Y. Bourne / P. Marchot’s team guest: Mickael Lafond, Fungal Biodiversity and Biotechnology (BBF) lab, Marseille – “Ruminococcins C: from an exotic structure to clinical properties.”

Abstract

Clarisse Roblin^1,2, Steve Chiumento³, Christian Basset³, Sylvie Kieffer-Jaquinod⁴, Cendrine Nicoletti¹, Cédric Jacqueline⁵, Lama Shamseddine³, Eric Pinloche², Iris Veyrier¹, Agnès Amouric¹, Elise Courvoisier-Dezord¹, Hamza Olleik^1, Olivier Bornet^6, Matthieu Nouailler⁶, Olga Iranzo¹, Marc Maresca¹, Michel Fons⁷, Katy Jeannot⁸, Estelle Devillard², Yohann Couté⁴, Nathalie Campo⁹, Mohamed Atta³, Patrice Pollard⁹, Josette Perrier¹, Victor Duarte³ & Mickael Lafond¹

1 Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France ;
2 ADISSEO France SAS, Centre d’Expertise et de Recherche en Nutrition, Commentry, France ;
3 Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, Grenoble, France ;
4 Univ. Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France ;
5 EA3826, IRS2 Nantes-Biotech, Université de Nantes, Nantes, France ;
6 LISM, IMM, Aix-Marseille Univ, CNRS, Marseille, France ;
7 Unité de Bioénergétique et Ingénierie des Protéines UMR7281, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ, CNRS, Marseille, France ;
8 Centre National de Référence de la Résistance aux Antibiotiques, Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France ;
9 Laboratoire de Microbiologie et de Génétique Moléculaires, CNRS, Université Paul Sabatier, Toulouse, France.

The multi-resistance of pathogens to antibiotics represents today an important problem of public-health, and the discovery of new antimicrobial molecules to fight bacterial resistant strains is nowadays a world-wide priority. Ribosomally synthesized and Post-translationally modified Peptides (RiPPs) with an antibacterial activity produced by bacteria also called bacteriocins, are part of this new generation of promising antimicrobial peptides (AMP). In this context, exploring the ability of the human gut symbionts to produce bacteriocins playing a barrier effect, we discovered and then produced a new synthetic RiPP from the Gram-positive dominant bacterium Ruminococcus gnavus. After characterizing in silico the Ruminococcin C biosynthetic genes cluster involved in the biosynthesis, maturation, export and immunity of five RumC isoforms (RumC1 to RumC5), we successfully isolated the five RumC isoforms in vivo using a mono-associated rat model, as well as produced the RumC1-5 in vitro using the Escherichia coli recombinant platform. A deep characterization using molecular and structural approaches and their biosynthetic pathway study, revealed that RumC peptides exhibits four thioether bridges build by a Radical-SAM enzyme. Such a post-translational modification gives to RumC1 an hitherto undescribed 3D structural folding into the sactipeptide family. At a functional level, we have shown that RumC1 is efficient to fight multi-drug resistant-clinical isolates in the micromolar range, and to cure a peritoneal infection in Clostridium perfringens challenged mice with a lower dose than the conventional antibiotic vancomycin. Also, while maintaining a global homeostasis of the microbiome, RumC1 exhibits additional beneficial properties for the human host, such as wound healing and anti-inflammatory activities. Our last investigations on the molecular mechanism revealed that, unlike known sactipeptides, RumC1 does not exert a pore-forming mode of action, colocalizes mainly at the septal ring, and exhibits a fast lethal effect with an inhibition of the main macromolecule biosynthetic pathways.