Gabriel Waksman

Birkbeck, University of London, Londinium, England, United Kingdom

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Publications (191)1541.7 Total impact

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    ABSTRACT: Types 1 and P pili are prototypical bacterial cell-surface appendages playing essential roles in mediating adhesion of bacteria to the urinary tract. These pili, assembled by the chaperone-usher pathway, are polymers of pilus subunits assembling into two parts: a thin, short tip fibrillum at the top, mounted on a long pilus rod. The rod adopts a helical quaternary structure and is thought to play essential roles: its formation may drive pilus extrusion by preventing backsliding of the nascent growing pilus within the secretion pore; the rod also has striking spring-like properties, being able to uncoil and recoil depending on the intensity of shear forces generated by urine flow. Here, we present an atomic model of the P pilus generated from a 3.8 Å resolution cryo-electron microscopy reconstruction. This structure provides the molecular basis for the rod's remarkable mechanical properties and illuminates its role in pilus secretion.
    Full-text · Article · Jan 2016 · Cell
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    ABSTRACT: The adaptor protein Grb2 is a key element of mitogenetically important signaling pathways. With its SH2 domain it binds to upstream targets while its SH3 domains bind to downstream proteins thereby relaying signals from the cell membranes to the nucleus. The Grb2 SH2 domain binds to its targets by recognizing a phosphotyrosine (pY) in a pYxNx peptide motif, requiring an Asn at the +2 position C-terminal to the pY with the residue either side of this Asn being hydrophobic. Structural analysis of the Grb2 SH2 domain in complex with its cognate peptide has shown that the peptide adopts a unique β-turn conformation, unlike the extended conformation that phosphopeptides adopt when bound to other SH2 domains. TrpEF1 (W121) is believed to force the peptide into this unusual conformation conferring this unique specificity to the Grb2 SH2 domain. Using X-ray crystallography, electron paramagnetic resonance (EPR) spectroscopy, and isothermal titration calorimetry (ITC), we describe here a series of experiments that explore the role of TrpEF1 in determining the specificity of the Grb2 SH2 domain. Our results demonstrate that the ligand does not adopt a pre-organized structure before binding to the SH2 domain, rather it is the interaction between the two that imposes the hairpin loop to the peptide. Furthermore, we find that the peptide adopts a similar structure when bound to both the wild-type Grb2 SH2 domain and a TrpEF1Gly mutant. This suggests that TrpEF1 is not the determining factor for the conformation of the phosphopeptide. This article is protected by copyright. All rights reserved.
    No preview · Article · Dec 2015 · Protein Science
  • Vidya Chandran Darbari · Gabriel Waksman
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    ABSTRACT: Type IV secretion systems (T4SSs) are large multisubunit translocons, found in both gram-negative and gram-positive bacteria and in some archaea. These systems transport a diverse array of substrates from DNA and protein-DNA complexes to proteins, and play fundamental roles in both bacterial pathogenesis and bacterial adaptation to the cellular milieu in which bacteria live. This review describes the various biochemical and structural advances made toward understanding the biogenesis, architecture, and function of T4SSs.
    No preview · Article · Jun 2015 · Annual review of biochemistry
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    ABSTRACT: Studying biomolecules at atomic resolution in their native environment is the ultimate aim of structural biology. We investigated the bacterial type IV secretion system core complex (T4SScc) by cellular dynamic nuclear polarization-based solid-state nuclear magnetic resonance spectroscopy to validate a structural model previously generated by combining in vitro and in silico data. Our results indicate that T4SScc is well folded in the cellular setting, revealing protein regions that had been elusive when studied in vitro.
    Full-text · Article · May 2015 · Nature Methods
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    ABSTRACT: Bacteria have evolved a remarkable array of sophisticated nanomachines to export various virulence factors across the bacterial cell envelope. In recent years, considerable progress has been made towards elucidating the structural and molecular mechanisms of the six secretion systems (types I-VI) of Gram-negative bacteria, the unique mycobacterial type VII secretion system, the chaperone-usher pathway and the curli secretion machinery. These advances have greatly enhanced our understanding of the complex mechanisms that these macromolecular structures use to deliver proteins and DNA into the extracellular environment or into target cells. In this Review, we explore the structural and mechanistic relationships between these single- and double-membrane-embedded systems, and we briefly discuss how this knowledge can be exploited for the development of new antimicrobial strategies.
    Full-text · Article · May 2015 · Nature Reviews Microbiology
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    Aravindan Ilangovan · Sarah Connery · Gabriel Waksman
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    ABSTRACT: Conjugation, the process by which plasmid DNA is transferred from one bacterium to another, is mediated by type IV secretion systems (T4SSs). T4SSs are versatile systems that can transport not only DNA, but also toxins and effector proteins. Conjugative T4SSs comprise 12 proteins named VirB1-11 and VirD4 that assemble into a large membrane-spanning exporting machine. Before being transported, the DNA substrate is first processed on the cytoplasmic side by a complex called the relaxosome. The substrate is then targeted to the T4SS for export into a recipient cell. In this review, we describe the recent progress made in the structural biology of both the relaxosome and the T4SS. Copyright © 2015 Elsevier Ltd. All rights reserved.
    Full-text · Article · Mar 2015 · Trends in Microbiology
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    Andreas Busch · Gilles Phan · Gabriel Waksman
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    ABSTRACT: The formation of adhesive surface structures called pili or fimbriae ('bacterial hair') is an important contributor towards bacterial pathogenicity and persistence. To fight often chronic or recurrent bacterial infections such as urinary tract infections, it is necessary to understand the molecular mechanism of the nanomachines assembling such pili. Here, we focus on the so far best-known pilus assembly machinery: the chaperone-usher pathway producing the type 1 and P pili, and highlight the most recently acquired structural knowledge. First, we describe the subunits' structure and the molecular role of the periplasmic chaperone. Second, we focus on the outer-membrane usher structure and the catalytic mechanism of usher-mediated pilus biogenesis. Finally, we describe how the detailed understanding of the chaperone-usher pathway at a molecular level has paved the way for the design of a new generation of bacterial inhibitors called 'pilicides'. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
    Full-text · Article · Mar 2015 · Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences
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    ABSTRACT: In view of the relentless increase in antibiotic resistance in human pathogens, efforts are needed to safeguard our future therapeutic options against infectious diseases. In addition to regulatory changes in our antibiotic use, this will have to include the development of new therapeutic compounds. One area that has received growing attention in recent years is the possibility to treat or prevent infections by targeting the virulence mechanisms that render bacteria pathogenic. Antivirulence targets include bacterial adherence, secretion of toxic effector molecules, bacterial persistence through biofilm formation, quorum sensing and immune evasion. Effective small molecule compounds have already been identified that suppress such processes. In this review we discuss the susceptibility of such compounds to the development of resistance, by comparison with known resistance mechanisms observed for classical bacteriostatic or -lytic antibiotics, and by review of available experimental case studies. Unfortunately, appearance of resistance mechanisms has already been demonstrated for some, showing that the quest of new, lasting drugs remains complicated. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    No preview · Article · Jan 2015 · Chemical Biology & Drug Design
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    ABSTRACT: Pseudomonas aeruginosa is a Gram-negative opportunistic bacterium, synonymous with cystic fibrosis patients, which can cause chronic infection of the lungs. This pathogen is a model organism to study biofilms: a bacterial population embedded in an extracellular matrix that provide protection from environmental pressures and lead to persistence. A number of chaperone-usher pathways, namely CupA-CupE, play key roles in these processes by assembling adhesive pili on the bacterial surface. One of these, encoded by the cupB operon, is unique as it contains a non-chaperone-usher gene product, CupB5. Two-partner secretion (TPS) systems are comprised of a C-terminal integral membrane β-barrel pore with tandem N-terminal POTRA (polypeptide transport associated) domains located in the periplasm (TpsB) and a secreted substrate (TpsA). Using NMR we show that TpsB4 (LepB) interacts with CupB5 and its predicted cognate partner TpsA4 (LepA), an extracellular protease. Moreover, using cellular studies we confirm that TpsB4 can translocate CupB5 across the P. aeruginosa outer membrane, which contrasts a previous observation that suggested the CupB3 P-usher secretes CupB5. In support of our findings we also demonstrate that tps4/cupB operons are co-regulated by the RocS1 sensor suggesting P. aeruginosa has developed synergy between these systems. Furthermore, we have determined the solution-structure of the TpsB4-POTRA1 domain and together with restraints from NMR chemical shift mapping and in vivo mutational analysis we have calculated models for the entire TpsB4 periplasmic region in complex with both TpsA4 and CupB5 secretion motifs. The data highlight specific residues for TpsA4/CupB5 recognition by TpsB4 in the periplasm and suggest distinct roles for each POTRA domain. This article is protected by copyright. All rights reserved.
    Full-text · Article · Jan 2015 · Protein Science
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    Adam Redzej · Gabriel Waksman · Elena V. Orlova
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    ABSTRACT: Type IV secretion (T4S) systems are large dynamic nanomachines that transport DNA and/or proteins through the membranes of bacteria. Analysis of T4S system architecture is an extremely challenging task taking into account their multi protein organisation and lack of overall global symmetry. Nonetheless the last decade demonstrated an amazing progress achieved by X-ray crystallography and cryo-electron microscopy. In this review we present a structural analysis of this dynamic complex based on recent advances in biochemical, biophysical and structural studies.
    Full-text · Article · Jan 2015 · AIMS Biophysics
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    Full-text · Dataset · Dec 2014
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    Full-text · Dataset · Nov 2014
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    Full-text · Dataset · Nov 2014
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    ABSTRACT: eLife digest Escherichia coli is a bacterium that commonly lives in the intestines of mammals, including humans, where it is usually harmless and can even be beneficial to its host. However, some types of E. coli produce hair-like filaments called P pili that allow the bacteria to attach to the human urinary tract and cause disease. To pass through the outer membrane of the E. coli cell, the filaments have to travel through a protein in the membrane called PapC usher. The PapC usher protein—which is also involved in the assembly of the P pili filaments—contains a tube-like part called a β-barrel that is usually blocked by another part of the protein called the ‘plug domain’. For the P pili to pass through the β-barrel, the plug domain has to move. This movement is controlled by two parts of the PapC protein, known as the α-helix and the β-hairpin, but it is not clear how. To address this question, Farabella et al. made computer models of the normal PapC protein and versions that lacked the α-helix and/or the β-hairpin. Looking at these structural models and analyzing the evolution of PapC proteins helped to predict that certain regions of the β-barrel may be involved in controlling the movement of the plug domain, and this was then confirmed experimentally. Farabella et al. propose that these regions—together with the α-helix and β-hairpin—control the opening and closing of the β-barrel. Further work is needed to investigate how other parts of the PapC protein are involved in P pili formation. These new insights could prove useful in the development of alternative treatments to fight bacterial infection. DOI: http://dx.doi.org/10.7554/eLife.03532.002
    Full-text · Article · Oct 2014 · eLife Sciences
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    ABSTRACT: A novel series of 8-amino imidazo[1,2-a] pyrazine derivatives has been developed as inhibitors of the VirB11 ATPase HP0525, a key component of the bacterial type IV secretion system. A flexible synthetic route to both 2- and 3-aryl substituted regioisomers has been developed. The resulting series of imidazo[1,2-a] pyrazines has been used to probe the structure-activity relationships of these inhibitors, which show potential as antibacterial agents. (C) 2014 The Authors. Published by Elsevier Ltd.
    Full-text · Article · Sep 2014 · Bioorganic & Medicinal Chemistry
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    Tamir Gonen · Gabriel Waksman

    Full-text · Article · Sep 2014 · Current Opinion in Structural Biology
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    ABSTRACT: Bacteria use type IV secretion (T4S) systems to deliver DNA and protein substrates to a diverse range of prokaryotic and eukaryotic target cells. T4S systems have great impact on human health, as they are a major source of antibiotic resistance spread among bacteria and are central to infection processes of many pathogens. Therefore, deciphering the structure and underlying translocation mechanism of T4S systems is crucial to facilitate development of new drugs. The last five years have witnessed considerable progress in unraveling the structure of T4S system subassemblies, notably that of the T4S system core complex, a large 1 MegaDalton (MDa) structure embedded in the double membrane of Gram-negative bacteria and made of 3 of the 12 T4S system components. However, the recent determination of the structure of ∼3 MDa assembly of 8 of these components has revolutionized our views of T4S system architecture and opened up new avenues of research, which are discussed in this review.
    Preview · Article · Aug 2014 · Current Opinion in Structural Biology
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    David Steadman · Alvin Lo · Gabriel Waksman · Han Remaut
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    ABSTRACT: The rise of multidrug resistant bacteria is a major worldwide health concern. There is currently an unmet need for the development of new and selective antibacterial drugs. Therapies that target and disarm the crucial virulence factors of pathogenic bacteria, while not actually killing the cells themselves, could prove to be vital for the treatment of numerous diseases. This article discusses the main surface architectures of pathogenic Gram-negative bacteria and the small molecules that have been discovered, which target their specific biogenesis pathways and/or actively block their virulence. The future perspective for the use of antivirulence compounds is also assessed.
    Full-text · Article · Jul 2014 · Future Microbiology
  • James Lillington · Sebastian Geibel · Gabriel Waksman
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    ABSTRACT: Uropathogenic Escherichia coli (UPEC) cause urinary tract infections (UTIs) in approximately 50% of women. These bacteria use type 1 and P pili for host recognition and attachment. These pili are assembled by the chaperone-usher pathway of pilus biogenesis. The review examines the biogenesis and adhesion of the UPEC type 1 and P pili. Particular emphasis is drawn to the role of the outer membrane usher protein. The structural properties of the complete pilus are also examined to highlight the strength and functionality of the final assembly. The usher orchestrates the sequential addition of pilus subunits in a defined order. This process follows a subunit-incorporation cycle which consists of four steps: recruitment at the usher N-terminal domain, donor-strand exchange with the previously assembled subunit, transfer to the usher C-terminal domains and translocation of the nascent pilus. Adhesion by the type 1 and P pili is strengthened by the quaternary structure of their rod sections. The rod is endowed with spring-like properties which provide mechanical resistance against urine flow. The distal adhesins operate differently from one another, targeting receptors in a specific manner. The biogenesis and adhesion of type 1 and P pili are being therapeutically targeted, and efforts to prevent pilus growth or adherence are described. The combination of structural and biochemical study has led to the detailed mechanistic understanding of this membrane spanning nano-machine. This can now be exploited to design novel drugs able to inhibit virulence. This is vital in the present era of resurgent antibiotics resistance. This article is part of a Special Issue entitled Structural biochemistry and biophysics of membrane proteins.
    No preview · Article · May 2014 · Biochimica et Biophysica Acta

Publication Stats

10k Citations
1,541.70 Total Impact Points

Institutions

  • 2004-2016
    • Birkbeck, University of London
      • Institute of Structural and Molecular Biology
      Londinium, England, United Kingdom
  • 2004-2015
    • The Institute of Structural and Molecular Biology
      Londinium, England, United Kingdom
    • University College London
      • • Institute of Structural and Molecular Biology
      • • Department of Structural and Molecular Biology
      Londinium, England, United Kingdom
  • 2010
    • MRC National Institute for Medical Research
      • Division of Molecular Structure
      Londinium, England, United Kingdom
  • 2009
    • Harvard Medical School
      Boston, Massachusetts, United States
  • 1997-2009
    • Washington University in St. Louis
      • • Department of Pediatrics
      • • Department of Biochemistry and Molecular Biophysics
      San Luis, Missouri, United States
  • 2005
    • Universität Basel
      Bâle, Basel-City, Switzerland
  • 2002
    • Vrije Universiteit Brussel
      Bruxelles, Brussels Capital, Belgium
  • 1999
    • Howard Hughes Medical Institute
      Ashburn, Virginia, United States
  • 1992
    • The Rockefeller University
      New York, New York, United States