M. tuberculosis as seen from M. avium.

Transcription

1 M. tuberculosis as seen from M. avium Marcel A. Behr

2 Overview Classic view of M. tuberculosis Reductive genomics M. avium work Evidence for horizontal gene transfer New view of M. tuberculosis M. kansasii as out-group Horizontal gene transfer in the emergence of M. tuberculosis

3 M. tuberculosis complex (MTC) M. tuberculosis M. microti M. bovis M. africanum

4 M. tuberculosis complex (MTC) M. tuberculosis M. microti M. bovis Oryx bacillus M. caprae Dassie bacillus M. pinnipedii M. africanum

5 Deletion-based MTC phylogeny Brosch et al, PNAS, > Mostowy et al., J Bact, 2005

6 Deletion-based phylogeny: problems Was it right? Would SNP-based analysis concur? Was our view biased by uni- directional perspective? Was it meaningful? How can loss of DNA explain evolution of a professional pathogen?

7 Mycobacterium avium M. avium hominissuis M. avium avium M. avium silvaticum M. avium paratuberculosis

8 M. avium variability M.tb BCG M. avium hominissuis M. avium paratuberculosis Shared ~ 4.6MB Behr et al, Science, 1999 Gordon et al, Mol Micro, 1999 MAH+ / MAP- 14 regions > ~730 kb Semret et al, J. Bact, 2004 MAP+ / MAH- 17 regions > ~220 kb Semret et al, JCM, 2005

9 Problems with M. avium data No obvious ancestor Large-sequence polymorphisms often complex Insertion/Deletion/Rearrangement Hard to predict sequence of events ~ 10x more variability than MTC

10 Genetics to understand genomics: Multi-locus sequence analysis: 56 isolates x 10 genes MAH M. avium subsp. hominissuis: High variability Low dn:ds Recombination Turenne et al, J. Bact, 2008

11 Pathogenic clones of M. avium MAH Restricted variability Elevated dn:ds No recombination Turenne et al, J. Bact, 2008

12 What is unique to MAP? Complete genome sequences: M. avium hominissuis (TIGR) M. avium paratuberculosis (U. Minn) Incomplete genome sequences: M. avium avium (U. Minn / McGill) M. intracellulare (McGill) Define elements found only in MAP

13 Bi-phasic evolution of MAP: Horizontal gene transfer + Deletions 6 Genomic Insertions 1 Genomic Deletion MAP-S Deletions MAP-C Deletions Alexander et al, J. Bact, 2009

14 Evolutionary model of M. avium M. avium hominissuis is an environmental generalist Largest genome M. avium paratuberculosis is a pathogenic clone HGT followed by reductive genomics Is this a general model? Contribution of horizontally acquired genomic islands to the evolution of the tubercle bacilli, Becq, Mol Biol Evol, 2007

15 Multi-locus sequence analysis of sequenced mycobacteria: 20 genes Veyrier et al, BMC Evol. Biol., 2009

16 Gene insertions: Lists A-D D A B C Veyrier et al, BMC Evol. Biol., 2009

17 Phylogenetic evidence for HGT List A: M. avium, M. marinum, M. kansasii, MTC (not rapid-growers) 28 proteins List B: M. marinum, M. kansasii, MTC 40 proteins List C: M.kansasii, MTC 14 proteins List D: MTC only 55 proteins

18 Notable acquisitions List B: Rv2949c Chorismate-formate lyase in phenolic glycolipid locus List D: Rv3377c/Rv3378c: Picked up in screen for phagosome maturation arrest Pethe et al, PNAS, 2004 Rv3377c and Rv3378c have a lower guanine/cytosine (GC) content (54.35% and 48.36%, respectively) than the surrounding chromosome (65%), implying that the locus was acquired by horizontal gene transfer.

19 Biphasic model of MTC evolution Phase 1: HGT events (pre-mtc): Gene acquisition greater capacity to survive in host and cause disease Infectious organism epidemic pathogen Phase 2: Reductive genomics (MTC): Established intracellular pathogen has limited opportunity for gene acquisition Deletion of excess genetic baggage Both phases: SNPs / rearrangements for neo-functionalization

20 Concluding thoughts Study of MTC isolates defines variability within the pathogen Study across mycobacteria genus reveals what is unique to MTC Also, what is unique to M. leprae, M. ulcerans, M. abscessus, etc. Like other genera, HGT has shaped evolution of pathogenic mycobacteria Although currently theoretical, this model lends itself to experimentation

21 Acknowledgements Serge Mostowy Makeda Semret Christine Turenne David Alexander Frédéric Veyrier Collaborators (McGill) Michael Reed Collaborators (other) Gerry Cangelosi Debby Cousins Des Collins Vivek Kapur Dick van Soolingen Funding: TB genomics: CIHR MAC genomics: CBDN NSERC NTMir