Genomes and Genes
Summary: A family of proteins that promote unwinding of RNA during splicing and translation.
- Kervestin S, Li C, Buckingham R, Jacobson A. Testing the faux-UTR model for NMD: analysis of Upf1p and Pab1p competition for binding to eRF3/Sup35p. Biochimie. 2012;94:1560-71 pubmed publisher..We conclude that activation of NMD at a premature termination codon is not solely based on the absence of Pab1p and suggest that a specific recruitment step must commit Upf1p to the process and Upf1p-associated mRNAs to NMD. ..
- Abudu A, Wang X, Dang Y, Zhou T, Xiang S, Zheng Y. Identification of molecular determinants from Moloney leukemia virus 10 homolog (MOV10) protein for virion packaging and anti-HIV-1 activity. J Biol Chem. 2012;287:1220-8 pubmed publisher..These results provide a molecular basis for further understanding the MOV10 antiretroviral mechanism. ..
- Lubas M, Christensen M, Kristiansen M, Domanski M, Falkenby L, Lykke Andersen S, et al. Interaction profiling identifies the human nuclear exosome targeting complex. Mol Cell. 2011;43:624-37 pubmed publisher..However, at least ZCCHC7 function is restricted to nucleoli. Our results suggest that human nuclear exosome degradation pathways comprise modules of spatially organized cofactors that diverge from the yeast model. ..
- Rodríguez Galán O, García Gómez J, de la Cruz J. Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives. Biochim Biophys Acta. 2013;1829:775-90 pubmed publisher..These factors include nucleases, RNA modifying enzymes, ATPases, GTPases, kinases and RNA helicases. Altogether, they likely confer speed, accuracy and directionality to the ribosome synthesis process, however, ..
- Ding S, Kohlway A, Pyle A. Unmasking the active helicase conformation of nonstructural protein 3 from hepatitis C virus. J Virol. 2011;85:4343-53 pubmed publisher..Our findings indicate that an open, extended conformation of NS3 is required for helicase activity and represents the biologically relevant conformation of the protein during viral replication. ..
- Fiorini F, Boudvillain M, Le Hir H. Tight intramolecular regulation of the human Upf1 helicase by its N- and C-terminal domains. Nucleic Acids Res. 2013;41:2404-15 pubmed publisher..This study underlines the tight and intricate regulation pathways required to activate multifunctional RNA helicases like Upf1.
- Fiorini F, Bonneau F, Le Hir H. Biochemical characterization of the RNA helicase UPF1 involved in nonsense-mediated mRNA decay. Methods Enzymol. 2012;511:255-74 pubmed publisher..This functional analysis is an important complement for structural studies of protein complexes containing RNA helicases.
- Chen C, Liu X, Boris Lawrie K, Sharma A, Jeang K. Cellular RNA helicases and HIV-1: insights from genome-wide, proteomic, and molecular studies. Virus Res. 2013;171:357-65 pubmed publisherb>RNA helicases are ubiquitous in plants and animals and function in many cellular processes...
- Khadka S, Vangeloff A, Zhang C, Siddavatam P, Heaton N, Wang L, et al. A physical interaction network of dengue virus and human proteins. Mol Cell Proteomics. 2011;10:M111.012187 pubmed publisher..This study provides a valuable starting point for additional investigations into the roles of human proteins in DENV infection. ..
- Park J, Heo I, Tian Y, Simanshu D, Chang H, Jee D, et al. Dicer recognizes the 5' end of RNA for efficient and accurate processing. Nature. 2011;475:201-5 pubmed publisher..Thus, 5'-end recognition by Dicer is important for precise and effective biogenesis of miRNAs. Insights from this study should also afford practical benefits to the design of small hairpin RNAs. ..
- Martin R, Straub A, Doebele C, Bohnsack M. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol. 2013;10:4-18 pubmed publisherRibosome synthesis requires a multitude of cofactors, among them DExD/H-box RNA helicases. Bacterial RNA helicases involved in ribosome assembly are not essential, while eukaryotes strictly require multiple DExD/H-box proteins that are ..
- Creamer T, Darby M, Jamonnak N, Schaughency P, Hao H, Wheelan S, et al. Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PLoS Genet. 2011;7:e1002329 pubmed publisher..In addition, we show that Sen1 does not cross-link efficiently to many expected non-coding RNAs but does cross-link to the 3' end of most pre-mRNA transcripts, suggesting an extensive role in mRNA 3' end formation and/or termination. ..
- Hardwick S, Luisi B. Rarely at rest: RNA helicases and their busy contributions to RNA degradation, regulation and quality control. RNA Biol. 2013;10:56-70 pubmed publisherb>RNA helicases are compact, machine-like proteins that can harness the energy of nucleoside triphosphate binding and hydrolysis to dynamically remodel RNA structures and protein-RNA complexes...
- Gargantini P, Lujan H, Pereira C. In silico analysis of trypanosomatids' helicases. FEMS Microbiol Lett. 2012;335:123-9 pubmed publisher..network, RNA editing, and trans-splicing; all of these unique features involve a wide variety of specific DNA/RNA helicases. In this work, the genomes of trypanosomatids were analyzed by data mining, searching for genes coding for DNA/..
- Lim S, Bowler M, Lai T, Song H. The Ighmbp2 helicase structure reveals the molecular basis for disease-causing mutations in DMSA1. Nucleic Acids Res. 2012;40:11009-22 pubmed publisher..Mapping of the pathogenic mutations of DSMA1 onto the helicase core structure provides a molecular basis for understanding the disease-causing consequences of Ighmbp2 mutations...
- Xing L, Niu M, Kleiman L. In vitro and in vivo analysis of the interaction between RNA helicase A and HIV-1 RNA. J Virol. 2012;86:13272-80 pubmed publisher..RHA is a member of the DExH subclass of RNA helicases that uniquely contains two double-stranded RNA binding domains (dsRBDs) at its N terminus...
- Cordin O, Hahn D, Beggs J. Structure, function and regulation of spliceosomal RNA helicases. Curr Opin Cell Biol. 2012;24:431-8 pubmed publisher..Here we discuss the potential family-specific mechanisms of spliceosomal RNA helicases and their regulation.
- Porrúa O, Libri D. A bacterial-like mechanism for transcription termination by the Sen1p helicase in budding yeast. Nat Struct Mol Biol. 2013;20:884-91 pubmed publisher..We also show that termination is inhibited by RNA-DNA hybrids. Our results elucidate the role of Sen1p in controlling pervasive transcription. ..
- Hwang J, Maquat L. Nonsense-mediated mRNA decay (NMD) in animal embryogenesis: to die or not to die, that is the question. Curr Opin Genet Dev. 2011;21:422-30 pubmed publisher..The critical roles of many NMD factors in other metabolic pathways undoubtedly also contribute to embryonic development if not viability. ..
- Al Tassan N, Khalil D, Shinwari J, Al Sharif L, Bavi P, Abduljaleel Z, et al. A missense mutation in PIK3R5 gene in a family with ataxia and oculomotor apraxia. Hum Mutat. 2012;33:351-4 pubmed publisher..Our characterization of the PIK3R5 protein and findings suggest that it may play a role in the development of the cerebellum and vermis...
- Watkins N, Bohnsack M. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Wiley Interdiscip Rev RNA. 2012;3:397-414 pubmed publisher..New snoRNA-rRNA interactions have been documented, and the roles of RNA helicases in releasing snoRNP complexes from the rRNA have been described.
- Gebhard L, Kaufman S, Gamarnik A. Novel ATP-independent RNA annealing activity of the dengue virus NS3 helicase. PLoS ONE. 2012;7:e36244 pubmed publisher..We propose that, according to the ATP availability, NS3 could function regulating the folding or unfolding of viral RNA structures. ..
- Prévost K, Desnoyers G, Jacques J, Lavoie F, Massé E. Small RNA-induced mRNA degradation achieved through both translation block and activated cleavage. Genes Dev. 2011;25:385-96 pubmed publisher..Thus, beyond translation initiation block, sRNA-induced mRNA cleavage requires several unexpected steps, many of which are determined by structural features of the target mRNA. ..
- Sabin L, Zheng Q, Thekkat P, Yang J, Hannon G, Gregory B, et al. Dicer-2 processes diverse viral RNA species. PLoS ONE. 2013;8:e55458 pubmed publisher..This study uncovered several novel, heavily targeted features within viral genomes, offering insight into viral replication, viral immune evasion strategies, and the mechanism of antiviral RNAi...
- Shi C, Baldwin I, Wu J. Arabidopsis plants having defects in nonsense-mediated mRNA decay factors UPF1, UPF2, and UPF3 show photoperiod-dependent phenotypes in development and stress responses. J Integr Plant Biol. 2012;54:99-114 pubmed publisher..These data suggest a complex regulatory network, likely composed of light signaling and NMD factor-mediated pathways, in influencing plant development and adaption to environmental stresses. ..
- Wagschal A, Rousset E, Basavarajaiah P, Contreras X, Harwig A, Laurent Chabalier S, et al. Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII. Cell. 2012;150:1147-57 pubmed publisher..Our study reveals RNAPII pausing and premature termination mediated by the co-operative activity of ribonucleases, Drosha/Dgcr8, Xrn2, and Rrp6, as a regulatory mechanism of RNAPII-dependent transcription elongation. ..
- Ranji A, Boris Lawrie K. RNA helicases: emerging roles in viral replication and the host innate response. RNA Biol. 2010;7:775-87 pubmedb>RNA helicases serve multiple roles at the virus-host interface...
- Ajamian L, Mouland A. Implications of RNA helicases in HIV-1 replication: possible roles in latency. Curr HIV Res. 2011;9:588-94 pubmed..In addition, we also raise the possibility that RNA helicases, while playing important roles at almost every step of the HIV-1 replication cycle, could be implicated in the ..
- Roux C, Demuth J, Dunman P. Characterization of components of the Staphylococcus aureus mRNA degradosome holoenzyme-like complex. J Bacteriol. 2011;193:5520-6 pubmed publisher..Results also revealed that the recently recognized RNase RnpA interacts with the S. aureus degradosome and that this interaction is conserved in other Gram-positive organisms. ..
- Fogel B, Lee J, Lane J, Wahnich A, Chan S, Huang A, et al. Mutations in rare ataxia genes are uncommon causes of sporadic cerebellar ataxia. Mov Disord. 2012;27:442-6 pubmed publisher..Rare genetic ataxias, reported only in specific populations or families, may contribute to a percentage of sporadic ataxia...
- Owttrim G. RNA helicases: diverse roles in prokaryotic response to abiotic stress. RNA Biol. 2013;10:96-110 pubmed publisher..b>RNA helicases rearrange RNA secondary structure and RNA-protein interactions in an ATP-dependent reaction, performing ..
- Rowland J, Simon W, Prakash J, Slabas A. Proteomics reveals a role for the RNA helicase crhR in the modulation of multiple metabolic pathways during cold acclimation of Synechocystis sp. PCC6803. J Proteome Res. 2011;10:3674-89 pubmed publisher..54-0.70). We propose functions for three previously hypothetical proteins. We suggest molecular targets for CrhR action and identify downstream regulated events in metabolism. ..
- Lehnik Habrink M, Newman J, Rothe F, Solovyova A, Rodrigues C, Herzberg C, et al. RNase Y in Bacillus subtilis: a Natively disordered protein that is the functional equivalent of RNase E from Escherichia coli. J Bacteriol. 2011;193:5431-41 pubmed publisher..In many bacteria, these RNases, as well as RNA helicases and other proteins, are organized in a protein complex called the RNA degradosome...
- Chang M, Collet B, Nie P, Lester K, Campbell S, Secombes C, et al. Expression and functional characterization of the RIG-I-like receptors MDA5 and LGP2 in Rainbow trout (Oncorhynchus mykiss). J Virol. 2011;85:8403-12 pubmed publisher..Interestingly, MDA5 expression was not affected by overexpressed LGP2 in transfected cells and vice versa, suggesting that they likely act in parallel as positive regulators for IFN production...
- Cenik E, Fukunaga R, Lu G, Dutcher R, Wang Y, Tanaka Hall T, et al. Phosphate and R2D2 restrict the substrate specificity of Dicer-2, an ATP-driven ribonuclease. Mol Cell. 2011;42:172-84 pubmed publisher..We propose that the Dicer-2 helicase domain uses ATP to generate many siRNAs from a single molecule of dsRNA before dissociating from its substrate. ..
- Wang Q, Han Y, Qiu Y, Zhang S, Tang F, Wang Y, et al. Identification and characterization of RNA duplex unwinding and ATPase activities of an alphatetravirus superfamily 1 helicase. Virology. 2012;433:440-8 pubmed publisher..Our study is the first to identify an alphatetravirus RNA helicase and further characterize its dsRNA unwinding and NTPase activities in detail and should foster our understanding of DpTV and other alphatetraviruses. ..
- Owttrim G. RNA helicases in cyanobacteria: biochemical and molecular approaches. Methods Enzymol. 2012;511:385-403 pubmed publisherb>RNA helicases are associated with every aspect of RNA metabolism and function. A diverse range of RNA helicases are encoded by essentially every organism...
- Childs K, Randall R, Goodbourn S. Paramyxovirus V proteins interact with the RNA Helicase LGP2 to inhibit RIG-I-dependent interferon induction. J Virol. 2012;86:3411-21 pubmed publisher..This is significant, because it demonstrates a general mechanism for the targeting of the RIG-I pathway by paramyxoviruses...
- Robert F, Pelletier J. Perturbations of RNA helicases in cancer. Wiley Interdiscip Rev RNA. 2013;4:333-49 pubmed publisher..Several RNA helicases have been implicated in the oncogenic process--either through altered expression levels, mutations, or due to ..
- Kemp C, Mueller S, Goto A, Barbier V, Paro S, Bonnay F, et al. Broad RNA interference-mediated antiviral immunity and virus-specific inducible responses in Drosophila. J Immunol. 2013;190:650-8 pubmed publisher..By contrast, the antiviral contribution of the JAK-STAT pathway appears to be virus specific. ..
- Bruns A, Pollpeter D, Hadizadeh N, Myong S, Marko J, Horvath C. ATP hydrolysis enhances RNA recognition and antiviral signal transduction by the innate immune sensor, laboratory of genetics and physiology 2 (LGP2). J Biol Chem. 2013;288:938-46 pubmed publisher..These results demonstrate previously unrecognized properties of LGP2 ATP hydrolysis and RNA interaction and provide a mechanistic basis for a positive regulatory role for LGP2 in antiviral signaling. ..
- Jamonnak N, Creamer T, Darby M, Schaughency P, Wheelan S, Corden J. Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. RNA. 2011;17:2011-25 pubmed publisher..This suggests a novel role for Nrd1 and Nab3 in destruction of ncRNAs in response to nutrient limitation. ..
- Cernilogar F, Onorati M, Kothe G, Burroughs A, Parsi K, Breiling A, et al. Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature. 2011;480:391-5 pubmed publisher..Taken together, our results show that DCR2 and AGO2 are globally associated with transcriptionally active loci and may have a pivotal role in shaping the transcriptome by controlling the processivity of RNA polymerase II. ..
- Avemaria F, Lunetta C, Tarlarini C, Mosca L, Maestri E, Marocchi A, et al. Mutation in the senataxin gene found in a patient affected by familial ALS with juvenile onset and slow progression. Amyotroph Lateral Scler. 2011;12:228-30 pubmed publisher..Diagnostic work-up revealed the diffuse involvement of central and peripheral motor neurons. Genetic analysis revealed a L389S mutation in the senataxin (SETX) gene. ..
- Byrd A, Raney K. Superfamily 2 helicases. Front Biosci (Landmark Ed). 2012;17:2070-88 pubmed..Some families translocate on single-stranded nucleic acid and unwind duplexes, some unwind double-stranded nucleic acids without translocation, and some translocate on double-stranded or single-stranded nucleic acids without unwinding. ..
- Pandiani F, Chamot S, Brillard J, Carlin F, Nguyen the C, Broussolle V. Role of the five RNA helicases in the adaptive response of Bacillus cereus ATCC 14579 cells to temperature, pH, and oxidative stresses. Appl Environ Microbiol. 2011;77:5604-9 pubmed publisher..The RNA helicases CshA, CshB, and CshC could participate in a general adaptation pathway to stressful conditions, with a ..
- Behrens M, He Y, Oliveira C, Andersen G, Pedersen J, Nielsen K. Structural analysis of RNA helicases with small-angle X-ray scattering. Methods Enzymol. 2012;511:191-212 pubmed publisher..Using such prior information relating to the systems studied and applying a variety of methods, substantial insight can be gained about solution structures and interactions of biological macromolecules through small-angle scattering. ..
- Malur M, Gale M, Krug R. LGP2 downregulates interferon production during infection with seasonal human influenza A viruses that activate interferon regulatory factor 3. J Virol. 2012;86:10733-8 pubmed publisher..It is intriguing that LGP2, a host protein induced during influenza A virus infection, downregulates the host antiviral IFN response. ..
- Fuller Pace F, Moore H. RNA helicases p68 and p72: multifunctional proteins with important implications for cancer development. Future Oncol. 2011;7:239-51 pubmed publisherThe DEAD box RNA helicases p68 (DDX5) and p72 (DDX17) play important roles in multiple cellular processes that are commonly dysregulated in cancers, including transcription, pre-mRNA processing/alternative splicing and miRNA processing...
- Ye P, Liu S, Zhu Y, Chen G, Gao G. DEXH-Box protein DHX30 is required for optimal function of the zinc-finger antiviral protein. Protein Cell. 2010;1:956-64 pubmed publisher..Downregulation of DHX30 with shRNAs reduced ZAP's antiviral activity. These data implicate that DHX30 is a cellular factor involved in the antiviral function of ZAP. ..
- Smibert P, Yang J, Azzam G, Liu J, Lai E. Homeostatic control of Argonaute stability by microRNA availability. Nat Struct Mol Biol. 2013;20:789-95 pubmed publisher..We conclude that Argonaute levels are finely tuned by cellular availability of mature miRNAs and the ubiquitin-proteasome system. ..
- Johnson S, Jackson R. Ski2-like RNA helicase structures: common themes and complex assemblies. RNA Biol. 2013;10:33-43 pubmed publisherSki2-like RNA helicases are large multidomain proteins involved in a variety of RNA processing and degradation events. Recent structures of Mtr4, Ski2 and Brr2 provide our first view of these intricate helicases...
- Palonen E, Lindstrom M, Somervuo P, Johansson P, Björkroth J, Korkeala H. Requirement for RNA helicase CsdA for growth of Yersinia pseudotuberculosis IP32953 at low temperatures. Appl Environ Microbiol. 2012;78:1298-301 pubmed publisher..The role of CsdA in Y. pseudotuberculosis under cold conditions was confirmed by impaired growth of insertional csdA mutants at 3°C. The results suggest that CsdA is crucial for Y. pseudotuberculosis survival in the chilled food chain...
- Newman J, Hewitt L, Rodrigues C, Solovyova A, Harwood C, Lewis R. Dissection of the network of interactions that links RNA processing with glycolysis in the Bacillus subtilis degradosome. J Mol Biol. 2012;416:121-36 pubmed publisher..Taken together, these data provide valuable insights into the structure and dynamics of the RNA degradosome, a fascinating and complex macromolecular assembly that links RNA degradation with central carbon metabolism. ..