Mycobacteriophage ZoeJ: A broad host-range close relative of mycobacteriophage TM4

Tuberculosis

Volumn 115, Issue , 2019, Pages 14-23

  Dedrick, Rebekah M ^a   Guerrero Bustamante, Carlos A ^a   Garlena, Rebecca A ^a   Pinches, R Seth ^b   Cornely, Kathleen ^b   Hatfull, Graham F ^a  

^a UNIVERSITY OF PITTSBURGH   (United States)

^b PROVIDENCE COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; RNA; BACTERIAL DNA; BACTERIAL PROTEIN; RECOMBINANT PROTEIN;

ARTICLE; BINDING SITE; DNA BINDING MOTIF; GENE EXPRESSION; GENE EXPRESSION LEVEL; GENOME ANALYSIS; HOST RANGE; LYSOGENIZATION; MYCOBACTERIOPHAGE; MYCOBACTERIOPHAGE TM4; MYCOBACTERIOPHAGE ZOEJ; MYCOBACTERIUM AVIUM; MYCOBACTERIUM SMEGMATIS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEIC ACID BASE SUBSTITUTION; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROPHAGE; RNA SEQUENCE; RNA TRANSLATION; SEQUENCE HOMOLOGY; SUPERINFECTION; TRANSLATION INITIATION; VIRUS CHARACTERIZATION; VIRUS ISOLATION; BACTERIAL GENE; BACTERIAL GENOME; CELLULAR IMMUNITY; GENETICS; HOST PATHOGEN INTERACTION; IMMUNOLOGY; MYCOBACTERIUM; PATHOGENICITY; PLASMID; WHOLE GENOME SEQUENCING;

BACTERIAL PROTEINS; DNA, BACTERIAL; GENES, BACTERIAL; GENOME, BACTERIAL; HOST-PATHOGEN INTERACTIONS; IMMUNITY, CELLULAR; MYCOBACTERIOPHAGES; MYCOBACTERIUM; MYCOBACTERIUM TUBERCULOSIS; PLASMIDS; RECOMBINANT PROTEINS; WHOLE GENOME SEQUENCING;

EID: 85060310976     PISSN: 14729792     EISSN: 1873281X     Source Type: Journal    
DOI: 10.1016/j.tube.2019.01.002     Document Type: Article

References (36)

1. Hatfull, G.F., Molecular genetics of mycobacteriophages. Microbiol Spectr 2 (2014), 1–36, 10.1128/microbiolspec.MGM2-0032-2013.
2. Hatfull, G.F., Mycobacteriophages: windows into tuberculosis. PLoS Pathog, 10, 2014, e1003953, 10.1371/journal.ppat.1003953.
3. 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 RL, Hendrix RW, Hatfull GF. On the nature of mycobacteriophage diversity and host preference. Virology 434 (2012), 187–201, 10.1016/j.virol.2012.09.026.
4. Russell, D.A., Hatfull, G.F., PhagesDB: the actinobacteriophage database. Bioinformatics 33 (2017), 784–786, 10.1093/bioinformatics/btw711.
5. Pope, W.H., Mavrich, T.N., Garlena, R.A., Guerrero-Bustamante, C.A., Jacobs-Sera, D., Montgomery, M.T., Russell, D.A., Warner, M.H., Science education alliance-phage hunters advancing G, evolutionary S, hatfull GF. Bacteriophages of Gordonia spp. display a spectrum of diversity and genetic relationships. MBio, 8, 2017, 10.1128/mBio.01069-17.
6. Pope, W.H., Bowman, C.A., Russell, D.A., Jacobs-Sera, D., Asai, D.J., Cresawn, S.G., Jacobs, W.R., Hendrix, R.W., Lawrence, J.G., Hatfull, G.F., Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science, Phage Hunters Integrating Research and Education, Mycobacterial Genetics Course. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife, 4, 2015, e06416, 10.7554/eLife.06416.
7. Hendrix, R.W., Smith, M.C., Burns, R.N., Ford, M.E., Hatfull, G.F., Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage. Proc Natl Acad Sci U S A 96 (1999), 2192–2197.
8. Pedulla, M.L., Ford, M.E., Houtz, J.M., Karthikeyan, T., Wadsworth, C., Lewis, J.A., Jacobs-Sera, D., Falbo, J., Gross, J., Pannunzio, N.R., Brucker, W., Kumar, V., Kandasamy, J., Keenan, L., Bardarov, S., Kriakov, J., Lawrence, J.G., Jacobs, W.R., Hendrix, R.W., Hatfull, G.F., Origins of highly mosaic mycobacteriophage genomes. Cell 113 (2003), 171–182.
9. Lawrence, J.G., Hatfull, G.F., Hendrix, R.W., Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches. J Bacteriol 184 (2002), 4891–4905.
10. 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., Hatfull, G.F., Cluster K Mycobacteriophages: insights into the Evolutionary Origins of Mycobacteriophage TM4. PLoS One, 6, 2011, e26750, 10.1371/journal.pone.0026750.
11. Jacobs, W.R. Jr., Tuckman, M., Bloom, B.R., Introduction of foreign DNA into mycobacteria using a shuttle phasmid. Nature 327 (1987), 532–535.
12. Ford, M.E., Stenstrom, C., Hendrix, R.W., Hatfull, G.F., Mycobacteriophage TM4: genome structure and gene expression. Tuber Lung Dis 79 (1998), 63–73, 10.1054/tuld.1998.0007 S0962-8479(98)90007-7 [pii].
13. Bardarov, S., Kriakov, J., Carriere, C., Yu, S., Vaamonde, C., McAdam, R.A., Bloom, B.R., Hatfull, G.F., Jacobs, W.R. Jr., Conditionally replicating mycobacteriophages: a system for transposon delivery to Mycobacterium tuberculosis. Proc Natl Acad Sci U S A 94 (1997), 10961–10966.
14. Sassetti, C.M., Boyd, D.H., Rubin, E.J., Comprehensive identification of conditionally essential genes in mycobacteria. Proc Natl Acad Sci U S A 98 (2001), 12712–12717.
15. Bardarov, S., Bardarov, S. Jr., Pavelka, M.S. Jr., Sambandamurthy, V., Larsen, M., Tufariello, J., Chan, J., Hatfull, G., Jacobs, W.R. Jr., Specialized transduction: an efficient method for generating marked and unmarked targeted gene disruptions in Mycobacterium tuberculosis, M. bovis BCG and M. smegmatis. Microbiology 148 (2002), 3007–3017.
16. Tufariello, J.M., Malek, A.A., Vilcheze, C., Cole, L.E., Ratner, H.K., Gonzalez, P.A., Jain, P., Hatfull, G.F., Larsen, M.H., Jacobs, W.R. Jr., Enhanced specialized transduction using recombineering in Mycobacterium tuberculosis. MBio, 5, 2014, 10.1128/mBio.01179-14 e01179-01114.
17. Jain, P., Weinrick, B.C., Kalivoda, E.J., Yang, H., Munsamy, V., Vilcheze, C., Weisbrod, T.R., Larsen, M.H., O'Donnell, M.R., Pym, A., Jacobs, W.R. Jr., Dual-Reporter mycobacteriophages (Phi2DRMs) reveal preexisting Mycobacterium tuberculosis persistent cells in human sputum. MBio, 7, 2016, 10.1128/mBio.01023-16.
18. Jain, P., Hartman, T.E., Eisenberg, N., O'Donnell, M.R., Kriakov, J., Govender, K., Makume, M., Thaler, D.S., Hatfull, G.F., Sturm, A.W., Larsen, M.H., Moodley, P., Jacobs, W.R. Jr., phi(2)GFP10, a high-intensity fluorophage, enables detection and rapid drug susceptibility testing of Mycobacterium tuberculosis directly from sputum samples. J Clin Microbiol 50 (2012), 1362–1369, 10.1128/JCM.06192-11 JCM.06192-11 [pii].
19. Jacobs, W.R. Jr., Barletta, R.G., Udani, R., Chan, J., Kalkut, G., Sosne, G., Kieser, T., Sarkis, G.J., Hatfull, G.F., Bloom, B.R., Rapid assessment of drug susceptibilities of Mycobacterium tuberculosis by means of luciferase reporter phages. Science 260 (1993), 819–822.
20. Sambandamurthy, V.K., Derrick, S.C., Hsu, T., Chen, B., Larsen, M.H., Jalapathy, K.V., Chen, M., Kim, J., Porcelli, S.A., Chan, J., Morris, S.L., Jacobs, W.R. Jr., Mycobacterium tuberculosis DeltaRD1 DeltapanCD: a safe and limited replicating mutant strain that protects immunocompetent and immunocompromised mice against experimental tuberculosis. Vaccine 24 (2006), 6309–6320.
21. Falkinham, J.O. 3rd, Factors influencing the chlorine susceptibility of Mycobacterium avium, Mycobacterium intracellulare, and Mycobacterium scrofulaceum. Appl Environ Microbiol 69 (2003), 5685–5689.
22. Dedrick, R.M., Jacobs-Sera, D., Bustamante, C.A., Garlena, R.A., Mavrich, T.N., Pope, W.H., Reyes, J.C., Russell, D.A., Adair, T., Alvey, R., Bonilla, J.A., Bricker, J.S., Brown, B.R., Byrnes, D., Cresawn, S.G., Davis, W.B., Dickson, L.A., Edgington, N.P., Findley, A.M., Golebiewska, U., Grose, J.H., Hayes, C.F., Hughes, L.E., Hutchison, K.W., Isern, S., Johnson, A.A., Kenna, M.A., Klyczek, K.K., Mageeney, C.M., Michael, S.F., Molloy, S.D., Montgomery, M.T., Neitzel, J., Page, S.T., Pizzorno, M.C., Poxleitner, M.K., Rinehart, C.A., Robinson, C.J., Rubin, M.R., Teyim, J.N., Vazquez, E., Ware, V.C., Washington, J., Hatfull, G.F., Prophage-mediated defence against viral attack and viral counter-defence. Nat Microbiol, 2, 2017, 16251, 10.1038/nmicrobiol.2016.251.
23. Marinelli, L.J., Piuri, M., Swigonova, Z., Balachandran, A., Oldfield, L.M., van Kessel, J.C., Hatfull, G.F., BRED: a simple and powerful tool for constructing mutant and recombinant bacteriophage genomes. PLoS One, 3, 2008, e3957, 10.1371/journal.pone.0003957.
24. van Kessel, J.C., Hatfull, G.F., Recombineering in Mycobacterium tuberculosis. Nat Methods 4 (2007), 147–152.
25. Russell, D.A., Sequencing, assembling, and finishing complete bacteriophage genomes. Methods Mol Biol 1681 (2018), 109–125, 10.1007/978-1-4939-7343-9_9.
26. Lee, M.H., Pascopella, L., Jacobs, W.R. Jr., Hatfull, G.F., Site-specific integration of mycobacteriophage L5: integration-proficient vectors for Mycobacterium smegmatis, Mycobacterium tuberculosis, and bacille Calmette-Guerin. Proc Natl Acad Sci U S A 88 (1991), 3111–3115.
27. Goulding, C.W., Parseghian, A., Sawaya, M.R., Cascio, D., Apostol, M.I., Gennaro, M.L., Eisenberg, D., Crystal structure of a major secreted protein of Mycobacterium tuberculosis-MPT63 at 1.5-A resolution. Protein Sci 11 (2002), 2887–2893, 10.1110/ps.0219002.
28. Horwitz, M.A., Lee, B.W., Dillon, B.J., Harth, G., Protective immunity against tuberculosis induced by vaccination with major extracellular proteins of Mycobacterium tuberculosis. Proc Natl Acad Sci U. S. A. 92 (1995), 1530–1534.
29. Sotello, D., Hata, D.J., Reza, M., Satyanarayana, R., Arunthari, V., Bosch, W., Disseminated Mycobacterium interjectum infection with bacteremia, hepatic and pulmonary involvement associated with a long-term catheter infection. Case Rep Infect Dis, 2017, 2017, 6958204, 10.1155/2017/6958204.
30. Daley, C.L., Mycobacterium avium complex disease. Microbiol Spectr, 5, 2017, 10.1128/microbiolspec.TNMI7-0045-2017.
31. Petrova, Z.O., Broussard, G.W., Hatfull, G.F., Mycobacteriophage-repressor-mediated immunity as a selectable genetic marker: Adephagia and BPs repressor selection. Microbiology 161 (2015), 1539–1551, 10.1099/mic.0.000120.
32. Dedrick, R.M., Mavrich, T.N., Ng, W.L., Hatfull, G.F., Expression and evolutionary patterns of mycobacteriophage D29 and its temperate close relatives. BMC Microbiol, 17, 2017, 225, 10.1186/s12866-017-1131-2.
33. Shell, S.S., Wang, J., Lapierre, P., Mir, M., Chase, M.R., Pyle, M.M., Gawande, R., Ahmad, R., Sarracino, D.A., Ioerger, T.R., Fortune, S.M., Derbyshire, K.M., Wade, J.T., Gray, T.A., Leaderless transcripts and small proteins are common features of the mycobacterial translational landscape. PLoS Genet, 11, 2015, 10.1371/journal.pgen.1005641.
34. Dedrick, R.M., Marinelli, L.J., Newton, G.L., Pogliano, K., Pogliano, J., Hatfull, G.F., Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles. Mol Microbiol 88 (2013), 577–589, 10.1111/mmi.12210.
35. Cumby, N., Edwards, A.M., Davidson, A.R., Maxwell, K.L., The bacteriophage HK97 gp15 moron element encodes a novel superinfection exclusion protein. J Bacteriol 194 (2012), 5012–5019, 10.1128/JB.00843-12.
36. Cresawn, S.G., Bogel, M., Day, N., Jacobs-Sera, D., Hendrix, R.W., Hatfull, G.F., Phamerator: a bioinformatic tool for comparative bacteriophage genomics. BMC Bioinf, 12, 2011, 395, 10.1186/1471-2105-12-395.