How Aromatic Compounds Block DNA Binding of HcaR Catabolite Regulator

Abstract

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.

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

“…The location and secondary structural composition of this hydrophobic cleft is analogous to those observed in structures of MarR family members bound to various phenolic acids and aldehyde ligands lacking CoA (3,8,18,19). Sufficient electron density was observed to model four pCCs bound to four CouR monomers in the crystallographic ASU.…”

“…D, sequence of oligonucleotide duplex used in crystallization. E, a multisequence alignment of MarR family proteins featuring CouR from R. palustris CGA009 (CouR-RP), CouR from R. jostii RHA1 (CouR-RJ), MepR, HcaR, MexR, and PcaV(3,4,17,19,31).…”

Tuning site-specific dynamics to drive allosteric activation in a pneumococcal zinc uptake regulator

“…show that apo-AdcR is less compact than the Zn II 2 state. As in the Zn II 2 state, the b-wing 239 tumbles independently of the rest of the molecule, revealing that a change in the flexibility or 240 orientation of the b-hairpin is likely not part of the allosteric mechanism, contrary to what has 241 been proposed for other MarRs on the basis of crystal structures alone (Liu et al, 2017, 242 Deochand & Grove, 2017, Kim et al, 2016). Overall, the 15 N relaxation data for backbone 243 amides show that Zn II binding leads to a reduction of mobility of the a1-a2 loop, which in turn, 244 decreases the dynamical independence the DNA-binding and dimerization domains, thereby 245 stabilizing a conformation that tumbles in solution as a single globular unit.…”

“…The generality of this simple paradigm is inconsistent with the findings that some MarR proteins 75 share very similar static structures in the active (DNA binding-competent) and inactive (DNA 76 binding-incompetent) states (Anandapadamanaban et al, 2016, Kim et al, 2016, Liguori et al, 77 2016; furthermore, several active states have been shown to require a significant rearrangement 78 to bind DNA (Alekshun et al, 2001, Zhu et al, 2017b, Hao et al, 2013, Gao et 79 al., 2017, Chin et al, 2006, Saridakis et al, 2008. In fact, a comprehensive analysis of all 80 available MarR family structures strongly suggests that the degree of structural reorganization 81 required to bind DNA, characterized by a narrow distribution of α4-α4' orientations, is 82 comparable whether transitioning from the inactive or active states of the repressor (Fig.…”

Caracterização funcional de fatores de transcrição da família MarR de Chromobacterium violaceum

“…A asa (winged) consiste de duas folhas- antiparalelas (2 e 3), sendo estabilizada em parte por uma cadeia beta curta (1), criando uma folha beta de três filamentos (PERERA; GROVE, 2010b). A hélice de reconhecimento (4) de cada monômero ligase à região do sulco maior no DNA, onde estão as sequências palindrômicas, enquanto os aminoácidos da asa interagem com a região do sulco menor (Figura 1C e 1D) (GROVE, 2017;KIM et al, 2016;KUMAREVEL, 2012).…”