How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator

• Published in: The Journal of biological chemistry 2016-06, Vol.291 (25), p.13243-13256
• Main Authors: Kim, Youngchang, Joachimiak, Grazyna, Bigelow, Lance, Babnigg, Gyorgy, Joachimiak, Andrzej
• Format: Article
• Language: English
• Subjects: Acinetobacter; Amino Acid Sequence; arabinose utilization; Bacterial Proteins - chemistry; bacterial transcription; BASIC BIOLOGICAL SCIENCES; Binding Sites; Conserved Sequence; Coumaric Acids - chemistry; Crystallography, X-Ray; DNA binding; DNA, Bacterial - chemistry; DNA-binding protein; Gene Expression Regulation, Bacterial; Gene Regulation; human gut bacteria; ligand-binding protein; ligand-induced conformational change; ligand-induced conformationional change; metabolic regulation; Models, Molecular; Molecular Sequence Data; NUDIX family; Protein Binding; protein conformation; Protein Stability; Protein Structure, Secondary; Protein Structure, Tertiary; Transcription Factors - chemistry
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M115.712067

Bacterial catabolism of aromatic compounds from various sources including phenylpropanoids and flavonoids that are abundant in soil plays an important role in the recycling of carbon in the ecosystem. We have determined the crystal structures of apo-HcaR from Acinetobacter sp. ADP1, a MarR/SlyA transcription factor, in complexes with hydroxycinnamates and a specific DNA operator. The protein regulates the expression of the hca catabolic operon in Acinetobacter and related bacterial strains, allowing utilization of hydroxycinnamates as sole sources of carbon. HcaR binds multiple ligands, and as a result the transcription of genes encoding several catabolic enzymes is increased. The 1.9–2.4 Å resolution structures presented here explain how HcaR recognizes four ligands (ferulate, 3,4-dihydroxybenzoate, p-coumarate, and vanillin) using the same binding site. The ligand promiscuity appears to be an adaptation to match a broad specificity of hydroxycinnamate catabolic enzymes while responding to toxic thioester intermediates. Structures of apo-HcaR and in complex with a specific DNA hca operator when combined with binding studies of hydroxycinnamates show how aromatic ligands render HcaR unproductive in recognizing a specific DNA target. The current study contributes to a better understanding of the hca catabolic operon regulation mechanism by the transcription factor HcaR.