Structural basis of thiol-based regulation of formaldehyde detoxification in H. influenzae by a MerR regulator with no sensor region

• Published in: Nucleic acids research 2016-08, Vol.44 (14), p.6981-6993
• Main Authors: Couñago, Rafael M, Chen, Nathan H, Chang, Chiung-Wen, Djoko, Karrera Y, McEwan, Alastair G, Kobe, Bostjan
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Crystallography, X-Ray; DNA, Bacterial - chemistry; DNA, Bacterial - metabolism; DNA-Binding Proteins - chemistry; DNA-Binding Proteins - metabolism; DNA-Directed RNA Polymerases - metabolism; Formaldehyde - metabolism; Gene Expression Regulation, Bacterial; Haemophilus influenzae - genetics; Haemophilus influenzae - metabolism; Inactivation, Metabolic - genetics; Kinetics; Models, Molecular; Operator Regions, Genetic - genetics; Promoter Regions, Genetic; Protein Binding; Structural Biology; Structure-Activity Relationship; Sulfhydryl Compounds - metabolism; Transcription Factors - metabolism; Transcription, Genetic
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkw543

Pathogenic bacteria such as Haemophilus influenzae, a major cause of lower respiratory tract diseases, must cope with a range of electrophiles generated in the host or by endogenous metabolism. Formaldehyde is one such compound that can irreversibly damage proteins and DNA through alkylation and cross-linking and interfere with redox homeostasis. Its detoxification operates under the control of HiNmlR, a protein from the MerR family that lacks a specific sensor region and does not bind metal ions. We demonstrate that HiNmlR is a thiol-dependent transcription factor that modulates H. influenzae response to formaldehyde, with two cysteine residues (Cys54 and Cys71) identified to be important for its response against a formaldehyde challenge. We obtained crystal structures of HiNmlR in both the DNA-free and two DNA-bound forms, which suggest that HiNmlR enhances target gene transcription by twisting of operator DNA sequences in a two-gene operon containing overlapping promoters. Our work provides the first structural insights into the mechanism of action of MerR regulators that lack sensor regions.