E. coli genome-wide promoter analysis in search for potential AtoC target elements

E. coli genome-wide promoter analysis in search for potential AtoC target elements

Kolisis, Fragiskos N.

Chatziioannou, Aristotelis

Panagiotidis, A.C.

Grigoroudis, A

Kyriakidis, D.A.

The AtoSC two-component system in E. coli activates atoDAEB operon genes to catabolize short-chain fatty acids, acetoacetate being the inducer. The AtoC response regulator was first described as the Antizyme of the polyamine biosynthetic ornithine decarboxylase. The AtoC binding site within the ato promoter was experimentally verified as an inverted 20 bp palindromic repeat. Transcriptome and phenotypic analyses however, indicated the involvement of atoSC to various other cellular activities, such as flagellar synthesis. Here we report a bioinformatic analysis for the localization of the AtoC binding motif within the E. coli genome that could indicate a putative implication, direct or indirect, of the AtoC in other operons regulation. A genome-wide promoter analysis was performed using a program for the de novo detection of overrepresented motifs within promoters. The motif sampling was initiated using the intergenic region where the AtoC binding site is located. By applying an iterative algorithm, including TCS regulated promoters, the program resulted to promoter sets comprising high-scoring putative cis-regulatory elements. The AtoC binding ability to these elements was tested by chromatin immunoprecipitation, using anti-AtoC polyclonal antibody. MotifScanner identified occurrences of different motifs connected to the ato palindromic sequence, and those related to established AtoC functions were singled out and used as templates for the design of primers, in order to analyse the immunoprecipitated chromatin in strains lacking or comprising atoSC, with or without acetoacetate induction. Experimental verification of predicted correlations could provide an insight to gene regulatory networks in bacteria, enabling us to foresee potential targets for response regulators.

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Εθνικό Ίδρυμα Ερευνών (ΕΙΕ)

Ήλιος - Αποθετήριο Εθνικού Ιδρύματος Ερευνών

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2010-04-23T10:52:30Z

2008-06

2012-06-12T12:23:29Z

http://hdl.handle.net/10442/8339

DOI: http://dx.doi.org/10.1111/j.1742-4658.2008.06448.x

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