Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

Archives of Virology

Volumn 159, Issue 2, 2014, Pages 235-248

  Biswas, Subhajit ^a,c   Li, Wilson ^a   Manktelow, Emily ^a   Lever, Jonathan ^b   Easton, Laura E ^b   Lukavsky, Peter J ^b   Desselberger, Ulrich ^a   Lever, Andrew M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^c UNIVERSITY OF LINCOLN   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

VIRUS RNA;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CLUSTER ANALYSIS; CONFORMATION; GENE DELETION; GENETICS; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; NUCLEOTIDE SEQUENCE; PHYLOGENY; ROTAVIRUS;

BASE SEQUENCE; CLUSTER ANALYSIS; DNA MUTATIONAL ANALYSIS; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; PHYLOGENY; RNA, VIRAL; ROTAVIRUS; SEQUENCE DELETION;

EID: 84895077165     PISSN: 03048608     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00705-013-1802-8     Document Type: Article

References (40)

1. Estes M, Kapikian A (2007) Rotaviruses. In: Knipe DM, Howley PM et al (eds) Fields virology, 5th edn. Wolters Kluwer Health/Lippincott Williams and Wilkins, Philadelphia, pp 1917-1974.
2. Li W, Manktelow E, von Kirchbach J, Gog J, Desselberger U, Lever A (2010) Genomic analyses of codon, sequence and structural conservation with selective biochemical structure mapping reveal highly conserved and dynamic structures in rotavirus RNAs with potential cis-acting functions. Nucleic Acids Res 38: 7718-7735.
3. Dreher TW, Tsai CH, Florentz C, Giegé R (1992) Specific valylation of turnip yellow mosaic virus RNA by wheat germ valyl-tRNA synthetase determined by three anticodon loop nucleotides. Biochemistry 31: 9183-9189.
4. Dreher TW (2009) Role of tRNA-like structures in controlling plant virus replication. Virus Res 139: 217-229.
5. Giegé R (2008) Towards a more complete view of tRNA biology. Nat Struct Mol Biol 15: 1007-1014.
6. Yue D, Weiner AM, Maizels N (1998) The CCA-adding enzyme has a single active site. J Biol Chem 273: 29693-29700.
7. Cho HD, Tomita K, Suzuki T, Weiner AM (2002) U2 small nuclear RNA is a substrate for the CCA-adding enzyme (tRNA nucleotidyltransferase). J Biol Chem 277: 3447-3455.
8. Dreher TW, Goodwin JB (1998) Transfer RNA mimicry among tymoviral genomic RNAs ranges from highly efficient to vestigial. Nucleic Acids Res 26: 4356-4364.
9. Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinform 9: 474.
10. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36: W70-W74.
11. L'Hernault A, Greatorex JS, Crowther RA, Lever AM (2007) Dimerisation of HIV-2 genomic RNA is linked to efficient RNA packaging, normal particle maturation and viral infectivity. Retrovirology 4: 90.
12. Yue D, Maizels N, Weiner AM (1996) CCA-adding enzymes and poly (A) polymerases are all members of the same nucleotidyltransferase superfamily: characterization of the CCA-adding enzyme from the archaeal hyperthermophile Sulfolobus shibatae. RNA 2: 895-908.
13. Nagaike T, Suzuki T, Tomari Y, Takemoto-Hori C, Negayama F, Watanabe K, Ueda T (2001) Identification and characterization of mammalian mitochondrial tRNA nucleotidyltransferases. J Biol Chem 276: 40041-40049.
14. Nishimura S, Harada F, Narushima U, Seno T (1967) Purification of methionine-, valine-, phenylalanine- and tyrosine-specific tRNA from Escherichia coli. Biochim Biophys Acta 142: 133-148.
15. Jia J, Xu F, Chen X, Chen L, Jin Y, Wang DT (2002) Two essential regions for tRNA recognition in Bacillus subtilis tryptophanyl-tRNA synthetase. Biochem J 365: 749-756.
16. Lukavsky PJ, Puglisi JD (2004) Large-scale preparation and purification of polyacrylamide-free RNA oligonucleotides. RNA 10: 889-893.
17. Easton LE, Shibata Y, Lukavsky PJ (2010) Rapid, nondenaturing RNA purification using weak anion-exchange fast performance liquid chromatography. RNA 16: 647-653.
18. Heus H, Pardi A (1991) Novel H-1 nuclear magnetic resonance assignment procedure for RNA duplexes. J Am Chem Soc 113: 4360-4361.
19. Tortorici MA, Shapiro BA, Patton JT (2006) A base-specific recognition signal in the 5' consensus sequence of rotavirus plus-strand RNAs promotes replication of the double-stranded RNA genome segments. RNA 12: 133-146.
20. Wilm A, Linnenbrink K, Steger G (2008) ConStruct: improved construction of RNA consensus structures. BMC Bioinform 9: 219.
21. Patton JT, Wentz M, Xiaobo J, Ramig RF (1996) Cis-acting signals that promote genome replication in rotavirus mRNA. J Virol 70: 3961-3971.
22. Chen D, Patton JT (1998) Rotavirus RNA replication requires a single-stranded 3' end for efficient minus-strand synthesis. J Virol 72: 7387-7396.
23. Barro M, Mandiola P, Chen D, Patton JT, Spencer E (2001) Identification of sequences in rotavirus mRNAs important for minus strand synthesis using antisense oligonucleotides. Virology 288: 71-80.
24. Chen D, Barros M, Spencer E, Patton JT (2001) Features of the 3'-consensus sequence of rotavirus mRNAs critical to minus strand synthesis. Virology 282: 221-229.
25. Giegé R, Briand JP, Mengual R, Ebel JP, Hirth L (1978) Valylation of the two RNA components of turnip-yellow mosaic virus and specificity of the tRNA aminoacylation reaction. Eur J Biochem 84: 251-256.
26. Dreher TW, Rao AL, Hall TC (1989) Replication in vivo of mutant brome mosaic virus RNAs defective in aminoacylation. J Mol Biol 206: 425-438.
27. Annamalai P, Rao A (2007) In vivo packaging of brome mosaic virus RNA3, but not RNAs 1 and 2, is dependent on a cis-acting 3' tRNA-like structure. J Virol 81: 173-181.
28. Gog JR, Afonso Edos S, Dalton RM, Leclercq I, Tiley L, Elton D, von Kirchbach JC, Naffakh N, Escriou N, Digard P (2007) Codon conservation in the influenza A virus genome defines RNA packaging signals. Nucleic Acids Res 35: 1897-1907.
29. Hutchinson EC, von Kirchbach JC, Gog JR, Digard P (2010) Genome packaging in influenza A virus. J Gen Virol 91: 313-328.
30. Matsuo E, Roy P (2009) Bluetongue virus VP6 acts early in the replication cycle and can form the basis of chimeric virus formation. J Virol 83: 8842-8848.
31. Friederich MW, Hagerman PJ (1997) The angle between the anticodon and aminoacyl acceptor stems of yeast tRNA(Phe) is strongly modulated by magnesium ions. Biochemistry 36: 6090-6099.
32. Klasens BI, Huthoff HT, Das AT, Jeeninga RE, Berkhout B (1999) The effect of template RNA structure on elongation by HIV-1 reverse transcriptase. Biochim Biophys Acta 1444: 355-370.
33. Madore E, Florentz C, Giege R, Lapointe J (1999) Magnesium-dependent alternative foldings of active and inactive Escherichia coli tRNA(Glu) revealed by chemical probing. Nucleic Acids Res 27: 3583-3588.
34. Simon AE, Gehrke L (2009) RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs. Biochim Biophys Acta 1789: 571-583.
35. Kenyon JC, Tanner SJ, Legiewicz M, Phillip PS, Rizvi TA, Le Grice SF, Lever AM (2011) SHAPE analysis of the FIV Leader RNA reveals a structural switch potentially controlling viral packaging and genome dimerization. Nucleic Acids Res 39: 6692-6704.
36. Olsthoorn RC, Mertens S, Brederode FT, Bol JF (1999) A conformational switch at the 3' end of a plant virus RNA regulates viral replication. EMBO J 18: 4856-4864.
37. Chen SC, Olsthoorn RC (2010) In vitro and in vivo studies of the RNA conformational switch in alfalfa mosaic virus. J Virol 84: 1423-1429.
38. Puglisi EV, Puglisi JD (2007) Probing the conformation of human tRNA(3)(Lys) in solution by NMR. FEBS Lett 581: 5307-5314.
39. Heerschap A, Mellema JR, Janssen HG, Walters JA, Haasnoot CA, Hilbers CW (1985) Imino-proton resonances of yeast tRNAPhe studied by two-dimensional nuclear Overhauser enhancement spectroscopy. Eur J Biochem 149: 649-655.
40. Figueroa N, Keith G, Leroy JL, Plateau P, Roy S, Gueron M (1983) NMR study of slowly exchanging imino protons in yeast tRNAasp. Proc Natl Acad Sci USA 80: 4330-4333.