Quantitative theory of entropic forces acting on constrained nucleotide sequences applied to viruses

Proceedings of the National Academy of Sciences of the United States of America

Volumn 111, Issue 13, 2014, Pages 5054-5059

  Greenbaum, Benjamin D ^a,b   Cocco, Simona ^c   Levine, Arnold J ^a   Monasson, Rémi ^d  

^a INSTITUTE FOR ADVANCED STUDY   (United States)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c CNRS   (France)

^d ECOLE NORMALE SUPÉRIEURE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DINUCLEOTIDE; SINGLE STRANDED RNA;

ARTICLE; CPG ISLAND; ENTROPY; FORCE; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS; INNATE IMMUNITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA VIRUS; VIRUS GENE; VIRUS GENOME;

BASE SEQUENCE; CODON; COMPUTER SIMULATION; DINUCLEOSIDE PHOSPHATES; ENTROPY; HUMANS; INFLUENZA A VIRUS, H1N1 SUBTYPE; MODELS, BIOLOGICAL; MOLECULAR MIMICRY; NUCLEOTIDE MOTIFS; VIRUSES;

EID: 84897506284     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1402285111     Document Type: Article

References (36)

1. Sharp PM, Li WH (1987) The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications.Nucleic Acids Res 15(3): 1281-1295.
2. Powell JR, Moriyama EN (1997) Evolution of codon usage bias in Drosophila. Proc Natl Acad Sci USA 94(15):7784-7790.
3. Rocha EP (2004) Codon usage bias from tRNA?s point of view: Redundancy, specialization, and efficient decoding for translation optimization. Genome Res 14(11): 2279-2286.
4. Karlin S, Doerfler W, Cardon LR (1994) Why is CpG suppressed in the genomes of virtually all small eukaryotic viruses but not in those of large eukaryotic viruses? J Virol 68(5):2889-2897.
5. Rabadan R, Levine AJ, Robins H (2006) Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes. J Virol 80(23):11887-11891.
6. Greenbaum BD, Levine AJ, Bhanot G, Rabadan R (2008) Patterns of evolution and host gene mimicry in influenza and other RNA viruses. PLoS Pathog 4(6):e1000079.
7. Greenbaum BD, Rabadan R, Levine AJ (2009) Patterns of oligonucleotide sequences in viral and host cell RNA identify mediators of the host innate immune system. PLoS ONE 4(6):e5969.
8. Jimenez-Baranda S, et al. (2011) Oligonucleotide motifs that disappear during the evolution of influenza virus in humans increase alpha interferon secretion by plasmacytoid dendritic cells. J Virol 85(8):3893-3904.
9. Pezda AC, Penn A, Barton GM, Coscoy L (2011) Suppression of TLR9 immunostimulatory motifs in the genome of a gammaherpesvirus. J Immunol 187(2):887-896.
10. Elde NC, Malik HS (2009) The evolutionary conundrum of pathogen mimicry.Nat Rev Microbiol 7(11):787-797.
11. Liddament MT, Brown WL, Schumacher AJ, Harris RS (2004) APOBEC3F properties and hypermutation preferences indicate activity against HIV-1 in vivo. Curr Biol 14(15): 1385-1391.
12. Wood N, et al. (2009) HIV evolution in early infection: Selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathog 5(5):e1000414.
13. Qian L, Kussell E (2012) Evolutionary dynamics of restriction site avoidance. Phys Rev Lett 108(15):158105.
14. Lin WH, Kussell E (2012) Evolutionary pressures on simple sequence repeats in prokaryotic coding regions.Nucleic Acids Res 40(6):2399-2413.
15. Brower-Sinning R, et al. (2009) The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. Genome Biol 10(2):R18.
16. Nelson P (2007) Biological Physics: Energy, Information, and Life (WH Freeman,New York), 1st Ed, Chap 7.
17. Baxter RJ (1982) Exactly Solved Models in Statistical Mechanics (Academic, Amsterdam), Chap 1-2.
18. Bao Y, et al. (2008) The influenza virus resource at theational Center for Biotechnology Information. J Virol 82(2):596-601.
19. HIV Sequence Compendium (2012) eds Kuiken C, et al. (Theoretical Biology and Biophysics Group, Los Alamosational Laboratory,M), LA-UR 12-24653.
20. Kent WJ, et al. (2002) The human genome browser at UCSC. Genome Res 12(6):996-1006.
21. Karolchik D, et al. (2004) The UCSC Table Browser data retrieval tool.Nucleic Acids Res 32(Database issue):D493-D496.
22. Lander ES, et al.; International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome.Nature 409(6822):860-921.
23. Zia RKP, Redish EF, McKay SR (2009) Making sense of the Legendre transform. Am J Phys 77:614.
24. Vabret N, et al. (2012) The biased nucleotide composition of HIV-1 triggers type I interferon response and correlates with subtype D increased pathogenicity. PLoS ONE 7(4):e33502.
25. Vabret N, et al. (2014) Large-scale nucleotide optimization of simian immunodeficiency virus (SIV) reduces its capacity to stimulate type-I IFN in vitro. J Virol, 10.1128/ JVI.03223-13.
26. Gumbel EJ (1958) Statistics of Extremes (Columbia Univ Press,New York), 1st Ed.
27. Hemmi H, et al. (2000) A Toll-like receptor recognizes bacterial DNA.Nature 408(6813): 740-745.
28. Nakajima K, Desselberger U, Palese P (1978) Recent human influenza A (H1N1) viruses are closely related genetically to strains isolated in 1950.Nature 274(5669):334-339.
29. Hanada K, Suzuki Y, Gojobori T (2004) A large variation in the rates of synonymous substitution for RNA viruses and its relationship to a diversity of viral infection and transmission modes. Mol Biol Evol 21(6):1074-1080.
30. Schwartz S, Felber BK, Pavlakis GN (1992) Distinct RNA sequences in the gag region of human immunodeficiency virus type 1 decrease RNA stability and inhibit expression in the absence of Rev protein. J Virol 66(1):150-159.
31. Schwartz S, et al. (1992) Mutational inactivation of an inhibitory sequence in human immunodeficiency virus type 1 results in Rev-independent gag expression. J Virol 66(12):7176-7182.
32. Chang JJ, Altfeld M (2009) TLR-mediated immune activation in HIV. Blood 113(2): 269-270.
33. van Weringh A, et al. (2011) HIV-1 modulates the tRNA pool to improve translation efficiency. Mol Biol Evol 28(6):1827-1834.
34. 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(19): 9687-9696.
35. Coleman JR, et al. (2008) Virus attenuation by genome-scale changes in codon pair bias. Science 320(5884):1784-1787.
36. Mueller S, et al. (2010) Live attenuated influenza virus vaccines by computer-aided rational design.Nat Biotechnol 28(7):723-726.