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Molecular Genetics of Bacillus subtilis

Prof. Kevin M. Devine

Signal transduction during cell wall synthesis in Bacillus subtilis: the YycFG two-component system.

The bacterial cell wall is an essential structure located outside the cytoplasmic membrane that is composed of approximately equal amounts of peptidoglycan and anionic polymers (eg. teichoic / teichuronic acid) and about 20% protein. It is a rigid structure that determines cell shape and acts as a barrier to turgor pressure. Cell wall synthesis involves cellular activities that occur in different cellular compartments: the precursors of peptidoglyan and teichoic acid are synthesized within the cytoplasm but their assembly into mature cell wall material occurs outside the cell. Similarly the cell wall synthetic enzymes (eg. penicillin binding proteins and autolysins) are produced intracellularly but their sites of action are extracellular, ie. within the cell wall. Therefore cell wall synthesis requires signaling between the cell wall and the cytoplasmic compartments to coordinate the production of precursors/enzymes with their utilization.

We have shown that the essential YycFG two-component signal transduction system of B. subtilis participates in signaling between the cell wall and cytoplasmic compartments in B. subtilis. YycFG controls cell wall metabolism in B. subtilis (Howell et al., 2003; Bisicchia et al., 2007). The YycG kinase senses and is activated by a signal, present during exponential growth, that we propose is associated with the cell wall synthetic precursor Lipid II (Dubrac et al., 2008). The YycF~P response regulator directs expression of the YocH, YvcE and LytE autolysins, while repressing expression of YoeB (IseA) and YjeA whose activities inhibit and modulate respectively autolysin activity. We have also shown that there is a relationship between YycFG, and the PhoPR two-component system that directs a cellular response to phosphate limitation (Howell et al., 2006).

We are further exploring how these two-component systems function in sensing conditions within the cell wall and transduce this information into the cell to control production of cell wall synthetic enzymes and intermediates. We are investigating the nature of the signals being detected and how they are transmitted into the cell. We are establishing the complete regulons of each two-component system, focusing on how cell wall synthetic processes are coordinately regulated during normal growth (by YycFG) and in response to phosphate stress (by PhoPR). An essential feature of this analysis will be the use of high throughput technology, using tiled arrays for detecting RNA transcripts and live cell arrays for real-time expression changes.

BaSysBio: Towards an understanding of dynamic transcriptional regulation at global scale in bacteria: a systems biology approach

The overall objective of BaSysBio is to establish the network of regulatory circuits of gene expression in B. subtilis to generate quantitative models how the cell functions as a system. The specific objectives are:

  • To unravel the global regulatory structure of B. subtilis metabolism to understand how transcriptional regulation is integrated with the other levels of control.
  • To achieve a quantitative understanding of the cellular transcriptional responses under conditions mimicking pathogenesis and to apply the acquired knowledge and the integrated modelling/experiments strategy developed in the model bacterium to understand the regulatory networks controlling pathogenesis in the closely related disease-causing bacteria Bacillus anthracis and Staphylococcus aureus.

The objectives will be achieved using high-throughput technologies at the transcriptomic (tiled arrays; live cell arrays), proteomic and metabolomic levels. These data will be utilized to generate dynamic and static models of the regulatory networks that comprise the B. subtilis cell.

This project is an EU-funded Integrated Project with 15 participant European groups and 1 Australian group. Further details about the project and the participant groups can be obtained at

Recent Publications

Dubrac, S., Bissicchia, P., Devine, K. M. & Msadek, T. (2008). A matter of life and death: cell wall homeostasis and the WalKR (YycFG) essential signal transduction pathway. Mol. Microbiol. 70:1307-1322. PubMed.

Westers, L., Westers, H., Zanen, G., Antelmann, H., Hecker, M., Noone, D., Devine, K. M., van Dijl, J. M. & Quax, W. J. (2008). Genetic or chemical protease inhibition causes significant changes in the Bacillus subtilis exoproteome. Proteomics 8, 2704-2713. PubMed.

Sheppard, K., Yuan, J., Hohn, M. J., Jester, B., Devine, K. M. & Soll, D. (2008). From one amino acid to another: tRNA-dependent amino acid biosynthesis. Nucleic Acids Res. 36, 1813-1825. PubMed.

Bisicchia, P., Noone, D., Lioliou, E., Howell, A., Quigley, S., Jensen, T., Jarmer, H. & Devine, K. M. (2007). The essential YycFG two-component system controls cell wall metabolism in Bacillus subtilis. Mol. Microbiol. 65, 180-200. PubMed.

Howell, A., Dubrac, S., Noone, D., Varughese, K. I. & Devine, K. (2006). Interactions between the YycFG and PhoPR two-component systems in Bacillus subtilis: the PhoR kinase phosphorylates the non-cognate YycF response regulator upon phosphate limitation. Mol. Microbiol. 59, 1199-1215. PubMed.

Hallin, P. F., Nielsen, N., Devine, K. M., Binnewies, T. T., Willenbrock, H. & Ussery, D. W. (2005). Genome update: base skews in 200+ bacterial chromosomes. Microbiology 151, 633-637. PubMed.

Ataide, S. F., Jester, B. C., Devine, K. M. & Ibba, M. (2005). Stationary-phase expression and aminoacylation of a transfer-RNA-like small RNA. EMBO Rep 6, 742-747. PubMed.

Westers, H., Dorenbos, R., van Dijl, J. M., Kabel, J., Flanagan, T., Devine, K. M., Jude, F., Seror, S. J., Beekman, A. C., Darmon, E., Eschevins, C., de Jong, A., Bron, S., Kuipers, O. P., Albertini, A. M., Antelmann, H., Hecker, M., Zamboni, N., Sauer, U., Bruand, C., Ehrlich, D. S., Alonso, J. C., Salas, M. & Quax, W. J. (2003). Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol. Biol. Evol. 20, 2076-2090. PubMed.

Kobayashi, K., Ehrlich, S. D., ..., Devine, K., ..., et al. (2003). Essential Bacillus subtilis genes. Proc. Natl. Acad. Sci. USA 100, 4678-4683. PubMed.

Jester, B. C., Levengood, J. D., Roy, H., Ibba, M. & Devine, K. M. (2003). Nonorthologous replacement of lysyl-tRNA synthetase prevents addition of lysine analogues to the genetic code. Proc. Natl. Acad. Sci. USA 100, 14351-14356. PubMed.

Howell, A., Dubrac, S., Andersen, K. K., Noone, D., Fert, J., Msadek, T. & Devine, K. (2003). Genes controlled by the essential YycG/YycF two-component system of Bacillus subtilis revealed through a novel hybrid regulator approach. Mol. Microbiol. 49, 1639-1655. PubMed.

Antelmann, H., Darmon, E., Noone, D., Veening, J. W., Westers, H., Bron, S., Kuipers, O. P., Devine, K. M., Hecker, M. & van Dijl, J. M. (2003). The extracellular proteome of Bacillus subtilis under secretion stress conditions. Mol. Microbiol. 49, 143-156. PubMed.

Weller, G. R., Kysela, B., Roy, R., Tonkin, L. M., Scanlan, E., Della, M., Devine, S. K., Day, J. P., Wilkinson, A., d'Adda di Fagagna, F., Devine, K. M., Bowater, R. P., Jeggo, P. A., Jackson, S. P. & Doherty, A. J. (2002). Identification of a DNA nonhomologous end-joining complex in bacteria. Science 297, 1686-1689. PubMed.

Darmon, E., Noone, D., Masson, A., Bron, S., Kuipers, O. P., Devine, K. M. & van Dijl, J. M. (2002). A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. J. Bacteriol. 184, 5661-5671. PubMed.

Noone, D., Howell, A., Collery, R. & Devine, K. M. (2001). YkdA and YvtA, HtrA-like serine proteases in Bacillus subtilis, engage in negative autoregulation and reciprocal cross-regulation of ykdA and yvtA gene expression. J. Bacteriol. 183, 654-663. PubMed.

Akbar, S., Gaidenko, T. A., Kang, C. M., O'Reilly, M., Devine, K. M. & Price, C. W. (2001). New family of regulators in the environmental signaling pathway which activates the general stress transcription factor sigma(B) of Bacillus subtilis. J. Bacteriol. 183, 1329-1338. PubMed.

Noone, D., Howell, A. & Devine, K. M. (2000). Expression of ykdA, encoding a Bacillus subtilis homologue of HtrA, is heat shock inducible and negatively autoregulated. J. Bacteriol. 182, 1592-1599. PubMed.

Derre, I., Rapoport, G., Devine, K., Rose, M. & Msadek, T. (1999). ClpE, a novel type of HSP100 ATPase, is part of the CtsR heat shock regulon of Bacillus subtilis. Mol. Microbiol. 32, 581-593. PubMed.