Dr David Whitworth PhD

Dr David Whitworth

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Contact Details

Teaching

Research

Signalling pathways in the social predator Myxococcus xanthus: the dynamics and specificity of protein-protein interactions.

  • Nutrient acquisition - (regulation of phosphate metabolism)
  • Responses to stress - (regulation of carotenoid synthesis, multicellular development)
  • Protein-protein interactions - (signalling pathway connectivity - experimental and computational)
  • Dynamic systems - (network properties, evolution and population behaviour/dynamics)
  • Bioinformatics - (comparative genomics, evolution of signalling networks)
  • Structural bioinformatics - (structure prediction, interaction modelling)

    My research focuses on bacterial signalling pathways and how they alter behaviour in response to a changing environment. In particular, I am interested in the social and predatory myxobacteria, and how they use two-component signalling pathways to co-ordinate group behaviour. Experimental work is investigating the protein-protein interactions between TCS transmitter and receiver domains, which define the structure of TCS pathways. As an extension of this work, we are also characterising the regulation of phosphate assimilation and its inter-relation with multicellular fruiting body formation, a regulon that involves at least seven TCS proteins. Benchwork is being complemented by theoretical studies. One such study uses comparative genomics to probe the evolution of TCSs, and has provided a method for predicting transmitter-receiver domain partnerships, many of which are being confirmed experimentally.

Publications

2017

Livingstone, P., Morphew, R., Whitworth, D. 2017. Myxobacteria are able to prey broadly upon clinically-relevant pathogens, exhibiting a prey range which cannot be explained by phylogeny. Frontiers in Microbiology 8 5193

Lloyd, D., Whitworth, D. 2017. The myxobacterium Myxococcus xanthus can sense and respond to the quorum signals secreted by potential prey organisms. Frontiers in Microbiology 8 439 Cadair

2016

Kara, A., Vickers, M., Swain, M., Whitworth, D., Fernandez-Fuentes, N. 2016. MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins. Bioinformatics 32 (21) pp. 3339-3341. Cadair

Whitworth, D.E. 2016. Recasting a traditional laboratory practical as a “Design-your-own protocol” to teach a universal research skill. Biochemistry and Molecular Biology Education 44 (4) pp. 377-380. Cadair

Edwards Rassner, S., Anesio, A., Girdwood, S.E., Hell, K., Gokul, J., Whitworth, D., Edwards, A. 2016. Can the bacterial community of a High Arctic glacier surface escape viral control? Frontiers in Microbiology 7 956 Cadair

2015

Whitworth, D.E., Slade, S.E., Mironas, A. 2015. Composition of distinct sub-proteomes in Myxococcus xanthus: metabolic cost and amino acid availability. Amino Acids 47 (12) pp. 2521-2531. Cadair

Whitworth, D. 2015. An off-the-shelf, authentic and versatile undergraduate molecular biology practical course. Biochemistry and Molecular Biology Education 43 (6) pp. 434-440. Cadair

Whitworth, D., Morgan, B. 2015. Synergism between bacterial GAPDH and OMVs: disparate mechanisms but co-operative action. Frontiers in Microbiology 6 1231 Cadair

Whitworth, D.E. 2015. Genome-wide analysis of myxobacterial two-component systems: genome relatedness and evolutionary changes. BMC Genomics 16 (1) 780 Cadair

Ortet, P., Whitworth, D.E., Santaella, C., Achouak, W., Barakat, M. 2015. P2CS: updates of the prokaryotic two-component systems database. Nucleic Acids Research 43 ((D1)) pp. D536-D541. Cadair

Kara, A., Vickers, M., Swain, M., Whitworth, D.E., Fernandez-Fuentes, N. 2015. Genome-wide prediction of prokaryotic two-component system networks using a sequence-based meta-predictor. BMC Bioinformatics 16 (1) 297 Cadair

2014

Mela, S., Whitworth, D.E. 2014. The fist bump: a more hygienic alternative to the handshake. American Journal of Infection Control 42 (8) pp. 916-917. Cadair

Whitworth, D.E., Wright, K. 2014. Online assessment of learning and engagement in university laboratory practicals. British Journal of Educational Technology Cadair

2013

Barakat, M., Ortet, P., Whitworth, D.E. 2013. P2RP: a Web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes. BMC Genomics 14 (1) pp. 269. Cadair

2012

Ortet, P., De Luca, G., Whitworth, D.E., Barakat, M. 2012. P2TF: a comprehensive resource for analysis of prokaryotic transcription factors. BMC Genomics 13 628 Cadair

Evans, A.G.L., Davey, H.M., Cookson, A.R., Currinn, H., Cooke-Fox, G., Stanczyk, P.J., Whitworth, D.E. 2012. Predatory activity of Myxococcus xanthus outer-membrane vesicles and properties of their hydrolase cargo. Microbiology 158 (Pt 11) pp. 2742-2752. Cadair

2011

Whitworth, D.E. 2011. Myxobacterial Vesicles: Death at a Distance? Advances in Applied Microbiology 75 pp. 1-31. Cadair

2010

Williams, R.H.N., Whitworth, D.E. 2010. The genetic organisation of prokaryotic two-component system signalling pathways. BMC Genomics 11 (720) 720 pp. 1-12.

Barakat, M., Ortet, P., Whitworth, D.E. 2010. P2CS: a database of prokaryotic two-component systems. Nucleic Acids Research 39 (1) pp. D771-D776. Cadair

Evans, A.R., Whitworth, D.E. 2010. Correlations between the role, sequence conservation, genomic location and severity of phenotype in myxobacterial developmental genes. FEMS Microbiology Letters 312 (1) pp. 40-45.

Holmes, A.B., Kalvala, S., Whitworth, D.E. 2010. Spatial simulations of myxobacterial development. PLoS Computational Biology 6 (2) e1000686 Cadair

Cock, P.J.A., Whitworth, D.E. 2010. Evolution of relative reading frame bias in unidirectional prokaryotic gene overlaps. Molecular Biology and Evolution 27 (4) pp. 753-756.

2009

Whitworth, D.E., Cock, P.J.A. 2009. Evolution of prokaryotic two-component systems: insights from comparative genomics. Amino Acids 37 (3) pp. 459-466.

Barakat, M., Ortet, P., Jourlin-Castelli, C., Ansaldi, M., Méjean, V., Whitworth, D.E. 2009. P2CS: a two-component system resource for prokaryotic signal transduction research. BMC Genomics 10 315

Whitworth, D.E., Young, M., McEwan, N.R., Newbold, C.J.Smith, S.P., Spikes, K.J. 2009. Life with little oxygen: lessons from microbes. Cadair

Holmes, A.B., Kalvala, S., Whitworth, D.E. 2009. Myxobacteria Motility: a novel 3D model of rippling behaviour in Myxococcus xanthus. Systemics and Informatics World Network 6 pp. 65-70.

2008

Whitworth, D.E. 2008. Genomes and knowledge - a questionable relationship? Trends in Microbiology 16 (11) pp. 512-519.

Whitworth, D.E., Millard, A., Hodgson, D.A., Hawkins, P.F. 2008. Protein-protein interactions between two-component system transmitter and receiver domains of Myxococcus xanthus. Proteomics 8 (9) pp. 1839-1842.

Whitworth, D.E., Holmes, A.B., Irvine, A.G., Hodgson, D.A., Scanlan, D.J. 2008. Phosphate acquisition components of the Myxococcus xanthus Pho regulon are regulated by both phosphate availability and development. Journal of Bacteriology 190 (6) pp. 1997-2003.

Whitworth, D.E., Cock, P.J.A. 2008. Two-component systems of the myxobacteria: structure, diversity and evolutionary relationships. Microbiology 154 (2) pp. 360-372.

2007

Cock, P.J.A., Whitworth, D.E. 2007. Evolution of prokaryotic two-component system signaling pathways: Gene fusions and fissions. Molecular Biology and Evolution 24 (11) pp. 2355-2357.

Whitworth, D.E. 2007. Myxobacteria: Multicellularity and Differentiation. 1stth edn, American Society for Microbiology Cadair

Whitworth, D.E., Cock, P.J.A. 2007. Two-Component Signal Transduction System of the Myxobacteria. In D. E. Whitworth. (ed) Myxobacteria: Multicellularity and Differentiation. American Society for Microbiology pp. 169-189. Cadair

Cock, P.J.A., Whitworth, D.E. 2007. Evolution of gene overlaps: relative reading frame bias in prokaryotic two-component system genes. Journal of Molecular Evolution 64 (4) pp. 457-462. Cadair

Schneiker, S., Perlova, O., Kaiser, O., Gerth, K., Alici, A., Altmeyer, M.O., Bartels, D., Bekel, T., Beyer, S., Bode, E., Bode, H.B., Bolten, C.J., Choudhuri, J.V., Doss, S., Elnakady, Y.A., Frank, B., Gaigalat, L., Goesmann, A., Groeger, C., Gross, F., Jelsbak, L., Jelsbak, L., Kalinowski, J., Kegler, C., Knauber, T., Konietzny, S., Kopp, M., Krause, L., Krug, D., Linke, B., Mahmud, T., Martinez-Arias, R., McHardy, A.C., Merai, M., Meyer, F., Mormann, S., Muñoz-Dorado, J., Perez, J., Pradella, S., Rachid, S., Raddatz, G., Rosenau, F., Rückert, C., Sasse, F., Scharfe, M., Schuster, S.C., Suen, G., Treuner-Lange, A., Velicer, G.J., Vorhölter, F., Weissman, K.J., Welch, R.D., Wenzel, S.C., Whitworth, D.E., Wilhelm, S., Wittmann, C., Blöcker, H., Pühler, A., Müller, R. 2007. Complete genome sequence of the myxobacterium Sorangium cellulosum. Nature Biotechnology 25 (11) pp. 1281-1289. Cadair

2006

Pham, V.D., Shebelut, C.W., Jose, I.R., Hodgson, D.A., Whitworth, D.E., Singer, M. 2006. The response regulator PhoP4 is required for late developmental events in Myxococcus xanthus. Microbiology 152 (6) pp. 1609-1620. Cadair

2005

Higgs, P.I., Cho, K., Whitworth, D.E., Evans, L.S., Zusman, D.R. 2005. Four Unusual Two-Component Signal Transduction Homologs, RedC to RedF, Are Necessary for Timely Development in Myxococcus xanthus. Journal of Bacteriology 187 (23) pp. 8191-8195.

2004

Whitworth, D.E., Bryan, S.J., Berry, A.E., McGowan, S.J., Hodgson, D.A. 2004. Genetic dissection of the light-inducible carQRS promoter region of Myxococcus xanthus. Journal of Bacteriology 186 (23) pp. 7836-7846.

2003

Browning, D.F., Whitworth, D.E., Hodgson, D.A. 2003. Light-induced carotenogenesis in Myxococcus xanthus functional characterization of the ECF sigma factor CarQ and antisigma factor CarR. Molecular Microbiology 48 (1) pp. 237-251. Cadair

2001

Whitworth, D.E., Hodgson, D.A. 2001. Light-induced carotenogenesis in Myxococcus xanthus: evidence that CarS acts as an anti-repressor of CarA. Molecular Microbiology 42 (3) pp. 809-819.