Home LiteratureArticle Details
PMID: 23439679 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Both endonucleolytic and exonucleolytic cleavage mediate ITS1 removal during human ribosomal RNA processing.

The Journal of cell biology ·Vol. 200 ·No. 5 ·2013-03-04 ·Pages 577-88

Sloan KE, Mattijssen S, Lebaron S, Tollervey D, Pruijn GJ, Watkins NJ

Abstract

Human ribosome production is up-regulated during tumorogenesis and is defective in many genetic diseases (ribosomopathies). We have undertaken a detailed analysis of human precursor ribosomal RNA (pre-rRNA) processing because surprisingly little is known about this important pathway. Processing in internal transcribed spacer 1 (ITS1) is a key step that separates the rRNA components of the large and small ribosomal subunits. We report that this was initiated by endonuclease cleavage, which required large subunit biogenesis factors. This was followed by 3' to 5' exonucleolytic processing by RRP6 and the exosome, an enzyme complex not previously linked to ITS1 removal. In contrast, RNA interference-mediated knockdown of the endoribonuclease MRP did not result in a clear defect in ITS1 processing. Despite the apparently high evolutionary conservation of the pre-rRNA processing pathway and ribosome synthesis factors, each of these features of human ITS1 processing is distinct from those in budding yeast. These results also provide significant insight into the links between ribosomopathies and ribosome production in human cells.

MeSH Terms
Endoribonucleases/genetics,metabolism Exoribonucleases/genetics,metabolism Exosome Multienzyme Ribonuclease Complex/genetics,metabolism HEK293 Cells HeLa Cells Humans Proteins/metabolism RNA Interference RNA Precursors/metabolism RNA Processing, Post-Transcriptional RNA, Fungal/metabolism RNA, Ribosomal/metabolism RNA, Ribosomal, 18S/metabolism RNA-Binding Proteins/metabolism Ribosomes/metabolism Saccharomyces cerevisiae/genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism Transfection
Chemicals
BOP1 protein, human Proteins RBM28 protein, human RNA Precursors RNA, Fungal RNA, Ribosomal RNA, Ribosomal, 18S RNA-Binding Proteins Saccharomyces cerevisiae Proteins Endoribonucleases Exoribonucleases Exosome Multienzyme Ribonuclease Complex mitochondrial RNA-processing endoribonuclease EXOSC10 protein, human
Authors & Affiliations
6 authors, click to expand affiliations / ORCID
Sloan Katherine E
Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, England, UK.
Mattijssen Sandy
Lebaron Simon
Tollervey David
Pruijn Ger J M
Watkins Nicholas J
References (41)
41 references, click to expand
  1. Analysis of two human pre-ribosomal factors, bystin and hTsr1, highlights differences in evolution of ribosome biogenesis between yeast and mammals.
    Nucleic Acids Res. 2011 Jan;39(1):280-91 PMID: 20805244
  2. The human core exosome interacts with differentially localized processive RNases: hDIS3 and hDIS3L.
    EMBO J. 2010 Jul 21;29(14):2342-57 PMID: 20531386
  3. Mutations in the RNA exosome component gene EXOSC3 cause pontocerebellar hypoplasia and spinal motor neuron degeneration.
    Nat Genet. 2012 Apr 29;44(6):704-8 PMID: 22544365
  4. Guarding the 'translation apparatus': defective ribosome biogenesis and the p53 signaling pathway.
    Wiley Interdiscip Rev RNA. 2011 Jul-Aug;2(4):507-22 PMID: 21957040
  5. Nuclear export and cytoplasmic processing of precursors to the 40S ribosomal subunits in mammalian cells.
    EMBO J. 2005 Aug 17;24(16):2862-72 PMID: 16037817
  6. Whole-exome re-sequencing in a family quartet identifies POP1 mutations as the cause of a novel skeletal dysplasia.
    PLoS Genet. 2011 Mar;7(3):e1002027 PMID: 21455487
  7. The ARF tumor suppressor controls ribosome biogenesis by regulating the RNA polymerase I transcription factor TTF-I.
    Mol Cell. 2010 May 28;38(4):539-50 PMID: 20513429
  8. Depletion of key protein components of the RISC pathway impairs pre-ribosomal RNA processing.
    Nucleic Acids Res. 2011 Jun;39(11):4875-89 PMID: 21321021
  9. Mapping the cleavage sites on mammalian pre-rRNAs: where do we stand?
    Biochimie. 2012 Jul;94(7):1521-32 PMID: 22342225
  10. An RNA conformational switch regulates pre-18S rRNA cleavage.
    J Mol Biol. 2011 Jan 7;405(1):3-17 PMID: 20934433
  11. Nucleolar Arf tumor suppressor inhibits ribosomal RNA processing.
    Mol Cell. 2003 Feb;11(2):415-24 PMID: 12620229
  12. In vivo disruption of Xenopus U3 snRNA affects ribosomal RNA processing.
    EMBO J. 1990 Jul;9(7):2299-308 PMID: 2357971
  13. 5'-end surveillance by Xrn2 acts as a shared mechanism for mammalian pre-rRNA maturation and decay.
    Nucleic Acids Res. 2011 Mar;39(5):1811-22 PMID: 21036871
  14. The yeast NOP4 gene product is an essential nucleolar protein required for pre-rRNA processing and accumulation of 60S ribosomal subunits.
    EMBO J. 1994 Jul 1;13(13):3127-35 PMID: 8039505
  15. Processing of the yeast pre-rRNA at sites A(2) and A(3) is linked.
    RNA. 1996 Jan;2(1):63-73 PMID: 8846297
  16. Degradation of ribosomal RNA precursors by the exosome.
    Nucleic Acids Res. 2000 Apr 15;28(8):1684-91 PMID: 10734186
  17. Alterations in the intracellular level of a protein subunit of human RNase P affect processing of tRNA precursors.
    Nucleic Acids Res. 2003 Aug 15;31(16):4836-46 PMID: 12907726
  18. Assembly of Saccharomyces cerevisiae 60S ribosomal subunits: role of factors required for 27S pre-rRNA processing.
    EMBO J. 2011 Sep 16;30(19):4020-32 PMID: 21926967
  19. A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease.
    EMBO J. 2011 Aug 02;30(19):4006-19 PMID: 21811236
  20. Synthetic lethality with fibrillarin identifies NOP77p, a nucleolar protein required for pre-rRNA processing and modification.
    EMBO J. 1994 Jul 1;13(13):3136-48 PMID: 8039506
  21. Disruption of U8 nucleolar snRNA inhibits 5.8S and 28S rRNA processing in the Xenopus oocyte.
    Cell. 1993 Jun 18;73(6):1233-45 PMID: 8513505
  22. RRP5 is required for formation of both 18S and 5.8S rRNA in yeast.
    EMBO J. 1996 Oct 15;15(20):5701-14 PMID: 8896463
  23. Processing of the precursors to small nucleolar RNAs and rRNAs requires common components.
    Mol Cell Biol. 1998 Mar;18(3):1181-9 PMID: 9488433
  24. The small subunit processome in ribosome biogenesis—progress and prospects.
    Wiley Interdiscip Rev RNA. 2011 Jan-Feb;2(1):1-21 PMID: 21318072
  25. A weak C' box renders U3 snoRNA levels dependent on hU3-55K binding.
    Mol Cell Biol. 2011 Jun;31(12):2404-12 PMID: 21505065
  26. Rcl1 protein, a novel nuclease for 18 S ribosomal RNA production.
    J Biol Chem. 2011 Sep 30;286(39):34082-7 PMID: 21849504
  27. Accurate processing of a eukaryotic precursor ribosomal RNA by ribonuclease MRP in vitro.
    Science. 1996 Apr 12;272(5259):268-70 PMID: 8602511
  28. A novel small-subunit processome assembly intermediate that contains the U3 snoRNP, nucleolin, RRP5, and DBP4.
    Mol Cell Biol. 2009 Jun;29(11):3007-17 PMID: 19332556
  29. C1D and hMtr4p associate with the human exosome subunit PM/Scl-100 and are involved in pre-rRNA processing.
    Nucleic Acids Res. 2007;35(8):2564-72 PMID: 17412707
  30. The post-transcriptional steps of eukaryotic ribosome biogenesis.
    Cell Mol Life Sci. 2008 Aug;65(15):2334-59 PMID: 18408888
  31. ERB1, the yeast homolog of mammalian Bop1, is an essential gene required for maturation of the 25S and 5.8S ribosomal RNAs.
    Nucleic Acids Res. 2001 Sep 1;29(17):3621-30 PMID: 11522832
  32. Rrp17p is a eukaryotic exonuclease required for 5' end processing of Pre-60S ribosomal RNA.
    Mol Cell. 2009 Dec 11;36(5):768-81 PMID: 20005841
  33. Mutations in the RNA component of RNase MRP cause a pleiotropic human disease, cartilage-hair hypoplasia.
    Cell. 2001 Jan 26;104(2):195-203 PMID: 11207361
  34. Nuclear RNase MRP is required for correct processing of pre-5.8S rRNA in Saccharomyces cerevisiae.
    Mol Cell Biol. 1993 Dec;13(12):7935-41 PMID: 8247008
  35. Alopecia, neurological defects, and endocrinopathy syndrome caused by decreased expression of RBM28, a nucleolar protein associated with ribosome biogenesis.
    Am J Hum Genet. 2008 May;82(5):1114-21 PMID: 18439547
  36. The eukaryotic RNA exosome: same scaffold but variable catalytic subunits.
    RNA Biol. 2011 Jan-Feb;8(1):61-6 PMID: 21289487
  37. The economics of ribosome biosynthesis in yeast.
    Trends Biochem Sci. 1999 Nov;24(11):437-40 PMID: 10542411
  38. Ribosomopathies: human disorders of ribosome dysfunction.
    Blood. 2010 Apr 22;115(16):3196-205 PMID: 20194897
  39. Viperin mRNA is a novel target for the human RNase MRP/RNase P endoribonuclease.
    Cell Mol Life Sci. 2011 Jul;68(14):2469-80 PMID: 21053045
  40. Yeast pre-rRNA processing and modification occur cotranscriptionally.
    Mol Cell. 2010 Mar 26;37(6):809-20 PMID: 20347423
  41. RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18 S rRNA processing catalyzed by the endonuclease Nob1.
    J Biol Chem. 2009 Dec 11;284(50):35079-91 PMID: 19801658
Article Info
Journal
The Journal of cell biology
Abbr.
J Cell Biol
ISSN
1540-8140
DOI
10.1083/jcb.201207131
Published
2013-03-04
Epub
2013-00-25
Pages
577-88
Language
English
Region
United States
NLM ID
0375356
PMCID
PMC3587827
Subset
IM
Grants
Wellcome Trust · United Kingdom
Wellcome Trust · 077248 · United Kingdom
Wellcome Trust · 092076 · United Kingdom
Biotechnology and Biological Sciences Research Council · United Kingdom
External Links
PubMed source DOI: 10.1083/jcb.201207131 PMC Full Text View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2