The IclR family of transcriptional activators and repressors can be defined by a single profile

Abstract

In the last decade enormous advances in life sciences have been possible due to the information obtained from DNA sequencing projects. The optimal interpretation and analysis of genome sequence data requires the precise annotation and classification of proteins deduced from open reading frames, which is usually done with the help of family-specific signatures. Here we report a novel profile for the IclR type of transcriptional activators and repressors. In contrast to profiles for other families of transcriptional regulators, the new IclR profile is located outside the helix-turn-helix DNA-binding motif. We provide evidence that the new profile is more specific than any of the existing signatures for this family of regulators. More than 500 representatives of this family were identified with this profile. A database on bacterial regulators (http://www.bactregulators.org) was built to compile and regroup the sequences with the aid of the new profile.

TtgV Represses Two Different Promoters by Recognizing Different Sequences

“…Below is the physical organization of the members of the IclR family, consisting of two domains, one involved in DNA recognition and another that includes a central segment of the proteins and extends toward the C-terminal end. The second domain seems to be involved in effector recognition and multimerization (5,10). PFAM refers to the HMM algorithm identifying IclR members in that region.…”

“…The high level of tolerance to toluene in Pseudomonas putida DOT-T1E is mediated mainly by three efflux pumps, two of which-TtgGHI and TtgDEF-are under crossregulation by the IclR family multidrug recognition regulators TtgV and TtgT (10,12). Of these two repressors, TtgV has been shown to play a dominant role in the transcriptional control of these two pumps in vivo (27).…”

Relevance of nucleotides of the PcaU binding site from Acinetobacter baylyi

“…Of all 540 recognized members of the IclR family Krell et al, 2006;Mulder et al, 2005) only a small number (20 regulators) have been investigated experimentally, and only for some of them is the binding site known. A conserved IclR-type DNA binding site cannot be found, but for a subgroup within the family (namely the PcaU/PobR/PcaR group) there is a conserved sequence motif (Fig.…”

Functional Identification of OphR, an IclR Family Transcriptional Regulator Involved in the Regulation of the Phthalate Catabolic Operon in Rhodococcus sp. Strain DK17

“…Helices a2 and a3 form a helix-loop-helix (HLH) motif, which is the DNAbinding motif (for DNA sequence recognition). Although the sequence in that region is specific for the DNA recognition sequence, conserved residues (D/E in helix a2 and M/L in helix a3 following G) [12] are also found in OphR. In particular, it is noteworthy that the amino acid substitutions observed between the pDK2-encoded and the pDK3-encoded OphR proteins are located at the positions corresponding to the loops connecting helices a1 and a2, b1 and b2, the b5 strand, and the end of helix a8 in the T. maritima IclR.…”