Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with <i>S. cerevisiae</i> ortholog Dbp2 in transcriptional control and glucose metabolism

Zheng, Xing; Wang, Siwen; Tran, Elizabeth

doi:10.1261/rna.060335.116

Cited by 46 publications

(67 citation statements)

References 80 publications

(128 reference statements)

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“…A further notable difference between DDX3X and Ded1p is the absence of pronounced strand annealing activity by DDX3X. This observation parallels a recent report for the DEAD-box helicase orthologs Dbp2p from S.cerevisae and DDX5X from human, where the yeast ortholog also shows stronger strand annealing activity than the human protein (47). …”

Section: Discussionsupporting

confidence: 84%

Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p

Sharma

Putnam

Jankowsky

2017

Journal of Molecular Biology

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DDX3X is a conserved DEAD-box RNA helicase involved in translation initiation and other processes of RNA metabolism. Mutations in human DDX3X and deregulation of its expression are linked to tumorigenesis and intellectual disability. The protein is also targeted by diverse viruses. Previous studies demonstrated helicase and NTPase activities for DDX3X, but important biochemical features of the enzyme remain unclear. Here, we systematically characterize enzymatic activities of human DDX3X and compare these to its closely related S. cerevisiae ortholog Ded1p. We show that DDX3X, like Ded1p, exclusively utilizes adenosine triphosphates to unwind helices, oligomerizes to function as efficient RNA helicase, and does not unwind DNA duplexes. The ATPase activity of DDX3X is markedly stimulated by RNA and weaker by DNA, although DNA binds to the enzyme. For RNA unwinding, DDX3X shows a greater preference than Ded1p for substrates with unpaired regions 3′ to the duplex over those with 5′ unpaired regions. DDX3X separates longer RNA duplexes faster than Ded1p and is less potent than Ded1p in facilitating strand annealing. Our results reveal that the biochemical activities of human DDX3X are typical for DEAD-box RNA helicases, but diverge quantitatively from its highly similar S. cerevisiae ortholog Ded1p.

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Section: Discussionsupporting

confidence: 84%

Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p

Sharma

Putnam

Jankowsky

2017

Journal of Molecular Biology

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“…Previous results from our laboratory showed that the ortholog of DDX5 in S. cerevisiae, Dbp2 (Xing et al 2019), is required for efficient termination of RNAPII transcription, as loss of DBP2 results in accumulation of a 39 extended GAL10 mRNA and GAL10s long, noncoding RNA (Cloutier et al 2012). Both Dbp2 and DDX5 exhibit highly efficient RNA duplex unwinding in vitro, consistent with a role in altering secondary structure Xing et al 2017). Furthermore, Dbp2 associates with actively transcribed chromatin in an RNA-dependent manner and is required for pre-mRNA maturation and messenger RNP assembly, as evidenced by reduced binding of export factors Nab2, Yra1, and Mex67 in dbp2D cells .…”

supporting

confidence: 53%

Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination

et al. 2019

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RNA helicases are a class of enzymes that unwind RNA duplexes in vitro but whose cellular functions are largely enigmatic. Here, we provide evidence that the DEAD-box protein Dbp2 remodels RNA-protein complex (RNP) structure to facilitate efficient termination of transcription in Saccharomyces cerevisiae via the Nrd1-Nab3-Sen1 (NNS) complex. First, we find that loss of DBP2 results in RNA polymerase II accumulation at the 39 ends of small nucleolar RNAs and a subset of mRNAs. In addition, Dbp2 associates with RNA sequence motifs and regions bound by Nrd1 and can promote its recruitment to NNS-targeted regions. Using Structure-seq, we find altered RNA/RNP structures in dbp2D cells that correlate with inefficient termination. We also show a positive correlation between the stability of structures in the 39 ends and a requirement for Dbp2 in termination. Taken together, these studies provide a role for RNA remodeling by Dbp2 and further suggests a mechanism whereby RNA structure is exploited for gene regulation.

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“…DDX5 resolves R-loops in vitro and in vivo DDX5 is an RGG/RG motif-containing helicase previously shown to unwind RNA:RNA and RNA:DNA duplexes (Hirling et al, 1989;Rossler et al, 2001;Xing et al, 2017). Dbp2, the S. cerevisiae homolog of DDX5, was shown to resolve RNA:DNA hybrids in the context of R-loops (Cloutier et al, 2016); however, whether DDX5 shares this R-loop resolving activity is unknown.…”

Section: Resultsmentioning

confidence: 99%

Arginine methylation of the DDX 5 helicase RGG / RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids

et al. 2019

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Aberrant transcription‐associated RNA : DNA hybrid (R‐loop) formation often causes catastrophic conflicts during replication, resulting in DNA double‐strand breaks and genomic instability. Preventing such conflicts requires hybrid dissolution by helicases and/or RN ase H. Little is known about how such helicases are regulated. Herein, we identify DDX 5, an RGG / RG motif‐containing DEAD ‐box family RNA helicase, as crucial player in R‐loop resolution. In vitro , recombinant DDX 5 resolves R‐loops in an ATP ‐dependent manner, leading to R‐loop degradation by the XRN 2 exoribonuclease. DDX 5‐deficient cells accumulate R‐loops at loci with propensity to form such structures based on RNA : DNA immunoprecipitation ( DRIP )‐ qPCR , causing spontaneous DNA double‐strand breaks and hypersensitivity to replication stress. DDX 5 associates with XRN 2 and resolves R‐loops at transcriptional termination regions downstream of poly(A) sites, to facilitate RNA polymerase II release associated with transcriptional termination. Protein arginine methyltransferase 5 ( PRMT 5) binds and methylates DDX 5 at its RGG / RG motif. This motif is required for DDX 5 interaction with XRN 2 and repression of cellular R‐loops, but not essential for DDX 5 helicase enzymatic activity. PRMT 5‐deficient cells accumulate R‐loops, resulting in increased formation of γH2 AX foci. Our findings exemplify a mechanism by which an RNA helicase is modulated by arginine methylation to resolve R‐loops, and its potential role in regulating transcription.

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Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism

Cited by 46 publications

References 80 publications

Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p

Biochemical Differences and Similarities between the DEAD-Box Helicase Orthologs DDX3X and Ded1p

Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination

Arginine methylation of the DDX 5 helicase RGG / RG motif by PRMT 5 regulates resolution of RNA:DNA hybrids

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