Differential effects of aromatic and charged residue substitutions in the RNA binding domains of the yeast poly(A)-binding protein

Journal of Molecular Biology

Volumn 269, Issue 1, 1997, Pages 67-81

  Deardorff, Julie A ^a   Sachs, Alan B ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

PAB; Poly(A) binding protein; Protein mutagenesis; RNA recognition motif; RNA protein interaction

Indexed keywords

FUNGAL PROTEIN; POLYADENYLATED RNA; RNA; RNA BINDING PROTEIN;

AMINO ACID SUBSTITUTION; ARTICLE; CELL VIABILITY; CONTROLLED STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN RNA BINDING; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION;

EID: 0031591391     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1013     Document Type: Article

References (47)

1. Adam S. A., Nakagawa T., Swanson M. S., Woodruff T. K., Dreyfuss G. mRNA polyadenylate binding protein: gene isolation and sequencing and identification of a ribonucleoprotein consensus sequence. Mol. Cell. Biol. 6:1986;2932-2943.
2. Anderson J. M., Paddy M., Swanson M. PUB1 is a major nuclear and cytoplasmic polyadenylated RNA-binding protein inSaccharomyces cerevisiae. Mol. Cell. Biol. 136:1993;102-112.
3. Baer B., Kornberg R. D. Repeating structure of cytoplasmic poly(A)-ribonucleoprotein. Proc. Natl Acad. Sci. USA. 77:1980;1890-1892.
4. Baer B., Kornberg R. D. The protein responsible for the repeating structure of cytoplasmic poly(A)-ribonucleoprotein. J. Cell Biol. 96:1983;717-721.
5. Birney E., Kumar S., Krainer A. R. Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors. Nucl. Acids Res. 21:1993;5803-5816.
6. Boeck R., Tarun S. Jr, Rieger M., Deardorff J. A., Müller-Auer S., Sachs A. B. The yeast Pan2 protein is required for poly(A)-binding protein-stimulated poly(A)-nuclease activity. J. Biol. Chem. 271:1996;432-438.
7. Brown C. E., Tarun S. Z. Jr, Boeck R., Sachs A. B. PAN3 encodes a subunit of the pab1p-dependent poly(A) nuclease inSaccharomyces cerevisiae. Mol. Cell. Biol. 16:1996;5744-5753.
8. Burd C. G., Dreyfuss G. Conserved structures and diversity of functions of RNA-binding proteins. Science. 265:1994;615-621.
9. Burd C. G., Matunis E. L., Dreyfuss G. The multiple RNA-binding domains of the mRNA poly(A) binding protein have different RNA-binding activities. Mol. Cell. Biol. 11:1991;3419-3424.
10. Cáceres J. F., Krainer A. R. Functional analysis of pre-mRNA splicing factor SF2/ASF structural domains. EMBO J. 12:1993;4715-4726.
11. Caponigro G., Parker R. Multiple functions for the poly(A)-binding protein in mRNA decapping and deadenylation in yeast. Genes Dev. 9:1995;2421-2432.
12. Dember L. M., Kim N. D., Liu K. Q., Anderson P. Individual RNA recognition motifs of TIA-1 and TIAR have different RNA binding specificities. J. Biol. Chem. 271:1996;2783-2788.
13. Elledge S. J., Davis R. W. A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay inSaccharomyces cerevisiae. Gene. 70:1988;303-312.
14. Garrett D. S., Lodi P. J., Shamoo Y., Williams K. R., Clore G. M., Gronenborn A. M. Determination of the secondary structure and folding topology of an RNA binding domain of mammalian hnRNP A1 protein using three-dimensional heteronuclear magnetic resonance spectroscopy. Biochemistry. 33:1994;2852-2858.
15. Geitz R. D., Sugino A. New yeast-Escherichia coli. Gene. 74:1988;527-534.
16. Gietz D., St. Jean A., Woods R. A., Schiestl R. H. Improved method for high efficiency transformation of intact yeast cells. Nucl. Acids Res. 20:1992;1425.
17. Görlach M., Wittekind M., Beckman R. A., Mueller L. Z., Dreyfuss G. Interaction of the RNA-binding domain of the hnRNPC proteins with RNA. EMBO J. 11:1992;3289-3295.
18. Görlach M., Burd C. G., Dreyfuss G. The mRNA poly(A) binding protein: localization, abundance, and RNA-binding specificity. Exp. Cell Res. 211:1994;400-407.
19. Guthrie C., Fink G. editors. Guide to Yeast Genetics and Molecular Biology, Methods in Enzymology. vol. 194. 1991;Academic Press, San Diego.
20. Hoffman D. W., Query C. C., Golden B. L., White S. W., Keene J. D. RNA-binding domain of the A protein component of the U1 small nuclear ribonucleoprotein analyzed by NMR spectroscopy is structurally similar to ribosomal proteins. Proc. Natl Acad. Sci. USA. 88:1991;2495-2499.
21. Jessen T. H., Oubridge C., Teo C. H., Pritchard C., Nagai K. Identification of molecular contacts between the U1A small nuclear ribonucleoprotein and U1 RNA. EMBO J. 10:1991;3447-3456.
22. Kanaar R. K., Lee A. L., Rudner D. Z., Wemmer D. E., Rio D. C. Interaction of the sex-lethal RNA binding domains with RNA. EMBO J. 14:1995;4530-4539.
23. Kenan D. J., Query C. C., Keene J. D. RNA recognition: towards identifying determinants of specificity. Trends Biochem. Sci. 16:1991;214-220.
24. Kuhn U., Pieler T. Xenopus. J. Mol. Biol. 256:1996;20-30.
25. Kunkel T. A., Katarzyna B., McClary J. Efficient site-directed mutagenesis using uracil-containing DNA. Methods Enzymol. 204:1991;125-139.
26. Lee A. L., Kanaar R., Rio D. C., Wemmer D. E. Resonance assignments and solution structure of the second RNA-binding domain of sex-lethal determined by multidimensional heteronuclear magnetic resonance. Biochemistry. 33:1994;13775-13786.
27. Lowell J. E., Rudner D. Z., Sachs A. B. 3′UTR-dependent deadenylation by the yeast poly(A) nuclease. Genes Dev. 6:1992;2088-2099.
28. Mayeda A., Munroe S. H., Cáceres J. F., Krainer A. R. Function of conserved domains of hnRNPA1 and other hnRNP A/B proteins. EMBO J. 13:1994;5483-5495.
29. Merrill B. M., Stone K. L., Cobianchi F., Wilson S. H., Williams K. R. Phenylalanines that are conserved among several RNA-binding proteins form part of a nucleic acid-binding pocket in the A1 heterogeneous nuclear ribonucleoprotein. J. Biol. Chem. 263:1988;3307-3313.
30. Nagai K., Oubridge C., Jessen T. H., Li J., Evans P. R. Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A. Nature. 348:1990;515-520.
31. Naranda T., Strong W. B., Menaya J., Fabbri B. J., Hershey J. W. B. Two structural domains of initiation factor eIF-4B are involved in binding to RNA. J. Biol. Chem. 269:1994;14465-14472.
32. Nietfeld W., Mentzel H., Pieler T. TheXenopus laevis. EMBO J. 9:1990;3699-3705.
33. Oubridge C., Ito N., Evans P. R., Teo C. H., Nagai K. Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin. Nature. 372:1994;432-438.
34. Proweller A., Butler J. S. Ribosomal association of poly(A) binding protein in poly(A) deficientSaccharomyces cerevisiae. J. Biol. Chem. 271:1996;10859-10865.
35. Sachs A. B., Davis R. W. The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation-initiation. Cell. 58:1989;857-867.
36. Sachs A. B., Deardorff J. A. Translation initiation requires the PAB-dependent poly(A) ribonuclease in yeast. Cell. 70:1992;961-973.
37. Sachs A. B., Kornberg R. D. Nuclear polyadenylate-binding protein. Mol. Cell. Biol. 5:1985;1993-1996.
38. Sachs A. B., Bond M. W., Kornberg R. D. A single gene from yeast for both nuclear and cytoplasmic polyadenylate-binding proteins: domain structure and expression. Cell. 45:1986;827-835.
39. Sachs A. B., Davis R. W., Kornberg R. D. A single domain of yeast poly(A) binding protein is necessary and sufficient for RNA binding and cell viability. Mol. Cell. Biol. 7:1987;3268-3276.
40. Samuels M. E., Bopp D., Colvin R. A., Roscigno R. F., Garcia-Blanco M. A., Schedl P. RNA binding by Sxl proteins in vitro and in vivo. Mol. Cell. Biol. 14:1994;4975-4990.
41. Scherly D., Dathan N. A., Boelens W., van Venrooij W. J., Mattaj I. W. The U2B″ RNP motif as a site of protein-protein interaction. EMBO J. 9:1990a;3675-3681.
42. Scherly D., Boelens W., Dathan N. A., van Venrooij W. J., Mattaj I. W. Major determinants of the specificity of interaction between small nuclear ribonucleoproteins U1A and U2B″ and their cognate RNAs. Nature. 345:1990b;502-506.
43. Shamoo Y., Abdul-Manan N., Williams K. R. Multiple RNA binding domains (RBDs) just don't add up. Nucl. Acids Res. 23:1995;725-728.
44. Surowy C. S., van Santen V. L., Scheib-Wixted S. M., Spritz R. A. Direct, sequence-specific binding of the human U1-70K ribonucleoprotein antigen protein to loop I of U1 small nuclear RNA. Mol. Cell. Biol. 9:1989;4179-4186.
45. Tarun S. Z. Jr, Sachs A. B. A common function for mRNA 5′ and 3′ ends in translation initiation in yeast. Genes Dev. 9:1995;2997-3007.
46. Tarun S. Z. Jr, Sachs A. B. Association of the yeast poly(A) tail binding protein with translation initiation factor eIF-4G. EMBO J. 15:1996;7168-7177.
47. Zuo P., Manley J. L. Functional domains of the human splicing factor ASF/SF2. EMBO J. 12:1993;4727-4737.