Presence of poly(A) and poly(A)-rich tails in a positive-strand RNA virus known to lack 3' poly(A) tails

Virology

Volumn 454-455, Issue 1, 2014, Pages 1-10

  Li, Weimin ^a   Zhang, Yongqiang ^a   Zhang, Chao ^a   Pei, Xinwu ^a   Wang, Zhixing ^a   Jia, Shirong ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Poly(A) tails; RNA polyadenylation; Tobacco mosaic virus

Indexed keywords

ADENOSINE; EXORIBONUCLEASE; GENOMIC RNA; NUCLEOTIDE DERIVATIVE; POLYADENYLIC ACID; POLYNUCLEOTIDE POLYMERASE; TRANSFER RNA; UNCLASSIFIED DRUG; VIRUS ENZYME; VIRUS RNA;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CHLOROPLAST; CONTROLLED STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYADENYLATION; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN POLYMERIZATION; RNA SEQUENCE; RNA STRUCTURE; RNA VIRUS; TOBACCO MOSAIC VIRUS; VIRUS CELL INTERACTION;

POLY(A) TAILS; RNA POLYADENYLATION; TOBACCO MOSAIC VIRUS;

ARABIDOPSIS; CHENOPODIUM; CHLOROPLASTS; RNA, MESSENGER; RNA, VIRAL; TOBACCO; TOBAMOVIRUS;

EID: 84896524526     PISSN: 00426822     EISSN: 10960341     Source Type: Journal    
DOI: 10.1016/j.virol.2014.02.002     Document Type: Article

References (63)

1. Ahlquist P., Noueiry A.O., Lee W.M., Kushner D.B., Dye B.T. Host factors in positive-strand RNA virus genome replication. J. Virol. 2003, 77:8181-8186.
2. Barr J.N., Fearns R. How RNA viruses maintain their genome integrity. J. Gen. Virol. 2010, 91:1373-1387.
3. Beachy R.N., Zaitlin M. Characterization and in vitro translation of the RNAs from less-than-full-length, virus-related, nucleoprotein rods present in tobacco mosaic virus preparations. Virology 1977, 81:160-169.
4. Bier K., York A., Fodor E. Cellular cap-binding proteins associate with influenza virus mRNAs. J. Gen. Virol. 2011, 92:1627-1634.
5. Bralley P., Jones G.H. cDNA cloning confirms the polyadenylation of RNA decay intermediates in Streptomyces coelicolor. Microbiology 2002, 148:1421-1425.
6. Buck K.W. Replication of tobacco mosaic virus RNA. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1999, 354:613-627.
7. Burton R.A., Gibeaut D.M., Bacic A., Findlay K., Roberts K., Hamilton A., Baulcombe D.C., Fincher G.B. Virus induced silencing of a plant cellulose synthase gene. Plant Cell 2000, 12:691-705.
8. Butler P.J. Self-assembly of tobacco mosaic virus: the role of an intermediate aggregate in generating both specificity and speed. Philos. Trans. R. Soc. Lond. B Biol. Sci. 1999, 354:537-550.
9. Campos-Guillén J., Bralley P., Jones G.H., Bechhofer D.H., Olmedo-Alvarez G. Addition of poly(A) and heteropolymeric 3' ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J. Bacteriol. 2005, 187:4698-4706.
10. Chen I.H., Chou W.J., Lee P.Y., Hsu Y.H., Tsai C.H. The AAUAAA motif of bamboo mosaic virus RNA is involved in minus-strand RNA synthesis and plus-strand RNA polyadenylation. J. Virol. 2005, 79:14555-14561.
11. Condon C. Maturation and degradation of RNA in bacteria. Curr. Opin. Microbiol. 2007, 10:271-278.
12. Creager A.N., Scholthof K.B., Citovsky V., Scholthof H.B. Tobacco mosaic virus. Pioneering research for a century. Plant Cell 1999, 11:301-308.
13. Cristodero M., Clayton C.E. Trypanosome MTR4 is involved in rRNA processing. Nucleic Acids Res. 2007, 35:7023-7030.
14. Dickson A.M., Wilusz J. Strategies for viral RNA stability: live long and prosper. Trends Genet. 2011, 27:286-293.
15. Dreher T.W. Funcations of the 3'-untranslated regions of positive strand RNA viral genomes. Annu. Rev. Phytopathol. 1999, 37:151-174.
16. Edmonds M. A history of poly A sequences: from formation to factors to function. Prog. Nucleic Acid Res. Mol. Biol. 2002, 71:285-389.
17. Feng Y., Cohen S.N. Unpaired terminal nucleotides and 5' monophosphorylation govern 3' polyadenylation by Escherichia coli poly(A) polymerase I. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:6415-6420.
18. Germain A., Herlich S., Larom S., Kim S.H., Schuster G., Stern D.B. Mutational analysis of Arabidopsis chloroplast polynucleotide phosphorylase reveals roles for both RNase PH core domains in polyadenylation, RNA 3'-end maturation and intron degradation. Plant J. 2011, 67:381-394.
19. Goelet P., Lomonossoff G.P., Butler P.J., Akam M.E., Gait M.J., Karn J. Nucleotide sequence of tobacco mosaic virus RNA. Proc. Natl. Acad. Sci. U.S.A. 1982, 79:5818-5822.
20. Guilley H., Jonard G., Kukla B., Richards K.E. Sequence of 1000 nucleotides at the 3' end of tobacco mosaic virus RNA. Nucleic Acids Res. 1979, 6:1287-1308.
21. Hayes R., Kudla J., Schuster G., Gabay L., Maliga P., Gruissem W. Chloroplast mRNA 3'-end processing by a high molecular weight protein complex is regulated by nuclear encoded RNA binding proteins. EMBO J. 1996, 15:1132-1141.
22. Houseley J., Tollervey D. The many pathways of RNA degradation. Cell 2009, 136:763-776.
23. King A.M.Q., Adams M.J., Carstens E.B., Lefkowitz E.J. Virus taxonomy: classification and nomenclature of viruses. Ninth Report of the International Committee on Taxonomy of Viruses 2012, Elsevier, San Diego, CA.
24. Kuai L., Das B., Sherman F. A nuclear degradation pathway controls the abundance of normal mRNAs in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2005, 102:13962-13967.
25. Kuai L., Fang F., Butler J.S., Sherman F. Polyadenylation of rRNA in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U.S.A. 2004, 101:8581-8586.
26. LaCava J., Houseley J., Saveanu C., Petfalski E., Thompson E., Jacquier A., Tollervey D. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 2005, 121:713-724.
27. Lange H., Gagliardi D. The exosome and 3'-5' RNA degradation in plants. Adv. Exp. Med. Biol. 2011, 702:50-62.
28. Lange H., Holec S., Cognat V., Pieuchot L., Le Ret M., Canaday J., Gagliardi D. Degradation of a polyadenylated rRNA maturation by-product involves one of the three RRP6-like proteins in Arabidopsis thaliana. Mol. Cell Biol. 2008, 28:3038-3044.
29. Lange H., Sement F.M., Canaday J., Gagliardi D. Polyadenylation-assisted RNA degradation processes in plants. Trends Plant Sci. 2009, 14:497-504.
30. Li Q.S., Gupta J.D., Hunt A.G. Polynucleotide phosphorylase is a component of a novel plant poly(A) polymerase. J. Biol. Chem. 1998, 273:17539-17543.
31. Lisitsky I., Klaff P., Schuster G. Addition of destabilizing poly (A)-rich sequences to endonuclease cleavage sites during the degradation of chloroplast mRNA. Proc. Natl. Acad. Sci. U.S.A. 1996, 93:13398-13403.
32. Liu Y., Schiff M., Marathe R., Dinesh-Kumar S.P. Tobacco Rar1, EDS1 and NPR1/NIM1 like genes are required for N-mediated resistance to tobacco mosaic virus. Plant J. 2002, 30:415-429.
33. Marchive C., Yehudai-Resheff S., Germain A., Fei Z., Jiang X., Judkins J., Wu H., Fernie A.R., Fait A., Stern D.B. Abnormal physiological and molecular mutant phenotypes link chloroplast polynucleotide phosphorylase to the phosphorus deprivation response in Arabidopsis. Plant Physiol. 2009, 151:905-924.
34. Más P., Beachy R.N. Replication of tobacco mosaic virus on endoplasmic reticulum and role of the cytoskeleton and virus movement protein in intracellular distribution of viral RNA. J. Cell Biol. 1999, 147:945-958.
35. Mohanty B.K., Kushner S.R. Polynucleotide phosphorylase functions both as a 3' right-arrow 5' exonuclease and a poly(A) polymerase in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 2000, 97:11966-11971.
36. Mohanty B.K., Kushner S.R. Bacterial/archaeal/organellar polyadenylation. Wiley Interdiscip. Rev. RNA 2010, 2:256-276.
37. Moon S.L., Barnhart M.D., Wilusz J. Inhibition and avoidance of mRNA degradation by RNA viruses. Curr. Opin. Microbiol. 2012, 15:500-505.
38. Moore M.J., Proudfoot N.J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 2009, 136:688-700.
39. Nakamura R., Takeuchi R., Takata K., Shimanouchi K., Abe Y., Kanai Y., Ruike T., Ihara A., Sakaguchi K. TRF4 is involved in polyadenylation of snRNAs in Drosophila melanogaster. Mol. Cell Biol. 2008, 28:6620-6631.
40. Ogram S.A., Flanegan J.B. Non-template functions of viral RNA in picornavirus replication. Curr. Opin. Virol. 2011, 1:339-346.
41. Ohno T., Aoyagi M., Yamanashi Y., Saito H., Ikawa S., Meshi T., Okada Y. Nucleotide sequence of the tobacco mosaic virus (tomato strain) genome and comparison with the common strain genome. J. Biochem. 1984, 96:1915-1923.
42. Poon L.L., Pritlove D.C., Fodor E., Brownlee G.G. Direct evidence that the poly(A) tail of influenza A virus mRNA is synthesized by reiterative copying of a U track in the virion RNA template. J. Virol. 1999, 73:3473-3476.
43. Regnier P., Hajnsdorf E. Poly(A)-assisted RNA decay and modulators of RNA stability. Prog. Mol. Biol. Transl. Sci. 2009, 85:137-185.
44. Sanfaçon H., Brodmann P., Hohn T. A dissection of the cauliflower mosaic virus polyadenylation signal. Genes Dev. 1991, 5:141-149.
45. Sauret-Güeto S., Botella-Pavía P., Flores-Pérez U., Martínez-García J.F., San Román C., León P., Boronat A., Rodríguez-Concepción M. Plastid cues posttranscriptionally regulate the accumulation of key enzymes of the methylerythritol phosphate pathway in Arabidopsis. Plant Physiol. 2006, 141:75-84.
46. Schoelz J.E., Zaitlin M. Tobacco mosaic virus RNA enters chloroplasts in vivo. Proc. Natl. Acad. Sci. U.S.A. 1989, 86:4496-4500.
47. Scholthof K.B., Adkins S., Czosnek H., Palukaitis P., Jacquot E., Hohn T., Hohn B., Saunders K., Candresse T., Ahlquist P., Hemenway C., Foster G.D. Top 10 plant viruses in molecular plant pathology. Mol. Plant Pathol. 2011, 12:938-954.
48. Schuster G., Stern D. RNA polyadenylation and decay in mitochondria and chloroplasts. Prog. Mol. Biol. Transl. Sci. 2009, 85:393-422.
49. Silver K.S.C., Pagano J.S. A noncanonical poly(A) signal, UAUAAA, and flanking elements in Epstein-Barr virus DNA polymerase mRNA function in cleavage and polyadenylation assays. Virology 1997, 234:147-159.
50. Slomovic S., Fremder E., Staals R.H., Pruijn G.J., Schuster G. Addition of poly(A) and poly(A)-rich tails during RNA degradation in the cytoplasm of human cells. Proc. Natl. Acad. Sci. U.S.A. 2010, 107:7407-7412.
51. Slomovic S., Portnoy V., Liveanu V., Schuster G. RNA polyadenylation in prokaryotes and organelles; different tails tell different tales. Crit. Rev. Plant Sci. 2006, 25:65-77.
52. Slomovic S., Laufer D., Geiger D., Schuster G. Polyadenylation of ribosomal RNA in human cells. Nucleic Acids Res. 2006, 34:2966-2975.
53. Slomovic S., Portnoy V., Yehudai-Resheff S., Bronshtein E., Schuster G. Polynucleotide phosphorylase and the archaeal exosome as poly(A)-polymerases. Biochim. Biophys. Acta 2008, 1779:247-255.
54. Slomovic S., Portnoy V., Schuster G. Detection and characterization of polyadenylated RNA in Eukarya, Bacteria, Archaea, and organelles. Methods Enzymol. 2008, 447:501-520.
55. Steil B.P., Kempf B.J., Barton D.J. Poly(A) at the 3' end of positive-strand RNA and VPg-linked poly(U) at the 5' end of negative-strand RNA are reciprocal templates during replication of poliovirus RNA. J. Virol. 2010, 84:2843-2858.
56. Vanácová S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A., Langen H., Keith G., Keller W. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 2005, 3:e189.
57. Walter M., Kilian J., Kudla J. PNPase activity determines the efficiency of mRNA 3'-end processing, the degradation of tRNA and the extent of polyadenylation in chloroplasts. EMBO J. 2002, 21:6905-6914.
58. Weichs an der Glon C., Ashe M., Eggermont J., Proudfoot N.J. Tat-dependent occlusion of the HIV poly(A) site. EMBO J. 1993, 12:2119-2128.
59. Win T.Z., Draper S., Read R.L., Pearce J., Norbury C.J., Wang S.W. Requirement of fission yeast Cid14 in polyadenylation of rRNAs. Mol. Cell Biol. 2006, 26:1710-1721.
60. Wyers F., Rougemaille M., Badis G., Rousselle J.C., Dufour M.E., Boulay J., Régnault B., Devaux F., Namane A., Séraphin B., Libri D., Jacquier A. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 2005, 121:725-737.
61. Zakrzewska-Placzek M., Souret F.F., Sobczyk G.J., Green P.J., Kufel J. Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Res. 2010, 38:4487-4502.
62. Zhang Y., Pei X., Zhang C., Lu Z., Wang Z., Jia S., Li W. De novo foliar transcriptome of Chenopodium amaranticolor and analysis of its gene expression during virus-induced hypersensitive response. PLoS One 2012, 7:e45953.
63. Zimmer S.L., Schein A., Zipor G., Stern D.B., Schuster G. Polyadenylation in Arabidopsis and Chlamydomonas organelles: the input of nucleotidyltransferases, poly(A) polymerases and polynucleotide phosphorylase. Plant J. 2009, 59:88-99.