Functional interactions between mRNA turnover and surveillance and the ubiquitin proteasome system

Wiley Interdisciplinary Reviews: RNA

Volumn 1, Issue 2, 2010, Pages 240-252

  Brooks, Seth A ^a  

^a VA MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INITIATION FACTOR 4E BINDING PROTEIN; MESSENGER RNA; POLYADENYLIC ACID BINDING PROTEIN; PROTEASOME; RIBONUCLEASE; UBIQUITIN;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; CYTOPLASM; ENZYME ACTIVITY; ENZYME LOCALIZATION; HUMAN; MRNA SURVEILLANCE; MRNA TURNOVER; NONHUMAN; NONSENSE MEDIATED MRNA DECAY; PRIORITY JOURNAL; REVIEW; RNA DEGRADATION; RNA METABOLISM; RNA PROCESSING; RNA SPLICING; RNA TRANSCRIPTION; RNA TRANSLATION; RNA TRANSPORT; AMINO ACID SEQUENCE; BIOLOGICAL MODEL; CHEMICAL STRUCTURE; GENETICS; HELA CELL; METABOLISM; MOLECULAR GENETICS; PHYSIOLOGY; PROTEIN DEGRADATION; RNA STABILITY;

AMINO ACID SEQUENCE; HELA CELLS; HUMANS; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEASOME ENDOPEPTIDASE COMPLEX; PROTEOLYSIS; RNA STABILITY; RNA, MESSENGER; UBIQUITIN;

EID: 84857695367     PISSN: 17577004     EISSN: 17577012     Source Type: Journal    
DOI: 10.1002/wrna.11     Document Type: Review

References (79)

1. Varshavsky A. Regulated protein degradation. Trends Biochem Sci 2005, 30: 283-286.
2. Ravid T, Hochstrasser M. Diversity of degradation signals in the ubiquitin-proteasome system. Nat Rev Mol Cell Biol 2008, 9: 679-690.
3. Chen ZJ, Sun LJ. Nonproteolytic functions of ubiquitin in cell signaling. Mol Cell 2009, 33: 275-286.
4. Pickart CM. Mechanisms underlying ubiquitination. Annu Rev Biochem 2001, 70: 503-533.
5. Li W, et al. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling. PLoS One 2008, 3: e1487.
6. Ardley HC, Robinson PA. E3 ubiquitin ligases. Essays Biochem 2005, 41: 15-30.
7. Komander D, Clague MJ, Urbe S. Breaking the chains: structure and function of the deubiquitinases. Nat Rev Mol Cell Biol 2009, 10: 550-563.
8. Dahlmann B. Proteasomes. Essays Biochem 2005, 41: 31-48.
9. Petit F, et al. Proteasome (prosome) associated endonuclease activity. Mol Biol Rep 1997, 24: 113-117.
10. Konstantinova IM, Tsimokha AS, Mittenberg AG. Role of proteasomes in cellular regulation. Int Rev Cell Mol Biol 2008, 267: 59-124.
11. Glickman MH, et al. The regulatory particle of the Saccharomyces cerevisiae proteasome. Mol Cell Biol 1998, 18: 3149-3162.
12. Glickman MH, et al. A subcomplex of the proteasome regulatory particle required for ubiquitin-conjugate degradation and related to the COP9-signalosome and eIF3. Cell 1998, 94: 615-623.
13. Lam YA, et al. A proteasomal ATPase subunit recognizes the polyubiquitin degradation signal. Nature 2002, 416: 763-767.
14. Pickart CM, Cohen RE. Proteasomes and their kin: proteases in the machine age. Nat Rev Mol Cell Biol 2004, 5: 177-187.
15. Kohler A, Hurt E. Exporting RNA from the nucleus to the cytoplasm. Nat Rev Mol Cell Biol 2007, 8: 761-773.
16. Aguilera A. Cotranscriptional mRNP assembly: from the DNA to the nuclear pore. Curr Opin Cell Biol 2005, 17: 242-250.
17. Reed R, Cheng H. TREX, SR proteins and export of mRNA. Curr Opin Cell Biol 2005, 17: 269-273.
18. Mitsui A, Sharp PA. Ubiquitination of RNA polymerase II large subunit signaled by phosphorylation of carboxyl-terminal domain. Proc Natl Acad Sci U S A 1999, 96: 6054-6059.
19. Maniatis T, Tasic B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 2002, 418: 236-243.
20. Lai MC, Lin RI, Tarn WY. Differential effects of hyperphosphorylation on splicing factor SRp55. Biochem J 2003, 371(Pt 3): 937-945.
21. Saeki K, et al. Proteomic analysis on insulin signaling in human hematopoietic cells: identification of CLIC1 and SRp20 as novel downstream effectors of insulin. Am J Physiol Endocrinol Metab 2005, 289: E419-E428.
22. Venables JP, et al. SIAH1 targets the alternative splicing factor T-STAR for degradation by the proteasome. Hum Mol Genet 2004, 13: 1525-1534.
23. Katzenberger RJ, Marengo MS, Wassarman DA. Control of alternative splicing by signal-dependent degradation of splicing-regulatory proteins. J Biol Chem 2009, 284: 10737-10746.
24. Gwizdek C, et al. The mRNA nuclear export factor Hpr1 is regulated by Rsp5-mediated ubiquitylation. J Biol Chem 2005, 280: 13401-13405.
25. Gwizdek C, et al. Ubiquitin-associated domain of Mex67 synchronizes recruitment of the mRNA export machinery with transcription. Proc Natl Acad Sci U S A 2006, 103: 16376-16381.
26. Saguez C, et al. Nuclear mRNA surveillance in THO/sub2 mutants is triggered by inefficient polyadenylation. Mol Cell 2008, 31: 91-103.
27. Keene JD. RNA regulons: coordination of post-transcriptional events. Nat Rev Genet 2007, 8: 533-543.
28. Moore MJ. From birth to death: the complex lives of eukaryotic mRNAs. Science 2005, 309: 1514-1518.
29. Shyu AB, Wilkinson MF, van Hoof A. Messenger RNA regulation: to translate or to degrade. Embo J 2008, 27: 471-481.
30. Sonenberg N, Hinnebusch AG. Regulation of translation initiation in eukaryotes: mechanisms and biological targets. Cell 2009, 136: 731-745.
31. Baugh JM, Pilipenko EV. 20S proteasome differentially alters translation of different mRNAs via the cleavage of eIF4F and eIF3. Mol Cell 2004, 16: 575-586.
32. Murata T, Shimotohno K. Ubiquitination and proteasome-dependent degradation of human eukaryotic translation initiation factor 4E. J Biol Chem 2006, 281: 20788-20800.
33. Mamane Y, et al. mTOR, translation initiation and cancer. Oncogene 2006, 25: 6416-6422.
34. Constantinou C, Elia A, Clemens MJ. Activation of p53 stimulates proteasome-dependent truncation of eIF4E-binding protein 1 (4E-BP1). Biol Cell 2008, 100: 279-289.
35. Elia A, Constantinou C, Clemens MJ. Effects of protein phosphorylation on ubiquitination and stability of the translational inhibitor protein 4E-BP1. Oncogene 2008, 27: 811-822.
36. Khaleghpour K, et al. Dual interactions of the translational repressor Paip2 with poly(A) binding protein. Mol Cell Biol 2001, 21: 5200-5213.
37. Roy G, et al. Paip1 interacts with poly(A) binding protein through two independent binding motifs. Mol Cell Biol 2002, 22: 3769-3782.
38. Craig AW, et al. Interaction of polyadenylate-binding protein with the eIF4G homologue PAIP enhances translation. Nature 1998, 392: 520-523.
39. Khaleghpour K, et al. Translational repression by a novel partner of human poly(A) binding protein, Paip2. Mol Cell 2001, 7: 205-216.
40. Berlanga JJ, Baass A, Sonenberg N. Regulation of poly(A) binding protein function in translation: characterization of the Paip2 homolog, Paip2B. RNA 2006, 12: 1556-1568.
41. Parker R, Sheth U. P bodies and the control of mRNA translation and degradation. Mol Cell 2007, 25: 635-646.
42. Franks TM, Lykke-Andersen J. The control of mRNA decapping and P-body formation. Mol Cell 2008, 32: 605-615.
43. Anderson P, Kedersha N. RNA granules: post-transcriptional and epigenetic modulators of gene expression. Nat Rev Mol Cell Biol 2009, 10: 430-436.
44. Eulalio A, et al. P-body formation is a consequence, not the cause, of RNA-mediated gene silencing. Mol Cell Biol 2007, 27: 3970-3981.
45. Lykke-Andersen S, Brodersen DE, Jensen TH. Origins and activities of the eukaryotic exosome. J Cell Sci 2009, 122(Pt 10): 1487-1494.
46. Ibrahim H, Wilusz J, Wilusz CJ. RNA recognition by 3′-to-5′ exonucleases: the substrate perspective. Biochim Biophys Acta 2008, 1779: 256-265.
47. Lin WJ, Duffy A, Chen CY. Localization of AU-rich element-containing mRNA in cytoplasmic granules containing exosome subunits. J Biol Chem 2007, 282: 19958-19968.
48. von Roretz C, Gallouzi IE. Decoding ARE-mediated decay: is microRNA part of the equation? J Cell Biol 2008, 181: 189-194.
49. Murray EL, Schoenberg DR. A + U-rich instability elements differentially activate 5′-3′ and 3′-5′ mRNA decay. Mol Cell Biol 2007, 27: 2791-2799.
50. Baou M, Jewell A, Murphy JJ. TIS11 family proteins and their roles in posttranscriptional gene regulation. J Biomed Biotechnol 2009, 2009: 634520.
51. Laroia G, et al. Control of mRNA decay by heat shock-ubiquitin-proteasome pathway. Science 1999, 284: 499-502.
52. Laroia G, Sarkar B, Schneider RJ. Ubiquitin-dependent mechanism regulates rapid turnover of AU-rich cytokine mRNAs. Proc Natl Acad Sci U S A 2002, 99: 1842-1846.
53. Laroia G, Schneider RJ. Alternate exon insertion controls selective ubiquitination and degradation of different AUF1 protein isoforms. Nucleic Acids Res 2002, 30: 3052-3058.
54. Paschoud S, et al. Destabilization of interleukin-6 mRNA requires a putative RNA stem-loop structure, an AU-rich element, and the RNA-binding protein AUF1. Mol Cell Biol 2006, 26: 8228-8241.
55. Mawji IA, et al. Role of the 3′-untranslated region of human endothelin-1 in vascular endothelial cells. Contribution to transcript lability and the cellular heat shock response. J Biol Chem 2004, 279: 8655-8667.
56. Torrisani J, et al. AUF1 cell cycle variations define genomic DNA methylation by regulation of DNMT1 mRNA stability. Mol Cell Biol 2007, 27: 395-410.
57. Deleault KM, Skinner SJ, Brooks SA. Tristetraprolin regulates TNF TNF-alpha mRNA stability via a proteasome dependent mechanism involving the combined action of the ERK and p38 pathways. Mol Immunol 2008, 45: 13-24.
58. Abdelmohsen K, et al. Ubiquitin-mediated proteolysis of HuR by heat shock. Embo J 2009, 28: 1271-1282.
59. Pioli PA, Rigby WF. The von Hippel-Lindau protein interacts with heteronuclear ribonucleoprotein a2 and regulates its expression. J Biol Chem 2001, 276: 40346-40352.
60. Peng Y, Liu X, Schoenberg DR. The 90-kDa heat shock protein stabilizes the polysomal ribonuclease 1 mRNA endonuclease to degradation by the 26S proteasome. Mol Biol Cell 2008, 19: 546-552.
61. Silva AL, Romao L. The mammalian nonsense-mediated mRNA decay pathway: to decay or not to decay! Which players make the decision? FEBS Lett 2009, 583: 499-505.
62. Neu-Yilik G, Kulozik AE. NMD: multitasking between mRNA surveillance and modulation of gene expression. Adv Genet 2008, 62: 185-243.
63. Kuroha K, Tatematsu T, Inada T. Upf1 stimulates degradation of the product derived from aberrant messenger RNA containing a specific nonsense mutation by the proteasome. EMBO Rep 2009.
64. Gatfield D, Izaurralde E. Nonsense-mediated messenger RNA decay is initiated by endonucleolytic cleavage in Drosophila. Nature 2004, 429: 575-578.
65. van Hoof A, et al. Exosome-mediated recognition and degradation of mRNAs lacking a termination codon. Science 2002, 295: 2262-2264.
66. Frischmeyer PA, et al. An mRNA surveillance mechanism that eliminates transcripts lacking termination codons. Science 2002, 295: 2258-2261.
67. Dimitrova LN, et al. Nascent peptide-dependent translation arrest leads to Not4p-mediated protein degradation by the proteasome. J Biol Chem 2009, 284: 10343-10352.
68. Doma MK, Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature 2006, 440: 561-564.
69. Petit F, et al. Involvement of proteasomal subunits zeta and iota in RNA degradation. Biochem J 1997, 326(Pt 1): 93-98.
70. Tsimokha AS, et al. Changes in composition and activities of 26S proteasomes under the action of doxorubicin-apoptosis inductor of erythroleukemic K562 cells. Cell Biol Int 2007, 31: 338-348.
71. Pouch MN, et al. Identification and initial characterization of a specific proteasome (prosome) associated RNase activity. J Biol Chem 1995, 270: 22023-22028.
72. Schmid HP, et al. The prosome: an ubiquitous morphologically distinct RNP particle associated with repressed mRNPs and containing specific ScRNA and a characteristic set of proteins. Embo J 1984, 3: 29-34.
73. Arrigo AP, et al. Characterization of the prosome from Drosophila and its similarity to the cytoplasmic structures formed by the low molecular weight heat-shock proteins. Embo J 1985, 4: 399-406.
74. Jarrousse AS, et al. Possible involvement of proteasomes (prosomes) in AUUUA-mediated mRNA decay. J Biol Chem 1999, 274: 5925-5930.
75. Jarrousse AS, et al. Relationships between proteasomes and viral gene products. Mol Biol Rep 1999, 26: 113-117.
76. Gautier-Bert K, et al. Substrate affinity and substrate specificity of proteasomes with RNase activity. Mol Biol Rep 2003, 30: 1-7.
77. Horsch A, et al. Prosomes discriminate between mRNA of adenovirus-infected and uninfected HeLa cells. FEBS Lett 1989, 246: 131-136.
78. Mazroui R, et al. Inhibition of the ubiquitin-proteasome system induces stress granule formation. Mol Biol Cell 2007, 18: 2603-2618.
79. Brennan CM, Steitz JA. HuR and mRNA stability. Cell Mol Life Sci 2001, 58: 266-277.