title: A single acetylation of 18 S rRNA is essential for biogenesis of the small ribosomal subunit in Saccharomyces cerevisiae.
abstract: Biogenesis of eukaryotic ribosome is a complex event involving a number of non-ribosomal factors. During assembly of the ribosome, rRNAs are post-transcriptionally modified by 2'-O-methylation, pseudouridylation, and several base-specific modifications, which are collectively involved in fine-tuning translational fidelity and/or modulating ribosome assembly. By mass-spectrometric analysis, we demonstrated that N(4)-acetylcytidine (ac(4)C) is present at position 1773 in the 18 S rRNA of Saccharomyces cerevisiae. In addition, we found an essential gene, KRE33 (human homolog, NAT10), that we renamed RRA1 (ribosomal RNA cytidine acetyltransferase 1) encoding an RNA acetyltransferase responsible for ac(4)C1773 formation. Using recombinant Rra1p, we could successfully reconstitute ac(4)C1773 in a model rRNA fragment in the presence of both acetyl-CoA and ATP as substrates. Upon depletion of Rra1p, the 23 S precursor of 18 S rRNA was accumulated significantly, which resulted in complete loss of 18 S rRNA and small ribosomal subunit (40 S), suggesting that ac(4)C1773 formation catalyzed by Rra1p plays a critical role in processing of the 23 S precursor to yield 18 S rRNA. When nuclear acetyl-CoA was depleted by inactivation of acetyl-CoA synthetase 2 (ACS2), we observed temporal accumulation of the 23 S precursor, indicating that Rra1p modulates biogenesis of 40 S subunit by sensing nuclear acetyl-CoA concentration.
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ito
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Yu
authors.initials: Y
authors.lastname: Akamatsu
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Akiko
authors.initials: A
authors.lastname: Noma
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Kimura
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Kenjyo
authors.initials: K
authors.lastname: Miyauchi
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Yoshiho
authors.initials: Y
authors.lastname: Ikeuchi
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
authors.forename: Takeo
authors.initials: T
authors.lastname: Suzuki
authors.affiliation: Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan. Electronic address: ts@chembio.t.u-tokyo.ac.jp.
authors.forename: Tsutomu
authors.initials: T
authors.lastname: Suzuki
mesh_terms: D000105:Acetyl Coenzyme A / Q000378:metabolism; D000107:Acetylation; D000123:Acetyltransferases / Q000502:physiology*; D001483:Base Sequence; D002467:Cell Nucleus / Q000378:metabolism; D008969:Molecular Sequence Data; D012323:RNA Processing, Post-Transcriptional; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism; D012337:RNA, Ribosomal, 18S / Q000235:genetics / Q000378:metabolism*; D012338:RNA, Ribosomal, 23S / Q000235:genetics / Q000378:metabolism; D054679:Ribosome Subunits, Small / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism* / Q000502:physiology; D013379:Substrate Specificity
chemical_list: D012331:RNA, Fungal; D012337:RNA, Ribosomal, 18S; D012338:RNA, Ribosomal, 23S; D029701:Saccharomyces cerevisiae Proteins; D000105:Acetyl Coenzyme A; D000123:Acetyltransferases; C000594846:RRA1 protein, S cerevisiae
keywords: Acetyl Coenzyme A (Acetyl-CoA); Acetyltransferase; RNA Modification; Ribosomal RNA Processing (rRNA Processing); Ribosome Assembly
references.citation: EMBO Rep. 2002 Jan;3(1):34-8
references.pmid: 11751581
references.citation: Mol Cell. 2006 Jul 21;23(2):207-17
references.pmid: 16857587
references.citation: Genes Dev. 1995 Oct 15;9(20):2470-81
references.pmid: 7590228
references.citation: Methods Enzymol. 2007;425:211-29
references.pmid: 17673085
references.citation: Am J Hum Genet. 2009 Jun;84(6):728-39
references.pmid: 19463982
references.citation: Dev Biol. 2010 Aug 15;344(2):1011-25
references.pmid: 20599896
references.citation: Cell Mol Life Sci. 2008 Aug;65(15):2334-59
references.pmid: 18408888
references.citation: J Am Soc Mass Spectrom. 1992 Jan;3(1):60-70
references.pmid: 24242838
references.citation: EMBO J. 2008 Aug 20;27(16):2194-203
references.pmid: 18668122
references.citation: Nat Chem Biol. 2013 Feb;9(2):105-11
references.pmid: 23242255
references.citation: Nature. 2003 Oct 16;425(6959):686-91
references.pmid: 14562095
references.citation: Mol Cell Biol. 2008 May;28(10):3151-61
references.pmid: 18332120
references.citation: EMBO Mol Med. 2013 Jul;5(7):1051-66
references.pmid: 23666744
references.citation: Sci STKE. 2004 Mar 02;2004(223):PL8
references.pmid: 15010550
references.citation: Nucleic Acids Res. 2010 Apr;38(7):2387-98
references.pmid: 20047967
references.citation: RNA. 2009 Dec;15(12):2083-104
references.pmid: 19850913
references.citation: PLoS Biol. 2009 Oct;7(10):e1000213
references.pmid: 19806183
references.citation: J Biol Chem. 1978 Feb 25;253(4):1101-5
references.pmid: 624721
references.citation: RNA. 2011 Dec;17(12):2235-48
references.pmid: 22028364
references.citation: Gene. 2003 Aug 14;313:17-42
references.pmid: 12957375
references.citation: Mol Cell. 2011 May 20;42(4):426-37
references.pmid: 21596309
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D178-83
references.pmid: 17947322
references.citation: Nucleic Acids Res. 2013 Jan;41(Database issue):D262-7
references.pmid: 23118484
references.citation: Curr Genet. 2002 Feb;40(5):326-38
references.pmid: 11935223
references.citation: Cell Mol Life Sci. 2004 Aug;61(16):2020-30
references.pmid: 15316652
references.citation: Mol Cell Biol. 2007 Aug;27(15):5414-29
references.pmid: 17515605
references.citation: Exp Cell Res. 2009 Jun 10;315(10):1653-67
references.pmid: 19303003
references.citation: Proc Natl Acad Sci U S A. 1988 Feb;85(4):1033-7
references.pmid: 3277187
references.citation: Nucleic Acids Res. 2007;35(5):1452-64
references.pmid: 17284456
references.citation: Exp Cell Res. 2004 May 15;296(1):43-50
references.pmid: 15120992
references.citation: EMBO J. 1991 Dec;10(13):4231-9
references.pmid: 1756730
references.citation: FASEB J. 1993 Jan;7(1):196-200
references.pmid: 8422966
references.citation: Gene. 1995 Aug 8;161(1):75-9
references.pmid: 7642141
references.citation: Mol Cell. 2002 Jul;10(1):105-15
references.pmid: 12150911
references.citation: Annu Rev Genet. 1999;33:261-311
references.pmid: 10690410
references.citation: Nat Rev Mol Cell Biol. 2005 Apr;6(4):318-27
references.pmid: 15803138
references.citation: Nucleic Acids Res. 2007;35(4):e24
references.pmid: 17251194
references.citation: RNA. 2002 Jul;8(7):948-58
references.pmid: 12166649
references.citation: J Bacteriol. 1998 Jun;180(11):2883-8
references.pmid: 9603876
references.citation: Biochem J. 1978 Jan 1;169(1):71-7
references.pmid: 629754
references.citation: Genetics. 2003 Mar;163(3):875-94
references.pmid: 12663529
references.citation: EMBO J. 2009 May 6;28(9):1362-73
references.pmid: 19322199
references.citation: Yeast. 1996 Dec;12(16):1607-33
references.pmid: 9123965
references.citation: Trends Biochem Sci. 1999 Nov;24(11):437-40
references.pmid: 10542411
references.citation: Biochem Biophys Res Commun. 2003 Nov 14;311(2):506-13
references.pmid: 14592445
references.citation: Genetics. 2013 Nov;195(3):643-81
references.pmid: 24190922
references.citation: Biochem Biophys Res Commun. 2012 May 25;422(1):1-4
references.pmid: 22575446
references.citation: Science. 2014 May 2;344(6183):527-32
references.pmid: 24786082
references.citation: Nat Protoc. 2006;1(2):581-5
references.pmid: 17406285
references.citation: J Biol Chem. 1984 Aug 10;259(15):9461-71
references.pmid: 6746655
references.citation: Biochimie. 2012 Jul;94(7):1521-32
references.pmid: 22342225
references.citation: Mol Cell. 2010 Mar 26;37(6):809-20
references.pmid: 20347423
references.citation: Microbiol Mol Biol Rev. 1998 Dec;62(4):1492-553
references.pmid: 9841679