Abstract
Carbohydrate metabolism plays a crucial role in the ecophysiology of human gut microbiota. Mechanisms of transcriptional regulation of sugar catabolism in commensal and prevalent human gut bacteria such as Bacteroides thetaiotaomicron remain mostly unknown. By a combination of bioinformatics and experimental approaches, we have identified an NrtR family transcription factor (BT0354 in B. thetaiotaomicron, BtAraR) as a novel regulator controlling the arabinose utilization genes. L-arabinose was confirmed to be a negative effector of BtAraR. We have solved the crystal structures of the apo and L-arabinose-bound BtAraR proteins, as well as the complex of apo-protein with a specific DNA operator. BtAraR forms a homodimer with each subunit comprised of the ligand-binding Nudix hydrolase-like domain and the DNA-binding winged-helix-turn-helix (wHTH) domain. We have identified the residues involved in binding of L-arabinose and recognition of DNA. The majority of these residues are well conserved in the AraR orthologs in Bacteroidetes. 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. Our analysis facilitates reconstruction of the metabolic and regulatory networks involved in carbohydrate utilization in human gut Bacteroides.
Highlights
The human gastrointestinal tract is predominantly a bacterial ecosystem that is largely represented by microorganisms from two divisions––the Bacteroidetes and the Firmicutes [1,2]
The Bacteroides genus includes commensal Gram-negative anaerobic bacteria that play a fundamental role in the breakdown of dietary polysaccharides in the host intestine [3,4], and that have evolved a divergent array of genes involved in sensing, regulation and polysaccharide degradation and utilization [5]
In this study we identified and characterized a novel L-arabinose-responsive transcription factor found in the Bacteroides species, which belongs to the NrtR family of Nudix-related transcriptional regulators [15]
Summary
The human gastrointestinal tract is predominantly a bacterial ecosystem that is largely represented by microorganisms from two divisions––the Bacteroidetes and the Firmicutes [1,2]. The Bacteroides genus includes commensal Gram-negative anaerobic bacteria that play a fundamental role in the breakdown of dietary polysaccharides in the host intestine [3,4], and that have evolved a divergent array of genes involved in sensing, regulation and polysaccharide degradation and utilization [5]. Decomposition and further utilization of complex and diverse oligosaccharides play a critical role in the ecophysiology of human gut microbiota. The ability to confidently reconstruct respective biochemical and regulatory networks from genomic and metagenomic data would strongly impact predictive modeling of microbial communities and their interactions with the host in health and disease. Presently this ability is hampered by a limited knowledge of functions of their key components (transporters, regulators, enzymes). Combining structural genomics with predictive bioinformatics and experimental functional characterization allows us to fill in major gaps in this knowledge and enables accurate reconstruction of carbohydrate metabolism in previously uncharacterized microbial species and communities
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