Activators Repressors and Dual Regulators Activators R - PDF document

Activators, Repressors and Dual Regulators Domain architecture, DNA binding domain or partner domain type is NOT indicative of the regulatory function Domain architecture, DNA binding domain or partner domain type is NOT indicative of the regulatory function 0246810121416 -600 -300 300 600 900 123456 -600 -300 600 900 Activator Binding SitesRepressor Binding SitesTranscription start siteTranscription start sitePosition of the TF binding sitePosition of the TF binding site Number of examples Number of examples Distance of the TF binding site from the transcription start site is the determining factor Distance of the TF binding site from the transcription start site is the determining factor 6A:1R:6D 1R 1A 1A 1D 1D RD1R1R1R1R1R1R M. Madan Babu http://www. Homeodomain“winged helix” DNA binding domain loop containing nucleotide triphosphate hydrolases(Pd)Putative DNA-binding domain Lambda repressor-like DNA binding domainPutative DNA-bending domain Cterminal effector domainof the Bipartite response regulatorFISlike Nucleic acid-binding proteinsDistribution of DBDs in the TF Regulatory Network CRP + +++_ __ _ _ + ++ + + Gene Product Negative regulationwith binding site data Positive regulationwith binding site data _Negative regulationwithout binding site data +Positive regulationwithout binding site data madanm@mrcM. Madan Babu http://www. Information on the regulated gene is available for 92 TFs from RegulonDB. We classified the 92 TFs in to nine functional classes according to what they respond to and what they regulate. Each of these functional classes have one to three proteins (global regulators) that regulate over 50 genes and the other proteins (fine tuners) control fewer than 20 genes Information on the regulated gene is available for 92 TFs from RegulonDB. We classified the 92 TFs in to nine functional classes according to what they respond to and what they regulate. Each of these functional classes have one to three proteins (global regulators) that regulate over 50 genes and the other proteins (fine tuners) control fewer than 20 genesTranscription Factors and their regulated genes Transcription Factors and their regulated genes Transcription Factors and their regulated TFs Transcription Factors and their regulated TFs 026810121618X = 1X = 2X = 3X = 4X = 17 Number of different TF genes (X) regulated by a transcription factor Number of Examples Very few TFs regulate more than one TF The TF network has four major regulatory hubs which are also global regulators in their respective functional class. The TF network has four major regulatory hubs which are also global regulators in their respective functional class.A relatively complex topology exists in a simple organism A relatively complex topology exists in a simple organism M. Madan Babu http://www. References Blattner FR, et al.(1997)The complete Genome Sequence of Escherichia coli K12. Science 277: 1453-Murzin AG, Brenner SE, et al.(1995)a structural classification of proteins database for the investigation of sequences and structures." Journal of Molecular Biology247: 536-Gough J and Chothia C (2002)"SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments." Nucleic Acids Res30: 268-Salgado H, Santos-Zavaleta A, Gama-Castro S, et al.(2001)RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli K-. Nucleic Acids Research29: 72-Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J(1998)From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. 20: 433-Rueda E and Collado-Vides J(2000)The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-Nucleic Acids Research28: 1838-Apic G, Gough J and Teichmann SA(2001)Domain combinations in archaeal, eubacterial and eukaryotic proteomes.Journal of Molecular Biology310: 311- M. Madan Babu http://www.