A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.
Bottom Line: L-arabinose was confirmed to be a negative effector of BtAraR.In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA.L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding.
Affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.Show MeSH
Mentions: Orthologs of the B. thetaiotaomicron AraR (BT0354) and XylR (BT0791) regulators were identified only within the Bacteroidetes phylum. AraR is present in 17 Bacteroides and 15 Prevotella spp., whereas XylR was found in 25 Bacteroides spp. and in several other Bacteroidetes (Figure 1A). We noted a strong tendency of araR and xylR genes to cluster on the chromosome with the arabinose and xylose utilization genes, respectively. Among 30 non-redundant Bacteroides species analyzed in this work, the AraR regulators and arabinose catabolic pathway genes were found in 17 species, while the other 13 Bacteroides species potentially have lost the arabinose catabolic genes. Multiple alignments of these AraR proteins revealed high overall conservation of their primary sequences (Supplementary Figure S1), suggesting the AraR orthologs are functionally identical with potentially preserved specificities toward the effector molecule and DNA sites. The Nudix signature motif GX5-EX7REUXEEXGU (where U is a hydrophobic residue and X is any residue) is strictly conserved in all known active Nudix hydrolases, but it is impaired in the NrtR regulators of NAD metabolism, several of which are known to be enzymatically inactive (15). Similarly to NrtR regulators, the Nudix signature motif is not conserved in the AraR proteins from Bacteroidetes, where two or three glutamate residues are substituted with other amino acids (Supplementary Figure S1). These observations suggest that AraR regulators are also enzymatically inactive and utilize their Nudix hydrolase-like domains for ligand binding.
Affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.