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Journal articles on the topic 'RNA helicase A'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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1

Shi, Rui-Zhu, Yuan-Qing Pan, and Li Xing. "RNA Helicase A Regulates the Replication of RNA Viruses." Viruses 13, no. 3 (2021): 361. http://dx.doi.org/10.3390/v13030361.

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The RNA helicase A (RHA) is a member of DExH-box helicases and characterized by two double-stranded RNA binding domains at the N-terminus. RHA unwinds double-stranded RNA in vitro and is involved in RNA metabolisms in the cell. RHA is also hijacked by a variety of RNA viruses to facilitate virus replication. Herein, this review will provide an overview of the role of RHA in the replication of RNA viruses.

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2

Robert-Paganin, Julien, Stéphane Réty, and Nicolas Leulliot. "Regulation of DEAH/RHA Helicases by G-Patch Proteins." BioMed Research International 2015 (2015): 1–9. http://dx.doi.org/10.1155/2015/931857.

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RNA helicases from the DEAH/RHA family are present in all the processes of RNA metabolism. The function of two helicases from this family, Prp2 and Prp43, is regulated by protein partners containing a G-patch domain. The G-patch is a glycine-rich domain discovered by sequence alignment, involved in protein-protein and protein-nucleic acid interaction. Although it has been shown to stimulate the helicase’s enzymatic activities, the precise role of the G-patch domain remains unclear. The role of G-patch proteins in the regulation of Prp43 activity has been studied in the two biological processes

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Donsbach, Pascal, and Dagmar Klostermeier. "Regulation of RNA helicase activity: principles and examples." Biological Chemistry 402, no. 5 (2021): 529–59. http://dx.doi.org/10.1515/hsz-2020-0362.

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Abstract RNA helicases are a ubiquitous class of enzymes involved in virtually all processes of RNA metabolism, from transcription, mRNA splicing and export, mRNA translation and RNA transport to RNA degradation. Although ATP-dependent unwinding of RNA duplexes is their hallmark reaction, not all helicases catalyze unwinding in vitro, and some in vivo functions do not depend on duplex unwinding. RNA helicases are divided into different families that share a common helicase core with a set of helicase signature motives. The core provides the active site for ATP hydrolysis, a binding site for no

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4

Wu, Yuliang. "Unwinding and Rewinding: Double Faces of Helicase?" Journal of Nucleic Acids 2012 (2012): 1–14. http://dx.doi.org/10.1155/2012/140601.

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Helicases are enzymes that use ATP-driven motor force to unwind double-stranded DNA or RNA. Recently, increasing evidence demonstrates that some helicases also possess rewinding activity—in other words, they can anneal two complementary single-stranded nucleic acids. All five members of the human RecQ helicase family, helicase PIF1, mitochondrial helicase TWINKLE, and helicase/nuclease Dna2 have been shown to possess strand-annealing activity. Moreover, two recently identified helicases—HARP and AH2 have only ATP-dependent rewinding activity. These findings not only enhance our understanding o

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5

Morozov, Sergey Y., Ekaterina A. Lazareva, and Andrey G. Solovyev. "RNA helicase domains of viral origin in proteins of insect retrotransposons: possible source for evolutionary advantages." PeerJ 5 (August 16, 2017): e3673. http://dx.doi.org/10.7717/peerj.3673.

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Recently, a novel phenomenon of horizontal gene transfer of helicase-encoding sequence from positive-stranded RNA viruses to LINE transposons in insect genomes was described. TRAS family transposons encoding an ORF2 protein, which comprised all typical functional domains and an additional helicase domain, were found to be preserved in many families during the evolution of the order Lepidoptera. In the present paper, in species of orders Hemiptera and Orthoptera, we found helicase domain-encoding sequences integrated into ORF1 of retrotransposons of the Jockey family. RNA helicases encoded by t

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Seo, Mihwa, Keunhee Seo, Wooseon Hwang, et al. "RNA helicase HEL-1 promotes longevity by specifically activating DAF-16/FOXO transcription factor signaling in Caenorhabditis elegans." Proceedings of the National Academy of Sciences 112, no. 31 (2015): E4246—E4255. http://dx.doi.org/10.1073/pnas.1505451112.

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The homeostatic maintenance of the genomic DNA is crucial for regulating aging processes. However, the role of RNA homeostasis in aging processes remains unknown. RNA helicases are a large family of enzymes that regulate the biogenesis and homeostasis of RNA. However, the functional significance of RNA helicases in aging has not been explored. Here, we report that a large fraction of RNA helicases regulate the lifespan of Caenorhabditis elegans. In particular, we show that a DEAD-box RNA helicase, helicase 1 (HEL-1), promotes longevity by specifically activating the DAF-16/forkhead box O (FOXO

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7

Cargill, Michael, Rasika Venkataraman, and Stanley Lee. "DEAD-Box RNA Helicases and Genome Stability." Genes 12, no. 10 (2021): 1471. http://dx.doi.org/10.3390/genes12101471.

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DEAD-box RNA helicases are important regulators of RNA metabolism and have been implicated in the development of cancer. Interestingly, these helicases constitute a major recurring family of RNA-binding proteins important for protecting the genome. Current studies have provided insight into the connection between genomic stability and several DEAD-box RNA helicase family proteins including DDX1, DDX3X, DDX5, DDX19, DDX21, DDX39B, and DDX41. For each helicase, we have reviewed evidence supporting their role in protecting the genome and their suggested mechanisms. Such helicases regulate the exp

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8

Chamot, Danuta, Wendy C. Magee, Esther Yu, and George W. Owttrim. "A Cold Shock-Induced Cyanobacterial RNA Helicase." Journal of Bacteriology 181, no. 6 (1999): 1728–32. http://dx.doi.org/10.1128/jb.181.6.1728-1732.1999.

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ABSTRACT The ability to modify RNA secondary structure is crucial for numerous cellular processes. We have characterized two RNA helicase genes, crhB and crhC, which are differentially expressed in the cyanobacterium Anabaena sp. strain PCC 7120. crhC transcription is limited specifically to cold shock conditions while crhB is expressed under a variety of conditions, including enhanced expression in the cold. This implies that both RNA helicases are involved in the cold acclimation process in cyanobacteria; however, they presumably perform different roles in this adaptation. Although both CrhB

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9

Gilman, Benjamin, Pilar Tijerina, and Rick Russell. "Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs." Biochemical Society Transactions 45, no. 6 (2017): 1313–21. http://dx.doi.org/10.1042/bst20170095.

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Structured RNAs and RNA–protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms. Recent studies have advanced our understanding of how th

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10

Du Pont, Kelly E., Russell B. Davidson, Martin McCullagh, and Brian J. Geiss. "Motif V regulates energy transduction between the flavivirus NS3 ATPase and RNA-binding cleft." Journal of Biological Chemistry 295, no. 6 (2019): 1551–64. http://dx.doi.org/10.1074/jbc.ra119.011922.

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The unwinding of dsRNA intermediates is critical for the replication of flavivirus RNA genomes. This activity is provided by the C-terminal helicase domain of viral nonstructural protein 3 (NS3). As a member of the superfamily 2 (SF2) helicases, NS3 requires the binding and hydrolysis of ATP/NTP to translocate along and unwind double-stranded nucleic acids. However, the mechanism of energy transduction between the ATP- and RNA-binding pockets is not well-understood. Previous molecular dynamics simulations conducted by our group have identified Motif V as a potential “communication hub” for thi

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Rudolph, Markus G., and Dagmar Klostermeier. "When core competence is not enough: functional interplay of the DEAD-box helicase core with ancillary domains and auxiliary factors in RNA binding and unwinding." Biological Chemistry 396, no. 8 (2015): 849–65. http://dx.doi.org/10.1515/hsz-2014-0277.

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Abstract DEAD-box helicases catalyze RNA duplex unwinding in an ATP-dependent reaction. Members of the DEAD-box helicase family consist of a common helicase core formed by two RecA-like domains. According to the current mechanistic model for DEAD-box mediated RNA unwinding, binding of RNA and ATP triggers a conformational change of the helicase core, and leads to formation of a compact, closed state. In the closed conformation, the two parts of the active site for ATP hydrolysis and of the RNA binding site, residing on the two RecA domains, become aligned. Closing of the helicase core is coupl

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12

Studer, Michael K., Lazar Ivanović, Marco E. Weber, Sabrina Marti, and Stefanie Jonas. "Structural basis for DEAH-helicase activation by G-patch proteins." Proceedings of the National Academy of Sciences 117, no. 13 (2020): 7159–70. http://dx.doi.org/10.1073/pnas.1913880117.

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RNA helicases of the DEAH/RHA family are involved in many essential cellular processes, such as splicing or ribosome biogenesis, where they remodel large RNA–protein complexes to facilitate transitions to the next intermediate. DEAH helicases couple adenosine triphosphate (ATP) hydrolysis to conformational changes of their catalytic core. This movement results in translocation along RNA, which is held in place by auxiliary C-terminal domains. The activity of DEAH proteins is strongly enhanced by the large and diverse class of G-patch activators. Despite their central roles in RNA metabolism, i

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Bohnsack, Katherine E., Ralf Ficner, Markus T. Bohnsack, and Stefanie Jonas. "Regulation of DEAH-box RNA helicases by G-patch proteins." Biological Chemistry 402, no. 5 (2021): 561–79. http://dx.doi.org/10.1515/hsz-2020-0338.

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Abstract RNA helicases of the DEAH/RHA family form a large and conserved class of enzymes that remodel RNA protein complexes (RNPs) by translocating along the RNA. Driven by ATP hydrolysis, they exert force to dissociate hybridized RNAs, dislocate bound proteins or unwind secondary structure elements in RNAs. The sub-cellular localization of DEAH-helicases and their concomitant association with different pathways in RNA metabolism, such as pre-mRNA splicing or ribosome biogenesis, can be guided by cofactor proteins that specifically recruit and simultaneously activate them. Here we review the

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14

Deng, Zengqin, Kathleen C. Lehmann, Xiaorong Li, et al. "Structural basis for the regulatory function of a complex zinc-binding domain in a replicative arterivirus helicase resembling a nonsense-mediated mRNA decay helicase." Nucleic Acids Research 42, no. 5 (2013): 3464–77. http://dx.doi.org/10.1093/nar/gkt1310.

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AbstractAll positive-stranded RNA viruses with genomes >∼7 kb encode helicases, which generally are poorly characterized. The core of the nidovirus superfamily 1 helicase (HEL1) is associated with a unique N-terminal zinc-binding domain (ZBD) that was previously implicated in helicase regulation, genome replication and subgenomic mRNA synthesis. The high-resolution structure of the arterivirus helicase (nsp10), alone and in complex with a polynucleotide substrate, now provides first insights into the structural basis for nidovirus helicase function. A previously uncharacterized domain 1B co

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15

DU, Mark X., Robert B. JOHNSON, Xin-Lai SUN, Kirk A. STASCHKE, Joseph COLACINO, and Q. May WANG. "Comparative characterization of two DEAD-box RNA helicases in superfamily II: human translation-initiation factor 4A and hepatitis C virus non-structural protein 3 (NS3) helicase." Biochemical Journal 363, no. 1 (2002): 147–55. http://dx.doi.org/10.1042/bj3630147.

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Eukaryotic initiation factor 4A (eIF4A) is an ATP-dependent RNA helicase and is homologous to the non-structural protein 3 (NS3) helicase domain encoded by hepatitis C virus (HCV). Reported here is the comparative characterization of human eIF4A and HCV NS3 helicase in an effort to better understand viral and cellular helicases of superfamily II and to assist in designing specific inhibitors against HCV infections. Both eIF4A and HCV NS3 helicase domain were expressed in bacterial cells as histidine-tagged proteins and purified to homogeneity. Purified eIF4A exhibited RNA-unwinding activity an

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16

Rho, Jaerang, Seeyoung Choi, Young Rim Seong, Joonho Choi, and Dong-Soo Im. "The Arginine-1493 Residue in QRRGRTGR1493G Motif IV of the Hepatitis C Virus NS3 Helicase Domain Is Essential for NS3 Protein Methylation by the Protein Arginine Methyltransferase 1." Journal of Virology 75, no. 17 (2001): 8031–44. http://dx.doi.org/10.1128/jvi.75.17.8031-8044.2001.

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ABSTRACT The NS3 protein of hepatitis C virus (HCV) contains protease and RNA helicase activities, both of which are likely to be essential for HCV propagation. An arginine residue present in the arginine-glycine (RG)-rich region of many RNA-binding proteins is posttranslationally methylated by protein arginine methyltransferases (PRMTs). Amino acid sequence analysis revealed that the NS3 protein contains seven RG motifs, including two potential RG motifs in the 1486-QRRGRTGRG-1494 motif IV of the RNA helicase domain, in which arginines are potentially methylated by PRMTs. Indeed, we found tha

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17

Grass, Lena M., Jan Wollenhaupt, Tatjana Barthel, et al. "Large-scale ratcheting in a bacterial DEAH/RHA-type RNA helicase that modulates antibiotics susceptibility." Proceedings of the National Academy of Sciences 118, no. 30 (2021): e2100370118. http://dx.doi.org/10.1073/pnas.2100370118.

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Many bacteria harbor RNA-dependent nucleoside-triphosphatases of the DEAH/RHA family, whose molecular mechanisms and cellular functions are poorly understood. Here, we show that the Escherichia coli DEAH/RHA protein, HrpA, is an ATP-dependent 3 to 5′ RNA helicase and that the RNA helicase activity of HrpA influences bacterial survival under antibiotics treatment. Limited proteolysis, crystal structure analysis, and functional assays showed that HrpA contains an N-terminal DEAH/RHA helicase cassette preceded by a unique N-terminal domain and followed by a large C-terminal region that modulates

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18

Delagoutte, Emmanuelle, and Peter H. von Hippel. "Helicase mechanisms and the coupling of helicases within macromolecular machines Part II: Integration of helicases into cellular processes." Quarterly Reviews of Biophysics 36, no. 1 (2003): 1–69. http://dx.doi.org/10.1017/s0033583502003864.

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1. Helicases as components of macromolecular machines 32. Helicases in replication 72.1 The loading of replicative helicases 72.1.1 Loading Rep helicase at the replication origin of bacteriophage ϕX174 72.1.2 How is a ssDNA strand passed through (and bound in?) the central channel of the hexameric replicative helicases? 82.1.3 Loading of E. coli DnaB helicase in the absence of an auxiliary protein-loading factor 82.1.4 The T7 gp4 primase-helicase is loaded by means of a facilitated ring-opening mechanism 102.1.5 Bacteriophage T4 gp61 primase can be viewed as a loading factor for the homologous

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Sengoku, T., O. Nureki, and S. Yokoyama. "Structural basis for RNA translocation by RNA helicase." Seibutsu Butsuri 43, supplement (2003): S98. http://dx.doi.org/10.2142/biophys.43.s98_2.

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20

El Mortaji, Lamya, Sylvie Aubert, Eloïse Galtier, et al. "The Sole DEAD-Box RNA Helicase of the Gastric PathogenHelicobacter pyloriIs Essential for Colonization." mBio 9, no. 2 (2018): e02071-17. http://dx.doi.org/10.1128/mbio.02071-17.

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ABSTRACTPresent in every kingdom of life, generally in multiple copies, DEAD-box RNA helicases are specialized enzymes that unwind RNA secondary structures. They play major roles in mRNA decay, ribosome biogenesis, and adaptation to cold temperatures. Most bacteria have multiple DEAD-box helicases that present both specialized and partially redundant functions. By using phylogenomics, we revealed that theHelicobactergenus, including the major gastric pathogenH. pylori, is among the exceptions, as it encodes a sole DEAD-box RNA helicase. InH. pylori, this helicase, designated RhpA, forms a mini

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Briguglio, Irene, Sandra Piras, Paola Corona, and Antonio Carta. "Inhibition of RNA Helicases of ssRNA+ Virus Belonging to Flaviviridae, Coronaviridae and Picornaviridae Families." International Journal of Medicinal Chemistry 2011 (December 16, 2011): 1–22. http://dx.doi.org/10.1155/2011/213135.

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Many viral pathogens encode the motor proteins named RNA helicases which display various functions in genome replication. General strategies to design specific and selective drugs targeting helicase for the treatment of viral infections could act via one or more of the following mechanisms: inhibition of the NTPase activity, by interferences with ATP binding and therefore by limiting the energy required for the unwinding and translocation, or by allosteric mechanism and therefore by stabilizing the conformation of the enzyme in low helicase activity state; inhibition of nucleic acids binding t

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Jankowsky, A., U. P. Guenther, and E. Jankowsky. "The RNA helicase database." Nucleic Acids Research 39, Database (2010): D338—D341. http://dx.doi.org/10.1093/nar/gkq1002.

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23

Sulkowska, Aleksandra, Andor Auber, Pawel J. Sikorski, et al. "RNA Helicases from the DEA(D/H)-Box Family Contribute to Plant NMD Efficiency." Plant and Cell Physiology 61, no. 1 (2019): 144–57. http://dx.doi.org/10.1093/pcp/pcz186.

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Abstract Nonsense-mediated mRNA decay (NMD) is a conserved eukaryotic RNA surveillance mechanism that degrades aberrant mRNAs comprising a premature translation termination codon. The adenosine triphosphate (ATP)-dependent RNA helicase up-frameshift 1 (UPF1) is a major NMD factor in all studied organisms; however, the complexity of this mechanism has not been fully characterized in plants. To identify plant NMD factors, we analyzed UPF1-interacting proteins using tandem affinity purification coupled to mass spectrometry. Canonical members of the NMD pathway were found along with numerous NMD c

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Rosana, Albert Remus R., Denise S. Whitford, Richard P. Fahlman, and George W. Owttrim. "Cyanobacterial RNA Helicase CrhR Localizes to the Thylakoid Membrane Region and Cosediments with Degradosome and Polysome Complexes in Synechocystis sp. Strain PCC 6803." Journal of Bacteriology 198, no. 15 (2016): 2089–99. http://dx.doi.org/10.1128/jb.00267-16.

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ABSTRACTThe cyanobacteriumSynechocystissp. strain PCC 6803 encodes a single DEAD box RNA helicase, CrhR, whose expression is tightly autoregulated in response to cold stress. Subcellular localization and proteomic analysis results indicate that CrhR localizes to both the cytoplasmic and thylakoid membrane regions and cosediments with polysome and RNA degradosome components. Evidence is presented that either functional RNA helicase activity or a C-terminal localization signal was required for polysome but not thylakoid membrane localization. Polysome fractionation and runoff translation analysi

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SINGH, MEGHNA, NIDHI SHRIVASTAVA, UZMA SAQIB, MOHAMMAD IMRAN SIDDIQI, and SHAILJA MISRA-BHATTACHARYA. "Structural modelling studies and immunoprophylactic potential ofBrugia malayiDEAD Box RNA helicase." Parasitology 140, no. 8 (2013): 1016–25. http://dx.doi.org/10.1017/s0031182013000322.

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SUMMARYDEAD Box RNA helicases are essential enzymes that are involved in RNA metabolic processes such as transcription, pre-mRNA splicing, translation initiation and RNA decay. We have previously over-expressed and biochemically characterized an immunodominant cDNA clone encoding DEAD box RNA helicase (BmL3-Helicase) isolated by immunoscreening of the larval stage cDNA library ofBrugia malayi.In the current study, the 3D structure was determined and the immunoprophylactic efficacy of BmL3-Helicase was investigated by immunizingMastomys couchawith the recombinant protein and subsequently challe

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Bernstein, Kara A., Sander Granneman, Alicia V. Lee, Swarnameenakshi Manickam, and Susan J. Baserga. "Comprehensive Mutational Analysis of Yeast DEXD/H Box RNA Helicases Involved in Large Ribosomal Subunit Biogenesis." Molecular and Cellular Biology 26, no. 4 (2006): 1195–208. http://dx.doi.org/10.1128/mcb.26.4.1195-1208.2006.

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ABSTRACT DEXD/H box putative RNA helicases are required for pre-rRNA processing in Saccharomyces cerevisiae, although their exact roles and substrates are unknown. To characterize the significance of the conserved motifs for helicase function, a series of five mutations were created in each of the eight essential RNA helicases (Has1, Dbp6, Dbp10, Mak5, Mtr4, Drs1, Spb4, and Dbp9) involved in 60S ribosomal subunit biogenesis. Each mutant helicase was screened for the ability to confer dominant negative growth defects and for functional complementation. Different mutations showed different degre

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Kukhanova, Marina K., Inna L. Karpenko, and Alexander V. Ivanov. "DEAD-box RNA Helicase DDX3: Functional Properties and Development of DDX3 Inhibitors as Antiviral and Anticancer Drugs." Molecules 25, no. 4 (2020): 1015. http://dx.doi.org/10.3390/molecules25041015.

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This short review is focused on enzymatic properties of human ATP-dependent RNA helicase DDX3 and the development of antiviral and anticancer drugs targeting cellular helicases. DDX3 belongs to the DEAD-box proteins, a large family of RNA helicases that participate in all aspects of cellular processes, such as cell cycle progression, apoptosis, innate immune response, viral replication, and tumorigenesis. DDX3 has a variety of functions in the life cycle of different viruses. DDX3 helicase is required to facilitate both the Rev-mediated export of unspliced/partially spliced human immunodeficie

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Johnson, Sean J., and Ryan N. Jackson. "Ski2-like RNA helicase structures." RNA Biology 10, no. 1 (2013): 33–43. http://dx.doi.org/10.4161/rna.22101.

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Phung, Duy Khanh, Clarisse Etienne, Manon Batista та ін. "RNA processing machineries in Archaea: the 5′-3′ exoribonuclease aRNase J of the β-CASP family is engaged specifically with the helicase ASH-Ski2 and the 3′-5′ exoribonucleolytic RNA exosome machinery". Nucleic Acids Research 48, № 7 (2020): 3832–47. http://dx.doi.org/10.1093/nar/gkaa052.

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Abstract A network of RNA helicases, endoribonucleases and exoribonucleases regulates the quantity and quality of cellular RNAs. To date, mechanistic studies focussed on bacterial and eukaryal systems due to the challenge of identifying the main drivers of RNA decay and processing in Archaea. Here, our data support that aRNase J, a 5′-3′ exoribonuclease of the β-CASP family conserved in Euryarchaeota, engages specifically with a Ski2-like helicase and the RNA exosome to potentially exert control over RNA surveillance, at the vicinity of the ribosome. Proteomic landscapes and direct protein–pro

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Gwack, Yousang, Hyouna Yoo, Inyoung Song, Joonho Choe, and Jang H. Han. "RNA-Stimulated ATPase and RNA Helicase Activities and RNA Binding Domain of Hepatitis G Virus Nonstructural Protein 3." Journal of Virology 73, no. 4 (1999): 2909–15. http://dx.doi.org/10.1128/jvi.73.4.2909-2915.1999.

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ABSTRACT Hepatitis G virus (HGV) nonstructural protein 3 (NS3) contains amino acid sequence motifs typical of ATPase and RNA helicase proteins. In order to examine the RNA helicase activity of the HGV NS3 protein, the NS3 region (amino acids 904 to 1580) was fused with maltose-binding protein (MBP), and the fusion protein was expressed inEscherichia coli and purified with amylose resin and anion-exchange chromatography. The purified MBP-HGV/NS3 protein possessed RNA-stimulated ATPase and RNA helicase activities. Characterization of the ATPase and RNA helicase activities of MBP-HGV/NS3 showed t

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31

Pause, A., N. Méthot, and N. Sonenberg. "The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis." Molecular and Cellular Biology 13, no. 11 (1993): 6789–98. http://dx.doi.org/10.1128/mcb.13.11.6789.

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eIF-4A is a eukaryotic translation initiation factor that is required for mRNA binding to ribosomes. It exhibits single-stranded RNA-dependent ATPase activity, and in combination with a second initiation factor, eIF-4B, it exhibits duplex RNA helicase activity. eIF-4A is the prototype of a large family of proteins termed the DEAD box protein family, whose members share nine highly conserved amino acid regions. The functions of several of these conserved regions in eIF-4A have previously been assigned to ATP binding, ATPase, and helicase activities. To define the RNA-binding region of eIF-4A, a

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Pause, A., N. Méthot, and N. Sonenberg. "The HRIGRXXR region of the DEAD box RNA helicase eukaryotic translation initiation factor 4A is required for RNA binding and ATP hydrolysis." Molecular and Cellular Biology 13, no. 11 (1993): 6789–98. http://dx.doi.org/10.1128/mcb.13.11.6789-6798.1993.

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eIF-4A is a eukaryotic translation initiation factor that is required for mRNA binding to ribosomes. It exhibits single-stranded RNA-dependent ATPase activity, and in combination with a second initiation factor, eIF-4B, it exhibits duplex RNA helicase activity. eIF-4A is the prototype of a large family of proteins termed the DEAD box protein family, whose members share nine highly conserved amino acid regions. The functions of several of these conserved regions in eIF-4A have previously been assigned to ATP binding, ATPase, and helicase activities. To define the RNA-binding region of eIF-4A, a

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Taschuk, Frances, and Sara Cherry. "DEAD-Box Helicases: Sensors, Regulators, and Effectors for Antiviral Defense." Viruses 12, no. 2 (2020): 181. http://dx.doi.org/10.3390/v12020181.

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DEAD-box helicases are a large family of conserved RNA-binding proteins that belong to the broader group of cellular DExD/H helicases. Members of the DEAD-box helicase family have roles throughout cellular RNA metabolism from biogenesis to decay. Moreover, there is emerging evidence that cellular RNA helicases, including DEAD-box helicases, play roles in the recognition of foreign nucleic acids and the modulation of viral infection. As intracellular parasites, viruses must evade detection by innate immune sensing mechanisms and degradation by cellular machinery while also manipulating host cel

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Zhang, Yandong, Jin You, Xingshun Wang, and Jason Weber. "The DHX33 RNA Helicase Promotes mRNA Translation Initiation." Molecular and Cellular Biology 35, no. 17 (2015): 2918–31. http://dx.doi.org/10.1128/mcb.00315-15.

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DEAD/DEAH box RNA helicases play essential roles in numerous RNA metabolic processes, such as mRNA translation, pre-mRNA splicing, ribosome biogenesis, and double-stranded RNA sensing. Herein we show that a recently characterized DEAD/DEAH box RNA helicase, DHX33, promotes mRNA translation initiation. We isolated intact DHX33 protein/RNA complexes in cells and identified several ribosomal proteins, translation factors, and mRNAs. Reduction of DHX33 protein levels markedly reduced polyribosome formation and caused the global inhibition of mRNA translation that was rescued with wild-type DHX33 b

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Xu, Shan, Yali Ci, Leijie Wang, et al. "Zika virus NS3 is a canonical RNA helicase stimulated by NS5 RNA polymerase." Nucleic Acids Research 47, no. 16 (2019): 8693–707. http://dx.doi.org/10.1093/nar/gkz650.

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Abstract Zika virus is a positive single-strand RNA virus whose replication involved RNA unwinding and synthesis. ZIKV NS3 contains a helicase domain, but its enzymatic activity is not fully characterized. Here, we established a dsRNA unwinding assay based on the FRET effect to study the helicase activity of ZIKV NS3, which provided kinetic information in real time. We found that ZIKV NS3 specifically unwound dsRNA/dsDNA with a 3′ overhang in the 3′ to 5′ direction. The RNA unwinding ability of NS3 significantly decreased when the duplex was longer than 18 base pairs. The helicase activity of

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Netterling, Sakura, Caroline Bäreclev, Karolis Vaitkevicius, and Jörgen Johansson. "RNA Helicase Important for Listeria monocytogenes Hemolytic Activity and Virulence Factor Expression." Infection and Immunity 84, no. 1 (2015): 67–76. http://dx.doi.org/10.1128/iai.00849-15.

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RNA helicases have been shown to be important for the function of RNA molecules at several levels, although their putative involvement in microbial pathogenesis has remained elusive. We have previously shown thatListeria monocytogenesDExD-box RNA helicases are important for bacterial growth, motility, ribosomal maturation, and rRNA processing. We assessed the importance of the RNA helicase Lmo0866 (here named CshA) for expression of virulence traits. We observed a reduction in hemolytic activity in a strain lacking CshA compared to the wild type. This phenomenon was less evident in strains lac

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Uson, Maria Loressa, Heather Ordonez, and Stewart Shuman. "Mycobacterium smegmatis HelY Is an RNA-Activated ATPase/dATPase and 3′-to-5′ Helicase That Unwinds 3′-Tailed RNA Duplexes and RNA:DNA Hybrids." Journal of Bacteriology 197, no. 19 (2015): 3057–65. http://dx.doi.org/10.1128/jb.00418-15.

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ABSTRACTMycobacteria have a large and distinctive ensemble of DNA helicases that function in DNA replication, repair, and recombination. Little is known about the roster of RNA helicases in mycobacteria or their roles in RNA transactions. The 912-amino-acidMycobacterium smegmatisHelY (MSMEG_3885) protein is a bacterial homolog of the Mtr4 and Ski2 helicases that regulate RNA 3′ processing and turnover by the eukaryal exosome. Here we characterize HelY as an RNA-stimulated ATPase/dATPase and an ATP/dATP-dependent 3′-to-5′ helicase. HelY requires a 3′ single-strand RNA tail (a loading RNA strand

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Li, Haitao, Stephen Clum, Shihyun You, Kurt E. Ebner, and R. Padmanabhan. "The Serine Protease and RNA-Stimulated Nucleoside Triphosphatase and RNA Helicase Functional Domains of Dengue Virus Type 2 NS3 Converge within a Region of 20 Amino Acids." Journal of Virology 73, no. 4 (1999): 3108–16. http://dx.doi.org/10.1128/jvi.73.4.3108-3116.1999.

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ABSTRACT NS3 protein of dengue virus type 2 has a serine protease domain within the N-terminal 180 residues. NS2B is required for NS3 to form an active protease involved in processing of the viral polyprotein precursor. The region carboxy terminal to the protease domain has conserved motifs present in several viral RNA-stimulated nucleoside triphosphatase (NTPase)/RNA helicases. To define the functional domains of protease and NTPase/RNA helicase activities of NS3, full-length and amino-terminal deletion mutants of NS3 were expressed inEscherichia coli and purified. Deletion of 160 N-terminal

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Mozaffari-Jovin, Sina, Traudy Wandersleben, Karine F. Santos, Cindy L. Will, Reinhard Lührmann, and Markus C. Wahl. "Inhibition of RNA Helicase Brr2 by the C-Terminal Tail of the Spliceosomal Protein Prp8." Science 341, no. 6141 (2013): 80–84. http://dx.doi.org/10.1126/science.1237515.

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The Ski2-like RNA helicase Brr2 is a core component of the spliceosome that must be tightly regulated to ensure correct timing of spliceosome activation. Little is known about mechanisms of regulation of Ski2-like helicases by protein cofactors. Here we show by crystal structure and biochemical analyses that the Prp8 protein, a major regulator of the spliceosome, can insert its C-terminal tail into Brr2’s RNA-binding tunnel, thereby intermittently blocking Brr2’s RNA-binding, adenosine triphosphatase, and U4/U6 unwinding activities. Inefficient Brr2 repression is the only recognizable phenotyp

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Shah, Abdullah, Farooq Rashid, Hassaan Mehboob Awan, et al. "The DEAD-Box RNA Helicase DDX3 Interacts with m6A RNA Demethylase ALKBH5." Stem Cells International 2017 (2017): 1–11. http://dx.doi.org/10.1155/2017/8596135.

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DDX3 is a member of the family of DEAD-box RNA helicases. DDX3 is a multifaceted helicase and plays essential roles in key biological processes such as cell cycle, stress response, apoptosis, and RNA metabolism. In this study, we found that DDX3 interacted with ALKBH5, an m6A RNA demethylase. The ATP domain of DDX3 and DSBH domain of ALKBH5 were indispensable to their interaction with each other. Furthermore, DDX3 could modulate the demethylation of mRNAs. We also showed that DDX3 regulated the methylation status of microRNAs and there was an interaction between DDX3 and AGO2. The dynamics of

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Hönig, Arnd, Didier Auboeuf, Marjorie M. Parker, Bert W. O'Malley, and Susan M. Berget. "Regulation of Alternative Splicing by the ATP-Dependent DEAD-Box RNA Helicase p72." Molecular and Cellular Biology 22, no. 16 (2002): 5698–707. http://dx.doi.org/10.1128/mcb.22.16.5698-5707.2002.

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ABSTRACT Although a number of ATP-dependent RNA helicases are important for constitutive RNA splicing, no helicases have been implicated in alternative RNA splicing. Here, we show that the abundant DEAD-box RNA helicase p72, but not its close relative p68, affects the splicing of alternative exons containing AC-rich exon enhancer elements. The effect of p72 was tested by using mini-genes that undergo different types of alternative splicing. When the concentration of p72 was increased in transient transfections, the inclusion of enhancer-containing CD44 alternative exons v4 and v5 increased usi

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Lin, Chao, and Joseph L. Kim. "Structure-Based Mutagenesis Study of Hepatitis C Virus NS3 Helicase." Journal of Virology 73, no. 10 (1999): 8798–807. http://dx.doi.org/10.1128/jvi.73.10.8798-8807.1999.

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ABSTRACT The NS3 protein of hepatitis C virus (HCV) is a bifunctional protein containing a serine protease in the N-terminal one-third, which is stimulated upon binding of the NS4A cofactor, and an RNA helicase in the C-terminal two-thirds. In this study, a C-terminal hexahistidine-tagged helicase domain of the HCV NS3 protein was expressed in Escherichia coli and purified to homogeneity by conventional chromatography. The purified HCV helicase domain has a basal ATPase activity, a polynucleotide-stimulated ATPase activity, and a nucleic acid unwinding activity and binds efficiently to single-

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Hamann, Florian, Lars C. Zimmerningkat, Robert A. Becker, et al. "The structure of Prp2 bound to RNA and ADP-BeF3−reveals structural features important for RNA unwinding by DEAH-box ATPases." Acta Crystallographica Section D Structural Biology 77, no. 4 (2021): 496–509. http://dx.doi.org/10.1107/s2059798321001194.

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Noncoding intron sequences present in precursor mRNAs need to be removed prior to translation, and they are excisedviathe spliceosome, a multimegadalton molecular machine composed of numerous protein and RNA components. The DEAH-box ATPase Prp2 plays a crucial role during pre-mRNA splicing as it ensures the catalytic activation of the spliceosome. Despite high structural similarity to other spliceosomal DEAH-box helicases, Prp2 does not seem to function as an RNA helicase, but rather as an RNA-dependent ribonucleoprotein particle-modifying ATPase. Recent crystal structures of the spliceosomal

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Hajj, Mirna, Petra Langendijk-Genevaux, Manon Batista, et al. "Phylogenetic Diversity of Lhr Proteins and Biochemical Activities of the Thermococcales aLhr2 DNA/RNA Helicase." Biomolecules 11, no. 7 (2021): 950. http://dx.doi.org/10.3390/biom11070950.

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Helicase proteins are known to use the energy of ATP to unwind nucleic acids and to remodel protein-nucleic acid complexes. They are involved in almost every aspect of DNA and RNA metabolisms and participate in numerous repair mechanisms that maintain cellular integrity. The archaeal Lhr-type proteins are SF2 helicases that are mostly uncharacterized. They have been proposed to be DNA helicases that act in DNA recombination and repair processes in Sulfolobales and Methanothermobacter. In Thermococcales, a protein annotated as an Lhr2 protein was found in the network of proteins involved in RNA

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Andreou, Alexandra Z., and Dagmar Klostermeier. "The DEAD-box helicase eIF4A." RNA Biology 10, no. 1 (2013): 19–32. http://dx.doi.org/10.4161/rna.21966.

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Koepsell, Scott A., Marilynn A. Larson, Mark A. Griep, and Steven H. Hinrichs. "Staphylococcus aureus Helicase but Not Escherichia coli Helicase Stimulates S. aureus Primase Activity and Maintains Initiation Specificity." Journal of Bacteriology 188, no. 13 (2006): 4673–80. http://dx.doi.org/10.1128/jb.00316-06.

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ABSTRACT Bacterial primases are essential for DNA replication due to their role in polymerizing the formation of short RNA primers repeatedly on the lagging-strand template and at least once on the leading-strand template. The ability of recombinant Staphylococcus aureus DnaG primase to utilize different single-stranded DNA templates was tested using oligonucleotides of the sequence 5′-CAGA (CA)5 XYZ (CA)3-3′, where XYZ represented the variable trinucleotide. These experiments demonstrated that S. aureus primase synthesized RNA primers predominately on templates containing 5′-d(CTA)-3′ or TTA

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Denison, Mark R., Willy J. M. Spaan, Yvonne van der Meer, et al. "The Putative Helicase of the Coronavirus Mouse Hepatitis Virus Is Processed from the Replicase Gene Polyprotein and Localizes in Complexes That Are Active in Viral RNA Synthesis." Journal of Virology 73, no. 8 (1999): 6862–71. http://dx.doi.org/10.1128/jvi.73.8.6862-6871.1999.

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ABSTRACT The coronavirus mouse hepatitis virus (MHV) translates its replicase gene (gene 1) into two co-amino-terminal polyproteins, polyprotein 1a and polyprotein 1ab. The gene 1 polyproteins are processed by viral proteinases to yield at least 15 mature products, including a putative RNA helicase from polyprotein 1ab that is presumed to be involved in viral RNA synthesis. Antibodies directed against polypeptides encoded by open reading frame 1b were used to characterize the expression and processing of the MHV helicase and to define the relationship of helicase to the viral nucleocapsid prot

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Kujat, Sonya L., and George W. Owttrim. "Redox-Regulated RNA Helicase Expression." Plant Physiology 124, no. 2 (2000): 703–14. http://dx.doi.org/10.1104/pp.124.2.703.

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Zhang, Jun, Hwan Ki Park, Haijing Sun, and Peiwen Fei. "RNA helicase and colon cancer." Cancer Biology & Therapy 7, no. 10 (2008): 1677–78. http://dx.doi.org/10.4161/cbt.7.10.6865.

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Koh, Hye Ran, Li Xing, Lawrence Kleiman, and Sua Myong. "Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing." Nucleic Acids Research 42, no. 13 (2014): 8556–64. http://dx.doi.org/10.1093/nar/gku523.

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