Contribution of Horizontal Gene Transfer to Virulence Acquisition in the Ancestor of the Tubercle Bacilli Jennifer Becq1, Maria C. Gutierrez2, Vania Rosas-Magallanes2, Jean Rauzier2, Brigitte Gicquel2, Olivier Neyrolles2 & Patrick Deschavanne1 1
Equipe de Bioinformatique Génomique et Moléculaire, Inserm U726, Université Paris 7, France -
2
Unité de Génétique Mycobactérienne, Institut Pasteur, France
[email protected]
III. Analysis of genomic island genes function
Introduction
Gene functional category
The tubercle bacilli comprise the Mycobacterium tuberculosis complex (MTcomplex) – M. tuberculosis, M. bovis, M. africanum, M. pinnipedii, and M. caprae species, the causative agents of tuberculosis. Very few of the genes of M. tuberculosis were initially thought to have been acquired by horizontal gene transfer (HGT). But further studies showed that Mycobacteria have been subject to average levels of HGT. A virulence operon was shown to be acquired from a proteobacterial specie. This raised the question of the contribution of HGT to the evolution of the ancestor of the tubercle bacilli and the emergence of MT-complex as major mammal pathogens.
Horizontal transfers ?
M. tuberculosis CDC1551 M. tuberculosis H37Rv
% in genomic islands
Average % in complete genomes
IS elements, repeated sequences & phages
40
15.6
3.7
Central intermediary metabolism
28
10.9
27.8
Virulence genes
21
8.2
6.5[5]
Regulatory functions
13
5.1
10.3
Cell envelope & possible membrane proteins
12
4.7
17.5
Others
10
3.9
NA
Unknown
132
51.6
48.0
Total
256
Virulence genes are slightly over-represented in the genomic islands, but a majority of genes have an unknown function.
MT-complex Mammal pathogens
M. bovis AF2122/97
M. marinum
No. of genes
IV. Search for putative origin using genomic signature
Wide host range
How did horizontal transfer contribute to the emergence of the pathogenic tubercle bacilli ?
Rv0986-8
166
virulence operon
d = 369
Plasmid PSAR-3
M. tuberculosis
I. Search for atypical genes
166 Yersinia mollaterii
151
164 156
Use of a consensus of 3 parametric methods to obtain rapidly atypical genes with good specificity
159
Desulforomonas Agrobacterium
Codon usage deviation[4]
162 Xylella
acetoxidans
Atypical GC %[3]
160
vitis
A species genomic database contains ~65,000 signatures of species, strains, organelles, viruses and plasmids (sequences over 1,5 kb available in GenBank). Potential « source » species can be attributed to genomic islands by looking for the nearest neighbours using euclidian distance between signatures.
fastidiosa Renibacterium
Alcaligenes Environmental sequence salmoninarum faecalis 3634299
Gene Rv2307B
genes Rv0986-8
Three major groups of donors can be identified :
Gene Rv2045c (lipT)
1. Actinobacteria (including the genus Mycobacterium) 2. Proteobacteria (including orders Burkholderiales, Pseudomonadales, Rhizobiales and Sphingomonadales).
Atypical signature[2] Complete genome
CONSENSUS
Gene Rv3538c
MT-complex genomic islands
To improve specificity,
200
3. Viruses
163
mean distance (AU)
a gene is considered atypical if 2 out
Potential origins for all the genomic islands described
of the 3 methods detect it
top row numbers : minimum, mean (color) and maximum distance between signatures bottom row / width : number of potential donor species in each taxonomic group
Selection of HGT regions specific to the tubercle bacilli by using comparative genomics in 3 steps :
These result suggest a substantial invasion of the tubercle bacilli ancestor by foreign DNA from soil bacteria (Rhizobiales) and bacteria capable of colonizing animals, including pathogens (Pseudomonadales and Burkholderiales).
1. Selection of common atypical genes in the 3 genomes (2 M. tuberculosis strains and M. bovis)
Conclusion & Perspectives
II. Focus on MT-complex specific genomic islands
2. Selection of the common atypical genes absent of other mycobacteria 3. Extention of these genes into genomic islands by adding adjacent genes with no syntenic ortholog in other mycobacteria
Island Rv1041c-Rv1055 Genes with orthologs in other mycobacteria
atypical gene common IS-like genes in MT-complex
leuX
Further analyses contributed to support the transferred status of these genomic islands[1]. They are still under host selection pressure, presenting many rearrangements within the MT-complex genomes. Future functional studies should investigate the precise role of the genes included in the genomic islands identified here. Conducting similar comparative genomics with various present-day M. tuberculosis genotypes should enlighten the mechanisms involved in tuberculosis pathogenicity. References
Gene names 1
M. tuberculosis H37Rv ppe15 pe8 M. marinum 4452v 4451
Direct DR Repeat
Rv1044
DR 1056 1057 4414 4413
J. Becq, M.C. Gutierrez, V. Rosas-Magallanes, J. Rauzier, B. Gicquel, O. Neyrolles and P. Deschavanne. Contribution of
horizontally acquired genomic islands to the evolution of the tubercle bacilli. Mol. Biol. Evol. Epub ahead of print, 2007. 2
C. Dufraigne, B. Fertil, S. Lespinats, A. Giron and P. Deschavanne, Detection and characterization of horizontal transfers in
prokaryotes using genomic signature. Nucleic Acids Res., 33(1):e6, 2005.
48 genomic islands were described. They account for 4.5 % of the genomes (199 kb) and include 256 genes. The majority display typical features of genomic islands (residual of mobile genetic elements, flanking direct repeats, insertion in the vicinity of tRNA sequences, etc.).
3 4
J. Lawrence and H. Ochman, Molecular archaeology of the Escherichia coli genome. PNAS, 95:9413-9417, 1998. C. Médigue, T. Rouxel, P. Vigier, A. Hénaut and A. Danchin, Evidence for Horizontal Gene Transfer in Escherichia coli
speciation. J. Mol. Biol., 222:851-856, 1991. 5
C.M. Sassetti and E.J. Rubin. Genetic requirements for mycobacterial survival during infection. PNAS, 100(22):12989-94, 2003.
Acknowledgements: M. marinum sequence data were produced by the M. marinum Sequencing Group at the Sanger Institute and can be obtained from http://www.sanger.ac.uk/Projects/M_marinum/.
