the biogenesis of archaic CU systems, structural analysis of the Csu fimbriae, which are used by Acinetobacter baumannii to form stable biofilms and cause nosocomial infection, was focused on. The major fimbriae subunit CsuA/B complexed with the CsuC chaperone was purified from the periplasm of Escherichia coli cells co-expressing CsuA/B and CsuC, and the complex was crystallized in PEG 3350 solution using the hanging-drop vapour-diffusion method. Selenomethionine-labelled CsuC-CsuA/B complex was purified and crystallized under the same conditions. The crystals diffracted to 2.40 Å resolution and belonged to the hexagonal space group P6(4)22, with unit-cell parameters a = b = 94.71, c = 187.05 Å, α = β = 90, γ = 120°. Initial phases were derived from a single anomalous diffraction (SAD) experiment using the selenomethionine derivative.
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Affiliation(s)
- Natalia Pakharukova
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Minna Tuittila
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Sari Paavilainen
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
| | - Anton Zavialov
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, Arcanum, Vatselankatu 2, 20500 Turku, Finland
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Garnett JA, Diallo M, Matthews SJ. Purification, crystallization and preliminary X-ray diffraction analysis of the Escherichia coli common pilus chaperone EcpB. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:676-9. [PMID: 26057794 PMCID: PMC4461329 DOI: 10.1107/s2053230x15006354] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 03/28/2015] [Indexed: 11/22/2022]
Abstract
In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher pathway that plays a major role in both early biofilm formation and host-cell adhesion. Initial attempts at crystallizing the chaperone EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. This is the first time that this refolding strategy has been used to purify CU chaperones. Pili are key cell-surface components that allow the attachment of bacteria to both biological and abiotic solid surfaces, whilst also mediating interactions between themselves. In Escherichia coli, the common pilus (Ecp) belongs to an alternative chaperone–usher (CU) pathway that plays a major role in both early biofilm formation and host-cell adhesion. The chaperone EcpB is involved in the biogenesis of the filament, which is composed of EcpA and EcpD. Initial attempts at crystallizing EcpB using natively purified protein from the bacterial periplasm were not successful; however, after the isolation of EcpB under denaturing conditions and subsequent refolding, crystals were obtained at pH 8.0 using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.4 Å resolution. These crystals belonged to the trigonal space group P3121 or P3221, with unit-cell parameters a = b = 62.65, c = 121.14 Å and one monomer in the asymmetric unit. Molecular replacement was unsuccessful, but selenomethionine-substituted protein and heavy-atom derivatives are being prepared for phasing. The three-dimensional structure of EcpB will provide invaluable information on the subtle mechanistic differences in biogenesis between the alternative and classical CU pathways. Furthermore, this is the first time that this refolding strategy has been used to purify CU chaperones, and it could be implemented in similar systems where it has not been possible to obtain highly ordered crystals.
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Affiliation(s)
- James A Garnett
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Mamou Diallo
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Steve J Matthews
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
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16
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Busch A, Phan G, Waksman G. Molecular mechanism of bacterial type 1 and P pili assembly. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2015; 373:rsta.2013.0153. [PMID: 25624519 DOI: 10.1098/rsta.2013.0153] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The formation of adhesive surface structures called pili or fimbriae ('bacterial hair') is an important contributor towards bacterial pathogenicity and persistence. To fight often chronic or recurrent bacterial infections such as urinary tract infections, it is necessary to understand the molecular mechanism of the nanomachines assembling such pili. Here, we focus on the so far best-known pilus assembly machinery: the chaperone-usher pathway producing the type 1 and P pili, and highlight the most recently acquired structural knowledge. First, we describe the subunits' structure and the molecular role of the periplasmic chaperone. Second, we focus on the outer-membrane usher structure and the catalytic mechanism of usher-mediated pilus biogenesis. Finally, we describe how the detailed understanding of the chaperone-usher pathway at a molecular level has paved the way for the design of a new generation of bacterial inhibitors called 'pilicides'.
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Affiliation(s)
- Andreas Busch
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gilles Phan
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology, University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
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17
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Lillington J, Geibel S, Waksman G. Reprint of "Biogenesis and adhesion of type 1 and P pili". Biochim Biophys Acta Gen Subj 2014; 1850:554-64. [PMID: 25063559 DOI: 10.1016/j.bbagen.2014.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 12/20/2022]
Abstract
BACKGROUND Uropathogenic Escherichia coli (UPEC) cause urinary tract infections (UTIs) in approximately 50% of women. These bacteria use type 1 and P pili for host recognition and attachment. These pili are assembled by the chaperone-usher pathway of pilus biogenesis. SCOPE OF REVIEW The review examines the biogenesis and adhesion of the UPEC type 1 and P pili. Particular emphasis is drawn to the role of the outer membrane usher protein. The structural properties of the complete pilus are also examined to highlight the strength and functionality of the final assembly. MAJOR CONCLUSIONS The usher orchestrates the sequential addition of pilus subunits in a defined order. This process follows a subunit-incorporation cycle which consists of four steps: recruitment at the usher N-terminal domain, donor-strand exchange with the previously assembled subunit, transfer to the usher C-terminal domains and translocation of the nascent pilus. Adhesion by the type 1 and P pili is strengthened by the quaternary structure of their rod sections. The rod is endowed with spring-like properties which provide mechanical resistance against urine flow. The distal adhesins operate differently from one another, targeting receptors in a specific manner. The biogenesis and adhesion of type 1 and P pili are being therapeutically targeted, and efforts to prevent pilus growth or adherence are described. GENERAL SIGNIFICANCE The combination of structural and biochemical study has led to the detailed mechanistic understanding of this membrane spanning nano-machine. This can now be exploited to design novel drugs able to inhibit virulence. This is vital in the present era of resurgent antibiotic resistance. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- James Lillington
- Institute of Structural and Molecular Biology (ISMB), University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Sebastian Geibel
- Institute of Structural and Molecular Biology (ISMB), University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology (ISMB), University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK.
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18
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Lillington J, Geibel S, Waksman G. Biogenesis and adhesion of type 1 and P pili. Biochim Biophys Acta Gen Subj 2014; 1840:2783-93. [PMID: 24797039 DOI: 10.1016/j.bbagen.2014.04.021] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 01/22/2023]
Abstract
BACKGROUND Uropathogenic Escherichia coli (UPEC) cause urinary tract infections (UTIs) in approximately 50% of women. These bacteria use type 1 and P pili for host recognition and attachment. These pili are assembled by the chaperone-usher pathway of pilus biogenesis. SCOPE OF REVIEW The review examines the biogenesis and adhesion of the UPEC type 1 and P pili. Particular emphasis is drawn to the role of the outer membrane usher protein. The structural properties of the complete pilus are also examined to highlight the strength and functionality of the final assembly. MAJOR CONCLUSIONS The usher orchestrates the sequential addition of pilus subunits in a defined order. This process follows a subunit-incorporation cycle which consists of four steps: recruitment at the usher N-terminal domain, donor-strand exchange with the previously assembled subunit, transfer to the usher C-terminal domains and translocation of the nascent pilus. Adhesion by the type 1 and P pili is strengthened by the quaternary structure of their rod sections. The rod is endowed with spring-like properties which provide mechanical resistance against urine flow. The distal adhesins operate differently from one another, targeting receptors in a specific manner. The biogenesis and adhesion of type 1 and P pili are being therapeutically targeted, and efforts to prevent pilus growth or adherence are described. GENERAL SIGNIFICANCE The combination of structural and biochemical study has led to the detailed mechanistic understanding of this membrane spanning nano-machine. This can now be exploited to design novel drugs able to inhibit virulence. This is vital in the present era of resurgent antibiotic resistance. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
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Affiliation(s)
- James Lillington
- Institute of Structural and Molecular Biology (ISMB), University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Sebastian Geibel
- Institute of Structural and Molecular Biology (ISMB), University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK
| | - Gabriel Waksman
- Institute of Structural and Molecular Biology (ISMB), University College London and Birkbeck College, Malet Street, London WC1E 7HX, UK.
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Pakharukova N, Tuittila M, Zavialov A. Crystallization and sulfur SAD phasing of AggA, the major subunit of aggregative adherence fimbriae type I from the Escherichia coli strain that caused an outbreak of haemolytic-uraemic syndrome in Germany. Acta Crystallogr Sect F Struct Biol Cryst Commun 2013; 69:1389-92. [PMID: 24316837 DOI: 10.1107/s1744309113029990] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 11/01/2013] [Indexed: 11/10/2022]
Abstract
The outbreak of Shiga toxin-producing Escherichia coli O104:H4 infection in Germany in 2011 was associated with significant mortality and morbidity owing to the progressive development of haemolytic-uraemic syndrome. The outbreak strain emerged recently as a result of horizontal transfer events leading to the acquisition of a number of virulence factors. Among them, aggregative adherence fimbriae type I (AAF/I) are considered to be particularly important since they are involved in the initial attachment of bacteria to the intestinal mucosa. Here, the crystallization and preliminary X-ray diffraction analysis of the major subunit of AAF/I, AggA, are reported. Crystallization of recombinant donor-strand complemented AggA was performed by the vapour-diffusion method. The crystals diffracted to 1.55 Å resolution and belonged to the orthorhombic space group C222(1), with unit-cell parameters a = 77.83, b = 80.17, c = 91.42 Å. Despite a low sulfur content of the protein [0.57%(w/w)], sufficiently accurate initial phases were derived from a sulfur SAD experiment.
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Affiliation(s)
- Natalia Pakharukova
- Department of Chemistry, University of Turku, Joint Biotechnology Laboratory, BioCity, Tykistökatu 6A, 20520 Turku, Finland
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20
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Ordered and ushered; the assembly and translocation of the adhesive type I and p pili. BIOLOGY 2013; 2:841-60. [PMID: 24833049 PMCID: PMC3960871 DOI: 10.3390/biology2030841] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 05/21/2013] [Accepted: 05/24/2013] [Indexed: 11/17/2022]
Abstract
Type I and P pili are chaperone-usher pili of uropathogenic Escherichia coli, which allow bacteria to adhere to host cell receptors. Pilus formation and secretion are orchestrated by two accessory proteins, a chaperone, which catalyses pilus subunit folding and maintains them in a polymerization-competent state, and an outer membrane-spanning nanomachine, the usher, which choreographs their assembly into a pilus and drives their secretion through the membrane. In this review, recent structures and kinetic studies are combined to examine the mechanism of type I and P pili assembly, as it is currently known. We also investigate how the knowledge of pilus biogenesis mechanisms has been exploited to design selective inhibitors of the process.
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21
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Piatek R, Zalewska-Piatek B, Dzierzbicka K, Makowiec S, Pilipczuk J, Szemiako K, Cyranka-Czaja A, Wojciechowski M. Pilicides inhibit the FGL chaperone/usher assisted biogenesis of the Dr fimbrial polyadhesin from uropathogenic Escherichia coli. BMC Microbiol 2013; 13:131. [PMID: 23758700 PMCID: PMC3706281 DOI: 10.1186/1471-2180-13-131] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 06/04/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The global spread of bacterial resistance has given rise to a growing interest in new anti-bacterial agents with a new strategy of action. Pilicides are derivatives of ring-fused 2-pyridones which block the formation of the pili/fimbriae crucial to bacterial pathogenesis. They impair by means of a chaperone-usher pathway conserved in the Gram-negative bacteria of adhesive structures biogenesis. Pili/fimbriae of this type belong to two subfamilies, FGS and FGL, which differ in the details of their assembly mechanism. The data published to date have shown that pilicides inhibit biogenesis of type 1 and P pili of the FGS type which are encoded by uropathogenic E. coli strains. RESULTS We evaluated the anti-bacterial activity of literature pilicides as blockers of the assembly of a model example of FGL-type adhesive structures--the Dr fimbriae encoded by a dra gene cluster of uropathogenic Escherichia coli strains. In comparison to the strain grown without pilicide, the Dr⁺ bacteria cultivated in the presence of the 3.5 mM concentration of pilicides resulted in a reduction of 75 to 87% in the adherence properties to CHO cells expressing Dr fimbrial DAF receptor protein. Using quantitative assays, we determined the amount of Dr fimbriae in the bacteria cultivated in the presence of 3.5 mM of pilicides to be reduced by 75 to 81%. The inhibition effect of pilicides is concentration dependent, which is a crucial property for their use as potential anti-bacterial agents. The data presented in this article indicate that pilicides in mM concentration effectively inhibit the adherence of Dr⁺ bacteria to the host cells--the crucial, initial step in bacterial pathogenesis. CONCLUSIONS Structural analysis of the DraB chaperone clearly showed it to be a model of the FGL subfamily of chaperones. This permits us to conclude that analyzed pilicides in mM concentration are effective inhibitors of the assembly of adhesins belonging to the Dr family, and more speculatively, of other FGL-type adhesive organelles. The presented data and those published so far permit to speculate that based on the conservation of chaperone-usher pathway in Gram-negative bacteria , the pilicides are potential anti-bacterial agents with activity against numerous pathogens, the virulence of which is dependent on the adhesive structures of the chaperone-usher type.
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Affiliation(s)
- Rafał Piatek
- Department of Microbiology, Gdańsk University of Technology, ul. Narutowicza 11/12, Gdańsk 80-233, Poland.
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Enterotoxigenic Escherichia coli CS1 pilus: not one structure but several. J Bacteriol 2013; 195:1357-9. [PMID: 23354749 DOI: 10.1128/jb.00053-13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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