Translational recoding as a feedback controller: Systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift

Nucleic Acids Research

Volumn 39, Issue 11, 2011, Pages 4587-4597

  Rato, Claudia ^a   Amirova, Svetlana R ^b   Bates, Declan G ^b   Stansfield, Ian ^a   Wallace, Heather M ^a  

^a UNIVERSITY OF ABERDEEN   (United Kingdom)

^b UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PLASMID VECTOR; PROTEIN OAZ1; PUTRESCINE; SACCHAROMYCES CEREVISIAE PROTEIN; SPERMIDINE; SPERMINE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CONTROLLED STUDY; FEEDBACK SYSTEM; FUNGAL STRAIN; FUNGUS GROWTH; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RIBOSOMAL FRAMESHIFTING; RIBOSOME; SACCHAROMYCES CEREVISIAE; STOP CODON; TRANSLATIONAL RECODING;

BINDING SITES; CODON, TERMINATOR; FEEDBACK, PHYSIOLOGICAL; FRAMESHIFTING, RIBOSOMAL; GENE DELETION; GENE EXPRESSION REGULATION, FUNGAL; MODELS, GENETIC; MUTATION; POLYAMINES; PUTRESCINE; RIBOSOMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPERMIDINE; SPERMINE;

EID: 79959446944     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1349     Document Type: Article

References (42)

1. Wallace, H.M., Fraser, A.V. and Hughes, A. (2003) A perspective of polyamine metabolism. Biochem. J., 376, 1-14. (Pubitemid 37487199)
2. Wallace, H.M. and Fraser, A.V. (2004) Inhibitors of polyamine metabolism. Amino Acids, 26, 353-365.
3. Poulin, R., Coward, J.K., Lakanen, J.R. and Pegg, A.E. (1993) Enhancement of the spermidine uptake system and lethal effects of spermidine overaccumulation in ornithine decarboxylaseoverproducing L1210 cells under hyposmotic stress. J. Biol. Chem., 268, 4690-4698. (Pubitemid 23081580)
4. Tobias, K.E. and Kahana, C. (1995) Exposure to ornithine results in excessive accumulation of putrescine and apoptotic cell death in ornithine decarboxylase overproducing mouse myeloma cells. Cell Growth Differ., 6, 1279-1285.
5. Ivanov, I.P. and Atkins, J.F. (2007) Ribosomal frameshifting in decoding antizyme mRNAs from yeast and protists to humans: close to 300 cases reveal remarkable diversity despite underlying conservation. Nucleic Acids Res., 35, 1842-1858. (Pubitemid 47064260)
6. Palanimurugan, R., Scheel, H., Hofmann, K. and Dohmen, R.J. (2004) Polyamines regulate their synthesis by inducing expression and blocking degradation of ODC antizyme. EMBO J., 23, 4857-4867. (Pubitemid 40069715)
7. Li, X. and Coffino, P. (1992) Regulated degradation of ornithine decarboxylase requires interaction with the polyamine-inducible protein antizyme. Mol. Cell. Biol., 12, 3556-3562.
8. Murakami, Y., Matsufuji, S., Kameji, T., Hayashi, S., Igarashi, K., Tamura, T., Tanaka, K. and Ichihara, A. (1992) Ornithine decarboxylase is degraded by the 26S proteasome without ubiquitination. Nature, 360, 597-599. (Pubitemid 23000711)
9. Kim, J., Bates, D.G., Postlethwaite, I., Ma, L. and Iglesias, P.A. (2006) Robustness analysis of biochemical network models. Syst. Biol., 153, 96-104. (Pubitemid 44251348)
10. Rodriguez-Caso, C., Montanez, R., Cascante, M., Sanchez- Jimenez, F. and Medina, M.A. (2006) Mathematical modeling of polyamine metabolism in mammals. J. Biol. Chem., 281, 21799-21812. (Pubitemid 44181884)
11. Vimaladithan, A. and Farabaugh, P.J. (1994) Special peptidyl-tRNA molecules can promote translational frameshifting without slippage. Mol. Cell. Biol., 14, 8107-8116. (Pubitemid 24373559)
12. Sundararajan, A., Michaud, W.A., Qian, Q., Stahl, G. and Farabaugh, P.J. (1999) Near-cognate peptidyl-tRNAs promote+1 programmed translational frameshifting in yeast. Mol. Cell, 4, 1005-1015. (Pubitemid 30054906)
13. Matsufuji, S., Matsufuji, T., Miyazaki, Y., Murakami, Y., Atkins, J.F., Gesteland, R.F. and Hayashi, S. (1995) Autoregulatory frameshifting in decoding mammalian ornithine decarboxylase antizyme. Cell, 80, 51-60.
14. Bonetti, B., Fu, L., Moon, J. and Bedwell, D.M. (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.
15. Hryniewicz, M.M. and Vonder Haar, R.A. (1983) Polyamines enhance readthrough of the UGA termination codon in a mammalian messenger RNA. Mol. Gen. Genet., 190, 336-343.
16. Yoshida, M., Kashiwagi, K., Kawai, G., Ishihama, A. and Igarashi, K. (2002) Polyamines enhance synthesis of the RNA polymerase sigma 38 subunit by suppression of an amber termination codon in the open reading frame. J. Biol. Chem., 277, 37139-37146.
17. Petros, L.M., Howard, M.T., Gesteland, R.F. and Atkins, J.F. (2005) Polyamine sensing during antizyme mRNA programmed frameshifting. Biochem. Biophys. Res. Commun., 338, 1478-1489. (Pubitemid 41608416)
18. Goldstein, A.L. and McCusker, J.H. (1999) Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast, 15, 1541-1553. (Pubitemid 29472165)
19. Sherman, F. (1991) Getting started with yeast. Methods Enzymol., 194, 3-21.
20. Fontaniella, B., Mateos, J.L., Vicente, C. and Legaz, M.E. (2001) Improvement of the analysis of dansylated derivatives of polyamines and their conjugates by high-performance liquid chromatography. J. Chromatogr. A, 919, 283-288. (Pubitemid 32568188)
21. Johnston, G.C., Ehrhardt, C.W., Lorincz, A. and Carter, B.L. (1979) Regulation of cell size in the yeast Saccharomyces cerevisiae. J. Bacteriol., 137, 1-5. (Pubitemid 9093910)
22. Sambrook, J., Fritsch, E.F. and and Maniatis, T. (1989) Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. Stahl, G., Bidou, L., Rousset, J.P. and Cassan, M. (1995) Versatile vectors to study recoding: conservation of rules between yeast and mammalian cells. Nucleic Acids Res., 23, 1557-1560.
24. Forbes, E.M., Nieduszynska, S.R., Brunton, F.K., Gibson, J., Glover, L.A. and Stansfield, I. (2007) Control of gag-pol gene expression in the Candida albicans retrotransposon Tca2. BMC Mol. Biol., 8, 94.
25. Gietz, R.D. and Woods, R.A. (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol., 350, 87-96. (Pubitemid 34619485)
26. Williams, I., Richardson, J., Starkey, A. and Stansfield, I. (2004) Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res., 32, 6605-6616. (Pubitemid 40220372)
27. Cohn, M.S., Tabor, C.W. and Tabor, H. (1980) Regulatory mutations affecting ornithine decarboxylase activity in Saccharomyces cerevisiae. J. Bacteriol., 142, 791-799. (Pubitemid 11230329)
28. Whitney, P.A. and Morris, D.R. (1978) Polyamine auxotrophs of Saccharomyces cerevisiae. J. Bacteriol., 134, 214-220. (Pubitemid 8334706)
29. Cohn, M.S., Tabor, C.W. and Tabor, H. (1978) Isolation and characterization of Saccharomyces cerevisiae mutants deficient in S-adenosylmethionine decarboxylase, spermidine, and spermine. J. Bacteriol., 134, 208-213. (Pubitemid 8334705)
30. Tabor, C.W. and Tabor, H. (1985) Polyamines in microorganisms. Microbiol. Rev., 49, 81-99. (Pubitemid 15134122)
31. Joets, J., Pousset, D., Marcireau, C. and Karst, F. (1996) Characterization of the Saccharomyces cerevisiae FMS1 gene related to Candida albicans corticosteroid-binding protein 1. Curr. Genet., 30, 115-120. (Pubitemid 26261675)
32. White, W.H., Gunyuzlu, P.L. and Toyn, J.H. (2001) Saccharomyces cerevisiae is capable of de novo pantothenic acid biosynthesis involving a novel pathway of beta-alanine production from spermine. J. Biol. Chem., 276, 10794-10800. (Pubitemid 38089254)
33. Chattopadhyay, M.K., Tabor, C.W. and Tabor, H. (2003) Spermidine but not spermine is essential for hypusine biosynthesis and growth in Saccharomyces cerevisiae: spermine is converted to spermidine in vivo by the FMS1-amine oxidase. Proc. Natl Acad. Sci. USA, 100, 13869-13874. (Pubitemid 37499158)
34. Liu, B., Sutton, A. and Sternglanz, R. (2005) A yeast polyamine acetyltransferase. J. Biol. Chem., 280, 16659-16664. (Pubitemid 41389123)
35. Balasundaram, D., Dinman, J.D., Tabor, C.W. and Tabor, H. (1994) SPE1 and SPE2: Two essential genes in the biosynthesis of polyamines that modulate+1 ribosomal frameshifting in Saccharomyces cerevisiae. J. Bacteriol., 176, 7126-7128. (Pubitemid 24349463)
36. Cornish-Bowden, A. (2004) Fundamentals of enzyme kinetics. Portland Press, London, UK.
37. Amarantos, I., Zarkadis, I.K. and Kalpaxis, D.L. (2002) The identification of spermine binding sites in 16S rRNA allows interpretation of the spermine effect on ribosomal 30S subunit functions. Nucleic Acids Res., 30, 2832-2843. (Pubitemid 34778143)
38. Xaplanteri, M.A., Petropoulos, A.D., Dinos, G.P. and Kalpaxis, D.L. (2005) Localization of spermine binding sites in 23S rRNA by photoaffinity labeling: parsing the spermine contribution to ribosomal 50S subunit functions. Nucleic Acids Res., 33, 2792-2805. (Pubitemid 41511219)
39. Amarantos, I. and Kalpaxis, D.L. (2000) Photoaffinity polyamines: Interactions with AcPhe-tRNA free in solution or bound at the P-site of Escherichia coli ribosomes. Nucleic Acids Res., 28, 3733-3742.
40. Howard, M.T., Shirts, B.H., Zhou, J., Carlson, C.L., Matsufuji, S., Gesteland, R.F., Weeks, R.S. and Atkins, J.F. (2001) Cell culture analysis of the regulatory frameshift event required for the expression of mammalian antizymes. Genes Cells, 6, 931-941. (Pubitemid 33100028)
41. Balasundaram, D., Dinman, J.D., Wickner, R.B., Tabor, C.W. and Tabor, H. (1994) Spermidine deficiency increases+1 ribosomal frameshifting efficiency and inhibits Ty1 retrotransposition in Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA, 91, 172-176. (Pubitemid 24018665)
42. Delbecq, P., Werner, M., Feller, A., Filipkowski, R.K., Messenguy, F. and Pierard, A. (1994) A segment of mRNA encoding the leader peptide of the CPA1 gene confers repression by arginine on a heterologous yeast gene transcript. Mol. Cell. Biol., 14, 2378-2390. (Pubitemid 24108220)