Extending the classification of bacterial transcription factors beyond the helix-turn-helix motif as an alternative approach to discover new cis/trans relationships

Nucleic Acids Research
Sébastien RigaliFritz Titgemeyer

Abstract

Transcription factors (TFs) of bacterial helix-turn-helix superfamilies exhibit different effector-binding domains (EBDs) fused to a DNA-binding domain with a common feature. In a previous study of the GntR superfamily, we demonstrated that classifying members into subfamilies according to the EBD heterogeneity highlighted unsuspected and accurate TF-binding site signatures. In this work, we present how such in silico analysis can provide prediction tools to discover new cis/trans relationships. The TF-binding site consensus of the HutC/GntR subfamily was used to (i) predict target sites within the Streptomyces coelicolor genome, (ii) discover a new HutC/GntR regulon and (iii) discover its specific TF. By scanning the S.coelicolor genome we identified a presumed new HutC regulon that comprises genes of the phosphotransferase system (PTS) specific for the uptake of N-acetylglucosamine (PTS(Nag)). A weight matrix was derived from the compilation of the predicted cis-acting elements upstream of each gene of the presumed regulon. Under the assumption that TFs are often subject to autoregulation, we used this matrix to scan the upstream region of the 24 HutC-like members of S.coelicolor. orf SCO5231 (dasR) was selected as the best c...Continue Reading

References

Jan 1, 1992·Annual Review of Biochemistry·C O Pabo, R T Sauer
Apr 15, 1991·FEMS Microbiology Letters·D J Haydon, J R Guest
May 5, 1986·Journal of Molecular Biology·F W Studier, B A Moffatt
Jan 1, 1993·Annual Review of Microbiology·M A Schell
Dec 16, 1997·Proceedings of the National Academy of Sciences of the United States of America·X Ni, J Westpheling
Jul 27, 1999·Molecular Microbiology·L J MotaI Sá-Nogueira
Sep 4, 1999·Journal of Molecular Evolution·J A Rosinski, W R Atchley
Mar 29, 2000·Nucleic Acids Research·E Pérez-Rueda, J Collado-Vides
May 17, 2000·Bioinformatics·G D Stormo
Jan 5, 2002·The Journal of Biological Chemistry·Sébastien RigaliJean Dusart
Apr 6, 2002·Current Opinion in Microbiology·Gary D Stormo, Kai Tan
Nov 9, 2002·FEMS Microbiology Letters·Yasuo OhnishiSueharu Horinouchi
Jun 28, 2003·FEMS Microbiology Reviews·Nigel L BrownJon L Hobman
Nov 18, 2003·Journal of Bacteriology·Harald NothaftFritz Titgemeyer
Dec 19, 2003·Nucleic Acids Research·Nicolas HuloAmos Bairoch

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Citations

Jan 6, 2010·Nucleic Acids Research·Marcus ReschYves A Muller
Apr 4, 2009·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Marcus ReschYves A Muller
May 24, 2011·Journal of Bacteriology·Ralph BertramFritz Titgemeyer
Jul 4, 2006·Journal of Bacteriology·Paul A HoskissonMark J Buttner
Aug 30, 2008·Journal of Bacteriology·Masakazu KataokaYusuke Kajiyama
Dec 22, 2006·Journal of Molecular Microbiology and Biotechnology·Séverine ColsonSébastien Rigali
Feb 4, 2012·PloS One·Adrien RichardAnnabelle Merieau
Oct 14, 2011·Yi chuan = Hereditas·Chi-Chu XieYue-Hua Chen
May 26, 2011·Natural Product Reports·Gilles P van Wezel, Kenneth J McDowall
Mar 10, 2010·Critical Reviews in Microbiology·Beatriz RuizElizabeth Langley
Apr 25, 2007·Biochemical and Biophysical Research Communications·Samuel HiardSébastien Rigali
Jul 14, 2006·Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution·Jianying GuYufeng Wang
Jun 14, 2013·Environmental Microbiology Reports·Matthias CraigSébastien Rigali
May 3, 2006·Current Opinion in Structural Biology·Mikhail S Gelfand
May 14, 2005·Journal of Molecular Biology·Michael E WallWilliam S Hlavacek
Jun 28, 2011·Biochemical and Biophysical Research Communications·Lei Ji, Jianping Xie
Nov 13, 2014·Molecular BioSystems·Sébastien RigaliPierre Tocquin
Jun 27, 2014·Frontiers in Microbiology·Dmitry A RavcheevDmitry A Rodionov
Jun 3, 2011·FEMS Microbiology Ecology·Behnam NazariTakeshi Fujii
Jun 8, 2017·Journal of the American Chemical Society·Fei XuMohammad R Seyedsayamdost
Sep 12, 2014·Molecular & Cellular Proteomics : MCP·Georgia Orfanoudaki, Anastassios Economou

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