Dead box rna helicases. Medical search. Frequent questions

DEAD/DEAH box helicases are proteins, and are putative RNA helicases. (wikipedia.org)
Activities of the DEAD box (Asp-Glu-Ala-Asp) family of proteins- including RNA-dependent ATPase and RNA helicase- function in all organisms to sculpt RNA-RNA duplex and RNA-protein complexes, ensuring that necessary rearrangements are rapidly and properly resolved during genetic information processing. (gsu.edu)
Altogether, the two host factors enhance TBSV replication synergistically by interacting with the viral (−)RNA and the replication proteins. (prolekarniky.cz)
After translation of their mRNA-sense genomic RNA(s), the viral RNA and the viral replication proteins are recruited to the site of viral replication in membranous compartments. (prolekarniky.cz)
For efficient replication, (+)RNA viruses recruit numerous host proteins [1] - [5] . (prolekarniky.cz)
Among the identified host proteins are RNA-binding proteins, such as translation factors, ribosomal proteins and RNA-modifying enzymes [1] . (prolekarniky.cz)
The co-opted host proteins likely affect several steps in viral RNA replication, including the assembly of the replicase complex and/or viral RNA synthesis. (prolekarniky.cz)
The single genomic RNA codes for two replication proteins, p33 and p92 pol , which are sufficient to support TBSV replicon (rep)RNA replication in yeast ( Saccharomyces cerevisiae ) model host [13] , [14] . (prolekarniky.cz)
When pieces of viral RNA are present inside a cell, multiple MDA5 proteins attach to it, one after another, forming a filament. (medlineplus.gov)
The altered protein may more readily attach to RNA, even pieces of RNA that are not from viruses, or to other MDA5 proteins to form filaments. (medlineplus.gov)
Studies suggest that the altered protein is unable to attach to viral RNA or to other MDA5 proteins to form filaments. (medlineplus.gov)
The prototype of DEAD-box proteins is the translation initiation factor eIF4A. (embl.de)
Long-term memory consolidation: The role of RNA-binding proteins with prion-like domains. (tcd.ie)
We uncovered the functions of ABCE proteins Rli1/ABCE1 and Arb1 in PIC assembly and ribosome biogenesis, and identified the tRNA methyltransferase Gcd10/Gcd14, which contributed to the discovery of the TRAMP-mediated RNA surveillance pathway. (nih.gov)
These distinctive flanking sequences inform the particular protein-protein and RNA-protein interactions for the diverse human DEAD-Box proteins. (bellbrooklabs.com)
One type of RNA protein cofactors are the ubiquitous DEAD-box proteins. (allegheny.edu)
DEAD-box proteins are essential in all aspects of RNA metabolism including pre-mRNA splicing, ribosome biogenesis, RNA interference, translation, mRNA transport, and decay. (allegheny.edu)
These motor proteins modulate RNA-RNA, RNA-protein, and/or protein-protein interactions by utilizing nine conserved motifs to convert RNA binding and ATP hydrolysis into distinct conformational changes. (allegheny.edu)
As part of the helicase superfamily 2 (SF2), DEAD-box proteins are formally putative RNA helicases. (allegheny.edu)
However, ATP driven unwinding of RNA duplexes has only been illustrated for a few proteins. (allegheny.edu)
The main focus and motivation of my research has been to biochemically understand the structural interactions and the role that proteins play in RNA catalysis and folding in eukaryotic RNA metabolism. (allegheny.edu)
DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. (syr.edu)
Numerous fundamental cellular processes, including virtually every aspect of gene expression and regulation, depend on the cooperation of RNAs and proteins. (fu-berlin.de)
Specific RNAs and proteins associate to build up some of the most complex macromolecular machineries of living cells, such as ribosomes and spliceosomes, which mediate particular steps of gene expression. (fu-berlin.de)
RNAs and proteins can also engage in more transient interactions, for example during co-transcriptional regulation of RNA polymerases or during post-transcriptional regulation of (pre-)mRNA life cycles. (fu-berlin.de)
We investigate the molecular mechanisms, by which RNAs and proteins cooperate to bring about the biological functions of selected RNPs involved in transcription and pre-mRNA splicing. (fu-berlin.de)

PeBoW, a trimeric complex consisting of pescadillo (Pes1), block of proliferation (Bop1), and the WD repeat protein 12 (WDR12), is essential for processing and maturation of mammalian 5.8S and 28S ribosomal RNAs. (cipsm.de)
This gene encodes a DEAD box protein with RNA helicase activity. (wikipedia.org)
BRCA1 protein is linked to the RNA polymerase II holoenzyme complex via RNA helicase A". Nature Genetics. (wikipedia.org)
In particular, the MDA5 protein recognizes a molecule called double-stranded RNA (a chemical cousin of DNA), which certain viruses, including rhinovirus (the virus that causes the common cold), respiratory syncytial virus (RSV), and the influenza (flu) virus, have as their genetic material or produce when they infect cells and copy (replicate) themselves. (medlineplus.gov)
Altered Ribostasis: RNA-Protein Granules in Degenerative Disorders. (tcd.ie)
In response to immune induction, uORF-inhibition is alleviated by three Ded1p/DDX3X-homologous RNA helicases which unwind the RNA structures, allowing ribosomes to bypass the inhibitory uORFs and upregulate defence protein production. (biorxiv.org)
Frick, D.N. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. (enzyme-database.org)
A fragment of the Trypanosoma brucei ZC3H41 protein encompassing the ATP-dependent RNA helicase domain was successfully subcloned for expression in a bacterial system (Escherichia coli). (iucc.ac.il)
Izhaki-Tavor, LS & Dessau, M 2020, ' ATP-dependent RNA helicase domain of the ZC3H41 protein from Trypanosoma brucei: Expression, purification and crystallization ', Acta Crystallographica Section F:Structural Biology Communications , vol. 76, pp. 604-608. (iucc.ac.il)
RNA polymerase-associated protein RapA (EC 3.6.4. (weizmann.ac.il)
DDX5 is a 614 amino acid protein consisting of an N-terminal Q motif, an ATP binding Rec A-like domain, a hinge region, a Rec A-like helicase domain, and a C-terminal RGS-RGG motif. (bellbrooklabs.com)
2017) Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism. (bellbrooklabs.com)
Hence, protein cofactors are usually necessary to stabilize or modulate RNA folding. (allegheny.edu)
Moreover, RNA-protein complexes (RNPs) provide glimpses at the molecular ancestry of modern cells, which most likely evolved from an RNA-dominated world. (fu-berlin.de)
In these processes, transcript-borne regulatory RNAs alone or in conjunction with protein factors assemble on the surface of RNAP and accompany the enzyme during further transcription by an RNA looping mechanism, rendering the elongation complex resistant to pause and/or termination signals downstream of the original modification site. (fu-berlin.de)
Background: The exon junction complex (EJC), which contains four core components, eukaryotic initiation factor 4AIII (eIF4AIII), MAGO/NASHI (MAGO), Y14/Tsunagi/RNA-binding protein 8A, and Barentsz/Metastatic lymph node 51, is formed in both nucleus and cytoplasm, and plays important roles in gene expression. (ncu.edu.tw)

Identified as a prototypic member of the DEAD box family and documented as an ATPase and RNA helicase, p68 plays essential and diverse functions in the control of gene expression ranging from pre-mRNA/rRNA processing and mRNA decay/stability to transcriptional activation and initiation. (gsu.edu)
Wang, X., Jia, H., Jankowsky, E. & Anderson, J.T. Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. (nature.com)
The data obtained with wt and ATPase deficient Ded1p mutants support the model that Ded1p unwinds local structures at the 3′-end of the TBSV (−)RNA, rendering the RNA compatible for initiation of (+)-strand synthesis. (prolekarniky.cz)
The N-terminal domain also contains motif III (S-A-T) which was proposed to participate in linking ATPase and helicase activities. (embl.de)
Members of this family also possess highly conserved ATPase and helicase domains, flanked by individually distinctive N and/or C-terminal motifs. (bellbrooklabs.com)

The conserved Saccharomyces cerevisiae Ski2-like RNA helicase Mtr4p plays essential roles in eukaryotic nuclear RNA processing. (nature.com)
All eukaryotic plus-stranded (+)RNA viruses have similar replication cycles in infected cells. (prolekarniky.cz)
Eukaryotic DNA repair helicase RAD3/ERCC-2, an ATP-dependent 5'-3' DNA helicase involved in nucleotide excision repair of UV-damaged DNA. (embl.de)
Eukaryotic TFIIH basal transcription factor complex helicase XPB subunit. (embl.de)
Eukaryotic ATP-dependent DNA helicase Q. A DNA helicase that may play a role in the repair of DNA that is damaged by ultraviolet light or other mutagens. (embl.de)
Bacterial and eukaryotic antiviral SKI2-like helicase. (embl.de)
Moreover, recent global ribosome-sequencing (Ribo-seq, sequencing of ribosome-protected RNA fragments) studies have shown that uORFs are a prevalent feature in eukaryotic mRNAs, not limited to these few well-studied examples 19 - 21 . (biorxiv.org)
Many eukaryotic precursor messenger RNAs (pre-mRNAs) bear coding regions (exons) interspersed with non-coding intervening sequences (introns). (fu-berlin.de)

A new yeast poly(A) polymerase complex involved in RNA quality control. (nature.com)
An ATP-dependent 3'-5' DNA helicase which is a component of the core-TFIIH basal transcription factor, involved in nucleotide excision repair (NER) of DNA and, when complexed to CAK, in RNA transcription by RNA polymerase II. (embl.de)
We identify an important role for DDX5 in G 1 -S-phase progression where it directly regulates DNA replication factor expression by promoting the recruitment of RNA polymerase II to E2F-regulated gene promoters. (aacrjournals.org)
4 On the other hand, DDX5 binds the SARS-CoV helicase to enhance viral proliferation, facilitates HIV-1 mRNA export, and enhances influenza virus polymerase activity. (bellbrooklabs.com)
RNA-based processive anti-termination is exemplified by the polymerase utilization ( put ) signal of phage HK022. (fu-berlin.de)

Sloan, K.E., Bohnsack, M.T., Schneider, C. & Watkins, N.J. The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA. (nature.com)
It functions as an RNA chaperone, a transcriptional regulator, a facilitator of mRNA processing, an enabler of nonsense-mediated decay, an important player in R loop resolution, an aid in micro-RNA processing, and an instrument of ribosomal biogenesis. (bellbrooklabs.com)
RNP-based processive anti-termination underlies the switching from immediate-early to delayed-early gene expression in other lambdoid phages as well as ribosomal RNA synthesis in Escherichia coli . (fu-berlin.de)
Huang YH, Said N, Loll B, Wahl MC (2019) Structural basis for the function of SuhB as a transcription factor in ribosomal RNA synthesis. (fu-berlin.de)

It may participate in melting of DNA:RNA hybrids, such as those that occur during transcription, and may play a role in X-linked gene expression. (wikipedia.org)
The mutation was found in a DEAD box RNA helicase gene that is identical to the previously identified low expression of osmotically responsive genes 4 (LOS4) locus, which was defined by the los4-1 mutation that reduces cold regulation of CBFs and their target genes and renders Arabidopsis plants chilling sensitive. (edu.sa)
Sixty-six Affymetrix microarray slides using lung adenocarcinoma tissue RNAs were analyzed by a statistical re-sampling method in order to detect genes with minimal variation in gene expression. (biomedcentral.com)
All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved. (syr.edu)

RNA helicases utilize the energy from ATP hydrolysis to unwind RNA. (enzyme-database.org)
Some of them unwind RNA with a 3′ to 5′ polarity [3], other show 5′ to 3′ polarity [8]. (enzyme-database.org)
Some helicases unwind DNA as well as RNA [7,8]. (enzyme-database.org)

DEAH-box RNA helicases. (embl.de)
In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. (syr.edu)

Replication of plus-strand RNA viruses depends on recruited host factors that aid several critical steps during replication. (prolekarniky.cz)
In this paper, we show that an essential translation factor, Ded1p DEAD-box RNA helicase of yeast, directly affects replication of Tomato bushy stunt virus (TBSV). (prolekarniky.cz)
Thus, two small RNA viruses, which do not code for their own helicases, seems to recruit a host RNA helicase to aid their replication in infected cells. (prolekarniky.cz)
However, the functions of host factors in (+)RNA virus replication are known only for a small number of host factors [1] - [9] . (prolekarniky.cz)
Gross, C.H. and Shuman, S. The nucleoside triphosphatase and helicase activities of vaccinia virus NPH-II are essential for virus replication. (enzyme-database.org)
Mathematical modeling of plus-strand RNA virus replication to identify broad-spectrum antiviral treatment strategies. (cdc.gov)

The Q motif is necessary for single-stranded RNA binding and for proper conformational dynamics in response to ATP binding and hydrolysis. (bellbrooklabs.com)
While both the ATP binding domain and the helicase domain share and cooperate in conformationally dictated ATP binding and hydrolysis, RNA binding, and helicase functions, the N-terminal Rec A-like domain principally orchestrates ATP binding and hydrolysis, while the C-terminal Rec A-like domain mainly controls RNA binding and helicase activities. (bellbrooklabs.com)
Use of the Transcreener ® ADP 2 assay for detection of helicase-linked ATP hydrolysis is a robust, HTS-proven method for identifying and characterizing DEAD-Box helicase inhibitors. (bellbrooklabs.com)

In situ poly(A) hybridization indicates that the export of poly(A) + RNAs is blocked in the cryophyte/los4-2 mutant at warm or high temperatures but not at low temperatures, whereas the los4-1 mutation weakens mRNA export at both low and warm temperatures. (edu.sa)
These results demonstrate an important role of the CRYOPHYTE/LOS4 RNA helicase in mRNA export, plant development, and stress responses. (edu.sa)

Here, single-molecule high-resolution optical trapping measurements reveal that Mtr4p unwinds RNA duplexes by 3′-to-5′ translocation on the loading strand, that strand separation occurs in discrete steps of 6 base pairs and that a single Mtr4p molecule performs consecutive unwinding steps. (nature.com)

RNA helicase activity of Mtr4p is critical for biological functions of the enzyme, but the molecular basis for RNA unwinding is not understood. (nature.com)
We further show that RNA unwinding by Mtr4p requires interaction with upstream RNA duplex. (nature.com)
Inclusion of Mtr4p within the TRAMP complex increases the rate constant for unwinding initiation but does not change the characteristics of Mtr4p's helicase mechanism. (nature.com)
Our data indicate that Mtr4p utilizes a previously unknown unwinding mode that combines aspects of canonical translocating helicases and non-canonical duplex-sensing helicases, thereby restricting directional translocation to duplex regions. (nature.com)
Figure 1: Observation of Mtr4p unwinding RNA duplex via high-resolution optical trapping. (nature.com)
Figure 2: Mtr4p unwinding rates versus tether tension and nucleotide composition for unwinding the 16-bp RNA hairpin. (nature.com)
Figure 3: Mtr4p unwinding 32-bp-long RNA hairpins. (nature.com)
Figure 5: Mtr4p RNA unwinding model. (nature.com)
Bernstein, J., Patterson, D.N., Wilson, G.M. & Toth, E.A. Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3′>5′ helicase partner of the nuclear exosome. (nature.com)
de la Cruz, J., Kressler, D., Tollervey, D. & Linder, P. Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3′ end formation of 5.8S rRNA in Saccharomyces cerevisiae . (nature.com)
The RNA helicase Mtr4p modulates polyadenylation in the TRAMP complex. (nature.com)

DDX5 (Dead-Box 5 or p68) is a member of a family of 37 "DEAD-Box" ATP-dependent RNA helicases that play a role in nearly all aspects of RNA processing and also act as nucleic acid recognition receptors for viral immunity. (bellbrooklabs.com)

Rodamilans, B. and Montoya, G. Expression, purification, crystallization and preliminary X-ray diffraction analysis of the DDX3 RNA helicase domain. (enzyme-database.org)
The C-terminal RGS-RGG (Arg-Gly-Ser-Arg-Gly-Gly) motif modulates DDX5-specific biological functions through its interaction with RNA and DDX3. (bellbrooklabs.com)
Like several other DDXs, most notably DDX3, it acts as a viral RNA sensor and contributes to immunity via type I interferon induction, but it is also hijacked by some viruses to enable their propagation. (bellbrooklabs.com)
Our DDX3 application provides an excellent example of using this assay to study DEAD-Box helicases, like DDX5. (bellbrooklabs.com)

IGCs are composed of particles measuring 20-25 nm in diameter, and they contain numerous factors that are involved in RNA synthesis and processing. (rupress.org)
RNA synthesis is terminated intrinsically, when the elongation complex transcribes a stable RNA hairpin followed by a uridine-rich stretch, or with the aid of transcription termination factor ρ. (fu-berlin.de)
e.g. they bind selectively to DNA, stimulate transcription resulting in tissue-specific RNA synthesis and undergo specific changes in response to various hormones or phytomitogens. (lookformedical.com)

We also find that Ded1p is a component of the tombusvirus replicase complex and Ded1p binds to the 3′-end of the viral minus-stranded RNA. (prolekarniky.cz)
In addition, we have developed an in vitro assay for Flock house virus (FHV), a small RNA virus of insects, that also demonstrated positive effect on FHV replicase activity by the added Ded1p helicase. (prolekarniky.cz)

After the assembly of the membrane-bound viral replicase complexes (VRC), the viral replicase uses the viral RNA as a template to produce complementary (−)RNA. (prolekarniky.cz)
Development of DDX5 inhibitors will help to delineate the complex roles of DDX5 and other DEAD-Box helicase in cancer and viral infection and hopefully lead to development of improved therapeutic strategies. (bellbrooklabs.com)

It contains 2 copies of a double-stranded RNA-binding domain, a DEXH core domain and an RGG box. (wikipedia.org)

To study the biological roles of OsRH2 and OsRH34 in rice, transgenic rice plants were generated by RNA interference. (ncu.edu.tw)

They are implicated in a number of cellular processes involving alteration of RNA secondary structure such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. (wikipedia.org)

Applying a mass spectrometric analysis, we identified the DEAD-box helicase DDX27 as stably associated factor of the PeBoW-complex. (cipsm.de)
Pausing and termination can be further modulated by elongation factors, such as N-utilization substances A and G. Some regulatory factors or RNAs can stably insulate RNAP from the destabilizing effects of terminators over long distances (processive anti-termination). (fu-berlin.de)

It acts by opening DNA either around the RNA transcription start site or the DNA. (embl.de)
The α 2 ββ'ω core enzyme cooperates with transcription factors and responds to signals on DNA templates and nascent RNAs to achieve full functionality in vivo . (fu-berlin.de)

For example, elongating RNAP frequently enters an elemental paused state, and pausing can be stabilized by an RNA hairpin invading the RNA exit tunnel or by RNAP backtracking. (fu-berlin.de)

Results: This study investigated two DEAD box RNA helicases, OsRH2 and OsRH34, which are homologous to eIF4AIII, in rice. (ncu.edu.tw)

Johnson, S.J. & Jackson, R.N. Ski2-like RNA helicase structures: common themes and complex assemblies. (nature.com)
It has been proposed that ribosome scanning and start codon selection are regulated by elements in the 5' leader sequence, such as RNA primary sequences (for example, the Kozak sequence context), upstream open reading frames (uORFs), secondary structures, and RNA modifications 4 - 7 . (biorxiv.org)

May be identical with EC 3.6.4.12 (DNA helicase). (enzyme-database.org)

Ataxin-2 interacts with the DEAD/H-box RNA helicase DDX6 and interferes with P-bodies and stress granules. (mpg.de)

Bacteria transcribe their genomes with the help of multi-subunit RNA polymerases (RNAPs), which comprise two large β and β' subunits that form the active site, two regulatory α subunits and an ω subunit that supports RNAP assembly. (fu-berlin.de)

RNA plays a crucial structural and catalytic role in a variety of important cellular processes. (allegheny.edu)

2019) The DDX5/Dbp2 subfamily of DEAD-box RNA helicases. (bellbrooklabs.com)

Li, S.C., Chung, M.C. and Chen, C.S. Cloning and characterization of a DEAD box RNA helicase from the viable seedlings of aged mung bean. (enzyme-database.org)

The RNA-binding domains and RGG box influence and regulate RNA helicase activity. (wikipedia.org)
It has a DNA unwinding activity characteristic of helicases with a 3' to 5' polarity. (embl.de)
Enables RNA binding activity. (nih.gov)

These findings suggested that RNA helicases may play important roles in sex development and differentiation in teleosts. (syr.edu)

RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. (nature.com)
Callahan, K.P. & Butler, J.S. TRAMP complex enhances RNA degradation by the nuclear exosome component Rrp6. (nature.com)

Conservation of the RNA helicases suggests that mRNA structurome remodelling is a general mechanism for stress-induced translation across kingdoms. (biorxiv.org)

These two superfamilies encompass a large number of DNA and RNA helicases from archaea, eubacteria, eukaryotes and viruses that seem to be active as monomers or dimers. (embl.de)
RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance. (cdc.gov)

Domain structure of human nuclear DNA helicase II (RNA helicase A)". The Journal of Biological Chemistry. (wikipedia.org)
This entry represents the DNA-binding domain of classical SF1 and SF2 helicases. (embl.de)

Anatomy1

Organisms1

Chemicals and Drugs20

Phenomena and Processes15

Information Science3

Proteins26

Protein16

ATPase5

Eukaryotic8

Polymerase5

Ribosomal4

Gene4

Unwind3

DEAH2

Replication6

Hydrolysis3

MRNA export2

Duplexes1

Mtr4p11

Nucleic acid1

DDX34

Synthesis3

Ded1p2

Viral2

DEXH1

Interference1

Initiation1

Stably2

Transcription2

Hairpin1

Homologous1

Structures2

4.121

Interacts1

Subunit1

Catalytic1

DBP21

Characterization1

Activity3

Roles1

Degradation2

Mechanism1

Viruses2

Domain2