2013-Annual Report. Name of the Structure: Integrated Mycobacterial Pathogenomics Unit

Transcription

1 2013-Annual Report Head of the structure: Dr. Roland BROSCH, Name of the Structure: Integrated Mycobacterial Pathogenomics Unit Secondary Affiliation: Name of the Institut Pasteur Department: Genetics and Genomics Staff Staff Eva BORITSCH Alessandro CASCIOFERRO Matthias GRÖSCHEL Nadine HONORE Laurence LANGLAIS Fabien LE CHEVALIER Laleh MAJLESSI Alexandre PAWLIK Fadel SAYES Roxane SIMEONE Wafa ZOUAOUI-FRIGUI Position and employer Engineer Secretary Permanent scientist Engineer Technician

2 Five Main publications (in years ): 1. 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, E.C., Debrie, A.S., Willery, E., Walker, D., Quail, M.A., Ma, L., Bouchier, C., Salvignol, G., Sayes, F, Cascioferro, A., Seemann, T., Barbe, V., Locht, C., Gutierrez, M.C., Leclerc, C., Bentley, S.D., Stinear, T.P., Brisse, S., Medigue, C., Parkhill, J., Cruveiller, S., and Brosch, R. (2013) Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis. Nature Genetics 45: Pawlik, A., Garnier, G., Orgeur, M., Tong, P., Lohan, A., Le Chevalier, F., Sapriel, G., Roux, A.L., Conlon, K., Honore, N., Dillies, M.A., Ma, L., Bouchier, C., Coppee, J.Y., Gaillard, J.L., Gordon, S.V., Loftus, B., Brosch, R., and Herrmann, J.L. (2013) Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus. Molecular Microbiology 90: Simeone, R., Bobard, A., Lippmann, J., Bitter, W., Majlessi, L., Brosch, R., and Enninga, J. (2012) Phagosomal Rupture by Mycobacterium tuberculosis Results in Toxicity and Host Cell Death. PLoS Pathogens 8:e Sayes, F., Sun, L., Di Luca, M., Simeone, R., Degaiffier, N., Fiette, L., Esin, S., Brosch, R., Bottai, D., Leclerc, C., and Majlessi, L. (2012) Strong Immunogenicity and Cross-Reactivity of Mycobacterium tuberculosis ESX-5 Type VII Secretion -Encoded PE-PPE Proteins Predicts Vaccine Potential. Cell Host & Microbe. 11: Bottai, D., Majlessi, L., Simeone, R., Frigui, W., Laurent, C., Lenormand, P., Chen, JM., Rosenkrands, I., Huerre, M., Leclerc, C., Cole, S.T., and Brosch, R. (2011). ESAT-6 secretion-independent impact of ESX-1 genes espf and espg1 on virulence of Mycobacterium tuberculosis. Journal of Infectious Disesases 203: Website address of your structure: Pathologies related to the research activities of your structure: Tuberculosis induced lung disease and disseminated tuberculosis infection

3 2013-Annual Report The research undertaken in our unit is centred on genomic features in relation to pathogenicity of Mycobacterium tuberculosis and close relatives. The goal of our research is to uncover novel aspects of mycobacterial pathogens in relation to evolution and host-pathogen interaction that may provide new insights how pathogenic mycobacteria succeed to infect and persist in their hosts and cause disease. Among the mycobacteria, the great majority of species represent harmless non-pathogenic bacteria of the environment. However, the genus Mycobacteria also contains pathogenic species, such as the members of the M. tuberculosis complex, which have very efficiently adapted to a pathogenic lifestyle and constitute some of most important human pathogens. Pathogenomics of tubercle bacilli. Genomics and comparative genomics are very powerful ways to get insights into the basic genetic structures that define whether or not a given bacterial strain may act as a pathogen. When the genomes of bacterial strains that show different degrees of virulence or different evolutionary success are compared among each other, factors that are responsible for these differences may then be identified. Our unit is particularly interested in using genomics and comparative genomics for characterising tubercle bacilli that show outstanding characteristics. Among the investigated strains are Mycobacterium canettii strains that show unusual smooth colony morphology and represent rare clinical isolates from the geographical region of Djibouti, East Africa. Fig. 1. A) Working model of the evolutionary scheme of tubercle bacilli (after Brosch et al., PNAS, 2002; Gordon et al., Bioessays, 2009; van Ingen et al., Emerg. Infect Dis., 2012; Supply et al., Nat. Genet., 2013); B) clustered regularly interspaced short palindromic repeat (CRISPR) loci and flanking CRISPR-associated (cas) genes of M. tuberculosis and different M. canettii strains (Supply et al., Nat. Genet., 2013). In a collaborative project implicating several major genome sequencing centres (Genoscope, Genopole, Sanger Institute) and Dr. Philip Supply from the Institut Pasteur in Lille we have subjected these rare strains to genome sequence- and pathogenomic analyses with the aim of comparing them with multiple phylogenetic

4 lineages of M. tuberculosis from different parts of the world and different members of the M. tuberculosis complex such as Mycobacterium africanum, Mycobacterium microti or Mycobacterium bovis. This analysis allowed defining the ancestral gene pool of the progenitor of M. tuberculosis named "Mycobacterium prototuberculosis" and the factors, which might be involved in the outstanding evolutionary success of M. tuberculosis as a human pathogen (Supply et al., 2013). This analysis also suggests that the lineage of tubercle bacilli characterized by the loss of region of difference 9 (RD9), which are represented by the M. africanum strains isolated from patients in West Africa and various tubercle bacilli isolated from animal sources, has undergone a different evolutionary pathway than the RD9 intact lineages, represented by M. tuberculosis isolates. ESX/type VII secretion systems and their impact on host-pathogen interaction Another main research theme of our unit is the genetic and functional characterization of ESX/type VII secretion systems in members of the M. tuberculosis complex. There are five paralogous systems present in M. tuberculosis that resemble each other in the organisation of the genomic locus and the core components of the system, but differ in the secreted effector proteins. In collaboration with the group of Dr. Jost Enninga at the Institut Pasteur we have recently shown that ESX-1, which is responsible for the secretion of the 6 kda early secreted antigenic target (ESAT-6) and the 10 kda culture filtrate protein (CFP-10), is implicated in the important cell biological phenomenon of phagosomal rupture in the host-cell during later stages of infection. (Simeone et al., PLoS Pathogens 2012; Houben et al., Cell. Microbiol. 2012). Fig. 2. A) Working model of the ESX/type VII secretion systems and genetic organisation of the ESX-1 and ESX-5 locus (after Bitter et al., PLoS Pathog. 2009) B) Example of FRET- inhibition induced by phagosomal rupture of M. tuberculosis in THP-1 cells that is not visible in the attenuated bacille de Calmette et Guérin (BCG) vaccine strain due to the absence of a functional ESX-1 system in this close relative of M. tuberculosis. Indeed, the absence of a functional ESX-1 secretion system causes attenuation and it is thought that loss of the region of difference 1 (RD1) from BCG, which deletes part of the genes of the ESX-1 machinery and its secreted products strongly contributed to the attenuation of the BCG vaccine.

5 However, apart from playing a role in virulence of M. tuberculosis, the proteins secreted by the various ESX secretion systems are known for inducing strong T-cell mediated immune responses, which is an important feature for vaccine development. In our unit, we are thus very interested and involved in the investigation of the cell-biological and immunological impact of the various ESX components in the host. Here we have recently investigated the immunogenicity of the PE and PPE proteins that are secreted via the ESX-5 secretion system of M. tuberculosis and found that they are highly immunogenic. Furthermore ESX-5 was found to be implicated in the virulence of M. tuberculosis, which is a feature important for vaccine development (Sayes et al., Cell Host & Microbe, 2012; Bottai et al., Mol. Microbiol. 2012). Apart from ESX-1 and ESX-5 there are three other paralogous ESX systems in M. tuberculosis, ESX-2, ESX-3 and ESX-4, which have not yet been subject of studies in our unit. Finally, ESX systems also exist in many other actinobacteria and Gram-positive bacteria, and may thus have a very broad importance for a large variety of bacterial pathogens.