The yeast THO complex and the associated RNA helicase Sub2p are important mRNP maturation factors. Transcripts produced in THO/sub2 mutants are subject to degradation by a surveillance mechanism that involves the nuclear RNA exosome. Here we show that inefficient polyadenylation forms the basis of this accelerated mRNA decay. A genetic screen reveals extensive interactions between deletions of THO subunits and mRNA 3' end processing mutants. Nuclear run-ons strengthen this link by showing premature transcription termination close to polyadenylation sites in THO/sub2 mutants in vivo. Moreover, in vitro, pre-mRNA substrates are poorly polyadenylated and consequently unstable in extracts from THO/sub2 mutant strains. Decreased polyadenylation correlates with a specific downregulation of the poly(A)-polymerase cofactor Fip1p by the ubiquitin/proteasome pathway. Both polyadenylation defects and Fip1p instability depend on the nuclear exosome component Rrp6p and its activator Trf4p. We suggest that removal of aberrant mRNA is facilitated by direct regulation of polyadenylation activity.

Before polyadenylated mRNA is exported from the nucleus, the 3-end processing complex is removed by a poorly described mechanism. In this study, we asked whether factors involved in mRNP maturation and export are also required for disassembly of the cleavage and polyadenylation complex. An RNA immunoprecipitation assay monitoring the amount of the cleavage factor (CF) IA component Rna15p associated with poly(A) ؉ RNA reveals defective removal of Rna15p in mutants of the nuclear export receptor Mex67p as well as other factors important for assembly of an export-competent mRNP. In contrast, Rna15p is not retained in mutants of export factors that function primarily on the cytoplasmic side of the nuclear pore. Consistent with a functional interaction between Mex67p and the 3-end processing complex, a mex67 mutant accumulates unprocessed SSA4 transcripts and exhibits a severe growth defect when this mutation is combined with mutation of Rna15p or another CF IA subunit, Rna14p. RNAs that become processed in a mex67 mutant have longer poly(A) tails both in vivo and in vitro. This influence of Mex67p on 3-end processing is conserved, as depletion of its human homolog, TAP/NXF1, triggers mRNA hyperadenylation. Our results indicate a function for nuclear mRNP assembly factors in releasing the 3-end processing complex once polyadenylation is complete.A significant advance in the area of eukaryotic gene expression has been the appreciation of multiple interrelationships between activities needed to get a functional mRNA to the cytoplasm for translation. Coordination occurs at the level of transcription, capping, splicing, 3Ј-end processing, and assembly of the mRNA into a ribonucleoprotein particle (RNP) that can be transported (for reviews, see references 2, 5, 12, 43, 51, and 55). Overseeing all of this is a nuclear mRNA surveillance mechanism which ensures that only correctly formed mRNP reaches the cytoplasm and that defective ones are degraded (for a review, see reference 70).Processing at the mRNA 3Ј end is accomplished by a multisubunit complex that recognizes signals on the nascent RNA, cleaves at the poly(A) site, and adds a poly(A) tract. The subunits of the complex are largely conserved across eukaryotes, and in the yeast Saccharomyces cerevisiae, this complex can be separated biochemically into three factors: cleavage and polyadenylation factor (CPF), cleavage factor (CF) IA, and Hrp1p (59). The length of the RNA poly(A) tail is restricted by the recruitment of specific poly(A)-binding proteins, such as Nab2p and Pab1p (6,19,22,40,80), and by the action of poly(A)-specific nucleases in the nucleus and the cytoplasm (59). Previous studies showed that 3Ј-end processing factors, with the exception of Hrp1p, Pab1p, and Nab2p, do not shuttle in and out of the nucleus (9, 38, 48). Thus, the exported mRNP does not include CF IA and CPF components, yet the signal sequences that stably hold these factors onto the mRNA as it receives its tail are present on the final polyadenylated product. Therefore, a mechanism must ex...

The cleavage/polyadenylation factor (CPF) of Saccharomyces cerevisiae is thought to provide the catalytic activities of the mRNA 3¢-end processing machinery, which include endonucleolytic cleavage at the poly(A) site, followed by synthesis of an adenosine polymer onto the new 3¢-end by the CPF subunit Pap1. Because of similarity to other nucleases in the metallo-blactamase family, the Brr5/Ysh1 subunit has been proposed to be the endonuclease. The C-terminal domain of Brr5 lies outside of b-lactamase homology, and its function has not been elucidated. We show here that this region of Brr5 is necessary for cell viability and mRNA 3¢-end processing. It is highly homologous to another CPF subunit, Syc1. Syc1 is not essential, but its removal improves the growth of other processing mutants at restrictive temperatures and restores in vitro processing activity to cleavage/ polyadenylation-defective brr5-1 extract. Our findings suggest that Syc1, by mimicking the essential Brr5 C-terminus, serves as a negative regulator of mRNA 3¢-end formation.

In the yeast Saccharomyces cerevisiae, mutation of some effectors of mRNA nuclear export leads to the rapid accumulation of HSP104 RNA in transcription site-associated foci. We have screened the S. cerevisiae complement of viable gene deletion mutants for their inability to export HSP104 RNA. The 15 strains identified comprise deletions of components of the THO, Thp1p/Sac3p, and nuclear pore complexes. In all three mutant classes, retained RNA overlaps the HSP104 transcription site. Thus, an early block to HSP104 RNA export is general. Incubation of the identified deletion strains, as well as seven additional mutants, under conditions where mRNA export is blocked results in rapid dissipation of nucleolar protein and RNA constituents. Time course experiments show that dissipation of nucleolar antigens succeeds mRNA retention and is reversed when the load of nuclear mRNA ceases. Consistent with a causal role of excess nuclear mRNA, nucleolar morphology in an mRNA export mutant environment remains intact when transcription by RNA polymerase II is inhibited.