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Chapter 2 : Mycobacterial Pathogenomics and Evolution

Authors: Daria Bottai1, Timothy P. Stinear2, Philip Supply3, Roland Brosch4
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Affiliations: 1: Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, Pisa, Italy; 2: Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia; 3: CNRS UMR 8204; INSERM, U1019; Center for Infection and Immunity of Lille, Institut Pasteur de Lille; and Université Lille Nord de France, Lille, France; 4: Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
Content Type: Monograph
Publication Year: 2014

Category: Microbial Genetics and Molecular Biology

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Abstract:

Mycobacteria are widespread microorganisms characterized by the high G+C content of their genomes and a lipid-rich cell envelope. The genus represents the only entity within the family , which belongs to the order and the phylum ( ). Whereas the great majority of the ∼130 described species in the genus are harmless environmental saprophytes, some mycobacteria have evolved to be major pathogens. With the exception of , which is recognized as an emerging human pathogen in cystic fibrosis patients ( ), the pathogenic species mainly belong to the slowly growing mycobacteria and comprise well-known human pathogens such as , , and as well as confirmed animal pathogens such as , , and ( ).

Citation: Bottai D, Stinear T, Supply P, Brosch R. 2014. Mycobacterial Pathogenomics and Evolution, p 27-47. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0025-2013
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Mycobacterial Pathogenomics and Evolution
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Citation: Bottai D, Stinear T, Supply P, Brosch R. 2014. Mycobacterial Pathogenomics and Evolution, p 27-47. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0025-2013
/content/10.1128/9781555818845.chap2.fig2-1
Figure 1
Proposed scenario of pathoadaptation of tubercle bacilli from a hypothetical mycobacterial common ancestor (most recent common ancestor, MRCA), adapted from reference . In the proposed evolutionary pathway strains gain specific functions (via horizontal gene transfer, recombination, mutation and/or gene loss, etc.), which allow them to better replicate and persist under the environment and temperature conditions of a niche such as human macrophages. It is plausible that the pathogenomic adaptation at some stage involved smooth tubercle bacilli/, which show a broader environmental adaptability and a genetically much larger diversity than the strains ( ).
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10.1128/9781555818845/fig2-1.gif
Image of Figure 1
Figure 1

Proposed scenario of pathoadaptation of tubercle bacilli from a hypothetical mycobacterial common ancestor (most recent common ancestor, MRCA), adapted from reference . In the proposed evolutionary pathway strains gain specific functions (via horizontal gene transfer, recombination, mutation and/or gene loss, etc.), which allow them to better replicate and persist under the environment and temperature conditions of a niche such as human macrophages. It is plausible that the pathogenomic adaptation at some stage involved smooth tubercle bacilli/, which show a broader environmental adaptability and a genetically much larger diversity than the strains ( ).

Citation: Bottai D, Stinear T, Supply P, Brosch R. 2014. Mycobacterial Pathogenomics and Evolution, p 27-47. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0025-2013
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Figure 2
Network phylogeny inferred among the five strains subjected to complete genome sequence analysis and 39 selected genome sequences from members of the classical complex by NeighborNet analysis, based on pairwise alignments of whole-genome SNP data, which in part are also listed in the lower right portion of the figure. The color code and the naming of different phylogenetic lineages within the complex refer to the nomenclature used in reference .
10.1128/9781555818845/fig2-2_thmb.gif
10.1128/9781555818845/fig2-2.gif
Image of Figure 2
Figure 2

Network phylogeny inferred among the five strains subjected to complete genome sequence analysis and 39 selected genome sequences from members of the classical complex by NeighborNet analysis, based on pairwise alignments of whole-genome SNP data, which in part are also listed in the lower right portion of the figure. The color code and the naming of different phylogenetic lineages within the complex refer to the nomenclature used in reference .

Citation: Bottai D, Stinear T, Supply P, Brosch R. 2014. Mycobacterial Pathogenomics and Evolution, p 27-47. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0025-2013
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Figure 3
Working model of the type VII secretion apparatus adapted from reference . Schematic representation of the core components and their interactions. Various ESX components belonging to different protein families are represented by different colors: orange, amino-terminal transmembrane protein; violet, amino-terminal transmembrane ATPase; green, integral membrane protein; red, mycosin (subtilisin-like serine protease); pink, AAA+ ATPase. Esx secreted substrates, PE and PPE proteins, as well as ESX-1-associated Esp proteins are also represented. Note that the channel drawn in the mycomembrane refers to a hypothetical protein, whose existence has not been experimentally demonstrated, and that the drawing of the mycomembrane follows a schematic representation of reference .
10.1128/9781555818845/fig2-3_thmb.gif
10.1128/9781555818845/fig2-3.gif
Image of Figure 3
Figure 3

Working model of the type VII secretion apparatus adapted from reference . Schematic representation of the core components and their interactions. Various ESX components belonging to different protein families are represented by different colors: orange, amino-terminal transmembrane protein; violet, amino-terminal transmembrane ATPase; green, integral membrane protein; red, mycosin (subtilisin-like serine protease); pink, AAA+ ATPase. Esx secreted substrates, PE and PPE proteins, as well as ESX-1-associated Esp proteins are also represented. Note that the channel drawn in the mycomembrane refers to a hypothetical protein, whose existence has not been experimentally demonstrated, and that the drawing of the mycomembrane follows a schematic representation of reference .

Citation: Bottai D, Stinear T, Supply P, Brosch R. 2014. Mycobacterial Pathogenomics and Evolution, p 27-47. In Hatfull G, Jacobs W (ed), Molecular Genetics of Mycobacteria, Second Edition. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.MGM2-0025-2013
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