Structural basis of transcriptional regulation by CouR, a repressor of coumarate catabolism, in Rhodopseudomonas palustris

Abstract

The MarR family transcriptional regulator CouR, from the soil bacterium CGA009, has recently been shown to negatively regulate a-coumarate catabolic operon. Unlike most characterized MarR repressors that respond to small metabolites at concentrations in the millimolar range, repression by CouR is alleviated by the 800-Da ligand -coumaroyl-CoA with high affinity and specificity. Here we report the crystal structures of ligand-free CouR as well as the complex with-coumaroyl-CoA, each to 2.1-Å resolution, and the 2.85-Å resolution cocrystal structure of CouR bound to an oligonucleotide bearing the cognate DNA operator sequence. In combination with binding experiments that uncover specific residues important for ligand and DNA recognition, these structures provide glimpses of a MarR family repressor in all possible states, providing an understanding of the molecular basis of DNA binding and the conformation alterations that accompany ligand-induced dissociation for activation of the operon.

Transcriptional Profiling Reveals the Importance of RcrR in the Regulation of Multiple Sugar Transportation and Biofilm Formation in Streptococcus mutans

“…Meanwhile, oligonucleotide 21 plus oligonucleotide 22 was a palindromic sequence with high AT content, suggesting that RcrR prefers binding to DNA regions with high AT content. This preference was also similar to those of the MarR family regulators CouR ( 26 ) and FabT ( 27 ).…”

Mechanism of transcription regulation by Acinetobacter baumannii HpaR in the catabolism of p‐hydroxyphenylacetate

“…Crystal structure of Ab HpaR in complex with 23‐bp oligonucleotide containing Box A sequence showed that both Ab HpaR and DNA need to undergo structural changes upon complex formation. Although the conformational difference of Ab HpaR between the apo and the DNA‐bound states [37,42] is not drastic, it is similar to what had been observed in other MarR proteins [21,46]. Deviation from ideal B‐form is also common for DNA in the protein‐bound state [53].…”

“…6B), which could play a role in stabilizing Arg88 in a position that is optimal for DNA contact. Similar Asp‐X‐Arg sequence motif is prevalent in the wing portion of MarR proteins [30,36–38,46–48].…”

Characterization of the first tetrameric transcription factor of the GntR superfamily with allosteric regulation from the bacterial pathogenAgrobacterium fabrum

“…Each dimer of Atu1419 within the tetramer can bind an identical palindrome. Similarly to regulators with a wHTH motif such as MarR regulators ( 40 , 41 ), FCD regulators bind to one half-site of the palindromic DNA, with the dimerization interface helping to establish the spacing between the two half-sites. The DNA binding domains of Atu1419, which are involved in the dimerization interface, allow Atu1419 to bind a short palindrome of 10 base pairs.…”