Yeast Lsm1p-7p/Pat1p Deadenylation-Dependent mRNA-Decapping Factors Are Required for Brome Mosaic Virus Genomic RNA Translation

REFERENCES

• Achsel, T., H. Brahms, B. Kastner, A. Bachi, M. Wilm, and R. Luhrmann. 1999. A doughnut-shaped heteromer of human Sm-like proteins binds to the 3′-end of U6 snRNA, thereby facilitating U4/U6 duplex formation in vitro. EMBO J. 18: 5789–5802.
   PubMed Web of Science ®Google Scholar
• Ahlquist, P. 1992. Bromovirus RNA replication and transcription. Curr. Opin. Genet. Dev. 2: 71–76.
   PubMedGoogle Scholar
• Ahlquist, P., R. Dasgupta, and P. Kaesberg. 1981. Near identity of 3- RNA secondary structure in bromoviruses and cucumber mosaic virus. Cell 23: 183–189.
   PubMed Web of Science ®Google Scholar
• Andino, R., N. Boddeker, D. Silvera, and A. V. Gamarnik. 1999. Intracellular determinants of picornavirus replication. Trends Microbiol. 7: 76–82.
   PubMedGoogle Scholar
• Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl (ed.). 1987. Current protocols in molecular biology. John Wiley & Sons, Inc., New York, N.Y.
   Google Scholar
• Bonnerot, C., R. Boeck, and B. Lapeyre. 2000. The two proteins Pat1p (Mrt1p) and Spb8p interact in vivo, are required for mRNA decay, and are functionally linked to Pab1p. Mol. Cell. Biol. 20: 5939–5946.
   PubMedGoogle Scholar
• Bouveret, E., G. Rigaut, A. Shevchenko, M. Wilm, and B. Seraphin. 2000. A Sm-like protein complex that participates in mRNA degradation. EMBO J. 19: 1661–1671.
   PubMedGoogle Scholar
• Brown, J. T., X. Yang, and A. W. Johnson. 2000. Inhibition of mRNA turnover in yeast by an xrn1 mutation enhances the requirement for eIF4E binding to eIF4G and for proper capping of transcripts by Ceg1p. Genetics 155: 31–42.
   PubMedGoogle Scholar
• Chartrand, P., X. H. Meng, S. Huttelmaier, D. Donato, and R. H. Singer. 2002. Asymmetric sorting of Ash1p in yeast results from inhibition of translation by localization elements in the mRNA. Mol. Cell 10: 1319–1330.
   PubMedGoogle Scholar
• Chen, J., and P. Ahlquist. 2000. Brome mosaic virus polymerase-like protein 2a is directed to the endoplasmic reticulum by helicase-like viral protein 1a. J. Virol. 74: 4310–4318.
   PubMedGoogle Scholar
• Chen, J., A. Noueiry, and P. Ahlquist. 2001. Brome mosaic virus protein 1a recruits viral RNA2 to RNA replication through a 5′ proximal RNA2 signal. J. Virol. 75: 3207–3219.
   PubMedGoogle Scholar
• Clark, I. E., D. Wyckoff, and E. R. Gavis. 2000. Synthesis of the posterior determinant Nanos is spatially restricted by a novel cotranslational regulatory mechanism. Curr. Biol. 10: 1311–1314.
   PubMedGoogle Scholar
• Coller, J. M., M. Tucker, U. Sheth, M. A. Valencia-Sanchez, and R. Parker. 2001. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes. RNA 7: 1717–1727.
   PubMedGoogle Scholar
• Collins, B. M., S. J. Harrop, G. D. Kornfeld, I. W. Dawes, P. M. Curmi, and B. C. Mabbutt. 2001. Crystal structure of a heptameric Sm-like protein complex from archaea: implications for the structure and evolution of snRNPs. J. Mol. Biol. 309: 915–923.
   PubMedGoogle Scholar
• Cormack, B., G. Bertram, M. Egerton, N. Gow, S. Falkow, and A. Brown. 1997. Yeast-enhanced green flourescent protein (yEGFP): a reporter of gene expression in Candida albicans. Microbiology 143: 303–311.
   PubMed Web of Science ®Google Scholar
• den Boon, J. A., J. Chen, and P. Ahlquist. 2001. Identification of sequences in brome mosaic virus replicase protein 1a that mediate association with endoplasmic reticulum membranes. J. Virol. 75: 12370–12381.
   PubMedGoogle Scholar
• Diez, J., M. Ishikawa, M. Kaido, and P. Ahlquist. 2000. Identification and characterization of a host protein required for efficient template selection in viral RNA replication. Proc. Natl. Acad. Sci. USA 97: 3913–3918.
   PubMed Web of Science ®Google Scholar
• Evans, D. R., C. Rasmussen, P. J. Hanic-Joyce, G. C. Johnston, R. A. Singer, and C. A. Barnes. 1995. Mutational analysis of the Prt1 protein subunit of yeast translation initiation factor 3. Mol. Cell. Biol. 15: 4525–4535.
   Google Scholar
• Felden, B., C. Florentz, R. Giege, and E. Westhof. 1994. Solution structure of the 3′-end of brome mosaic virus genomic RNAs: conformational mimicry with canonical tRNAs. J. Mol. Biol. 235: 508–531.
   PubMedGoogle Scholar
• Gamarnik, A. V., and R. Andino. 1996. Replication of poliovirus in Xenopus oocytes requires two human factors. EMBO J. 15: 5988–5998.
   PubMedGoogle Scholar
• Gebauer, F., D. F. Corona, T. Preiss, P. B. Becker, and M. W. Hentze. 1999. Translational control of dosage compensation in Drosophila by Sex-lethal: cooperative silencing via the 5′ and 3′ UTRs of msl-2 mRNA is independent of the poly(A) tail. EMBO J. 18: 6146–6154.
   PubMedGoogle Scholar
• Gray, N. K., and M. Wickens. 1998. Control of translation initiation in animals. Annu. Rev. Cell Dev. Biol. 14: 399–458.
   PubMed Web of Science ®Google Scholar
• Gunkel, N., T. Yano, F. H. Markussen, L. C. Olsen, and A. Ephrussi. 1998. Localization-dependent translation requires a functional interaction between the 5′ and 3′ ends of oskar mRNA. Genes Dev. 12: 1652–1664.
   PubMedGoogle Scholar
• Guthrie, C., and G. R. Fink (ed.). 1991 Guide to yeast genetics and molecular biology, vol. 194. Academic Press, Inc., San Diego, Calif.
   Google Scholar
• He, W., and R. Parker. 2000. Functions of Lsm proteins in mRNA degradation and splicing. Curr. Opin. Cell Biol. 12: 346–350.
   PubMed Web of Science ®Google Scholar
• Hilleren, P., and R. Parker. 1999. Mechanisms of mRNA surveillance in eukaryotes. Annu. Rev. Genet. 33: 229–260.
   PubMedGoogle Scholar
• Ishikawa, M., J. Diez, M. Restrepo-Hartwig, and P. Ahlquist. 1997. Yeast mutations in multiple complementation groups inhibit brome mosaic virus RNA replication and transcription and perturb regulated expression of the viral polymerase-like gene. Proc. Natl. Acad. Sci. USA 94: 13810–13815.
   PubMedGoogle Scholar
• Ishikawa, M., M. Janda, M. A. Krol, and P. Ahlquist. 1997. In vivo DNA expression of functional brome mosaic virus RNA replicons in Saccharomyces cerevisiae. J. Virol. 71: 7781–7790.
   PubMed Web of Science ®Google Scholar
• Jacobson, A., and S. W. Peltz. 1999. Tools for turnover: methods for analysis of mRNA stability in eukaryotic cells. Methods 17: 1–2.
   PubMedGoogle Scholar
• Janda, M., and P. Ahlquist. 1998. Brome mosaic virus RNA replication protein 1a dramatically increases in vivo stability but not translation of viral genomic RNA3. Proc. Natl. Acad. Sci. USA 95: 2227–2232.
   PubMedGoogle Scholar
• Janda, M., and P. Ahlquist. 1993. RNA-dependent replication, transcription, and persistence of brome mosaic virus RNA replicons in S. cerevisiae. Cell 72: 961–970.
   PubMedGoogle Scholar
• Johnstone, O., and P. Lasko. 2001. Translational regulation and RNA localization in Drosophila oocytes and embryos. Annu. Rev. Genet. 35: 365–406.
   PubMedGoogle Scholar
• Kambach, C., S. Walke, R. Young, J. M. Avis, E. de la Fortelle, V. A. Raker, R. Luhrmann, J. Li, and K. Nagai. 1999. Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. Cell 96: 375–387.
   PubMed Web of Science ®Google Scholar
• Kohl, R. J., and T. C. Hall. 1974. Aminoacylation of RNA from several viruses: amino acid specificity and differential activity of plant, yeast and bacterial synthetases. J. Gen. Virol. 25: 257–261.
   PubMed Web of Science ®Google Scholar
• Krol, M. A., N. H. Olson, J. Tate, J. E. Johnson, T. S. Baker, and P. Ahlquist. 1999. RNA-controlled polymorphism in the in vivo assembly of 180-subunit and 120-subunit virions from a single capsid protein. Proc. Natl. Acad. Sci. USA 96: 13650–13655.
   PubMedGoogle Scholar
• Kufel, J., C. Allmang, L. Verdone, J. D. Beggs, and D. Tollervey. 2002. Lsm proteins are required for normal processing of pre-tRNAs and their efficient association with La-homologous protein Lhp1p. Mol. Cell. Biol. 22: 5248–5256.
   PubMed Web of Science ®Google Scholar
• Kuhn, K. M., J. L. DeRisi, P. O. Brown, and P. Sarnow. 2001. Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source. Mol. Cell. Biol. 21: 916–927.
   PubMedGoogle Scholar
• Lee, W. M., M. Ishikawa, and P. Ahlquist. 2001. Mutation of host delta9 fatty acid desaturase inhibits brome mosaic virus RNA replication between template recognition and RNA synthesis. J. Virol. 75: 2097–2106.
   PubMedGoogle Scholar
• Miglietta, J. 1987. Ph.D. thesis. University of Wisconsin, Madison.
   Google Scholar
• Moller, T., T. Franch, P. Hojrup, D. R. Keene, H. P. Bachinger, R. G. Brennan, and P. Valentin-Hansen. 2002. Hfq: a bacterial Sm-like protein that mediates RNA-RNA interaction. Mol. Cell 9: 23–30.
   PubMed Web of Science ®Google Scholar
• Noueiry, A. O., J. Chen, and P. Ahlquist. 2000. A mutant allele of essential, general translation initiation factor DED1 selectively inhibits translation of a viral mRNA. Proc. Natl. Acad. Sci. USA 97: 12985–12990.
   PubMedGoogle Scholar
• Olsen, P. H., and V. Ambros. 1999. The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev. Biol. 216: 671–680.
   PubMed Web of Science ®Google Scholar
• Restrepo-Hartwig, M., and P. Ahlquist. 1996. Brome mosaic virus helicase- and polymerase-like proteins colocalize on the endoplasmic reticulum at sites of viral RNA synthesis. J. Virol. 70: 8908–8916.
   PubMedGoogle Scholar
• Restrepo-Hartwig, M., and P. Ahlquist. 1999. Brome mosaic virus RNA replication proteins 1a and 2a colocalize and 1a independently localizes on the yeast endoplasmic reticulum. J. Virol. 73: 10303–10309.
   PubMedGoogle Scholar
• Richter, J. D. 1999. Cytoplasmic polyadenylation in development and beyond. Microbiol. Mol. Biol. Rev. 63: 446–456.
   PubMedGoogle Scholar
• Rietveld, K., C. W. A. Pleij, and L. Bosch. 1983. Three dimensional models of the tRNA-like 3′ termini of some plant viral RNAs. EMBO J. 2: 1079–1085.
   PubMed Web of Science ®Google Scholar
• Ruegsegger, U., J. H. Leber, and P. Walter. 2001. Block of HAC1 mRNA translation by long-range base pairing is released by cytoplasmic splicing upon induction of the unfolded protein response. Cell 107: 103–114.
   PubMed Web of Science ®Google Scholar
• Salgado-Garrido, J., E. Bragado-Nilsson, S. Kandels-Lewis, and B. Seraphin. 1999. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J. 18: 3451–3462.
   PubMed Web of Science ®Google Scholar
• Saunders, C., and R. S. Cohen. 1999. The role of oocyte transcription, the 5′UTR, and translation repression and derepression in Drosophila gurken mRNA and protein localization. Mol. Cell 3: 43–54.
   PubMedGoogle Scholar
• Schwartz, M., J. Chen, M. Janda, M. Sullivan, J. den Boon, and P. Ahlquist. 2002. A positive-strand RNA virus replication complex parallels form and function of retrovirus capsids. Mol. Cell 9: 505–514.
   PubMedGoogle Scholar
• Seggerson, K., L. Tang, and E. G. Moss. 2002. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev. Biol. 243: 215–225.
   PubMed Web of Science ®Google Scholar
• Seraphin, B. 1995. Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4, and U5 snRNPs. EMBO J. 14: 2089–2098.
   PubMedGoogle Scholar
• Seto, A. G., A. J. Zaug, S. G. Sobel, S. L. Wolin, and T. R. Cech. 1999. Saccharomyces cerevisiae telomerase is an Sm small nuclear ribonucleoprotein particle. Nature 401: 177–180.
   PubMed Web of Science ®Google Scholar
• Strauss, J. H., and E. G. Strauss. 1999. With a little help from the host. Science 283: 802–804.
   PubMedGoogle Scholar
• Sullivan, M., and P. Ahlquist. 1999. A brome mosaic virus intergenic RNA3 replication signal functions with viral replication protein 1a to dramatically stabilize RNA in vivo. J. Virol. 73: 2622–2632.
   PubMedGoogle Scholar
• Sullivan, M., and P. Ahlquist. 1997. cis-Acting signals in bromovirus RNA replication and gene expression: networking with viral proteins and host factors. Semin. Virol. 8: 221–230.
   Google Scholar
• Tharun, S., W. He, A. E. Mayes, P. Lennertz, J. D. Beggs, and R. Parker. 2000. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 404: 515–518.
   PubMed Web of Science ®Google Scholar
• Tharun, S., and R. Parker. 2001. Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs. Mol. Cell 8: 1075–1083.
   PubMedGoogle Scholar
• Thio, G. L., R. P. Ray, G. Barcelo, and T. Schupbach. 2000. Localization of gurken RNA in Drosophila oogenesis requires elements in the 5′ and 3′ regions of the transcript. Dev. Biol. 221: 435–446.
   PubMedGoogle Scholar
• Tomasevic, N., and B. A. Peculis. 2002. Xenopus LSm proteins bind U8 snoRNA via an internal evolutionarily conserved octamer sequence. Mol. Cell. Biol. 22: 4101–4112.
   PubMed Web of Science ®Google Scholar
• Tucker, M., and R. Parker. 2000. Mechanisms and control of mRNA decapping in Saccharomyces cerevisiae. Annu. Rev. Biochem. 69: 571–595.
   PubMedGoogle Scholar
• Tucker, M., M. A. Valencia-Sanchez, R. R. Staples, J. Chen, C. L. Denis, and R. Parker. 2001. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae. Cell 104: 377–386.
   PubMed Web of Science ®Google Scholar
• Valasek, L., K. H. Nielsen, and A. G. Hinnebusch. 2002. Direct eIF2-eIF3 contact in the multifactor complex is important for translation initiation in vivo. EMBO J. 21: 5886–5898.
   PubMed Web of Science ®Google Scholar
• van Regenmortel, M. H. V. (ed.). 2000 Virus taxonomy. Academic Press, Inc., San Diego, Calif.
   Google Scholar
• Vasudevan, S., and S. W. Peltz. 2001. Regulated ARE-mediated mRNA decay in Saccharomyces cerevisiae. Mol. Cell 7: 1191–1200.
   PubMed Web of Science ®Google Scholar
• Wilusz, C. J., M. Wormington, and S. W. Peltz. 2001. The cap-to-tail guide to mRNA turnover. Nat. Rev. Mol. Cell. Biol. 2: 237–246.
   PubMed Web of Science ®Google Scholar
• Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. El Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, R. W. Davis, et al. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285: 901–906.
   PubMed Web of Science ®Google Scholar
• Wyers, F., M. Minet, M. E. Dufour, L. T. Vo, and F. Lacroute. 2000. Deletion of the PAT1 gene affects translation initiation and suppresses a PAB1 gene deletion in yeast. Mol. Cell. Biol. 20: 3538–3549.
   PubMedGoogle Scholar
• Zhang, A., K. M. Wassarman, J. Ortega, A. C. Steven, and G. Storz. 2002. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9: 11–22.
   PubMed Web of Science ®Google Scholar