Ruminococcins C: from an exotic structure to clinical properties
Clarisse Roblin1,2, Steve Chiumento3, Christian Basset3, Sylvie Kieffer-Jaquinod4, Cendrine Nicoletti1, Cédric Jacqueline5, Lama Shamseddine3, Eric Pinloche2, Iris Veyrier1, Agnès Amouric1, Elise Courvoisier-Dezord1, Hamza Olleik1, Olivier Bornet6, Matthieu Nouailler6, Olga Iranzo1, Marc Maresca1, Michel Fons7, Katy Jeannot8, Estelle Devillard2, Yohann Couté4, Nathalie Campo9, Mohamed Atta3, Patrice Pollard9Josette Perrier1, Victor Duarte3 & Mickael Lafond1

1Aix-Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France ; 2ADISSEO France SAS, Centre d’Expertise et de Recherche en Nutrition, Commentry, France ; 3Univ. Grenoble Alpes, CEA, CNRS, CBM-UMR5249, Grenoble, France ; 4Univ. Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France ; 5EA3826, IRS2 Nantes-Biotech, Université de Nantes, Nantes, France ; 6LISM, IMM, Aix-Marseille Univ, CNRS, Marseille, France ; 7Unité de Bioénergétique et Ingénierie des Protéines UMR7281, Institut de Microbiologie de la Méditerranée, Aix-Marseille Univ, CNRS, Marseille, France ; 8Centre National de Référence de la Résistance aux Antibiotiques, Laboratoire de Bactériologie, Centre Hospitalier Universitaire de Besançon, Besançon, France ; 9Laboratoire 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 for human and animal, and the discovery of new antimicrobial molecules to fight bacterial resistant strains is nowadays a world-wide priority. Ribosomally synthesized and Posttranslationally 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, but penetrates the target bacteria, colocalizes at the septal ring, and exhibits a fast lethal effect with an inhibition of the main macromolecule biosynthetic pathways.