Phage phenomics: Physiological approaches to characterize novel viral proteins

Journal of Visualized Experiments

Volumn 2015, Issue 100, 2015, Pages

  Sanchez, Savannah E ^a   Cuevas, Daniel A ^b   Rostron, Jason E ^a   Liang, Tiffany Y ^b   Pivaroff, Cullen G ^a   Haynes, Matthew R ^a   Nulton, Jim ^a   Felts, Ben ^a   Bailey, Barbara A ^a   Salamon, Peter ^a   Edwards, Robert A ^a,c,d   Burgin, Alex B ^e   Segall, Anca M ^a   Rohwer, Forest ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c San Diego State University   (United States)

^d ARGONNE NATIONAL LABORATORY   (United States)

^e BROAD INSTITUTE OF MIT AND HARVARD   (United States)

Author keywords

Continuous culture; Immunology; Issue 100; Metabolomics; Multi phenotype assay plates (MAPs); Phage; Phenomics; Viral metagenome

Indexed keywords

VIRUS PROTEIN;

BACTERIOPHAGE; BIOSYNTHESIS; ESCHERICHIA COLI; GENETICS; GENOMICS; METABOLISM; PROCEDURES; VIROLOGY; VIRUS GENOME;

BACTERIOPHAGES; ESCHERICHIA COLI; GENOME, VIRAL; GENOMICS; VIRAL PROTEINS;

EID: 84941241991     PISSN: 1940087X     EISSN: None     Source Type: Journal    
DOI: 10.3791/52854     Document Type: Article

References (37)

1. Wommack, K. E., Colwell, R. R. Virioplankton: Viruses in Aquatic Ecosystems. Microbiology and Molecular Biology Reviews. 64, (1), 69-114 (2000).
2. Hendrix, R. W. Recoding in Bacteriophages. Recoding: Expansion of decoding rules enriches gene expression. 24, 249-258 (2010).
3. Breitbart, M., et al. Genomic analysis of uncultured marine viral communities. Proceedings of the National Academy of Sciences. 99, (22), 14250-14255 (2002).
4. Breitbart, M., et al. Diversity and population structure of a near-shore marine-sediment viral community. Proceedings. Biological sciences/The Royal Society. 271, (1539), 565-574 (2004).
5. Dinsdale, E. A., et al. Functional metagenomic profiling of nine biomes. Nature. 452, (7187), 629-632 (2008).
6. Vega Thurber, R. L., et al. Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa. Proceedings of the National Academy of Sciences of the United States of America. 105, (47), 18413-18418 (2008).
7. Pedulla, M. L., et al. Origins of highly mosaic mycobacteriophage genomes. Cell. 113, (2), 171-182 (2003).
8. Calendar, R., Abedon, S. T. The bacteriophages. Oxford Univeresity Press (2006).
9. Breitbart, M., Miyake, J. H., Rohwer, F. Global distribution of nearly identical phage-encoded DNA sequences. FEMS microbiology letters. 236, (2), 249-256 (2004).
10. Klenk, H. -P., Palm, P., Zillig, W. DNA-Dependent RNA Polymerases as Phylogenetic Marker Molecules. Systematic and Applied Microbiology. 16, (4), 638-647 (1993).
11. Breitbart, M., Thompson, L., Suttle, C., Sullivan, M. Exploring the Vast Diversity of Marine Viruses. Oceanography. 20, (2), 135-139 (2007).
12. Mann, N. H., Cook, A., Millard, A., Bailey, S., Clokie, M. Marine ecosystems: bacterial photosynthesis genes in a virus. Nature. 424, (6950), 741 (2003).
13. Mann, N. H., et al. The genome of S-PM2, a “photosynthetic” T4-type bacteriophage that infects marine Synechococcus strains. Journal of bacteriology. 187, (9), 3188-3200 (2005).
14. Lindell, D., et al. Transfer of photosynthesis genes to and from Prochlorococcus viruses. Proceedings of the National Academy of Sciences of the United States of America. 101, (30), 11013-11018 (2004).
15. Millard, A., Clokie, M. R. J., Shub, D. A., Mann, N. H. Genetic organization of the psbAD region in phages infecting marine Synechococcus strains. Proceedings of the National Academy of Sciences of the United States of America. 101, (30), 11007-11012 (2004).
16. Sullivan, M. B., Coleman, M. L., Weigele, P., Rohwer, F., Chisholm, S. W. Three Prochlorococcus cyanophage genomes: signature features and ecological interpretations. PLoS biology. 3, (5), e144 (2005).
17. Rohwer, F., et al. The complete genomic sequence of the marine phage Roseophage SIOI shares homology with nonmarine phages. Limnology and Oceanography. 45, (2), 408-418 (2000).
18. Miller, E. S., et al. Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage. Journal of bacteriology. 185, (17), 5220-5233 (2003).
19. Thompson, L. R., et al. Phage auxiliary metabolic genes and the redirection of cyanobacterial host carbon metabolism. Proceedings of the National Academy of Sciences of the United States of America. 108, (39), E757-E764 (2011).
20. Paterson, S., et al. Antagonistic coevolution accelerates molecular evolution. Nature. 464, (7286), 275-278 (2010).
21. Seguritan, V., et al. Artificial neural networks trained to detect viral and phage structural proteins. PLoS computational biology. 8, (8), e1002657 (2012).
22. Neidhardt, F. C., Bloch, P. L., Smith, D. F. Culture Medium for Enterobacteria. Journal of Bacteriology. 119, (3), 736-747 (1974).
23. Khlebnikov, A., Datsenko, K. A., Skaug, T., Wanner, B. L., Keasling, J. D. Homogeneous expression of the P(BAD) promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology (Reading, England). 147, (Pt 2), 3241-3247 (2001).
24. Cuevas, D. A., et al. Elucidating genomic gaps using phenotypic profiles. F1000Research. (2014).
25. Zwietering, M. H., Jongenburger, I., Rombouts, F. M., van’t Riet, K. Modeling of the bacterial growth curve. Applied and environmental microbiology. 56, (6), 1875-1881 (1990).
26. Venables, W. N., Smith, D. M. An introduction to R. Available from: http://cran.r-project.org/doc/manuals/R-intro.pdf (2014).
27. Schmieder, R., Lim, Y. W., Rohwer, F., Edwards, R. TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets. BMC bioinformatics. 11, 341 (2010).
28. Schmieder, R., Edwards, R. Quality control and preprocessing of metagenomic datasets. Bioinformatics (Oxford, England). 27, (6), 863-864 (2011).
29. Schmieder, R., Edwards, R. Fast identification and removal of sequence contamination from genomic and metagenomic datasets. PloS One. 6, (3), e17288 (2011).
30. Welch, M., et al. Design parameters to control synthetic gene expression in Escherichia coli. PloS One. 4, (9), e7002 (2009).
31. Fiehn, O., et al. Quality control for plant metabolomics: reporting MSI-compliant studies. The Plant journal: for cell and molecular biology. 53, (4), 691-704 (2008).
32. Zeng, Q., Chisholm, S. W. Marine viruses exploit their host’s two-component regulatory system in response to resource limitation. Current biology: CB. 22, (2), 124-128 (2012).
33. Shindy, W. W., Smith, O. E. Identification of plant hormones from cotton ovules. Plant physiology. 55, (3), 550-554 (1975).
34. Lee, H. I., Leon, J., Raskin, I. Biosynthesis and metabolism of salicylic acid. Proceedings of the National Academy of Sciences of the United States of America. 92, (10), 4076-4079 (1995).
35. Chappell, J. The Biochemistry and Molecular Biology of Isoprenoid Metabolism. Plant Physiology. 107, (1), 1-6 (1995).
36. Kitagawa, M., et al. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA research: an international journal for rapid publication of reports on genes and genomes. 12, (5), 291-299 (2005).
37. Baran, R., et al. Metabolic footprinting of mutant libraries to map metabolite utilization to genotype. ACS chemical biology. 8, (1), 189-199 (2013).