Structure/function analysis of yeast ribosomal protein L2

Nucleic Acids Research

Volumn 36, Issue 6, 2008, Pages 1826-1835

  Meskauskas, Arturas ^a   Russ, Johnathan R ^a   Dinman, Jonathan D ^a  

^a University of Maryland   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASPARTIC ACID; GLUTAMINE; HISTIDINE; LEUCINE; PEPTIDYLTRANSFERASE; PROTEIN L2; RIBOSOME PROTEIN; RIBOSOME RNA; TRANSFER RNA; TYROSINE; UNCLASSIFIED DRUG; VALINE;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; FUNGAL GENETICS; GENE IDENTIFICATION; MOLECULAR INTERACTION; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; RIBOSOME; RNA BINDING; RNA STRUCTURE; RNA TRANSLATION; SACCHAROMYCES CEREVISIAE; YEAST;

ALLELES; AMINO ACID SUBSTITUTION; BASE SEQUENCE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PEPTIDYL TRANSFERASES; PHENOTYPE; POLYRIBOSOMES; PROTEIN BIOSYNTHESIS; RIBOSOMAL PROTEINS; RIBOSOME SUBUNITS, LARGE, EUKARYOTIC; RIBOSOMES; RNA, RIBOSOMAL; SACCHAROMYCES CEREVISIAE PROTEINS;

EID: 41849145258     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn034     Document Type: Article

References (48)

1. Inoue,T., Sullivan,F.X. and Cech,T.R. (1985) Intermolecular exon ligation of the rRNA precursor of Tetrahymena: Oligonucleotides can function as 5′ exons. Cell, 43, 431-437.
2. Kazemie,M. (1976) Binding of aminoacyl-tRNA to reconstituted subparticles of Escherichia coli large ribosomal subunits. Eur. J. Biochem., 67, 373-378.
3. Schulze,H. and Nierhaus,K.H. (1982) Minimal set of ribosomal components for reconstitution of the peptidyltransferase activity. EMBO J., 1, 609-613.
4. Khaitovich,P., Mankin,A.S., Green,R., Lancaster,L. and Noiler,H.F. (1999) Characterization of functionally active subribosomal particles from Thermus aquaticus. Proc. Natl Acad. Sci. USA, 96, 85-90.
5. Fahnestook,S.R. (1975) Evidence of the involvement of a 50S ribosomal protein in several active sites. Biochemistry, 14, 5321-5327.
6. Sonenberg,N., Wilchek,M. and Zamir,A. (1973) Mapping of Escherichia coli ribosomal components involved in peptidyl transferase activity. Proc. Natl Acad. Sci USA, 70, 1423-1426.
7. Harada,N., Maemura,K., Yamasaki,N. and Kimura,M. (1998) Identification by site-directed mutagenesis of amino acid residues in ribosomal ptbtein L2 that are essential for binding to 23S ribosomal RNA. Biochim. Biophys. Acta, 1429, 176-186.
8. Uhlein,M., Weglohner,W., Urlaub,H. and Wittmann-Liebold,B. (1998) Functional implications of ribosomal protein L2 in protein biosynthesis as shown by in vivo replacement studies. Biochem. J., 331, 423-430.
9. Diedrich,G., Spahn,C.M., Stelzl,U., Schafer,M.A., Wooten,T., Bochkariov,D.E., Cooperman,B.S., Traut,R.R. and Nierhaus,K.H. (2000) Ribosomal protein L2 is involved in the association of the ribosomal subunits, tRNA binding to A and P sites and peptidyl transfer. EMBO J., 19, 5241-5250.
10. Yusupov,M.M., Yusupova,G.Z., Baucom,A., Lieberman,K., Earnest,T.N., Cate,J.H. and Noller,H.F. (2001) Crystal structure of the ribosome at 5.5_A resolution. Science, 292, 883-896.
11. Ban,N., Nissen,P., Hansen,J., Moore,P.B. and Steitz,T.A. (2000) The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science, 289, 905-920.
12. Klein,D.J., Moore,P.B. and Steitz,T.A. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol., 340, 141-177.
13. Spahn,C.M., Beckmann,R., Eswar,N., Penczek,P.A., Sali,A., Blobel,G. and Frank,J. (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae-tRNA- ribosome and subunit-subunit interactions. Cell, 107, 373-386.
14. Oen,H.,Pellegrini,M. and Cantor,C.R. (1974) Peptidyl-transferase inhibitors alter the covalent reaction of BrAcPhe-tRNA with the E. coli ribosome. FEBS Lett., 45, 218-222.
15. Wower,J., Hixson,S.S. and Zimmermann,R.A. (1988) Photochemical cross-linking of yeast tRNA(Phe) containing 8-azidoadenosine at positions 73 and 76 to the Escherichia coli ribosome. Biochemistry 27, 8114-8121.
16. Nakagawa,A., Nakashima,T., Taniguchi,M., Hosaka,H., Kimura,M. and Tanaka,I. (1999) The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome. EMBQ J., 18, 1459-1467.
17. Perez-Gosalbez,M., Vazquez,D. and Ballesta,J.P. (1979) Affinity labelling of yeast ribosomal peptidyl transferase. Mol. Gen. Genet. 163, 29-34.
18. Reyes,R., Vazquez,D. and Ballesta,J.P. (1978) Structure of the yeast ribosomes. Proteins associated with the rRNA. Biochim. Biophys. Acta 521, 229-234.
19. Kudlicki,W., Szyszka,R., Palen,E. and Gasior,E. (1980) Evidence for a highly specific protein kinase phosphorylating two strongly acidic proteins of yeast 60 S ribosomal subunit. Biochim. Biophys. Acta, 633, 376-385.
20. Otaka,E., Higo,K. and Itoh,T. (1983) Yeast ribosomal proteins: VII. Cytoplasmic ribosomal proteins from Schizosaccharomyces pombe. Mol. Gen. Genet., 191, 519-524.
21. Lucioli,A., Presutti,C., Ciafre,S., Caffarelli,E., Fragapane,P. and Bozzoni,I. (1988) Gene dosage alteration of L2 ribosomal protein genes in Saccharomyces cerevisiae: Effects on ribosome synthesis. Mol. Cell. Biol., 8, 4792-4798.
22. Kudlicki,W., Grankowski,N. and Gasior,E. (1976) Ribosomal protein as substrate for a GTP-dependent protein kinase from yeast. Mol. Biol. Rep., 3, 121-129.
23. 1 double-stranded RNA virus propagation. J. Virol., 66, 3669-3676.
24. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning, a Laboratory Manual. Cold Spring Harbor Press, Cold Spring Harbor, NY.
25. Ito,H., Fukuda,Y., Murata,K. and Kimura,A. (1983) Transformation of intact yeast cells treated with alkali cations. J. Bacteriol., 153, 163-168.
26. Dinman,J.D. and Wickner,R.B. (1994) Translational maintenance of frame: mutants of Saccharomyces cerevisiae with altered -1 ribosomal frameshifting efficiencies. Genetics, 136, 75-86.
27. Wickner,R.B. and Leibowitz,M.J. (1979) Mak mutants of yeast: Mapping and characterization. J. Bact., 140, 154-160.
28. Sikorski,R.S. and Hieter,P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122, 19-27.
29. Muhlrad,D., Hunter,R. and Parker,R, (1992) A rapid method for localized mutagenesis of yeast genes. Yeast, 8, 79-82.
30. Dimman,J.D. and Kinzy,T.G. (1997) Translational misreading: Mutations in translation elongation factor 1α differentially affect programmed ribosomal frameshifting and drug sensitivity. RNA, 3, 870-881.
31. Harger,J.W. and Dinman,J.D. (2003) An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae. RNA, 9, 1019-1024.
32. Jacobs,J.L. and Dinman,J.D. (2004) Systematic analysis of bicistronic reporter assay data. Nucleic Acids Res., 32, e160-e170.
33. Sachs,A.B. and Davis,R.W. (1989) The poly(A) binding protein is required for poly(A) shortening and 60S ribosomal subunit-dependent translation initiation. Cell, 58, 857-867.
34. Meskauskas,A., Petrov,A.N. and Dinman,J.D. (2005) Identification of functionally important amino acids of ribosomal protein L3 by saturation mutagenesis. Mol. Cell. Biol., 25, 10863-10874.
35. Stern,S., Moazed,D. and Noller,H.F. (1988) Structural analysis of RNA using chemical and enzymatic probing monitored by primer extension. Methods Enzymol., 164, 481-489.
36. Lowe,T.M. and Eddy,S.R. (1999) A computational screen for methylation guide snoRNAs in yeast. Science, 283, 1168-1171.
37. DeLano,W.L. The PyMOL Molecular Graphics System. http://www.pymol.org. 2006.
38. Ohtake,Y. and Wickner,R.B. (1995) Yeast virus propagation depends critically on free 60S ribosomal subunit concentration. Mol. Cell. Biol., 15, 2772-2781.
39. Dinman,J.D. and Berry,M.J. (2006) Regulation of termination and recoding. In Mathews,M.B., Sonenberg,N. and Hershey,J.W.B. (eds), Translational Control in Biology and Medicine. Cold Spring Harbor Press, Cold Spring Harbor, NY.
40. Harger,J.W. and Dinman,J.D. (2004) Evidence against a direct role for the Upf proteins in frameshfiting or nonsense codon read-through. RNA 10, 1721-1729.
41. Komili,S., Farny,N.G., Roth,F.P. and Silver,P.A. (2007) Functional specificity among ribosomal proteins regulates gene expression. Cell 131, 557-571.
42. Pestka,S. (1977) Inhibitors of protein synthesis. In Weissbach,H. and Pestka,S. (eds), Molecular Mechanismns of Protein Biosynthesis. Academic Press, New York, pp. 467-553.
43. Ogle,J.M., Carter,A.P. and Ramakrishnan,V. (2003) Insights into the decoding mechanism from recent ribosome structures. Trends Biochem. Sci., 28, 259-266.
44. Meskauskas,A., Harger,J.W., Jacobs,K.L.M. and Dinman,J.D. (2003) Decreased peptidyltransferase activity correlates with increased programmed -1 ribosomal frameshifting and viral maintenance defects in the yeast Saccharomyces cerevisiae. RNA, 9, 982-992.
45. Kitahara,K., Kajiura,A., Sato,N.S. and Suzuki,T. (2007) Functional genetic selection of Helix 66 in Escherichia coli 23S rRNA identified the eukaryotic-binding sequence for ribosomal protein L2. Nucleic Acids Res., 35, 4018-4029.
46. Meskauskas,A. and Dinman,J.D. (2007) Ribosomal protein L3: Gatekeeper to the A site. Molecular Cell, 25, 877-888.
47. Hansen,J.L., Moore,P.B. and Steitz,T.A. (2003) Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J. Mol. Biol., 330, 1061-1075.
48. Ohtake,Y. and Wickner,R.B. (1995) KRB1, a suppressor of mak7-1 (a mutant RPL4A), is RPL4B, a second ribosomal protein L4 gene, on a fragment of Saccharomyces chromosome XII. Genetics, 140, 129-137.