M. tuberculosis as seen from M. avium

Marcel A. Behr Marcel A. Behr marcel.behr@mcgill.cawww.molepi.mcgill.ca

Overview

�Classic view of M. tuberculosis– Reductive genomics

�M. avium work– Evidence for horizontal gene transfer– Evidence for horizontal gene transfer

�New view of M. tuberculosis– M. kansasii as out-group– Horizontal gene transfer in the

emergence of M. tuberculosis

M. tuberculosis complex (MTC)

M. microtiM. tuberculosis M. bovis

M. africanum

M. tuberculosis complex (MTC)

M. microtiM. tuberculosis M. bovis

Oryx bacillus

M. caprae

M. africanum

Dassie bacillus M. pinnipedii

Deletion-based MTC phylogeny

Brosch et al, PNAS, 2002-> Mostowy et al., J Bact, 2005

Deletion-based phylogeny: problems

� Was it right? – Would SNP-based analysis concur?– Was our view biased by uni-

directional perspective?directional perspective?

� Was it meaningful?– How can loss of DNA explain

evolution of a professional pathogen?

Mycobacterium avium

M. avium hominissuis

M. avium avium

M. avium silvaticum

M. avium paratuberculosis

M. avium variabilityM. avium paratuberculosis

M. aviumhominissuis

Shared~ 4.6MB

M.tb BCG

MAP+ / MAH-17 regions > ~220 kB

Semret et al, JCM, 2005

MAH+ / MAP-14 regions > ~730 kB

Semret et al, J. Bact, 2004

~ 4.6MB

Behr et al, Science, 1999Gordon et al, Mol Micro, 1999

Problems with M. avium data

� No obvious ancestor� Large-sequence polymorphisms

often complex– Insertion/Deletion/Rearrangement– Insertion/Deletion/Rearrangement– Hard to predict sequence of events

� ~ 10x more variability than MTC

Genetics to understand genomics: Multi-locus sequence analysis: 56 isolates x 10 gen es

MAH

M. avium subsp . hominissuis:High variabilityLow dN:dS

Turenne et al, J. Bact, 2008

Low dN:dSRecombination

Pathogenic clones of M. aviumMAH

Turenne et al, J. Bact, 2008

Restricted variabilityElevated dN:dS

No recombination

What is unique to MAP?

� Complete genome sequences: – M. avium hominissuis (TIGR)– M. avium paratuberculosis (U. Minn)

Incomplete genome sequences: � Incomplete genome sequences: – M. avium avium (U. Minn / McGill)– M. intracellulare (McGill)

� Define elements found only in MAP

6 Genomic Insertions

Bi-phasic evolution of MAP: Horizontal gene transfer + Deletions

Alexander et al, J. Bact, 2009

1 Genomic Deletion

MAP-S Deletions

MAP-C Deletions

Evolutionary model of M. avium

� M. avium hominissuis is an environmental generalist

– Largest genome

� M. avium paratuberculosis is a pathogenic clonepathogenic 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

Multi-locus sequence analysis of sequenced mycobacteria: 20 genes

Veyrier et al, BMC Evol. Biol., 2009

Gene insertions: Lists A-D

Veyrier et al, BMC Evol. Biol., 2009

A

B C

D

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� List B: M. marinum, M. kansasii, MTC– 40 proteins

� List C: M.kansasii, MTC– 14 proteins

� List D: MTC only– 55 proteins

Notable acquisitions

� List B: Rv2949c– Chorismate-formate lyase in phenolic

glycolipid locus

� List D: Rv3377c/Rv3378c: Picked up in screen for phagosome maturation 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.”

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):� 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

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. – 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

Acknowledgementswww.molepi.mcgill.ca� Serge Mostowy

� Makeda Semret� Christine Turenne� David Alexander

Funding:TB genomics:CIHR

MAC genomics:CBDNNSERC

Collaborators (McGill)�Michael Reed

Collaborators (other)�Gerry Cangelosi �Debby Cousins�Des Collins

� Frédéric VeyrierNSERCNTMir

�Des Collins�Vivek Kapur �Dick van Soolingen