The Mycobacterium phlei Genome: Expectations and Surprises

Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898–1899. We present the complete genome sequence for the M. phlei CCUG21000T type strain and the draft genomes for four additional strains. The genome size for all fiveis 5.3 Mb with 69.4% Guanine-Cytosine content...

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Main Authors:	Das, Sarbashis, Pettersson, B. M. Fredrik, Behra, Phani Rama Krishna, Ramesh, Malavika, Dasgupta, Santanu, Bhattacharya, Alok, Kirsebom, Leif A.
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860684/

id	pubmed-4860684
recordtype	oai_dc
spelling	pubmed-48606842016-05-10 The Mycobacterium phlei Genome: Expectations and Surprises Das, Sarbashis Pettersson, B. M. Fredrik Behra, Phani Rama Krishna Ramesh, Malavika Dasgupta, Santanu Bhattacharya, Alok Kirsebom, Leif A. Genome Report Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898–1899. We present the complete genome sequence for the M. phlei CCUG21000T type strain and the draft genomes for four additional strains. The genome size for all fiveis 5.3 Mb with 69.4% Guanine-Cytosine content. This is ≈0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport (potAD, potF) that are absent in other mycobacteria, and 3) strain-specific variations in the number of σ-factor genes. Moreover, M. phlei has as many as 82 mce (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155. Oxford University Press 2016-03-03 /pmc/articles/PMC4860684/ /pubmed/26941228 http://dx.doi.org/10.1093/gbe/evw049 Text en © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Das, Sarbashis Pettersson, B. M. Fredrik Behra, Phani Rama Krishna Ramesh, Malavika Dasgupta, Santanu Bhattacharya, Alok Kirsebom, Leif A.
spellingShingle	Das, Sarbashis Pettersson, B. M. Fredrik Behra, Phani Rama Krishna Ramesh, Malavika Dasgupta, Santanu Bhattacharya, Alok Kirsebom, Leif A. The Mycobacterium phlei Genome: Expectations and Surprises
author_facet	Das, Sarbashis Pettersson, B. M. Fredrik Behra, Phani Rama Krishna Ramesh, Malavika Dasgupta, Santanu Bhattacharya, Alok Kirsebom, Leif A.
author_sort	Das, Sarbashis
title	The Mycobacterium phlei Genome: Expectations and Surprises
title_short	The Mycobacterium phlei Genome: Expectations and Surprises
title_full	The Mycobacterium phlei Genome: Expectations and Surprises
title_fullStr	The Mycobacterium phlei Genome: Expectations and Surprises
title_full_unstemmed	The Mycobacterium phlei Genome: Expectations and Surprises
title_sort	mycobacterium phlei genome: expectations and surprises
description	Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898–1899. We present the complete genome sequence for the M. phlei CCUG21000T type strain and the draft genomes for four additional strains. The genome size for all fiveis 5.3 Mb with 69.4% Guanine-Cytosine content. This is ≈0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E (cas3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport (potAD, potF) that are absent in other mycobacteria, and 3) strain-specific variations in the number of σ-factor genes. Moreover, M. phlei has as many as 82 mce (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4860684/
_version_	1613576955910684672

The Mycobacterium phlei Genome: Expectations and Surprises

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