Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA

Long-range conformational changes in the nucleotide-bound states of the DEAD-box helicase Vasa

DEAD-box helicases use ATP to unwind short double-stranded RNA (dsRNA). The helicase core consists of two discrete domains, termed RecA_N and RecA_C. The nucleotide binding site is harbored in RecA_N, while both RecA_N and RecA_C are involved in RNA recognition and ATP hydrolysis. In the absence of nucleotides or RNA, RecA_N and RecA_C do not interact ("open" form of the enzyme). In the presence of both RNA and ATP the two domains come together ("closed" form), building the composite RNA binding site and stimulating ATP hydrolysis. Because of the different roles and thermodynamic properties of the ADP-bound and ATP-bound states in the catalytic cycle, the conformations of DEAD-box helicases in complex with ATP and ADP are assumed to be different. However, the available crystal structures do not recapitulate these supposed differences and show identical conformations of DEAD-box helicases independent of the identity of the bound nucleotide. Here, we use NMR to demonstrate that the conformations of the ATP- and ADP-bound forms of the DEAD-box helicase Vasa are indeed different, contrary to the results from x-ray crystallography. These differences do not relate to the populations of the open and closed forms, but are intrinsic to the RecA_N domain. NMR chemical shift analysis reveals the regions of RecA_N where the average conformations of Vasa-ADP and Vasa-ATP are most different and indicates that these differences may contribute to modulating the affinity of the two nucleotide-bound complexes for RNA substrates.

Communication between DNA and nucleotide binding sites facilitates stepping by the RecBCD helicase

Double-strand DNA breaks are the severest type of genomic damage, requiring rapid response to ensure survival. RecBCD helicase in prokaryotes initiates processive and rapid DNA unzipping, essential for break repair. The energetics of RecBCD during translocation along the DNA track are quantitatively not defined. Specifically, it's essential to understand the mechanism by which RecBCD switches between its binding states to enable its translocation. Here, we determine, by systematic affinity measurements, the degree of coupling between DNA and nucleotide binding to RecBCD. In the presence of ADP, RecBCD binds weakly to DNA that harbors a double overhang mimicking an unwinding intermediate. Consistently, RecBCD binds weakly to ADP in the presence of the same DNA. We did not observe coupling between DNA and nucleotide binding for DNA molecules having only a single overhang, suggesting that RecBCD subunits must both bind DNA to 'sense' the nucleotide state. On the contrary, AMPpNp shows weak coupling as RecBCD remains strongly bound to DNA in its presence. Detailed thermodynamic analysis of the RecBCD reaction mechanism suggests an 'energetic compensation' between RecB and RecD, which may be essential for rapid unwinding. Our findings provide the basis for a plausible stepping mechanism' during the processive translocation of RecBCD.

Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA

DEAD-box RNA helicases are implicated in most aspects of RNA biology, where these enzymes unwind short RNA duplexes in an ATP-dependent manner. During the central step of the unwinding cycle, the two domains of the helicase core form a distinct closed conformation that destabilizes the RNA duplex, which ultimately leads to duplex melting. Despite the importance of this step for the unwinding process no high-resolution structures of this state are available. Here, I used nuclear magnetic resonance spectroscopy and X-ray crystallography to determine structures of the DEAD-box helicase DbpA in the closed conformation, complexed with substrate duplexes and single-stranded unwinding product. These structures reveal that DbpA initiates duplex unwinding by interacting with up to three base-paired nucleotides and a 5' single-stranded RNA duplex overhang. These high-resolution snapshots, together with biochemical assays, rationalize the destabilization of the RNA duplex and are integrated into a conclusive model of the unwinding process.

Auxiliary ATP binding sites support DNA unwinding by RecBCD

The RecBCD helicase initiates double-stranded break repair in bacteria by processively unwinding DNA with a rate approaching ∼1,600 bp·s⁻¹, but the mechanism enabling such a fast rate is unknown. Employing a wide range of methodologies — including equilibrium and time-resolved binding experiments, ensemble and single-molecule unwinding assays, and crosslinking followed by mass spectrometry — we reveal the existence of auxiliary binding sites in the RecC subunit, where ATP binds with lower affinity and distinct chemical interactions as compared to the known catalytic sites. The essentiality and functionality of these sites are demonstrated by their impact on the survival of E.coli after exposure to damage-inducing radiation. We propose a model by which RecBCD achieves its optimized unwinding rate, even when ATP is scarce, by using the auxiliary binding sites to increase the flux of ATP to its catalytic sites.

RecBCD is a remarkably fast DNA helicase. Using a battery of biophysical methods, Zananiri et. al reveal additional, non-catalytic ATP binding sites that increase the ATP flux to the catalytic sites that allows fast unwinding when ATP is scarce.

Measuring the impact of cofactors on RNA helicase activities

RNA helicases are the largest class of enzymes in eukaryotic RNA metabolism. In cells, protein cofactors regulate RNA helicase functions and impact biochemical helicase activities. Understanding how cofactors affect enzymatic activities of RNA helicases is thus critical for delineating physical roles and regulation of RNA helicases in cells. Here, we discuss approaches and conceptual considerations for the design of experiments to interrogate cofactor effects on RNA helicase activities in vitro. We outline the mechanistic frame for helicase reactions, discuss optimization of experimental setup and reaction parameters for measuring cofactor effects on RNA helicase activities, and provide basic guides to data analysis and interpretation. The described approaches are also instructive for determining the impact of small molecule inhibitors of RNA helicases.

OUP accepted manuscript

The DEAD-box protein Dbp5 is essential for RNA export, which involves regulation by the nucleoporins Gle1 and Nup159 at the cytoplasmic face of the nuclear pore complex (NPC). Mechanistic understanding of how these nucleoporins regulate RNA export requires analyses of the intrinsic and activated Dbp5 ATPase cycle. Here, kinetic and equilibrium analyses of the Saccharomyces cerevisiae Gle1-activated Dbp5 ATPase cycle are presented, indicating that Gle1 and ATP, but not ADP-P_i or ADP, binding to Dbp5 are thermodynamically coupled. As a result, Gle1 binds Dbp5-ATP > 100-fold more tightly than Dbp5 in other nucleotide states and Gle1 equilibrium binding of ATP to Dbp5 increases >150-fold via slowed ATP dissociation. Second, Gle1 accelerated Dbp5 ATPase activity by increasing the rate-limiting P_i release rate constant ∼20-fold, which remains rate limiting. These data show that Gle1 activates Dbp5 by modulating ATP binding and P_i release. These Gle1 activities are expected to facilitate ATPase cycling, ensuring a pool of ATP bound Dbp5 at NPCs to engage RNA during export. This work provides a mechanism of Gle1-activation of Dbp5 and a framework to understand the joint roles of Gle1, Nup159, and other nucleoporins in regulating Dbp5 to mediate RNA export and other Dbp5 functions in gene expression.

Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome

DEAD-box RNA helicases are essential cellular enzymes that remodel misfolded RNA structures in an adenosine triphosphate (ATP)-dependent process. The DEAD-box helicase DbpA is involved in the complex and highly regulated process of ribosome maturation. To prevent wasteful hydrolysis of ATP by DbpA, the enzyme is only active when bound to maturing ribosomes. Here, we elucidate the structural basis behind this important regulatory mechanism and find that the recruited ribosome substrate is able to stabilize the catalytically important closed state of the helicase. In addition, our data identify the natural site of action for DbpA in the maturing ribosome and provide a molecular explanation for the observed ribosome maturation defects that result from the overexpression of a DbpA mutant form.

The adenosine triphosphate (ATP)-dependent DEAD-box RNA helicase DbpA from Escherichia coli functions in ribosome biogenesis. DbpA is targeted to the nascent 50S subunit by an ancillary, carboxyl-terminal RNA recognition motif (RRM) that specifically binds to hairpin 92 (HP92) of the 23S ribosomal RNA (rRNA). The interaction between HP92 and the RRM is required for the helicase activity of the RecA-like core domains of DbpA. Here, we elucidate the structural basis by which DbpA activity is endorsed when the enzyme interacts with the maturing ribosome. We used nuclear magnetic resonance (NMR) spectroscopy to show that the RRM and the carboxyl-terminal RecA-like domain tightly interact. This orients HP92 such that this RNA hairpin can form electrostatic interactions with a positively charged patch in the N-terminal RecA-like domain. Consequently, the enzyme can stably adopt the catalytically important, closed conformation. The substrate binding mode in this complex reveals that a region 5′ to helix 90 in the maturing ribosome is specifically targeted by DbpA. Finally, our results indicate that the ribosome maturation defects induced by a dominant negative DbpA mutation are caused by a delayed dissociation of DbpA from the nascent ribosome. Taken together, our findings provide unique insights into the important regulatory mechanism that modulates the activity of DbpA.

IRC3 regulates mitochondrial translation in response to metabolic cues in Saccharomyces cerevisiae

Mitochondrial oxidative phosphorylation (OXPHOS) enzymes are made up of dual genetic origin. Mechanisms regulating the expression of nuclear-encoded OXPHOS subunits in response to metabolic cues (glucose vs. glycerol), is significantly understood while regulation of mitochondrially encoded OXPHOS subunits is poorly defined. Here, we show that IRC3 a DEAD/H box helicase, previously implicated in mitochondrial DNA maintenance, is central to integrating metabolic cues with mitochondrial translation. Irc3 associates with mitochondrial small ribosomal subunit in cells consistent with its role in regulating translation elongation based on Arg8^m reporter system. IRC3 deleted cells retained mitochondrial DNA despite growth defect on glycerol plates. Glucose grown Δirc3ρ⁺ and irc3 temperature-sensitive cells at 37⁰C have reduced translation rates from majority of mRNAs. In contrast, when galactose was the carbon source, reduction in mitochondrial translation was observed predominantly from Cox1 mRNA in Δirc3ρ⁺ but no defect was observed in irc3 temperature-sensitive cells, at 37⁰C. In support, of a model whereby IRC3 responds to metabolic cues to regulate mitochondrial translation, suppressors of Δirc3 isolated for restoration of growth on glycerol media restore mitochondrial protein synthesis differentially in presence of glucose vs. glycerol.

Assignment of the Ile, Leu, Val, Met and Ala methyl group resonances of the DEAD-box RNA helicase DbpA from E. coli

ATP-dependent DEAD-box helicases constitute one of the largest families of RNA helicases and are important regulators of most RNA-dependent cellular processes. The functional core of these enzymes consists of two RecA-like domains. Changes in the interdomain orientation of these domains upon ATP and RNA binding result in the unwinding of double-stranded RNA. The DEAD-box helicase DbpA from E. coli is involved in ribosome maturation. It possesses a C-terminal RNA recognition motif (RRM) in addition to the canonical RecA-like domains. The RRM recruits DbpA to nascent ribosomes by binding to hairpin 92 of the 23S rRNA. To follow the conformational changes of Dbpa during the catalytic cycle we initiated solution state NMR studies. We use a divide and conquer approach to obtain an almost complete resonance assignment of the isoleucine, leucine, valine, methionine and alanine methyl group signals of full length DbpA (49 kDa). In addition, we also report the backbone resonance assignments of two fragments of DbpA that were used in the course of the methyl group assignment. These assignments are the first step towards a better understanding of the molecular mechanism behind the ATP-dependent RNA unwinding process catalyzed by DEAD-box helicases.

Interconnected assembly factors regulate the biogenesis of mitoribosomal large subunit

Mitoribosomes consist of ribosomal RNA and protein components, coordinated assembly of which is critical for function. We used mitoribosomes from Trypanosoma brucei with reduced RNA and increased protein mass to provide insights into the biogenesis of the mitoribosomal large subunit. Structural characterization of a stable assembly intermediate revealed 22 assembly factors, some of which have orthologues/counterparts/homologues in mammalian genomes. These assembly factors form a protein network that spans a distance of 180 Å, shielding the ribosomal RNA surface. The central protuberance and L7/L12 stalk are not assembled entirely and require removal of assembly factors and remodeling of the mitoribosomal proteins to become functional. The conserved proteins GTPBP7 and mt‐EngA are bound together at the subunit interface in proximity to the peptidyl transferase center. A mitochondrial acyl‐carrier protein plays a role in docking the L1 stalk, which needs to be repositioned during maturation. Additional enzymatically deactivated factors scaffold the assembly while the exit tunnel is blocked. Together, this extensive network of accessory factors stabilizes the immature sites and connects the functionally important regions of the mitoribosomal large subunit.

ATP utilization by a DEAD-box protein during refolding of a misfolded group I intron ribozyme

DEAD-box helicase proteins perform ATP-dependent rearrangements of structured RNAs throughout RNA biology. Short RNA helices are unwound in a single ATPase cycle, but the ATP requirement for more complex RNA structural rearrangements is unknown. Here we measure the amount of ATP used for native refolding of a misfolded group I intron ribozyme by CYT-19, a Neurospora crassa DEAD-box protein that functions as a general chaperone for mitochondrial group I introns. By comparing the rates of ATP hydrolysis and ribozyme refolding, we find that several hundred ATP molecules are hydrolyzed during refolding of each ribozyme molecule. After subtracting nonproductive ATP hydrolysis that occurs in the absence of ribozyme refolding, we find that approximately 100 ATPs are hydrolyzed per refolded RNA as a consequence of interactions specific to the misfolded ribozyme. This value is insensitive to changes in ATP and CYT-19 concentration and decreases with decreasing ribozyme stability. Because of earlier findings that ∼90% of global ribozyme unfolding cycles lead back to the kinetically preferred misfolded conformation and are not observed, we estimate that each global unfolding cycle consumes ∼10 ATPs. Our results indicate that CYT-19 functions as a general RNA chaperone by using a stochastic, energy-intensive mechanism to promote RNA unfolding and refolding, suggesting an evolutionary convergence with protein chaperones.

General and Target-Specific DExD/H RNA Helicases in Eukaryotic Translation Initiation

DExD (DDX)- and DExH (DHX)-box RNA helicases, named after their Asp-Glu-x-Asp/His motifs, are integral to almost all RNA metabolic processes in eukaryotic cells. They play myriad roles in processes ranging from transcription and mRNA-protein complex remodeling, to RNA decay and translation. This last facet, translation, is an intricate process that involves DDX/DHX helicases and presents a regulatory node that is highly targetable. Studies aimed at better understanding this family of conserved proteins have revealed insights into their structures, catalytic mechanisms, and biological roles. They have also led to the development of chemical modulators that seek to exploit their essential roles in diseases. Herein, we review the most recent insights on several general and target-specific DDX/DHX helicases in eukaryotic translation initiation.

Kinetics and Thermodynamics of DbpA Protein's C-Terminal Domain Interaction with RNA

DbpA is an Escherichia coli DEAD-box RNA helicase implicated in RNA structural isomerization in the peptide bond formation site. In addition to the RecA-like catalytic core conserved in all of the members of DEAD-box family, DbpA contains a structured C-terminal domain, which is responsible for anchoring DbpA to hairpin 92 of 23S ribosomal RNA during the ribosome assembly process. Here, surface plasmon resonance was used to determine the equilibrium dissociation constant and the microscopic rate constants of the DbpA C-terminal domain association and dissociation to a fragment of 23S ribosomal RNA containing hairpin 92. Our results show that the DbpA protein's residence time on the RNA is 10 times longer than the time DbpA requires to hydrolyze one ATP. Thus, our data suggest that once bound to the intermediate ribosomal particles via its RNA-binding domain, DbpA could unwind a number of double-helix substrates before its dissociation from the ribosomal particles.

ATPase activity of the DEAD-box protein Dhh1 controls processing body formation

Translational repression and mRNA degradation are critical mechanisms of posttranscriptional gene regulation that help cells respond to internal and external cues. In response to certain stress conditions, many mRNA decay factors are enriched in processing bodies (PBs), cellular structures involved in degradation and/or storage of mRNAs. Yet, how cells regulate assembly and disassembly of PBs remains poorly understood. Here, we show that in budding yeast, mutations in the DEAD-box ATPase Dhh1 that prevent ATP hydrolysis, or that affect the interaction between Dhh1 and Not1, the central scaffold of the CCR4-NOT complex and an activator of the Dhh1 ATPase, prevent PB disassembly in vivo. Intriguingly, this process can be recapitulated in vitro, since recombinant Dhh1 and RNA, in the presence of ATP, phase-separate into liquid droplets that rapidly dissolve upon addition of Not1. Our results identify the ATPase activity of Dhh1 as a critical regulator of PB formation.

DOI:http://dx.doi.org/10.7554/eLife.18746.001

Most cells and organisms live in changeable environments. Adapting to environmental changes means that organisms must quickly alter which of their genes they express. Varying which genes are switched on or off is not enough; cells must also degrade existing messenger RNAs (or mRNAs for short), which contain the genetic instructions of the previously active genes. Therefore, cells must tightly regulate the machinery needed to degrade mRNAs.

When Baker’s yeast (also known as budding yeast) cells experience certain stressful conditions, the proteins that break down mRNAs localize into specific structures inside the cell known as ‘processing bodies’. These structures are found in many other organisms across evolution, from yeast to human. Processing bodies also form in a variety of biological contexts, such as in nerve cells and developing embryos. Still, why cells form processing bodies, and how their assembly is regulated, is not well understood.

One essential component of processing bodies is an enzyme called Dhh1. This enzyme has been conserved throughout evolution and is known to promote the decay of mRNAs as well as to repress their translation into proteins. Now, Mugler, Hondele et al. show that Dhh1’s must break down molecules of the energy carrier ATP (referred to as its “ATPase activity”) in order to regulate the dynamic nature of processing bodies. Mutant Dhh1 proteins that lack ATPase activity form permanent processing bodies in non-stressed yeast cells. This shows that that the breakdown of ATP by Dhh1 is required for the disassembly of processing bodies. Similar results were seen for mutant Dhh1 proteins that cannot interact with Not1, a protein which enhances the ATPase activity of Dhh1.

Next Mugler, Hondele et al. mixed purified Dhh1 with ATP and RNA molecules and saw that the mixture underwent a “liquid-liquid phase separation” and formed observable granules, similar to oil droplets in water. These granules dissolved when Not1 was added to stimulate the Dhh1 enzyme to turnover ATP. This showed that several important biochemical and biophysical aspects of processing bodies seen within living cells could be recreated outside of a cell.

Armed with a greater understanding of the rules that govern the formation of processing bodies, future work can now address how important processing bodies are for regulating gene expression. Another challenge for the future will be to examine the specific roles that processing bodies play in yeast and other cells, like human egg cells or nerve cells.

DOI:http://dx.doi.org/10.7554/eLife.18746.002

Recent adaptations of fluorescence techniques for the determination of mechanistic parameters of helicases and translocases

Helicases and translocases are nucleic acid (NA)-based molecular motors that use the free energy liberated during the nucleoside triphosphate (NTP, usually ATP) hydrolysis cycle for unidirectional translocation along their NA (DNA, RNA or heteroduplex) substrates. Determination of the kinetic and thermodynamic parameters of their mechanoenzymatic cycle serves as a basis for the exploration of their physiological behavior and various cellular functions. Here we describe how recent adaptations of fluorescence-based solution kinetic methods can be used to determine practically all important mechanistic parameters of NA-based motor proteins. We outline practically useful analysis procedures for equilibrium, steady-state and transient kinetic data. This analysis can be used to quantitatively characterize the enzymatic steps of the NTP hydrolytic cycle, the binding site size, stoichiometry and energetics of protein-NA interactions, the rate and processivity of translocation along and unwinding of NA strands, and the mechanochemical coupling between these processes. The described methods yield insights into the functional role of the enzymes, and also greatly aid the design and interpretation of single-molecule experiments as well as the engineering of enzymatic properties for biotechnological applications.

The organization and contribution of helicases to RNA splicing

Splicing is an essential step of gene expression. It occurs in two consecutive chemical reactions catalyzed by a large protein-RNA complex named the spliceosome. Assembled on the pre-mRNA substrate from five small nuclear proteins, the spliceosome acts as a protein-controlled ribozyme to catalyze the two reactions and finally dissociates into its components, which are re-used for a new round of splicing. Upon following this cyclic pathway, the spliceosome undergoes numerous intermediate stages that differ in composition as well as in their internal RNA-RNA and RNA-protein contacts. The driving forces and control mechanisms of these remodeling processes are provided by specific molecular motors called RNA helicases. While eight spliceosomal helicases are present in all organisms, higher eukaryotes contain five additional ones potentially required to drive a more intricate splicing pathway and link it to an RNA metabolism of increasing complexity. Spliceosomal helicases exhibit a notable structural diversity in their accessory domains and overall architecture, in accordance with the diversity of their task-specific functions. This review summarizes structure-function knowledge about all spliceosomal helicases, including the latter five, which traditionally are treated separately from the conserved ones. The implications of the structural characteristics of helicases for their functions, as well as for their structural communication within the multi-subunits environment of the spliceosome, are pointed out.

Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin

RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-binding proteins Yra1, Nab2, and Mex67 onto poly(A)(+)RNA. We also found that Yra1 associates directly with Dbp2 and functions as an inhibitor of Dbp2-dependent duplex unwinding, suggestive of a cycle of unwinding and inhibition by Dbp2. To test this, we undertook a series of experiments to shed light on the order of events for Dbp2 in co-transcriptional mRNP assembly. We now show that Dbp2 is recruited to chromatin via RNA and forms a large, RNA-dependent complex with Yra1 and Mex67. Moreover, single-molecule fluorescence resonance energy transfer and bulk biochemical assays show that Yra1 inhibits unwinding in a concentration-dependent manner by preventing the association of Dbp2 with single-stranded RNA. This inhibition prevents over-accumulation of Dbp2 on mRNA and stabilization of a subset of RNA polymerase II transcripts. We propose a model whereby Yra1 terminates a cycle of mRNP assembly by Dbp2.

P(I) Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5)

mRNA export from the nucleus depends on the ATPase activity of the DEAD-box protein Dbp5/DDX19. Although Dbp5 has measurable ATPase activity alone, several regulatory factors (e.g., RNA, nucleoporin proteins, and the endogenous small molecule InsP₆) modulate catalytic activity in vitro and in vivo to facilitate mRNA export. An analysis of the intrinsic and regulator-activated Dbp5 ATPase cycle is necessary to define how these factors control Dbp5 and mRNA export. Here, we report a kinetic and equilibrium analysis of the Saccharomyces cerevisiae Dbp5 ATPase cycle, including the influence of RNA on Dbp5 activity. These data show that ATP binds Dbp5 weakly in rapid equilibrium with a binding affinity (K_T ~ 4 mM) comparable to the K_M for steady-state cycling, while ADP binds an order of magnitude more tightly (K_D ~ 0.4 mM). The overall intrinsic steady-state cycling rate constant (k_cat) is limited by slow, near-irreversible ATP hydrolysis and even slower subsequent phosphate release. RNA increases k_cat and rate-limiting P_i release 20-fold, although P_i release continues to limit steady-state cycling in the presence of RNA, in conjunction with RNA binding. Together, this work identifies RNA binding and P_i release as important biochemical transitions within the Dbp5 ATPase cycle and provides a framework for investigating the means by which Dbp5 and mRNA export is modulated by regulatory factors.

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mRNA export from the nucleus requires DEAD-box protein Dbp5/DDX19 ATPase activity.

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Kinetics and thermodynamics of intrinsic Dbp5 ATPase reveal RNA's effect on Dbp5.

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Intrinsic Dbp5 ATPase is limited by slow ATP hydrolysis and slower P_i release.

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RNA activates P_i release, but it and RNA binding still limit RNA-stimulated ATPase.

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RNA binding and P_i release define RNA-stimulated Dbp5 ATPase for further regulation.

Myo19 is an outer mitochondrial membrane motor and effector of starvation-induced filopodia

Mitochondria respond to environmental cues and stress conditions. Additionally, the disruption of the mitochondrial network dynamics and its distribution is implicated in a variety of neurodegenerative diseases. Here, we reveal a new function for Myo19 in mitochondrial dynamics and localization during the cellular response to glucose starvation. Ectopically expressed Myo19 localized with mitochondria to the tips of starvation-induced filopodia. Corollary to this, RNA interference (RNAi)-mediated knockdown of Myo19 diminished filopodia formation without evident effects on the mitochondrial network. We analyzed the Myo19-mitochondria interaction, and demonstrated that Myo19 is uniquely anchored to the outer mitochondrial membrane (OMM) through a 30-45-residue motif, indicating that Myo19 is a stably attached OMM molecular motor. Our work reveals a new function for Myo19 in mitochondrial positioning under stress.

A gating mechanism for Pi release governs the mRNA unwinding by eIF4AI during translation initiation

Eukaryotic translation initiation factor eIF4AI, the founding member of DEAD-box helicases, undergoes ATP hydrolysis-coupled conformational changes to unwind mRNA secondary structures during translation initiation. However, the mechanism of its coupled enzymatic activities remains unclear. Here we report that a gating mechanism for Pi release controlled by the inter-domain linker of eIF4AI regulates the coupling between ATP hydrolysis and RNA unwinding. Molecular dynamic simulations and experimental results revealed that, through forming a hydrophobic core with the conserved SAT motif of the N-terminal domain and I357 from the C-terminal domain, the linker gated the release of Pi from the hydrolysis site, which avoided futile hydrolysis cycles of eIF4AI. Further mutagenesis studies suggested this linker also plays an auto-inhibitory role in the enzymatic activity of eIF4AI, which may be essential for its function during translation initiation. Overall, our results reveal a novel regulatory mechanism that controls eIF4AI-mediated mRNA unwinding and can guide further mechanistic studies on other DEAD-box helicases.

Bacterial versatility requires DEAD-box RNA helicases

RNA helicases of the DEAD-box and DEAH-box families are important players in many processes involving RNA molecules. These proteins can modify RNA secondary structures or intermolecular RNA interactions and modulate RNA-protein complexes. In bacteria, they are known to be involved in ribosome biogenesis, RNA turnover and translation initiation. They thereby play an important role in the adaptation of bacteria to changing environments and to respond to stress conditions.

The Ded1/DDX3 subfamily of DEAD-box RNA helicases

In eukaryotic organisms, the orthologs of the DEAD-box RNA helicase Ded1p from yeast and DDX3 from human form a well-defined subfamily that is characterized by high sequence conservation in their helicase core and their N- and C- termini. Individual members of this Ded1/DDX3 subfamily perform multiple functions in RNA metabolism in both nucleus and cytoplasm. Ded1/DDX3 subfamily members have also been implicated in cellular signaling pathways and are targeted by diverse viruses. In this review, we discuss the considerable body of work on the biochemistry and biology of these proteins, including the recently discovered link of human DDX3 to tumorigenesis.

Synergistic effects of ATP and RNA binding to human DEAD-box protein DDX1

RNA helicases of the DEAD-box protein family form the largest group of helicases. The human DEAD-box protein 1 (DDX1) plays an important role in tRNA and mRNA processing, is involved in tumor progression and is also hijacked by several virus families such as HIV-1 for replication and nuclear export. Although important in many cellular processes, the mechanism of DDX1′s enzymatic function is unknown. We have performed equilibrium titrations and transient kinetics to determine affinities for nucleotides and RNA. We find an exceptional tight binding of DDX1 to adenosine diphosphate (ADP), one of the strongest affinities observed for DEAD-box helicases. ADP binds tighter by three orders of magnitude when compared to adenosine triphosphate (ATP), arresting the enzyme in a potential dead-end ADP conformation under physiological conditions. We thus suggest that a nucleotide exchange factor leads to DDX1 recycling. Furthermore, we find a strong cooperativity in binding of RNA and ATP to DDX1 that is also reflected in ATP hydrolysis. We present a model in which either ATP or RNA binding alone can partially shift the equilibrium from an ‘open’ to a ‘closed’-state; this shift appears to be not further pronounced substantially even in the presence of both RNA and ATP as the low rate of ATP hydrolysis does not change.

ATPase site configuration of the RNA helicase DbpA probed by ENDOR spectroscopy

Electron-nuclear double resonance (ENDOR) is a method that probes the local structure of paramagnetic centers via their hyperfine interactions with nearby magnetic nuclei. Here we describe the use of this technique to structurally characterize the ATPase active site of the RNA helicase DbpA, where Mg(2+)-ATP binds. This is achieved by substituting the EPR (electron paramagnetic resonance) silent Mg(2+) ion with paramagnetic, EPR active, Mn(2+) ion. (31)P ENDOR provides the interaction of the Mn(2+) with the nucleotide (ADP, ATP and its analogs) through the phosphates. The ENDOR spectra clearly distinguish between ATP- and ADP-binding modes. In addition, by preparing (13)C-enriched DbpA, (13)C ENDOR is used to probe the interaction of the Mn(2+) with protein residues. This combination allows tracking structural changes in the Mn(2+) coordination shell, in the ATPase site, in different states of the protein, namely with and without RNA and with different ATP analogs. Here, a detailed description of sample preparation and the ENDOR measurement methodology is provided, focusing on measurements at W-band (95 GHz) where sensitivity is high and spectral interpretations are relatively simple.

Mutational analysis of the functional sites in porcine reproductive and respiratory syndrome virus non-structural protein 10

Porcine reproductive and respiratory syndrome virus (PRRSV) is prevalent throughout the world and has caused major economic losses to the pig industry. Arterivirus non-structural protein 10 (nsp10) is a superfamily 1 helicase participating in multiple processes of virus replication. PRRSV nsp10, however, has not yet been well characterized. In this study, a series of nsp10 mutants were constructed and analysed for functional sites of different enzymic activities. We found that nsp10 could bind both ssDNA and dsDNA, and this binding activity could be inactivated by mutations at Cys25 and His32. These two mutations also abolished unwinding activity without affecting ATPase activity. In addition, substitution of Ala227 by Ser eliminated helicase activity, whilst substitution by Val enhanced unwinding activity. Taken together, our results showed that Cys25 and His32 in PRRSV nsp10 were critical for nucleic acid binding and unwinding, and that Ala227 played an important role in helicase activity.

Fluorescence methods in the investigation of the DEAD-box helicase mechanism

DEAD-box proteins catalyze the ATP-dependent unwinding of RNA duplexes and accompany RNA molecules throughout their cellular life. Conformational changes in the helicase core of DEAD-box proteins are intimately linked to duplex unwinding. In the absence of ligands, the two RecA domains of the helicase core are separated. ATP and RNA binding induces a closure of the cleft between the RecA domains that is coupled to the distortion of bound RNA, leading to duplex destabilization and dissociation of one RNA strand. Reopening of the helicase core occurs after ATP hydrolysis and is coupled to phosphate release and dissociation of the second RNA strand.Fluorescence spectroscopy provides an array of approaches to study intermolecular interactions, local structural rearrangements, or large conformational changes of biomolecules. The fluorescence intensity of a fluorophore reports on its environment, and fluorescence anisotropy reflects the size of the molecular entity the fluorophore is part of. Fluorescence intensity and anisotropy are therefore sensitive probes to report on binding and dissociation events. Fluorescence resonance energy transfer (FRET) reports on the distance between two fluorophores and thus on conformational changes. Single-molecule FRET experiments reveal the distribution of conformational states and the kinetics of their interconversion. This chapter summarizes fluorescence approaches for monitoring individual aspects of DEAD-box protein activity, from nucleotide and RNA binding and RNA unwinding to protein and RNA conformational changes in the catalytic cycle, and illustrates exemplarily how fluorescence-based methods have contributed to understanding the mechanism of DEAD-box helicase-catalyzed RNA unwinding.

The RNA helicase DHX34 activates NMD by promoting a transition from the surveillance to the decay-inducing complex

Nonsense-mediated decay (NMD) is a surveillance mechanism that degrades aberrant mRNAs. A complex comprising SMG1, UPF1, and the translation termination factors eRF1 and eRF3 (SURF) is assembled in the vicinity of a premature termination codon. Subsequently, an interaction with UPF2, UPF3b, and the exon junction complex induces the formation of the decay-inducing complex (DECID) and triggers NMD. We previously identified the RNA helicase DHX34 as an NMD factor in C. elegans and in vertebrates. Here, we investigate the mechanism by which DHX34 activates NMD in human cells. We show that DHX34 is recruited to the SURF complex via its preferential interaction with hypophosphorylated UPF1. A series of molecular transitions induced by DHX34 include enhanced recruitment of UPF2, increased UPF1 phosphorylation, and dissociation of eRF3 from UPF1. Thus, DHX34 promotes mRNP remodeling and triggers the conversion from the SURF complex to the DECID complex resulting in NMD activation.

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DHX34 interacts with Nonsense-mediated decay factors and the mRNA decay factory

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Hypophosphorylated UPF1 recruits DHX34 to the SURF complex

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DHX34 promotes the recruitment of UPF2, UPF1 phosphorylation, and eRF3 release

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DHX34 remodels mRNPs and promotes the transition from the SURF to DECID complex

Single-molecule kinetics of the eukaryotic initiation factor 4AI upon RNA unwinding

The eukaryotic translation initiation factor 4AI (eIF4AI) is the prototypical DEAD-box RNA helicase. It has a "dumbbell" structure consisting of two domains connected by a flexible linker. Previous studies demonstrated that eIF4AI, in conjunction with eIF4H, bind to loop structures and repetitively unwind RNA hairpins. Here, we probe the conformational dynamics of eIF4AI in real time using single-molecule FRET. We demonstrate that eIF4AI/eIF4H complex can repetitively unwind RNA hairpins by transitioning between an eIF4AI "open" and a "closed" conformation using the energy derived from ATP hydrolysis. Our experiments directly track the conformational changes in the catalytic cycle of eIF4AI and eIF4H, and this correlates precisely with the kinetics of RNA unwinding. Furthermore, we show that the small-molecule eIF4A inhibitor hippuristanol locks eIF4AI in the closed conformation, thus efficiently inhibiting RNA unwinding. These results indicate that the large conformational changes undertaken by eIF4A during the helicase catalytic cycle are rate limiting.

DDX6 and its orthologs as modulators of cellular and viral RNA expression

DDX6 (Rck/p54), a member of the DEAD-box family of helicases, is highly conserved from unicellular eukaryotes to vertebrates. Functions of DDX6 and its orthologs in dynamic ribonucleoproteins contribute to global and transcript-specific messenger RNA (mRNA) storage, translational repression, and decay during development and differentiation in the germline and somatic cells. Its role in pathways that promote mRNA-specific alternative translation initiation has been shown to be linked to cellular homeostasis, deregulated tissue development, and the control of gene expression in RNA viruses. Recently, DDX6 was found to participate in mRNA regulation mediated by miRNA-mediated silencing. DDX6 and its orthologs have versatile functions in mRNA metabolism, which characterize them as important post-transcriptional regulators of gene expression.

RNA helicase proteins as chaperones and remodelers

Superfamily 2 helicase proteins are ubiquitous in RNA biology and have an extraordinarily broad set of functional roles. Central among these roles are the promotion of rearrangements of structured RNAs and the remodeling of ribonucleoprotein complexes (RNPs), allowing formation of native RNA structure or progression through a functional cycle of structures. Although all superfamily 2 helicases share a conserved helicase core, they are divided evolutionarily into several families, and it is principally proteins from three families, the DEAD-box, DEAH/RHA, and Ski2-like families, that function to manipulate structured RNAs and RNPs. Strikingly, there are emerging differences in the mechanisms of these proteins, both between families and within the largest family (DEAD-box), and these differences appear to be tuned to their RNA or RNP substrates and their specific roles. This review outlines basic mechanistic features of the three families and surveys individual proteins and the current understanding of their biological substrates and mechanisms.

DEAD-box helicases form nucleotide-dependent, long-lived complexes with RNA

DEAD-box RNA helicases bind and remodel RNA and RNA-protein complexes in an ATP-dependent fashion. Several lines of evidence suggest that DEAD-box RNA helicases can also form stable, persistent complexes with RNA in a process referred to as RNA clamping. The molecular basis of RNA clamping is not well understood. Here we show that the yeast DEAD-box helicase Ded1p forms exceptionally long-lived complexes with RNA and the nonhydrolyzable ATP ground-state analogue ADP-BeFx or the nonhydrolyzable ATP transition state analogue ADP-AlFx. The complexes have lifetimes of several hours, and neither nucleotide nor Mg(2+) is released during this period. Mutation of arginine 489, which stabilizes the transition state, prevents formation of long-lived complexes with the ATP transition state analogue, but not with the ground state analogue. We also show that two other yeast DEAD-box helicases, Mss116p and Sub2p, form comparably long-lived complexes with RNA and ADP-BeFx. Like Ded1p, Mss116p forms long-lived complexes with ADP-AlFx, but Sub2p does not. These data suggest that the ATP transition state might vary for distinct DEAD-box helicases, or that the transition state triggers differing RNA binding properties in these proteins. In the ATP ground state, however, all tested DEAD-box helicases establish a persistent grip on RNA, revealing an inherent capacity of the enzymes to function as potent, ATP-dependent RNA clamps.

Molecular insights into RNA and DNA helicase evolution from the determinants of specificity for a DEAD-box RNA helicase

How different helicase families with a conserved catalytic 'helicase core' evolved to function on varied RNA and DNA substrates by diverse mechanisms remains unclear. In this study, we used Mss116, a yeast DEAD-box protein that utilizes ATP to locally unwind dsRNA, to investigate helicase specificity and mechanism. Our results define the molecular basis for the substrate specificity of a DEAD-box protein. Additionally, they show that Mss116 has ambiguous substrate-binding properties and interacts with all four NTPs and both RNA and DNA. The efficiency of unwinding correlates with the stability of the 'closed-state' helicase core, a complex with nucleotide and nucleic acid that forms as duplexes are unwound. Crystal structures reveal that core stability is modulated by family-specific interactions that favor certain substrates. This suggests how present-day helicases diversified from an ancestral core with broad specificity by retaining core closure as a common catalytic mechanism while optimizing substrate-binding interactions for different cellular functions.

Take advantage of time in your experiments: a guide to simple, informative kinetics assays

Understanding virtually any process in cellular and molecular biology depends on knowledge of the rates of the biochemical reactions, so it is regrettable that few cellular and molecular biologists take advantage of kinetics experiments in their work. Fortunately, the kinetics experiments that are most useful for understanding cellular systems are within reach for everyone whose research would benefit from this information. This essay describes simple methods to measure the valuable kinetic parameters that characterize the dynamics of life processes. These “transient-state” methods not only differ in concept from traditional approaches used to analyze enzyme reactions at steady state, but they are also applicable to learning about the dynamics of any biological process.

ATPase mechanism of the 5'-3' DNA helicase, RecD2: evidence for a pre-hydrolysis conformation change

The superfamily 1 helicase, RecD2, is a monomeric, bacterial enzyme with a role in DNA repair, but with 5′-3′ activity unlike most enzymes from this superfamily. Rate constants were determined for steps within the ATPase cycle of RecD2 in the presence of ssDNA. The fluorescent ATP analog, mantATP (2′(3′)-O-(N-methylanthraniloyl)ATP), was used throughout to provide a complete set of rate constants and determine the mechanism of the cycle for a single nucleotide species. Fluorescence stopped-flow measurements were used to determine rate constants for adenosine nucleotide binding and release, quenched-flow measurements were used for the hydrolytic cleavage step, and the fluorescent phosphate biosensor was used for phosphate release kinetics. Some rate constants could also be measured using the natural substrate, ATP, and these suggested a similar mechanism to that obtained with mantATP. The data show that a rearrangement linked to Mg²⁺ coordination, which occurs before the hydrolysis step, is rate-limiting in the cycle and that this step is greatly accelerated by bound DNA. This is also shown here for the PcrA 3′-5′ helicase and so may be a general mechanism governing superfamily 1 helicases. The mechanism accounts for the tight coupling between translocation and ATPase activity.

AMP sensing by DEAD-box RNA helicases

In eukaryotes, cellular levels of adenosine monophosphate (AMP) signal the metabolic state of the cell. AMP concentrations increase significantly upon metabolic stress, such as glucose deprivation in yeast. Here, we show that several DEAD-box RNA helicases are sensitive to AMP, which is not produced during ATP hydrolysis by these enzymes. We find that AMP potently inhibits RNA binding and unwinding by the yeast DEAD-box helicases Ded1p, Mss116p, and eIF4A. However, the yeast DEAD-box helicases Sub2p and Dbp5p are not inhibited by AMP. Our observations identify a subset of DEAD-box helicases as enzymes with the capacity to directly link changes in AMP concentrations to RNA metabolism.

Structures of the phage Sf6 large terminase provide new insights into DNA translocation and cleavage

Many DNA viruses use powerful molecular motors to cleave concatemeric viral DNA into genome-length units and package them into preformed procapsid powered by ATP hydrolysis. Here we report the structures of the DNA-packaging motor gp2 of bacteriophage Sf6, which reveal a unique clade of RecA-like ATPase domain and an RNase H-like nuclease domain tethered by a regulatory linker domain, exhibiting a strikingly distinct domain arrangement. The gp2 structures complexed with nucleotides reveal, at the atomic detail, the catalytic center embraced by the ATPase domain and the linker domain. The gp2 nuclease activity is modulated by the ATPase domain and is stimulated by ATP. An extended DNA-binding surface is formed by the linker domain and the nuclease domain. These results suggest a unique mechanism for translation of chemical reaction into physical motion of DNA and provide insights into coordination of DNA translocation and cleavage in a viral DNA-packaging motor, which may be achieved via linker-domain-mediated interdomain communication driven by ATP hydrolysis.

Looking back on the birth of DEAD-box RNA helicases

DEAD-box proteins represent the largest family of RNA helicases, present in all three kingdoms of life. They are involved in a variety of processes involving RNA metabolism and in some instances also in processes that use guide RNAs. Since their first descriptions in the late 1980s, the perception of their molecular activities has dramatically changed. At the time when only eight proteins with 9 conserved motifs constituted the DEAD-box protein family, it was the biochemical characterization of mammalian eIF4A that first suggested a local unwinding activity. This was confirmed in vitro using partially double stranded RNA substrates with the unexpected result of a bidirectional unwinding activity. A real change of paradigm from the classical helicase activity to localized RNA unwinding occurred with the publication of the vasa•RNA structure with a bend in the RNA substrate and the insightful work from several laboratories demonstrating local unwinding without translocation. Finally, elegant work on the exon-junction complex revealed how DEAD-box proteins can bind to RNA to serve as clamps to function as nucleation centers to form RNP complexes. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.

Packing them up and dusting them off: RNA helicases and mRNA storage

Cytoplasmic mRNA can be translated, translationally repressed, localized or degraded. Regulation of translation is an important step in control of gene expression and the cell can change whether and to what extent an mRNA is translated. If an mRNA is not translating, it will associate with translation repression factors; the mRNA can be stored in these non-translating states. The movement of mRNA into storage and back to translation is dictated by the recognition of the mRNA by trans factors. So, remodeling the factors that bind mRNA is critical for changing the fate of mRNA. RNA helicases, which have the ability to remodel RNA or RNA-protein complexes, are excellent candidates for facilitating such rearrangements. This review will focus on the RNA helicases implicated in translation repression and/or mRNA storage and how their study has illuminated mechanisms of mRNA regulation. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.

DEAD-box helicases as integrators of RNA, nucleotide and protein binding

DEAD-box helicases perform diverse cellular functions in virtually all steps of RNA metabolism from Bacteria to Humans. Although DEAD-box helicases share a highly conserved core domain, the enzymes catalyze a wide range of biochemical reactions. In addition to the well established RNA unwinding and corresponding ATPase activities, DEAD-box helicases promote duplex formation and displace proteins from RNA. They can also function as assembly platforms for larger ribonucleoprotein complexes, and as metabolite sensors. This review aims to provide a perspective on the diverse biochemical features of DEAD-box helicases and connections to structural information. We discuss these data in the context of a model that views the enzymes as integrators of RNA, nucleotide, and protein binding. This article is part of a Special Issue entitled: The Biology of RNA helicases - Modulation for life.

Roles of helicases in translation initiation: a mechanistic view

The goal of this review is to summarize our current knowledge about the helicases involved in translation initiation and their roles in both general and mRNA-specific translation. The main topics covered are the mechanisms of helicase action, with emphasis on the roles of accessory domains and proteins; the functions performed by helicases in translation initiation; and the interplay between direct and indirect effects of helicases that also function in steps preceding translation initiation. Special attention is given to the dynamics of eIF4A binding and dissociation from eIF4F during mRNA unwinding. It is proposed that DHX29, as well as other helicases and translation initiation factors could also cycle on and off the translation initiation complexes, similar to eIF4A. The evidence in favor of this hypothesis and its possible implications for the mechanisms of translation initiation is discussed. This article is part of a Special Issue entitled: The biology of RNA helicases - Modulation for life.

Roles for Helicases as ATP-Dependent Molecular Switches

On the basis of the familial name, a "helicase" might be expected to have an enzymatic activity that unwinds duplex polynucleotides to form single strands. A more encompassing taxonomy that captures alternative enzymatic roles has defined helicases as a sub-class of molecular motors that move directionally and processively along nucleic acids, the so-called "translocases". However, even this definition may be limiting in capturing the full scope of helicase mechanism and activity. Discussed here is another, alternative view of helicases-as machines which couple NTP-binding and hydrolysis to changes in protein conformation to resolve stable nucleoprotein assembly states. This "molecular switch" role differs from the classical view of helicases as molecular motors in that only a single catalytic NTPase cycle may be involved. This is illustrated using results obtained with the DEAD-box family of RNA helicases and with a model bacterial system, the ATP-dependent Type III restriction-modification enzymes. Further examples are discussed and illustrate the wide-ranging examples of molecular switches in genome metabolism.

Helicase-mediated changes in RNA structure at the single-molecule level

RNA helicases are a diverse group of RNA-dependent ATPases known to play a large number of biological roles inside the cell, such as RNA unwinding, remodeling, export and degradation. Understanding how helicases mediate changes in RNA structure is therefore of fundamental interest. The advent of single-molecule spectroscopic techniques has unveiled with unprecedented detail the interplay of RNA helicases with their substrates. In this review, we describe the characterization of helicase-RNA interactions by single-molecule approaches. State-of-the-art techniques are presented, followed by a discussion of recent advancements in this exciting field.

Duplex destabilization by four ribosomal DEAD-box proteins

DEAD-box proteins are believed to participate in the folding of RNA by destabilizing RNA secondary or tertiary structures. Although these proteins bind and hydrolyze ATP, the mechanism by which nucleotide hydrolysis is coupled to helix destabilization may vary among different DEAD-box proteins. To investigate their abilities to disrupt helices and couple ATP hydrolysis to unwinding, we assayed the Saccharomyces cerevisiae ribosomal DEAD-box proteins, Dbp3p, Dbp4p, Rok1p, and Rrp3p utilizing a series of RNA substrates containing a short duplex and either a 5' or 3' single-stranded region. All four proteins unwound a 10 bp helix in vitro in the presence of ATP; however, significant dissociation of longer helices was not observed. While Dbp3p did not require a single-stranded extension to disrupt a helix, the unwinding activities of Dbp4p, Rok1p, and Rrp3p were substantially stimulated by either a 5' or 3' single-stranded extension. Interestingly, these proteins showed a clear length dependency with 3' extensions that was not observed with 5' extensions, suggesting that they bind substrates with a preferred orientation. In the presence of AMPPNP or ADP, all four proteins displayed displacement activity suggesting that nucleotide binding is sufficient to facilitate duplex disruption. Further enhancement of the strand displacement rate in the presence of ATP was observed for only Dbp3p and Rrp3p.

Reverse gyrase transiently unwinds double-stranded DNA in an ATP-dependent reaction

Reverse gyrase is a unique DNA topoisomerase that catalyzes the introduction of positive supercoils into DNA in an ATP-dependent reaction. It consists of a helicase domain that functionally cooperates with a topoisomerase domain. Different models for the catalytic mechanism of reverse gyrase that predict a central role of the helicase domain have been put forward. The helicase domain acts as a nucleotide-dependent conformational switch that alternates between open and closed states with different affinities for single- and double-stranded DNA. It has been suggested that the helicase domain can unwind double-stranded regions, but helicase activity has not been demonstrated as yet. Here, we show that the isolated helicase domain and full-length reverse gyrase can transiently unwind double-stranded regions in an ATP-dependent reaction. The latch region of reverse gyrase, an insertion into the helicase domain, is required for DNA supercoiling. Strikingly, the helicase domain lacking the latch cannot unwind DNA, linking unwinding to DNA supercoiling. The unwinding activity may provide and stabilize the single-stranded regions required for strand passage by the topoisomerase domain, either de novo or by expanding already existing unpaired regions that may form at high temperatures.

Analysis of duplex unwinding by RNA helicases using stopped-flow fluorescence spectroscopy

The characterization of unwinding reactions by RNA helicases often requires the determination of rate constants that are too fast to be measured by traditional, manual gel-based methods. Stopped-flow fluorescence measurements allow access to fast unwinding rate constants. In this chapter, we outline strategies and experimental considerations for the design of stopped-flow fluorescence experiments to monitor duplex unwinding by RNA helicases, with focus on DEAD-box helicases. We discuss advantages, disadvantages, and technical considerations for stopped-flow approaches, as well as substrate design. In addition, we list protocols and explain functional information obtained with these experiments.

Oxygen isotopic exchange probes of ATP hydrolysis by RNA helicases

It is often possible to obtain a detailed understanding of the forward steps in ATP hydrolysis because they are thermodynamically favored and usually occur rapidly. However, it is difficult to obtain the reverse rates for ATP resynthesis because they are thermodynamically disfavored and little of their product, ATP, accumulates. Isotopic exchange reactions provide access to these reverse reactions because isotopic changes accumulate over time due to multiple reversals of hydrolysis, even in the absence of net resynthesis of significant amounts of ATP. Knowledge of both the forward and reverse rates allows calculation of the free energy changes at each step and how it changes when coupled to an energy-requiring conformational step such as unwinding of an RNA helix. This chapter describes the principal types of oxygen isotopic exchange reactions that are applicable to ATPases, in general, and helicases, in particular, their application and their interpretation.

Mss116p: a DEAD-box protein facilitates RNA folding

RNA folding is an essential aspect underlying RNA-mediated cellular processes. Many RNAs, including large, multi-domain ribozymes, are capable of folding to the native, functional state without assistance of a protein cofactor in vitro. In the cell, trans-acting factors, such as proteins, are however known to modulate the structure and thus the fate of an RNA. DEAD-box proteins, including Mss116p, were recently found to assist folding of group I and group II introns in vitro and in vivo. The underlying mechanism(s) have been studied extensively to explore the contribution of ATP hydrolysis and duplex unwinding in helicase-stimulated intron splicing. Here we summarize the ongoing efforts to understand the novel role of DEAD-box proteins in RNA folding.