A 5'-proximal stem-loop structure of 5' untranslated region of porcine reproductive and respiratory syndrome virus genome is key for virus replication

Virology Journal

Volumn 8, Issue , 2011, Pages

  Lu, Jiaqi ^a   Gao, Fei ^a,b   Wei, Zuzhang ^a   Liu, Ping ^a,b   Liu, Changlong ^a   Zheng, Haihong ^a   Li, Yanhua ^a   Lin, Tao ^a,b   Yuan, Shishan ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b NANJING AGRICULTURAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; GENOMIC RNA; GUANOSINE; VIRUS RNA;

5' UNTRANSLATED REGION; ANIMAL CELL; ARTERIVIRUS; ARTICLE; BASE PAIRING; CONTROLLED STUDY; GENE FUNCTION; GENE SEQUENCE; MESSENGER RNA SYNTHESIS; MOLECULAR PHYLOGENY; NONHUMAN; RNA STRUCTURE; RNA SYNTHESIS; VIRUS GENOME; VIRUS REPLICATION; ANIMAL; CELL LINE; CONFORMATION; GENE DELETION; GENETIC RECOMBINATION; GENETICS; HAMSTER; NUCLEOTIDE SEQUENCE; PHYSIOLOGY;

ARTERIVIRUS; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; RNA VIRUSES; SUS;

5' UNTRANSLATED REGIONS; ANIMALS; CELL LINE; CONSERVED SEQUENCE; CRICETINAE; NUCLEIC ACID CONFORMATION; PORCINE RESPIRATORY AND REPRODUCTIVE SYNDROME VIRUS; RECOMBINATION, GENETIC; RNA, VIRAL; SEQUENCE DELETION; VIRUS REPLICATION;

EID: 79955125674     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-8-172     Document Type: Article

References (48)

1. The molecular biology of arteriviruses. EJ Snijder JJ Meulenberg, J Gen Virol 1998 79 Pt 5 961 979 9603311 (Pubitemid 28203837)
2. Novel Structural Protein in Porcine Reproductive and Respiratory Syndrome Virus Encoded in an Alternative Open Reading Frame 5 Present in All Arteriviruses. CR Johnson TF Griggs JS Gnanandarajah MP Murtaugh, J Gen Virol 2011 21307222
3. Discovery of a small arterivirus gene that overlaps the GP5 coding sequence and is important for virus production. AE Firth JC Zevenhoven-Dobbe NM Wills YY Go U Balasuriya JF Atkins EJ Snijder CC Posthuma, J Gen Virol 2011 21307223
4. Secondary structure and function of the 5'-proximal region of the equine arteritis virus RNA genome. E Van den Born AP Gultyaev EJ Snijder, RNA 2004 10 424 437 10.1261/rna.5174804 14970388 (Pubitemid 38241003)
5. Nidovirus transcription: how to make sense.? AO Pasternak WJ Spaan EJ Snijder, J Gen Virol 2006 87 1403 1421 10.1099/vir.0.81611-0 16690906 (Pubitemid 43827196)
6. Coronaviruses use discontinuous extension for synthesis of subgenome-length negative strands. SG Sawicki DL Sawicki, Adv Exp Med Biol 1995 380 499 506 8830530
7. Arterivirus discontinuous mRNA transcription is guided by base pairing between sense and antisense transcription-regulating sequences. G van Marle JC Dobbe AP Gultyaev W Luytjes WJ Spaan EJ Snijder, Proc Natl Acad Sci USA 1999 96 12056 12061 10.1073/pnas.96.21.12056 10518575 (Pubitemid 29502857)
8. Sequence requirements for RNA strand transfer during nidovirus discontinuous subgenomic RNA synthesis. AO Pasternak E van den Born WJ Spaan EJ Snijder, EMBO J 2001 20 7220 7228 10.1093/emboj/20.24.7220 11742998 (Pubitemid 34062313)
9. Sequence motifs involved in the regulation of discontinuous coronavirus subgenomic RNA synthesis. S Zuniga I Sola S Alonso L Enjuanes, J Virol 2004 78 980 994 10.1128/JVI.78.2.980-994.2004 14694129 (Pubitemid 38067619)
10. Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark. K Tian X Yu T Zhao Y Feng Z Cao C Wang Y Hu X Chen D Hu X Tian, et al. PLoS One 2007 2 526 10.1371/journal.pone.0000526 17565379
11. Porcine reproductive and respiratory syndrome in China. L Zhou H Yang, Virus Res 2010 154 31 37 10.1016/j.virusres.2010.07.016 20659506
12. Mouse hepatitis virus stem-loop 2 adopts a uYNMG(U)a-like tetraloop structure that is highly functionally tolerant of base substitutions. P Liu L Li SC Keane D Yang JL Leibowitz DP Giedroc, J Virol 2009 83 12084 12093 10.1128/JVI.00915-09 19759148
13. A U-turn motif-containing stem-loop in the coronavirus 5' untranslated region plays a functional role in replication. P Liu L Li JJ Millership H Kang JL Leibowitz DP Giedroc, RNA 2007 13 763 780 10.1261/rna.261807 17353353 (Pubitemid 46641536)
14. Putative cis-acting stem-loops in the 5' untranslated region of the severe acute respiratory syndrome coronavirus can substitute for their mouse hepatitis virus counterparts. H Kang M Feng ME Schroeder DP Giedroc JL Leibowitz, J Virol 2006 80 10600 10614 10.1128/JVI.00455-06 16920822 (Pubitemid 44628906)
15. The leader RNA of coronavirus mouse hepatitis virus contains an enhancer-like element for subgenomic mRNA transcription. Y Wang X Zhang, J Virol 2000 74 10571 10580 10.1128/JVI.74.22.10571-10580.2000 11044101
16. The 5'-terminal region of the Aichi virus genome encodes cis-acting replication elements required for positive- and negative-strand RNA synthesis. S Nagashima J Sasaki K Taniguchi, J Virol 2005 79 6918 6931 10.1128/JVI.79.11. 6918-6931.2005 15890931 (Pubitemid 40677323)
17. Functional analysis of the stem-loop structures at the 5' end of the Aichi virus genome. S Nagashima J Sasaki K Taniguchi, Virology 2003 313 56 65 10.1016/S0042-6822(03)00346-5 12951021 (Pubitemid 37013595)
18. 3'-Terminal sequence in poliovirus negative-strand templates is the primary cis-acting element required for VPgpUpU-primed positive-strand initiation. N Sharma BJ O'Donnell JB Flanegan, J Virol 2005 79 3565 3577 10.1128/JVI.79.6.3565-3577.2005 15731251 (Pubitemid 40327945)
19. Cis-acting RNA elements at the 5' end of Sindbis virus genome RNA regulate minus- and plus-strand RNA synthesis. I Frolov R Hardy CM Rice, RNA 2001 7 1638 1651 10.1017/S135583820101010X 11720292 (Pubitemid 33078938)
20. Lelystad virus, the cause of porcine epidemic abortion and respiratory syndrome: a review of mystery swine disease research at Lelystad. G Wensvoort EP de Kluyver JM Pol F Wagenaar RJ Moormann MM Hulst R Bloemraad A den Besten T Zetstra C Terpstra, Vet Microbiol 1992 33 185 193 10.1016/0378-1135(92)90046-V 1481355
21. Characterization of swine infertility and respiratory syndrome (SIRS) virus (isolate ATCC VR-2332). DA Benfield E Nelson JE Collins L Harris SM Goyal D Robison WT Christianson RB Morrison D Gorcyca D Chladek, J Vet Diagn Invest 1992 4 127 133 1616976
22. The origin and evolution of porcine reproductive and respiratory syndrome viruses. K Hanada Y Suzuki T Nakane O Hirose T Gojobori, Mol Biol Evol 2005 22 1024 1031 10.1093/molbev/msi089 15659555 (Pubitemid 40471415)
23. Divergence time of porcine reproductive and respiratory syndrome virus subtypes. R Forsberg, Mol Biol Evol 2005 22 2131 2134 10.1093/molbev/msi208 16000650 (Pubitemid 41437812)
24. Comparison of the 5' leader sequences of North American isolates of reference and field strains of porcine reproductive and respiratory syndrome virus (PRRSV). C Tan L Chang S Shen DX Liu J Kwang, Virus Genes 2001 22 209 217 10.1023/A:1008179726163 11324758 (Pubitemid 32291093)
25. Determination of 5'-leader sequences from radically disparate strains of porcine reproductive and respiratory syndrome virus reveals the presence of highly conserved sequence motifs. MB Oleksiewicz A Botner J Nielsen T Storgaard, Arch Virol 1999 144 981 987 10.1007/s007050050560 10416379 (Pubitemid 29284859)
26. Identification of 5' and 3' cis-acting elements of the porcine reproductive and respiratory syndrome virus: acquisition of novel 5' AU-rich sequences restored replication of a 5'-proximal 7-nucleotide deletion mutant. YJ Choi SI Yun SY Kang YM Lee, J Virol 2006 80 723 736 10.1128/JVI.80.2.723-736. 2006 16378975
27. Discontinuous subgenomic RNA synthesis in arteriviruses is guided by an RNA hairpin structure located in the genomic leader region. E Van den Born CC Posthuma AP Gultyaev EJ Snijder, J Virol 2005 79 6312 6324 10.1128/JVI.79.10. 6312-6324.2005 15858015 (Pubitemid 40617235)
28. Construction of infectious cDNA clones of PRRSV: separation of coding regions for nonstructural and structural proteins. S Yuan Z Wei, Sci China C Life Sci 2008 51 271 279 10.1007/s11427-008-0023-y 18246315 (Pubitemid 351208376)
29. Mfold web server for nucleic acid folding and hybridization prediction. M Zuker, Nucleic Acids Res 2003 31 3406 3415 10.1093/nar/gkg595 12824337 (Pubitemid 37442169)
30. An infectious cDNA clone of a highly pathogenic porcine reproductive and respiratory syndrome virus variant associated with porcine high fever syndrome. J Lv J Zhang Z Sun W Liu S Yuan, J Gen Virol 2008 89 2075 2079 10.1099/vir.0.2008/001529-0 18753215
31. Recombinant PRRSV expressing porcine circovirus sequence reveals novel aspect of transcriptional control of porcine arterivirus. H Zheng Z Sun XQ Zhu J Long J Lu J Lv S Yuan, Virus Res 2010 148 8 16 10.1016/j.virusres.2009.11.014 19951727
32. Reverse genetic manipulation of the overlapping coding regions for structural proteins of the type II porcine reproductive and respiratory syndrome virus. D Yu J Lv Z Sun H Zheng J Lu S Yuan, Virology 2009 383 22 31 10.1016/j.virol.2008.09.013 18977502
33. Identification of dispensable nucleotide sequence in 3' untranslated region of porcine reproductive and respiratory syndrome virus. Z Sun C Liu F Tan F Gao P Liu A Qin S Yuan, Virus Res 2010 154 38 47 10.1016/j.virusres.2010.08. 027 20833212
34. Stem-loop III in the 5' untranslated region is a cis-acting element in bovine coronavirus defective interfering RNA replication. S Raman P Bouma GD Williams DA Brian, J Virol 2003 77 6720 6730 10.1128/JVI.77.12.6720-6730.2003 12767992 (Pubitemid 36666866)
35. Higher-order RNA structural requirements and small-molecule induction of tombusvirus subgenomic mRNA transcription. S Wang L Mortazavi KA White, J Virol 2008 82 3864 3871 10.1128/JVI.02416-07 18256151 (Pubitemid 351521223)
36. The 3a accessory protein of SARS coronavirus specifically interacts with the 5'UTR of its genomic RNA, Using a unique 75 amino acid interaction domain. K Sharma M Surjit N Satija B Liu VT Chow SK Lal, Biochemistry 2007 46 6488 6499 10.1021/bi062057p 17488094 (Pubitemid 46870115)
37. Three different cellular proteins bind to complementary sites on the 5'-end-positive and 3'-end-negative strands of mouse hepatitis virus RNA. T Furuya MM Lai, J Virol 1993 67 7215 7222 8230443 (Pubitemid 23343847)
38. An apical GAGA loop within 5' UTR of the coxsackievirus B3 RNA maintains structural organization of the IRES element required for efficient ribosome entry. S Bhattacharyya S Das, RNA Biol 2006 3 60 68 10.4161/rna.3.2.2990 17114941 (Pubitemid 44435345)
39. A 5' RNA element promotes dengue virus RNA synthesis on a circular genome. CV Filomatori MF Lodeiro DE Alvarez MM Samsa L Pietrasanta AV Gamarnik, Genes Dev 2006 20 2238 2249 10.1101/gad.1444206 16882970
40. Structural and functional studies of the promoter element for dengue virus RNA replication. MF Lodeiro CV Filomatori AV Gamarnik, J Virol 2009 83 993 1008 10.1128/JVI.01647-08 19004935
41. Genetic interactions among the West Nile virus methyltransferase, the RNA-dependent RNA polymerase, and the 5' stem-loop of genomic RNA. B Zhang H Dong Y Zhou PY Shi, J Virol 2008 82 7047 7058 10.1128/JVI.00654-08 18448528 (Pubitemid 351977724)
42. The arterivirus replicase is the only viral protein required for genome replication and subgenomic mRNA transcription. R Molenkamp H van Tol BC Rozier Y van der Meer WJ Spaan EJ Snijder, J Gen Virol 2000 81 2491 2496 10993938
43. The 5' and 3' downstream AUG region elements are required for mosquito-borne flavivirus RNA replication. P Friebe PY Shi E Harris, J Virol 2011 85 1900 1905 10.1128/JVI.02037-10 21123391
44. Identification of mutated cyclization sequences that permit efficient replication of West Nile virus genomes: use in safer propagation of a novel vaccine candidate. R Suzuki R Fayzulin I Frolov PW Mason, J Virol 2008 82 6942 6951 10.1128/JVI.00662-08 18480453 (Pubitemid 351977715)
45. Functional analysis of dengue virus cyclization sequences located at the 5' and 3'UTRs. DE Alvarez CV Filomatori AV Gamarnik, Virology 2008 375 223 235 10.1016/j.virol.2008.01.014 18289628
46. Long-range RNA-RNA interactions circularize the dengue virus genome. DE Alvarez MF Lodeiro SJ Luduena LI Pietrasanta AV Gamarnik, J Virol 2005 79 6631 6643 10.1128/JVI.79.11.6631-6643.2005 15890901 (Pubitemid 40677294)
47. Genome cyclization as strategy for flavivirus RNA replication. SM Villordo AV Gamarnik, Virus Res 2009 139 230 239 10.1016/j.virusres.2008.07.016 18703097
48. Heteroclite subgenomic RNAs are produced in porcine reproductive and respiratory syndrome virus infection. S Yuan MP Murtaugh KS Faaberg, Virology 2000 275 158 169 10.1006/viro.2000.0639 11183205