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A New Yeast Poly(A) Polymerase Complex Involved in RNA Quality Control
Open accessAbstract
Eukaryotic cells contain several unconventional poly(A) polymerases in addition to the canonical enzymes responsible for the synthesis of poly(A) tails of nuclear messenger RNA precursors. The yeast protein Trf4p has been implicated in a quality control pathway that leads to the polyadenylation and subsequent exosome-mediated degradation of hypomethylated initiator tRNAMet (tRNAiMet). Here we show that Trf4p is the catalytic subunit of a new poly(A) polymerase complex that contains Air1p or Air2p as potential RNA-binding subunits, as well as the putative RNA helicase Mtr4p. Comparison of native tRNAiMet with its in vitro transcribed unmodified counterpart revealed that the unmodified RNA was preferentially polyadenylated by affinity-purified Trf4 complex from yeast, as well as by complexes reconstituted from recombinant components. These results and additional experiments with other tRNA substrates suggested that the Trf4 complex can discriminate between native tRNAs and molecules that are incorrectly folded. Moreover, the polyadenylation activity of the Trf4 complex stimulated the degradation of unmodified tRNAiMet by nuclear exosome fractions in vitro. Degradation was most efficient when coupled to the polyadenylation activity of the Trf4 complex, indicating that the poly(A) tails serve as signals for the recruitment of the exosome. This polyadenylation-mediated RNA surveillance resembles the role of polyadenylation in bacterial RNA turnover.
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Citations
Cites
Analytical Properties of the Nanoelectrospray Ion Source
Wilm, M., & Mann, M. (1996) · Analytical Chemistry · doi:10.1021/ac9509519 · Cited by 1,868
The Tandem Affinity Purification (TAP) Method: A General Procedure of Protein Complex Purification
Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M., & Séraphin, B. (2001) · Methods · doi:10.1006/meth.2001.1183 · Cited by 1,783
The protein–protein interaction map of Helicobacter pylori
Rain, J.-C., Selig, L., De Reuse, H., Battaglia, V., Reverdy, C., Simon, S., Lenzen, G., Petel, F., Wojcik, J., Schächter, V., et al. (2001) · Nature · doi:10.1038/35051615 · Cited by 1,146
Zhao, J., Hyman, L., & Moore, C. (1999) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.63.2.405-445.1999 · Cited by 1,033
Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M., & Tollervey, D. (1997) · Cell · doi:10.1016/s0092-8674(00)80432-8 · Cited by 954
Toward a functional analysis of the yeast genome through exhaustive two-hybrid screens
Fromont-Racine, M., Rain, J.-C., & Legrain, P. (1997) · Nature Genetics · doi:10.1038/ng0797-277 · Cited by 908
The enzymes and control of eukaryotic mRNA turnover
Parker, R., & Song, H. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb724 · Cited by 730
Nuclear surveillance and degradation of hypomodified initiator tRNA Met in S. cerevisiae
Kadaba, S., Krueger, A., Trice, T., Krecic, A. M., Hinnebusch, A. G., & Anderson, J. (2004) · Genes & Development · doi:10.1101/gad.1183804 · Cited by 486
van Hoof, A., Lennertz, P., & Parker, R. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.2.441-452.2000 · Cited by 359
Amarasinghe, G. K., De Guzman, R. N., Turner, R. B., Chancellor, K. J., Wu, Z. R., & Summers, M. F. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3979 · Cited by 345
Isolation and characterization of pre-mRNA splicing mutants of Saccharomyces cerevisiae.
Vijayraghavan, U., Company, M., & Abelson, J. (1989) · Genes & Development · doi:10.1101/gad.3.8.1206 · Cited by 331
Aravind, L. (1999) · Nucleic Acids Research · doi:10.1093/nar/27.7.1609 · Cited by 322
de la Cruz, J. (1998) · The EMBO Journal · doi:10.1093/emboj/17.4.1128 · Cited by 321
3′-End processing of pre-mRNA in eukaryotes
Wahle, E., & Rüegsegger, U. (1999) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.1999.tb00400.x · Cited by 293
A regulatory cytoplasmic poly(A) polymerase in Caenorhabditis elegans
Wang, L., Eckmann, C. R., Kadyk, L. C., Wickens, M., & Kimble, J. (2002) · Nature · doi:10.1038/nature01039 · Cited by 293
New perspectives on connecting messenger RNA 3′ end formation to transcription
Proudfoot, N. (2004) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2004.03.007 · Cited by 285
Anderson, J., Phan, L., Cuesta, R., Carlson, B. A., Pak, M., Asano, K., Björk, G. R., Tamame, M., & Hinnebusch, A. G. (1998) · Genes & Development · doi:10.1101/gad.12.23.3650 · Cited by 281
DNA polymerase β belongs to an ancient nucleotidyltransferase superfamily
Holm, L. (1995) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(00)89071-4 · Cited by 257
Polyadenylylation helps regulate mRNA decay in Escherichia coli.
O'Hara, E. B., Chekanova, J. A., Ingle, C. A., Kushner, Z. R., Peters, E., & Kushner, S. R. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.6.1807 · Cited by 256
An Important Role for RNase R in mRNA Decay
Cheng, Z.-F., & Deutscher, M. P. (2005) · Molecular Cell · doi:10.1016/j.molcel.2004.11.048 · Cited by 246
Dreyfus, M., & Régnier, P. (2002) · Cell · doi:10.1016/s0092-8674(02)01137-6 · Cited by 237
mRNA Decay in Escherichia coli Comes of Age
Kushner, S. R. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.17.4658-4665.2002 · Cited by 224
Basavappa, R., & Sigler, P. B. (1991) · The EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07864.x · Cited by 216
Fountoulakis, M., & Langen, H. (1997) · Analytical Biochemistry · doi:10.1006/abio.1997.2213 · Cited by 216
Self-citationDannull, J., Surovoy, A., Jung, G., & Moelling, K. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06414.x · Cited by 207
A history of poly A sequences: from formation to factors to function
(2002) · Progress in Nucleic Acid Research and Molecular Biology · doi:10.1016/s0079-6603(02)71046-5 · Cited by 194
Martin, G., & Keller, W. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00617.x · Cited by 190
Self-citationPol κ: A DNA Polymerase Required for Sister Chromatid Cohesion
Wang, Z., Castaño, I. B., De Las Peñas, A., Adams, C., & Christman, M. F. (2000) · Science · doi:10.1126/science.289.5480.774 · Cited by 186
mRNA polyadenylation and its coupling to other RNA processing reactions and to transcription
Minvielle-Sebastia, L., & Keller, W. (1999) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(99)80049-0 · Cited by 177
Self-citationFunctional Domains of the Rsp5 Ubiquitin-Protein Ligase
Wang, G., Yang, J., & Huibregtse, J. M. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.1.342 · Cited by 173
A Role for SSU72 in Balancing RNA Polymerase II Transcription Elongation and Termination
Dichtl, B., Blank, D., Ohnacker, M., Friedlein, A., Roeder, D., Langen, H., & Keller, W. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00707-4 · Cited by 168
Self-citationRunning rings around RNA: a superfamily of phosphate-dependent RNases.
Symmons, M., Williams, M. G., Luisi, B., Jones, G. H., & Carpousis, A. (2002) · TIBS -Trends in Biochemical Sciences. Regular ed · doi:10.1016/s0968-0004(01)01999-5 · Cited by 168
Processing of 3′-Extended Read-Through Transcripts by the Exosome Can Generate Functional mRNAs
Torchet, C., Bousquet-Antonelli, C., Milligan, L., Thompson, E., Kufel, J., & Tollervey, D. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00544-0 · Cited by 163
Crystal structure of mammalian poly(A) polymerase in complex with an analog of ATP
Martin, G., Keller, W., & Doublié, S. (2000) · The EMBO Journal · doi:10.1093/emboj/19.16.4193 · Cited by 153
Self-citationPolyadenylation of rRNA in Saccharomyces cerevisiae
Kuai, L., Fang, F., Butler, J. S., & Sherman, F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0402888101 · Cited by 149
Gerber, A. P., Grosjean, H., Melcher, T., & Keller, W. (1998) · The EMBO Journal · doi:10.1093/emboj/17.16.4780 · Cited by 148
Self-citationMusing on the structural organization of the exosome complex.
Mitchell, P., & Tollervey, D. W. (2000) · Nature Structural Biology · doi:10.1038/82817 · Cited by 136
Mammalian GLD-2 homologs are poly(A) polymerases
Kwak, J. E., Wang, L., Ballantyne, S. M., Kimble, J. E., & Wickens, M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400779101 · Cited by 136
Cid13 Is a Cytoplasmic Poly(A) Polymerase that Regulates Ribonucleotide Reductase mRNA
Saitoh, S., Chabes, A., McDonald, W. H., Thelander, L., Yates, J. R., & Russell, P. R. (2002) · Cell · doi:10.1016/s0092-8674(02)00753-5 · Cited by 132
Primary, Secondary, and Tertiary Structures of tRNAs
Dirheimer, G., Keith, G., Dumas, P., & Westhof, É. (2014) · ASM Press eBooks · doi:10.1128/9781555818333.ch8 · Cited by 129
Self-citationStructure of Yeast Poly(A) Polymerase Alone and in Complex with 3'-dATP
Bard, J., Zhelkovsky, A. M., Helmling, S., Earnest, T. N., Moore, C. L., & Bohm, A. (2000) · Science · doi:10.1126/science.289.5483.1346 · Cited by 117
Ohnacker, M., Barabino, S. M. L., Preker, P., & Keller, W. (2000) · The EMBO Journal · doi:10.1093/emboj/19.1.37 · Cited by 116
Self-citationChristofori, G., & Keller, W. (1989) · Molecular and Cellular Biology · doi:10.1128/mcb.9.1.193 · Cited by 110
Self-citationCytoplasmic poly(A) polymerases mediate cellular responses to S phase arrest
Read, R. L., Martinho, R. G., Wang, S.-W., Carr, A. M., & Norbury, C. J. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.192467799 · Cited by 102
Regulation of the mitosis/meiosis decision in the Caenorhabditis elegans germline
Crittenden, S. L., Eckmann, C. R., Wang, L., Bernstein, D. S., Wickens, M., & Kimble, J. E. (2003) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2003.1333 · Cited by 96
Preker, P., Ohnacker, M., Minvielle-Sébastia, L., et al. (1997) · The EMBO Journal · doi:10.1093/emboj/16.15.4727 · Cited by 91
Purification and characterization of poly(A) polymerase from Saccharomyces cerevisiae
Lingner, J., Radtke, I., Wahle, E., & Keller, W. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)31508-4 · Cited by 84
Self-citationRecognition of polyadenylation sites in yeast pre‐mRNAs by cleavage and polyadenylation factor
Dichtl, B., & Keller, W. (2001) · The EMBO Journal · doi:10.1093/emboj/20.12.3197 · Cited by 83
Self-citationCastaño, I., Heath‐Pagliuso, S., Sadoff, B. U., Fitzhugh, D. J., & Christman, M. F. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.12.2404 · Cited by 77
Primary structure of three tRNAs from brewer's yeast: tRNAPro2, tRNAHis1 and tRNAHis2
Keith, G., Pixa, G., Fix, C., & Dirheimer, G. (1984) · Biochimie · doi:10.1016/s0300-9084(84)80030-9 · Cited by 55
Self-citationInoue, K., Mizuno, T., Wada, K., & Hagiwara, M. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m004560200 · Cited by 55
MARTIN, G., & KELLER, W. (2004) · RNA · doi:10.1261/rna.5242304 · Cited by 50
Self-citationMartin, G., Möglich, A., Keller, W., & Doublié, S. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.047 · Cited by 49
Self-citationStructure/Function Analysis of the Saccharomyces cerevisiae Trf4/Pol σ DNA Polymerase
Wang, Z., Castaño, I., Adams, C., Vu, C., Fitzhugh, D. J., & Christman, M. F. (2002) · Genetics · doi:10.1093/genetics/160.2.381 · Cited by 33
Senger, B., Aphasizhev, R., Walter, P., & Fasiolo, F. (1995) · Journal of Molecular Biology · doi:10.1006/jmbi.1995.0279 · Cited by 23
Keller, W., & Martin, G. (2002) · Nature · doi:10.1038/419267a · Cited by 13
Self-citation
Cited by
The highways and byways of mRNA decay
Garneau, N. L., Wilusz, J., & Wilusz, C. J. (2007) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2104 · Cited by 1,294
RNA Quality Control in Eukaryotes
Doma, M. K., & Parker, R. (2007) · Cell · doi:10.1016/j.cell.2007.10.041 · Cited by 345
Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts
Meola, N., Domanski, M., Karadoulama, E., Chen, Y., Gentil, C., Pultz, D., Vitting-Seerup, K., Lykke-Andersen, S., Andersen, J. S., Sandelin, A., et al. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.09.025 · Cited by 290
Extensive Degradation of RNA Precursors by the Exosome in Wild-Type Cells
Gudipati, R. K., Xu, Z., Lebreton, A., Séraphin, B., Steinmetz, L. M., Jacquier, A., & Libri, D. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.08.018 · Cited by 236
The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex
Halbach, F., Reichelt, P., Rode, M., & Conti, E. (2013) · Cell · doi:10.1016/j.cell.2013.07.017 · Cited by 210
Metadata
- Authors
- Vaňáčová, Š., Wolf, J., Martin, G., Blank, D., Dettwiler, S., Friedlein, A., Langen, H., Keith, G., & Keller, W.
- Venue
- PLoS Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2005-04-19
- Volume
- 3
- Issue
- 6
- Pages
- e189
- ISSN
- 1544-9173 (ISSN-L)
- 1545-7885
- OpenAlex
- W2032501207
- Cited by
- 567
- References
- 56
- FWCI
- 17.63
- Type
- journal article
- Language
- en
- Open access
- gold
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