Evolutionarily Conserved Roles of the Dicer Helicase Domain in Regulating RNA Interference Processing

Kidwell, Mary Anne; Chan, Jessica M.; Doudna, Jennifer A.

doi:10.1074/jbc.m114.589051

Cited by 17 publications

(25 citation statements)

References 35 publications

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“…Dicer1 (dmDcr1), in contrast, is specialized on miRNA processing and is supported by the dsRBP Loquacious (Loqs) (Forstemann et al 2005;Jiang et al 2005;Saito et al 2005;Ye et al 2007). Like other Dicer proteins, dmDcr1 is characterized by several different domains (Tsutsumi et al 2011): two RNase III domains that cleave the two strands of the miRNA precursor (Zhang et al 2004), a dsRBD that supports the cleavage activity (Kidwell et al 2014), a PAZ domain, which interacts with the ds end of the pre-miRNA and positions it on human Dicer for cleavage ) and a helicase domain, which binds ATP and might be involved in substrate recognition (Sinha et al 2015). Loqs contains three dsRBDs (Fig.…”

Section: Introductionmentioning

confidence: 99%

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Jakob¹,

Treiber²,

Treiber³

et al. 2016

RNA

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In the microRNA (miRNA) pathway, Dicer processes precursors to mature miRNAs. For efficient processing, double-stranded RNA-binding proteins support Dicer proteins. In flies, Loquacious (Loqs) interacts with Dicer1 (dmDcr1) to facilitate miRNA processing. Here, we have solved the structure of the third double-stranded RNA-binding domain (dsRBD) of Loqs and define specific structural elements that interact with dmDcr1. In addition, we show that the linker preceding dsRBD3 contributes significantly to dmDcr1 binding. Furthermore, our structural work demonstrates that the third dsRBD of Loqs forms homodimers. Mutations in the dimerization interface abrogate dmDcr1 interaction. Loqs, however, binds to dmDcr1 as a monomer using the identified dimerization surface, which suggests that Loqs might form dimers under conditions where dmDcr1 is absent or not accessible. Since critical sequence elements are conserved, we suggest that dimerization might be a general feature of dsRBD proteins in gene silencing.

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Section: Introductionmentioning

confidence: 99%

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Jakob¹,

Treiber²,

Treiber³

et al. 2016

RNA

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“…During the course of our biochemical studies, we constantly detected in our purified preparations of full length DDX3X an unexpected exoribonuclease activity of this enzyme. Being aware of preliminary implications of DDX3X in genome stability ( 10 ) and of the existence of double-functioning enzymes with helicase/RNase activities ( 26 , 27 ) we tested a possible DDX3X RNaseH2-like activity. When incubated in the presence of a specific oligonucleotide dsDNA substrate containing a single rCMP embedded in one strand at a specific position (Substrate * D 39 R 1 D 15 : D 55 Figure 1A ), recombinant purified human DDX3X ( Supplementary Figure S1a and b ) cut at the 5′ side of the single rNMP, generating a product identical to the one of RNaseH2 (Figure 1A , compare lanes 1–5 with lanes 6–10), albeit with lower efficiency (Figure 1B ).…”

Section: Resultsmentioning

confidence: 99%

Novel alternative ribonucleotide excision repair pathways in human cells by DDX3X and specialized DNA polymerases

Riva

Garbelli

Casiraghi

et al. 2020

Nucleic Acids Research

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Removal of ribonucleotides (rNMPs) incorporated into the genome by the ribonucleotide excision repair (RER) is essential to avoid genetic instability. In eukaryotes, the RNaseH2 is the only known enzyme able to incise 5′ of the rNMP, starting the RER process, which is subsequently carried out by replicative DNA polymerases (Pols) δ or ϵ, together with Flap endonuclease 1 (Fen-1) and DNA ligase 1. Here, we show that the DEAD-box RNA helicase DDX3X has RNaseH2-like activity and can support fully reconstituted in vitro RER reactions, not only with Pol δ but also with the repair Pols β and λ. Silencing of DDX3X causes accumulation of rNMPs in the cellular genome. These results support the existence of alternative RER pathways conferring high flexibility to human cells in responding to the threat posed by rNMPs incorporation.

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“…The helicase domain is considered to be one of the most conserved regions among all Dicer proteins [ 50 ], and shows a high sequence similarity to the helicases of the superfamily SF2 [ 42 , 43 , 44 ]. SF2 is the largest and most diverse of the helicase superfamilies.…”

Section: Dicer Structure and The Importance Of Its Domainsmentioning

confidence: 99%

Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases

Ciechanowska

Pokornowska

Kurzyńska-Kokorniak

2021

IJMS

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Ribonuclease Dicer belongs to the family of RNase III endoribonucleases, the enzymes that specifically hydrolyze phosphodiester bonds found in double-stranded regions of RNAs. Dicer enzymes are mostly known for their essential role in the biogenesis of small regulatory RNAs. A typical Dicer-type RNase consists of a helicase domain, a domain of unknown function (DUF283), a PAZ (Piwi-Argonaute-Zwille) domain, two RNase III domains, and a double-stranded RNA binding domain; however, the domain composition of Dicers varies among species. Dicer and its homologues developed only in eukaryotes; nevertheless, the two enzymatic domains of Dicer, helicase and RNase III, display high sequence similarity to their prokaryotic orthologs. Evolutionary studies indicate that a combination of the helicase and RNase III domains in a single protein is a eukaryotic signature and is supposed to be one of the critical events that triggered the consolidation of the eukaryotic RNA interference. In this review, we provide the genetic insight into the domain organization and structure of Dicer proteins found in vertebrate and invertebrate animals, plants and fungi. We also discuss, in the context of the individual domains, domain deletion variants and partner proteins, a variety of Dicers’ functions not only related to small RNA biogenesis pathways.

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Evolutionarily Conserved Roles of the Dicer Helicase Domain in Regulating RNA Interference Processing

Cited by 17 publications

References 35 publications

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Structural and functional insights into the fly microRNA biogenesis factor Loquacious

Novel alternative ribonucleotide excision repair pathways in human cells by DDX3X and specialized DNA polymerases

Genetic Insight into the Domain Structure and Functions of Dicer-Type Ribonucleases

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