Congratulations to Mudassar on publication of his paper on transcription regulator activities in Streptomyces coelicolor

Congratulations to Mudassar on the publication of his latest paper in Nucleic Acids Research, Volume . This is work from his previous post with Nigel Burroughs.

Iqbal, M., Mast, Y., Amin, R., Hodgson, D.A., The STREAM Consortium, Wohlleben, W. and Burroughs, N.J. 2012. Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor.

Abstract

Determining transcriptional regulator activities is a major focus of systems biology, providing key insight into regulatory mechanisms and co-regulators. For organisms such as Escherichia coli, transcriptional regulator binding site data can be integrated with expression data to infer transcriptional regulator activities. However, for most organisms there is only sparse data on their transcriptional regulators, while their associated binding motifs are largely unknown. Here, we address the challenge of inferring activities of unknown regulators by generating de novo (binding) motifs and integrating with expression data. We identify a number of key regulators active in the metabolic switch, including PhoP with its associated directed repeat PHO box, candidate motifs for two SARPs, a CRP family regulator, an iron response regulator and that for LexA. Experimental validation for some of our predictions was obtained using gel-shift assays. Our analysis is applicable to any organism for which there is a reasonable amount of complementary expression data and for which motifs (either over represented or evolutionary conserved) can be identified in the genome.

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Congratulations to Hiroki Takahashi

Congratulations to Hiroki Takahashi who will be moving to Chiba University as a PI from 1st April 2012. Hiroki’s group will be based in the Medical Mycology Research Center and he expects the main focus of his research will be in analysis of next generation sequence data in a medical mycology context. We will, of course, be continuing our collaboration on metal regulation in pathogenic E. coli strains.