Home LiteratureArticle Details
PMID: 17429074 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Analysis of P-body assembly in Saccharomyces cerevisiae.

Molecular biology of the cell ·Vol. 18 ·No. 6 ·2007-06-00 ·Pages 2274-87

Teixeira D, Parker R

Abstract

Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), that contain untranslating mRNAs in conjunction with proteins involved in translation repression and mRNA decapping and degradation. However, the order of protein assembly into P-bodies and the interactions that promote P-body assembly are unknown. To gain insight into how yeast P-bodies assemble, we examined the P-body accumulation of Dcp1p, Dcp2p, Edc3p, Dhh1p, Pat1p, Lsm1p, Xrn1p, Ccr4p, and Pop2p in deletion mutants lacking one or more P-body component. These experiments revealed that Dcp2p and Pat1p are required for recruitment of Dcp1p and of the Lsm1-7p complex to P-bodies, respectively. We also demonstrate that P-body assembly is redundant and no single known component of P-bodies is required for P-body assembly, although both Dcp2p and Pat1p contribute to P-body assembly. In addition, our results indicate that Pat1p can be a nuclear-cytoplasmic shuttling protein and acts early in P-body assembly. In contrast, the Lsm1-7p complex appears to primarily function in a rate limiting step after P-body assembly in triggering decapping. Taken together, these results provide insight both into the function of individual proteins involved in mRNA degradation and the mechanisms by which yeast P-bodies assemble.

MeSH Terms
Cytoplasmic Granules/metabolism DEAD-box RNA Helicases/genetics,metabolism DNA-Binding Proteins/genetics,metabolism Endoribonucleases/genetics,metabolism Protein Biosynthesis RNA Cap-Binding Proteins RNA Caps/metabolism RNA, Messenger/metabolism RNA-Binding Proteins/genetics,metabolism Ribonucleases/genetics,metabolism Saccharomyces cerevisiae/cytology,genetics,metabolism Saccharomyces cerevisiae Proteins/genetics,metabolism
Chemicals
DNA-Binding Proteins LSM1 protein, S cerevisiae PAT1 protein, S cerevisiae RNA Cap-Binding Proteins RNA Caps RNA, Messenger RNA-Binding Proteins Saccharomyces cerevisiae Proteins CCR4 protein, S cerevisiae DCP2 protein, S cerevisiae Endoribonucleases Ribonucleases POP2 protein, S cerevisiae DHH1 protein, S cerevisiae DEAD-box RNA Helicases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Teixeira Daniela
Department of Molecular and Cellular Biology and Howard Hughes Medical Institute, University of Arizona, Tucson, AZ 85721-0106, USA.
Parker Roy
References (63)
63 references, click to expand
  1. Cytoplasmic foci are sites of mRNA decay in human cells.
    J Cell Biol. 2004 Apr12;165(1):31-40 PMID: 15067023
  2. Loss of translational control in yeast compromised for the major mRNA decay pathway.
    Mol Cell Biol. 2004 Apr;24(7):2998-3010 PMID: 15024087
  3. A complex containing the CCR4 and CAF1 proteins is involved in mRNA deadenylation in Drosophila.
    EMBO J. 2004 Jul 21;23(14):2862-71 PMID: 15215893
  4. Differential effects of translational inhibition in cis and in trans on the decay of the unstable yeast MFA2 mRNA.
    J Biol Chem. 1994 Apr 1;269(13):9687-92 PMID: 8144558
  5. An essential component of the decapping enzyme required for normal rates of mRNA turnover.
    Nature. 1996 Aug 15;382(6592):642-6 PMID: 8757137
  6. Mutations in trans-acting factors affecting mRNA decapping in Saccharomyces cerevisiae.
    Mol Cell Biol. 1996 Oct;16(10):5830-8 PMID: 8816497
  7. A mouse cytoplasmic exoribonuclease (mXRN1p) with preference for G4 tetraplex substrates.
    J Cell Biol. 1997 Feb 24;136(4):761-73 PMID: 9049243
  8. Dhh1p, a putative RNA helicase, associates with the general transcription factors Pop2p and Ccr4p from Saccharomyces cerevisiae.
    Genetics. 1998 Feb;148(2):571-9 PMID: 9504907
  9. Recognition of yeast mRNAs as "nonsense containing" leads to both inhibition of mRNA translation and mRNA degradation: implications for the control of mRNA decapping.
    Mol Biol Cell. 1999 Nov;10(11):3971-8 PMID: 10564284
  10. Glucose depletion rapidly inhibits translation initiation in yeast.
    Mol Biol Cell. 2000 Mar;11(3):833-48 PMID: 10712503
  11. A Sm-like protein complex that participates in mRNA degradation.
    EMBO J. 2000 Apr 3;19(7):1661-71 PMID: 10747033
  12. Yeast Sm-like proteins function in mRNA decapping and decay.
    Nature. 2000 Mar 30;404(6777):515-8 PMID: 10761922
  13. mRNA decapping in yeast requires dissociation of the cap binding protein, eukaryotic translation initiation factor 4E.
    Mol Cell Biol. 2000 Nov;20(21):7933-42 PMID: 11027264
  14. Identification of novel Saccharomyces cerevisiae proteins with nuclear export activity: cell cycle-regulated transcription factor ace2p shows cell cycle-independent nucleocytoplasmic shuttling.
    Mol Cell Biol. 2000 Nov;20(21):8047-58 PMID: 11027275
  15. The transcription factor associated Ccr4 and Caf1 proteins are components of the major cytoplasmic mRNA deadenylase in Saccharomyces cerevisiae.
    Cell. 2001 Feb 9;104(3):377-86 PMID: 11239395
  16. Targeting an mRNA for decapping: displacement of translation factors and association of the Lsm1p-7p complex on deadenylated yeast mRNAs.
    Mol Cell. 2001 Nov;8(5):1075-83 PMID: 11741542
  17. The DEAD box helicase, Dhh1p, functions in mRNA decapping and interacts with both the decapping and deadenylase complexes.
    RNA. 2001 Dec;7(12):1717-27 PMID: 11780629
  18. Composition and functional characterization of the yeast spliceosomal penta-snRNP.
    Mol Cell. 2002 Jan;9(1):31-44 PMID: 11804584
  19. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry.
    Nature. 2002 Jan 10;415(6868):180-3 PMID: 11805837
  20. RNA helicase p54 (DDX6) is a shuttling protein involved in nuclear assembly of stored mRNP particles.
    J Cell Sci. 2002 Jan 15;115(Pt 2):395-407 PMID: 11839790
  21. Identification of a human decapping complex associated with hUpf proteins in nonsense-mediated decay.
    Mol Cell Biol. 2002 Dec;22(23):8114-21 PMID: 12417715
  22. Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures.
    EMBO J. 2002 Dec 16;21(24):6915-24 PMID: 12486012
  23. The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci.
    RNA. 2002 Dec;8(12):1489-501 PMID: 12515382
  24. Analysis of recombinant yeast decapping enzyme.
    RNA. 2003 Feb;9(2):231-8 PMID: 12554866
  25. Decapping and decay of messenger RNA occur in cytoplasmic processing bodies.
    Science. 2003 May 2;300(5620):805-8 PMID: 12730603
  26. The enzymes and control of eukaryotic mRNA turnover.
    Nat Struct Mol Biol. 2004 Feb;11(2):121-7 PMID: 14749774
  27. Crystal structure of Dcp1p and its functional implications in mRNA decapping.
    Nat Struct Mol Biol. 2004 Mar;11(3):249-56 PMID: 14758354
  28. Capped mRNA degradation intermediates accumulate in the yeast spb8-2 mutant.
    Mol Cell Biol. 1998 Sep;18(9):5062-72 PMID: 9710590
  29. Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae.
    Yeast. 1998 Jul;14(10):953-61 PMID: 9717241
  30. The cis acting sequences responsible for the differential decay of the unstable MFA2 and stable PGK1 transcripts in yeast include the context of the translational start codon.
    RNA. 1999 Mar;5(3):420-33 PMID: 10094310
  31. Mutations in translation initiation factors lead to increased rates of deadenylation and decapping of mRNAs in Saccharomyces cerevisiae.
    Mol Cell Biol. 1999 Aug;19(8):5247-56 PMID: 10409716
  32. The DCP2 protein is required for mRNA decapping in Saccharomyces cerevisiae and contains a functional MutT motif.
    EMBO J. 1999 Oct 1;18(19):5411-22 PMID: 10508173
  33. SMG7 acts as a molecular link between mRNA surveillance and mRNA decay.
    Mol Cell. 2004 Nov 19;16(4):587-96 PMID: 15546618
  34. Messenger RNA turnover in eukaryotes: pathways and enzymes.
    Crit Rev Biochem Mol Biol. 2004 Jul-Aug;39(4):197-216 PMID: 15596551
  35. The yeast EDC1 mRNA undergoes deadenylation-independent decapping stimulated by Not2p, Not4p, and Not5p.
    EMBO J. 2005 Mar 9;24(5):1033-45 PMID: 15706350
  36. Processing bodies require RNA for assembly and contain nontranslating mRNAs.
    RNA. 2005 Apr;11(4):371-82 PMID: 15703442
  37. A role for eIF4E and eIF4E-transporter in targeting mRNPs to mammalian processing bodies.
    RNA. 2005 May;11(5):717-27 PMID: 15840819
  38. Mutations in the Saccharomyces cerevisiae LSM1 gene that affect mRNA decapping and 3' end protection.
    Genetics. 2005 May;170(1):33-46 PMID: 15716506
  39. Stress granules and processing bodies are dynamically linked sites of mRNP remodeling.
    J Cell Biol. 2005 Jun 20;169(6):871-84 PMID: 15967811
  40. MicroRNA-dependent localization of targeted mRNAs to mammalian P-bodies.
    Nat Cell Biol. 2005 Jul;7(7):719-23 PMID: 15937477
  41. Inhibition of translational initiation by Let-7 MicroRNA in human cells.
    Science. 2005 Sep 2;309(5740):1573-6 PMID: 16081698
  42. A role for the eIF4E-binding protein 4E-T in P-body formation and mRNA decay.
    J Cell Biol. 2005 Sep 12;170(6):913-24 PMID: 16157702
  43. General translational repression by activators of mRNA decapping.
    Cell. 2005 Sep 23;122(6):875-86 PMID: 16179257
  44. Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies.
    Science. 2005 Oct 21;310(5747):486-9 PMID: 16141371
  45. A crucial role for GW182 and the DCP1:DCP2 decapping complex in miRNA-mediated gene silencing.
    RNA. 2005 Nov;11(11):1640-7 PMID: 16177138
  46. Disruption of GW bodies impairs mammalian RNA interference.
    Nat Cell Biol. 2005 Dec;7(12):1267-74 PMID: 16284622
  47. A role for the P-body component GW182 in microRNA function.
    Nat Cell Biol. 2005 Dec;7(12):1261-6 PMID: 16284623
  48. Identification of novel argonaute-associated proteins.
    Curr Biol. 2005 Dec 6;15(23):2149-55 PMID: 16289642
  49. Multiple processing body factors and the ARE binding protein TTP activate mRNA decapping.
    Mol Cell. 2005 Dec 22;20(6):905-15 PMID: 16364915
  50. Virus-like particles of the Ty3 retrotransposon assemble in association with P-body components.
    RNA. 2006 Jan;12(1):94-101 PMID: 16373495
  51. Crystal structure and functional analysis of Dcp2p from Schizosaccharomyces pombe.
    Nat Struct Mol Biol. 2006 Jan;13(1):63-70 PMID: 16341225
  52. RNA granules.
    J Cell Biol. 2006 Mar 13;172(6):803-8 PMID: 16520386
  53. Proteome survey reveals modularity of the yeast cell machinery.
    Nature. 2006 Mar 30;440(7084):631-6 PMID: 16429126
  54. Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.
    Nature. 2006 Mar 30;440(7084):637-43 PMID: 16554755
  55. Targeting of aberrant mRNAs to cytoplasmic processing bodies.
    Cell. 2006 Jun 16;125(6):1095-109 PMID: 16777600
  56. Relief of microRNA-mediated translational repression in human cells subjected to stress.
    Cell. 2006 Jun 16;125(6):1111-24 PMID: 16777601
  57. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes.
    Genes Dev. 2006 Jul 15;20(14):1885-98 PMID: 16815998
  58. Formation of GW bodies is a consequence of microRNA genesis.
    EMBO Rep. 2006 Sep;7(9):904-10 PMID: 16906129
  59. P bodies: at the crossroads of post-transcriptional pathways.
    Nat Rev Mol Cell Biol. 2007 Jan;8(1):9-22 PMID: 17183357
  60. P bodies and the control of mRNA translation and degradation.
    Mol Cell. 2007 Mar 9;25(5):635-46 PMID: 17349952
  61. Accumulation of polyadenylated mRNA, Pab1p, eIF4E, and eIF4G with P-bodies in Saccharomyces cerevisiae.
    Mol Biol Cell. 2007 Jul;18(7):2592-602 PMID: 17475768
  62. Identification of Edc3p as an enhancer of mRNA decapping in Saccharomyces cerevisiae.
    Genetics. 2004 Feb;166(2):729-39 PMID: 15020463
  63. Eukaryotic mRNA decapping.
    Annu Rev Biochem. 2004;73:861-90 PMID: 15189161
Article Info
Journal
Molecular biology of the cell
Abbr.
Mol Biol Cell
ISSN
1059-1524
DOI
10.1091/mbc.e07-03-0199
Published
2007-06-00
Epub
2007-00-11
Pages
2274-87
Language
English
Region
United States
NLM ID
9201390
PMCID
PMC1877105
Subset
IM
Grants
NIGMS NIH HHS · R37 GM045443 · United States
NIGMS NIH HHS · R37 GM45443 · United States
External Links
PubMed source DOI: 10.1091/mbc.e07-03-0199 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