Public Health Research Institute Center
UMDNJ - New Jersey Medical School
225 Warren Street
Newark, New Jersey 07103

Phone: (973) 854-3400
e-mail: dubnauda@umdnj.edu





An introduction by Dr. David Dubnau on the research carried out in his laboratory.




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.





Selected Publications


Mirouze N, Desai Y, Raj A, Dubnau D (2012) Spo0A~P imposes a temporal gate for the bimodal expression of competence in Bacillus subtilis. PLoS Genet 8: e1002586. PMI: 22412392

Prepiak P, Defrancesco M, Spadavecchia S, Mirouze N, Albano M, Persuh M, Fujita M, Dubnau D (2011) MecA dampens transitions to spore, biofilm exopolysaccharide and competence expression by two different mechanisms. Mol Microbiol 80: 1014-1030. PMI: 21435029

Parashar V, Mirouze N, Dubnau DA, Neiditch MB (2011) Structural basis of response regulator dephosphorylation by Rap phosphatases. PLoS Biol 9: e1000589. PMI: 21346797

Mirouze N, Prepiak P, Dubnau D (2011) Fluctuations in spo0A transcription control rare developmental transitions in Bacillus subtilis. PLoS Genet 7: e1002048. PMI: 21552330

Mirouze N, Parashar V, Baker MD, Dubnau DA, Neiditch MB (2011) An atypical Phr peptide regulates the developmental switch protein RapH. J Bacteriol 193: 6197-6206. PMI: 21908671

Dubnau D (2011) Winner takes all in a race for cell fate. Mol Syst Biol 7: 558. PMI: 22146302

Briley K, Jr., Prepiak P, Dias MJ, Hahn J, Dubnau D (2011) Maf acts downstream of ComGA to arrest cell division in competent cells of B. subtilis. Mol Microbiol 81: 23-39. PMI: 21564336

Briley K, Jr., Dorsey-Oresto A, Prepiak P, Dias MJ, Mann JM, Dubnau D (2011) The secretion ATPase ComGA is required for the binding and transport of transforming DNA. Mol Microbiol 81: 818-830. PMI: 21707789

Dubnau D (2010) Swim or chill: lifestyles of a bacillus. Genes Dev 24: 735-737. PMI: 20395361

Burton B, Dubnau D (2010) Membrane-associated DNA transport machines. Cold Spring Harb Perspect Biol 2: a000406. PMI: 20573715

Kojetin DJ, McLaughlin PD, Thompson RJ, Dubnau D, Prepiak P, Rance M, Cavanagh J (2009) Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions. J Mol Biol 387: 639-652. PMI: 19361434

Johnsen PJ, Dubnau D, Levin BR (2009) Episodic selection and the maintenance of competence and natural transformation in Bacillus subtilis. Genetics 181: 1521-1533. PMI: 19189946

Hahn J, Kramer N, Briley K, Jr., Dubnau D (2009) McsA and B mediate the delocalization of competence proteins from the cell poles of Bacillus subtilis. Mol Microbiol 72: 202-215. PMI: 19226326

Okada M, Yamaguchi H, Sato I, Tsuji F, Dubnau D, Sakagami Y (2008) Chemical structure of posttranslational modification with a farnesyl group on tryptophan. Biosci Biotechnol Biochem 72: 914-918. PMI: 18323630

Smits WK, Hoa TT, Hamoen LW, Kuipers OP, Dubnau D (2007) Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein. Mol Microbiol 64: 368-381. PMI: 17493123

Prepiak P, Dubnau D (2007) A peptide signal for adapter protein-mediated degradation by the AAA+ protease ClpCP. Mol Cell 26: 639-647. PMI: 17560370

Okada M, Yamaguchi H, Sato I, Tsuji F, Qi J, Dubnau D, Sakagami Y (2007) Acid labile ComX pheromone from Bacillus mojavensis RO-H-1. Biosci Biotechnol Biochem 71: 1807-1810. PMI: 17617699

Okada M, Yamaguchi H, Sato I, Cho SJ, Dubnau D, Sakagami Y (2007) Structure-activity relationship studies on quorum sensing ComX(RO-E-2) pheromone. Bioorg Med Chem Lett 17: 1705-1707. PMI: 17240141

Maamar H, Raj A, Dubnau D (2007) Noise in gene expression determines cell fate in Bacillus subtilis. Science 317: 526-529. PMI: 17569828

Kramer N, Hahn J, Dubnau D (2007) Multiple interactions among the competence proteins of Bacillus subtilis. Mol Microbiol 65: 454-464. PMI: 17630974

Dubnau D, Losick R (2006) Bistability in bacteria. Mol Microbiol 61: 564-572. PMI: 16879639

Chen I, Provvedi R, Dubnau D (2006) A macromolecular complex formed by a pilin-like protein in competent Bacillus subtilis. J Biol Chem 281: 21720-21727. PMI: 16751195

Okada M, Sato I, Cho SJ, Iwata H, Nishio T, Dubnau D, Sakagami Y (2005) Structure of the Bacillus subtilis quorum-sensing peptide pheromone ComX. Nat Chem Biol 1: 23-24. PMI: 16407988

Maamar H, Dubnau D (2005) Bistability in the Bacillus subtilis K-state (competence) system requires a positive feedback loop. Mol Microbiol 56: 615-624. PMI: 15819619

Hahn J, Maier B, Haijema BJ, Sheetz M, Dubnau D (2005) Transformation proteins and DNA uptake localize to the cell poles in Bacillus subtilis. Cell 122: 59-71. PMI: 16009133

Draskovic I, Dubnau D (2005) In Mullaney P (ed.), The Dynamic bacterial genome and its biological consequences. Cambridge University Press, Cambridge, UK.

Draskovic I, Dubnau D (2005) Biogenesis of a putative channel protein, ComEC, required for DNA uptake: membrane topology, oligomerization and formation of disulphide bonds. Mol Microbiol 55: 881-896. PMI: 15661011

Chen I, Christie PJ, Dubnau D (2005) The ins and outs of DNA transfer in bacteria. Science 310: 1456-1460. PMI: 16322448

Albano M, Smits WK, Ho LT, Kraigher B, Mandic-Mulec I, Kuipers OP, Dubnau D (2005) The Rok protein of Bacillus subtilis represses genes for cell surface and extracellular functions. J Bacteriol 187: 2010-2019. PMI: 15743949

Okada M, Sato I, Cho SJ, Suzuki Y, Ojika M, Dubnau D, Sakagami Y (2004) Towards structural determination of the ComX pheromone: synthetic studies on peptides containing geranyltryptophan. Biosci Biotechnol Biochem 68: 2374-2387. PMI: 15564679

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 11: 643-649. PMI: 15184891

Chen I, Dubnau D (2004) DNA uptake during bacterial transformation. Nat Rev Microbiol 2: 241-249. PMI: 15083159

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 186: 15-21. PMI: 14679219

Chen I, Dubnau D (2003) DNA transport during transformation. Front Biosci 8: s544-556. PMI: 12700070

Persuh M, Mandic-Mulec I, Dubnau D (2002) A MecA paralog, YpbH, binds ClpC, affecting both competence and sporulation. J Bacteriol 184: 2310-2313. PMI: 11914365

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 277: 6994-7001. PMI: 11744713

Hoa TT, Tortosa P, Albano M, Dubnau D (2002) Rok (YkuW) regulates genetic competence in Bacillus subtilis by directly repressing comK. Mol Microbiol 43: 15-26. PMI: 11849533

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 43: 1331-1345. PMI: 11918817

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 44: 1561-1573. PMI: 12067344

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 42: 717-727. PMI: 11722737

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 183: 451-460. PMI: 11133937

Provvedi R, Chen I, Dubnau D (2001) NucA is required for DNA cleavage during transformation of Bacillus subtilis. Mol Microbiol 40: 634-644. PMI: 11359569

Haijema BJ, Hahn J, Haynes J, Dubnau D (2001) A ComGA-dependent checkpoint limits growth during the escape from competence. Mol Microbiol 40: 52-64. PMI: 11298275

Tortosa P, Albano M, Dubnau D (2000) Characterization of ylbF, a new gene involved in competence development and sporulation in Bacillus subtilis. Mol Microbiol 35: 1110-1119. PMI: 10712692

Dubnau D, Turgay K (2000) In Storz G and Hengge-Aronis R (eds.), Bacterial Stress Responses. American Society for Microbiology, Washington, DC, pp. 249-260.

Tortosa P, Dubnau D (1999) Competence for transformation: a matter of taste. Curr Opin Microbiol 2: 588-592. PMI: 10607621

Piazza F, Tortosa P, 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. PMI: 10419951

Persuh M, Turgay K, Mandic-Mulec I, Dubnau D (1999) The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch. Mol Microbiol 33: 886-894. PMI: 10447896

Dubnau D (1999) DNA uptake in bacteria. Annu Rev Microbiol 53: 217-244. PMI: 10547691

Turgay K, Hahn J, Burghoorn J, Dubnau D (1998) Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J 17: 6730-6738. PMI: 9890793