DEAD-Box Helicase Proteins Disrupt RNA Tertiary Structure Through Helix Capture

Pan, Cynthia; Potratz, Jeffrey P.; Cannon, Brian; Simpson, Zachary Booth; Ziehr, Jessica L.; Tijerina, Pilar; Russell, Rick

doi:10.1371/journal.pbio.1001981

Cited by 22 publications

(36 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We focused on Mss116p, a DEAD-box helicase found in yeast mitochondria that has been particularly well characterized in vitro (Huang et al 2005;Tijerina et al 2006;Del Campo et al 2007;Chen et al 2008;Liu et al 2008;Markov et al 2009;Karunatilaka et al 2010;Henn et al 2012;Mallam et al 2012;Russell et al 2013;Pan et al 2014). Our findings are entirely consistent with previous studies of the effects of Mss116p on RNA folding reactions in vitro and suggest that DEAD-box helicase activity might account for the unique discrepancy in the kinetics of secondary structure exchange exhibited between hairpin ribozyme pathways in vitro and in yeast.…”

Section: Introductionsupporting

confidence: 83%

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo

Ruminski

Watson

Mahen

et al. 2016

RNA

View full text Add to dashboard Cite

RNAs must assemble into specific structures in order to carry out their biological functions, but in vitro RNA folding reactions produce multiple misfolded structures that fail to exchange with functional structures on biological time scales. We used carefully designed self-cleaving mRNAs that assemble through well-defined folding pathways to identify factors that differentiate intracellular and in vitro folding reactions. Our previous work showed that simple base-paired RNA helices form and dissociate with the same rate and equilibrium constants in vivo and in vitro. However, exchange between adjacent secondary structures occurs much faster in vivo, enabling RNAs to quickly adopt structures with the lowest free energy. We have now used this approach to probe the effects of an extensively characterized DEAD-box RNA helicase, Mss116p, on a series of well-defined RNA folding steps in yeast. Mss116p overexpression had no detectable effect on helix formation or dissociation kinetics or on the stability of interdomain tertiary interactions, consistent with previous evidence that intracellular factors do not affect these folding parameters. However, Mss116p overexpression did accelerate exchange between adjacent helices. The nonprocessive nature of RNA duplex unwinding by DEAD-box RNA helicases is consistent with a branch migration mechanism in which Mss116p lowers barriers to exchange between otherwise stable helices by the melting and annealing of one or two base pairs at interhelical junctions. These results suggest that the helicase activity of DEAD-box proteins like Mss116p distinguish intracellular RNA folding pathways from nonproductive RNA folding reactions in vitro and allow RNA structures to overcome kinetic barriers to thermodynamic equilibration in vivo.

show abstract

Section: Introductionsupporting

confidence: 83%

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo

Ruminski

Watson

Mahen

et al. 2016

RNA

View full text Add to dashboard Cite

show abstract

“…In agreement with this model, a recent study shows that DEAD-box helicases can disrupt tertiary contacts by binding a secondary structure only after it spontaneously loses its tertiary contacts. After binding, they use ATP to unwind the helix (Pan et al 2014). Interestingly, the requirement for spontaneous dynamics implies a preference of DEAD-box helicases for less stable RNA structures, which are likely to experience greater dynamic fluctuations (Pan et al 2014).…”

Section: Discussionmentioning

confidence: 99%

“…After binding, they use ATP to unwind the helix (Pan et al 2014). Interestingly, the requirement for spontaneous dynamics implies a preference of DEAD-box helicases for less stable RNA structures, which are likely to experience greater dynamic fluctuations (Pan et al 2014). One would expect such low stable structures to exist in mRNA CDSs given that vastly fewer structures are identified by RNA probing in vivo than in vitro (Rouskin et al 2014).…”

Section: Discussionmentioning

confidence: 99%

A novel translational control mechanism involving RNA structures within coding sequences

et al. 2016

View full text Add to dashboard Cite

The impact of RNA structures in coding sequences (CDS) within mRNAs is poorly understood. Here, we identify a novel and highly conserved mechanism of translational control involving RNA structures within coding sequences and the DEADbox helicase Dhh1. Using yeast genetics and genome-wide ribosome profiling analyses, we show that this mechanism, initially derived from studies of the Brome Mosaic virus RNA genome, extends to yeast and human mRNAs highly enriched in membrane and secreted proteins. All Dhh1-dependent mRNAs, viral and cellular, share key common features. First, they contain long and highly structured CDSs, including a region located around nucleotide 70 after the translation initiation site; second, they are directly bound by Dhh1 with a specific binding distribution; and third, complementary experimental approaches suggest that they are activated by Dhh1 at the translation initiation step. Our results show that ribosome translocation is not the only unwinding force of CDS and uncover a novel layer of translational control that involves RNA helicases and RNA folding within CDS providing novel opportunities for regulation of membrane and secretome proteins.

show abstract

“…However, greater overexpression of Ded1 from an inducible GAL1 promoter represses translation, causing sequestration of eIF4E, eIF4G, and Pab1 in cytoplasmic granules (Hilliker et al 2011). Ded1 can form very stable complexes with RNA in vitro (Liu et al 2014) and it is important for resolving misfolded RNA structures and preventing higher-order structural contacts that would otherwise destabilize RNA architecture (Pan et al 2014).…”

Section: Mrna Recruitment Of the 43s Picmentioning

confidence: 99%

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

2016

View full text Add to dashboard Cite

In this review, we provide an overview of protein synthesis in the yeast Saccharomyces cerevisiae. The mechanism of protein synthesis is well conserved between yeast and other eukaryotes, and molecular genetic studies in budding yeast have provided critical insights into the fundamental process of translation as well as its regulation. The review focuses on the initiation and elongation phases of protein synthesis with descriptions of the roles of translation initiation and elongation factors that assist the ribosome in binding the messenger RNA (mRNA), selecting the start codon, and synthesizing the polypeptide. We also examine mechanisms of translational control highlighting the mRNA cap-binding proteins and the regulation of GCN4 and CPA1 mRNAs.

show abstract

DEAD-Box Helicase Proteins Disrupt RNA Tertiary Structure Through Helix Capture

Abstract: Single-molecule fluorescence experiments reveal how DEAD-box proteins unfold structured RNAs to promote conformational transitions and refolding to the native functional state.

Cited by 22 publications

References 62 publications

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo

A DEAD-box RNA helicase promotes thermodynamic equilibration of kinetically trapped RNA structures in vivo

A novel translational control mechanism involving RNA structures within coding sequences

Mechanism and Regulation of Protein Synthesis in Saccharomyces cerevisiae

Contact Info

Product

Resources

About