Research Summary

Many bacteria take up environmental DNA in macromolecular form in a process known as transformation. To accomplish this, cells must be in a physiological state called "competence." Dr. Dubnau's lab studies this process of DNA uptake in the model organism Bacillus subtilis. He and his co-workers are attempting to find out how this large molecule is transported across the cell membrane into the cell. They have identified about 20 proteins associated with the cell membrane that are needed for transformation, and are exploring how these proteins do their jobs. Many of these proteins, including both those attached to the cell membrane and those found in the cytosol, are co-localized preferentially at the poles of the rod shaped bacterial cells. Many of them interact with one another, forming a remarkable DNA uptake and processing machine that is not only responsible for internalizing DNA, but conducting it to the chromosome where it can recombine with homologous DNA sequences. The lab is mapping these protein-protein interactions and determining how the machine manipulates and protects the DNA during transformation. A major focus of the lab is to understand how the polar localization takes place and to explore the signals that lead to the assembly and disassembly of the transformation machine as the cells enter and leave the competent state. Interestingly, these 20 or so proteins are ordinarily not produced. When cells become crowded and starved for food, the synthesis of the DNA uptake proteins is turned on. Dr. Dubnau's lab is exploring the complex regulatory mechanisms that accomplish this synthesis in response to nutritional and crowding signals. Regulation occurs on the level of transcription and also by the modulation of protein stability. An interesting aspect is that in B. subtilis only about 10% of the cells in a genetically homogeneous culture express the transformation proteins, an example of "bistable" gene expression. The basis of this phenomenon is stochastic, depending on noise in the basal expression of the master transcriptional regulator, ComK, and on the presence of a positive feedback loop in which ComK is needed for the transcription of its own gene. The mechanism of bistable competence expression is under investigation, using a combined experimental and modeling approach.



     

     Bistability in comK expression. The cells are stained red with
     propidium iodide and the competence expressing cells can be
     identified by the green fluorescence from a comK-gfp fusion.






Research Data

ROK microarray data
ROK microarray data




Recent Articles


Maamar H, Raj A, Dubnau D.
Noise in Gene Expression Determines Cell Fate in Bacillus subtilis.
Science, 2007, in press.

Prepiak P, Dubnau D.
A Peptide Signal for Adapter Protein-Mediated Degradation by the AAA(+) Protease ClpCP.
Mol Cell, 2007, 26(5): p. 639-647.

Smits WK, Hoa TT, Hamoen LW, Kuipers OP, Dubnau D.
Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein.
Mol Microbiol, 2007 64(2): p. 368-381.

Okada M, Yamaguchi H, Sato I, Cho SJ, Dubnau D, Sakagami Y.
Structure-activity relationship studies on quorum sensing ComX(RO-E-2) pheromone.
Bioorg Med Chem Lett, 2007, 17(6): p. 1705-1707.

Okada, M., et al.
Chemical synthesis of ComX pheromone and related peptides containing isoprenoidal tryptophan residues.
Tetrahedron, 2006, 62: p. 8907-8918.

Dubnau, D. and Losick, R.
Bistability in bacteria.
Mol. Microbiol. , 2006. 61: p. 564-572.

Chen, I., Provvedi, R. and Dubnau, D.
A Macromolecular Complex Formed by a Pilin-like Protein in Competent Bacillus subtilis.
J. Biol. Chem. , 2006. 281: p. 21720-7.

Maamar, H. and Dubnau, D.
Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop.
Mol Microbiol, 2005. 56: p. 615-24.

Okada, M., et al.
Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX.
Nature Chem. Biol., 2005. 1: p. 1-2.

Hahn, J., et al.
Transformation proteins and DNA uptake localize to the cell poles in Bacillus subtilis.
Cell, 2005. 122: p. 59-71.

Draskovic, I. and Dubnau, D.
Biogenesis of a putative channel protein, ComEC, required for DNA uptake: membrane topology, oligomerization and formation of disulphide bonds.
Mol Microbiol, 2005. 55: p. 881-96.

Albano, M., et al.
The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions.
J. Bacteriol., 2005. 187: p. 2010.

I. Chen and Dubnau, D.
The ins and outs of DNA transfer in bacteria.
Science, 2005. 310: 1456-60.

Okada, M. et al.
Towards structural determination of the ComX pheromone: synthetic studies on peptides containing geranyltruptophan.
Biosci. Biotenol. Biochem. 2004. 68: 2374-87.


Maier B, Chen I, Dubnau D, Sheetz MP. (2004).
DNA transport into Bacillus subtilis requires proton motive force to generate large molecular forces.
Nat Struct Mol Biol. 2004 Jul;11(7):643-9. Epub 2004 Jun 06.
PMID: 15184891
Abstract

Chen I, Dubnau D. (2004).
DNA Uptake During Bacterial Transformation
Nat Rev Microbiol. 2004 Mar;2(3):241-9
PMID: 15083159
Abstract  |  Full Article

Ansaldi M, Dubnau D. (2004).
Diversifying selection at the Bacillus quorum-sensing locus and determinants of modification specificity during synthesis of the ComX pheromone.
J Bacteriol. 2004 Jan;186(1):15-21
PMID: 14679219
Abstract  |  Full Article

Chen I, Dubnau D. (2003).
DNA transport during transformation.
Front Biosci. 2003 May 1;8:s544-5
PMID: 12700070
Abstract

Ansaldi M, Marolt D, Stebe T, Mandic-Mulec I, Dubnau D. (2002).
Specific activation of the Bacillus quorum-sensing systems by isoprenylated pheromone variants.
Mol Microbiol 2002 Jun;44(6):1561-73
PMID: 12067344
Abstract  |  Full Article

Berka RM, Hahn J, Albano M, Draskovic I, Persuh M, Cui X, Sloma A, Widner W, Dubnau D. (2002).
Microarray analysis of the Bacillus subtilis K-state: genome-wide expression changes dependent on ComK.
Mol Microbiol 2002 Mar;43(5):1331-45
PMID: 11918817
Abstract  |  Full Article

Persuh M, Mandic-Mulec I, Dubnau, D. (2002).
A MecA paralog, YpbH, binds ClpC, affecting both competence and sporulation.
J Bacteriol 2002 Apr;184(8):2310-3
PMID: 11914365
Abstract  |  Full Article

Hoa TT, Tortosa P, Albano M, Dubnau D. (2002).
Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK.
Mol Microbiol 2002 Jan;43(1):15-26
PMID: 11849533
Abstract  l  Full Article

Meima R, Eschevins C, Fillinger S, Bolhuis A, Hamoen LW, Dorenbos R, Quax WJ, van Dijl JM, Provvedi R, Chen I, Dubnau D, Bron S (2002).
The bdbDC operon of Bacillus subtilis encodes thiol-disulfide oxidoreductases required for competence development.
J Biol Chem 2002 Mar 1;277(9):6994-7001
PMID: 11744713
Abstract  |  Full Article

Turgay K, Persuh M, Hahn J, Dubnau D. (2001).
Roles of the two ClpC ATP binding sites in the regulation of competence and the stress response.
Mol Microbiol 2001 Nov;42(3):717-27
PMID: 11722737
Abstract  |  Full Article

Provvedi R, Chen I, Dubnau D (2001).
NucA is required for DNA cleavage during transformation of Bacillus subtilis.
Mol Microbiol 2001 May;40(3):634-44
PMID: 11359569
Abstract  |  Full Article

Haijema BJ, Hahn J, Haynes J, Dubnau D. (2001).
A ComGA-dependent checkpoint limits growth during the escape from competence.
Mol Microbiol 2001 Apr;40(1):52-64
PMID: 11298275
Abstract  |  Full Article

Tortosa P, Logsdon L, Kraigher B, Itoh Y, Mandic-Mulec I, Dubnau D. (2001).
Specificity and genetic polymorphism of the Bacillus competence quorum-sensing system.
J Bacteriol 2001 Jan;183(2):451-60
PMID: 11133937
Abstract  |  Full Article



Dubnau, D. and Turgay, K. (2000)
The regulation of competence in Bacillus subtilis and its relation to stress response.
In Bacterial Stress Responses. G. Storz and R. Hengge-Aronis (eds). Washington, DC, American Society for Microbiology, 249-260.

Tortosa, P., Albano, M. and Dubnau, D. (2000)
Characterization of ylbF, a new gene involved in competence development and sporulation in Bacillus subtilis.
Mol. Microbiol. 35 : 1110-1119.

Dubnau, D. (1999)
DNA Uptake in Bacteria.
Ann. Rev. Microbiol. 53 : 214-244.

Persuh, M., Turgay, K., Mandic-Mulec, I. and Dubnau, D. (1999)
The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch.
Mol Microbiol 33 : 886-894.

Piazza, F., Tortosa, P. and Dubnau, D. (1999)
Mutational analysis and membrane topology of ComP, a quorum-sensing histidine kinase of Bacillus subtilis controlling competence development.
J Bacteriol 181 : 4540-4548.

Tortosa, P. and Dubnau, D. (1999)
Competence for transformation: a matter of taste.
Current Opinion in Microbiology 2 : 588-592.

Turgay, K., Hahn, J., Burghoorn, J. and Dubnau, D. (1998)
Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor.
EMBO J. 17 : 6730-6738.

PubMed Lisitings>




Book Chapters

Draskovic, I. and D. Dubnau
Competence for genetic transformation
In "The Dynamic bacterial genome and its biological consequences"
P. Mullaney, Editor. 2005, Cambridge University Press: Cambridge, UK.