Identification of Allosteric Hotspots regulating the ribosomal RNA-binding by Antibiotic Resistance-Conferring Erm Methyltransferases.

Fiche publication

Date publication

juin 2022

Journal

The Journal of biological chemistry

Auteurs

Membres identifiés du Cancéropôle Est :
Pr MELY Yves

Tous les auteurs :
Bhujbalrao R, Gavvala K, Singh RK, Singh J, Boudier C, Chakrabarti S, Patwari GN, Mély Y, Anand R

Lien Pubmed

https://www.ncbi.nlm.nih.gov/pubmed/35772496

Résumé

Antibiotic resistance via epigenetic methylation of ribosomal RNA is one of the most prevalent strategies adopted by multi-drug resistant pathogens. The erythromycin-resistance methyltransferase (Erm) methylates rRNA at the conserved A2058 position and imparts resistance to macrolides such as erythromycin. However, the precise mechanism adopted by Erm methyltransferases for locating the target base within a complicated rRNA scaffold remains unclear. Here, we show that a conserved RNA architecture, including specific bulge sites, present more than 15 Å from the reaction center, is key to methylation at the pathogenic site. Using a set of RNA sequences site-specifically labeled by fluorescent nucleotide surrogates, we show that base flipping is a pre-requisite for effective methylation and that distal bases assist in the recognition and flipping at the reaction center. The Erm-RNA complex model revealed that intrinsically flipped-out bases in the RNA serve as a putative anchor point for the Erm. Molecular dynamic simulation studies demonstrated the RNA undergoes a substantial change in conformation to facilitate an effective protein-rRNA handshake. This study highlights the importance of unique architectural features exploited by RNA to impart fidelity to RNA methyltransferases via enabling allosteric crosstalk. Moreover, the distal trigger sites identified here serve as attractive hotspots for the development of combination drug therapy aimed at reversing resistance.