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Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis.

Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE - MBio (2014)

Bottom Line: Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition.Our results clearly placed M. indicus pranii as an ancestor of the M. avium complex.Analyses of comparative metabolic pathways between M. indicus pranii (NP), M. tuberculosis (TP), and M. intracellulare (OP) pointed to the presence of novel alternative pathways in M. tuberculosis with implications for pathogenesis and survival in the human host and identification of new drug targets.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom asad@ebi.ac.uk seyedhasnain@gmail.com.

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Comparative genomics of selected mycobacterial genomes. The genomes of Mycobacterium indicus pranii (shown in green; an NP), Mycobacterium intracellulare ATCC 13950 (orange; an OP), and Mycobacterium tuberculosis H37Rv (pink; a TP) were selected for comparative genomic analyses. We used BLASTp, with a cutoff of 20% identity and e value of 10e–4, to determine the number of homologous protein-coding genes common between them (shown as edge labels between the nodes). The arrowhead represents the query genome, whereas the arrow tail represents the subject genome.
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fig4: Comparative genomics of selected mycobacterial genomes. The genomes of Mycobacterium indicus pranii (shown in green; an NP), Mycobacterium intracellulare ATCC 13950 (orange; an OP), and Mycobacterium tuberculosis H37Rv (pink; a TP) were selected for comparative genomic analyses. We used BLASTp, with a cutoff of 20% identity and e value of 10e–4, to determine the number of homologous protein-coding genes common between them (shown as edge labels between the nodes). The arrowhead represents the query genome, whereas the arrow tail represents the subject genome.

Mentions: For further comparative analyses, a 20% sequence identity cutoff with an e value of <1e−4 was used to analyze BLASTp results. This cutoff was used to determine the number of homologous protein-coding genes shared between M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv. Our analysis of homologous protein-coding genes shared between M. indicus pranii (NP), M. intracellulare ATCC 13950 (OP), and M. tuberculosis H37Rv (TP) revealed 4,995 (~95%) M. indicus pranii proteins had homology with M. intracellulare ATCC 13950, whereas homologies between M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively (Fig. 4; see also Table S2 in the supplemental material).


Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis.

Rahman SA, Singh Y, Kohli S, Ahmad J, Ehtesham NZ, Tyagi AK, Hasnain SE - MBio (2014)

Comparative genomics of selected mycobacterial genomes. The genomes of Mycobacterium indicus pranii (shown in green; an NP), Mycobacterium intracellulare ATCC 13950 (orange; an OP), and Mycobacterium tuberculosis H37Rv (pink; a TP) were selected for comparative genomic analyses. We used BLASTp, with a cutoff of 20% identity and e value of 10e–4, to determine the number of homologous protein-coding genes common between them (shown as edge labels between the nodes). The arrowhead represents the query genome, whereas the arrow tail represents the subject genome.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222108&req=5

fig4: Comparative genomics of selected mycobacterial genomes. The genomes of Mycobacterium indicus pranii (shown in green; an NP), Mycobacterium intracellulare ATCC 13950 (orange; an OP), and Mycobacterium tuberculosis H37Rv (pink; a TP) were selected for comparative genomic analyses. We used BLASTp, with a cutoff of 20% identity and e value of 10e–4, to determine the number of homologous protein-coding genes common between them (shown as edge labels between the nodes). The arrowhead represents the query genome, whereas the arrow tail represents the subject genome.
Mentions: For further comparative analyses, a 20% sequence identity cutoff with an e value of <1e−4 was used to analyze BLASTp results. This cutoff was used to determine the number of homologous protein-coding genes shared between M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv. Our analysis of homologous protein-coding genes shared between M. indicus pranii (NP), M. intracellulare ATCC 13950 (OP), and M. tuberculosis H37Rv (TP) revealed 4,995 (~95%) M. indicus pranii proteins had homology with M. intracellulare ATCC 13950, whereas homologies between M. indicus pranii, M. intracellulare ATCC 13950, and M. tuberculosis H37Rv were significantly lower. A total of 4,153 (~79%) M. indicus pranii proteins and 4,093 (~79%) M. intracellulare ATCC 13950 proteins exhibited homology with the M. tuberculosis H37Rv proteome, while 3,301 (~82%) and 3,295 (~82%) M. tuberculosis H37Rv proteins showed homology with M. indicus pranii and M. intracellulare ATCC 13950 proteomes, respectively (Fig. 4; see also Table S2 in the supplemental material).

Bottom Line: Mycobacterial evolution involves various processes, such as genome reduction, gene cooption, and critical gene acquisition.Our results clearly placed M. indicus pranii as an ancestor of the M. avium complex.Analyses of comparative metabolic pathways between M. indicus pranii (NP), M. tuberculosis (TP), and M. intracellulare (OP) pointed to the presence of novel alternative pathways in M. tuberculosis with implications for pathogenesis and survival in the human host and identification of new drug targets.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom asad@ebi.ac.uk seyedhasnain@gmail.com.

Show MeSH
Related in: MedlinePlus