Mycobacteriophages are emerging as a premiere model system for understanding fundamental questions In gene expression, protein structure and function, and genome evolution. Mycobacteriophages are viruses that infect mycobacteria, and are easy to Isolate, grow, and genomically characterize. Over 100 mycobacteriophage genomes have been sequenced - the largest group of phages infecting a single common host - but a tiny fraction of the global population of 1031 particles dominating the biosphere. Mycobacteriophages are amazingly diverse and 85% of their genes are of unknown function. Elucidating gene functions and unraveling the biological secrets of the mycobacteriophages has not been possible for lack of a system for genetic manipulations to make gene knockouts, insertions, and to add gene tags. This problem was circumvented with development of BRED technology for genome manipulation. For the first time, development of a facile and broadly applicable mycobacteriophage genetic system is possible. With nearly 10,000 genes, mostly of unknown function, there is an emerging and critical need for these tools. While the number of mycobacteriophage researchers has been fairly modest, it is currently exploding because of two main events. First is the implementation of mycobacteriophage discovery and genomics by the HHMI Science Education Alliance in colleges and universities across the US, with inclusion by 2011 of 36 institutions, 75 faculty, and many hundreds of student researchers, many who need to extend their investigations to address specific questions in mycobacteriophage biology and need the tools to do so. Secondly, the simplicity of the new BRED technology makes it generally applicable. The genetic tools we will develop will enable construction of simple unmarked gene knockouts, gene essentiality determination, creation of insertion mutants and tagged genes, and s transposition mutagenesis systems. We will also generate resources including phage-specific primers, plasmid vectors, and transcriptome data. The phagesdb.org web site will provide a central location for mycobacteriophage genome data, dissemination of resources, material requests, establishment of collaborations, and sharing of materials.

Public Health Relevance

Mycobacteriophages offer new paradigms for gene function, expression and regulation, as well as understanding the mechanisms of genome evolution. In addition to being a simple and powerful model organism, they also provide powerful tools for understanding their host, Mycobacterium tuberculosis, which kills more people than any other single infectious agent.

Agency
National Institute of Health (NIH)
Type
Resource-Related Research Projects (R24)
Project #
5R24GM093901-04
Application #
8655899
Study Section
Genomics, Computational Biology and Technology Study Section (GCAT)
Program Officer
Reddy, Michael K
Project Start
Project End
Budget Start
Budget End
Support Year
4
Fiscal Year
2014
Total Cost
Indirect Cost
Name
University of Pittsburgh
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
City
Pittsburgh
State
PA
Country
United States
Zip Code
15213
Oldfield, Lauren M; Hatfull, Graham F (2014) Mutational analysis of the mycobacteriophage BPs promoter PR reveals context-dependent sequences for mycobacterial gene expression. J Bacteriol 196:3589-97
Hatfull, Graham F (2014) Molecular Genetics of Mycobacteriophages. Microbiol Spectr 2:1-36
Pope, Welkin H; Jacobs-Sera, Deborah; Russell, Daniel A et al. (2014) Genomics and proteomics of mycobacteriophage patience, an accidental tourist in the Mycobacterium neighborhood. MBio 5:e02145
Dedrick, Rebekah M; Marinelli, Laura J; Newton, Gerald L et al. (2013) Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles. Mol Microbiol 88:577-89
Broussard, Gregory W; Oldfield, Lauren M; Villanueva, Valerie M et al. (2013) Integration-dependent bacteriophage immunity provides insights into the evolution of genetic switches. Mol Cell 49:237-48
Smith, Margaret C M; Hendrix, Roger W; Dedrick, Rebekah et al. (2013) Evolutionary relationships among actinophages and a putative adaptation for growth in Streptomyces spp. J Bacteriol 195:4924-35
Hatfull, Graham F; Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science Program; KwaZulu-Natal Research Institute for Tuberculosis and HIV Mycobacterial Genetics Course Students et al. (2012) Complete genome sequences of 138 mycobacteriophages. J Virol 86:2382-4
Hatfull, Graham F (2012) The secret lives of mycobacteriophages. Adv Virus Res 82:179-288
Mageeney, Catherine; Pope, Welkin H; Harrison, Melinda et al. (2012) Mycobacteriophage Marvin: a new singleton phage with an unusual genome organization. J Virol 86:4762-75
Payne, Kimberly M; Hatfull, Graham F (2012) Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PLoS One 7:e34052

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