CodonShuffle: A tool for generating and analyzing synonymously mutated sequences

Virus Evolution

Volumn 1, Issue 1, 2015, Pages

  De Melo Jorge, Daniel Macedo ^a   Mills, Ryan E ^a   Lauring, Adam S ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Bioinformatics; Codon; RNA virus; Synonymous mutation; Synthetic

Indexed keywords

EID: 85027046544     PISSN: None     EISSN: 20571577     Source Type: Journal    
DOI: 10.1093/ve/vev012     Document Type: Article

References (37)

1. Belalov, I. S., and Lukashev, A. N. (2013) 'Causes and Implications of Codon Usage Bias in RNA Viruses', PLoS One, 8: e56642.
2. Bull, J. J., Molineux, I. J., and Wilke, C. O. (2012) 'Slow Fitness Recovery in a Codon-Modified Viral Genome', Molecular Biology and Evolution, 29: 2997-3004.
3. Burns, C. C. et al. (2006) 'Modulation of Poliovirus Replicative Fitness in HeLa Cells by Deoptimization of Synonymous Codon Usage in the Capsid Region', Journal of Virology, 80: 3259-72.
4. Burns, C. C. et al. (2009) 'Genetic Inactivation of Poliovirus Infectivity by Increasing the Frequencies of CpG and UpA Dinucleotides within and across Synonymous Capsid Region Codons', Journal of Virology, 83: 9957-69.
5. Cello, J., Paul, A. V., and Wimmer, E. (2002) 'Chemical Synthesis of Poliovirus cDNA: Generation of Infectious Virus in the Absence of Natural Template', Science, 297: 1016-8.
6. Coleman, J. R. et al. (2008) 'Virus Attenuation by Genome-Scale Changes in Codon Pair Bias', Science, 320: 1784-7.
7. Cuevas, J. M., Domingo-Calap, P., and Sanjuán, R. (2012) 'The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses', Molecular Biology and Evolution, 29: 17-20.
8. Fields, B. N., Knipe, D. M., and Howley, P. M. (2013) Fields Virology. Philadelphia, PA: Lippincott Williams & Wilkins.
9. Goodman, D. B., Church, G. M., and Kosuri, S. (2013) 'Causes and Effects of N-Terminal Codon Bias in Bacterial Genes', Science, 342: 475-9.
10. Gutman, G. A., and Hatfield, G.W. (1989) 'Nonrandom Utilization of Codon Pairs in Escherichia coli', Proceedings of the National Academy of Sciences of the United States of America, 86: 3699-703.
11. Jenkins, G. M., and Holmes, E. C. (2003) 'The Extent of Codon Usage Bias in Human RNA Viruses and Its Evolutionary Origin', Virus Research, 92: 1-7.
12. Karlin, S., Doerfler, W., and Cardon, L. R. (1994) 'Why is CpG Suppressed in the Genomes of Virtually All Small Eukaryotic Viruses But Not in Those of Large Eukaryotic Viruses?', Journal of Virology, 68: 2889-97.
13. Hartl, D.L. (1988) A Primer of Population Genetics, 3rd edn. Sunderland, MA: Sinauer.
14. Lauring, A. S. et al. (2012) 'Codon Usage Determines the Mutational Robustness, Evolutionary Capacity, and Virulence of an RNA Virus', Cell Host and Microbe, 12: 623-32.
15. Lorenz, R. et al. (2011) 'ViennaRNA Package 2.0', Algorithms for Molecular Biology, 6: 26.
16. Markham, N. R., and Zuker, M. (2008) 'UNAFold: Software for Nucleic Acid Folding and Hybridization', Methods in Molecular Biology, 453: 3-31.
17. Mueller, S. et al. (2006) 'Reduction of the Rate of Poliovirus Protein Synthesis through Large-Scale Codon Deoptimization Causes Attenuation of Viral Virulence by Lowering Specific Infectivity', Journal of Virology, 80: 9687-96.
18. Nogales, A. et al. (2014) 'Influenza A Virus Attenuation by Codon Deoptimization of the NS Gene for Vaccine Development', Journal of Virology, 88: 10525-40.
19. Nougairede, A. et al. (2013) 'Random Codon Re-encoding Induces Stable Reduction of Replicative Fitness of Chikungunya Virus in Primate and Mosquito Cells', PLoS Pathogens, 9: e1003172.
20. Palmenberg, A. C. et al. (2009) 'Sequencing and Analyses of All Known Human Rhinovirus Genomes Reveal Structure and Evolution', Science, 324: 55-9.
21. Plotkin, J. B., and Dushoff, J. (2003) 'Codon Bias and Frequency-Dependent Selection on the Hemagglutinin Epitopes of Influenza A Virus', Proceedings of the National Academy of Sciences of the United States of America, 100: 7152-7.
22. Plotkin, J. B., and Dushoff, J. (2011) 'Synonymous But Not the Same: The Causes and Consequences of Codon Bias', Nature Reviews Genetics, 12: 32-42.
23. Rabadan, R., Levine, A. J., and Robins, H. (2006) 'Comparison of Avian and Human Influenza A Viruses Reveals a Mutational Bias on the Viral Genomes', Journal of Virology, 80: 11887-91.
24. Sharp, P. M., and Li, W. H. (1987) 'The Codon Adaptation Index- A Measure of Directional Synonymous Codon Usage Bias, and Its Potential Applications', Nucleic Acids Research, 15: 1281-95.
25. Sharp, P. M., and Li, W. H. (1993) 'Codon Usage: Mutational Bias, Translational Selection, or Both?', Biochemical Society Transactions, 21: 835-41.
26. Shen, S. H. et al. (2015) 'Large-Scale Recoding of an Arbovirus Genome to Rebalance Its Insect Versus Mammalian Preference', Proceedings of the National Academy of Sciences of the United States of America, 112: 4749-54.
27. Simmonds, P., and Smith, D. B. (1999) 'Structural Constraints on RNA Virus Evolution', Journal of Virology, 73: 5787-94.
28. Simmonds, P., and Smith, D. B. (2004) 'Detection of Genome-Scale Ordered RNA Structure (GORS) in Genomes of Positive-Stranded RNA Viruses: Implications for Virus Evolution and Host Persistence', RNA, 10: 1337-51.
29. Steil, B. P., and Barton, D. J. (2009) 'Cis-Active RNA Elements (CREs) and Picornavirus RNA Replication', Virus Research, 139: 240-52.
30. Tuller, T. et al. (2010) 'An Evolutionarily Conserved Mechanism for Controlling the Efficiency of Protein Translation', Cell, 141: 344-54.
31. Tulloch, F., et al. (2014) 'RNA Virus Attenuation by Codon Pair Deoptimisation is an Artefact of Increases in CpG/UpA Dinucleotide Frequencies', eLife, 3: e04531.
32. Wang, B. et al. (2015) 'Recoding of the Vesicular Stomatitis Virus L Gene by Computer-Aided Design Provides a Live, Attenuated Vaccine Candidate', MBio, 6: e00237-15.
33. Wimmer, E., and Paul, A. V. (2011) 'Synthetic Poliovirus and Other Designer Viruses: What have We Learned from Them?', Annual Review of Microbiology, 65: 583-609.
34. Wong, E. H. M. et al. (2010) 'Codon Usage Bias and the Evolution of Influenza A viruses. Codon Usage Biases of Influenza Virus', BMC Evolutionay Biology, 10: 253.
35. Wright, F. (1990) 'The "Effective Number of Codons" Used in a Gene', Gene, 87: 23-9.
36. Yang, Z. (2006) Molecular Evolution: A Statistical Approach. Oxford: OUP.
37. Zuker, M. (2003) 'Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction', Nucleic Acids Research, 31: 3406-15.