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Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

Wee WY, Tan TK, Jakubovics NS, Choo SW - PLoS ONE (2016)

Bottom Line: It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism.These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans.The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.

ABSTRACT
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

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Related in: MedlinePlus

The pathway for urea cycle derived from KEGG pathway analysis.UM_WWY possess a gene encoding for a putative enzyme arginase (EC 3.5.3.1) which hydrolyzes arginine into ornithine and urea. EC 6.3.4.5 = Argininosuccinate synthetase; EC 4.3.2.1 = Argininosuccinate lyase; EC 2.1.3.3 = Ornithine transcarbamoylase.
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pone.0152682.g005: The pathway for urea cycle derived from KEGG pathway analysis.UM_WWY possess a gene encoding for a putative enzyme arginase (EC 3.5.3.1) which hydrolyzes arginine into ornithine and urea. EC 6.3.4.5 = Argininosuccinate synthetase; EC 4.3.2.1 = Argininosuccinate lyase; EC 2.1.3.3 = Ornithine transcarbamoylase.

Mentions: Interestingly, further examinations of these genes revealed a gene encoding arginase (EC3.5.3.1), which is an enzyme found in some eubacteria and eukaryotes [25]. Arginase is one of the key enzymes in the urea cycle (Fig 5). This enzyme plays an important role in the hydrolysis of L-arginine to ornithine and urea. We examined the urea cycle KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and we found that the genome of UM_WWY also encodes other enzymes needed to form a complete urea cycle such as argininosuccinate synthetase (EC 6.3.4.5), argininosuccinate lyase (EC 4.3.2.1) and ornithine transcarbamoylase (EC 2.1.3.3) (Fig 5). In addition, gene encoding urease present in UM_WWY indicating that arginine or urea could be sources of nitrogen for this organism [26].Overall, this analysis indicates that UM_WWY is likely the first or the only known mycobacterial species which possesses the genetic basis for a complete urea cycle.


Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

Wee WY, Tan TK, Jakubovics NS, Choo SW - PLoS ONE (2016)

The pathway for urea cycle derived from KEGG pathway analysis.UM_WWY possess a gene encoding for a putative enzyme arginase (EC 3.5.3.1) which hydrolyzes arginine into ornithine and urea. EC 6.3.4.5 = Argininosuccinate synthetase; EC 4.3.2.1 = Argininosuccinate lyase; EC 2.1.3.3 = Ornithine transcarbamoylase.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4816395&req=5

pone.0152682.g005: The pathway for urea cycle derived from KEGG pathway analysis.UM_WWY possess a gene encoding for a putative enzyme arginase (EC 3.5.3.1) which hydrolyzes arginine into ornithine and urea. EC 6.3.4.5 = Argininosuccinate synthetase; EC 4.3.2.1 = Argininosuccinate lyase; EC 2.1.3.3 = Ornithine transcarbamoylase.
Mentions: Interestingly, further examinations of these genes revealed a gene encoding arginase (EC3.5.3.1), which is an enzyme found in some eubacteria and eukaryotes [25]. Arginase is one of the key enzymes in the urea cycle (Fig 5). This enzyme plays an important role in the hydrolysis of L-arginine to ornithine and urea. We examined the urea cycle KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and we found that the genome of UM_WWY also encodes other enzymes needed to form a complete urea cycle such as argininosuccinate synthetase (EC 6.3.4.5), argininosuccinate lyase (EC 4.3.2.1) and ornithine transcarbamoylase (EC 2.1.3.3) (Fig 5). In addition, gene encoding urease present in UM_WWY indicating that arginine or urea could be sources of nitrogen for this organism [26].Overall, this analysis indicates that UM_WWY is likely the first or the only known mycobacterial species which possesses the genetic basis for a complete urea cycle.

Bottom Line: It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism.These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans.The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

View Article: PubMed Central - PubMed

Affiliation: Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia.

ABSTRACT
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

Show MeSH
Related in: MedlinePlus