Evolutionary specialization of recoding: Frameshifting in the expression of S. cerevisiae antizyme mRNA is via an atypical antizyme shift site but is still +1

RNA

Volumn 12, Issue 3, 2006, Pages 332-337

  Ivanov, Ivaylo P ^a,b   Gesteland, Raymond F ^b   Atkins, John F ^a,b  

^a UNIVERSITY COLLEGE CORK   (Ireland)

^b UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Antizyme; Frameshifting; ODC; Polyamines

Indexed keywords

ANTIZYME; MESSENGER RNA; TRANSFER RNA;

ARTICLE; BUDDING; FUNGAL GENETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; SACCHAROMYCES CEREVISIAE;

ANIMALS; BASE SEQUENCE; CONSERVED SEQUENCE; FRAMESHIFTING, RIBOSOMAL; FUNGI; MAMMALS; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; ORNITHINE DECARBOXYLASE; PROTEINS; RNA, FUNGAL; RNA, MESSENGER; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, NUCLEIC ACID; SPECIES SPECIFICITY;

EUKARYOTA; FUNGI; MAMMALIA; SACCHAROMYCES CEREVISIAE; SACCHAROMYCETALES; VERTEBRATA;

EID: 33344477344     PISSN: 13558382     EISSN: None     Source Type: Journal    
DOI: 10.1261/rna.2245906     Document Type: Article

References (48)

1. Atkins, J.F., Gesteland, R.F., Reid, B.R., and Anderson, C.W. 1979. Normal tRNAs promote ribosomal frameshifting. Cell 18: 1119-1131.
2. Baranov, P.V., Gesteland, R.F., and Atkins, J.F. 2004. P-site tRNA is a crucial initiator of ribosomal frameshifting. RNA 10: 221-230.
3. Baranov, P.V., Fayet, O., Hendrix, R.W., and Atkins, J.F. 2006. Recoding in bacteriophages and bacterial IS elements. Trends Genet. (in press).
4. Belting, M., Mani, K., Jonsson, M., Cheng, F., Sandgren, S., Jonsson, S., Ding, K., Delcros, J.G., and Fransson, L.A. 2003. Glypican-1 is a vehicle for polyamine uptake in mammalian cells: A pivotal role for nitrosthiol-derived nitric oxide. J. Biol. Chem. 278: 47181-47189.
5. Bercovich, Z. and Kahana, C. 2004. Degradation of antizyme inhibitor, an ornithine decarboxylase homologous protein, is ubiquitin-dependent and is inhibited by antizyme. J. Biol. Chem. 279: 54097-54102.
6. Cai, J., Roberts, I.N., and Collins, M.D. 1996. Phylogenetic relationships among members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences. Int. J. Syst. Bacteriol. 46: 542-549.
7. Childs, A.C., Mehta, D.J., and Gerner, E.W. 2003. Polyamine-dependent gene expression. Cell. Mol. Life Sci. 60: 1394-1406.
8. Coffino, P. 2001. Regulation of cellular polyamines by antizyme. Nat. Rev. Mol. Cell Biol. 2: 188-194.
9. Dietrich, F.S., Voegeli, S., Brachat, S., Lerch, A., Gates, K., Steiner, S., Mohr, C., Pohlmann, R., Luedi, P., Choi, S., et al. 2004. The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304: 304-307.
10. Farabaugh, P.J., Zhao, H., and Vimaladithan, A. 1993. A novel programmed frameshift expresses the POL3 gene of retrotransposon Ty3 of yeast: Frameshifting without tRNA slippage. Cell 74: 93-103.
11. Hansen, T.M., Baranov, T.M., Ivanov, I.P., Gesteland, R.F., and Atkins, J.F. 2003. Maintenance of the correct open reading frame by the ribosome. EMBO Rep. 4: 499-504.
12. Hayashi, S., Murakami, Y., and Matsufuji, S. 1996. Ornithine decarboxylase antizyme: A novel type of regulatory protein. Trends Biochem. Sci. 21: 27-30.
13. 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 expression of mammalian antizymes. Genes Cells 6: 931-941.
14. Ivanov, I.P., Gesteland, R.F., and Atkins, J.F. 1998a. A second mammalian antizyme: Conservation of programmed ribosomal frameshifting. Genomics 52: 119-129.
15. Ivanov, I.P., Gesteland, R.F., Matsufuji, S., and Atkins, J.F. 1998b. Programmed frameshifting in the synthesis of mammalian antizyme is +1 in mammals, predominantly +1 in fission yeast, but -2 in budding yeast. RNA 4: 1230-1238.
16. Ivanov, I.P., Gesteland, R.F., and Atkins, J.F. 2000a. Antizyme expression: A subversion of triplet decoding, which is remarkably conserved by evolution, is a sensor for an autoregulatory circuit. Nucleic Acids Res. 28: 3185-3196.
17. Ivanov, I.P., Matsufuji, S., Murakami, Y., Gesteland, R.F., and Atkins, J.F. 2000b. Conservation of polyamine regulation by translational frameshifting from yeast to mammals. EMBO J. 19: 1907-1917.
18. Ivanov, I.P., Rohrwasser, A., Terreros, D.A., Gesteland, R.F., and Atkins, J.F. 2000c. Discovery of a spermatogenesis stage-specific ornithine decarboxylase antizyme: Antizyme 3. Proc. Natl. Acad. Sci. 97: 4808-4813.
19. Ivanov, I.P., Gurvich, O.L., Gesteland, R.F., and Atkins, J.F. 2003. Recoding: Site- or mRNA-specific alteration of genetic readout utilized for gene expression. In Translation mechanisms (eds. J. Lapointe and L. Brakier-Gingras), pp. 354-369. Landes Bioscience, Austin, TX.
20. Ivanov, I.P., Anderson, C.B., Gesteland, R.F., and Atkins, J.F. 2004. Identification of a new antizyme mRNA +1 frameshifting stimulatory pseudoknot in a subset of diverse invertebrates and its apparent absence in intermediate species. J. Mol. Biol. 339: 495-504.
21. Jacobs, G.H., Rackham, O., Stockwell, P.A., Tate, W., and Brown, C.M. 2002. Transterm: A database of mRNAs and translational control elements. Nucleic Acids Res. 30: 310-311
22. Karamysheva, Z., Wang, L., Shrode, T., Bednenko, J., Hurley, L.A., and Shippen, D.E. 2003. Developmentally programmed gene elimination in Euplotes crassus facilitates a switch in the telomerase catalytic subunit. Cell 113: 565-576
23. Klobutcher, L.A. and Farabaugh, P.J. 2002. Shifty ciliates: Frequent programmed translational frameshifting in euplotids. Cell 111: 763-766.
24. Le Roy, F., Salehzada, T., Bisbal, C., Dougherty, J.P., and Peltz, S.W. 2005. A newly discovered function of RNase L in regulating translation termination. Nat. Struct. Mol. Biol. 12: 505-512.
25. Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25: 955-964.
26. 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.
27. Matsufuji, S., Matsufuji, T., Wills, N.M., Gesteland, R.F., and Atkins, J.F. 1996. Reading two bases twice: Mammalian antizyme frameshifting in yeast. EMBO J. 15: 1360-1370.
28. Murakami, Y., Matsufuji, S., Kameji, T., Hayashi, S., Igarashi, K., Tamur, T., Tanaka, K., and Ichihara, A. 1992. Ornithine decarboxylase is degraded by the 26S proteasome without ubiquitination. Nature 360: 597-599.
29. Namy, O., Hatin, I., and Rousset, J.-P. 2001. Impact of the six nucleotides downstream of the stop codon on translation termination. EMBO Rep. 2: 787-793.
30. Newman, R.M., Mobascher, A., Mangold, U., Koike, C., Diah, S., Schmidt, M., Finley, D., and Zetter, B.R. 2004. Antizyme targets cyclin D1 for degradation. J. Biol. Chem. 279: 41504-41511.
31. 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.
32. Pande, S., Vimaladithan, A., Zhao, H., and Farabaugh, P.J. 1995. Pulling the ribosome out of frame by +1 at a programmed frameshift site by cognate binding of aminoacyl-tRNA. Mol. Cell. Biol. 15: 298-304.
33. Petros, L.M., Howard, M.T., Gesteland, R.F., and Atkins, J.F. 2005. Polyamine sensing during antizyme mRNA programmed frameshifting. Biochem. Biophys. Res. Comm. 338: 1478-1489.
34. Sakata, K., Kashiwagi, K., and Igarashi, K. 2000. Properties of a polyamine transporter regulated by antizyme. Biochem. J. 347: 297-303.
35. Stahl, G., Ben Salem, S., Li, Z., McCarty, G., Raman, A., Shah, M., and Farabaugh, P.J. 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.
36. Stahl, G., Salem, S.N., Chen, L., Zhao, B., and Farabaugh, P.J. 2004. Translational accuracy during exponential, postdiauxic, and stationary growth phases in Saccharomyces cerevisiae. Eukaryot. Cell 3: 331-338.
37. 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.
38. Tate, W.P., Poole, E.S., Horsfield, J.A., Mannering, S.A., Brown, C.M., Moffat, J.G., Dalphin, M.E., McCaughan, K.K., Major, L.L., and Wilson, D.N. 1995. Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon. Biochem. Cell Biol. 73: 1095-1103.
39. Tosaka, Y., Tanaka, H., Yano, Y., Masai, K., Nozaki, M., Yomogida, K., Otani, S., Nojima, H., and Nishimune, Y. 2000. Identification and characterization of testis specific ornithine decarboxylase antizyme (OAZ-t) gene: Expression in haploid germ cells and polyamineinduced frameshifting. Genes Cells 5: 265-276.
40. Vied, C., Halachmi, N., Salzberg, A., and Horabin, J.I. 2003. Antizyme is a target of sex-lethal in the Drosophila germline and appears to act downstream of hedgehog to regulate sex-lethal and cyclin B. Dev. Biol. 253: 214-229.
41. Vimaladithan, A. and Farabaugh, P.J. 1994. Special peptidyl-tRNA molecules can promote translational frameshifting without slippage. Mol. Cell. Biol. 14: 8107-8116.
42. Wallace, H.M., Fraser, A.V., and Hughes, A. 2003 A perspective of polyamine metabolism. Biochem. J. 376: 1-14.
43. Weiss, R. and Gallant, J. 1983. Mechanism of ribosome frameshifting during translation of the genetic code. Nature 302: 389-393.
44. Weiss, R.B., Dunn, D.M., Atkins, J.F., and Gesteland, R.F. 1987. Slippery runs, shifty stops, backward steps, and forward hops: -2, -1, +1, +2, +5, and +6 ribosomal frameshifting. Cold Spring Harbor Symp. Quant. Biol. 52: 687-693.
45. Weiss, R.B., Dunn, D.M., Atkins, J.F., and Gesteland, R.F. 1990. Ribosomal frameshifting from -2 to +50 nucleotides. Prog. Nucleic Acids Res. Mol. Biol. 39: 159-183.
46. Xu, J., Hendrix, R.W., and Duda, R.L. 2004. Conserved translational frameshift in dsDNA bacteriophage tail assembly genes. Mol. Cell 16: 11-21.
47. Zhang, M., Pickart, C.M., and Coffino, P. 2003. Determinants of proteasome recognition on ornithine decarboxylase, a ubiquitin independent substrate. EMBO J. 22: 1488-1496.
48. Zhang, J., Wang, Y., Zhou, Y., Cao, Z., Huang, P., and Lu, B. 2005. Yeast two-hybrid screens imply that GGNBP1, GGNBP2 and OAZ3 are potential interaction partners of testicular germ cell-specific protein GGN1. FEBS Lett. 579: 559-566.