Molecular chaperones and quality control in noncoding RNA biogenesis

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 71, Issue , 2006, Pages 505-511

  Wolin, S L ^a   Wurtmann, E J ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAPERONE; HFQ PROTEIN; LA ANTIGEN; RO PROTEIN; TRANSFER RNA; UNCLASSIFIED DRUG; UNTRANSLATED RNA; BACTERIAL RNA; FUNGAL RNA; RNA BINDING PROTEIN;

ARTICLE; BACTERIUM; BIOGENESIS; EUKARYOTE; INTERACTIONS WITH RNA; NONHUMAN; POLYADENYLATION; PRIORITY JOURNAL; PROKARYOTE; QUALITY CONTROL; RNA BINDING; RNA FOLDING; RNA STABILITY; YEAST; BIOSYNTHESIS; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETICS; METABOLISM; MUTATION; REVIEW; SACCHAROMYCES CEREVISIAE;

BACTERIA; MODELS, MOLECULAR; MOLECULAR CHAPERONES; MUTATION; NUCLEIC ACID CONFORMATION; RNA, BACTERIAL; RNA, FUNGAL; RNA, UNTRANSLATED; RNA-BINDING PROTEINS; SACCHAROMYCES CEREVISIAE;

EID: 34250628082     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2006.71.051     Document Type: Conference Paper

References (67)

1. Achsel T., Brahms H., Kastner B., Bachi A., Wilm M., and Luhrmann R. 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.
2. Alexandrov A., Chernyakov I., Gu W., Hiley S.L., Hughes T.R., Grayhack E.J., and Phizicky E.M. 2006. Rapid tRNA decay can result from lack of nonessential modifications. Mol. Cell 21: 87.
3. Alfano C., Sanfelice D., Babon J., Kelly G., Jacks A., Curry S., and Conte M.R. 2004. Structural analysis of cooperative RNA binding by the La motif and central RRM domain of human La protein. Nat. Struct. Mol. Biol. 11: 323.
4. Anderson J.T. 2005. RNA turnover: Unexpected consequences of being tailed. Curr. Biol. 15: R635.
5. Anderson J., Phan L., and Hinnebusch A.G. 2000. The Gcd10p/Gcd14p complex is the essential two-subunit tRNA(1-methyladenosine) methyltransferase of Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 97: 5173.
6. Anderson J., Phan L., Cuesta R., Carlson B.A., Pak M., Asano K., Bjork G.R., Tamame M., and Hinnebusch A.G. 1998. The essential Gcd10p-Gcd14p nuclear complex is required for 1-methyladenosine modification and maturation of initiator methionyl-tRNA. Genes Dev. 12: 3650.
7. Arhin G.K., Shen S., Perez I.F., Tschudi C., and Ullu E. 2005. Downregulation of the essential Trypanosoma brucei La protein affects accumulation of elongator methionyl-tRNA. Mol. Biochem. Parasitol. 144: 104.
8. Brescia C.C., Mikulecky P.J., Feig A.L., and Sledjeski D.D. 2003. Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structure. RNA 9: 33.
9. Calvo O., Cuesta R., Anderson J., Gutierrez N., Garcia-Barrio M.T., Hinnebusch A.G., and Tamame M. 1999. GCD14p, a repressor of GCN4 translation, cooperates with Gcd10p and Lhp1p in the maturation of initiator methionyl-tRNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 19: 4167.
10. Chakshusmathi G., Kim S.D., Rubinson D.A., and Wolin S.L. 2003. A La protein requirement for efficient pre-tRNA folding. EMBO J. 22: 6562.
11. Chen X., Smith J.D., Shi H., Yang D.D., Flavell R.A., and Wolin S.L. 2003. The Ro autoantigen binds misfolded U2 small nuclear RNAs and assists mammalian cell survival after UV irradiation. Curr. Biol. 13: 2206.
12. Cheng Z.F. and Deutscher M.P. 2003. Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proc. Natl. Acad. Sci. 100: 6388.
13. Copela L.A., Chakshusmathi G., Sherrer R.L., and Wolin S.L. 2006. The La protein functions redundantly with tRNA modification enzymes to ensure tRNA structural stability. RNA 12: 644.
14. Deutscher M.P. 2006. Degradation of RNA in bacteria: Comparison of mRNA and stable RNA. Nucleic Acids Res. 34: 659.
15. Dong G., Chakshusmathi G., Wolin S.L., and Reinisch K.M. 2004. Structure of the La motif: A winged helix domain mediates RNA binding via a conserved aromatic patch. EMBO J. 23: 1000.
16. Egecioglu D.E., Henras A.K., and Chanfreau G.F. 2006. Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome. RNA 12: 26.
17. Fernandez C.F., Pannone B.K., Chen X., Fuchs G., and Wolin S.L. 2004. An Lsm2-Lsm7 complex in Saccharomyces cerevisiae associates with the small nucleolar RNA snR5. Mol. Biol. Cell 15: 2842.
18. Foldynova-Trantirkova S., Paris Z., Sturm N.R., Campbell D.A., and Lukes J. 2005. The Trypanosoma brucei La protein is a candidate poly(U) shield that impacts spliced leader RNA maturation and tRNA intron removal. Int. J. Parasitol. 35: 359.
19. Fuchs G., Stein A.J., Fu C., Reinisch K.M., and Wolin S.L. 2006. Structural and biochemical basis for misfolded RNA recognition by the Ro protein. Nat. Struct. Mol. Biol. 13: 1002.
20. Geissmann T.A. and Touati D. 2004. Hfq, a new chaperoning role: Binding to messenger RNA determines access for small RNA regulator. EMBO J. 23: 396.
21. Goodier J.L., Fan H., and Maraia R.J. 1997. A carboxy-terminal basic region controls RNA polymerase III transcription factor activity of human La protein. Mol. Cell. Biol. 17: 5823.
22. He W. and Parker R. 2001. The yeast cytoplasmic LsmI/Pat1p complex protects mRNA 3′ termini from partial degradation. Genetics 158: 1445.
23. Herschlag D. 1995. RNA chaperones and the RNA folding problem. J. Biol. Chem. 270: 20871.
24. Houseley J. and Tollervey D. 2006. Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep. 7: 205.
25. Huang H.R., Rowe C.E., Mohr S., Jiang Y., Lambowitz A.M., and Perlman P.S. 2005. The splicing of yeast mitochondrial group I and group II introns requires a DEAD-box protein with RNA chaperone function. Proc. Natl. Acad. Sci. 102: 163.
26. Huang Y., Bayfield M.A., Intine R.V., and Maraia R.J. 2006. Separate RNA-binding surfaces on the multifunctional La protein mediate distinguishable activities in tRNA maturation. Nat. Struct. Mol. Biol. 13: 611.
27. Inada M. and Guthrie C. 2004. Identification of Lhp1p-associated RNAs by microarray analysis in Saccharomyces cerevisiae reveals association with coding and noncoding RNAs. Proc. Natl. Acad. Sci. 101: 434.
28. Johansson M.J. and Bystrom A.S. 2002. Dual function of the tRNA(m(5)U54)methyltransferase in tRNA maturation. RNA 8: 324.
29. Kadaba S., Wang X., and Anderson J.T. 2006. Nuclear RNA surveillance in Saccharomyces cerevisiae: Trf4p-dependent polyadenylation of nascent hypomethylated tRNA and an aberrant form of 5S rRNA. RNA 12: 508.
30. Met in S. cerevisiae. Genes Dev. 18: 1227.
31. LaCava J., Houseley J., Saveanu C., Petfalski E., Thompson E., Jacquier A., and Tollervey D. 2005. RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121: 713.
32. Lease R.A. and Woodson S.A. 2004. Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNA. J. Mol. Biol. 344: 1211.
33. Li Z., Pandit S., and Deutscher M.P. 1998. Polyadenylation of stable RNA precursors in vivo. Proc. Natl. Acad. Sci. 95: 12158.
34. Li Z., Reimers S., Pandit S., and Deutscher M.P. 2002. RNA quality control: Degradation of defective transfer RNA. EMBO J. 21: 1132.
35. Mayes A.E., Verdone L., Legrain P., and Beggs J.D. 1999. Characterization of Sm-like proteins in yeast and their association with U6 snRNA. EMBO J. 18: 4321.
36. Mikulecky P.J., Kaw M.K., Brescia C.C., Takach J.C., Sledjeski D.D., and Feig A.L. 2004. Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat. Struct. Mol. Biol. 11: 1206.
37. Mohanty B.K. and Kushner S.R. 1999. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol. Microbiol. 34: 1094.
38. Mohanty B.K., Maples V.F., and Kushner S.R. 2004. The Smlike protein Hfq regulates polyadenylation dependent mRNA decay in Escherichia coli. Mol. Microbiol. 54: 905.
39. Mohr S., Stryker J.M., and Lambowitz A.M. 2002. A DEADbox protein functions as an ATP-dependent RNA chaperone in group I intron splicing. Cell 109: 769.
40. Moll I., Leitsch D., Steinhauser T., and Blasi U. 2003a. RNA chaperone activity of the Sm-like Hfq protein. EMBO Rep. 4: 284.
41. Moll I., Afonyushkin T., Vytvytska O., Kaberdin V.R., and Blasi U. 2003b. Coincident Hfq binding and RNase E cleavage sites on mRNA and small regulatory RNAs. RNA 9: 1308.
42. Moller T., Franch T., Hojrup P., Keene D.R., Bachinger H.P., Brennan R.G., and Valentin-Hansen P. 2002. Hfq: A bacterial Sm-like protein that mediates RNA-RNA interaction. Mol. Cell 9: 23.
43. Moore P.B. and Steitz T.A. 2003. The structural basis of large ribosomal subunit function. Annu. Rev. Biochem. 72: 813.
44. O'Brien C.A. and Wolin S.L. 1994. A possible role for the 60 kd Ro autoantigen in a discard pathway for defective 5S ribosomal RNA precursors. Genes Dev. 8: 2891.
45. Pannone B.K., Xue D., and Wolin S.L. 1998. A role for the yeast La protein in U6 snRNP assembly: Evidence that the La protein is a molecular chaperone for RNA polymerase III transcripts. EMBO J. 17: 7442.
46. Pannone B.K., Kim S.D., Noe D.A., and Wolin S.L. 2001. Multiple functional interactions between components of the Lsm2-Lsm8 complex, U6 snRNA, and the yeast La protein. Genetics 158: 187.
47. Park J.M., Kohn M.J., Bruinsma M.W., Vech C., Intine R.V., Fuhrmann S., Grinberg A., Mukherjee I., Love P.E., Ko M.S., et al. 2006. The multifunctional RNA-binding protein La is required for mouse development and for the establishment of embryonic stem cells. Mol. Cell Biol. 26: 1445.
48. Salgado-Garrido J., Bragado-Nilsson E., Kandels-Lewis S., and Seraphin B. 1999. Sm and Sm-like proteins assemble in two related complexes of deep evolutionary origin. EMBO J. 18: 3451.
49. Schroeder R., Barta A., and Semrad K. 2004. Strategies for RNA folding and assembly. Nat. Rev. Mol. Cell Biol. 5: 908.
50. Schumacher M.A., Pearson R.F., Moller T., Valentin-Hansen P., and Brennan R.G. 2002. Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: A bacterial Sm-like protein. EMBO J. 21: 3546.
51. Schumperli D. and Pillai R.S. 2004. The special Sm core structure of the U7 snRNP: Far-reaching significance of a small nuclear ribonucleoprotein. Cell. Mol. Life Sci. 61: 2560.
52. Shi H., O'Brien C.A., Van Horn D.J., and Wolin S.L. 1996. A misfolded form of 5S rRNA is associated with the Ro and La autoantigens. RNA 2: 769.
53. Shimaoka M., Takagi J., and Springer T.A. 2002. Conformational regulation of integrin structure and function. Annu. Rev. Biophys. Biomol. Struct. 31: 485.
54. Stein A.J., Fuchs G., Fu C., Wolin S.L., and Reinisch K.M. 2005. Structural insights into RNA quality control: The Ro autoantigen binds misfolded RNAs via its central cavity. Cell 121: 529.
55. Storz G., Altuvia S., and Wassarman K.M. 2005. An abundance of RNA regulators. Annu. Rev. Biochem. 74: 199.
56. Storz G., Opdyke J.A., and Zhang A. 2004. Controlling mRNA stability and translation with small, noncoding RNAs. Curr. Opin. Microbiol. 7: 140.
57. Teplova M., Yuan Y.R., Phan A.T., Malinina L., Ilin S., Teplov A., and Patel D.J. 2006. Structural basis for recognition and sequestration of UUU(OH) 3′ temini of nascent RNA polymerase III transcripts by La, a rheumatic disease autoantigen. Mol. Cell 21: 75.
58. Tharun S., He W., Mayes A.E., Lennertz P., Beggs J.D., and Parker R. 2000. Yeast Sm-like proteins function in mRNA decapping and decay. Nature 404: 515.
59. Vanacova S., Wolf J., Martin G., Blank D., Dettwiler S., Friedlein A., Langen H., Keith G., and Keller W. 2005. A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3: e189.
60. Verdone L., Galardi S., Page D., and Beggs J.D. 2004. Lsm proteins promote regeneration of pre-mRNA splicing activity. Curr. Biol. 14: 1487.
61. Wolin S.L. and Cedervall T. 2002. The La protein. Annu. Rev. Biochem. 71: 375.
62. Wyers F., Rougemaille M., Badis G., Rousselle J.-C., Dufour M.-E., Boulay J., Regnault B., Devaux F., Namane A., Seraphin B., et al. 2005. Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121: 725.
63. Xue D., Rubinson D.A., Pannone B.K., Yoo C.J., and Wolin S.L. 2000. U snRNP assembly in yeast involves the La protein. EMBO J. 19: 1650.
64. Yoo C.J. and Wolin S.L. 1997. The yeast La protein is required for the 3′ endonucleolytic cleavage that matures tRNA precursors. Cell 89: 393.
65. Zaric B., Chami M., Remigy H., Engel A., Ballmer-Hofer K., Winkler F.K., and Kambach C. 2005. Reconstitution of two recombinant LSm protein complexes reveals aspects of their architecture, assembly and function. J. Biol. Chem. 22: 16066.
66. Zhang A., Wassarman K.M., Ortega J., Steven A.C., and Storz G. 2002. The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAs. Mol. Cell 9: 11.
67. Zhang A., Wassarman K.M., Rosenow C., Tjaden B.C., Storz G., and Gottesman S. 2003. Global analysis of small RNA and mRNA targets of Hfq. Mol. Microbiol. 50: 1111.