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Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4.


ABSTRACT: Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, in that it was reportedly recovered from a lysogenic strain of Mycobacterium avium, but it is not capable of forming lysogens in any mycobacterial host. Like TM4, all of the Cluster K phages infect both fast- and slow-growing mycobacteria, and all of them--with the exception of TM4--form stable lysogens in both Mycobacterium smegmatis and Mycobacterium tuberculosis; immunity assays show that all five of these phages share the same immune specificity. TM4 infects these lysogens suggesting that it was either derived from a heteroimmune temperate parent or that it has acquired a virulent phenotype. We have also characterized a widely-used conditionally replicating derivative of TM4 and identified mutations conferring the temperature-sensitive phenotype. All of the Cluster K phages contain a series of well conserved 13 bp repeats associated with the translation initiation sites of a subset of the genes; approximately one half of these contain an additional sequence feature composed of imperfectly conserved 17 bp inverted repeats separated by a variable spacer. The K1 phages integrate into the host tmRNA and the Cluster K phages represent potential new tools for the genetics of M. tuberculosis and related species.

SUBMITTER: Pope WH 

PROVIDER: S-EPMC3203893 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Cluster K mycobacteriophages: insights into the evolutionary origins of mycobacteriophage TM4.

Pope Welkin H WH   Ferreira Christina M CM   Jacobs-Sera Deborah D   Benjamin Robert C RC   Davis Ariangela J AJ   DeJong Randall J RJ   Elgin Sarah C R SC   Guilfoile Forrest R FR   Forsyth Mark H MH   Harris Alexander D AD   Harvey Samuel E SE   Hughes Lee E LE   Hynes Peter M PM   Jackson Arrykka S AS   Jalal Marilyn D MD   MacMurray Elizabeth A EA   Manley Coreen M CM   McDonough Molly J MJ   Mosier Jordan L JL   Osterbann Larissa J LJ   Rabinowitz Hannah S HS   Rhyan Corwin N CN   Russell Daniel A DA   Saha Margaret S MS   Shaffer Christopher D CD   Simon Stephanie E SE   Sims Erika F EF   Tovar Isabel G IG   Weisser Emilie G EG   Wertz John T JT   Weston-Hafer Kathleen A KA   Williamson Kurt E KE   Zhang Bo B   Cresawn Steven G SG   Jain Paras P   Piuri Mariana M   Jacobs William R WR   Hendrix Roger W RW   Hatfull Graham F GF  

PloS one 20111028 10


Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a centr  ...[more]

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