Influenza B virus has global ordered RNA structure in (+) and (-) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence

BMC Research Notes

Volumn 6, Issue 1, 2013, Pages

  Priore, Salvatore F ^a   Moss, Walter N ^a   Turner, Douglas H ^a  

^a UNIVERSITY OF ROCHESTER MEDICAL CENTER   (United States)

Author keywords

GORS; Influenza; Influenza A; Influenza B; RNA; RNA secondary structure; Structural bioinformatics

Indexed keywords

M1 MATRIX PROTEIN, INFLUENZA B VIRUS; MATRIX PROTEIN; NUCLEOPROTEIN; PB2 PROTEIN, INFLUENZA VIRUS; VIRUS PROTEIN;

CHEMISTRY; CONFORMATION; DNA BASE COMPOSITION; GENETICS; INFLUENZA VIRUS A; INFLUENZA VIRUS B; RNA FOLDING; THERMODYNAMICS;

BASE COMPOSITION; INFLUENZA A VIRUS; INFLUENZA B VIRUS; NUCLEIC ACID CONFORMATION; NUCLEOPROTEINS; RNA FOLDING; THERMODYNAMICS; VIRAL MATRIX PROTEINS; VIRAL NONSTRUCTURAL PROTEINS; VIRAL PROTEINS;

EID: 84883583978     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-6-330     Document Type: Article

References (40)

1. Influenza B virus in seals. Osterhaus AD, Rimmelzwaan GF, Martina BE, Bestebroer TM, Fouchier RA, Science 2000 288 1051 1053 10.1126/science.288.5468. 1051 10807575 (Pubitemid 30324237)
2. Mass mortality of harbor seals: pneumonia associated with influenza A virus. Geraci JR, St Aubin DJ, Barker IK, Webster RG, Hinshaw VS, Bean WJ, Ruhnke HL, Prescott JH, Early G, Baker AS, et al. Science 1982 215 1129 1131 10.1126/science.7063847 7063847 (Pubitemid 12114099)
3. The evolution of human influenza viruses. Hay AJ, Gregory V, Douglas AR, Lin YP, Phil Trans R Soc Lond B Biol Sci 2001 356 1861 1870 (Pubitemid 34099091)
4. The annual impact of seasonal influenza in the US: measuring disease burden and costs. Molinari NA, Ortega-Sanchez IR, Messonnier ML, Thompson WW, Wortley PM, Weintraub E, Bridges CB, Vaccine 2007 25 5086 5096 10.1016/j.vaccine.2007.03.046 17544181 (Pubitemid 46879994)
5. Mortality associated with influenza and respiratory syncytial virus in the United States. Thompson WW, Shay DK, Weintraub E, Brammer L, Cox N, Anderson LJ, Fukuda K, JAMA 2003 289 179 186 10.1001/jama.289.2.179 12517228 (Pubitemid 36068705)
6. The economic value of a quadrivalent versus trivalent influenza vaccine. Lee BY, Bartsch SM, Willig AM, Vaccine 2012 30 7443 7446 10.1016/j.vaccine.2012. 10.025 23084849
7. The rationale for quadrivalent influenza vaccines. Ambrose CS, Levin MJ, Hum Vaccin Immunother 2012 8 81 88 22252006
8. The biology of influenza viruses. Bouvier NM, Palese P, Vaccine 2008 26 Suppl 4 49 D53 19230160
9. RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. Pfingsten JS, Kieft JS, RNA 2008 14 1255 1263 10.1261/rna.987808 18515544 (Pubitemid 351872182)
10. Role of RNA structure in regulating pre-mRNA splicing. Warf MB, Berglund JA, Trends Biochem Sci 2010 35 169 178 10.1016/j.tibs.2009.10.004 19959365
11. Poly(A) tail recognition by a viral RNA element through assembly of a triple helix. Mitton-Fry RM, DeGregorio SJ, Wang J, Steitz TA, Steitz JA, Science 2010 330 1244 1247 10.1126/science.1195858 21109672
12. Noncoding RNPs of viral origin. Steitz JA, Borah S, Cazalla D, Fok V, Lytle R, Mitton-Fry R, Riley K, Samji T, Cold Spring Harb Perspect Biol 2011 3 005165 10.1101/cshperspect.a005165 20719877
13. A comparative method for finding and folding RNA secondary structures within protein-coding regions. Pedersen JS, Meyer IM, Forsberg R, Simmonds P, Hein J, Nucleic Acids Res 2004 32 4925 4936 10.1093/nar/gkh839 15448187 (Pubitemid 39429696)
14. Importance of mRNA secondary structural elements for the expression of influenza virus genes. Ilyinskii PO, Schmidt T, Lukashev D, Meriin AB, Thoidis G, Frishman D, Shneider AM, OMICS 2009 13 421 430 10.1089/omi.2009.0036 19594376
15. An RNA conformational shift in recent H5N1 influenza A viruses. Gultyaev AP, Heus HA, Olsthoorn RC, Bioinformatics 2007 23 272 276 10.1093/ bioinformatics/btl559 17090581 (Pubitemid 46323147)
16. A family of non-classical pseudoknots in influenza A and B viruses. Gultyaev AP, Olsthoorn RC, RNA Biol 2010 7 125 129 10.4161/rna.7.2.11287 20200490
17. Fast and reliable prediction of noncoding RNAs. Washietl S, Hofacker IL, Stadler PF, Proc Natl Acad Sci U S A 2005 102 2454 2459 10.1073/pnas.0409169102 15665081 (Pubitemid 40279397)
18. Identification of potential conserved RNA secondary structure throughout influenza A coding regions. Moss WN, Priore SF, Turner DH, RNA 2011 17 991 1011 10.1261/rna.2619511 21536710
19. The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH, PLoS One 2012 7 38323 10.1371/journal.pone. 0038323 22685560
20. Influenza A virus coding regions exhibit host-specific global ordered RNA structure. Priore SF, Moss WN, Turner DH, PLoS One 2012 7 35989 10.1371/journal.pone.0035989 22558296
21. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. Clote P, Ferre F, Kranakis E, Krizanc D, RNA 2005 11 578 591 10.1261/rna.7220505 15840812 (Pubitemid 40594326)
22. Sperschneider J, Datta A, An introduction to RNA structure and pseudoknot prediction. In Algorithms in Computational Molecular Biology John Wiley & Sons, Inc 2011 521 546 10.1002/9780470892107.ch24
23. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH, Proc Natl Acad Sci U S A 2004 101 7287 7292 10.1073/pnas.0401799101 15123812 (Pubitemid 38638025)
24. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Mathews DH, Sabina J, Zuker M, Turner DH, J Mol Biol 1999 288 911 940 10.1006/jmbi.1999.2700 10329189 (Pubitemid 29248642)
25. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: implications for virus evolution and host persistence. Simmonds P, Tuplin A, Evans DJ, RNA 2004 10 1337 1351 10.1261/rna.7640104 15273323 (Pubitemid 39122104)
26. Bioinformatic and physical characterizations of genome-scale ordered RNA structure in mammalian RNA viruses. Davis M, Sagan SM, Pezacki JP, Evans DJ, Simmonds P, J Virol 2008 82 11824 11836 10.1128/JVI.01078-08 18799591
27. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Katz L, Burge CB, Genome Res 2003 13 2042 2051 10.1101/gr.1257503 12952875 (Pubitemid 37161761)
28. Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Deutscher MP, Nucleic Acids Res 2006 34 659 666 10.1093/nar/gkj472 16452296 (Pubitemid 43240252)
29. The influenza virus resource at the national center for biotechnology information. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D, J Virol 2008 82 596 601 10.1128/JVI.02005-07 17942553
30. Fast folding and comparison of RNA secondary structures. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, Schuster P, Monatsh Chem 1994 125 167 188 10.1007/BF00818163
31. Structural constraints on RNA virus evolution. Simmonds P, Smith DB, J Virol 1999 73 5787 5794 10364330 (Pubitemid 29274865)
32. SSE: a nucleotide and amino acid sequence analysis platform. Simmonds P, BMC Res Notes 2012 5 50 10.1186/1756-0500-5-50 22264264
33. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP, Proc Natl Acad Sci U S A 2011 108 11063 11068 10.1073/pnas.1106501108 21642531
34. Genome-wide measurement of RNA secondary structure in yeast. Kertesz M, Wan Y, Mazor E, Rinn JL, Nutter RC, Chang HY, Segal E, Nature 2010 467 103 107 10.1038/nature09322 20811459
35. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Underwood JG, Uzilov AV, Katzman S, Onodera CS, Mainzer JE, Mathews DH, Lowe TM, Salama SR, Haussler D, Nat Meth 2010 7 995 1001 10.1038/nmeth.1529
36. Characterization of the termination-reinitiation strategy employed in the expression of influenza B virus BM2 protein. Powell ML, Napthine S, Jackson RJ, Brierley I, Brown TD, RNA 2008 14 2394 2406 10.1261/rna.1231008 18824510
37. Eukaryotic coupled translation of tandem cistrons: identification of the influenza B virus BM2 polypeptide. Horvath CM, Williams MA, Lamb RA, EMBO J 1990 9 2639 2647 2114979
38. Patterns of evolution and host gene mimicry in influenza and other RNA viruses. Greenbaum BD, Levine AJ, Bhanot G, Rabadan R, PLoS Pathog 2008 4 1000079 10.1371/journal.ppat.1000079 18535658 (Pubitemid 351930631)
39. Comparison of avian and human influenza A viruses reveals a mutational bias on the viral genomes. Rabadan R, Levine AJ, Robins H, J Virol 2006 80 11887 11891 10.1128/JVI.01414-06 16987977 (Pubitemid 44788900)
40. Inhibition of influenza A virus replication by influenza B virus nucleoprotein: an insight into interference between influenza A and B viruses. Wanitchang A, Narkpuk J, Jaru-ampornpan P, Jengarn J, Jongkaewwattana A, Virology 2012 432 194 203 10.1016/j.virol.2012.06.016 22770925