Nop5 interacts with the archaeal <scp>RNA</scp> exosome

Gauernack, A. Susann; Lassek, Christian; Hou, Linlin; Dzieciolowski, Julia; Evguenieva‐Hackenberg, Elena; Klug, Gabriele

doi:10.1002/1873-3468.12915

Cited by 5 publications

(4 citation statements)

References 39 publications

(82 reference statements)

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“…The archaeal and eukaryotic exosome complexes are the main cellular machineries responsible for 3ʹ to 5ʹ mRNA degradation . In the genus Sulfolobus , the archaeal exosome is also responsible for polyadenylation, which plays a role in assisting exoribonucleases in overcoming complicated secondary structures during nucleolytic degradation .…”

Section: Polyadenylation‐assisted Rna Degradationmentioning

confidence: 79%

“…The archaeal and eukaryotic exosome complexes are the main cellular machineries responsible for 3ʹ to 5ʹ mRNA degradation. 57 In the genus Sulfolobus, the archaeal exosome is also responsible for polyadenylation, which plays a role in assisting exoribonucleases in overcoming complicated secondary structures during nucleolytic degradation. 58,59 The addition of an A-rich RNA tail to a synthetic RNA molecule improved the degradation of this RNA by the Rrp4 exosome, supporting the idea that the presence of A-rich tails at the 3 end of mRNAs is important for RNA destabilization in S. solfataricus.…”

Section: Polyadenylation-assisted Rna Degradationmentioning

confidence: 99%

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RNA stabilization in hyperthermophilic archaea

Gomes-Filho

Randau

2019

Annals of the New York Academy of Sciences

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Analyses of the RNA metabolism of hyperthermophilic archaea highlight the efficiency of regulatory RNAs and RNA‐guided processes at extreme temperatures. These organisms must overcome the intrinsic thermolability of RNAs. Elevated levels of RNA modifications and structured GC‐rich regions are observed for many universal noncoding RNA families. Guide RNAs are often protected from degradation by their presence within ribonucleoprotein complexes. Modification and ligation of RNA termini can be employed to impair exonucleolytic degradation. Finally, antisense strand transcription promotes the formation of RNA duplexes and can be used to stabilize RNA regions. In our review, we provide examples of these RNA stabilization mechanisms that have been observed in hyperthermophilic archaeal model organisms.

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Section: Polyadenylation‐assisted Rna Degradationmentioning

confidence: 79%

Section: Polyadenylation-assisted Rna Degradationmentioning

confidence: 99%

RNA stabilization in hyperthermophilic archaea

Gomes-Filho

Randau

2019

Annals of the New York Academy of Sciences

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“…Further, aDnaG (and the exosome) interacts with the Sm-like proteins SmAP1 and SmAP2, and this interaction seems to influence the subcellular localization of the exosome and the levels of the A-rich RNA tails in the cell [13]. Finally, the exosome was found to interact with aNop5 in the stationary growth phase, and this interaction depends on aRrp4 [14]. Nop5 is part of an RNA methylating protein complex [15].…”

Section: Introductionmentioning

confidence: 95%

iCLIP analysis of RNA substrates of the archaeal exosome

et al. 2020

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Background The archaeal exosome is an exoribonucleolytic multiprotein complex, which degrades single-stranded RNA in 3′ to 5′ direction phosphorolytically. In a reverse reaction, it can add A-rich tails to the 3′-end of RNA. The catalytic center of the exosome is in the aRrp41 subunit of its hexameric core. Its RNA-binding subunits aRrp4 and aDnaG confer poly(A) preference to the complex. The archaeal exosome was intensely characterized in vitro, but still little is known about its interaction with natural substrates in the cell, particularly because analysis of the transcriptome-wide interaction of an exoribonuclease with RNA is challenging. Results To determine binding sites of the exosome to RNA on a global scale, we performed individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP) analysis with antibodies directed against aRrp4 and aRrp41 of the chrenarchaeon Sulfolobus solfataricus. A relatively high proportion (17–19%) of the obtained cDNA reads could not be mapped to the genome. Instead, they corresponded to adenine-rich RNA tails, which are post-transcriptionally synthesized by the exosome, and to circular RNAs (circRNAs). We identified novel circRNAs corresponding to 5′ parts of two homologous, transposase-related mRNAs. To detect preferred substrates of the exosome, the iCLIP reads were compared to the transcript abundance using RNA-Seq data. Among the strongly enriched exosome substrates were RNAs antisense to tRNAs, overlapping 3′-UTRs and RNAs containing poly(A) stretches. The majority of the read counts and crosslink sites mapped in mRNAs. Furthermore, unexpected crosslink sites clustering at 5′-ends of RNAs was detected. Conclusions In this study, RNA targets of an exoribonuclease were analyzed by iCLIP. The data documents the role of the archaeal exosome as an exoribonuclease and RNA-tailing enzyme interacting with all RNA classes, and underlines its role in mRNA turnover, which is important for adaptation of prokaryotic cells to changing environmental conditions. The clustering of crosslink sites near 5′-ends of genes suggests simultaneous binding of both RNA ends by the S. solfataricus exosome. This may serve to prevent translation of mRNAs dedicated to degradation in 3′-5′ direction.

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“…The core of this archaeal RNA-degrading machine is composed of Rrp41 (3′−5′ exoribonuclease and poly-RNA tailing), Rrp42 (non-catalytic scaffold), Rrp4 (RNA-binding), Csl4 (RNA presentation), and DnaG (DNA primase) ( 11 ). Additional subunits include Nop5 (rRNA/tRNA 2′- O -methyl-transferase) ( 12 ), aRNase J, and a Ski2-like RNA helicase ( 13 ). Halophilic archaea and certain methanogens, however, do not encode an RNA exosome.…”

Section: Introductionmentioning

confidence: 99%

RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii

Jia

Dantuluri

Margulies

et al. 2023

mBio

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Nucleases are strictly regulated and often localized in the cell to avoid the uncontrolled degradation of DNA and RNA. Here, a new type of nuclease complex, composed of RecJ3, RecJ4, and aRNase J, was identified through its ATP-dependent association with the ubiquitin-like SAMP1 and AAA-ATPase Cdc48a. The complex was discovered in Haloferax volcanii , an archaeon lacking an RNA exosome. Genetic analysis revealed aRNase J to be essential and RecJ3, RecJ4, and Cdc48a to function in the recovery from DNA damage including genotoxic agents that generate double-strand breaks. The RecJ3:RecJ4:aRNase J complex (isolated in 2:2:1 stoichiometry) functioned primarily as a 3′−5′ exonuclease in hydrolyzing RNA and ssDNA, with the mechanism non-processive for ssDNA. aRNase J could also be purified as a homodimer that catalyzed endoribonuclease activity and, thus, was not restricted to the 5′−3′ exonuclease activity typical of aRNase J homologs. Moreover, RecJ3 and RecJ4 could be purified as a 560-kDa subcomplex in equimolar subunit ratio with nuclease activities mirroring the full RecJ3/4-aRNase J complex. These findings prompted reconstitution assays that suggested RecJ3/4 could suppress, alter, and/or outcompete the nuclease activities of aRNase J. Based on the phenotypic results, this control mechanism of aRNase J by RecJ3/4 is not necessary for cell growth but instead appears important for DNA repair. IMPORTANCE Nucleases are critical for various cellular processes including DNA replication and repair. Here, a dynamic type of nuclease complex is newly identifiedidentifiedidentifiedin the archaeon Haloferax volcanii , which is missing the canonical RNA exosome. The complex, composed of RecJ3, RecJ4, and aRNase J, functions primarily as a 3′−5′ exonuclease and was discovered through its ATP-dependent association with the ubiquitin-like SAMP1 and Cdc48a. aRNase J alone forms a homodimer that has endonuclease function and, thus, is not restricted to 5′−3′ exonuclease activity typical of other aRNase J enzymes. RecJ3/4 appears to suppress, alter, and/or outcompete the nuclease activities of aRNase J. While aRNase J is essential for growth, RecJ3/4, Cdc48a, and SAMPs are important for recovery against DNA damage. These biological distinctions may correlate with the regulated nuclease activity of aRNase J in the RecJ3/4-aRNaseJ complex.

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Nop5 interacts with the archaeal RNA exosome

Cited by 5 publications

References 39 publications

RNA stabilization in hyperthermophilic archaea

RNA stabilization in hyperthermophilic archaea

iCLIP analysis of RNA substrates of the archaeal exosome

RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii

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