Alternative 3′ Pre-mRNA Processing in Saccharomyces cerevisiae Is Modulated by Nab4/Hrp1 In Vivo

Guisbert, Karen S. Kim; Li, Hao; Guthrie, Christine

doi:10.1371/journal.pbio.0050006

Cited by 39 publications

(53 citation statements)

References 42 publications

(57 reference statements)

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“…In agreement with this conclusion, the L205S (hrp1-5) and I313N (hrp1-6) alleles were found to be synthetically lethal with the rna14-1 and rna15-1 mutants, respectively (14). These defects in the rna14/15 mutants can be attributed to the disruption of the interface between Hrp1 and Rna14, an interaction known to be important to make a functional CF I complex (11,20,21,31).…”

Section: Discussionsupporting

confidence: 57%

“…Cleavage and polyadenylation can be uncoupled in vitro but in vivo they are connected with each other and with transcription termination. Defects in 3′-end processing have also been associated with several diseases in humans (9), but this process may be even more critical in yeast that has shorter intergenic regions and much rarer alternative splicing (10,11). In this organism, efficient mRNA transport is mostly dependent on polyadenylation rather than splicing.…”

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confidence: 99%

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Structural and biochemical analysis of the assembly and function of the yeast pre-mRNA 3′ end processing complex CF I

Barnwal

Lee

Moore

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The accuracy of the 3′-end processing by cleavage and polyadenylation is essential for mRNA biogenesis and transcription termination. In yeast, two poorly conserved neighboring elements upstream of cleavage sites are important for accuracy and efficiency of this process. These two RNA sequences are recognized by the RNA binding proteins Hrp1 and Rna15, but efficient processing in vivo requires a bridging protein (Rna14), which forms a stable dimer of heterodimers with Rna15 to stabilize the RNA-protein complex. We earlier reported the structure of the ternary complex of Rna15 and Hrp1 bound to the RNA processing element. We now report the use of solution NMR to study the interaction of Hrp1 with the Rna14-Rna15 heterodimer in the presence and absence of 3′-end processing signals. By using methyl selective labeling on Hrp1, in vivo activity and pull-down assays, we were able to study this complex of several hundred kDa, identify the interface within Hrp1 responsible for recruitment of Rna14 and validate the functional significance of this interaction through structure-driven mutational analysis.mRNA processing | mRNA transport | protein-RNA | methyl-TROSY | modeling E ukaryotic messenger RNA precursors (pre-mRNA) undergo extensive cotranscriptional processing before their transport to the cytoplasm and subsequent translation (1, 2). The processing events include 5′-end capping, splicing to remove intronic sequences and cleavage and polyadenylation at the 3′-end (3, 4). Correct 3′-end processing is necessary for mRNA biogenesis and transcription termination, preserves RNAs from degradation (5), promotes its export to the cytoplasm (6), enhances translation (7) and promotes transcriptional activation (4, 8). Cleavage and polyadenylation can be uncoupled in vitro but in vivo they are connected with each other and with transcription termination. Defects in 3′-end processing have also been associated with several diseases in humans (9), but this process may be even more critical in yeast that has shorter intergenic regions and much rarer alternative splicing (10, 11). In this organism, efficient mRNA transport is mostly dependent on polyadenylation rather than splicing.In yeast, the 3′-end processing reaction is executed by a complex machine containing more than 20 proteins (4) which share significant similarities with human 3′-end processing proteins. The entire yeast 3′-end processing complex is divided into two subcomplexes, called cleavage factor I (CF I) and cleavage and polyadenylation factor (CPF) (4). CF I binds to the pre-mRNA upstream of the cleavage signal within the pre-mRNA, whereas CPF binds at the cleavage site as well as upstream and downstream of the cleavage site. Several sequences within yeast pre-mRNAs, which are surprisingly poorly conserved, direct the recruitment of cleavage and polyadenylation factors (12, 13). In the 5′-3′ direction, they include AU-rich efficiency element (EE) responsible for polyadenylation efficiency; A-rich positioning element (PE) critical for precise 3′-end processing; t...

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Section: Discussionsupporting

confidence: 57%

mentioning

confidence: 99%

Structural and biochemical analysis of the assembly and function of the yeast pre-mRNA 3′ end processing complex CF I

Barnwal

Lee

Moore

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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“…Interestingly, some mRNAs produce different isoforms of the same transcript that vary in their 3= UTR lengths. Transcripts with varying 3= UTR lengths can be produced as a result of alternative 3=-end processing, which can be sensitive to growth conditions (71).…”

Section: Atypically Long 3= Utrs Can Target Mrnas To the Nmd Pathwaymentioning

confidence: 99%

Regulation of Natural mRNAs by the Nonsense-Mediated mRNA Decay Pathway

Peccarelli

Kebaara

2014

Eukaryot Cell

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The nonsense-mediated mRNA decay (NMD) pathway is a specialized mRNA degradation pathway that degrades select mRNAs. This pathway is conserved in all eukaryotes examined so far, and it triggers the degradation of mRNAs that prematurely terminate translation. Originally identified as a pathway that degrades mRNAs with premature termination codons as a result of errors during transcription, splicing, or damage to the mRNA, NMD is now also recognized as a pathway that degrades some natural mRNAs. The degradation of natural mRNAs by NMD has been identified in multiple eukaryotes, including Saccharomyces cerevisiae, Drosophila melanogaster, Arabidopsis thaliana, and humans. S. cerevisiae is used extensively as a model to study natural mRNA regulation by NMD. Inactivation of the NMD pathway in S. cerevisiae affects approximately 10% of the transcriptome. Similar percentages of natural mRNAs in the D. melanogaster and human transcriptomes are also sensitive to the pathway, indicating that NMD is important for the regulation of gene expression in multiple organisms. NMD can either directly or indirectly regulate the decay rate of natural mRNAs. Direct NMD targets possess NMD-inducing features. This minireview focuses on the regulation of natural mRNAs by the NMD pathway, as well as the features demonstrated to target these mRNAs for decay by the pathway in S. cerevisiae. We also compare NMD-targeting features identified in S. cerevisiae with known NMDtargeting features in other eukaryotic organisms.

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“…As examples, the CBP1 gene is processed in two mRNAs (2.2 and 1.2kb) by alternative 3´-end processing, the predominance being regulated by the carbon source (Sparks et al, 1997). The SUA7 transcript predominance changes with the growth phase (Hoppes et al, 2000), after a heat shock or when copper concentrations cause stress to cells (Kim Guisbert et al, 2007). Alternative polyadenylation is a widespread mechanism in eukaryotes.…”

Section: Genes With Alternative Polyadenylationmentioning

confidence: 99%

“…The effects on RNA14 processing, with truncated alternatives (T), were shown in Ssu72 and Npl3 (Wong et al, 2007) mutants. However, until more recently with Hrp1 (Kim Guisbert et al, 2007) or with Pta1 and Pcf11 (Seoane et al, 2009a), little was known about the factors specifically involved in alternative 3'-end selection in yeast genes with regulated (and non-truncated) 3'-end alternatives, or their possible interaction with specific elements at the 3'-UTR. Pta1 establishes a physical interaction with Pcf11 (GST pull-down assays) (Ghazy et al, 2009).…”

Section: Genes With Alternative Polyadenylationmentioning

confidence: 99%

Alternative Polyadenylation in Yeast: 3 ́-UTR Elements and Processing Factors Acting at a Distance

Lamas-Maceiras¹,

Seoane²,

Freire-Picos³

2011

RNA Processing

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Alternative 3′ Pre-mRNA Processing in Saccharomyces cerevisiae Is Modulated by Nab4/Hrp1 In Vivo

Cited by 39 publications

References 42 publications

Structural and biochemical analysis of the assembly and function of the yeast pre-mRNA 3′ end processing complex CF I

Structural and biochemical analysis of the assembly and function of the yeast pre-mRNA 3′ end processing complex CF I

Regulation of Natural mRNAs by the Nonsense-Mediated mRNA Decay Pathway

Alternative Polyadenylation in Yeast: 3 ́-UTR Elements and Processing Factors Acting at a Distance

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