Translational accuracy during exponential, postdiauxic, and stationary growth phases in Saccharomyces cerevisiae

Eukaryotic Cell

Volumn 3, Issue 2, 2004, Pages 331-338

  Stahl, Guillaume ^a,b   Salem, Samia N Ben ^a   Chen, Lifeng ^a   Zhao, Bing ^a   Farabaugh, Philip J ^a  

^a UNIVERSITY OF MARYLAND BALTIMORE COUNTY   (United States)

^b UPS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; AMINOACYL TRANSFER RNA; GLUCOSE; TRNA, ARGININE; TRNA, ARGININE-;

ARTICLE; CODON; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLISM; PHYSIOLOGY; PROTEIN SYNTHESIS; RETROPOSON; RIBOSOMAL FRAMESHIFTING; SACCHAROMYCES CEREVISIAE;

CODON; ETHANOL; FRAMESHIFTING, RIBOSOMAL; GLUCOSE; PROTEIN BIOSYNTHESIS; RETROELEMENTS; RNA, TRANSFER, AMINO ACYL; SACCHAROMYCES CEREVISIAE;

EUKARYOTA; MYXOGASTRIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 16544363622     PISSN: 15359778     EISSN: None     Source Type: Journal    
DOI: 10.1128/EC.3.2.331-338.2004     Document Type: Article

References (48)

1. Aigner, S., J. Lingner, K. J. Goodrich, C. A. Grosshans, A. Shevchenko, M. Mann, and T. R. Cech. 2000. Euplotes telomerase contains an La motif protein produced by apparent translational frameshifting. EMBO J. 19: 6230-6239.
2. Andersson, D. I., H. W. van Verseveld, A. H. Stouthamer, and C. G. Kurland. 1986. Suboptimal growth with hyper-accurate ribosomes. Arch. Microbiol. 144:96-101.
3. Asakura, T., T. Sasaki, F. Nagano, A. Satoh, H. Obaishi, H. Nishioka, H. Imamura, K. Hotta, K. Tanaka, H. Nakanishi, and Y. Takai. 1998. Isolation and characterization of a novel actin filament-binding protein from Saccharomyces cerevisiae. Oncogene 16:121-130.
4. Barak, Z., J. Gallant, D. Lindsley, B. Kwieciszewki, and D. Heidel. 1996. Enhanced ribosome frameshifting in stationary phase cells. J. Mol. Biol. 263:140-148.
5. Belcourt, M. F., and P. J. Farabaugh. 1990. Ribosomal frameshifting in the yeast retrotransposon Ty: tRNAs induce slippage on a 7 nucleotide minimal site. Cell 62:339-352.
6. Bidou, L., G. Stahl, I. Hatin, O. Namy, J. P. Rousset, and P. J. Farabaugh. 2000. Nonsense-mediated decay mutants do not affect programmed -1 frameshifting. RNA 6:952-961.
7. Bonetti, B., L. W. Fu, J. Moon, and D. M. Bedwell. 1995. The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae. J. Mol. Biol. 251:334-345.
8. Bradford, M. 1976. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72:248-254.
9. Brierley, I. 1995. Ribosomal frameshifting on viral RNAs. J. Gen. Virol. 76:1885-1892.
10. Burke, D., D. Dawson, and T. Stearns. 2000. Methods in yeast genetics: a Cold Spring Harbor Laboratory course manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
11. Craigen, W. J., and C. T. Caskey. 1986. Expression of peptide chain release factor 2 requires high-efficiency frameshifting. Nature 322:273-275.
12. DeRisi, J. L., V. R. Iyer, and P. O. Brown. 1997. Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 278:680-686.
13. Dujon, B., D. Alexandraki, B. Andre, W. Ansorge, V. Baladron, J. P. Ballesta, A. Banrevi, P. A. Bolle, M. Bolotin-Fukuhara, P. Bossier, and J. Doofus. 1994. Complete DNA sequence of yeast chromosome XI. Nature 369:371-377.
14. Farabaugh, P. J. 1996. Programmed translational frameshifting. Microbiol. Rev. 60:103-134.
15. Farabaugh, P. J., H. Zhao, and A. Vimaladithan. 1993. A novel programed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: frame-shifting without tRNA slippage. Cell 74:93-103.
16. Fu, C., and J. Parker. 1994. A ribosomal frameshifting error during translation of the argI mRNA of Escherichia coli. Mol. Gen. Genet. 243:434-441.
17. Fuge, E. K., E. L. Braun, and M. Werner-Washburne. 1994. Protein synthesis in long-term stationary-phase cultures of Saccharomyces cerevisiae. J. Bacteriol. 176:5802-5813.
18. Gietz, D., A. St. Jean, R. A. Woods, and R. H. Schiestl. 1992. Improved method for high efficiency transformation of intact yeast cells. Nucleic Acids Res. 20:1425.
19. Hopfield, J. J. 1974. Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc. Natl. Acad. Sci. USA 71:4135-4139.
20. Ikemura, T. 1985. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:13-34.
21. Ishihama, A. 1997. Adaptation of gene expression in stationary phase bacteria. Curr. Opin. Genet. Dev. 7:582-588.
22. Ju, Q., and J. R. Warner. 1994. Ribosome synthesis during the growth cycle of Saccharomyces cerevisiae. Yeast 10:151-157.
23. Kawakami, K., S. Pande, B. Faiola, D. P. Moore, J. D. Boeke, P. J. Farabaugh, J. N. Strathern, Y. Nakamura, and D. J. Garfinkel. 1993. A rare tRNA-Arg(CCU) that regulates Ty1 element ribosomal frameshifting is essential for Ty1 retrotransposition in Saccharomyces cerevisiae. Genetics 135: 309-320.
24. Kurland, C. G. 1992. Translational accuracy and the fitness of bacteria. Annu. Rev. Genet. 26:29-50.
25. Li, Z., G. Stahl, and P. J. Farabaugh. 2001. Programmed +1 frameshifting stimulated by complementarity between a downstream mRNA sequence and an error-correcting region of rRNA. RNA 7:275-284.
26. Matsufuji, S., T. Matsufuji, Y. Miyazaki, Y. Murakami, J. F. Atkins, R. F. Gesteland, and S. Hayashi. 1995. Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell 80:51-60.
27. Morris, D. K., and V. Lundblad. 1997. Programmed translational frameshifting in a gene required for yeast telomere replication. Curr. Biol. 7:969-976.
28. Nakamura, Y., T. Gojobori, and T. Ikemura. 2000. Codon usage tabulated from international DNA sequence databases: status for the year 2000. Nucleic Acids Res. 28:292.
29. Ninio, J. 1975. Kinetic amplification of enzyme discrimination. Biochimie 57:587-595.
30. Percudani, R., A. Pavesi, and S. Ottonello. 1997. Transfer RNA gene redundancy and translational selection in Saccharomyces cerevisiae. J. Mol. Biol. 268:322-330.
31. Peter, K., D. Lindsley, L. Peng, and J. A. Gallant 1992. Context rules of rightward overlapping reading. New Biol. 4:520-526.
32. Rom, E., and C. Kahana. 1994. Polyamines regulate the expression of ornithine decarboxylase antizyme in vitro by inducing ribosomal frame-shifting. Proc. Natl. Acad. Sci. USA 91:3959-3963.
33. Ruusala, T., D. Andersson, M. Ehrenberg, and C. G. Kurland. 1984. Hyper-accurate ribosomes inhibit growth. EMBO J. 3:2575-2580.
34. Schwartz, R., and J. F. Curran. 1997. Analyses of frameshifting at UUU-pyrimidine sites. Nucleic Acids Res. 25:2005-2011.
35. Shigemoto, K., J. Brennan, E. Walls, C. J. Watson, D. Stott, P. W. Rigby, and A. D. Reith. 2001. Identification and characterisation of a developmentally regulated mammalian gene that utilises -1 programmed ribosomal frame-shifting. Nucleic Acids Res. 29:4079-4088.
36. Skuzeski, J. M., L. M. Nichols, R. F. Gesteland, and J. F. Atkins. 1991. The signal for a leaky UAG stop codon in several plant viruses includes the two downstream codons. J. Mol. Biol. 218:365-373.
37. Stahl, G., L. Bidou, J. P. Rousset, and M. Cassan. 1995. Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. Nucleic Acids Res. 23:1557-1560.
38. Stahl, G., G. P. McCarty, and P. J. Farabaugh. 2002. Ribosome structure: revisiting the connection between translational accuracy and unconventional decoding. Trends Biochem. Sci. 27:178-183.
39. Stahl, G., S. B. Salem, Z. Li, G. McCarty, A. Raman, M. Shah, and P. J. Farabaugh. 2001. Programmed +1 translational frameshifting in the yeast Saccharomyces cerevisiae results from disruption of translational error correction. Cold Spring Harbor Symp. Quant. Biol. 66:249-258.
40. Steneberg, P., C. Englund, J. Kronhamn, T. A. Weaver, and C. Samakovlis. 1998. Translational readthrough in the hdc mRNA generates a novel branching inhibitor in the Drosophila trachea. Genes Dev. 12:956-967.
41. Sundararajan, A., W. A. Michaud, Q. Qian, G. Stahl, and P. J. Farabaugh. 1999. Near-cognate peptidyl-tRNAs promote +1 programmed translational frameshifting in yeast. Mol. Cell 4:1005-1015.
42. Tan, M., K. Heckmann, and C. Brunen-Nieweler. 2001. Analysis of micronuclear, macronuclear and cDNA sequences encoding the regulatory subunit of cAMP-dependent protein kinase of Euplotes octocarinatus: evidence for a ribosomal frameshift. J. Eukaryot. Microbiol. 48:80-87.
43. Tan, M., A. Liang, C. Brunen-Nieweler, and K. Heckmann. 2001. Programmed translational frameshifting is likely required for expressions of genes encoding putative nuclear protein kinases of the ciliate Euplotes octocarinatus. J. Eukaryot. Microbiol. 48:575-582.
44. Thompson, R. C. 1988. EFTu provides an internal kinetic standard for translational accuracy. Trends Biochem. Sci. 13:91-93.
45. Tsuchihashi, Z., and P. O. Brown. 1992. Sequence requirements for efficient translational frameshifting in the Escherichia coli dnaX gene and the role of an unstable interaction between tRNA(Lys) and an AAG lysine codon. Genes Dev. 6:511-519.
46. Warner, J. R. 1999. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24:437-440.
47. Wenthzel, A. M., M. Stancek, and L. A. Isaksson. 1998. Growth phase dependent stop codon readthrough and shift of translation reading frame in Escherichia coli. FEBS Lett. 421:237-242.
48. Werner-Washburne, M., E. Braun, M. Crawford, and V. Peck. 1996. Stationary phase in Saccharomyces cerevisiae. Mol. Microbiol. 19:1159-1166.