title: The Mycobacterium phlei Genome: Expectations and Surprises.
abstract: Mycobacterium phlei, a nontuberculosis mycobacterial species, was first described in 1898-1899. We present the complete genome sequence for theM. phlei CCUG21000(T)type strain and the draft genomes for four additional strains. The genome size for all five is 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 theM. 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 toM. smegmatis mc2 155.
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala, Sweden.
authors.forename: Sarbashis
authors.initials: S
authors.lastname: Das
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala, Sweden.
authors.forename: B M Fredrik
authors.initials: BM
authors.lastname: Pettersson
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala, Sweden.
authors.forename: Phani Rama Krishna
authors.initials: PR
authors.lastname: Behra
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala, Sweden.
authors.forename: Malavika
authors.initials: M
authors.lastname: Ramesh
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala, Sweden.
authors.forename: Santanu
authors.initials: S
authors.lastname: Dasgupta
authors.affiliation: School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
authors.forename: Alok
authors.initials: A
authors.lastname: Bhattacharya
authors.affiliation: Department of Cell and Molecular Biology, Box 596, Biomedical Centre, Uppsala, Sweden leif.kirsebom@icm.uu.se.
authors.forename: Leif A
authors.initials: LA
authors.lastname: Kirsebom
mesh_terms: D000818:Animals; D064113:CRISPR-Cas Systems; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D005990:Glycerol / Q000378:metabolism; D009168:Mycobacterium phlei / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D010802:Phylogeny; D011073:Polyamines / Q000378:metabolism
chemical_list: D011073:Polyamines; D005990:Glycerol
keywords: Mycobacterium phlei genome sequence; comparative genome analysis; mycobacterial growth; mycobacterial phylogeny