Slow fitness recovery in a codon-modified viral genome

Molecular Biology and Evolution

Volumn 29, Issue 10, 2012, Pages 2997-3004

  Bull, J J ^a   Molineux, I J ^a   Wilke, C O ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

codon modification; fitness suppression; genome engineering; vaccine design

Indexed keywords

VIRUS VACCINE;

ADAPTATION; AMINO ACID SUBSTITUTION; ARTICLE; BACTERIOPHAGE; CODON; COPY NUMBER VARIATION; DNA FLANKING REGION; DNA MODIFICATION; ESCHERICHIA COLI; GENE EXPRESSION; GENE FREQUENCY; GENE REPLICATION; GENE TRANSFER; GENETIC ENGINEERING; MOLECULAR EVOLUTION; MUTATIONAL ANALYSIS; NONHUMAN; POINT MUTATION; REPRODUCTIVE FITNESS; STOP CODON; VIRION; VIRUS GENOME; VIRUS ISOLATION; VIRUS STRAIN; VIRUS VIRULENCE; WILD TYPE;

ADAPTATION, BIOLOGICAL; BACTERIOPHAGE T7; BASE SEQUENCE; CODON; EVOLUTION, MOLECULAR; GENETIC FITNESS; GENOME, VIRAL; NUCLEOTIDES;

BACTERIA (MICROORGANISMS); MIRIDAE;

EID: 84866904061     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mss119     Document Type: Article

References (25)

1. Antia R, Regoes RR, Koella JC, Bergstrom CT. 2003. The role of evolution in the emergence of infectious diseases. Nature 426:658-661. (Pubitemid 38009372)
2. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol. 2:2006. 0008.
3. Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, Lenski RE, Kim JF. 2009. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461:1243-1247.
4. Bull JJ, Badgett MR, Wichman HA, Huelsenbeck JP, Hillis DM, Gulati A, Ho C, Molineux IJ. 1997. Exceptional convergent evolution in a virus. Genetics 147:1497-1507. (Pubitemid 27525448)
5. Bull JJ, Heineman RH, Wilke CO. 2011. The phenotype fitness map in phage experimental evolution. PLoS One 6:e27796.
6. Bull JJ, Millstein J, Orcutt J, Wichman HA. 2006. Evolutionary feedback mediated through population density, illustrated with viruses in chemostats. Am Nat. 167:E39-E51.
7. Bull JJ, Molineux IJ. 2008. Predicting evolution from genomics: experimental evolution of bacteriophage T7. Heredity 100: 453-463. (Pubitemid 351574181)
8. Burns CC, Campagnoli R, Shaw J, Vincent A, Jorba J, Kew O. 2009. Genetic inactivation of poliovirus infectivity by increasing the frequencies of CpG and UpA dinucleotides within and across synonymous capsid region codons. J Virol. 83:9957-9969.
9. Burns CC, Shaw J, Campagnoli R, Jorba J, Vincent A, Quay J, Kew O. 2006. Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. J Virol. 80:3259-3272.
10. Coleman JR, Papamichail D, Skiena S, Futcher B, Wimmer E, Mueller S. 2008. Virus attenuation by genome-scale changes in codon pair bias. Science 320:1784-1787. (Pubitemid 351931294)
11. Dunn JJ, Studier FW. 1983. Complete nucleotide sequence of bacteriophage T7 DNA and the locations of T7 genetic elements. J Mol Biol. 166:477-535. (Pubitemid 13027896)
12. Gu W, Zhou T, Wilke CO. 2010. A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput Biol. 6:e1000664.
13. Harcombe WR, Springman R, Bull JJ. 2009. Compensatory evolution for a gene deletion is not limited to its immediate functional network. BMC Evol Biol. 9:106.
14. Heineman RH, Molineux IJ, Bull JJ. 2005. Evolutionary robustness of an optimal phenotype: re-evolution of lysis in a bacteriophage deleted for its lysin gene. J Mol Evol. 61:181-191. (Pubitemid 41298102)
15. Keller TE, Mis SD, Jia KE, Wilke CO. 2012. Reduced mRNA secondary-structure stability near the start codon indicates functional genes in prokaryotes. Genome Biol Evol. 4:80-88.
16. Kew OM, Sutter RW, de Gourville EM, Dowdle WR, Pallansch MA. 2005. Vaccine-derived polioviruses and the endgame strategy for global polio eradication. Annu Rev Microbiol. 59:587-635. (Pubitemid 41507443)
17. Kudla G, Murray AW, Tollervey D, Plotkin JB. 2009. Codingsequence determinants of gene expression in Escherichia coli. Science 324:255-258.
18. Molineux IJ. 2005. T7 group. In: Calendar R, editor. The bacteriophages. Oxford: Oxford University Press. pp. 277-301.
19. Mueller S, Coleman JR, Papamichail D, Ward CB, Nimnual A, Futcher B, Skiena S, Wimmer E. 2010. Live attenuated influenza virus vaccines by computer-aided rational design. Nat Biotechnol. 28:723-726.
20. Mueller S, Papamichail D, Coleman JR, Skiena S, Wimmer E. 2006. Reduction of the rate of poliovirus protein synthesis through large-scale codon deoptimization causes attenuation of viral virulence by lowering specific infectivity. J Virol. 80:9687-9696. (Pubitemid 44435643)
21. Rokyta D, Badgett MR, Molineux IJ, Bull JJ. 2002. Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Mol Biol Evol. 19:230-238. (Pubitemid 34184595)
22. Studier FW, Rosenberg AH. 1981. Genetic and physical mapping of the late region of bacteriophage T7 DNA by use of cloned fragments of T7 DNA. J Mol Biol. 153:503-525. (Pubitemid 12180288)
23. Wichman HA, Millstein J, Bull JJ. 2005. Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170: 19-31. (Pubitemid 40799968)
24. Zhou T, Weems M, Wilke CO. 2009. Translationally optimal codons associate with structurally sensitive sites in proteins. Mol Biol Evol. 26:1571-1580.
25. Zhou T, Wilke CO. 2011. Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses. BMC Evol Biol. 11:59.