Eberly Family Professor of Biotechnology, HHMI Professor
Phages and tuberculosis
Dr. Hatfull received his Ph.D. in 1981 with Willie Donachie at the University of Edinburgh, Scotland, performed postdoctoral studies with Nigel Grindley at Yale University and with Fred Sanger at the MRC, and joined the Department in 1988.
Mycobacterium tuberculosis kills more people than any other single infectious agent. Since antibiotics are available and the BCG vaccine is in widespread use, why do two million people die each year from TB? The answer, in part, is that we really don't understand this curious bacterium or what parts of its genetic instructions make this such a deadly pathogen. At the heart of our strategies to understand mycobacterial genetics is the mycobacteriophages - viruses that infect the mycobacteria. These are easy to grow and manipulate and offer advantages over working with the slow-growing mycobacteria (such as M. tuberculosis) that can take up to a month to produce a colony on an agar plate. Phages are also rich sources of potential genetic and molecular tools that can be used to study - and to modify - their bacterial hosts.
Here's just a flavor of some of the current studies going on in the lab:
Exploring bacteriophage genomics. In collaboration with Dr. Hendrix we have spearheaded an initiative to understand viral diversity and evolution. Our specific focus is on the genomic characterization of mycobactriophages, and a collection of about 250 complete genome sequences have been determined. Many of these phages were isolated and sequenced through three programs in which phage discovery and genomics is a platform for integrating our science and educational missions. These are the Pittsburgh Phage Hunters Integrating Research and Education (PHIRE) program, the Howard Hughes Medical Institute Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (HHMI SEA-PHAGES) program, and a Univiersity of KwaZulu-Natal and KwaZulu-Nalat Research in TB and HIV (UKZN/K-RITH) workshop. These studies have not only provided valuable insights into phage diveristy and evolution, but present a rich and easily-accessible reservoir of genetic and mechanistic novelty for further study. A database of mycobaectriophage genomic infomration is available at http://www.phagesdb.org.
Exploiting mycobacteriophages. We are dissecting the mycobacteriophages to understand the functional roles of the thousands of genes we have identified, and to deternine if and when they are expressed, and how this expression is regulated. We are exploiting this information to develop tools and approaches that not only generate new tools for genetic manipulation for tuberculosis, but also to gain advances in diagnosis, prevention and treatment of the disease.
Site-specific recombination. Many if not most of the mycobacteriophages we have sequenced integrate their DNA into the host chromosome (and can excise them too). We are studying the mechanism of integrase-mediated site-specific recombination with a primary current focus on the serine-integrases. We are partiualrly interested in understanding how recomibnational directionality is determine in phage integration systems.
Tools - Genetic and Clinical. Studying the mycobacteria and their phages has great potential for the development of novel tools for their genetics but also for a more direct clinical involvement. Two systems we have been involved in developing are multivalent recombinant BCG vaccines and Luciferase Reporter Phages, but there are numerous additional strategies awaiting further development!
Hatfull, G. F. Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program, KwaZulu-Natal Research Institute for Tuberculosis and HIV (K-RITH) Mycobacterial Genetics Course, University of California Los Angeles Research Immersion Laboratory in Virology, Phage Hunters Integrating Research and Education (PHIRE) program. (2013). The complete genome sequences of 63 mycobacteriophages. GenomeA 1, doi:pii: e00847-13. 10.1128/genomeA.00847-13.
Singh, S., Plaks, S. G., Homa, N. J., Amrich, C. G., Heroux, A., Hatfull, G. F., & VanDemark, A. P. (2013). The structure of Xis reveals the basis for filament fomration and insight into DNA bending within a mycobacteriophage Intasome. J. Mol. Biol., In press.
Singh. S., Rockenbach, K., Dedrick, R. M., Vandemark, A., & Hatfull, G. F. (2013) Cross-talk between Diverse Serine Integrases. J Mol Biol In press.
Smith, M. C., Hendrix, R. W., Dedrick, R., Mitchell, K., Ko, CC., Russell, D., Bell, E., Gregory, M., Bibb, M. J., Pethick, F., Jacobs-Sera, D., Herron, P., Buttner, M. J., and Hatull, G. F. (2013). Evolutionary relationships within actinophages and a putative adaptation for growth in Streptomyces spp. J. Bacteriol. 195, 4924-4935.
Piuri, M., Rondon, L., Urdaniz, E., and Hatfull, G. F. (2013). Generation of affinity-tagged fluoromycobacteriophages by mixed assembly of phage capsids. Appl Environ Microbiol. 79, 5608-5615.
Pope, W. H., Jacobs-Sera, D., Best, A. A., Broussard, G. W., Connerly, P. L., Dedrick, R. M., Kremer, T. A., Offner, S., Ogiefo, A. H., Pizzorno, M. C., Rockenbach, K., Russell, D. A., Stowe, E. L., Stukey, J., Thibault, S. A., Conway, J. F., Hendrix, R. W., Hatfull, G. F. (2013) Cluster J mycobacteriophages: intron splicing in capsid and tail genes. PLoS One 8:e69273.
Broussard, G. W. and Hatfull, G. F. (2013) Evolution of genetic switch complexity. Bacteriophage 3:e24186.
Singh, S., Ghosh, P., and Hatfull, G. F. (2013). Attachment site selection and identity in Bxb1 serine integrase-mediated site-specific recombination. PLoS Genetics. 9, e1003490
Sambandan, D., D.N. Dao, B.C. Weinrick, C. Vilcheze, S.S. Gurcha, A. Ojha, L. Kremer, G.S. Besra, G.F. Hatfull & W.R. Jacobs, Jr., (2013) Keto-mycolic acid-dependent pellicle formation confers tolerance to drug-sensitive Mycobacterium tuberculosis. MBio 4: e00222-00213.
Silva, J.L., M. Piuri, G. Broussard, L. Marinelli, G.M. Bastos, R.D. Hirata, G.F. Hatfull & M.H. Hirata, (2013) Application of BRED technology to construct recombinant D29 reporter phage expressing EGFP. FEMS Microbiol Lett. 344, 166-172.
Dedrick, R. M., Marinelli, L. J., Newton, G. L., Pogliano, K., Pogliano, J ., Hatfull, G. F. (2013). FUnctional requirements for bacetriophage growth: gene essentiality and expression in mycobacteriophage Giles. Mol. Microbiology EPub head of print.
Sencilo, A., Jacobs-Sera, D., Russell, D. A., Ko, C-C., Bowman, C. A., Atanasova, N., Österlund, E., Oksanen, H. M., Bamford, D. H., Hatfull, G. F., Roine, E., & Hendrix, R.W. (2013). Snapshot of haloarchaeal tailed virus genomes. RNA Biology. In Press
Broussard, G.W., L.M. Oldfield, V.M. Villanueva, B.L. Lunt, E.E. Shine & G.F. Hatfull, (2013) Integration-Dependent Bacteriophage Immunity Provides Insights into the Evolution of Genetic Switches. Mol Cell. 49, 237-248.
Jacobs-Sera, D., Marinelli, L. J., Bowman, C., Broussard, G. W., Guerrero Bustamante, C., Boyle, M. M., Petrova, Z. O., Dedrick, R. M., Pope, W. H., Science Education Alliance Phage Hunters Advancing, G., Evolutionary Science Sea-Phages, P., Modlin, R. L., Hendrix, R. W., and Hatfull, G. F. (2012) On the nature of mycobacteriophage diversity and host preference. Virology 434, 187-201.
Marinelli, L.J., Fitz-Gibbon, S., Hayes, C., Bowman, C., Inkeles, M., Loncaric, A., Russell, D.A., Jacobs-Sera, D., Cokus, S., Pellegrini, M., Kim, J., Miller, J. F., Hatfull, G. F., and Modlin, R. L. (2012). Propionibacterium acnes Bacteriophages Display Limited Genetic Diversity and Broad Killing Activity against Bacterial Skin Isolates. mBio 3. e00279-12
Bai, H., Kath, J.E., Zorgiebel, F.M., Sun, M., Ghosh, P., Hatfull, G.F., Grindley, N.D., and Marko, J.F. (2012). Remote control of DNA-acting enzymes by varying the Brownian dynamics of a distant DNA end. Proc Natl Acad Sci U S A. Epub
Marinelli, L. J. , Hatfull, G. F., Piuri, M. (2012) Recombineering: A powerful tool for modification of bacteriophage genomes. Bacteriophage 2, 5-14.
Payne, K.M., and Hatfull, G.F. (2012). Mycobacteriophage endolysins: diverse and modular enzymes with multiple catalytic activities. PLoS One 7, e34052
Mageeney, C., W. Pope, M. Harrison, D. Moran, T. Cross, D. Jacobs-Sera, R. W. Hendrix, D. Dunbar & G. F. Hatfull, (2012) Mycobacteriophage Marvin: A new singleton phage with an unusual genome organization. J Virol. 86:4762-75.
Hatfull (2012). The Secret Lives of Mycobacteriophages. Advances in Virus Research. 82,179-288.
Hatfull, G. F., et al (2012) Complete genome sequences of 138 mycobacteriophages. J. Virol. 86: 2382-2384.
Kulka, K., Hatfull, G., and Ojha, A.K. (2012). Growth of Mycobacterium tuberculosis biofilms. J. Vis. Exp. 15:3820
Savinov, A., Pan, J., Ghosh, P. and Hatfull, G. F. (2012) The Bxb1 gp47 recombination directionality factor is required not only for prophage excision but also for phage DNA replication. Gene 495: 42-48.
Jain, P., Hartman, T.E., Eisenberg, N., O'Donnell, M. R., Kriakov, J., Govender, K., Makume, M., Thaler, D.S., Maiga, M., Timmins, G.S., Bishai, W.R., Hatfull, G.F., Sturm, A.W., Larsen, M.H., Moodley, P., and Jacobs, W.R. (2012) A high intensity fluorophage enables detection and rapid drug susceptibility testing of Mycobacterium tuberculosis directy from sputum samples. J. Clin. Microbiol. 50, 1362-1369
Cresawn, S.G., Bogel, M., Day, N., Jacobs-Sera, D., Hendrix, R.W. and Hatfull, G.F. (2011) Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinformatics 12:395.
Anderson, W.A., Amasino, R.M., Ares, M., Jr., Banerjee, U., Bartel, B., Corces, V.G., Drennan, C.L., Elgin, S.C., Epstein, I.R., Fanning, E., Guillette, L.J., Jr., Handelsman, J., Hatfull, G.F., Hoy, R.R., Kelley, D., Leinwand, L.A., Losick, R., Lu, Y., Lynn, D.G., Neuhauser, C., ODowd, D.K., Olivera, T., Pevzner, P., Richards-Kortum, R.R., Rine, J., Sah, R.L., Strobel, S.A., Walker, G.C., Walt, D.R., Warner, I.M., Wessler, S., Willard, H.F. and Zare, R.N. (2011) Competencies: a cure for pre-med curriculum. Science 334: 760-761
Pope, W.H., Ferreira, C.M., Jacobs-Sera, D., Benjamin, R.C., Davis, A.J., DeJong, R.J., Elgin, S.C.R., Guilfoile, F.R., Forsyth, M.H., Harris, A.D., Harvey, S.E., Hughes, L.E., Hynes, P.M., Jackson, A.S., Jalal, M.D., MacMurray, E.A., Manley, C.M., McDonough, M.J., Mosier, J.L., Osterbann, L.J., Rabinowitz, H.S., Rhyan, C.N., Russell, D.A., Saha, M.S., Shaffer, C.D., Simon, S.E., Sims, E.F., Tovar, I.G., Weisser, E.G., Wertz, J.T., Weston-Hafer, K.A., Williamson, K.E., Zhang, B., Cresawn, S.G., Jain, P., Piuri, M., Jacobs, W.R., Jr., Hendrix, R.W. and Hatfull, G.F. (2011) Cluster K Mycobacteriophages: Insights into the Evolutionary Origins of Mycobacteriophage TM4. PLoS ONE 6:e26750.
Hatfull, G.F. and Hendrix, R.W. (2011) Bacteriophages and their Genomes. Current Opinions in Virology 1: 298-303
Bai, H., Sun, M., Ghosh, P., Hatfull, G.F., Grindley, N.D. and Marko, J.F. (2011) Single-molecule analysis reveals the molecular bearing mechanism of DNA strand exchange by a serine recombinase. Proc Natl Acad Sci U S A 108:7419-24.
Huang, J., Ghosh, P., Hatfull, G.F. and Hong, Y. (2011) Successive and targeted DNA integrations in the Drosophila genome by Bxb1 and phiC31 integrases. Genetics 189:391-5.
Marine, R., Polson, S.W., Ravel, J., Hatfull, G., Russell, D., Sullivan, M., Syed, F., Dumas, M. and Wommack, K.E. (2011) Evaluation of a transposase protocol for rapid generation of shotgun high-throughput sequencing libraries from nanogram quantities of DNA. Appl Environ Microbiol 77: 8071-9.
Jain, P., Thaler, D.S., Maiga, M., Timmins, G.S., Bishai, W.R., Hatfull, G.F., Larsen, M.H. and Jacobs, W.R. (2011) Reporter phage and breath tests: emerging phenotypic assays for diagnosing active tuberculosis, antibiotic resistance, and treatment efficacy. J Infect Dis 204: 1142-1150.
Anderson, W.A., Banerjee, U., Drennan, C.L., Elgin, S.C., Epstein, I.R., Handelsman, J., Hatfull, G.F., Losick, R., ODowd, D.K., Olivera, B.M., Strobel, S.A., Walker, G.C. and Warner, I.M. (2011) Science education. Changing the culture of science education at research universities. Science 331:152-153.
Pope, W.H., D. Jacobs-Sera, D.A. Russell, C.L. Peebles, Z. Al-Atrache, T.A. Alcoser, L.M. Alexander, M.B. Alfano, S.T. Alford, N.E. Amy, M.D. Anderson, A.G. Anderson, A.A. Ang, J.r Ares M, A.J. Barber, L.P. Barker, J.M. Barrett, W.D. Barshop, C.M. Bauerle, I.M. Bayles, K.L. Belfield, A.A. Best, J.r Borjon A, C.A. Bowman, C.A. Boyer, K.W. Bradley, V.A. Bradley, L.N. Broadway, K. Budwal, K.N. Busby, I.W. Campbell, A.M. Campbell, A. Carey, S.M. Caruso, R.D. Chew, C.L. Cockburn, L.B. Cohen, J.M. Corajod, S.G. Cresawn, K.R. Davis, L. Deng, D.R. Denver, B.R. Dixon, S. Ekram, S.C. Elgin, A.E. Engelsen, B.E. English, M.L. Erb, C. Estrada, L.Z. Filliger, A.M. Findley, L. Forbes, M.H. Forsyth, T.M. Fox, M.J. Fritz, R. Garcia, Z.D. George, A.E. Georges, C.R. Gissendanner, S. Goff, R. Goldstein, K.C. Gordon, R.D. Green, S.L. Guerra, K.R. Guiney-Olsen, B.G. Guiza, L. Haghighat, G.V. Hagopian, C.J. Harmon, J.S. Harmson, G.A. Hartzog, S.E. Harvey, S. He, K.J. He, K.E. Healy, E.R. Higinbotham, E.N. Hildebrandt, J.H. Ho, G.M. Hogan, V.G. Hohenstein, N.A. Holz, V.J. Huang, E.L. Hufford, P.M. Hynes, A.S. Jackson, E.C. Jansen, J. Jarvik, P.G. Jasinto, T.C. Jordan, T. Kasza, M.A. Katelyn, J.S. Kelsey, L.A. Kerrigan, D. Khaw, J. Kim, J.Z. Knutter, C.C. Ko, G.V. Larkin, J.R. Laroche, A. Latif, K.D. Leuba, S.I. Leuba, L.O. Lewis, K.E. Loesser-Casey, C.A. Long, A.J. Lopez, N. Lowery, T.Q. Lu, V. Mac, I.R. Masters, J.J. McCloud, M.J. McDonough, A.J. Medenbach, A. Menon, R. Miller, B.K. Morgan, P.C. Ng, E. Nguyen, K.T. Nguyen, E.T. Nguyen, K.M. Nicholson, L.A. Parnell, C.E. Peirce, A.M. Perz, L.J. Peterson, R.E. Pferdehirt, S.V. Philip, K. Pogliano, J. Pogliano, T. Polley, E.J. Puopolo, H.S. Rabinowitz, M.J. Resiss, C.N. Rhyan, Y.M. Robinson, L.L. Rodriguez, A.C. Rose, J.D. Rubin, J.A. Ruby, M.S. Saha, J.W. Sandoz, J. Savitskaya, D.J. Schipper, C.E. Schnitzler, A.R. Schott, J.B. Segal, C.D. Shaffer, K.E. Sheldon, E.M. Shepard, J.W. Shepardson, M.K. Shroff, J.M. Simmons, E.F. Simms, B.M. Simpson, K.M. Sinclair, R.L. Sjoholm, I.J. Slette, B.C. Spaulding, C.L. Straub, J. Stukey, T. Sughrue, T.Y. Tang, L.M. Tatyana, S.B. Taylor, B.J. Taylor, L.M. Temple, J.V. Thompson, M.P. Tokarz, S.E. Trapani, A.P. Troum, J. Tsay, A.T. Tubbs, J.M. Walton, D.H. Wang, H. Wang, J.R. Warner, E.G. Weisser, S.C. Wendler, K.A. Weston-Hafer, H.M. Whelan, K.E. Williamson, A.N. Willis, H.S. Wirtshafter, T.W. Wong, P. Wu, Y. Yang, B.C. Yee, D.A. Zaidins, B. Zhang, M.Y. Zuniga, R.W. Hendrix, and G.F. Hatfull (2011) Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution. PLoS One 6:e16329e16329
Rondon, L., M. Piuri, J.r Jacobs WR, J. de Waard, G.F. Hatfull, and H. Takiff (2011) Evaluation of Fluoromycobacteriophages for detecting drug resistance in Mycobacterium tuberculosis. J Clin Microbiol :
Traag, B.A., A. Driks, P. Stragier, W. Bitter, G. Broussard, G. Hatfull, F. Chu, K.N. Adams, L. Ramakrishnan, and R. Losick (2010) Do mycobacteria produce endospores? Proc Natl Acad Sci U S A 107:878-881
Hatfull, G.F. (2010) Mycobacteriophages: genes and genomes. Annu Rev Microbiol 64:331-356
Alibaud, L., A. Alahari, X. Trivelli, A.K. Ojha, G.F. Hatfull, Y. Guerardel, and L. Kremer (2010) Temperature-dependent regulation of mycolic acid cyclopropanation in saprophytic mycobacteria: role of the Mycobacterium smegmatis 1351 gene (MSMEG_1351) in CIS-cyclopropanation of alpha-mycolates. J Biol Chem 285:21698-21707
Ojha, A.K., X. Trivelli, Y. Guerardel, L. Kremer, and G.F. Hatfull (2010) Enzymatic hydrolysis of trehalose dimycolate releases free mycolic acids during mycobacterial growth in biofilms. J Biol Chem 285:17380-17389
Sampson, T., G.W. Broussard, L.J. Marinelli, D. Jacobs-Sera, M. Ray, C.C. Ko, D. Russell, R.W. Hendrix, and G.F. Hatfull (2009) Mycobacteriophages BPs, Angel and Halo: comparative genomics reveals a novel class of ultra-small mobile genetic elements. Microbiology 155:2962-2977
Payne, K., Q. Sun, J. Sacchettini, and G.F. Hatfull (2009) Mycobacteriophage Lysin B is a novel mycolylarabinogalactan esterase. Mol. Microbiol. 73:367-381
Stewart, C.R., S.R. Casjens, S.G. Cresawn, J.M. Houtz, A.L. Smith, M.E. Ford, C.L. Peebles, G.F. Hatfull, R.W. Hendrix, W.M. Huang, and M.L. Pedulla (2009) The genome of Bacillus subtilis bacteriophage SPO1. J. Mol. Biol. 388:48-70
Comeau, A.M., G.F. Hatfull, H.M. Krisch, D. Lindell, N.H. Mann, and D. Prangishvili (2008) Exploring the prokaryotic virosphere. Res. Microbiol. 159:306-313
Hatfull, G.F., S.G. Cresawn, and R.W. Hendrix (2008) Comparative genomics of the mycobacteriophages: insights into bacteriophage evolution. Res. Microbiol. 159:332-339
van Kessel, J.C., L.J. Marinelli, and G.F. Hatfull (2008) Recombineering mycobacteria and their phages. Nat. Rev. Microbiol. 6:851-857
Marinelli, L.J., M. Piuri, Z. Swigonova, A. Balachandran, L.M. Oldfield, K.e.s.s.e. van, and G.F. Hatfull (2008) BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLoS ONE 3:e3957
van Kessel, J.C., and G.F. Hatfull (2008) Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets. Mol. Microbiol. 67:1094-1107
- Charles Bowman, Staff
- Gregory Broussard, Post Doc
- Rebekah Dedrick, Post Doc
- Max Garber, Research Assistant
- Pallavi Ghosh, Research Assistant Professor
- Carlos Guerrero, Staff
- Deborah Jacobs-Sera, Lab Instructor
- Ching-Chung Ko, Graduate Student
- Bryce Lunt, Graduate Student
- Chris Meier, Research Assistant
- Lauren Oldfield, Graduate Student
- Zaritza Petrova, Staff
- Welkin Pope, Research Assistant Professor
- Daniel Russell, Lab Instructor
- Valerie Villanueva, Graduate Student