Phylogenetic prediction of cis-acting elements: A cre-like sequence in Norovirus genome?

BMC Research Notes

Volumn 2, Issue , 2009, Pages

  Victoria, Matías ^a   Colina, Rodney ^b   Miagostovich, Marize ^a   Leite, José ^a   Cristina, Juan ^b  

^a INSTITUTO OSWALDO CRUZ   (Brazil)

^b FACULTAD DE CIENCIAS   (Uruguay)

Author keywords

[No Author keywords available]

Indexed keywords

CALICIVIRIDAE; HEPATITIS A VIRUS; HEPATOVIRUS; NOROVIRUS; PICORNAVIRIDAE; RNA VIRUSES;

EID: 77249124868     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-2-176     Document Type: Article

References (30)

1. Evidence for a functional RNA element in the hepatitis C virus core gene. McMullar LK Grakoui A, Evans MJ Mihalik M, Puig AD Branch AD, Feinstone SM Rice CM, Proc Natl Acad Sci USA 2007 104 2879 2884 10.1073/pnas.0611267104 17299041
2. Detailed mapping of RNA secondary structures in core and NS5B-encoding sequences of hepatitis C virus by RNase cleavage and novel bioinformatic prediction methods. Tuplin A Evans DJ Simmonds P, J Gen Virol 2004 85 3037 3047 10.1099/vir.0.80141-0 15448367
3. A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for hepatitis C virus RNA replication. You S Stump DD, Branch AD Rice CM, J Virol 2004 78 1352 1366 10.1128/JVI.78.3.1352-1366.2004 14722290
4. pro. Gerber K Wimmer E Paul AV, Virology 2001 75 10979 10990 10.1128/JVI.75.22.10979-10990.2001 (Pubitemid 33031565)
5. 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
6. The rhinovirus type 14 genome contains an internally located RNA structure that is required for viral replication. McKnight KL Lemon SM, RNA 1998 4 1569 1584 10.1017/S1355838298981006 9848654
7. RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Knudsen B Hein J, Bioinformatics 1999 15 446 454 10.1093/bioinformatics/15.6.446 10383470
8. Secondary structure prediction for aligned RNA sequences. Hofacker IL Fekete M Stadler PF, J Mol Biol 2002 319 1059 1066 10.1016/S0022-2836(02)00308-X 12079347
9. Calculating nucleic acid secondary structure. Zuker M, Curr Opin Struct Biol 2000 10 303 310 10.1016/S0959-440X(00)00088-9 10851192
10. pol-coding sequence of Hepatoviruses. Yang Y Yi M Evans DJ Simmonds P, Lemon SM, J Virol 2008 82 10118 10128 10.1128/JVI.00787-08 18684812
11. New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features. Tapparel C Junier T, Gerlach D Cordey S, Van Belle S Perrin L, Zdobnov EM Kaiser L, BMC Genomics 2007 8 224 10.1186/1471-2164-8-224 17623054
12. Goodfellow: Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses. Simmonds P Karakasiliotis I Bailey D Chaudhry Y, Evans DJ, Nucleic Acids Res 2008 36 2530 2546 10.1093/nar/gkn096 18319285
13. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC, Nucleic Acids Res 2004 32 1792 1797 10.1093/nar/gkh340 15034147
14. Genetic differences between blood- and brain-derived viral sequences from human immunodeficiency virus type 1-infected patients: evidence of conserved elements in the V3 region of the envelope protein of brain derived sequences. Korber BT Kuntsman K Patterson B Furtado M, McEvilly M Levy R, Wolinsky S, J Virol 1994 68 7467 7481 7933130
15. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. Mathews DH Sabina J, Zucker M Turner H, J Mol Biol 1999 288 911 940 10.1006/jmbi.1999.2700 10329189
16. The Vienna RNA websuite. Gruber AR Lorenz R Bernhart SH Neubock R, Hofacker IL, Nucleic Acids Res 2008 36 Web Server 70 74 10.1093/nar/gkn188 18424795
17. La, PTB and PAB proteins bind to the 3' untranslated regián of Norwalk virus genomic RNA. Gutierrez-Escolano AL Vazquez-Ochoa M, Escobar-Herrera J Hernandez-Acosta J, Biochem Biophys Res Commun 2003 311 759 766 10.1016/j.bbrc.2003.10.066 14623338
18. Predicted stem-loop structures and variation in nucleotide sequence of 3' noncoding regions among animal calicivirus genomes. Seal BS Neill JD Ridpath JF, Virus Genes 1994 8 243 247 10.1007/BF01704518 7975270
19. Constrained evolution with respect to gene overlap of hepatitis B virus. Mizokami M Orito E, Ohba K Ikeo K, Lau JY Gojobori T, J Mol Evol 1997 44 83 S90 10.1007/PL00000061 9071016
20. Sequence and genomic organization of Norwalk virus. Jiang X Wang M, Wang K Estes MK, Virology 1993 195 51 61 10.1006/viro.1993.1345 8391187
21. Large outbreak of Norovirus: the baker who should have known better. De Wit MA Widdowson MA, Vennema H de Bruin E, Fernandes T Koopmans M, J Infect 2007 55 188 193 10.1016/j.jinf.2007.04.005 17602749
22. The molecular biology of caliciviruses. Clarke IN Lambden PR, J Gen Virol 1997 78 291 301 9018049
23. The phylogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. Koonin EV, J Gen Virol 1991 72 2197 2206 10.1099/0022-1317-72-9-2197 1895057
24. Genetic and biochemical studies of poliovirus cis-acting replication element cre in relation to VPg uridylylation. Rieder E Paul AV Kim DW Van Boom JH, Wimmer E, J Virol 2000 74 10371 10380 10.1128/JVI.74.22.10371-10380.2000 11044081
25. Functional dissection of a poliovirus cis-acting replication element [PV-cre(2C)]: analysis of single and dual-cre viral genomes and proteins that bind specifically to PV-cre RNA. Yin J Paul AV, Wimmer E Rieder E, J Virol 2003 77 5152 5166 10.1128/JVI.77.9.5152-5166.2003 12692218
26. A "slide-back" mechanism for the initiation of protein-primer RNA synthesis by the RNA polymerase of poliovirus. Paul AV Yin J, Mugavero J Rieder E, Liu Y Wimmer E, J Biol Chem 2003 278 43951 43960 10.1074/jbc. M307441200 12937178
27. Identification of an RNA hairpin in poliovirus RNA that served as the primary template in the in vitro uridylylation of VPg. Paul AV Rieder E Kim DW Van Boom JH, Wimmer E, J Virol 2000 74 10359 10370 10.1128/JVI.74.22.10359- 10370.2000 11044080
28. Protein primed RNA synthesis by purified poliovirus RNA polymerase. Paul AV Van Boom JH, Filippov D Wimmer E, Nature 1998 393 280 284 10.1038/30529 9607767
29. pol. Rohayem J Robel I Jager K Scheffler U, Rudoph W, J Virol 2006 80 7060 7069 10.1128/JVI.02195-05 16809311
30. The active form of the norovirus RNA-dependent RNA polymerase is a homodimer with cooperative activity. Hogbom M Jager K, Robel I Unge T, Rohayem J, J Gen Virol 2009 90 281 291 10.1099/vir.0.005629-0 19141436