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Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium.

Prasanna AN, Mehra S - PLoS ONE (2013)

Bottom Line: Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order.It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree.It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.

ABSTRACT
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.

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Related in: MedlinePlus

Classification of mycobacterial genes into functional classes.The genes are categorized into 16 different role categories based on the TIGR classification system, where AAB represents Amino acid and Biosynthesis; BSC- Biosynthesis of Co-factors; CEN- Cell envelope; CEP- Cellular processes; CIM- Central intermediary metabolism; DME- DNA Metabolism; EME-Energy metabolism; FPM – Fatty acid and Phospholipid metabolism; HPR – Hypothetical proteins; PFA – Protein Fate; PSY – Protein synthesis; PPN – Purine, pyrimidine and nucleotide metabolism; RFU – Regulatory functions (Regulatory functions+Transcription); TBP – Transport and Binding proteins; UNK – Unknown & Unclassified proteins; MEE – Mobile extrachromosomal elements.
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pone-0071248-g001: Classification of mycobacterial genes into functional classes.The genes are categorized into 16 different role categories based on the TIGR classification system, where AAB represents Amino acid and Biosynthesis; BSC- Biosynthesis of Co-factors; CEN- Cell envelope; CEP- Cellular processes; CIM- Central intermediary metabolism; DME- DNA Metabolism; EME-Energy metabolism; FPM – Fatty acid and Phospholipid metabolism; HPR – Hypothetical proteins; PFA – Protein Fate; PSY – Protein synthesis; PPN – Purine, pyrimidine and nucleotide metabolism; RFU – Regulatory functions (Regulatory functions+Transcription); TBP – Transport and Binding proteins; UNK – Unknown & Unclassified proteins; MEE – Mobile extrachromosomal elements.

Mentions: The distribution of genes into various functional classes is presented in Figure 1 based on the TIGR classification system. Data is shown for 8 out of the 10 species as the TIGR classification is not available for M. marinum and M. ulcerans. Most of the genomes have a large number (∼1000) of hypothetical proteins and proteins with unknown functions (∼1000). Among the primary metabolism genes, energy metabolism has a large presence in all genomes with an average of 600 genes. Genes coding for amino acid biosynthesis are less than 200. Purine and pyrimidine metabolism related genes are also fewer in number compared to other categories (<100). Most Mycobacterium genomes have a large number of regulatory genes. The number of genes in some categories such as nucleotide metabolism (PPN), protein fate (PFA) and cofactor biosynthesis (BSA) are fairly constant across all species considered in this work.


Comparative phylogenomics of pathogenic and non-pathogenic mycobacterium.

Prasanna AN, Mehra S - PLoS ONE (2013)

Classification of mycobacterial genes into functional classes.The genes are categorized into 16 different role categories based on the TIGR classification system, where AAB represents Amino acid and Biosynthesis; BSC- Biosynthesis of Co-factors; CEN- Cell envelope; CEP- Cellular processes; CIM- Central intermediary metabolism; DME- DNA Metabolism; EME-Energy metabolism; FPM – Fatty acid and Phospholipid metabolism; HPR – Hypothetical proteins; PFA – Protein Fate; PSY – Protein synthesis; PPN – Purine, pyrimidine and nucleotide metabolism; RFU – Regulatory functions (Regulatory functions+Transcription); TBP – Transport and Binding proteins; UNK – Unknown & Unclassified proteins; MEE – Mobile extrachromosomal elements.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3756022&req=5

pone-0071248-g001: Classification of mycobacterial genes into functional classes.The genes are categorized into 16 different role categories based on the TIGR classification system, where AAB represents Amino acid and Biosynthesis; BSC- Biosynthesis of Co-factors; CEN- Cell envelope; CEP- Cellular processes; CIM- Central intermediary metabolism; DME- DNA Metabolism; EME-Energy metabolism; FPM – Fatty acid and Phospholipid metabolism; HPR – Hypothetical proteins; PFA – Protein Fate; PSY – Protein synthesis; PPN – Purine, pyrimidine and nucleotide metabolism; RFU – Regulatory functions (Regulatory functions+Transcription); TBP – Transport and Binding proteins; UNK – Unknown & Unclassified proteins; MEE – Mobile extrachromosomal elements.
Mentions: The distribution of genes into various functional classes is presented in Figure 1 based on the TIGR classification system. Data is shown for 8 out of the 10 species as the TIGR classification is not available for M. marinum and M. ulcerans. Most of the genomes have a large number (∼1000) of hypothetical proteins and proteins with unknown functions (∼1000). Among the primary metabolism genes, energy metabolism has a large presence in all genomes with an average of 600 genes. Genes coding for amino acid biosynthesis are less than 200. Purine and pyrimidine metabolism related genes are also fewer in number compared to other categories (<100). Most Mycobacterium genomes have a large number of regulatory genes. The number of genes in some categories such as nucleotide metabolism (PPN), protein fate (PFA) and cofactor biosynthesis (BSA) are fairly constant across all species considered in this work.

Bottom Line: Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order.It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree.It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India.

ABSTRACT
Mycobacterium species are the source of a variety of infectious diseases in a range of hosts. Genome based methods are used to understand the adaptation of each pathogenic species to its unique niche. In this work, we report the comparison of pathogenic and non-pathogenic Mycobacterium genomes. Phylogenetic trees were constructed using sequence of core orthologs, gene content and gene order. It is found that the genome based methods can better resolve the inter-species evolutionary distances compared to the conventional 16S based tree. Phylogeny based on gene order highlights distinct evolutionary characteristics as compared to the methods based on sequence, as illustrated by the shift in the relative position of M. abscessus. This difference in gene order among the Mycobacterium species is further investigated using a detailed synteny analysis. It is found that while rearrangements between some Mycobacterium genomes are local within synteny blocks, few possess global rearrangements across the genomes. The study illustrates how a combination of different genome based methods is essential to build a robust phylogenetic relationship between closely related organisms.

Show MeSH
Related in: MedlinePlus