Subdivision of the Helix-Turn-Helix GntR Family of Bacterial Regulators in the FadR, HutC, MocR, and YtrA Subfamilies

Abstract

Among transcription factors, several groups have been identified according to their conserved motifs and their modes of DNA binding such as helix-turn-helix, zinc-fingers, leucinezipper, homeodomain, and ␤-sheet DNA-binding proteins (2, 3). The most studied and best characterized is the HTH 1 group (1, 4 -8) in which the conserved DNA recognition motif consists of an ␣-helix, a turn, and a second ␣-helix, often called the "recognition" helix as it is the part of the HTH motif that fits into the DNA major groove. Generally, HTH proteins bind as dimers, 2-fold symmetric DNA sequences in which each monomer recognizes a half-site. This group is now considered as a reference for understanding the general rules that govern protein-DNA interactions (9, 10) and has also become a favorite target for evolutionary studies (8,11).Among HTH transcriptional regulators, families have been identified throughout sequence comparisons and phylogenetic, structural, and functional analyses focused on DNA-binding domains and almost exclusively on the HTH structure, which is the only active motif that shows strong similarities among all members of the group (1, 4, 6 -8, 11). These comparative studies have led to the determination of a specific HTH consensus pattern or signature for each family, providing the basis for a simple method of classification and detection of new members (12).The lack of significant similarity among regions involved in effector binding or oligomerization systematically excludes these domains during families signature establishment, although they have important roles in the regulating process. In fact, it is often the oligomerization between regulatory subunits and/or the conformational changes due to the binding or the removal of the inducing/repressing molecule that allows correct HTH motif disposition and the subsequent DNA binding ability of the whole regulatory protein. The link between the two regions is therefore more intimate than it first appears from a unique amino acids comparison and may also be reflected in the DNA operator sequences, the third structural element involved in gene regulation.To argue for the existence of a link between regions involved in the regulating process, we analyzed the HTH GntR family of bacterial regulators. As determined thus far, the family comprises about 270 members distributed among the most diverse bacterial groups and regulating the most various biological processes. This family was first described by Haydon and Guest in 1991 (1) and was named after GntR, the repressor of the gluconate operon in Bacillus subtilis (13,14). Our interest in the properties of these bacterial regulators arises from the identification by our laboratory of the xlnR gene (15) in which chromosomal disruption in Streptomyces lividans relieves various extracellular enzymatic systems from glucose repression.The first purpose of this report is to present, 10 years after the first comparative study, an update of the GntR family description. Moreover, we decided to analyze the full-length sequenc...

Positive transcriptional control of the pyridoxal phosphate biosynthesis genes pdxST by the MocR-type regulator PdxR of Corynebacterium glutamicum ATCC 13032

“…The corresponding gene region was isolated by complementing the pdx-4 mutation of S. venezuelae, indicating a relationship between the expression of ORF1 and the availability of pyridoxal. The protein encoded by ORF1 can be classified as a member of the MocR subfamily of GntR-type transcription regulators (Magarvey et al, 2001;Rigali et al, 2002). The PdxR protein from C. glutamicum was also grouped into this subfamily of regulatory proteins (Brune et al, 2005;McHardy et al, 2003).…”

“…These DNA motifs are therefore likely candidates for DNA-binding sites of the transcription regulator PdxR. As knowledge of DNA-binding sites of MocR-type transcription regulators is very scarce (Rigali et al, 2002), the functional relevance of the three motifs was investigated in vitro by DNA band shift assays with purified PdxR protein.…”

“…Protein domain predictions performed with the SUPERFAMILY tools (Gough et al, 2001) (Hoskisson & Rigali, 2009;Rigali et al, 2002). Aspartate aminotransferases are part of a large superfamily of PLP-binding enzymes (Schneider et al, 2000) sharing a prominent mechanistic feature in such a way that the PLP group is bound covalently to a conserved lysine residue (Sigrist et al, 2010).…”

Actinomycete integrative and conjugative pMEA-like elements of Amycolatopsis and Saccharopolyspora decoded

“…KorA of pMEA100 shows 38% identity to the N-terminal GntR-containing part of a regulatory protein of Ralstonia eutropha JMP134. This protein is approximately 2 times larger (235 aa) than KorA of pMEA100 and contains an additional C-terminal FadR domain, which is often found in regulators of fatty acid metabolism (Rigali et al, 2002). pSE222 lacks a GntR transcriptional regulator, but encodes a second XRE-family regulator (SACE_1139) instead.…”

“…The impA gene together with the translationally coupled impC, constitute the imp (inhibition of plasmid maintenance) locus of SLP1 and also prevents replication and transfer of the integrated SLP1 (Shiffman and Cohen, 1993). GntR domains are often located at the N-terminal part of transcriptional regulators with a variable effector-binding/oligomerisation domain at the C-terminus that modulates the activity of the DNA-binding protein (Rigali et al, 2002). The pMEA-related Kor proteins, however, are approximately half the size of other AICE Kor proteins and do not have an additional known conserved domain besides the DNA-binding domain.…”