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Barton DL, Chang YR, Ducker W, Dobnikar J. Data-driven modelling makes quantitative predictions regarding bacteria surface motility. PLoS Comput Biol 2024; 20:e1012063. [PMID: 38743804 PMCID: PMC11125545 DOI: 10.1371/journal.pcbi.1012063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/24/2024] [Accepted: 04/09/2024] [Indexed: 05/16/2024] Open
Abstract
In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states.
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Affiliation(s)
- Daniel L. Barton
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Yow-Ren Chang
- National Institute of Standards and Technology (NIST), 100 Bureau Dr, Gaithersburg, Maryland, United States of America
| | - William Ducker
- Department of Chemical Engineering and Center for Soft Matter and Biological Physics, Virginia Tech, Blacksburg, Virgina, United States of America
| | - Jure Dobnikar
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing, China
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2
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de Amorim GC, Bardiaux B, Izadi-Pruneyre N. Structural Analysis of Proteins from Bacterial Secretion Systems and Their Assemblies by NMR Spectroscopy. Methods Mol Biol 2024; 2715:503-517. [PMID: 37930547 DOI: 10.1007/978-1-0716-3445-5_30] [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] [Indexed: 11/07/2023]
Abstract
Bacterial secretion systems are built up from proteins with different physicochemical characteristics, such as highly hydrophobic transmembrane polypeptides, and soluble periplasmic or intracellular domains. A single complex can be composed of more than ten proteins with distinct features, spreading through different cellular compartments. The membrane and multicompartment nature of the proteins, and their large molecular weight make their study challenging. However, information on their structure and assemblies is required to understand their mechanisms and interfere with them. An alternative strategy is to work with soluble domains and peptides corresponding to the regions of interest of the proteins.Here, we describe a simple and fast protocol to evaluate the stability, folding, and interaction of protein sub-complexes by using solution-state Nuclear Magnetic Resonance (NMR) spectroscopy. This technique is widely used for protein structure and protein-ligand interaction analysis in solution.
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Affiliation(s)
- Gisele Cardoso de Amorim
- Núcleo Multidisciplinar de Pesquisa em Biologia, Campus Duque de Caxias, Universidade Federal do Rio de Janeiro, Duque de Caxias, RJ, Brazil
| | - Benjamin Bardiaux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France
| | - Nadia Izadi-Pruneyre
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Transmembrane Systems Unit, Paris, France.
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3
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Christensen AH, Gupta A, Chen G, Peters WS, Knoblauch M, Stone HA, Jensen KH. Locally optimal geometry for surface-enhanced diffusion. Phys Rev E 2023; 108:045101. [PMID: 37978587 DOI: 10.1103/physreve.108.045101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 08/16/2023] [Indexed: 11/19/2023]
Abstract
Molecular diffusion in bulk liquids proceeds according to Fick's law, which stipulates that the particle current is proportional to the conductive area. This constrains the efficiency of filtration systems in which both selectivity and permeability are valued. Previous studies have demonstrated that interactions between the diffusing species and solid boundaries can enhance or reduce particle transport relative to bulk conditions. However, only cases that preserve the monotonic relationship between particle current and conductive area are known. In this paper, we expose a system in which the diffusive current increases when the conductive area diminishes. These examples are based on the century-old theory of a charged particle interacting with an electrical double layer. This surprising discovery could improve the efficiency of filtration and may advance our understanding of biological pore structures.
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Affiliation(s)
| | - Ankur Gupta
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Colorado 80309, USA
| | - Guang Chen
- Department of Advanced Manufacturing and Robotics, College of Engineering, Peking University, Beijing 100871, People's Republic of China
| | - Winfried S Peters
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Michael Knoblauch
- School of Biological Sciences, Washington State University, Pullman, Washington 99164, USA
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Kaare H Jensen
- Department of Physics, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
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4
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Ma L, Feng J, Zhang J, Lu X. Campylobacter biofilms. Microbiol Res 2022; 264:127149. [DOI: 10.1016/j.micres.2022.127149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/27/2022]
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5
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Ptak-Kaczor M, Banach M, Stapor K, Fabian P, Konieczny L, Roterman I. Solubility and Aggregation of Selected Proteins Interpreted on the Basis of Hydrophobicity Distribution. Int J Mol Sci 2021; 22:ijms22095002. [PMID: 34066830 PMCID: PMC8125953 DOI: 10.3390/ijms22095002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/03/2021] [Accepted: 05/06/2021] [Indexed: 11/30/2022] Open
Abstract
Protein solubility is based on the compatibility of the specific protein surface with the polar aquatic environment. The exposure of polar residues to the protein surface promotes the protein’s solubility in the polar environment. The aquatic environment also influences the folding process by favoring the centralization of hydrophobic residues with the simultaneous exposure to polar residues. The degree of compatibility of the residue distribution, with the model of the concentration of hydrophobic residues in the center of the molecule, with the simultaneous exposure of polar residues is determined by the sequence of amino acids in the chain. The fuzzy oil drop model enables the quantification of the degree of compatibility of the hydrophobicity distribution observed in the protein to a form fully consistent with the Gaussian 3D function, which expresses an idealized distribution that meets the preferences of the polar water environment. The varied degrees of compatibility of the distribution observed with the idealized one allow the prediction of preferences to interactions with molecules of different polarity, including water molecules in particular. This paper analyzes a set of proteins with different levels of hydrophobicity distribution in the context of the solubility of a given protein and the possibility of complex formation.
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Affiliation(s)
- Magdalena Ptak-Kaczor
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
| | - Mateusz Banach
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
| | - Katarzyna Stapor
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Piotr Fabian
- Institute of Computer Science, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland; (K.S.); (P.F.)
| | - Leszek Konieczny
- Chair of Medical Biochemistry—Jagiellonian University—Medical College, Kopernika 7, 31-034 Kraków, Poland;
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Jagiellonian University—Medical College, Medyczna 7, 30-688 Kraków, Poland; (M.P.-K.); (M.B.)
- Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Łojasiewicza 11, 30-348 Kraków, Poland
- Correspondence:
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6
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Sainz-Mejías M, Jurado-Martín I, McClean S. Understanding Pseudomonas aeruginosa-Host Interactions: The Ongoing Quest for an Efficacious Vaccine. Cells 2020; 9:cells9122617. [PMID: 33291484 PMCID: PMC7762141 DOI: 10.3390/cells9122617] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas aeruginosa is a leading cause of chronic respiratory infections in people with cystic fibrosis (CF), bronchiectasis or chronic obstructive pulmonary disease (COPD), and acute infections in immunocompromised individuals. The adaptability of this opportunistic pathogen has hampered the development of antimicrobial therapies, and consequently, it remains a major threat to public health. Due to its antimicrobial resistance, vaccines represent an alternative strategy to tackle the pathogen, yet despite over 50 years of research on anti-Pseudomonas vaccines, no vaccine has been licensed. Nevertheless, there have been many advances in this field, including a better understanding of the host immune response and the biology of P. aeruginosa. Multiple antigens and adjuvants have been investigated with varying results. Although the most effective protective response remains to be established, it is clear that a polarised Th2 response is sub-optimal, and a mixed Th1/Th2 or Th1/Th17 response appears beneficial. This comprehensive review collates the current understanding of the complexities of P. aeruginosa-host interactions and its implication in vaccine design, with a view to understanding the current state of Pseudomonal vaccine development and the direction of future efforts. It highlights the importance of the incorporation of appropriate adjuvants to the protective antigen to yield optimal protection.
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Graham KJ, Burrows LL. More than a feeling: microscopy approaches to understanding surface-sensing mechanisms. J Bacteriol 2020; 203:JB.00492-20. [PMID: 33077631 PMCID: PMC8095462 DOI: 10.1128/jb.00492-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The mechanisms by which bacteria sense and respond to surface attachment have long been a mystery. Our understanding of the structure and dynamics of bacterial appendages, notably type IV pili (T4P), provided new insights into the potential ways that bacteria sense surfaces. T4P are ubiquitous, retractable hair-like adhesins that until recently were difficult to image in the absence of fixation due to their nanoscale size. This review focuses on recent microscopy innovations used to visualize T4P in live cells to reveal the dynamics of their retraction and extension. We discuss recently proposed mechanisms by which T4P facilitate bacterial surface sensing, including the role of surface-exposed PilY1, two-component signal transduction pathways, force-induced structural modifications of the major pilin, and altered dynamics of the T4P motor complex.
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Affiliation(s)
- Katherine J Graham
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton ON Canada L8S4K1
| | - Lori L Burrows
- Department of Biochemistry and Biomedical Sciences, and the Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton ON Canada L8S4K1
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8
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Audette GF, Yaseen A, Bragagnolo N, Bawa R. Protein Nanotubes: From Bionanotech towards Medical Applications. Biomedicines 2019; 7:biomedicines7020046. [PMID: 31234611 PMCID: PMC6630890 DOI: 10.3390/biomedicines7020046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 01/21/2023] Open
Abstract
Nanobiotechnology involves the study of structures found in nature to construct nanodevices for biological and medical applications with the ultimate goal of commercialization. Within a cell most biochemical processes are driven by proteins and associated macromolecular complexes. Evolution has optimized these protein-based nanosystems within living organisms over millions of years. Among these are flagellin and pilin-based systems from bacteria, viral-based capsids, and eukaryotic microtubules and amyloids. While carbon nanotubes (CNTs), and protein/peptide-CNT composites, remain one of the most researched nanosystems due to their electrical and mechanical properties, there are many concerns regarding CNT toxicity and biodegradability. Therefore, proteins have emerged as useful biotemplates for nanomaterials due to their assembly under physiologically relevant conditions and ease of manipulation via protein engineering. This review aims to highlight some of the current research employing protein nanotubes (PNTs) for the development of molecular imaging biosensors, conducting wires for microelectronics, fuel cells, and drug delivery systems. The translational potential of PNTs is highlighted.
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Affiliation(s)
- Gerald F Audette
- Department of Chemistry and the Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada.
| | - Ayat Yaseen
- Department of Chemistry and the Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada.
| | - Nicholas Bragagnolo
- Department of Chemistry and the Centre for Research on Biomolecular Interactions, York University, Toronto, ON M3J 1P3, Canada.
| | - Raj Bawa
- Patent Law Department, Bawa Biotech LLC, Ashburn, VA 20147, USA.
- Guanine Inc., Rensselaer, NY 12144-3463, USA.
- Pharmaceutical Research Institute of Albany College of Pharmacy and Health Sciences, Albany, NY 12208, USA.
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9
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Abstract
Type IV pilus (T4P)-like systems have been identified in almost every major phylum of prokaryotic life. They include the type IVa pilus (T4aP), type II secretion system (T2SS), type IVb pilus (T4bP), Tad/Flp pilus, Com pilus, and archaeal flagellum (archaellum). These systems are used for adhesion, natural competence, phage adsorption, folded-protein secretion, surface sensing, swimming motility, and twitching motility. The T4aP allows for all of these functions except swimming and is therefore a good model system for understanding T4P-like systems. Recent structural analyses have revolutionized our understanding of how the T4aP machinery assembles and functions. Here we review the structure and function of the T4aP.
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10
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Solanki V, Kapoor S, Thakur KG. Structural insights into the mechanism of Type IVa pilus extension and retraction ATPase motors. FEBS J 2018; 285:3402-3421. [PMID: 30066435 DOI: 10.1111/febs.14619] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/26/2018] [Accepted: 07/30/2018] [Indexed: 11/27/2022]
Abstract
Type IVa pili are bacterial appendages involved in diverse physiological processes, including electron transfer in Geobacter sulfurreducens. ATP hydrolysis coupled with conformational changes powers the extension (PilB) and retraction (PilT) motors in the pilus machinery. We report the unliganded crystal structures of the core ATPase domain of PilB and PilT-4 from G. sulfurreducens at 3.1 and 2.6 Å resolution, respectively. PilB structure revealed three distinct conformations, that is, open, closed, and open' which were previously proposed to be mediated by ATP/ADP binding. PilT-4 subunits, on the other hand, were observed in the closed state conformation. We further report that both PilB and PilT-4 hexamers have two high-affinity ATP-binding sites. Comparative structural analysis and solution data presented here supports the "symmetric rotary model" for these ATPase motors. Our data further suggest that pores of these motors rotate either clockwise or counterclockwise to facilitate assembly or disassembly of right-handed or left-handed pilus. DATABASE Structural data are available in the RCSB PDB database under the PDB ID 5ZFQ (PilT-4), 5ZFR (PilB).
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Affiliation(s)
- Vipul Solanki
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
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11
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Nguyen Y, Boulton S, McNicholl ET, Akimoto M, Harvey H, Aidoo F, Melacini G, Burrows LL. A Highly Dynamic Loop of the Pseudomonas aeruginosa PA14 Type IV Pilin Is Essential for Pilus Assembly. ACS Infect Dis 2018; 4:936-943. [PMID: 29342354 DOI: 10.1021/acsinfecdis.7b00229] [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] [Indexed: 11/30/2022]
Abstract
Type IVa pili (T4aP) are long, thin surface filaments involved in attachment, motility, biofilm formation, and DNA uptake. They are important virulence factors for many bacteria, including Pseudomonas aeruginosa, an opportunistic pathogen and common cause of hospital-acquired infections. Each helical filament contains thousands of monomers of the major pilin subunit, PilA. Each P. aeruginosa strain expresses one of five phylogenetically distinct major pilins, which vary in sequence and the nature of their associated accessory protein(s). Here, we present the backbone resonance assignment of the C-terminal domain of the group III PilA from strain PA14, a highly virulent, globally distributed clone. Secondary structure probabilities calculated from chemical shifts were in excellent agreement with previous homology modeling using a group V pilin structural template. The analysis revealed that the distal segment of the αβ loop had high microsecond-millisecond dynamics compared with other loop regions. Shortening of this segment by internal deletion abrogated pilus assembly in a dominant negative manner, suggesting a potential role in pilin polymerization. Pilin conformations that support optimal interactions of both the conserved hydrophobic N-termini in the pilus core and hydrophilic loops creating the filament surface may be necessary to produce stable filaments.
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12
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Fibre diffraction studies of biological macromolecules. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 127:43-87. [DOI: 10.1016/j.pbiomolbio.2017.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/21/2017] [Accepted: 04/05/2017] [Indexed: 12/27/2022]
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13
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Naidoo N, Pillay M. Bacterial pili, with emphasis on Mycobacterium tuberculosis curli pili: potential biomarkers for point-of care tests and therapeutics. Biomarkers 2016; 22:93-105. [PMID: 27797276 DOI: 10.1080/1354750x.2016.1252960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
CONTEXT Novel biomarkers are essential for developing rapid diagnostics and therapeutic interventions Objective: This review aimed to highlight biomarker characterisation and assessment of unique bacterial pili. METHODS A PubMed search for bacterial pili, diagnostics, vaccine and therapeutics was performed, with emphasis on the well characterised pili. RESULTS In total, 46 papers were identified and reviewed. CONCLUSION Extensive analyses of pili enabled by advanced nanotechnology and whole genome sequencing provide evidence that they are strong biomarker candidates. Mycobacterium tuberculosis curli pili are emphasised as important epitopes for the development of much needed point-of-care diagnostics and therapeutics.
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Affiliation(s)
- Natasha Naidoo
- a Medical Microbiology and Infection Control , School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Congella , Durban , South Africa
| | - Manormoney Pillay
- a Medical Microbiology and Infection Control , School of Laboratory Medicine and Medical Sciences, College of Health Science, University of KwaZulu-Natal, Congella , Durban , South Africa
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Saeb ATM. Presence of Bacterial Virulence Gene Homologues in the dibenzo-p-dioxins degrading bacterium Sphingomonas wittichii. Bioinformation 2016; 12:241-248. [PMID: 28197061 PMCID: PMC5290665 DOI: 10.6026/97320630012241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 11/28/2022] Open
Abstract
Sphingomonas wittichii, a close relative of the human pathogen Sphingomonas paucimobilis, is a microorganism of great interest to the bioremediation community for its ability of biodegradation to a large number of toxic polychlorinated dioxins. In the present study we investigated the presence of different virulence factors and genes in S. wittichii. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of S. wittichii as a potential virulent pathogen. The 16SrDNA phylogenetic tree showed that the closest bacterial taxon to S. wittichii is Brucella followed by Helicobacter, Campylobacter, Pseudomonas then Legionella. Despite their close phylogenetic relationship, S. wittichii did not share any virulence factors with Helicobacter or Campylobacter. On the contrary, in spite of the phylogenetic divergence between S. wittichii and Pseudomonas spp., they shared many major virulence factors, such as, adherence, antiphagocytosis, Iron uptake, proteases and quorum sensing. S. wittichii contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp. and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. S. wittichii is a potential virulent bacterium. Another possibility is that reductive evolution process attenuated S. wittichii pathogenic capabilities. Thus plenty of care must be taken when using this bacterium in soil remediation purposes.
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Affiliation(s)
- Amr T. M. Saeb
- Biotechnology Department, Strategic Center for Diabetes Research, College of medicine, King Saud University, Saudi Arabia
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15
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Lento C, Wilson DJ, Audette GF. Dimerization of the type IV pilin from Pseudomonas aeruginosa strain K122-4 results in increased helix stability as measured by time-resolved hydrogen-deuterium exchange. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2016; 3:012001. [PMID: 26798830 PMCID: PMC4711513 DOI: 10.1063/1.4929597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/20/2015] [Indexed: 06/05/2023]
Abstract
Truncated pilin monomers from Pseudomonas aeruginosa strain K122-4 (ΔK122) have been shown to enter a monomer-dimer equilibrium in solution prior to oligomerization into protein nanotubes. Here, we examine the structural changes occurring between the monomeric and dimeric states of ΔK122 using time-resolved hydrogen-deuterium exchange mass spectrometry. Based on levels of deuterium uptake, the N-terminal α-helix and the loop connecting the second and third strands of the anti-parallel β-sheet contribute significantly to pilin dimerization. Conversely, the antiparallel β-sheet and αβ loop region exhibit increased flexibility, while the receptor binding domain retains a rigid conformation in the equilibrium state.
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Affiliation(s)
- Cristina Lento
- Department of Chemistry, York University , Toronto, Ontario M3J 1P3, Canada
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16
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Abstract
Proteinaceous, nonflagellar surface appendages constitute a variety of structures, including those known variably as fimbriae or pili. Constructed by distinct assembly pathways resulting in diverse morphologies, fimbriae have been described to mediate functions including adhesion, motility, and DNA transfer. As these structures can represent major diversifying elements among Escherichia and Salmonella isolates, multiple fimbrial classification schemes have been proposed and a number of mechanistic insights into fimbrial assembly and function have been made. Herein we describe the classifications and biochemistry of fimbriae assembled by the chaperone/usher, curli, and type IV pathways.
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17
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Saeb AT, David SK, Al-Brahim H. In silico detection of virulence gene homologues in the human pathogen sphingomonas spp. Evol Bioinform Online 2014; 10:229-38. [PMID: 25574122 PMCID: PMC4266192 DOI: 10.4137/ebo.s20710] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/09/2014] [Accepted: 11/11/2014] [Indexed: 11/05/2022] Open
Abstract
There is an ongoing debate about the clinical significance of Sphingomonas paucimobilis as a virulent bacterial pathogen. In the present study, we investigated the presence of different virulence factors and genes in Sphingomonas bacteria. We utilized phylogenetic, comparative genomics and bioinformatics analysis to investigate the potentiality of Sphingomonas bacteria as virulent pathogenic bacteria. The 16S ribosomal RNA gene (16S rDNA) phylogenetic tree showed that the closest bacterial taxon to Sphingomonas is Brucella with a bootstrap value of 87 followed by Helicobacter, Campylobacter, Pseudomonas, and then Legionella. Sphingomonas shared no virulence factors with Helicobacter or Campylobacter, despite their close phylogenic relationship. In spite of the phylogenetic divergence between Sphingomonas and Pseudomonas, they shared many major virulence factors, such as adherence, antiphagocytosis, iron uptake, proteases, and quorum sensing. In conclusion, Sphingomonas spp. contains several major virulence factors resembling Pseudomonas sp., Legionella sp., Brucella sp., and Bordetella sp. virulence factors. Similarity of virulence factors did not match phylogenetic relationships. These findings suggest horizontal gene transfer of virulence factors rather than sharing a common pathogenic ancestor. Sphingomonas spp. is potential virulent bacterial pathogen.
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Affiliation(s)
- Amr Tm Saeb
- Biotechnology Department, Strategic Center for Diabetes Research, King Saud University, Riyadh, Saudi Arabia
| | - Satish Kumar David
- Information Technology Department, Strategic Center for Diabetes Research, King Saud University, Riyadh, Saudi Arabia
| | - Hissa Al-Brahim
- Biotechnology Department, Strategic Center for Diabetes Research, King Saud University, Riyadh, Saudi Arabia
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18
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The 1.59Å resolution structure of the minor pseudopilin EpsH of Vibrio cholerae reveals a long flexible loop. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:406-15. [DOI: 10.1016/j.bbapap.2013.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 11/01/2013] [Accepted: 11/24/2013] [Indexed: 01/25/2023]
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19
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Pera NP, Pieters RJ. Towards bacterial adhesion-based therapeutics and detection methods. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00346a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bacterial adhesion is an important first step towards bacterial infection and plays a role in colonization, invasion and biofilm formation.
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Affiliation(s)
- Núria Parera Pera
- Department of Medicinal Chemistry and Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Utrecht University
- 3508 TB Utrecht
- The Netherlands
| | - Roland J. Pieters
- Department of Medicinal Chemistry and Chemical Biology
- Utrecht Institute for Pharmaceutical Sciences
- Utrecht University
- 3508 TB Utrecht
- The Netherlands
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20
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Abstract
Type IV pili (T4P) are multifunctional protein fibers produced on the surfaces of a wide variety of bacteria and archaea. The major subunit of T4P is the type IV pilin, and structurally related proteins are found as components of the type II secretion (T2S) system, where they are called pseudopilins; of DNA uptake/competence systems in both Gram-negative and Gram-positive species; and of flagella, pili, and sugar-binding systems in the archaea. This broad distribution of a single protein family implies both a common evolutionary origin and a highly adaptable functional plan. The type IV pilin is a remarkably versatile architectural module that has been adopted widely for a variety of functions, including motility, attachment to chemically diverse surfaces, electrical conductance, acquisition of DNA, and secretion of a broad range of structurally distinct protein substrates. In this review, we consider recent advances in this research area, from structural revelations to insights into diversity, posttranslational modifications, regulation, and function.
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Tan Z, Li H, Pan H, Zhou X, Liu X, Luo N, Hu W, Li Y. Characterization of four type IV pilin homologues in Stigmatella aurantiaca DSM17044 by heterologous expression in Myxococcus xanthus. PLoS One 2013; 8:e75105. [PMID: 24058653 PMCID: PMC3776727 DOI: 10.1371/journal.pone.0075105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/09/2013] [Indexed: 11/19/2022] Open
Abstract
As prokaryotic models for multicellular development, Stigmatella aurantiaca and Myxococcus xanthus share many similarities in terms of social behaviors, such as gliding motility. Our current understanding of myxobacterial grouped-cell motilities comes mainly from the research on M. xanthus, which shows that filamentous type IV pili (TFP), composed of type IV pilin (also called PilA protein) subunits, are the key apparatus for social motility (S-motility). However, little is known about the pilin protein in S. aurantiaca. We cloned and sequenced four genes (pilA(Sa1~4)) from S. aurantiaca DSM17044 that are homologous to pilA(Mx) (pilA gene in M. xanthus DK1622). The homology and similarities among pilA(Sa) proteins and other myxobacterial homologues were systematically analyzed. To determine their potential biological functions, the four pilA(Sa) genes were expressed in M. xanthus DK10410 (ΔpilA(Mx)), which did not restore S-motility on soft agar or EPS production to host cells. After further analysis of the motile behaviors in a methylcellulose solution, the M. xanthus strains were categorized into three types. YL6101, carrying pilA(Sa1), and YL6104, carrying pilA(Sa4), produced stable but unretractable surface pili; YL6102, carrying pilA(Sa2), produced stable surface pili and exhibited reduced TFP-dependent motility in methylcellulose; YL6103, carrying pilA(Sa3), produced unstable surface pili. Based on these findings, we propose that pilA(Sa2) might be responsible for the type IV pilin production involved in group motility in S. aurantiaca DSM17044. After examining the developmental processes, it was suggested that the expression of PilA(Sa4) protein might have positive effects on the fruiting body formation of M. xanthus DK10410 cells. Moreover, the formation of fruiting body in M. xanthus cells with stable exogenous TFPSa were compensated by mixing them with S. aurantiaca DSM17044 cells. Our results shed some light on the features and functions of type IV pilin homologues in S. aurantiaca.
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Affiliation(s)
- Zaigao Tan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Haoming Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Hongwei Pan
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Xiuwen Zhou
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Xin Liu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Ningning Luo
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
| | - Wei Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
- * E-mail:
| | - Yuezhong Li
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan, Shandong, China
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22
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Petrov A, Lombardo S, Audette GF. Fibril-mediated oligomerization of pilin-derived protein nanotubes. J Nanobiotechnology 2013; 11:24. [PMID: 23829476 PMCID: PMC3704941 DOI: 10.1186/1477-3155-11-24] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 07/01/2013] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Self-assembling protein nanotubes (PNTs) are an intriguing alternative to carbon nanotubes for applications in bionanotechnology, in part due to greater inherent biocompatibility. The type IV pilus of the gram negative bacteria Pseudomonas aeruginosa is a protein-based fibre composed of a single subunit, the type IV pilin. Engineered pilin monomers from P. aeruginosa strain K122-4 (ΔK122) have been shown to oligomerize into PNTs both in solution and at surfaces. In order to fully exploit PNTs in bionanotechonological settings, an in-depth understanding of their assembly, physical characteristics and robustness, both in solution and when constrained to surfaces, is required. RESULTS This study details the effectiveness of multiple initiators of ΔK122-derived PNT oligomerization and characterize the formation of PNTs in solution. The optimal initiator for the oligomerization of ΔK122 in solution was observed to be 2-methyl-2,4-pentanediol (MPD). Conversely, larger PEG molecules do not trigger oligomerization. Multi-angle light scattering analysis indicates that the pilin protein exists in a monomer-dimer equilibrium in solution, and that an intermediate species forms within three hours that then coalesces over time into high molecular weight PNTs. Transmission Electron Microscopic analysis was used to observe the formation of oligomerized ΔK122 fibrils prior to assembly into full-length PNTs. CONCLUSIONS The oligomerization of ΔK122 pilin derived PNTs is a fibril mediated process. The optimal trigger for PNT oligomerization in solution is MPD, and the observation that PEGs do not induce oligomerization may enable the oligomerization of pilin-derived PNTs on PEG-functionalized surfaces for implantable bionanodevices.
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Affiliation(s)
- Anna Petrov
- Department of Chemistry, York University, Toronto, ON M3J1P3, Canada
| | | | - Gerald F Audette
- Department of Chemistry, York University, Toronto, ON M3J1P3, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, Canada
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Srivastava SK, Gayathri S, Manjasetty BA, Gopal B. Analysis of conformational variation in macromolecular structural models. PLoS One 2012; 7:e39993. [PMID: 22808083 PMCID: PMC3392262 DOI: 10.1371/journal.pone.0039993] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 05/30/2012] [Indexed: 11/18/2022] Open
Abstract
Experimental conditions or the presence of interacting components can lead to variations in the structural models of macromolecules. However, the role of these factors in conformational selection is often omitted by in silico methods to extract dynamic information from protein structural models. Structures of small peptides, considered building blocks for larger macromolecular structural models, can substantially differ in the context of a larger protein. This limitation is more evident in the case of modeling large multi-subunit macromolecular complexes using structures of the individual protein components. Here we report an analysis of variations in structural models of proteins with high sequence similarity. These models were analyzed for sequence features of the protein, the role of scaffolding segments including interacting proteins or affinity tags and the chemical components in the experimental conditions. Conformational features in these structural models could be rationalized by conformational selection events, perhaps induced by experimental conditions. This analysis was performed on a non-redundant dataset of protein structures from different SCOP classes. The sequence-conformation correlations that we note here suggest additional features that could be incorporated by in silico methods to extract dynamic information from protein structural models.
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Affiliation(s)
| | - Savitha Gayathri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Babu A. Manjasetty
- European Molecular Biology Laboratory, Grenoble Outstation and Unit of Virus Host-Cell Interactions (UVHCI), Grenoble, France
| | - Balasubramanian Gopal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- * E-mail: (SKS); (BG)
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24
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Petrov A, Audette GF. Peptide and protein-based nanotubes for nanobiotechnology. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2012; 4:575-85. [PMID: 22753264 DOI: 10.1002/wnan.1180] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The development of biologically relevant nanosystems such as biomolecular probes and sensors requires systems that effectively interface specific biochemical environments with abiotic architectures. The most widely studied nanomaterial, carbon nanotubes, has proven challenging in their adaptation for biomedical applications despite their numerous advantageous physical and electrochemical properties. On the other hand, development of bionanosystems through adaptation of existing biological systems has several advantages including their adaptability through modern recombinant DNA strategies. Indeed, the use of peptides, proteins and protein assemblies as nanotubes, scaffolds, and nanowires has shown much promise as a bottom-up approach to the development of novel bionanosystems. We highlight several unique peptide and protein systems that generate protein nanotubes (PNTs) that are being explored for the development of biosensors, probes, bionanowires, and drug delivery systems.
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Affiliation(s)
- Anna Petrov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
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25
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Hu W, Yang Z, Lux R, Zhao M, Wang J, He X, Shi W. Direct visualization of the interaction between pilin and exopolysaccharides of Myxococcus xanthus with eGFP-fused PilA protein. FEMS Microbiol Lett 2011; 326:23-30. [PMID: 22092602 DOI: 10.1111/j.1574-6968.2011.02430.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/13/2011] [Accepted: 09/27/2011] [Indexed: 10/17/2022] Open
Abstract
Type IV pili (TFP) and exopolysaccharides (EPS) are important components for social behaviors in Myxococcus xanthus, including gliding motility and fruiting body formation. Although specific interactions between TFP and EPS have been proposed, there have as yet been no direct observations of these interactions under native conditions. In this study, we found that a truncated PilA protein (PilACt) containing only the C-terminal domain (amino acids 32-208) is sufficient for EPS binding in vitro. Furthermore, an enhanced green fluorescent protein (eGFP) and PilACt fusion protein were constructed and used to label the native EPS in M. xanthus. Under confocal laser scanning microscope, the eGFP-PilACt-bound fruiting bodies, trail structures and biofilms exhibited similar patterns as the wheat germ agglutinin lectin-labeled EPS structures. This study showed that eGFP-PilACt fusion protein was able efficiently to label the EPS of M. xanthus, providing evidence for the first time of the direct interaction between the PilA protein and EPS under native conditions.
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Affiliation(s)
- Wei Hu
- School of Dentistry, UCLA, Los Angeles, CA 90095, USA
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26
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Sharma A, Krause A, Worgall S. Recent developments for Pseudomonas vaccines. HUMAN VACCINES 2011; 7:999-1011. [PMID: 21941090 DOI: 10.4161/hv.7.10.16369] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Infections with Pseudomonas aeruginosa are a major health problem for immune-compromised patients and individuals with cystic fibrosis. A vaccine against: P. aeruginosa has long been sought after, but is so far not available. Several vaccine candidates have been assessed in experimental animals and humans, which include sub-cellular fractions, capsule components, purified and recombinant proteins. Unique characteristics of the host and the pathogen have complicated the vaccine development. This review summarizes the current state of vaccine development for this ubiquitous pathogen, in particular to provide mucosal immunity against infections of the respiratory tract in susceptible individuals with cystic fibrosis.
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Affiliation(s)
- Anurag Sharma
- Department of Genetic Medicine, Weill Medical College of Cornell University, New York, NY, USA
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27
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Rodgers K, Arvidson CG, Melville S. Expression of a Clostridium perfringens type IV pilin by Neisseria gonorrhoeae mediates adherence to muscle cells. Infect Immun 2011; 79:3096-105. [PMID: 21646450 PMCID: PMC3147591 DOI: 10.1128/iai.00909-10] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 05/28/2011] [Indexed: 11/20/2022] Open
Abstract
Clostridium perfringens is an anaerobic, Gram-positive bacterium that causes a range of diseases in humans, including lethal gas gangrene. We have recently shown that strains of C. perfringens move across the surface of agar plates by a unique type IV pilus (TFP)-mediated social motility that had not been previously described. Based on sequence homology to pilins in Gram-negative bacteria, C. perfringens appears to have two pilin subunits, PilA1 and PilA2. Structural prediction analysis indicated PilA1 is similar to the pseudopilin found in Klebsiella oxytoca, while PilA2 is more similar to true pilins found in the Gram-negative pathogens Pseudomonas aeruginosa and Neisseria gonorrhoeae. Strains of N. gonorrhoeae that were genetically deficient in the native pilin, PilE, but supplemented with inducible expression of PilA1 and PilA2 of C. perfringens were constructed. Genetic competence, wild-type twitching motility, and attachment to human urogenital epithelial cells were not restored by expression of either pilin. However, attachment to mouse and rat myoblast (muscle) cell lines was observed with the N. gonorrhoeae strain expressing PilA2. Significantly, wild-type C. perfringens cells adhered to mouse myoblasts under anaerobic conditions, and adherence was 10-fold lower in a pilT mutant that lacked functional TFP. These findings implicate C. perfringens TFP in the ability of C. perfringens to adhere to and move along muscle fibers in vivo, which may provide a therapeutic approach to limiting this rapidly spreading and highly lethal infection.
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Affiliation(s)
- Katherine Rodgers
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia
| | - Cindy Grove Arvidson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
| | - Stephen Melville
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia
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28
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Yang Z, Hu W, Chen K, Wang J, Lux R, Zhou ZH, Shi W. Alanine 32 in PilA is important for PilA stability and type IV pili function in Myxococcus xanthus. MICROBIOLOGY-SGM 2011; 157:1920-1928. [PMID: 21493683 DOI: 10.1099/mic.0.049684-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Type IV pili (TFP) are membrane-anchored filaments with a number of important biological functions. In the model organism Myxococcus xanthus, TFP act as molecular engines that power social (S) motility through cycles of extension and retraction. TFP filaments consist of several thousand copies of a protein called PilA or pilin. PilA contains an N-terminal α-helix essential for TFP assembly and a C-terminal globular domain important for its activity. The role of the PilA sequence and its structure-function relationship in TFP-dependent S motility remain active areas of research. In this study, we identified an M. xanthus PilA mutant carrying an alanine to valine substitution at position 32 in the α-helix, which produced structurally intact but retraction-defective TFP. Characterization of this mutant and additional single-residue variants at this position in PilA demonstrated the critical role of alanine 32 in PilA stability, TFP assembly and retraction.
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Affiliation(s)
- Zhe Yang
- Molecular Biology Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
| | - Wei Hu
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, Shandong, PR China.,School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Kevin Chen
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095-7364, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Jing Wang
- State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, Shandong, PR China.,School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Renate Lux
- School of Dentistry, University of California, Los Angeles, CA 90095, USA
| | - Z Hong Zhou
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095-7364, USA.,California NanoSystems Institute, UCLA, Los Angeles, CA 90095, USA
| | - Wenyuan Shi
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, CA 90095-7364, USA.,School of Dentistry, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA
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29
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Shewmaker F. The application of NMR techniques to bacterial adhesins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2011; 715:241-56. [PMID: 21557068 DOI: 10.1007/978-94-007-0940-9_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Extracellular adhesins frequently compose large, highly-ordered structural assemblies that project away from the bacterial surface. These assemblies, known as pili or fimbriae, are rod-like polymeric structures that in some cases can extend up to several micrometers from the cell surface. Because these adhesin structures are critical to bacterial colonization of host cell surfaces, there is an incentive to understand their structure, assembly and mechanism of host cell attachment. Various methods in Nuclear Magnetic Resonance (NMR) spectroscopy have been used to address these topics, yielding structural information at the atomic level. Also, new methods in solid-state NMR spectroscopy have thus far been under-utilized in the study of large adhesin structures and offer a powerful approach to overcoming problems with crystallization to better understand the structures of these complexes. The following is a brief overview of the contributions of NMR to the study of bacterial adhesins with an emphasis on the future potential of solid-state NMR.
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Affiliation(s)
- Frank Shewmaker
- Department of Pharmacology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
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30
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Modeling pilus structures from sparse data. J Struct Biol 2010; 173:436-44. [PMID: 21115127 DOI: 10.1016/j.jsb.2010.11.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 11/11/2010] [Accepted: 11/15/2010] [Indexed: 11/23/2022]
Abstract
Bacterial Type II secretion systems (T2SS) and type IV pili (T4P) biogenesis machineries share the ability to assemble thin filaments from pilin protein subunits in the plasma membrane. Here we describe in detail the calculation strategy that served to determine a detailed atomic model of the T2SS pilus from Klebsiella oxytoca (Campos et al., PNAS 2010). The strategy is based on molecular modeling with generalized distance restraints and experimental validation (salt bridge charge inversion; double cysteine substitution and crosslinking). It does not require directly fitting structures into an envelope obtained from electron microscopy, but relies on lower resolution information, in particular the symmetry parameters of the helix forming the pilus. We validate the strategy with T4P where either a higher resolution structure is available (for the gonococcal (GC) pilus from Neisseria gonorrhoeae), or where we can compare our results to additional experimental data (for Vibrio cholerae TCP). The models are of sufficient precision to compare the architecture of the different pili in detail.
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31
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Adak AK, Leonov AP, Ding N, Thundimadathil J, Kularatne S, Low PS, Wei A. Bishydrazide glycoconjugates for lectin recognition and capture of bacterial pathogens. Bioconjug Chem 2010; 21:2065-75. [PMID: 20925370 DOI: 10.1021/bc100288c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bishydrazides are versatile linkers for attaching glycans to substrates for lectin binding and pathogen detection schemes. The α,ω-bishydrazides of carboxymethylated hexa(ethylene glycol) (4) can be conjugated at one end to unprotected oligosaccharides, then attached onto carrier proteins, tethered onto activated carboxyl-terminated surfaces, or functionalized with a photoactive cross-linking agent for lithographic patterning. Glycoconjugates of bishydrazide 4 can also be converted into dithiocarbamates (DTCs) by treatment with CS(2) under mild conditions, for attachment onto gold substrates. The immobilized glycans serve as recognition elements for cell-surface lectins and enable the detection and capture of bacterial pathogens such as Pseudomonas aeruginosa by their adsorption onto micropatterned substrates. A detection limit of 10³ cfu/mL is demonstrated, using a recently introduced method based on optical pattern recognition.
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Affiliation(s)
- Avijit Kumar Adak
- Department of Chemistry, Purdue University, West Lafayette, Indiana, United States
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32
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Hackbarth C, Hodges RS. Synthetic peptide vaccine development: designing dual epitopes into a single pilin peptide immunogen generates antibody cross-reactivity between two strains of Pseudomonas aeruginosa. Chem Biol Drug Des 2010; 76:293-304. [PMID: 20807222 DOI: 10.1111/j.1747-0285.2010.01021.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the main challenges of Pseudomonas aeruginosa vaccine development is the design of an antigen that elicits cross-reactive antibodies against multiple virulent strains. Using a rational design approach, we have developed a single 17-residue peptide immunogen that generates antibodies that target the receptor-binding domain of the type IV pilus of more than one strain of P. aeruginosa. Using the receptor-binding domain sequence, of native strain PAO as a template, we have systematically changed up to five residues in the PAO sequence of the peptide immunogen into that of the PAK sequence. We show by indirect and competitive ELISA that the mutant peptide immunogens elicit the development of polyclonal sera that is cross-reactive to both native strain PAO and PAK pilin. We further show that there are at least two separate antibody populations in the polyclonal sera that possess closely related epitopes but which are each strain specific. Moreover, part of the epitope for the PAO-specific antibodies consists of several residues outside the disulfide loop of the receptor-binding domain. This allows us to create two unique epitopes within the same receptor-binding domain sequence.
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Affiliation(s)
- Clifton Hackbarth
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Program in Structural Biology and Biophysics, 12801 E. 17th Ave, MS 8101, Aurora, CO 80045, USA
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33
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Structural Characterization of Novel Pseudomonas aeruginosa Type IV Pilins. J Mol Biol 2010; 395:491-503. [DOI: 10.1016/j.jmb.2009.10.070] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2009] [Revised: 10/28/2009] [Accepted: 10/28/2009] [Indexed: 11/19/2022]
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34
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Single-residue changes in the C-terminal disulfide-bonded loop of the Pseudomonas aeruginosa type IV pilin influence pilus assembly and twitching motility. J Bacteriol 2009; 191:6513-24. [PMID: 19717595 DOI: 10.1128/jb.00943-09] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PilA, the major pilin subunit of Pseudomonas aeruginosa type IV pili (T4P), is a principal structural component. PilA has a conserved C-terminal disulfide-bonded loop (DSL) that has been implicated as the pilus adhesinotope. Structural studies have suggested that DSL is involved in intersubunit interactions within the pilus fiber. PilA mutants with single-residue substitutions, insertions, or deletions in the DSL were tested for pilin stability, pilus assembly, and T4P function. Mutation of either Cys residue of the DSL resulted in pilins that were unable to assemble into fibers. Ala replacements of the intervening residues had a range of effects on assembly or function, as measured by changes in surface pilus expression and twitching motility. Modification of the C-terminal P-X-X-C type II beta-turn motif, which is one of the few highly conserved features in pilins across various species, caused profound defects in assembly and twitching motility. Expression of pilins with suspected assembly defects in a pilA pilT double mutant unable to retract T4P allowed us to verify which subunits were physically unable to assemble. Use of two different PilA antibodies showed that the DSL may be an immunodominant epitope in intact pili compared with pilin monomers. Sequence diversity of the type IVa pilins likely reflects an evolutionary compromise between retention of function and antigenic variation. The consequences of DSL sequence changes should be evaluated in the intact protein since it is technically feasible to generate DSL-mimetic peptides with mutations that will not appear in the natural repertoire due to their deleterious effects on assembly.
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35
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Kao DJ, Hodges RS. Advantages of a synthetic peptide immunogen over a protein immunogen in the development of an anti-pilus vaccine for Pseudomonas aeruginosa. Chem Biol Drug Des 2009; 74:33-42. [PMID: 19519742 DOI: 10.1111/j.1747-0285.2009.00825.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The type IV pilus is an important adhesin in the establishment of infection by Pseudomonas aeruginosa. We have previously reported on a synthetic peptide vaccine targeting the receptor-binding domain of the main structural subunit of the pilus, PilA. The receptor-binding domain is a 14-residue disulfide loop at the C-terminal end of the pilin protein. The objective of this study was to compare the immunogenicity of a peptide-conjugate to a protein subunit immunogen to determine which was superior for use in an anti-pilus vaccine. BALB/c mice were immunized with the native PAK strain pilin protein and a synthetic peptide of the receptor-binding domain conjugated to keyhole limpet haemocyanin. A novel pilin protein with a scrambled receptor-binding domain was used to characterize receptor-binding domain-specific antibodies. The titres against the native pilin of the animals immunized with the synthetic peptide-conjugate were higher than the titres of animals immunized with the pilin protein. In addition, the affinities of anti-peptide sera for the intact pilin receptor-binding domain were significantly higher than affinities of anti-pilin protein sera. These results have significant implications for vaccine design and show that there are significant advantages in using a synthetic peptide-conjugate over a subunit pilin protein for an anti-pilus vaccine.
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Affiliation(s)
- Daniel J Kao
- Department of Biochemistry and Molecular Genetics, University of Colorado Denver, School of Medicine, Biomolecular Structure, MS 8101, P.O. Box 6511, Aurora, CO 80045, USA
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36
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Korotkov KV, Gray MD, Kreger A, Turley S, Sandkvist M, Hol WGJ. Calcium is essential for the major pseudopilin in the type 2 secretion system. J Biol Chem 2009; 284:25466-70. [PMID: 19640838 DOI: 10.1074/jbc.c109.037655] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The pseudopilus is a key feature of the type 2 secretion system (T2SS) and is made up of multiple pseudopilins that are similar in fold to the type 4 pilins. However, pilins have disulfide bridges, whereas the major pseudopilins of T2SS do not. A key question is therefore how the pseudopilins, and in particular, the most abundant major pseudopilin, GspG, obtain sufficient stability to perform their function. Crystal structures of Vibrio cholerae, Vibrio vulnificus, and enterohemorrhagic Escherichia coli (EHEC) GspG were elucidated, and all show a calcium ion bound at the same site. Conservation of the calcium ligands fully supports the suggestion that calcium ion binding by the major pseudopilin is essential for the T2SS. Functional studies of GspG with mutated calcium ion-coordinating ligands were performed to investigate this hypothesis and show that in vivo protease secretion by the T2SS is severely impaired. Taking all evidence together, this allows the conclusion that, in complete contrast to the situation in the type 4 pili system homologs, in the T2SS, the major protein component of the central pseudopilus is dependent on calcium ions for activity.
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Affiliation(s)
- Konstantin V Korotkov
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, Washington 98195, USA
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37
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Averhoff B. Shuffling genes around in hot environments: the unique DNA transporter ofThermus thermophilus. FEMS Microbiol Rev 2009; 33:611-26. [DOI: 10.1111/j.1574-6976.2008.00160.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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38
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Allemand JF, Maier B. Bacterial translocation motors investigated by single molecule techniques. FEMS Microbiol Rev 2009; 33:593-610. [PMID: 19243443 DOI: 10.1111/j.1574-6976.2009.00166.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Translocation of DNA and protein fibers through narrow constrictions is a ubiquitous and crucial activity of bacterial cells. Bacteria use specialized machines to support macromolecular movement. A very important step toward a mechanistic understanding of these translocation machines is the characterization of their physical properties at the single molecule level. Recently, four bacterial transport processes have been characterized by nanomanipulation at the single molecule level, DNA translocation by FtsK and SpoIIIE, DNA import during transformation, and the related process of a type IV pilus retraction. With all four processes, the translocation rates, processivity, and stalling forces were remarkably high as compared with single molecule experiments with other molecular motors. Although substrates of all four processes proceed along a preferential direction of translocation, directionality has been shown to be controlled by distinct mechanisms.
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39
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Marczak M, Mazur A, Gruszecki WI, Skorupska A. PssO, a unique extracellular protein important for exopolysaccharide synthesis in Rhizobium leguminosarum bv. trifolii. Biochimie 2008; 90:1781-90. [PMID: 18835420 DOI: 10.1016/j.biochi.2008.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 08/25/2008] [Indexed: 11/29/2022]
Abstract
Synthesis and secretion of polysaccharides by Gram-negative bacteria are a result of a concerted action of enzymatic and channel-forming proteins localized in different compartments of the cell. The presented work comprises functional characterization of PssO protein encoded within the previously identified, chromosomal exopolysaccharide (EPS) biosynthesis region (Pss-I) of symbiotic bacterium Rhizobium leguminosarum bv. trifolii TA1 (RtTA1). pssO gene localization between pssN and pssP genes encoding proteins engaged in exopolysaccharide synthesis and transport, suggested its role in EPS synthesis and/or secretion. RtTA1 pssO deletion mutant and the PssO protein overproducing strains were constructed. The mutant strain was EPS-deficient, however, this mutation was not complemented. The PssO-overproducing strain was characterized by increase in EPS secretion. Subcellular fractionation, pssO-phoA/lacZ translational fusion analyses and immunolocalisation of PssO on RtTA1 cell surface by electron microscopy demonstrated that PssO is secreted to the extracellular medium and remains attached to the cell. Western blotting analysis revealed the presence of immunologically related proteins within the species R. leguminosarum bv. trifolii, bv. viciae and Rhizobium etli. The secondary structure of PssO-His(6), as determined by FTIR spectroscopy, consists of at least 32% alpha-helical and 12% beta-sheet structures. A putative function of PssO in EPS synthesis and/or transport is discussed in the context of its cellular localization and the phenotypes of the deletion mutant and pssO-overexpressing strain.
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Affiliation(s)
- M Marczak
- Department of Genetics and Microbiology, Institute of Microbiology and Biotechnology, Maria Curie-Skłodowska University, Lublin, Poland
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40
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Novel proteins that modulate type IV pilus retraction dynamics in Pseudomonas aeruginosa. J Bacteriol 2008; 190:7022-34. [PMID: 18776014 DOI: 10.1128/jb.00938-08] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas aeruginosa uses type IV pili to colonize various materials and for surface-associated twitching motility. We previously identified five phylogenetically distinct alleles of pilA in P. aeruginosa, four of which occur in genetic cassettes with specific accessory genes (J. V. Kus, E. Tullis, D. G. Cvitkovitch, and L. L. Burrows, Microbiology 150:1315-1326, 2004). Each of the five pilin alleles, with and without its associated pilin accessory gene, was used to complement a group II PAO1 pilA mutant. Expression of group I or IV pilA genes restored twitching motility to the same extent as the PAO1 group II pilin. In contrast, poor twitching resulted from complementation with group III or group V pilA genes but increased significantly when the cognate tfpY or tfpZ accessory genes were cointroduced. The enhanced motility was linked to an increase in recoverable surface pili and not to alterations in total pilin pools. Expression of the group III or V pilins in a PAO1 pilA-pilT double mutant yielded large amounts of surface pili, regardless of the presence of the accessory genes. Therefore, poor piliation in the absence of the TfpY and TfpZ accessory proteins results from a net increase in PilT-mediated retraction. Similar phenotypes were observed for tfpY single and tfpY-pilT double knockout mutants of group III strain PA14. A PilAV-TfpY chimera produced few surface pili, showing that the accessory proteins are specific for their cognate pilin. The genetic linkage between specific pilin and accessory genes may be evolutionarily conserved because the accessory proteins increase pilus expression on the cell surface, thereby enhancing function.
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41
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Korotkov KV, Hol WGJ. Structure of the GspK-GspI-GspJ complex from the enterotoxigenic Escherichia coli type 2 secretion system. Nat Struct Mol Biol 2008; 15:462-8. [PMID: 18438417 DOI: 10.1038/nsmb.1426] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2007] [Accepted: 04/01/2008] [Indexed: 11/09/2022]
Abstract
Gram-negative bacteria translocate various proteins including virulence factors across their outer membrane via type 2 secretion systems (T2SSs). T2SSs are thought to contain a pseudopilus, a subcomplex formed by one major and several minor pseudopilins. We report the crystal structure of the complex formed by three minor pseudopilins from enterotoxigenic Escherichia coli. The GspK-GspI-GspJ complex has quasihelical characteristics and an architecture consistent with a localization at the pseudopilus tip. The alpha-domain of GspK has a previously unobserved fold with an unexpected dinuclear metal binding site. The area surrounding its disulfide bridge is conserved and might interact with other T2SS components or with secreted proteins.
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Affiliation(s)
- Konstantin V Korotkov
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Box 357742, Seattle, Washington 98195, USA
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42
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Hazes B, Frost L. Towards a systems biology approach to study type II/IV secretion systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2008; 1778:1839-50. [PMID: 18406342 DOI: 10.1016/j.bbamem.2008.03.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Revised: 02/22/2008] [Accepted: 03/17/2008] [Indexed: 10/22/2022]
Abstract
Many gram-negative bacteria produce thin protein filaments, named pili, which extend beyond the confines of the outer membrane. The importance of these pili is illustrated by the fact that highly complex, multi-protein pilus-assembly machines have evolved, not once, but several times. Their many functions include motility, adhesion, secretion, and DNA transfer, all of which can contribute to the virulence of bacterial pathogens or to the spread of virulence factors by horizontal gene transfer. The medical importance has stimulated extensive biochemical and genetic studies but the assembly and function of pili remains an enigma. It is clear that progress in this field requires a more holistic approach where the entire molecular apparatus that forms the pilus is studied as a system. In recent years systems biology approaches have started to complement classical studies of pili and their assembly. Moreover, continued progress in structural biology is building a picture of the components that make up the assembly machine. However, the complexity and multiple-membrane spanning nature of these secretion systems pose formidable technical challenges, and it will require a concerted effort before we can create comprehensive and predictive models of these remarkable molecular machines.
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Affiliation(s)
- Bart Hazes
- Department of Medical Microbiology and Immunology, University of Alberta, Edmonton, Alberta, Canada
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Structure of the minor pseudopilin EpsH from the Type 2 secretion system of Vibrio cholerae. J Mol Biol 2008; 377:91-103. [PMID: 18241884 PMCID: PMC2275911 DOI: 10.1016/j.jmb.2007.08.041] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2007] [Revised: 08/16/2007] [Accepted: 08/16/2007] [Indexed: 01/07/2023]
Abstract
Many Gram-negative bacteria use the multi-protein type II secretion system (T2SS) to selectively translocate virulence factors from the periplasmic space into the extracellular environment. In Vibrio cholerae the T2SS is called the extracellular protein secretion (Eps) system,which translocates cholera toxin and several enzymes in their folded state across the outer membrane. Five proteins of the T2SS, the pseudopilins, are thought to assemble into a pseudopilus, which may control the outer membrane pore EpsD, and participate in the active export of proteins in a "piston-like" manner. We report here the 2.0 A resolution crystal structure of an N-terminally truncated variant of EpsH, a minor pseudopilin from Vibrio cholerae. While EpsH maintains an N-terminal alpha-helix and C-terminal beta-sheet consistent with the type 4a pilin fold, structural comparisons reveal major differences between the minor pseudopilin EpsH and the major pseudopilin GspG from Klebsiella oxytoca: EpsH contains a large beta-sheet in the variable domain, where GspG contains an alpha-helix. Most importantly, EpsH contains at its surface a hydrophobic crevice between its variable and conserved beta-sheets, wherein a majority of the conserved residues within the EpsH family are clustered. In a tentative model of a T2SS pseudopilus with EpsH at its tip, the conserved crevice faces away from the helix axis. This conserved surface region may be critical for interacting with other proteins from the T2SS machinery.
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Shimoda E, Muto T, Horiuchi T, Furuya N, Komano T. Novel class of mutations of pilS mutants, encoding plasmid R64 type IV prepilin: interface of PilS-PilV interactions. J Bacteriol 2008; 190:1202-8. [PMID: 18065540 PMCID: PMC2238207 DOI: 10.1128/jb.01204-07] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2007] [Accepted: 11/21/2007] [Indexed: 12/25/2022] Open
Abstract
The type IV pili of plasmid R64 belonging to the type IVB group are required only for liquid mating. They consist of the major and minor components PilS pilin and PilV adhesin, respectively. PilS pilin is first synthesized as a 22-kDa prepilin from the pilS gene and is then processed to a 19-kDa mature pilin by PilU prepilin peptidase. In a previous genetic analysis, we identified four classes of the pilS mutants (T. Horiuchi and T. Komano, J. Bacteriol. 180:4613-4620, 1998). The products of the class I pilS mutants were not processed by prepilin peptidase; the products of the class II mutants were not secreted; in the class III mutants type IV pili with reduced activities in liquid mating were produced; and in the class IV mutants type IV pili with normal activities were produced. Here, we describe a novel class, class V, of pilS mutants. Mutations in the pilS gene at Gly-56 or Tyr-57 produced type IV pili lacking PilV adhesin, which were inactive in liquid mating. Residues 56 and 57 of PilS pilin are suggested to function as an interface of PilS-PilV interactions.
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Affiliation(s)
- Eriko Shimoda
- Department of Biology, Tokyo Metropolitan University, Minamiohsawa, Hachioji, Tokyo 192-0397, Japan
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45
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Yanez ME, Korotkov KV, Abendroth J, Hol WGJ. The crystal structure of a binary complex of two pseudopilins: EpsI and EpsJ from the type 2 secretion system of Vibrio vulnificus. J Mol Biol 2008; 375:471-86. [PMID: 18022192 PMCID: PMC2219201 DOI: 10.1016/j.jmb.2007.10.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 10/10/2007] [Accepted: 10/12/2007] [Indexed: 11/20/2022]
Abstract
Type II secretion systems (T2SS) translocate virulence factors from the periplasmic space of many pathogenic bacteria into the extracellular environment. The T2SS of Vibrio cholerae and related species is called the extracellular protein secretion (Eps) system that consists of a core of multiple copies of 11 different proteins. The pseudopilins, EpsG, EpsH, EpsI, EpsJ and EpsK, are five T2SS proteins that are thought to assemble into a pseudopilus, which is assumed to interact with the outer membrane pore, and may actively participate in the export of proteins. We report here biochemical evidence that the minor pseudopilins EpsI and EpsJ from Vibrio species interact directly with one another. Moreover, the 2.3 A resolution crystal structure of a complex of EspI and EpsJ from Vibrio vulnificus represents the first atomic resolution structure of a complex of two different pseudopilin components from the T2SS. Both EpsI and EpsJ appear to be structural extremes within the family of type 4a pilin structures solved to date, with EpsI having the smallest, and EpsJ the largest, "variable pilin segment" seen thus far. A high degree of sequence conservation in the EpsI:EpsJ interface indicates that this heterodimer occurs in the T2SS of a large number of bacteria. The arrangement of EpsI and EpsJ in the heterodimer would correspond to a right-handed helical character of proteins assembled into a pseudopilus.
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Affiliation(s)
- Marissa E Yanez
- Department of Biochemistry, Biomolecular Structure Center, University of Washington, Box 357742, Seattle, WA 98195, USA
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46
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Li J, Lim MS, Li S, Brock M, Pique ME, Woods VL, Craig L. Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry. Structure 2008; 16:137-48. [PMID: 18184591 PMCID: PMC2238685 DOI: 10.1016/j.str.2007.10.027] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2007] [Revised: 10/05/2007] [Accepted: 10/13/2007] [Indexed: 10/22/2022]
Abstract
The bacterial pathogen Vibrio cholerae uses toxin-coregulated pili (TCP) to colonize the human intestine, causing the severe diarrheal disease cholera. TCP are long, thin, flexible homopolymers of the TcpA subunit that self-associate to hold cells together in microcolonies and serve as the receptor for the cholera toxin phage. To better understand TCP's roles in pathogenesis, we characterized its structure using hydrogen/deuterium exchange mass spectrometry and computational modeling. We show that the pilin subunits are held together by tight packing of the N-terminal alpha helices, but loose packing of the C-terminal globular domains leaves substantial gaps on the filament surface. These gaps expose a glycine-rich, amphipathic segment of the N-terminal alpha-helix, contradicting the consensus view that this region is buried in the filament core. Our results explain extreme filament flexibility, suggest a molecular basis for pilus-pilus interactions, and reveal a previously unrecognized therapeutic target for V. cholerae and other enteric pathogens.
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Affiliation(s)
- Juliana Li
- Molecular Biology and Biochemistry Department, Simon Fraser University, 8888 University Dr., Burnaby, BC Canada V5A 1S6
| | - Mindy S. Lim
- Molecular Biology and Biochemistry Department, Simon Fraser University, 8888 University Dr., Burnaby, BC Canada V5A 1S6
| | - Sheng Li
- Department of Medicine and Biomedical Sciences Graduate Program, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0656, USA
| | - Melissa Brock
- Department of Medicine and Biomedical Sciences Graduate Program, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0656, USA
| | - Michael E. Pique
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA
| | - Virgil L. Woods
- Department of Medicine and Biomedical Sciences Graduate Program, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0656, USA
| | - Lisa Craig
- Molecular Biology and Biochemistry Department, Simon Fraser University, 8888 University Dr., Burnaby, BC Canada V5A 1S6
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47
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Kao DJ, Churchill MEA, Irvin RT, Hodges RS. Animal protection and structural studies of a consensus sequence vaccine targeting the receptor binding domain of the type IV pilus of Pseudomonas aeruginosa. J Mol Biol 2007; 374:426-42. [PMID: 17936788 DOI: 10.1016/j.jmb.2007.09.032] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Revised: 08/27/2007] [Accepted: 09/11/2007] [Indexed: 11/15/2022]
Abstract
One of the main obstacles in the development of a vaccine against Pseudomonas aeruginosa is the requirement that it is protective against a wide range of virulent strains. We have developed a synthetic-peptide consensus-sequence vaccine (Cs1) that targets the host receptor-binding domain (RBD) of the type IV pilus of P. aeruginosa. Here, we show that this vaccine provides increased protection against challenge by the four piliated strains that we have examined (PAK, PAO, KB7 and P1) in the A.BY/SnJ mouse model of acute P. aeruginosa infection. To further characterize the consensus sequence, we engineered Cs1 into the PAK monomeric pilin protein and determined the crystal structure of the chimeric Cs1 pilin to 1.35 A resolution. The substitutions (T130K and E135P) used to create Cs1 do not disrupt the conserved backbone conformation of the pilin RBD. In fact, based on the Cs1 pilin structure, we hypothesize that the E135P substitution bolsters the conserved backbone conformation and may partially explain the immunological activity of Cs1. Structural analysis of Cs1, PAK and K122-4 pilins reveal substitutions of non-conserved residues in the RBD are compensated for by complementary changes in the rest of the pilin monomer. Thus, the interactions between the RBD and the rest of the pilin can either be mediated by polar interactions of a hydrogen bond network in some strains or by hydrophobic interactions in others. Both configurations maintain a conserved backbone conformation of the RBD. Thus, the backbone conformation is critical in our consensus-sequence vaccine design and that cross-reactivity of the antibody response may be modulated by the composition of exposed side-chains on the surface of the RBD. This structure will guide our future vaccine design by focusing our investigation on the four variable residue positions that are exposed on the RBD surface.
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Affiliation(s)
- Daniel J Kao
- Department of Biochemistry and Molecular Genetics, University of Colorado at Denver and Health Sciences Center, Biomolecular Structure, MS 8101, P.O. Box 6511, Aurora, CO 80045, USA
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48
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Pier G. Application of vaccine technology to prevention of Pseudomonas aeruginosa infections. Expert Rev Vaccines 2007; 4:645-56. [PMID: 16221066 DOI: 10.1586/14760584.4.5.645] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Development of an effective vaccine against the multiple presentations of Pseudomonas aeruginosa infection, including nosocomial pneumonia, bloodstream infections, chronic lung infections in cystic fibrosis patients and potentially sight-threatening keratitis in users of contact lenses, is a high priority. As with vaccine development for any pathogen, key information about the most effective immunologic effectors of immunity and target antigens needs to be established. For P. aeruginosa, although there is a role for cell-mediated immunity in animals following active vaccination, the bulk of the data indicate that opsonically-active antibodies provide the most effective mediators of acquired immunity. Major target antigens include the lipopolysaccharide O-polysaccharides, cell-surface alginate, flagella, components of the Type III secretion apparatus and outer membrane proteins with a potentially additive effect achieved by including immune effectors to toxins and proteases. A variety of active vaccination approaches have the potential for efficacy such as vaccination with purified or recombinant antigens incorporating multiple epitopes, conjugate vaccines incorporating proteins and carbohydrate antigens, and live attenuated vaccines, including heterologous antigen delivery systems expressing immunogenic P. aeruginosa antigens. A diverse range of passive immunotherapeutic approaches are also candidates for effective immunity, with a variety of human monoclonal antibodies described over the years with good preclinical efficacy and some early Phase I and II studies in humans. Finding an effective active and/or passive vaccination strategy for P. aeruginosa infections could be realized in the next 5 to 10 years, but will require that advances are made in the understanding of antigen expression and immune effectors that work in different human tissues and clinical settings, and also require a means to validate that clinical outcomes achieved in Phase III trials represent meaningful advances in management and treatment of P. aeruginosa infections.
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Affiliation(s)
- Gerald Pier
- Brigham and Women's Hospital, Department of Medicine, Harvard Medical School, Boston, MA 02115, USA.
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Abstract
Bacterial adhesion is often a prelude to infection. In many cases, this process is governed by protein-carbohydrate interactions. Intervention at this early stage of infection is a conceptually highly attractive alternative to conventional antibiotics that are increasingly prone to resistance. The lack of high-affinity inhibitors of adhesion has proven to be a hurdle for further exploitation of this concept; however, new developments indicate a positive change. Structure-based design at the monovalent level and also evaluation of glycodendrimers and glycopolymers have yielded structures of high affinity. In addition to the development of inhibitors, topics of this review include available structural information of adhesion proteins, carbohydrate specificities of the various pathogens and their adhesion proteins. Other new developments aimed at affecting bacterial adhesion and the use of the adhesins for bacterial detection are also discussed.
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Affiliation(s)
- Roland J Pieters
- Department of Medicinal Chemistry and Chemical Biology, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, NL-3508 TB Utrecht, The Netherlands.
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50
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Ng SYM, Chaban B, Jarrell KF. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J Mol Microbiol Biotechnol 2006; 11:167-91. [PMID: 16983194 DOI: 10.1159/000094053] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The archaeal flagellum is a unique motility organelle. While superficially similar to the bacterial flagellum, several similarities have been reported between the archaeal flagellum and the bacterial type IV pilus system. These include the multiflagellin nature of the flagellar filament, N-terminal sequence similarities between archaeal flagellins and bacterial type IV pilins, as well as the presence of homologous proteins in the two systems. Recent advances in archaeal flagella research add to the growing list of similarities. First, the preflagellin peptidase that is responsible for processing the N-terminal signal peptide in preflagellins has been identified. The preflagellin peptidase is a membrane-bound enzyme topologically similar to its counterpart in the type IV pilus system (prepilin peptidase); the two enzymes are demonstrated to utilize the same catalytic mechanism. Second, it has been suggested that the archaeal flagellum and the bacterial type IV pilus share a similar mode of assembly. While bacterial flagellins and type IV pilins can be modified with O-linked glycans, N-linked glycans have recently been reported on archaeal flagellins. This mode of glycosylation, as well as the observation that the archaeal flagellum lacks a central channel, are both consistent with the proposed assembly model. On the other hand, the failure to identify other genes involved in archaeal flagellation by homology searches likely implies a novel aspect of the archaeal flagellar system. These interesting features remain to be deciphered through continued research. Such knowledge would be invaluable to motility and protein export studies in the Archaea.
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Affiliation(s)
- Sandy Y M Ng
- Department of Microbiology and Immunology, Queen's University, Kingston, Canada
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