Structural basis for DNA recognition by the transcription regulator MetR

Abstract

MetR, a LysR-type transcriptional regulator (LTTR), has been extensively studied owing to its role in the control of methionine biosynthesis in proteobacteria. A MetR homodimer binds to a 24-base-pair operator region of the met genes and specifically recognizes the interrupted palindromic sequence 5'-TGAA-N5-TTCA-3'. Mechanistic details underlying the interaction of MetR with its target DNA at the molecular level remain unknown. In this work, the crystal structure of the DNA-binding domain (DBD) of MetR was determined at 2.16 Å resolution. MetR-DBD adopts a winged-helix-turn-helix (wHTH) motif and shares significant fold similarity with the DBD of the LTTR protein BenM. Furthermore, a data-driven macromolecular-docking strategy was used to model the structure of MetR-DBD bound to DNA, which revealed that a bent conformation of DNA is required for the recognition helix α3 and the wing loop of the wHTH motif to interact with the major and minor grooves, respectively. Comparison of the MetR-DBD-DNA complex with the crystal structures of other LTTR-DBD-DNA complexes revealed residues that may confer operator-sequence binding specificity for MetR. Taken together, the results show that MetR-DBD uses a combination of direct base-specific interactions and indirect shape recognition of the promoter to regulate the transcription of met genes.

Engineering CatM, a LysR-Type Transcriptional Regulator, to Respond Synergistically to Two Effectors

“…Consistent with this possibility, CatM(K38N) increased muconate-activated transcription of P benA better than the wild-type CatM (Figure 4). Similar interactions are observed in other LTTRs, such as CbnR (A38, R34, and D42) [31], MetR (S38, S34, H35, and Q42) [32], DntR (R43, N39, T46 and A47) [33] and Tsar (Q38, D42, and S34) [34].…”

Enteric Chromosomal Islands: DNA Packaging Specificity and Role of λ-like Helper Phage Terminase

“…The crystallographic structure of RppC shows a DBD, residues 1-64, that is remarkably like the DBDs of TerS-λ and the MetR transcription activator [30] and other members of the LysR group. The predicted DBDs of RppC and its relatives RppA, RppB, and RppG have two α-helices, α1 and α2, and two short β strands forming a "wing", with a positively charged residue at the tip.…”

Laboratory evolution ofE. coliwith a natural vitamin B12analog reveals roles for cobamide uptake and adenosylation in methionine synthase-dependent growth

“…4A, Cultures 1-5) (33). It is unclear how these mutations affect metH expression; the metH mutation is not located in the promoter, RBS, or MetR binding site (34), while the metR mutation is located in its DNA-binding domain (35). Taken together, these results suggest that increasing cobamide uptake and adenosylation are effective strategies for improving growth in limiting to moderate pCbl concentrations, while changing expression of metH facilitates adaptation at higher concentrations of pCbl.…”