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

Abstract

DEAD-box proteins are a class of nonprocessive RNA helicases that dynamically modulate the structure of RNA and ribonucleoprotein complexes (RNPs). However, the precise roles of individual members are not well understood. Work from our laboratory revealed that the DEAD-box protein Dbp2 in is an active RNA helicase in vitro that functions in transcription by promoting mRNP assembly, repressing cryptic transcription initiation, and regulating long noncoding RNA activity. Interestingly, Dbp2 is also linked to glucose sensing and hexose transporter gene expression. DDX5 is the mammalian ortholog of Dbp2 that has been implicated in cancer and metabolic syndrome, suggesting that the role of Dbp2 and DDX5 in glucose metabolic regulation is conserved. Herein, we present a refined biochemical and biological comparison of yeast Dbp2 and human DDX5 enzymes. We find that human DDX5 possesses a 10-fold higher unwinding activity than Dbp2, which is partially due to the presence of a mammalian/avian specific C-terminal extension. Interestingly, ectopic expression of rescues the cold sensitivity, cryptic initiation defects, and impaired glucose import in Δ cells, suggesting functional conservation. Consistently, we show that DDX5 promotes glucose uptake and glycolysis in mouse AML12 hepatocyte cells, suggesting that mammalian DDX5 and Dbp2 share conserved roles in cellular metabolism.

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

“…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). …”

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

“…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 .…”

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

“…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.…”