1. Domain Assignment to Transcription Factors 416 Proteins with at least one SCOP DBD assignment 416 Proteins with at least one SCOP DBD assignment PFAM assignments 416 proteins with DBD assignment 271 Transcription Factors 113 with regulated gene information + 158 with DBD 271 Transcription Factors 113 with regulated gene information + 158 with DBD Remove 145 proteins (Transposases, Replication/Repair and Restriction Enzymes) Remove 145 proteins (Transposases, Replication/Repair and Restriction Enzymes) To gain insight into the evolution and organisation of the transcription factors in E. coli, we used the information available in RegulonDB (Salgado et al., 2001) on TFs and their regulated genes. To find out about the domain architecture and family membership of E. coli TFs, we used the SUPERFAMILY (Gough et al., 2001) database of structural assignments to predicted proteins from the E. coli genome, and extracted all those with DNA-binding domains (DBDs). Using the functional annotation for the E. coli genome, we removed proteins involved in replication & repair, restriction enzymes and transposases.

2. Repertoire of DNA Binding Domains in E. coli TFs “Winged” helix Lambda repressor-like C-terminal effector domain of the bipartite response regulator Homeodomain-likeFIS-like Nucleic acid binding proteinTrp repressor Met repressor-like 1jhf 1efa 1rnl 1bl0 1etx 1jhg 1cmb 1mjc Putative DNA binding protein 1exi 1ihf IHF-like DNA-binding proteins Flagellar transcriptional activator FlhD 1g8e

3. Domain Analysis of E. coli TFs On average each TF has two domains: one DBD and a partner domain which is generally the control domain On average each TF has two domains: one DBD and a partner domain which is generally the control domain 1 Domain TFs 3 Domain TFs 2 Domain TFs 2% 4 Domain TFs 76% 13% 9% Small Molecule Binding Domain Enzyme Domain Receiver Domain Protein Interaction Domain DNA Binding Domain Domain of unknown function The activity of ~90% of transcription factors is controlled by a second domain and only ~10% is controlled at the transcriptional level In E. coli, there are 271 TFs that belong to 11 DBD families and 46 different partner domains as identified in SUPERFAMILY. The domains can be broadly classified into six functional classes as mentioned above. About two thirds of the 271 proteins have the same domain architecture as at least one other protein, and have thus arisen as a consequence of duplication of a complete gene (Apic et al., 2001 show that proteins with identical domain architecture are highly likely to be direct duplicates.) On average, each TF is made up of two domains, and the neighbouring domains to the DBD are of the small molecule binding type in 120 of the 240 multidomain proteins. 44% 11% 5% 7% 12% 22%