An extensive network of information flow through the B1b/c intersubunit bridge of the yeast ribosome

PLoS ONE

Volumn 6, Issue 5, 2011, Pages

  Rhodin, Michael H J ^a   Dinman, Jonathan D ^a  

^a Bldg 142   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PEPTIDYLTRANSFERASE; RIBOSOME RNA; TRANSFER RNA;

ALLELE; ARTICLE; CELL VIABILITY; FUNGAL STRAIN; FUNGUS MUTANT; FUNGUS MUTATION; GENETIC ANALYSIS; NONHUMAN; PHENOTYPE; RIBOSOME; RNA BINDING; SACCHAROMYCES CEREVISIAE; CHEMICAL STRUCTURE; FUNGAL GENE; GENETICS; PROTEIN SYNTHESIS; YEAST;

GENES, FUNGAL; MODELS, MOLECULAR; PROTEIN BIOSYNTHESIS; RIBOSOMES; YEASTS;

EID: 79956268777     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020048     Document Type: Article

References (53)

1. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA, (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905-920.
2. Fischer N, Konevega AL, Wintermeyer W, Rodnina MV, Stark H, (2010) Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy. Nature 466: 329-333.
3. Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, et al. (2005) Structures of the bacterial ribosome at 3.5 Å resolution. Science 310: 827-834.
4. Spahn CM, Beckmann R, Eswar N, Penczek PA, Sali A, et al. (2001) Structure of the 80S ribosome from Saccharomyces cerevisiae--tRNA- ribosome and subunit-subunit interactions. Cell 107: 373-386.
5. Taylor DJ, Devkota B, Huang AD, Topf M, Narayanan E, et al. (2009) Comprehensive molecular structure of the eukaryotic ribosome. Structure 17: 1591-1604.
6. Yusupov MM, Yusupova GZ, Baucom A, Lieberman K, Earnest TN, et al. (2001) Crystal Structure of the Ribosome at 5.5 Å Resolution. Science 292: 883-896.
7. Gabashvili IS, Agrawal RK, Spahn CM, Grassucci RA, Svergun DI, et al. (2000) Solution structure of the E. coli 70S ribosome at 11.5 A resolution. Cell 100: 537-549.
8. Ben-Shem A, Jenner L, Yusupova G, Yusupov M, (2010) Crystal structure of the eukaryotic ribosome. Science 330: 1203-1209.
9. Rhodin MHJ, Dinman JD, (2010) A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding. Nucleic Acids Res 38: 8377-8389.
10. Sergiev PV, Kiparisov SV, Burakovsky DE, Lesnyak DV, Leonov AA, et al. (2005) The conserved A-site finger of the 23S rRNA: just one of the intersubunit bridges or a part of the allosteric communication pathway? Journal of Molecular Biology 353: 116-123.
11. Valle M, Zavialov A, Sengupta J, Rawat U, Ehrenberg M, et al. (2003) Locking and unlocking of ribosomal motions. Cell 114: 123-134.
12. Zhang W, Dunkle JA, Cate JH, (2009) Structures of the ribosome in intermediate states of ratcheting. Science 325: 1014-1017.
13. Frank J, Gao H, Sengupta J, Gao N, Taylor DJ, (2007) The process of mRNA-tRNA translocation. Proceedings of the National Academy of Sciences of the United States of America 104: 19671-19678.
14. Frank J, Agrawal RK, (2000) A ratchet-like inter-subunit reorganization of the ribosome during translocation. Nature 406: 318-322.
15. Shasmal M, Chakraborty B, Sengupta J, (2010) Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome. Biochemical and Biophysical Research Communications 399: 192-197.
16. Cmejla R, Cmejlova J, Handrkova H, Petrak J, Petrtylova K, et al. (2009) Identification of mutations in the ribosomal protein L5 (RPL5) and ribosomal protein L11 (RPL11) genes in Czech patients with Diamond-Blackfan anemia. Human Mutation Journal 30: 321-327.
17. Gazda HT, Sheen MR, Vlachos A, Choesmel V, O'Donohue MF, et al. (2008) Ribosomal protein L5 and L11 mutations are associated with cleft palate and abnormal thumbs in Diamond-Blackfan anemia patients. Am J Hum Genet 83: 769-780.
18. Quarello P, Garelli E, Carando A, Brusco A, Calabrese R, et al. (2010) Diamond-Blackfan anemia: genotype-phenotype correlations in Italian patients with RPL5 and RPL11 mutations. Haematologica 95: 206-213.
19. Dai MS, Shi D, Jin Y, Sun XX, Zhang Y, et al. (2006) Regulation of the MDM2-p53 pathway by ribosomal protein L11 involves a post-ubiquitination mechanism. Journal of Biological Chemistry 281: 24304-24313.
20. Dai MS, Sun XX, Lu H, (2010) Ribosomal protein L11 associates with c-Myc at 5 S rRNA and tRNA genes and regulates their expression. Journal of Biological Chemistry 285: 12587-12594.
21. Sun XX, Wang YG, Xirodimas DP, Dai MS, (2010) Perturbation of 60 S ribosomal biogenesis results in ribosomal protein L5- and L11-dependent p53 activation. Journal of Biological Chemistry 285: 25812-25821.
22. Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V, (2002) Selection of tRNA by the Ribosome Requires a Transition from an Open to a Closed Form. Cell 111: 721-732.
23. Grollman AP, (1967) Inhibitors of protein biosynthesis. II. Mode of action of anisomycin. JBiolChem 242: 3226-3233.
24. Hansen JL, Moore PB, Steitz TA, (2003) Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. JMolBiol 330: 1061-1075.
25. Schlunzen F, Zarivach R, Harms R, Bashan A, Tocilj A, et al. (2001) Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413: 814-821.
26. Fredrick K, Noller HF, (2003) Catalysis of ribosomal translocation by sparsomycin. Science 300: 1159-1162.
27. Icho T, Wickner RB, (1988) The MAK11 protein is essential for cell growth and replication of M double-stranded RNA and is apparently a membrane-associated protein. JBiolChem 263: 1467-1475.
28. Dinman JD, Icho T, Wickner RB, (1991) A-1 ribosomal frameshift in a double-stranded RNA virus forms a Gag-pol fusion protein. Proc Natl Acad Sci U S A 88: 174-178.
29. Dinman JD, Wickner RB, (1992) Ribosomal frameshifting efficiency and Gag/Gag-pol ratio are critical for yeast M1 double-stranded RNA virus propagation. JVirol 66: 3669-3676.
30. Wickner RB, (1996) Double-stranded RNA viruses of Saccharomyces cerevisiae Microbiol Rev 60: 250-265.
31. Breinig F, Tipper DJ, Schmitt MJ, (2002) Kre1p, the plasma membrane receptor for the yeast K1 viral toxin. Cell 108: 395-405.
32. Dinman JD, (1995) Ribosomal frameshifting in yeast viruses. Yeast 11: 1115-1127.
33. Ohtake Y, Wickner RB, (1995) Yeast virus propagation depends critically on free 60S ribosomal subunit concentration. Molecular & Cellular Biology 15: 2772-2781.
34. Harger JW, Dinman JD, (2003) An in vivo dual-luciferase assay system for studying translational recoding in the yeast Saccharomyces cerevisiae RNA 9: 1019-1024.
35. Plant EP, Nguyen P, Russ JR, Pittman YR, Nguyen T, et al. (2007) Differentiating between near- and non-cognate codons in Saccharomyces cerevisiae. PLoS ONE 2: e517.
36. Jacobs JL, Dinman JD, (2004) Systematic analysis of bicistronic reporter assay data. Nucleic Acids Res 32: e160-e170.
37. Liao PY, Choi YS, Dinman JD, Lee KH, (2011) The many paths to frameshifting: kinetic modelling and analysis of the effects of different elongation steps on programmed-1 ribosomal frameshifting. Nucleic Acids Res 39: 300-312.
38. Clare J, Farabaugh P, (1985) Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression. Proceedings of the National Academy of Sciences of the United States of America 82: 2829-2833.
39. Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM, (2005) RNA structure analysis at single nucleotide resolution by selective 2′-hydroxyl acylation and primer extension (SHAPE). Journal of the American Chemical Society 127: 4223-4231.
40. Mortimer SA, Weeks KM, (2007) A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. Journal of the American Chemical Society 129: 4144-4145.
41. Wilkinson KA, Merino EJ, Weeks KM, (2006) Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat Protoc 1: 1610-1616.
42. Petrov AN, Meskauskas A, Roshwalb SC, Dinman JD, (2008) Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit. Nucleic Acids Res 36: 6187-6198.
43. Meskauskas A, Dinman JD, (2008) Ribosomal protein L3 functions as a 'rocker switch' to aid in coordinating of large subunit-associated functions in eukaryotes and Archaea. Nucleic Acids Res 36: 6175-6186.
44. Rakauskaite R, Dinman JD, (2008) rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance. Nucleic Acids Res 36: 1497-1507.
45. Dinman JD, (2005) 5S rRNA: Structure and Function from Head to Toe. International Journal of Biomedical Science 1: 2-7.
46. Kiparisov S, Petrov A, Meskauskas A, Sergiev PV, Dontsova OA, et al. (2005) Structural and functional analysis of 5S rRNA. Molecular Genetics and Genomics 27: 235-247.
47. Besseova I, Reblova K, Leontis NB, Sponer J, (2010) Molecular dynamics simulations suggest that RNA three-way junctions can act as flexible RNA structural elements in the ribosome. Nucleic Acids Research 38: 6247-6264.
48. Cochella L, Green R, (2005) An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308: 1178-1180.
49. Rodnina MV, Gromadski KB, Kothe U, Wieden HJ, (2005) Recognition and selection of tRNA in translation. FEBS Letters 579: 938-942.
50. Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, et al. (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340-348.
51. Spahn CM, Gomez-Lorenzo MG, Grassucci RA, Jorgensen R, Andersen GR, et al. (2004) Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. EMBO J 23: 1008-1019.
52. DeLano WL, (2006) The PyMOL Molecular Graphics System, version 1.4. Available:http://www.pymol.org/.
53. Dresios J, Derkatch IL, Liebman SW, Synetos D, (2000) Yeast ribosomal protein L24 affects the kinetics of protein synthesis and ribosomal protein L39 improves translational accuracy, while mutants lacking both remain viable. Biochemistry 39: 7236-7244.