Genetic regulation & genome evolution
Project leader:
Loic Coutte
Loïc's ORCID
Loïc's Contact
Copper homeostasis in Bordetella pertussis
Copper is an essential micronutrient for most bacteria, serving notably as a co-factor of various enzymes and in electron transfer complexes, but it is also toxic and used as a killing agent by phagocytes. We have discovered that unlike other Gram-negative bacteria, the host-restricted pathogen Bordetella pertussis has few defenses against copper other than a custom-made system that fends off both metal and oxidative stresses. Conversely, this bacterium has acquired an original two-protein copper acquisition system that we are investigating, composed of a TonB-dependent transporter of a new subfamily and a heme-containing inner membrane protein. We have revealed a sophisticated mode of regulation of this system by copper involving a novel upstream Open Reading Frame (‘uORF’). Our results indicate that this system is involved in the provision of copper to the respiratory heme-copper oxidases. We are currently addressing the structure of the two proteins and their functions in B. pertussis.
We have also identified a new family of ribosomally produced, post-translationally modified peptides (‘RiPPs’) that we have called ‘bufferins’, in B. pertussis and other pathogenic and environmental bacteria. We have shown that model bufferins contribute to the protection against copper by chelating Cu(I) and Cu(II) ions. In the ANR CuRiPP grant we have discovered that conserved cysteines of bufferins are modified into thiooxazole by enzymes of the superfamily of multi-nuclear non-heme, iron-dependent oxidases (MNIO). In silico analyses have shown that bufferins represent a widespread family of MNIO-modified RiPPs. Our goals are to decipher the mechanisms of bufferin biogenesis, their structure and their mode of copper chelation.
Project leader:
Philip Supply
Philip's ORCID
Philip's Contact
Evolutionary history and factors driving the spread of tuberculosis
Mycobacterium tuberculosis is the deadliest bacterial infectious agent globally and the first contributor to antimicrobial mortality. Using comparative genomics and pathophysiological approaches applied to strain lineages with different epidemic and/or antibiotic resistance profiles, we aim at identifying the factors that have contributed to its emergence and its exceptional evolutionary success, including in multidrug-resistant (MDR) forms. This work has led to the discovery of exceptional ancestral branches of tubercle bacilli in East Africa, including a new sister clade of the M. tuberculosis complex (MTBC), as well as outstanding TB clinical isolates with a smooth colony morphotype, named M. canettii, showing mosaic genomes and inter-strain recombination in contrast to the highly clonal structure of the MTBC. The latter strains that are also less persistent during host infection than M. tuberculosis likely represent an extant reflection of the ancestral, free-living bacterial pool from which the MTBC emerged. With help of Cyril Gaudin (internal collaboration with ERA4TB team), whole genome sequencing (WGS) analysis of M. canettii mutants obtained after experimental evolution revealed that mechanisms conferring increased resistance to host-induced stress were key in the emergence of persistent TB strains. We also used WGS to reveal molecular and historical factors that favored the emergence and the longitudinal spread of major epidemic multi-drug resistant clones, member of the major Beijing/L2 lineage of the MTBC. The extensive resistance and the outstanding genetic arsenal of these geographically widespread MDR strains represent a “perfect storm” that jeopardizes the successful introduction of new anti-MDR-TB antibiotic regimens. With the CRyPTIC consortium, genetic determinants of drug resistance are further comprehensively catalogued across the genomes of globally circulating M. tuberculosis strains. The development and international deployment with GenoScreen of the innovative next generation sequencing-based diagnostics Deeplex Myc-TB, which has a uniquely extended diagnostic spectrum (see Translational Research), represents a new powerful tool to combat the spread of such highly resistant clones.
