Genetic regulation & genome evolution
Stephanie Slupek, Technician
Sophie Lecher, Engineer
Rudy Antoine, CRCN INSERM
Camille Locht, DRE INSERM
0000-0002-8626-8109
Bordetellae’s gene expression regulation
The Bordetellae, encompassing the human pathogen B. pertussis and the veterinary pathogen B. bronchiseptica, produce an arsenal of virulence factors such as adhesins and toxins, that allow the bacteria to transmit, infect and colonize the respiratory tract of the host. These bacteria regulate their virulence factor expressions according to environmental conditions. The regulation of Bordetella virulence is mediated by the two-component system BvgA/S. In the virulence phase phosphorylated BvgA activates the transcription of virulence-activated genes (vags). In the a-virulent phase, the vags are not expressed but instead, virulence-repressed genes (vrgs) are expressed. The expression of the vrgs is regulated by another two-component system, RisA/K and by the action of BvgR, a c-di-GMP phosphodiesterase. Using molecular biology and omics’s technologies, our goal is to define the regulation network and the mode of regulation involving the BvgASR and the RisAK systems. Surprisingly, we have shown that some genes are regulated by both BvgA and RisA. Additionally, some genes not shown to be regulated in omics’s studies show a binding site for BvgA and/ or RisA in their promoter regions increasing the complexity of the RisAK/BvgASR network in Bordetella virulence regulation. B. pertussis encodes for up to 16 different two-component systems arguing on the extreme complexity of the Bordetella gene expression biology.
Combined RNAseq and ChIPseq Analyses of the BvgA Virulence Regulator of Bordetella pertussis
mSystems
DOI: 10.1128/mSystems.00208-20
Coutte L; Antoine R; Slupek S; Solans L; Derop J; Bonnefond A; Hot D; Locht C;
Distinct virulence ranges for infection of mice by Bordetella pertussis revealed by engineering of the sensor-kinase BvgS.
PloS one
DOI: 10.1371/journal.pone.0204861
Coutte L; Lesne E; Solans L; Slupek S; Debrie AS; Dhennin V; Froguel P; Hot D; Locht C; Antoine R Jacob-Dubuisson
The multifaceted RisA regulon of Bordetella pertussis.
Scientific reports
DOI: 10.1038/srep32774
Coutte L; Huot L; Antoine R; Slupek S; Merkel TJ; Chen Q; Stibitz S; Hot D; Locht C
Stephanie Slupek, Technician
Carine Rouanet, Senior Scientist, Institut Pasteur de Lille
Christine Demanche, lecturer (MCU), Université Lille 2
Rudy Antoine, Senior Scientist INSERM
Philip Supply, Research Director CNRS
0000-0003-3690-3853
Evolutionary history and factors driving the spread of tuberculosis
Mycobacterium tuberculosis is the deadliest single bacterial infectious agent 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. We showed that 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 MDR 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, including compensatory, drug tolerance and hypervirulence mutations, represent a “perfect storm” that jeopardizes the successful introduction of new anti-MDR-TB antibiotic regimens. 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.
1. Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, Kohl TA, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P*, Niemann S*, Wirth T*. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun. 2022 13:5105. doi: 10.1038/s41467-022-32455-1. *Co-last authors
2. Allen AC, Malaga W, Gaudin C, Volle A, Moreau F, Hassan A, Astarie-Dequeker C, Peixoto A, Antoine R, Pawlik A, Frigui W, Berrone C, Brosch R, Supply P, Guilhot C. Parallel in vivo experimental evolution reveals that increased stress resistance was key for the emergence of persistent tuberculosis bacilli. Nat Microbiol. 2021 6:1082-1093. doi: 10.1038/s41564-021-00938-4
3. Ngabonziza JCS, Loiseau C, Marceau M, Jouet A, Menardo F, Tzfadia O, Antoine R, Niyigena EB, Mulders W, Fissette K, Diels M, Gaudin C, Duthoy S, Ssengooba W, André E, Kaswa MK, Habimana YM, Brites D, Affolabi D, Mazarati JB, de Jong BC, Rigouts L, Gagneux S, Meehan CJ, Supply P. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun. 2020 11:2917. doi: 10.1038/s41467-020-16626-6
4. Merker M, Blin C, Mona S, Duforet-Frebourg N, Lecher S, Willery E, […], Supply P*, Niemann S*, Wirth T*. Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage. Nat Genet. 2015 Mar;47(3):242-9. doi: 10.1038/ng.3195. *Co-last authors
5. Supply P, Marceau M, Mangenot S, Roche D, Rouanet C, Khanna V, Majlessi L, Criscuolo A, Tap J, Pawlik A, Fiette L, Orgeur M, Fabre M, Parmentier C, Frigui W, Simeone R, Boritsch EC, Debrie AS, Willery E, Walker D, Quail MA, Ma L, Bouchier C, Salvignol G, Sayes F, Cascioferro A, Seemann T, Barbe V, Locht C, Gutierrez MC, Leclerc C, Bentley SD, Stinear TP, Brisse S, Médigue C, Parkhill J, Cruveiller S, Brosch R. Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nat Genet. 2013 45:172-9. doi: 10.1038/ng.2517
