name: Actinobacteriophage_554 version: 3 date: 2016-07-19 owner: name: Graham Hatfull email: gfh@pitt.edu url: https://www.biology.pitt.edu/person/graham-hatfull description: > This database contains the 554 manually annotated Actinobacteriophages analyzed in Lima-Junior et al. 2016 & Dedrick et al. 2017. publications: 1: doi: 10.1186/s12866-016-0734-3 pmid: 27316672 title: > Characterization of mycobacteria and mycobacteriophages isolated from compost at the São Paulo Zoo Park Foundation in Brazil and creation of the new mycobacteriophage Cluster U authors: > James Daltro Lima-Junior, Cristina Viana-Niero, Daniel V Conde Oliveira, Gabriel Esquitini Machado, Michelle Cristiane da Silva Rabello, Joaquim Martins-Junior, Layla Farage Martins, Luciano Antonio Digiampietri, Aline Maria da Silva, João Carlos Setubal, Daniel A Russell, Deborah Jacobs-Sera, Welkin H Pope, Graham F Hatfull, Sylvia Cardoso Leão abstract: > A large collection of sequenced mycobacteriophages capable of infecting a single host strain of Mycobacterium smegmatis shows considerable genomic diversity with dozens of distinctive types (clusters) and extensive variation within those sharing evident nucleotide sequence similarity. Here we profiled the mycobacterial components of a large composting system at the São Paulo zoo. We isolated and sequenced eight mycobacteriophages using Mycobacterium smegmatis mc(2)155 as a host. None of these eight phages infected any of mycobacterial strains isolated from the same materials. The phage isolates span considerable genomic diversity, including two phages (Barriga, Nhonho) related to Subcluster A1 phages, two Cluster B phages (Pops, Subcluster B1; Godines, Subcluster B2), three Subcluster F1 phages (Florinda, Girafales, and Quico), and Madruga, a relative of phage Patience with which it constitutes the new Cluster U. Interestingly, the two Subcluster A1 phages and the three Subcluster F1 phages have genomic relationships indicating relatively recent evolution within a geographically isolated niche in the composting system. We predict that composting systems such as those used to obtain these mycobacteriophages will be a rich source for the isolation of additional phages that will expand our view of bacteriophage diversity and evolution. 2: doi: 10.1038/nmicrobiol.2016.251 pmid: 28067906 title: > Prophage-mediated defense against viral attack and viral counter-defense authors: > Rebekah M Dedrick, Deborah Jacobs-Sear, Carlos A Guerrero Bustamante, Rebecca A Garlena, Travis N Mavrich, Welkin H Pope, Juan C Cervantes Reyes, Daniel A Russel, Tamarah Adair, Richard Alvey, J Alfred Bonilla, Jerald S Bricker, Bryony R Brown, Deanna Byrnes, Steven G Cresawn, William B Davis, Leon A Dickson, Nicholas P Edgington, Ann M Findley, Urszula Golebiewska, Julianne H Grose, Cory F Hayes, Lee E Hughes, Keith W Hutchison, Sharon Isern, Allison A Johnson, Margaret A Kenna, Karen K Klyczek, Catherine M Mageeney, Scott F Michael, Sally D Molloy, Matthew T Montgomery, James Neitzel, Shallee T Page, Marie C Pizzorno, Marianne K Poxleitner, Claire A Rinehart, Courtney J Robinson, Michael R Rubin, Joseph N Teyim, Edwin Vazquez, Vassie C Ware, Jacqueline Washington, Graham F Hatfull abstract: > Temperate phages are common and prophages are abundant residents of sequenced bacterial genomes. Mycobacteriophages are viruses infecting mycobacterial hosts including Mycobacterium tuberculosis and Mycobacterium smegmatis, encompass substantial genetic diversity, and are commonly temperate. Characterization of ten Cluster N temperate mycobacteriophages reveals at least five distinct prophage-expressed viral defense systems that interfere with infection of lytic and temperate phages that are either closely-related (homotypic defense) or unrelated (heterotypic defense). Target specificity is unpredictable, ranging from a single target phage to one-third of those tested. The defense systems include a single-subunit restriction system, a heterotypic exclusion system, and a predicted (p)ppGpp synthetase, which blocks lytic phage growth, promotes bacterial survival, and enables efficient lysogeny. The predicted (p)ppGpp synthetase coded by the Phrann prophage defends against phage Tweety infection, but Tweety codes for a tetrapeptide repeat protein, gp54, that acts as a highly effective counter-defense system. Prophage-mediated viral defense offers an efficient mechanism for bacterial success in host-virus dynamics, and counter-defense promotes phage co-evolution. resources: ~