Challenges in predicting the evolutionary maintenance of a phage transgene

Journal of Biological Engineering

Volumn 8, Issue 1, 2014, Pages

  Schmerer, Matthew ^a   Molineux, Ian J ^a   Ally, Dilara ^b   Tyerman, Jabus ^c   Cecchini, Nicole ^a   Bull, James J ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b BAYER CROPSCIENCE   (United States)

^c Total Gas and Power New Energies USA Inc   (United States)

Author keywords

Biofilm; Evolution; Phage; Synthetic biology; Tragedy of the commons

Indexed keywords

AMMONIUM SULFATE;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERICIDAL ACTIVITY; BACTERIOPHAGE; BIOENGINEERING; BIOFILM; CLONING; DELETION MUTANT; ENZYMATIC DEGRADATION; ENZYME ACTIVITY; EVOLUTION; FREEZE THAWING; GENE EXPRESSION; LONGEVITY; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; TRANSGENE; TRANSGENIC ORGANISM;

EID: 84949117015     PISSN: None     EISSN: 17541611     Source Type: Journal    
DOI: 10.1186/1754-1611-8-21     Document Type: Article

References (39)

1. Donlan RM, Costerton JW: Biofilms: survival mechanisms of clinically relevant microorganisms . Clin Microbiol Rev 2002,15(2):167-193.
2. Worthington RJ, Richards JJ, Melander C: Small molecule control of bacterial biofilms . Org Biomol Chem 2012,10(37):7457-7474.
3. Cornelissen A, Ceyssens P, Van Praet H, Noben J, Shaburova OV, Krylov VN, Volckaert G, Lavigne R, T'Syen J: The T7-related Pseudomonas putida phage 15 displays virion-associated biofilm degradation properties . PloS One 2011,6(4):e18597.
4. Lu TK, Collins JJ: Dispersing biofilms with engineered enzymatic bacteriophage . PNAS 2007,104(27):11197-11202.
5. West SA, Griffin AS, Gardner A, Diggle SP: Social evolution theory for microorganisms . Nat Rev Microbiol 2006,4(8):597-607.
6. Xavier JB, Foster KR: Cooperation and conflict in microbial biofilms . Proc Natl Acad Sci U S A 2007,104(3):876-881.
7. MacLean RC: The tragedy of the commons in microbial populations insights from theoretical, comparative and experimental studies . Heredity 2008,100(5):471-477.
8. Bull JJ, Harcombe WR: Population dynamics constrain the cooperative evolution of cross-feeding . PloS One 2009, 4:e4115.
9. Kummerli R, Griffin AS, West SA, Buckling A, Harrison F: Viscous medium promotes cooperation in the pathogenic bacterium Pseudomonas aeruginosa . Proc Biol Sci R Soc 2009,276(1672):3531-3538.
10. Eshelman CM, Vouk R, Stewart JL, Halsne E, Lindsey HA, Schneider S, Gualu M, Dean AM, Kerr B: Unrestricted migration favours virulent pathogens in experimental metapopulations: evolutionary genetics of a rapacious life history . Philos Trans R Soc Lond B Biol Sci 2010,365(1552):2503-2513.
11. Frank SA: Demography and the tragedy of the commons . J Evol Biol 2010, 23:32-39.
12. Smith J: Tragedy of the commons among antibiotic resistance plasmids . Evolution 2012,66(4):1269-1274.
13. Levin BR, Stewart FM, Chao L: Resource-limited growth, competition, and predation - a model and experimental studies with bacteria and bacteriophage . Am Nat 1977,111(977):3-24.
14. Levin BR, Bull JJ: Population and evolutionary dynamics of phage therapy . Nat Rev Microbiol 2004,2(2):166-173.
15. Gladstone EG, Molineux IJ, Bull JJ: Evolutionary principles and synthetic biology: avoiding a molecular tragedy of the commons with an engineered phage . J Biol Eng 2012, 6:13.
16. Doolittle MM, Cooney JJ, Caldwell DE: Tracing the interaction of bacteriophage with bacterial biofilms using fluorescent and chromogenic probes . J Ind Microbiol 1996,16(6):331-341.
17. Manuel SGA, Ragunath C, Sait HBR, Izano EA, Kaplan JB, Ramasubbu N: Role of actie-site residues of dispersin B, a biofilm-releasing beta-hexosaminidase from a periodontal pathogen, in substrate hydrolysis . FEBS J 2007,274(22):5987-5999.
18. Schrag SJ, Mittler JE: Host-parasite coexistence: the role of spatial refuges in stabilizing bacteria-phage interactions . Amer Natur 1996,148(2):348-377.
19. Molineux I: The T7 group . In The Bacteriophages. Edited by: Calendar R. Oxford: Oxford University Press; 2005:277-301.
20. Dunn JJ, Studier FW: Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements . J Mol Biol 1983,166(4):477-535. [PMID: 6864790]
21. Rokyta D, Badgett MR, Molineux IJ, Bull JJ: Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus . Mol Biol Evol 2002,19(3):230-238.
22. Burns CC, Campagnoli R, Shaw J, Vincent A, Jorba J, Kew OM: Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG, and UpA dinucleotides within and across synonymous capsid region codons . J Virol 2009,83(19):9957-9969. [PMID: 19605476]
23. Gould F: Broadening the application of evolutionarily based genetic pest management . Evolution 2008,62(2):500-510.
24. Bull JJ, Turelli M: Wolbachia versus dengue: evolutionary forecasts . Evol Med Public Health 2013, 2013:197-207.
25. Paddon CJ, Keasling JD: Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development . Nat Rev Microbiol 2014,12(5):355-367.
26. Cecchini N, Schmerer M, Molineux IJ, Springman R, Bull JJ: Evolutionarily stable attenuation by genome rearrangement in a virus . G3 (Bethesda, Md.) 2013,3(8):1389-1397.
27. Springman R, Molineux IJ, Duong C, Bull RJ, Bull JJ: Evolutionary stability of a refactored phage genome . ACS Synthetic Biol 2012,1(9):425-430.
28. Sleight SC, Bartley BA, Lieviant JA, Sauro HM: Designing and engineering evolutionary robust genetic circuits . J Biol Eng 2010, 4:12.
29. Hanlon GW, Denyer SP, Olliff CJ, Ibrahim LJ: Reduction in exopolysaccharide viscosity as an aid to bacteriophage penetration through Pseudomonas aeruginosa biofilms . Appl Environ Microbiol 2001,67(6):2746-2753.
30. Hughes KA, Sutherland IW, Jones MV: Biofilm susceptibility to bacteriophage attack: the role of phage-borne polysaccharide depolymerase . Microbiology 1998, 144(Pt 11):3039-3047.
31. García LR, Molineux IJ: Rate of translocation of bacteriophage T7, DNA across the membranes of Escherichia coli . J Bacteriol 1995,177(14):4066-4076.
32. Studier FW, Moffatt BA: Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes . J Mol Biol 1986, 189:113-130.
33. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H: Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection . Mol Syst Biol 2006, 2:2006.0008.
34. Romeo T, Gong M, Liu MY, Brun-Zinkernagel AM: Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties . J Bacteriol 1993,175(15):4744-4755.
35. Kaplan JB, Ragunath C, Ramasubbu N, Fine DH: Detachment of Actinobacillus actinomycetemcomitans biofilm cells by an endogenous beta-hexosaminidase activity . J Bacteriol 2003,185(16):4693-4698.
36. Heineman RH, Bull JJ: Testing optimality with experimental evolution lysis time in a bacteriophage . Evolution 2007,61(7):1695-1709.
37. Bull JJ, Heineman RH, Wilke CO: The phenotype-fitness map in experimental evolution of phages . PloS One 2011,6(11):e27796.
38. Bull JJ: Optimality models of phage life history and parallels in disease evolution . J Theor Biol 2006,241(4):928-38.
39. R Development Core Team: R: A Language and Environment for Statistical Computing. Vienna: R Foundation for Statistical Computing; 2012. [ http://www.R-project.org/ ]. [ISBN 3-900051-0