Profile

Career

Research

Overview

Our interest lies in understanding how bacteria are successful in their environment, focusing mainly on bacterial pathogens (E coli (UPEC), Salmonella and Klebsiella). Bacterial populations are not homogenous, and we work to identify and understand how this is controlled, by studying gene regulation and regulatory networks at a molecular level. A main interest is DNA methylation and phase variation. This is studied both as a model system for heritable gene regulation (epigenetic regulation) and to understand the relevance in context of bacterial pathogenesis. Related to this we are studying how this regulation contributes bacterial biofilm formation and dispersal. Our work involves a wide range of techniques, from bacterial genetics to biochemistry and advanced imaging technology.

Discoveries

Epigenetic regulation can be altered by changing just the genome sequence context of the gene. Identified that important Salmonella virulence factors are controlled by phase variation. The laser of the MP-LSM can be used as a biofilm manipulation tool, which can be developed as a model to analyze effects of antimicrobials on the biofilm.

Current projects

• The immunodominant O-antigen and Salmonella enterica pathogenesis (Funding body: Wellcome Trust)
• Bacterial biofilm formation (Funding body: BBSRC studentship)

Research group(s)

Available PhD research projects

O-antigen modification and Salmonella virulence (for 2012-13)
Salmonella enterica sp is an important food borne pathogen that spreads as a result of its persistence in the animal reservoir.  To combat this problem, detailed insight is required into the underlying mechanisms of its persistence, spread and virulence.  We are interested in the molecular biology of bacterial pathogens and in this project the student will focus on a family of operons that are involved in modifying the O-antigen of the lipopolysaccharide (Broadbent et al 2010).  The O-antigen structure and composition is a main feature of serotyping, which is an essential epidemiological tool.  Furthermore, the O-antigen is a dominant immunogen, and thus changes may allow immune evasion.  Finally, these genes are phage derived, and expression may influence horizontal gene transfer.  The exact contribution to the success of Salmonella however needs to be defined, and the activities of  the gene products identified.  The student will contribute to our ongoing efforts in this area using a range of techniques including in molecular biology, genetics and protein biochemistry to assess gene regulation and to identify basic biochemical features of the gene products.  Furthermore the student  assess the role of these enzymes in influencing host-pathogen interactions.  Collaborations are in place to facilitate the studies.

How to kill a biofilm: role of population heterogeneity (for 2012-13)
Biofilms are communities of microbes that are attached to a surface, and in health care, biofilms on catheters, stents and implants can lead to infections that are difficult to eradicate. Understanding how they form, disperse and persist is key towards combating their occurrence This project will combine genetic and imaging approaches to examine the effects of population heterogeneity among bacteria and of interactions between strains on biofilm “fitness” parameters (i.e. dispersal, matrix, packing, resistance). Heterogeneity in growth and single cell fitness will be examined using diverse antimicrobial strategies. Using our new protocols, localized death and killing will be induced by laser and the effect compared with chemical and biological induced death (colicins, antibiotics, CDI). You will use E. coli and Salmonella model and pathogenic strains. Outcomes will provide insight into the effect of partial killing of biofilm, which is relevant in general in clinical settings. Training will be obtained in microbiology, bacterial genetics, molecular biology, bacterial physiology, pathognesis, advanced imaging with further methodology development.

References: 

1. Lakins, M.A., Marrison, J.L., O’Toole, P.J and Van der Woude, M.W. (2009) Exploiting advances in imaging technology to study biofilms by applying multiphoton laser scanning microscopy as an imaging and manipulation tool. Journal of Microscopy. 235:128-137
2. van der Woude, M.W. (2006) Re-examining the role and random nature of phase variation. FEMS Microbiol Lett. 254:190-197.

Defining molecular rules that govern epigenetic gene regulation in bacteria (for 2012-13)
DNA methylation-dependent phase variation, a heritable yet reversible regulation, controls expression of virulence factors in certain bacteria, specifically E coli and Salmonella spp. Our work has identified key elements yet much remains to be learned about the mechanism. This project aims to identify molecular rules governing this epigenetic regulation. The approach is to define essential genetic elements, analyse protein (OxyR)-DNA interactions, examine the role of RNA polymerase for inheritance of expression state, and manipulate two identified systems (manuscript in preparation). The data will also contribute to developing and testing a mathematical model for this stochastic regulation (modeling carried out by collaborators). Identifying the rules may allow engineering a synthetic switch and inform links between cell physiology and gene regulation. Using the findings genome sequences can be mined to identify similar systems in other genera to inform virulence and vaccine studies. Techniques include cloning, mutational analysis, protein purification, DNA-protein interactions (EMSA, fluorescence anisotropy), FACS, qRT-PCR, and bioinformatics/genome analysis. Suitable for applicants with some molecular biology/microbiology/ biochemistry background. References (please enquire - manuscripts are in preparation):

1. Van der Woude, M. W., and Henderson, I.R. (2008) Regulation and Function of Ag43 (Flu). Annu. Rev. Microbiol. 62: 153-69

2. Wallecha, A., Munster, V., Correnti, J., Chan, T. and van der Woude, M.W. (2002) Dam- and OxyR-dependent phase variation of agn43: essential elements and evidence for a new role of DNA methylation. J. Bacteriol. 184:3338-3347.

Publications

Selected publications

• Wagenaars, E.,Van der Woude M. and Vann, R. (2011) An Atmospheric –Pressulr Low-Temperature Plasma Jet for Growth Inhibition of Escherchia coli.  IEEE Transactions on Plasma Science (accepted)
• Broadbent, S. E., Davies M. R, and van der Woude, M.W. (2010) Phase variation controls expression of Salmonella LPS modification genes by a DNA methylation dependent mechanism.  Mol Microbiol.  77: 337-353. This has article was identified as important by F1000.  Read the evaluation at http://f1000.com/4434956 until 04/20/2012.
• Broadbent, S., van der Woude, M. and Aziz, N. (2010) Accurate and simple sizing of primer extension products using a non-radioactive approach facilitates identification of transcription initiation sites. J. Microbiol. Methods.  81:256-8.
• Kaminska, R. and Van der Woude, M.W. (2010) Establishing and maintaining sequestration of Dam target sites for phase variation of agn43 in E. coli.  J. Bacteriol. 192(7): 1937-1945
• Lakins, M.A., Marrison, J.L., O’Toole, P.J and Van der Woude, M.W.  (2009) Exploiting advances in imaging technology to study biofilms by applying multiphoton laser scanning microscopy as an imaging and manipulation tool.  Journal of Microscopy. 235:128-137
• Wallecha, A. Correnti, J., Munster, V., and van der Woude, M.W.  (2003) Transcriptional repression of agn43 by OxyR is independent of its oxidation state. J. Bacteriol.185: 2203-2209
• Haagmans, W. and van der Woude, M. (2000)  Phase variation of Ag43 in E. coli: Dam-dependent methylation abrogates OxyR binding and OxyR-mediated repression of transcription.  Mol. Microbiol.  35: 877-887.
• Van der Woude, M. W., Braaten, B.  and Low, D. A. (1996)  Epigenetic phase variation of the pap operon in Escherichia coli .  Trends in Microbiology 4:5-9.

Selected review and book chapters

• van der Woude, M.W. (2011)  Phase variation: how to create and coordinate population diversity. Current Opinion in Microbiology 14 (2): 205-211
• Broadbent, S. E. and van der Woude, M. W.  (2010)  Phase variation  in: “Bacterial Stress Responses” 2nd edition. eds. G. Storz and R. Hengge. ASM Press in press
• van der Woude, M. W., and Henderson, I.R. (2008) Regulation and Function of Ag43 (Flu).  Annu. Rev. Microbiol. 62: 153-69
• van der Woude, M.W. (2008)  Some types of bacterial phase variation are epigenetic. Microbe, 3(1): 21-26  (News Magazine for the Americn Society for Microbiology)
• van der Woude, M.W. (2006)  Re-examining the role and random nature of phase variation.  FEMS Microbiol Lett. 254:190-197.
• van der Woude, M.W. and Baumler, A. (2004) Phase variation and antigenic variation in bacteria. Clin. Microbiol. Rev. 17:581-611.

Other publications

• van der Woude, M.W., and Berks, R. (2011) Trains, games, microbes and microscopes - a winning recipe for a great day. Microbiology Today 38/2:126-127.
  

Full publications list

External activities

Memberships

• The American Society for Microbiology
  Member
• Biochemical Society
  Member
• The Society for General Microbiology
  Member
• StoMP network: “A collaborative research network between mathematical modellers and microbiologists.”
  Member
  

Editorial duties

• Biochemical Journal
  Editor (2004 - )

Other Professional Activities

• BBSRC Research Committee B
  Core member (2011 - )
  

Invited talks and conferences

• How to generate population heterogeneity in E. coli and Salmonella using Dam and OxyR
  CNRS Marseille, 03/12/2010
• Why should health care professionals care about biofilms at Infection Matters?
  University of Hull and the NHS invited presentation, 26/11/2010   
• Diversity in a culture is a good thing: an introduction to bacterial phase variation
  Utrecht University of Applied Sciences (NL), special lecture, 24/11/2010
• Dam regulates phase variation in E. coli and Salmonella
  6th NEB meeting on DNA restriction and modification, August 2010
• StoMP workshop
  July 2010, York (co-developer)
• Stochastic effects in microbial infection: experiments and modelling, workshop
  Edinburgh, 2010 ; part of e-science institute supported series  on "Modelling and microbiology" (Co-organiser)