Roles of DEAD-box proteins in RNA and RNP Folding

Pan, Cynthia; Russell, Rick

doi:10.4161/rna.7.6.13571

Cited by 43 publications

(36 citation statements)

References 149 publications

(212 reference statements)

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“…DEAD-box proteins are part of the helicase 2 superfamily of enzymes (Caruthers and McKay 2002) and, in vitro, most, but not all, show nonprocessive RNA helicase activity on model substrates (Cordin et al 2006;Linder and Jankowsky 2011). However, unlike the DNA and viral RNA helicases of the SF2 family, which start their actions at the single-stranded region of the helical substrate and translocate toward the opposite end, DEADbox proteins directly load on the double-helix substrate and unwind it without translocation (Pyle 2008;FairmanWilliams et al 2010;Pan and Russell 2010).…”

Section: Introductionmentioning

confidence: 99%

“…DEAD-box proteins are a family of enzymes that use the energy of ATP binding and hydrolysis to facilitate RNA conformational changes in many pathways of RNA metabolism, including RNA splicing, ribosome maturation, transcription, RNA transport, and RNA degradation (Tanner and Linder 2001;Cordin et al 2006;Pyle 2008;Pan and Russell 2010;Linder and Jankowsky 2011). DEAD-box proteins are part of the helicase 2 superfamily of enzymes (Caruthers and McKay 2002) and, in vitro, most, but not all, show nonprocessive RNA helicase activity on model substrates (Cordin et al 2006;Linder and Jankowsky 2011).…”

Section: Introductionmentioning

confidence: 99%

“…For the DEAD-box family of proteins, the observed rate constant of double-helix unwinding is dependent on the unwinding catalytic efficiency of the enzyme, which is dependent on the rate of ATP hydrolysis, the stability of double helix, and the ability of the enzyme to perform annealing (Pyle 2008;Pan and Russell 2010;Henn et al 2012;Putnam and Jankowsky 2013). Previous experiments have shown that the observed rate constant of DbpA-facilitated annealing is very similar to the observed rate constant of BSA-facilitated annealing; hence the DbpA protein does not seem to actively facilitate double-helix unwinding (O Uhlenbeck and C Diges, pers.…”

mentioning

confidence: 99%

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The DbpA catalytic core unwinds double-helix substrates by directly loading on them

Childs

Gentry

Moore

et al. 2016

RNA

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DbpA is a DEAD-box RNA helicase implicated in the assembly of the large ribosomal subunit. Similar to all the members of the DEAD-box family, the DbpA protein has two N-terminal RecA-like domains, which perform the RNA unwinding. However, unlike other members of this family, the DbpA protein also possesses a structured C-terminal RNA-binding domain that mediates specific tethering of DbpA to hairpin 92 of the Escherichia coli 23S ribosomal RNA. Previous studies using model RNA molecules containing hairpin 92 show that the RNA molecules support the DbpA protein's double-helix unwinding activity, provided that the double helix has a 3 ′ single-stranded region. The 3 ′ single-stranded region was suggested to be the start site of the DbpA protein's catalytic unwinding activity. The data presented here demonstrate that the single-stranded region 3′ of the doublehelix substrate is not required for the DbpA protein's unwinding activity and the DbpA protein unwinds the double-helix substrates by directly loading on them.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

mentioning

confidence: 99%

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The DbpA catalytic core unwinds double-helix substrates by directly loading on them

Childs

Gentry

Moore

et al. 2016

RNA

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“…To ensure this, cells use a number of different protein and RNA maturation factors (El Hage et al 2001;Charollais et al 2003Charollais et al , 2004El Hage and Alix 2004;Jain 2008). One class of RNA maturation factors used by the cell during ribosome assembly is DEAD-box RNA helicases (Cordin et al 2006;Linder 2006;Pyle 2008;Pan and Russell 2010;Shajani et al 2011;Henn et al 2012;Putnam and Jankowsky 2013). In vitro, these enzymes use the energy of ATP binding and hydrolysis to unwind short RNA double helices.…”

Section: Introductionmentioning

confidence: 99%

Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein

Gentry

Childs

Gevorkyan³

et al. 2016

RNA

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DbpA is a DEAD-box RNA helicase implicated in Escherichia coli large ribosomal subunit assembly. Previous studies have shown that when the ATPase and helicase inactive DbpA construct, R331A, is expressed in E. coli cells, a large ribosomal subunit intermediate accumulates. The large subunit intermediate migrates as a 45S particle in a sucrose gradient. Here, using a number of structural and fluorescent assays, we investigate the ribosome profiles of cells lacking wild-type DbpA and overexpressing the R331A DbpA construct. Our data show that in addition to the 45S particle previously described, 27S and 35S particles are also present in the ribosome profiles of cells overexpressing R331A DbpA. The 27S, 35S, and 45S independently convert to the 50S subunit, suggesting that ribosome assembly in the presence of R331A and the absence of wild-type DbpA occurs via multiple pathways.

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“…Finally, DDX6 belongs to the family of DEAD box helicases. These highly conserved enzymes accelerate structural transitions of RNAs and RNPs in an ATP-dependent manner that resembles the activities of certain groups of protein chaperones (13,14). Interestingly, in contrast to their decay function in cellular mRNAs, PatL1, LSm1-7, and DDX6 have all or in part been shown to be required for replication of diverse (ϩ)RNA viruses, including human hepatitis C virus (HCV), West Nile virus (WNV), and Dengue virus (DNV), as well as the plant brome mosaic virus (BMV) (15)(16)(17)(18)(19)(20)(21)(22).…”

mentioning

confidence: 99%

The Cellular Decapping Activators LSm1, Pat1, and Dhh1 Control the Ratio of Subgenomic to Genomic Flock House Virus RNAs

Giménez‐Barcons

Alves-Rodrigues

Jungfleisch

et al. 2013

J Virol

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, and Dhh1 control the ratio of subgenomic RNA3 to genomic RNA1 production, a key feature in the FHV life cycle mediated by a long-distance base pairing within RNA1. Depletion of LSM1, PAT1, or DHH1 dramatically increased RNA3 accumulation during replication. This was not caused by differences between RNA1 and RNA3 steady-state levels in the absence of replication. Importantly, coimmunoprecipitation assays indicated that LSm1-7, Pat1, and Dhh1 interact with the FHV RNA genome and the viral polymerase. By using a strategy that allows dissecting different stages of the replication process, we found that LSm1-7, Pat1, and Dhh1 did not affect the early replication steps of RNA1 recruitment to the replication complex or RNA1 synthesis. Furthermore, their function on RNA3/RNA1 ratios was independent of the membrane compartment, where replication occurs and requires ATPase activity of the Dhh1 helicase. Together, these results support that LSm1-7, Pat1, and Dhh1 control RNA3 synthesis. Their described function in mediating cellular mRNP rearrangements suggests a parallel role in mediating key viral RNP transitions, such as the one required to maintain the balance between the alternative FHV RNA1 conformations that control RNA3 synthesis.

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Roles of DEAD-box proteins in RNA and RNP Folding

Cited by 43 publications

References 149 publications

The DbpA catalytic core unwinds double-helix substrates by directly loading on them

The DbpA catalytic core unwinds double-helix substrates by directly loading on them

Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein

The Cellular Decapping Activators LSm1, Pat1, and Dhh1 Control the Ratio of Subgenomic to Genomic Flock House Virus RNAs

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