Dr. Wendy Smith

Senior Research Associate

I am a research associate based in our wet lab in the Centre for Bacterial Cell Biology, Newcastle University. I studied Medical Microbiology at Newcastle University and my PhD was analysing functional genomics of group A streptococcal virulence factors.

My initial research involved investigating the mechanisms of pathogenicity utilized by the Gram positive bacteria Streptococcus pyogenes. This experience equipped me with considerable expertise in the physiology/molecular biology of Gram-positive bacteria.

I first encountered the concept of synthetic biology (at local seminars) in the context of a Gram-positive bacterium (Bacillus subtilis) and my interest stemmed initially from recognizing that this was a completely new and ‘exciting’ area, where I could make a valuable contribution exploiting my existing expertise.

I have now extended my interests into the field of synthetic biology and am specifically researching into synthetic quorum peptide mediated communication systems in Bacillus subtilis.

Research Interests

  • Synthetic biology
  • Molecular biology
  • Bacterial communication systems
  • B. subtilis genomics and transcriptomics
  • Publications

    • [DOI] G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, and J. S. Hallinan, “Bacillondex: an integrated data resource for systems and synthetic biology,” J integr bioinform, vol. 10, iss. 2, pp. 224-224, 2013.
      author = "Misirli, G and Wipat, A and Mullen, J and James, K and Pocock, M and Smith, W and Allenby, N and Hallinan, J S",
      title = {BacillOndex: an integrated data resource for systems and synthetic biology},
      abstract = {BacillOndex is an extension of the Ondex data integration system, providing a semantically annotated, integrated knowledge base for the model Gram-positive bacterium Bacillus subtilis. This application allows a user to mine a variety of B. subtilis data sources, and analyse the resulting integrated dataset, which contains data about genes, gene products and their interactions. The data can be analysed either manually, by browsing using Ondex, or computationally via a Web services interface. We describe the process of creating a BacillOndex instance, and describe the use of the system for the analysis of single nucleotide polymorphisms in B. subtilis Marburg. The Marburg strain is the progenitor of the widely-used laboratory strain B. subtilis 168. We identified 27 SNPs with predictable phenotypic effects, including genetic traits for known phenotypes. We conclude that BacillOndex is a valuable tool for the systems-level investigation of, and hypothesis generation about, this important biotechnology workhorse. Such understanding contributes to our ability to construct synthetic genetic circuits in this organism.},
      journal = "J Integr Bioinform",
      year = "2013",
      volume = "10",
      number = "2",
      pages = "224-224",
      month = "",
      pmid = "23571273",
      url = "http://www.hubmed.org/display.cgi?uids=23571273",
      doi = "10.2390/biecoll-jib-2013-224"
    • [DOI] S. Bell, A. Howard, J. A. Wilson, E. L. Abbot, W. D. Smith, C. L. Townes, B. H. Hirst, and J. Hall, “Streptococcus pyogenes infection of tonsil explants is associated with a human ?-defensin 1 response from control but not recurrent acute tonsillitis patients,” Mol oral microbiol, vol. 27, iss. 3, pp. 160-171, 2012.
      author = "Bell, S and Howard, A and Wilson, J A and Abbot, E L and Smith, W D and Townes, C L and Hirst, B H and Hall, J",
      title = {Streptococcus pyogenes infection of tonsil explants is associated with a human ?-defensin 1 response from control but not recurrent acute tonsillitis patients},
      abstract = {Host defence peptides (HDP), including the defensins and hCAP-18, function as part of the innate immune defences, protecting the host epithelia from microbial attachment and invasion. Recurrent acute tonsillitis (RAT), in which patients suffer repeated symptomatic tonsil infections, is linked to Streptococcus pyogenes, a group A streptococcus, and may reflect the impaired expression of such peptides. To address this, the defensin and hCAP-18 messenger RNA expression profiles of 54 tonsils excised from control and RAT patients undergoing tonsillectomy were quantified and compared. Marked variation in expression was observed between individuals from the two groups, but statistically no significant differences were identified, suggesting that at the time of surgery the tonsil epithelial HDP barrier was not compromised in RAT subjects. Surgical removal of the tonsils occurs in a quiescent phase of disease, and so to assess the effects of an active bacterial infection, HaCaT cells an in vitro model of the tonsil epithelium, and explants of patient tonsils maintained in vitro were challenged with S. pyogenes. The HaCaT data supported the reduced expression of hCAP-18/LL-37, human ?-defensin 1 (HBD1;P < 0.01) and HBD2 (P < 0.05), consistent with decreased protection of the epithelial barrier. The tonsil explant data, although not as definitive, showed similar trends apart from HBD1 expression, which in the control tonsils but not the RAT patient tonsils was characterized by increased expression (P < 0.01). These data suggest that in vivo HBD1 may play a critical role in protecting the tonsil epithelia from S. pyogenes.},
      journal = "Mol Oral Microbiol",
      year = "2012",
      volume = "27",
      number = "3",
      pages = "160-171",
      month = "Jun",
      pmid = "22520386",
      url = "http://www.hubmed.org/display.cgi?uids=22520386",
      doi = "10.1111/j.2041-1014.2012.640.x"
    • [DOI] A. Faulds-Pain, C. Birchall, C. Aldridge, W. D. Smith, G. Grimaldi, S. Nakamura, T. Miyata, J. Gray, G. Li, J. X. Tang, K. Namba, T. Minamino, and P. D. Aldridge, "Flagellin redundancy in caulobacter crescentus and its implications for flagellar filament assembly," J bacteriol, vol. 193, iss. 11, pp. 2695-2707, 2011.
      author = "Faulds-Pain, A and Birchall, C and Aldridge, C and Smith, W D and Grimaldi, G and Nakamura, S and Miyata, T and Gray, J and Li, G and Tang, J X and Namba, K and Minamino, T and Aldridge, P D",
      title = {Flagellin redundancy in Caulobacter crescentus and its implications for flagellar filament assembly},
      abstract = {Bacterial flagella play key roles in surface attachment and host-bacterial interactions as well as driving motility. Here, we have investigated the ability of Caulobacter crescentus to assemble its flagellar filament from six flagellins: FljJ, FljK, FljL, FljM, FljN, and FljO. Flagellin gene deletion combinations exhibited a range of phenotypes from no motility or impaired motility to full motility. Characterization of the mutant collection showed the following: (i) that there is no strict requirement for any one of the six flagellins to assemble a filament; (ii) that there is a correlation between slower swimming speeds and shorter filament lengths in ?fljK ?fljM mutants; (iii) that the flagellins FljM to FljO are less stable than FljJ to FljL; and (iv) that the flagellins FljK, FljL, FljM, FljN, and FljO alone are able to assemble a filament.},
      journal = "J Bacteriol",
      year = "2011",
      volume = "193",
      number = "11",
      pages = "2695-2707",
      month = "Jun",
      pmid = "21441504",
      url = "http://www.hubmed.org/display.cgi?uids=21441504",
      doi = "10.1128/JB.01172-10"
    • [DOI] J. A. Pointon, W. D. Smith, G. Saalbach, A. Crow, M. A. Kehoe, and M. J. Banfield, "A highly unusual thioester bond in a pilus adhesin is required for efficient host cell interaction," J biol chem, vol. 285, iss. 44, pp. 33858-33866, 2010.
      author = "Pointon, J A and Smith, W D and Saalbach, G and Crow, A and Kehoe, M A and Banfield, M J",
      title = {A highly unusual thioester bond in a pilus adhesin is required for efficient host cell interaction},
      abstract = {Many bacterial pathogens present adhesins at the tips of long macromolecular filaments known as pili that are often important virulence determinants. Very little is known about how pili presented by Gram-positive pathogens mediate host cell binding. The crystal structure of a pilus adhesin from the important human pathogen Streptococcus pyogenes reveals an internal thioester bond formed between the side chains of a cysteine and a glutamine residue. The presence of the thioester was verified using UV-visible spectroscopy and mass spectrometry. This unusual bond has only previously been observed in thioester domains of complement and complement-like proteins where it is used to form covalent attachment to target molecules. The structure also reveals two intramolecular isopeptide bonds, one of these formed through a Lys/Asp residue pair, which are strategically positioned to confer protein stability. Removal of the internal thioester by allele-replacement mutagenesis in S. pyogenes severely compromises bacterial adhesion to model host cells. Although current paradigms of bacterial/host cell interaction envisage strong non-covalent interactions, the present study suggests cell adhesion could also involve covalent bonds.},
      journal = "J Biol Chem",
      year = "2010",
      volume = "285",
      number = "44",
      pages = "33858-33866",
      month = "Oct",
      pmid = "20729215",
      url = "http://www.hubmed.org/display.cgi?uids=20729215",
      doi = "10.1074/jbc.M110.149385"
    • [DOI] W. D. Smith, J. A. Pointon, E. Abbot, H. J. Kang, E. N. Baker, B. H. Hirst, J. A. Wilson, M. J. Banfield, and M. A. Kehoe, "Roles of minor pilin subunits spy0125 and spy0130 in the serotype m1 streptococcus pyogenes strain sf370," J bacteriol, vol. 192, iss. 18, pp. 4651-4659, 2010.
      author = "Smith, W D and Pointon, J A and Abbot, E and Kang, H J and Baker, E N and Hirst, B H and Wilson, J A and Banfield, M J and Kehoe, M A",
      title = {Roles of minor pilin subunits Spy0125 and Spy0130 in the serotype M1 Streptococcus pyogenes strain SF370},
      abstract = {Adhesive pili on the surface of the serotype M1 Streptococcus pyogenes strain SF370 are composed of a major backbone subunit (Spy0128) and two minor subunits (Spy0125 and Spy0130), joined covalently by a pilin polymerase (Spy0129). Previous studies using recombinant proteins showed that both minor subunits bind to human pharyngeal (Detroit) cells (A. G. Manetti et al., Mol. Microbiol. 64:968-983, 2007), suggesting both may act as pilus-presented adhesins. While confirming these binding properties, studies described here indicate that Spy0125 is the pilus-presented adhesin and that Spy0130 has a distinct role as a wall linker. Pili were localized predominantly to cell wall fractions of the wild-type S. pyogenes parent strain and a spy0125 deletion mutant. In contrast, they were found almost exclusively in culture supernatants in both spy0130 and srtA deletion mutants, indicating that the housekeeping sortase (SrtA) attaches pili to the cell wall by using Spy0130 as a linker protein. Adhesion assays with antisera specific for individual subunits showed that only anti-rSpy0125 serum inhibited adhesion of wild-type S. pyogenes to human keratinocytes and tonsil epithelium to a significant extent. Spy0125 was localized to the tip of pili, based on a combination of mutant analysis and liquid chromatography-tandem mass spectrometry analysis of purified pili. Assays comparing parent and mutant strains confirmed its role as the adhesin. Unexpectedly, apparent spontaneous cleavage of a labile, proline-rich (8 of 14 residues) sequence separating the N-terminal approximately 1/3 and C-terminal approximately 2/3 of Spy0125 leads to loss of the N-terminal region, but analysis of internal spy0125 deletion mutants confirmed that this has no significant effect on adhesion.},
      journal = "J Bacteriol",
      year = "2010",
      volume = "192",
      number = "18",
      pages = "4651-4659",
      month = "Sep",
      pmid = "20639332",
      url = "http://www.hubmed.org/display.cgi?uids=20639332",
      doi = "10.1128/JB.00071-10"
    • [DOI] A. S. Solovyova, J. A. Pointon, P. R. Race, W. D. Smith, M. A. Kehoe, and M. J. Banfield, "Solution structure of the major (spy0128) and minor (spy0125 and spy0130) pili subunits from streptococcus pyogenes," Eur biophys j, vol. 39, iss. 3, pp. 469-480, 2010.
      author = "Solovyova, A S and Pointon, J A and Race, P R and Smith, W D and Kehoe, M A and Banfield, M J",
      title = {Solution structure of the major (Spy0128) and minor (Spy0125 and Spy0130) pili subunits from Streptococcus pyogenes},
      abstract = {Adhesion of the serotype M1 Streptococcus pyogenes strain SF370 to human tonsil explants and cultured keratinocytes requires extended polymeric surface structures called pili. In this important human pathogen, pili are assembled from three protein subunits: Spy0125, Spy0128 and Spy0130 through the action of sortase enzymes. For this study, the structural properties of these pili proteins have been investigated in solution. Spy0125 and Spy0128 display characteristics of globular, folded proteins. Circular dichroism suggests a largely beta-sheet composition for Spy0128 and Spy0125; Spy0130 appears to contain little secondary structure. Each of the proteins adopts a monodisperse, monomeric state in solution as assessed by analytical ultracentrifugation. Further, small-angle X-ray scattering curves for Spy0125, Spy0128 and Spy0130 suggest each protein adopts an elongated shape, likely comprised of two domains, with similar maximal dimensions. Based on the scattering data, dummy atom models of each of the pili subunits have been reconstructed ab initio. This study provides the first insights into the structure of Streptococcus pyogenes minor pili subunits, and possible implications for protein function are discussed.},
      journal = "Eur Biophys J",
      year = "2010",
      volume = "39",
      number = "3",
      pages = "469-480",
      month = "Feb",
      pmid = "19290517",
      url = "http://www.hubmed.org/display.cgi?uids=19290517",
      doi = "10.1007/s00249-009-0432-2"
    • [DOI] P. R. Race, M. L. Bentley, J. A. Melvin, A. Crow, R. K. Hughes, W. D. Smith, R. B. Sessions, M. A. Kehoe, D. G. McCafferty, and M. J. Banfield, "Crystal structure of streptococcus pyogenes sortase a: implications for sortase mechanism," J biol chem, vol. 284, iss. 11, pp. 6924-6933, 2009.
      author = "Race, P R and Bentley, M L and Melvin, J A and Crow, A and Hughes, R K and Smith, W D and Sessions, R B and Kehoe, M A and McCafferty, D G and Banfield, M J",
      title = {Crystal structure of Streptococcus pyogenes sortase A: implications for sortase mechanism},
      abstract = {Sortases are a family of Gram-positive bacterial transpeptidases that anchor secreted proteins to bacterial cell surfaces. These include many proteins that play critical roles in the virulence of Gram-positive bacterial pathogens such that sortases are attractive targets for development of novel antimicrobial agents. All Gram-positive pathogens express a "housekeeping" sortase that recognizes the majority of secreted proteins containing an LPXTG wall-sorting motif and covalently attaches these to bacterial cell wall peptidoglycan. Many Gram-positive pathogens also express additional sortases that link a small number of proteins, often with variant wall-sorting motifs, to either other surface proteins or peptidoglycan. To better understand the mechanisms of catalysis and substrate recognition by the housekeeping sortase produced by the important human pathogen Streptococcus pyogenes, the crystal structure of this protein has been solved and its transpeptidase activity established in vitro. The structure reveals a novel arrangement of key catalytic residues in the active site of a sortase, the first that is consistent with kinetic analysis. The structure also provides a complete description of residue positions surrounding the active site, overcoming the limitation of localized disorder in previous structures of sortase A-type proteins. Modification of the active site Cys through oxidation to its sulfenic acid form or by an alkylating reagent supports a role for a reactive thiol/thiolate in the catalytic mechanism. These new insights into sortase structure and function could have important consequences for inhibitor design.},
      journal = "J Biol Chem",
      year = "2009",
      volume = "284",
      number = "11",
      pages = "6924-6933",
      month = "Mar",
      pmid = "19129180",
      url = "http://www.hubmed.org/display.cgi?uids=19129180",
      doi = "10.1074/jbc.M805406200"
    • [DOI] E. L. Abbot, W. D. Smith, G. P. Siou, C. Chiriboga, R. J. Smith, J. A. Wilson, B. H. Hirst, and M. A. Kehoe, "Pili mediate specific adhesion of streptococcus pyogenes to human tonsil and skin," Cell microbiol, vol. 9, iss. 7, pp. 1822-1833, 2007.
      author = "Abbot, E L and Smith, W D and Siou, G P and Chiriboga, C and Smith, R J and Wilson, J A and Hirst, B H and Kehoe, M A",
      title = {Pili mediate specific adhesion of Streptococcus pyogenes to human tonsil and skin},
      abstract = {Very little is known about the biological functions of pili that have recently been found to be expressed by important Gram-positive pathogens such as Corynebacterium diphtheriae, Streptococcus agalacticae, S. pneumoniae and S. pyogenes. Using various ex vivo tissue and cellular models, here we show that pili mediate adhesion of serotype M1 S. pyogenes strain SF370 to both human tonsil epithelium and primary human keratinocytes, which represent the two main sites of infection by this human-specific pathogen. Mutants lacking minor pilus subunits retained the ability to express cell-surface pili, but these were functionally defective. In contrast to above, pili were not required for S. pyogenes adhesion to either immortalized HEp-2 or A549 cells, highlighting an important limitation of these extensively used adhesion/invasion models. Adhering bacteria were internalized very effectively by both HEp-2 and A549 cells, but not by tonsil epithelium or primary keratinocytes. While pili acted as the primary adhesin, the surface M1 protein clearly enhanced adhesion to tonsil, but surprisingly, had the opposite effect on adhesion to keratinocytes. These studies provide clear evidence that S. pyogenes pili display an adhesive specificity for clinically relevant human tissues and are likely to play a critical role in the initial stages of infection.},
      journal = "Cell Microbiol",
      year = "2007",
      volume = "9",
      number = "7",
      pages = "1822-1833",
      month = "Jul",
      pmid = "17359232",
      url = "http://www.hubmed.org/display.cgi?uids=17359232",
      doi = "10.1111/j.1462-5822.2007.00918.x"