Different nuclease requirements for exosome-mediated degradation of normal and nonstop mRNAs.
Two general pathways of mRNA decay have been characterized in yeast. In one pathway, the mRNA is degraded by the cytoplasmic form of the exosome. The exosome has both 3' to 5' exoribonuclease and endoribonuclease activity, and the available evidence suggests that the exonuclease activity is required for the degradation of mRNAs. We confirm here that this is true for normal mRNAs, but that aberrant mRNAs that lack a stop codon can be efficiently degraded in the absence of the exonuclease activity of the exosome. Specifically, we show that the endo- and exonuclease activities of the exosome are both capable of rapidly degrading nonstop mRNAs and ribozyme-cleaved mRNAs. Additionally, the endonuclease activity of the exosome is not required for endonucleolytic cleavage in no-go decay. In vitro, the endonuclease domain of the exosome is active only under nonphysiological conditions, but our findings show that the in vivo activity is sufficient for the rapid degradation of nonstop mRNAs. Thus, whereas normal mRNAs are degraded by two exonucleases (Xrn1p and Rrp44p), several endonucleases contribute to the decay of many aberrant mRNAs, including transcripts subject to nonstop and no-go decay. Our findings suggest that the nuclease requirements for general and nonstop mRNA decay are different, and describe a molecular function of the core exosome that is not disrupted by inactivating its exonuclease activity.
Department of Microbiology and Molecular Genetics, University of Texas Health Science Center, Houston, TX 77030, USA.
Daneen
D
Schaeffer
Ambro
A
van Hoof
D018388:Codon, Terminator / Q000235:genetics / Q000378:metabolism*; D055354:Exosomes / Q000235:genetics / Q000378:metabolism*; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability / Q000502:physiology*; D012331:RNA, Fungal / Q000235:genetics / Q000378:metabolism*; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D012260:Ribonucleases / Q000235:genetics / Q000378:metabolism*; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism*
D018388:Codon, Terminator; D005656:Fungal Proteins; D012331:RNA, Fungal; D012333:RNA, Messenger; D012260:Ribonucleases
Cell. 2006 Dec 15;127(6):1223-37
17174896
Science. 2002 Mar 22;295(5563):2262-4
11910110
Genetics. 2005 Dec;171(4):1455-61
15965245
Nature. 2006 Mar 23;440(7083):561-4
16554824
Cell. 1997 Nov 14;91(4):457-66
9390555
Genes Dev. 1993 Aug;7(8):1632-43
8393418
Science. 2002 Mar 22;295(5563):2258-61
11910109
Nucleic Acids Res. 2009 Mar;37(4):1127-40
19129231
Mol Cell Biol. 1993 Aug;13(8):4826-35
8336719
Genes Dev. 1999 Aug 15;13(16):2148-58
10465791
RNA. 2001 Sep;7(9):1192-212
11565744
Genes Dev. 1991 Feb;5(2):221-31
1899842
EMBO J. 1998 Mar 2;17(5):1497-506
9482746
Genes Dev. 1992 Nov;6(11):2100-11
1427074
Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12741-6
12242335
Mol Cell Biol. 2000 Nov;20(21):8230-43
11027292
Genes Dev. 1994 Apr 1;8(7):855-66
7926773
Mol Cell. 2004 Jul 23;15(2):173-83
15260969
EMBO J. 2010 Jul 21;29(14):2342-57
20531386
Science. 2006 Jul 7;313(5783):104-7
16825573
RNA. 2008 Dec;14(12):2609-17
18974281
RNA. 2006 Jul;12(7):1323-37
16714281
Cell. 2009 Oct 30;139(3):547-59
19879841
Nature. 2008 Dec 18;456(7224):993-6
19060886
Nat Struct Mol Biol. 2007 Jan;14(1):15-22
17173052
EMBO J. 1998 Mar 2;17(5):1487-96
9482745
Science. 2001 Aug 10;293(5532):1146-50
11498593
Nat Struct Mol Biol. 2009 Jan;16(1):49-55
19060897
J Biol Chem. 2004 Jan 2;279(1):755-64
14573594
Mol Cell. 2006 Oct 6;24(1):149-56
16996291
Mol Cell. 2008 Mar 28;29(6):717-28
18374646
EMBO J. 2010 Jul 21;29(14):2358-67
20531389
Mol Biol Cell. 2009 Jul;20(13):3025-32
19420139
Nature. 2004 Jun 3;429(6991):575-8
15175755
Nature. 2006 Sep 7;443(7107):110-4
16957732
RNA. 2005 Apr;11(4):459-69
15703439
Nature. 1996 Aug 15;382(6592):642-6
8757137
RNA. 2003 Sep;9(9):1157-67
12923263
Nat Struct Mol Biol. 2009 Jan;16(1):56-62
19060898
Mol Cell Biol. 1995 May;15(5):2719-27
7739552