Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome

Egecioglu, Defne E.; Henras, Anthony K.; Chanfreau, Guillaume

doi:10.1261/rna.2207206

Cited by 102 publications

(103 citation statements)

References 22 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These data suggest that, depending on the gene context, snoRNA terminators possess the potential to direct polyadenylation. Previous data, indeed, reported polyadenylation of some sn/ snoRNAs precursors in an exosome-defective yeast strain (van Hoof et al 2000;Egecioglu et al 2006). Accordingly, a strain deleted for RRP6 showed that one to four adenines are present at the 39-end of C/D-box snoRNA precursors that had been incompletely processed (Grzechnik and Kufel 2008).…”

Section: The Nrd1 Complexmentioning

confidence: 82%

“…In yeast, noncanonical nuclear PAPs, Trf4/5 (Haracska et al 2005;Egecioglu et al 2006;, function in a nuclear RNA surveillance pathway as part of the TRAMP (Trf-Air-Mtr4 polyadenylation) complex, which activates degradation by the exosome of a variety of aberrant nuclear precursors of many types of RNAs after addition of a poly(A) tail (LaCava et al 2005). Although not well studied, this RNA surveillance function is likely conserved in humans since homologs of the TRAMP and exosome complexes are present in mammals.…”

Section: -End Processing Machinerymentioning

confidence: 99%

See 1 more Smart Citation

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

291

326

View full text Add to dashboard Cite

Gene transcription in the cell nucleus is a complex and highly regulated process. Transcription in eukaryotes requires three distinct RNA polymerases, each of which employs its own mechanisms for initiation, elongation, and termination. Termination mechanisms vary considerably, ranging from relatively simple to exceptionally complex. In this review, we describe the present state of knowledge on how each of the three RNA polymerases terminates and how mechanisms are conserved, or vary, from yeast to human.

show abstract

Section: The Nrd1 Complexmentioning

confidence: 82%

Section: -End Processing Machinerymentioning

confidence: 99%

Transcription termination by nuclear RNA polymerases

Richard

Manley²

2009

Genes Dev.

291

326

View full text Add to dashboard Cite

show abstract

“…In addition to targeting unstable pre-tRNAs for decay, TRAMP is involved in the decay of a mutant U6 snRNA, several precursors to rRNAs and snRNAs, and transcripts of intergenic regions (LaCava et al 2005;Wyers et al 2005;Kadaba et al 2006). Yeast also contain a related poly(A) polymerase complex, consisting of the Trf4p-related protein Trf5p, Air1p, and Mtr4p, that has overlapping functions with the TRAMP complex (Egecioglu et al 2006;Houseley and Tollervey 2006;Kadaba et al 2006).…”

Section: Similar Pathways For Noncoding Rna Quality Control In Bactermentioning

confidence: 99%

Molecular Chaperones and Quality Control in Noncoding RNA Biogenesis

Wolin¹,

Wurtmann²

2006

Cold Spring Harbor Symposia on Quantitative Biology

View full text Add to dashboard Cite

Although noncoding RNAs have critical roles in all cells, both the mechanisms by which these RNAs fold into functional structures and the quality control pathways that monitor correct folding are only beginning to be elucidated. Here, we discuss several proteins that likely function as molecular chaperones for noncoding RNAs and review the existing knowledge on noncoding RNA quality control. One protein, the La protein, binds many nascent noncoding RNAs in eukaryotes and is required for efficient folding of certain pre-tRNAs. In prokaryotes, the Sm-like protein Hfq is required for the function of many noncoding RNAs. Recent work in bacteria and yeast has revealed the existence of quality control systems involving polyadenylation of unstable noncoding RNAs followed by exonucleolytic degradation. In addition, the Ro protein, which is present in many animal cells and also certain bacteria, binds misfolded noncoding RNAs and is proposed to function in RNA quality control.

show abstract

“…Critically, budding yeast-derived TRAMP4 complex or recombinant Trf4-Air1/2 complex exclusively polyadenylates hypomodified tRNA i Met , suggesting that the TRAMP4 complex recognizes the structure/folding of an RNA substrate (22). Besides aberrant tRNAs, Trf4 also polyadenylates and stimulates the degradation of snRNAs, snoRNAs, rRNAs, and CUT RNAs, including the prototypic CUT, NEL025c (14,21,32,33).…”

mentioning

confidence: 99%

Air1 Zinc Knuckles 4 and 5 and a Conserved IWRXY Motif Are Critical for the Function and Integrity of the Trf4/5-Air1/2-Mtr4 Polyadenylation (TRAMP) RNA Quality Control Complex

Fasken

Leung

Banerjee

et al. 2011

Journal of Biological Chemistry

View full text Add to dashboard Cite

In Saccharomyces cerevisiae, non-coding RNAs, including cryptic unstable transcripts (CUTs), are subject to degradation by the exosome. The Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex in S. cerevisiae is a nuclear exosome cofactor that recruits the exosome to degrade RNAs. Trf4/5 are poly(A) polymerases, Mtr4 is an RNA helicase, and Air1/2 are putative RNA-binding proteins that contain five CCHC zinc knuckles (ZnKs). One central question is how the TRAMP complex, especially the Air1/2 protein, recognizes its RNA substrates. To characterize the function of the Air1/2 protein, we used random mutagenesis of the AIR1/2 gene to identify residues critical for Air protein function. We identified air1-C178R and air2-C167R alleles encoding air1/2 mutant proteins with a substitution in the second cysteine of ZnK5. Mutagenesis of the second cysteine in AIR1/2 ZnK1-5 reveals that Air1/2 ZnK4 and -5 are critical for Air protein function in vivo. In addition, we find that the level of CUT, NEL025c, in air1 ZnK1-5 mutants is stabilized, particularly in air1 ZnK4, suggesting a role for Air1 ZnK4 in the degradation of CUTs. We also find that Air1/2 ZnK4 and -5 are critical for Trf4 interaction and that the Air1-Trf4 interaction and Air1 level are critical for TRAMP complex integrity. We identify a conserved IWRXY motif in the Air1 ZnK4-5 linker that is important for Trf4 interaction. We also find that hZC-CHC7, a putative human orthologue of Air1 that contains the IWRXY motif, localizes to the nucleolus in human cells and interacts with both mammalian Trf4 orthologues, PAPD5 and PAPD7 (PAP-associated domain containing 5 and 7), suggesting that hZCCHC7 is the Air component of a human TRAMP complex.Production of mature RNAs in eukaryotes requires a complex set of processing steps, including 5Ј-end capping, splicing, 3Ј-end cleavage, polyadenylation, nucleolytic cleavage/trimming, and base modifications, by numerous processing components. Incorrectly processed RNAs are rapidly degraded by RNA quality control machinery to prevent deleterious effects on the cell. Processing and degradation of multiple classes of RNA are performed by RNA endo/exoribonucleases that are recruited to their RNA substrates by specific protein cofactors. These nucleases and their cofactors are highly regulated and evolutionarily conserved.In Saccharomyces cerevisiae, non-coding RNAs (ncRNAs), 2 including precursors of rRNAs, snoRNAs, and snRNAs, are processed and/or degraded by the nuclear exosome, an evolutionarily conserved ringlike riboexonuclease complex containing two active 3Ј-5Ј-riboexonucleases, Rrp44/Dis3 and Rrp6 (1-8). Hypomodified initiator tRNAs (tRNA i Met ) from cells with an impaired tRNA methyltransferase and aberrant pre-mRNAs from cells with defective 3Ј-end processing, splicing, or nuclear export factors are also degraded by the nuclear exosome (9 -13). More recently, a novel class of small (250 -300-nucleotide) intergenic RNA polymerase II transcripts, termed cryptic unstable transcripts (CUTs), was discovered in cells that lack ...

show abstract

Contributions of Trf4p- and Trf5p-dependent polyadenylation to the processing and degradative functions of the yeast nuclear exosome

Cited by 102 publications

References 22 publications

Transcription termination by nuclear RNA polymerases

Transcription termination by nuclear RNA polymerases

Molecular Chaperones and Quality Control in Noncoding RNA Biogenesis

Air1 Zinc Knuckles 4 and 5 and a Conserved IWRXY Motif Are Critical for the Function and Integrity of the Trf4/5-Air1/2-Mtr4 Polyadenylation (TRAMP) RNA Quality Control Complex

Contact Info

Product

Resources

About