Gateway Arch to the RNA Exosome

Losh, Jillian S.; Hoof, Ambro van

doi:10.1016/j.cell.2015.08.013

Cited by 4 publications

(6 citation statements)

References 10 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…S6A), similar to results reported in Arabidopsis (Abbasi et al, 2010;Lange et al, 2011;Hang et al, 2014;Sikorski et al, 2015;Shanmugam et al, 2017). The results suggested that active polyadenylationdependent RNA processing systems, such as those mediated by the TRAMP (Jia et al, 2011;Lange et al, 2014) and nuclear RNA exosome (LaCava et al, 2005;Houseley et al, 2006;Doma and Parker, 2007;Lange et al, 2009;Losh and van Hoof, 2015;Sikorski et al, 2015;Thoms et al, 2015), exist in rice and take part in pre-18S rRNA processing.…”

Section: Identification Of Pre-18s Rrna Intermediates For the Pre-40ssupporting

confidence: 84%

“…In eukaryotic cells, aberrant rRNA biogenesis activates RNA quality control in the nucleus, which triggers higher polyadenylation of certain rRNA intermediates and by-products catalyzed by the Trf/Air/Mtr4 polyadenylation complex (TRAMP; Jia et al, Lange et al, 2014). These intermediates are degraded sequentially by the nuclear exosome complex (LaCava et al, 2005;Houseley et al, 2006;Doma and Parker, 2007;Lange et al, 2009;Losh and van Hoof, 2015;Thoms et al, 2015). Dysfunction of ribosomal biogenesis (Gallagher et al, 2004;Ferreira-Cerca et al, 2005Tafforeau et al, 2013) results in severe developmental defects in higher plants (Byrne, 2009;Fujikura et al, 2009;Horiguchi et al, 2011;Weis et al, 2015aWeis et al, , 2015b and serious genetic diseases in mammals (Choesmel et al, 2007;Narla and Ebert, 2010;McCann and Baserga, 2013;Sondalle and Baserga, 2014;Bai et al, 2016).…”

mentioning

confidence: 99%

See 1 more Smart Citation

Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa

et al. 2018

View full text Add to dashboard Cite

Ribosome biogenesis is crucial for plant growth and environmental acclimation. Processing of ribosomal RNAs (rRNAs) is an essential step in ribosome biogenesis and begins with transcription of the rDNA. The resulting precursor-rRNA (pre-rRNA) transcript undergoes systematic processing, where multiple endonucleolytic and exonucleolytic cleavages remove the external and internal transcribed spacers (ETS and ITS). The processing sites and pathways for pre-rRNA processing have been deciphered in and, to some extent, in, mammalian cells, and Arabidopsis (). However, the processing sites and pathways remain largely unknown in crops, particularly in monocots such as rice (), one of the most important food resources in the world. Here, we identified the rRNA precursors produced during rRNA biogenesis and the critical endonucleolytic cleavage sites in the transcribed spacer regions of pre-rRNAs in rice. We further found that two pre-rRNA processing pathways, distinguished by the order of 5' ETS removal and ITS1 cleavage, coexist in vivo. Moreover, exposing rice to chilling stress resulted in the inhibition of rRNA biogenesis mainly at the pre-rRNA processing level, suggesting that these energy-intensive processes may be reduced to increase acclimation and survival at lower temperatures. Overall, our study identified the pre-rRNA processing pathway in rice and showed that ribosome biogenesis is quickly inhibited by low temperatures, which may shed light on the link between ribosome biogenesis and environmental acclimation in crop plants.

show abstract

Section: Identification Of Pre-18s Rrna Intermediates For the Pre-40ssupporting

confidence: 84%

mentioning

confidence: 99%

Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa

et al. 2018

View full text Add to dashboard Cite

show abstract

“…Specifically, ZCCHC8 CTD interacts with a highly conserved surface at the base of the helicase core modules, unique from the binding sites reported for TRAMP subunits Trf4p and Air2p. While NEXT and TRAMP subunits contact MTR4 through the helicase core, several exosome partners are recruited to MTR4 via its arch domain ( 43 ). Hence, in addition to being an RNA helicase, MTR4 serves as an interaction hub, providing a platform for multiple exosome accessory factors to access the exosome.…”

Section: Discussionmentioning

confidence: 99%

Structural basis for MTR4–ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex

Puno

Lima

2018

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

View full text Add to dashboard Cite

SignificanceAberrant or unwanted transcripts can be degraded by the RNA exosome with the help of the nuclear exosome-targeting (NEXT) complex. NEXT, composed of RNA-binding protein RBM7, scaffold ZCCHC8, and helicase MTR4, is implicated in stress response, neurodegeneration, and viral ribogenesis. Here, we characterize the activities of NEXT that support its role in exosome-mediated decay. NEXT catalyzes 3′→5′ helicase activity and disrupts RNA:RNA and DNA:RNA duplexes more efficiently than MTR4. Optimal activity is observed when substrates include a uridine-rich motif, for interactions with RBM7, and a 3′ poly(A) tail. The ZCCHC8 C-terminal domain binds the helicase core and can stimulate MTR4 helicase/ATPase activities. Our results highlight the interplay among NEXT subunits to ensure effective targeting of substrates.

show abstract

“…118,131−134 Interestingly, the Air2 contacts with the Mtr4 arch resemble those of Utp18 and Nop53, suggesting that these adaptor proteins may compete with Air2 for Mtr4 binding. 118,119 The N-terminus of Trf4 also interacts with the Mtr4 helicase core, with Trf4/Air2 positioned such that RNA could thread from Mtr4 to the Trf4 active site. 118 3.3.3.2.…”

Section: Role Of the Yeast Nuclear Exosome Nucleases In Ncrna Surveil...mentioning

confidence: 99%

“…Both Trf4 and Air2 contact Mtr4. Air2 interacts with both the Mtr4 helicase domain and the arch domain, with the contacts to the Mtr4 arch resembling those of Nop53 and Utp18. , (C) For RNA polymerase II transcripts, the Nrd1–Nab3 heterodimer of the Nrd1–Nab3–Sen1 complex recognizes short motifs on the nascent ncRNA. Nrd1 also interacts with the C-terminal domain of the large subunit of the polymerase.…”

Section: The Rna Exosomementioning

confidence: 99%

Noncoding RNA Surveillance: The Ends Justify the Means

2017

View full text Add to dashboard Cite

Numerous surveillance pathways sculpt eukaryotic transcriptomes by degrading unneeded, defective, and potentially harmful noncoding RNAs (ncRNAs). Because aberrant and excess ncRNAs are largely degraded by exoribonucleases, a key characteristic of these RNAs is an accessible, protein-free 5' or 3' end. Most exoribonucleases function with cofactors that recognize ncRNAs with accessible 5' or 3' ends and/or increase the availability of these ends. Noncoding RNA surveillance pathways were first described in budding yeast, and there are now high-resolution structures of many components of the yeast pathways and significant mechanistic understanding as to how they function. Studies in human cells are revealing the ways in which these pathways both resemble and differ from their yeast counterparts, and are also uncovering numerous pathways that lack equivalents in budding yeast. In this review, we describe both the well-studied pathways uncovered in yeast and the new concepts that are emerging from studies in mammalian cells. We also discuss the ways in which surveillance pathways compete with chaperone proteins that transiently protect nascent ncRNA ends from exoribonucleases, with partner proteins that sequester these ends within RNPs, and with end modification pathways that protect the ends of some ncRNAs from nucleases.

show abstract

Gateway Arch to the RNA Exosome

Abstract: The RNA exosome degrades many different RNAs. Thoms et al. now fill an important gap in our understanding of how the exosome recognizes distinct subsets of target RNAs.

Cited by 4 publications

References 10 publications

Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa

Ribosomal RNA Biogenesis and Its Response to Chilling Stress in Oryza sativa

Structural basis for MTR4–ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex

Noncoding RNA Surveillance: The Ends Justify the Means

Contact Info

Product

Resources

About