Cluster k mycobacteriophages: Insights into the evolutionary origins of mycobacteriophage tm4

Pope, WH and Ferreira, CM and Jacobs-Sera, D and Benjamin, RC and Davis, AJ and DeJong, RJ and Elgin, SCR and Guilfoile, FR and Forsyth, MH and Harris, AD and Harvey, SE and Hughes, LE and Hynes, PM and Jackson, AS and Jalal, MD and MacMurray, EA and Manley, CM and McDonough, MJ and Mosier, JL and Osterbann, LJ and Rabinowitz, HS and Rhyan, CN and Russell, DA and Saha, MS and Shaffer, CD and Simon, SE and Sims, EF and Tovar, IG and Weisser, EG and Wertz, JT and Weston-Hafer, KA and Williamson, KE and Zhang, B and Cresawn, SG and Jain, P and Piuri, M and Jacobs, WR and Hendrix, RW and Hatfull, GF (2011) Cluster k mycobacteriophages: Insights into the evolutionary origins of mycobacteriophage tm4. PLoS ONE, 6 (10).

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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. © 2011 Pope et al.

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Details

Item Type:	Article
Status:	Published
Creators/Authors:	Creators Email Pitt Username ORCID Pope, WH Ferreira, CM Jacobs-Sera, D djs@pitt.edu DJS 0000-0001-7838-3257 Benjamin, RC Davis, AJ DeJong, RJ Elgin, SCR Guilfoile, FR Forsyth, MH Harris, AD Harvey, SE Hughes, LE Hynes, PM Jackson, AS Jalal, MD MacMurray, EA Manley, CM McDonough, MJ Mosier, JL Osterbann, LJ Rabinowitz, HS Rhyan, CN Russell, DA dar78@pitt.edu DAR78 0000-0001-6894-2748 Saha, MS Shaffer, CD Simon, SE Sims, EF Tovar, IG Weisser, EG Wertz, JT Weston-Hafer, KA Williamson, KE Zhang, B Cresawn, SG Jain, P Piuri, M Jacobs, WR Hendrix, RW rhx@pitt.edu RHX Hatfull, GF gfh@pitt.edu GFH
Contributors:	Contribution Contributors Name Email Pitt Username ORCID Editor Bereswill, Stefan UNSPECIFIED UNSPECIFIED UNSPECIFIED
Date:	2 November 2011
Date Type:	Publication
Journal or Publication Title:	PLoS ONE
Volume:	6
Number:	10
DOI or Unique Handle:	10.1371/journal.pone.0026750
Schools and Programs:	Dietrich School of Arts and Sciences > Biological Sciences
Refereed:	Yes
MeSH Headings:	Attachment Sites, Microbiological; Base Sequence; Chromosome Mapping; Cluster Analysis; Conserved Sequence--genetics; Evolution, Molecular; Gene Deletion; Genome, Viral--genetics; Molecular Sequence Annotation; Molecular Sequence Data; Multigene Family--genetics; Mutation--genetics; Mycobacteriophages--genetics; Mycobacteriophages--growth & development; Mycobacteriophages--isolation & purification; Mycobacteriophages--ultrastructure; Sequence Analysis, DNA; Temperature; Viral Proteins--genetics; Virion--genetics; Virion--ultrastructure; Virus Integration--genetics; Virus Replication--physiology
Other ID:	NLM PMC3203893
PubMed Central ID:	PMC3203893
PubMed ID:	22053209
Date Deposited:	07 Sep 2012 20:40
Last Modified:	31 Jul 2020 15:57
URI:	http://d-scholarship.pitt.edu/id/eprint/13992

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