Pat1 Contains Distinct Functional Domains That Promote P-Body Assembly and Activation of Decapping

REFERENCES

• Anderson, J. S., and R. P. Parker. 1998. The 3′ to 5′ degradation of yeast mRNAs is a general mechanism for mRNA turnover that requires the SKI2 DEVH box protein and 3′ to 5′ exonucleases of the exosome complex. EMBO J. 17:1497–1506.
   PubMed Web of Science ®Google Scholar
• Anderson, P., and N. Kedersha. 2006. RNA granules. J. Cell Biol. 172:803–808.
   PubMed Web of Science ®Google Scholar
• Beelman, C. A., and R. Parker. 1994. Differential effects of translational inhibition in cis and in trans on the decay of the unstable yeast MFA2 mRNA. J. Biol. Chem. 269:9687–9692.
   PubMedGoogle Scholar
• Beelman, C. A., A. Stevens, G. Caponigro, T. E. LaGrandeur, L. Hatfield, D. M. Fortner, and R. Parker. 1996. An essential component of the decapping enzyme required for normal rates of mRNA turnover. Nature 382:642–646.
   PubMedGoogle Scholar
• Beliakova-Bethell, N., C. Beckham, T. H. Giddings, Jr., M. Winey, R. Parker, and S. Sandmeyer. 2006. Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components. RNA 12:94–101.
   PubMed Web of Science ®Google Scholar
• Bhattacharyya, S. N., R. Habermacher, U. Martine, E. I. Closs, and W. Filipowicz. 2006. Relief of microRNA-mediated translational repression in human cells subjected to stress. Cell 125:1111–1124.
   PubMed Web of Science ®Google Scholar
• Bonnerot, C., R. Boeck, and B. Lapeyre. 2000. The two proteins Pat1 (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
• Brengues, M., D. Teixeira, and R. Parker. 2005. Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies. Science 310:486–489.
   PubMed Web of Science ®Google Scholar
• Cagney, G., P. Uetz, and S. Fields. 2000. High-throughput screening for protein-protein interactions using two-hybrid assay. Methods Enzymol. 328:3–14.
   PubMedGoogle Scholar
• Cao, D., and R. Parker. 2001. Computational modeling of eukaryotic mRNA turnover. RNA 7:1192–1212.
   PubMedGoogle Scholar
• Caponigro, G., D. Muhlrad, and R. Parker. 1993. A small segment of the MATα1 transcript promotes mRNA decay in Saccharomyces cerevisiae: a stimulatory role for rare codons. Mol. Cell. Biol. 13:5141–5148.
   PubMed Web of Science ®Google Scholar
• Caponigro, G., and R. Parker. 1995. Multiple functions for the poly(A)-binding protein in mRNA decapping and deadenylation in yeast. Genes Dev. 9:2421–2432.
   PubMedGoogle Scholar
• Coller, J., and R. Parker. 2004. Eukaryotic mRNA decapping. Annu. Rev. Biochem. 73:861–890.
   PubMed Web of Science ®Google Scholar
• Coller, J., and R. Parker. 2005. General translational repression by activators of mRNA decapping. Cell 122:875–886.
   PubMed Web of Science ®Google 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
• Cougot, N., S. Babajko, and B. Seraphin. 2004. Cytoplasmic foci are sites of mRNA decay in human cells. J. Cell Biol. 165:31–40.
   PubMed Web of Science ®Google Scholar
• Decker, C. J., and R. Parker. 1993. A turnover pathway for both stable and unstable mRNAs in yeast: evidence for a requirement for deadenylation. Genes Dev. 7:1632–1643.
   PubMed Web of Science ®Google Scholar
• Dunckley, T., and R. Parker. 1999. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif. EMBO J. 18:5411–5422.
   PubMed Web of Science ®Google Scholar
• Eulalio, A., I. Behm-Ansmant, and E. Izaurralde. 2007. P bodies: at the crossroads of post-transcriptional pathways. Nat. Rev. Mol. Cell Biol. 8:9–22.
   PubMed Web of Science ®Google Scholar
• Hatfield, L., C. A. Beelman, A. Stevens, and R. Parker. 1996. Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae. Mol. Cell. Biol. 16:5830–5838.
   PubMedGoogle 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
• Holmes, L. E., S. G. Campbell, S. K. De Long, A. B. Sachs, and M. P. Ashe. 2004. Loss of translational control in yeast compromised for the major mRNA decay pathway. Mol. Cell. Biol. 24:2998–3010.
   PubMed Web of Science ®Google Scholar
• Hsu, C. L., and A. Stevens. 1993. Yeast cells lacking 5′→3′ exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5′ cap structure. Mol. Cell. Biol. 13:4826–4835.
   PubMedGoogle Scholar
• Ingelfinger, D., D. J. Arndt-Jovin, R. Luhrmann, and T. Achsel. 2002. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci. RNA 8:1489–1501.
   PubMed Web of Science ®Google Scholar
• Jakymiw, A., S. Lian, T. Eystathioy, S. Li, M. Satoh, J. C. Hamel, M. J. Fritzler, and E. K. Chan. 2005. Disruption of GW bodies impairs mammalian RNA interference. Nat. Cell Biol. 7:1267–1274.
   PubMed Web of Science ®Google Scholar
• James, P., J. Halladay, and E. A. Craig. 1996. Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144:1425–1436.
   PubMed Web of Science ®Google Scholar
• LaGrandeur, T., and R. Parker. 1999. The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast include the context of the translational start codon. RNA 5:420–433.
   PubMedGoogle Scholar
• Liu, J., M. A. Valencia-Sanchez, G. J. Hannon, and R. Parker. 2005. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies. Nat. Cell Biol. 7:719–723.
   PubMed Web of Science ®Google Scholar
• Lykke-Andersen, J. 2002. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay. Mol. Cell. Biol. 22:8114–8121.
   PubMed Web of Science ®Google Scholar
• Meyer, S., C. Temme, and E. Wahle. 2004. Messenger RNA turnover in eukaryotes: pathways and enzymes. Crit. Rev. Biochem. Mol. Biol. 39:197–216.
   PubMed Web of Science ®Google Scholar
• Muhlrad, D., C. J. Decker, and R. Parker. 1994. Deadenylation of the unstable mRNA encoded by the yeast MFA2 gene leads to decapping followed by 5′→3′ digestion of the transcript. Genes Dev. 8:855–866.
   PubMed Web of Science ®Google Scholar
• Muhlrad, D., and R. Parker. 1999. Recognition of yeast mRNAs as “nonsense containing” leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping. Mol. Biol. Cell 10:3971–3978.
   PubMed Web of Science ®Google Scholar
• Parker, R., and U. Sheth. 2007. P bodies and the control of mRNA translation and degradation. Mol. Cell 25:635–646.
   PubMed Web of Science ®Google Scholar
• Parker, R., and H. Song. 2004. The enzymes and control of eukaryotic mRNA turnover. Nat. Struct. Mol. Biol. 11:121–127.
   PubMed Web of Science ®Google Scholar
• Pillai, R. S., S. N. Bhattacharyya, C. G. Artus, T. Zoller, N. Cougot, E. Basyuk, E. Bertrand, and W. Filipowicz. 2005. Inhibition of translational initiation by Let-7 MicroRNA in human cells. Science 309:1573–1576.
   PubMed Web of Science ®Google Scholar
• Rother, R. P., M. B. Frank, and P. S. Thomas. 1992. Purification, primary structure, bacterial expression and subcellular distribution of an oocyte-specific protein in Xenopus. Eur. J. Biochem. 206:673–683.
   PubMedGoogle Scholar
• Scheller, N., P. Resa-Infante, S. de la Luna, R. P. Galao, M. Albrecht, L. Kaestner, P. Lipp, T. Lengauer, A. Meyerhans, and J. Diez. 6 September 2007, posting date. Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim. Biophys. Acta. doi:10.1016/j.bbamcr.2007.08.009.
   Google Scholar
• Schwartz, D. C., and R. Parker. 1999. Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:5247–5256.
   PubMedGoogle Scholar
• Sheth, U., and R. Parker. 2003. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies. Science 300:805–808.
   PubMed Web of Science ®Google Scholar
• Sheth, U., and R. Parker. 2006. Targeting of aberrant mRNAs to cytoplasmic processing bodies. Cell 125:1095–1109.
   PubMed Web of Science ®Google Scholar
• Teixeira, D., and R. Parker. 2007. Analysis of P-body assembly in Saccharomyces cerevisiae. Mol. Biol. Cell 18:2274–2287.
   PubMed Web of Science ®Google Scholar
• Teixeira, D., U. Sheth, M. A. Valencia-Sanchez, M. Brengues, and R. Parker. 2005. Processing bodies require RNA for assembly and contain nontranslating mRNAs. RNA 11:371–382.
   PubMed Web of Science ®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 Lsm1-7p complex on deadenylated yeast mRNAs. Mol. Cell 8:1075–1083.
   PubMedGoogle Scholar
• Unterholzner, L., and E. Izaurralde. 2004. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay. Mol. Cell 16:587–596.
   PubMed Web of Science ®Google Scholar
• Wyers, F., M. Minet, M. E. Dufour, L. T. A. 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