Research Topics
| I B DoddSummaryAffiliation: University of Adelaide Country: Australia Publications
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Publications
Octamerization of lambda CI repressor is needed for effective repression of P(RM) and efficient switching from lysogenyI B Dodd
Department of Molecular Biosciences, University of Adelaide, South Australia 5005, Australia
Genes Dev 15:3013-22. 2001..We propose the octameric CI:O(R)-O(L) complex increases the affinity of CI for O(R)3 by allowing a CI tetramer to link O(R)3 and the third operator at O(L), O(L)3...- Action at a distance in CI repressor regulation of the bacteriophage 186 genetic switchIan B Dodd
Department of Molecular Biosciences Biochemistry, University of Adelaide, South Australia, Australia
Mol Microbiol 45:697-710. 2002..We propose that the 186 switch is regulated by a novel mechanism in which a CI octamer bound at pR forms alternative DNA loops to pL or to a flanking site, depending on CI concentration... - Cooperativity in long-range gene regulation by the lambda CI repressorIan B Dodd
Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
Genes Dev 18:344-54. 2004..The results establish the lambda system as a powerful tool for examining long-range gene regulatory interactions in vivo... - Revisited gene regulation in bacteriophage lambdaIan B Dodd
Discipline of Biochemistry, School of Molecular and Biomedical Science, University of Adelaide, South Australia 5005, Australia
Curr Opin Genet Dev 15:145-52. 2005..New genetic and quantitative analysis of the lambda gene network is challenging cherished ideas about how complex behaviours emerge from this regulatory system... - Modelling transcriptional interference and DNA looping in gene regulationIan B Dodd
Centre for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
J Mol Biol 369:1200-13. 2007..Our results demonstrate the power of mathematical modelling for the extraction of detailed biochemical information from in vivo data... - Barriers and silencers: a theoretical toolkit for control and containment of nucleosome-based epigenetic statesIan B Dodd
Center for Models of Life, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, 2100 Copenhagen Ø, Denmark
J Mol Biol 414:624-37. 2011..Thus, a relatively simple set of nucleosome-modifying enzymes and recognition domains is all that is needed to make chromatin-based epigenetics useful and safe... - Potent transcriptional interference by pausing of RNA polymerases over a downstream promoterAdam C Palmer
School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia
Mol Cell 34:545-55. 2009..Gene regulation by pausing-enhanced occlusion provides a general and potentially widespread mechanism by which even weak converging or tandem transcription, either coding or noncoding, can bring about strong in cis repression... - The helix-turn-helix motif of the coliphage 186 immunity repressor binds to two distinct recognition sequencesKeith E Shearwin
Department of Molecular Biosciences, University of Adelaide, Adelaide, Australia 5005
J Biol Chem 277:3186-94. 2002..Site-directed mutation of the putative 186 HTH motif eliminates binding to both A and B type sites, supporting the idea that binding to the two distinct DNA sequences is mediated by a variant HTH motif... - Cro's role in the CI Cro bistable switch is critical for {lambda}'s transition from lysogeny to lytic developmentRachel A Schubert
Molecular and Biomedical Sciences Biochemistry, University of Adelaide, Adelaide, SA 5005, Australia
Genes Dev 21:2461-72. 2007..Thus a bistable CI-Cro circuit reinforces the commitment to a developmental transition... - The late-expressed region of the temperate coliphage 186 genomeR Portelli
Department of Biochemistry, University of Adelaide, Adelaide, 5005, Australia
Virology 248:117-30. 1998..The relative absence of lysogenic conversion genes in 186 suggests that the two phages have evolved to use the lytic and lysogenic reproductive modes to different extents... - A mathematical model for transcriptional interference by RNA polymerase traffic in Escherichia coliKim Sneppen
NORDITA, Nordic Institute for Theoretical Physics, Niels Bohr Institute, Blegdamsvej 17, DK 2100 Copenhagen, Denmark
J Mol Biol 346:399-409. 2005..The model provides a framework for using transcriptional interference to investigate various dynamic processes on DNA in vivo... - Minimal gene regulatory circuits that can count like bacteriophage lambdaM Avlund
Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
J Mol Biol 394:681-93. 2009..Our study suggests that additional regulatory mechanisms to decouple Cro and CII levels may exist in lambda and that infection counting could be widespread among temperate bacteriophages, many of which contain CI-Cro-like circuits... - Why do phage play dice?Mikkel Avlund
Center for Models of Life, Niels Bohr Institute, Copenhagen, Denmark
J Virol 83:11416-20. 2009..Crucial to the argument is the clonal identity of the phage... - Theory for the stability and regulation of epigenetic landscapesMille A Micheelsen
Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, DK 2100, Copenhagen Ø, Denmark
Phys Biol 7:026010. 2010..This combined treatment of noisy dynamics both between and during cell division provides an efficient way to calculate the stability of alternative states in a broad range of epigenetic systems... - The generation of promoter-mediated transcriptional noise in bacteriaNamiko Mitarai
Department of Physics, Kyushu University, Fukuoka, Japan
PLoS Comput Biol 4:e1000109. 2008..Both mechanisms are tunable by the alteration of promoter kinetics and therefore allow the optimization of promoter mediated noise... - Bacteriophage P4 Vis protein is needed for prophage excisionSimona Calì
Dipartimento di Scienze Biomolecolari e Biotecnologie, Universita degli Studi di Milano, 20133 Milan, Italy
Virology 322:82-92. 2004..Furthermore, we mapped by primer extension the 5' end of the int transcript and found that ectopic expression of Vis reduced its signal intensity, suggesting that Vis is also involved in negative regulation of the int promoter... - The structural basis of cooperative regulation at an alternate genetic switchHeather W Pinkett
Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, 37th and Hamilton Walk, Philadelphia, 19102, USA
Mol Cell 21:605-15. 2006..Whereas the overall fold of the 186 and lambda repressor monomers is remarkably similar, the way the two repressors cooperatively assemble is quite different and explains in part the differences in their regulatory activity... - Functional alignment of regulatory networks: a study of temperate phagesAla Trusina
Department of Theoretical Physics, Umea University, Umea, Sweden
PLoS Comput Biol 1:e74. 2005..We finally discuss how network alignment can be used to pinpoint protein similarities viewed from the network perspective...