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Rna helicase

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https://www.readbyqxmd.com/read/28431250/nuclear-proximity-of-mtr4-to-rna-exosome-restricts-dna-mutational-asymmetry
#1
Junghyun Lim, Pankaj Kumar Giri, David Kazadi, Brice Laffleur, Wanwei Zhang, Veronika Grinstein, Evangelos Pefanis, Lewis M Brown, Erik Ladewig, Ophélie Martin, Yuling Chen, Raul Rabadan, François Boyer, Gerson Rothschild, Michel Cogné, Eric Pinaud, Haiteng Deng, Uttiya Basu
The distribution of sense and antisense strand DNA mutations on transcribed duplex DNA contributes to the development of immune and neural systems along with the progression of cancer. Because developmentally matured B cells undergo biologically programmed strand-specific DNA mutagenesis at focal DNA/RNA hybrid structures, they make a convenient system to investigate strand-specific mutagenesis mechanisms. We demonstrate that the sense and antisense strand DNA mutagenesis at the immunoglobulin heavy chain locus and some other regions of the B cell genome depends upon localized RNA processing protein complex formation in the nucleus...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28428796/expression-profiling-coupled-with-in-silico-mapping-identifies-candidate-genes-for-reducing-aflatoxin-accumulation-in-maize
#2
Ramesh Dhakal, Chenglin Chai, Ratna Karan, Gary L Windham, William P Williams, Prasanta K Subudhi
Aflatoxin, produced by Aspergillus flavus, is hazardous to health of humans and livestock. The lack of information about large effect QTL for resistance to aflatoxin accumulation is a major obstacle to employ marker-assisted selection for maize improvement. The understanding of resistance mechanisms of the host plant and the associated genes is necessary for improving resistance to A. flavus infection. A suppression subtraction hybridization (SSH) cDNA library was made using the developing kernels of Mp715 (resistant inbred) and B73 (susceptible inbred) and 480 randomly selected cDNA clones were sequenced to identify differentially expressed genes (DEGs) in response to A...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28427210/dependence-of-p53-deficient-cells-on-the-dhx9-dexh-box-helicase
#3
Teresa Lee, Jerry Pelletier
DHX9 is a DExH-box helicase family member with key regulatory roles in a broad range of cellular processes. It participates at multiple levels of gene regulation, including DNA replication, transcription, translation, RNA transport, and microRNA processing. It has been implicated in tumorigenesis and recent evidence suggests that it may be a promising chemotherapeutic target. Previous studies have determined that DHX9 suppression elicits an apoptotic or senescence response by activating p53 signaling. Here, we show that DHX9 inhibition can also have deleterious effects in cells lacking functional p53...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426938/high-throughput-screening-to-identify-inhibitors-of-dead-box-helicase-ddx41
#4
Mariko Yoneyama-Hirozane, Mitsuyo Kondo, Shin-Ichi Matsumoto, Akiko Morikawa-Oki, Daisuke Morishita, Atsushi Nakanishi, Tomohiro Kawamoto, Masaharu Nakayama
The human DEAD (Asp-Glu-Ala-Asp) box protein DDX41, a member of the DEXDc helicase family, has nucleic acid-dependent ATPase and RNA and DNA translocase and unwinding activities. DDX41 is affected by somatic mutations in sporadic cases of myeloid neoplasms as well as in a biallelic fashion in 50% of patients with germline DDX41 mutations. The R525H mutation in DDX41 is thought to play important roles in the development of hereditary myelodysplastic syndrome and acute myelocytic leukemia. In this study, human DDX41 and its R525H mutant (R525H) were expressed in Escherichia coli and purified...
April 1, 2017: SLAS Discovery
https://www.readbyqxmd.com/read/28416567/the-c-terminal-dsrna-binding-domain-of-drosophila-dicer-2-is-crucial-for-efficient-and-high-fidelity-production-of-sirna-and-loading-of-sirna-to-argonaute2
#5
Suresh K Kandasamy, Li Zhu, Ryuya Fukunaga
Drosophila Dicer-2 efficiently and precisely produces 21-nt siRNAs from long double-stranded RNA (dsRNA) substrates and loads these siRNAs onto the effector protein Argonaute2 for RNA silencing. The functional roles of each domain of the multi-domain Dicer-2 enzyme in the production and loading of siRNAs are not fully understood. Here we characterized Dicer-2 mutants lacking either the N-terminal helicase domain or C-terminal dsRNA-binding domain (CdsRBD) (ΔHelicase and ΔCdsRBD, respectively) in vivo and in vitro...
April 17, 2017: RNA
https://www.readbyqxmd.com/read/28416566/structure-of-deah-rha-atpase-prp43p-bound-to-rna-implicates-a-pair-of-hairpins-and-motif-va-in-translocation-along-rna
#6
Yangzi He, Jonathan P Staley, Gregers Rom Andersen, Klaus H Nielsen
Three families of nucleic acid-dependent ATPases (DEAH/RHA, Ski2-like and NS3/NPH-II), termed the DExH ATPases, are thought to execute myriad functions by processive, ATP-dependent, 3' to 5' translocation along single-stranded nucleic acid. While the mechanism of translocation of the viral NS3/NPH-II family has been studied extensively, it has not been clear if or how the principles that have emerged for this family extend to the other two families. Here we report the crystal structure of the yeast DEAH/RHA family ATPase Prp43p, which functions in splicing and ribosome biogenesis, in complex with poly-uracil and a non-hydrolysable ATP analogue...
April 17, 2017: RNA
https://www.readbyqxmd.com/read/28411239/discrimination-of-cytosolic-self-and-non-self-rna-by-rig-i-like-receptors
#7
Charlotte Laessig, Karl-Peter Hopfner
RIG-I-like receptors (RLRs) are cytosolic innate immune sensors that detect pathogenic RNA and induce a systemic antiviral response. During the last decade many studies focused on their molecular characterization and the identification of RNA agonists. Thereby it became more and more clear that RLR activation needs to be carefully regulated, since constitutive signalling or detection of endogenous RNA through loss of specificity is detrimental. Here, we review the current understanding of RLR activation and selectivity...
April 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28411202/characterization-of-the-mammalian-dead-box-protein-ddx5-reveals-functional-conservation-with-s-cerevisiae-ortholog-dbp2-in-transcriptional-control-and-glucose-metabolism
#8
Zheng Xing, Siwen Wang, Elizabeth J Tran
DEAD-box proteins are a class of non-processive RNA helicases that dynamically modulate the structure of RNA and ribonucleoprotein complexes (RNPs). However, the precise roles of individual members are not well understood. Work from our lab revealed that the DEAD-box protein Dbp2 in Saccharomyces cerevisiae is an active RNA helicase in vitro that functions in transcription by promoting mRNP assembly, repressing cryptic transcription initiation, and regulating long non-coding RNA activity. Interestingly, Dbp2 is also linked to glucose sensing and hexose transporter gene expression...
April 14, 2017: RNA
https://www.readbyqxmd.com/read/28408439/sen1-has-unique-structural-features-grafted-on-the-architecture-of-the-upf1-like-helicase-family
#9
Bronislava Leonaitė, Zhong Han, Jérôme Basquin, Fabien Bonneau, Domenico Libri, Odil Porrua, Elena Conti
The superfamily 1B (SF1B) helicase Sen1 is an essential protein that plays a key role in the termination of non-coding transcription in yeast. Here, we identified the ~90 kDa helicase core of Saccharomyces cerevisiae Sen1 as sufficient for transcription termination in vitro and determined the corresponding structure at 1.8 Å resolution. In addition to the catalytic and auxiliary subdomains characteristic of the SF1B family, Sen1 has a distinct and evolutionarily conserved structural feature that "braces" the helicase core...
April 13, 2017: EMBO Journal
https://www.readbyqxmd.com/read/28402257/-dead-box-rna-helicase-3-modulates-nf-%C3%AE%C2%BAb-signal-pathway-by-controlling-the-phosphorylation-of-pp2a-c-subunit
#10
Xin Wang, Rui Wang, Miao Luo, Chen Li, Hua-Xia Wang, Chang-Chao Huan, Yu-Rong Qu, Ying Liao, Xiang Mao
Asp-Glu-Ala-Asp (DEAD)-box RNA helicase 3 (DDX3), an ATP-dependent RNA helicase, is associated with RNA splicing, mRNA export, transcription, translation, and RNA decay. Recent studies revealed that DDX3 participates in innate immune response during virus infection by interacting with TBK1 and regulating the production of IFN-β. In our studies, we demonstrated that DDX3 regulated NF-κB signal pathway. We found that DDX3 knockdown reduced the phosphorylation of p65 and IKK-β and ultimately attenuated the production of inflammatory cytokines induced by poly(I:C) or TNF-α stimulation...
March 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/28400277/high-sensitive-one-step-rt-pcr-using-mmlv-reverse-transcriptase-dna-polymerase-with-reverse-transcriptase-activity-and-dna-rna-helicase
#11
Hiroyuki Okano, Misato Baba, Tomomi Yamasaki, Ryota Hidese, Shinsuke Fujiwara, Itaru Yanagihara, Takeshi Ujiiye, Tsukasa Hayashi, Kenji Kojima, Teisuke Takita, Kiyoshi Yasukawa
No abstract text is available yet for this article.
April 8, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28396352/association-of-the-cold-shock-dead-box-rna-helicase-rhle-to-the-rna-degradosome-in-caulobacter-crescentus
#12
Angel A Aguirre, Alexandre M Vicente, Steven W Hardwick, Daniela M Alvelos, Ricardo R Mazzon, Ben F Luisi, Marilis V Marques
In diverse bacterial lineages, multi-enzyme assemblies have evolved that are central elements of RNA metabolism and RNA-mediated regulation. The aquatic, Gram-negative bacteria Caulobacter crescentus, which has been a model system for studying the bacterial cell cycle, has an RNA degradosome assembly that is formed by the endoribonuclease RNase E and includes the DEAD-box RNA helicase RhlB. Immunoprecipitations of extracts from cells expressing an epitope-tagged RNase E reveal that RhlE, another member of the DEAD-box helicase family, associates with the degradosome at temperatures below the optimum for growth...
April 10, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28396347/serotype-specific-interactions-among-functional-domains-of-dengue-virus-2-non-structural-proteins-ns-5-and-ns3-are-crucial-for-viral-rna-replication
#13
Tadahisa Teramoto, Anuradha Balasubramanian, Kyung H Choi, Radhakrishnan Padmanabhan
Four serotypes of mosquito-borne Dengue virus (DENV), evolved from a common ancestor, are human pathogens of global significance, and there is no vaccine or antiviral drug available. The N-terminal domain of DENV NS5 has guanylyltransferase and methyltransferase (MTase) and the C-terminal region has the polymerase (POL) which are important for 5'-capping and RNA replication. The crystal structure of NS5 showed it as a dimer but the functional evidence for NS5 dimer is lacking. The results of our studies show that the substitution of DENV2 NS5 MTase or POL with that of DENV4 NS5 within DENV2 RNA resulted in severe attenuation of replication in the transfected BHK-21 cells...
April 10, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28388677/the-barley-stripe-mosaic-virus-%C3%AE-b-protein-promotes-chloroplast-targeted-replication-by-enhancing-unwinding-of-rna-duplexes
#14
Kun Zhang, Yongliang Zhang, Meng Yang, Songyu Liu, Zhenggang Li, Xianbing Wang, Chenggui Han, Jialin Yu, Dawei Li
RNA viruses encode various RNA binding proteins that function in many steps of viral infection cycles. These proteins function as RNA helicases, methyltransferases, RNA-dependent RNA polymerases, RNA silencing suppressors, RNA chaperones, movement proteins, and so on. Although many of the proteins bind the viral RNA genome during different stages of infection, our knowledge about the coordination of their functions is limited. In this study, we describe a novel role for the Barley stripe mosaic virus (BSMV) γb as an enhancer of αa RNA helicase activity, and we show that the γb protein is recruited by the αa viral replication protein to chloroplast membrane sites of BSMV replication...
April 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28388433/rna-helicase-ddx5-inhibits-reprogramming-to-pluripotency-by-mirna-based-repression-of-rybp-and-its-prc1-dependent-and-independent-functions
#15
Huanhuan Li, Ping Lai, Jinping Jia, Yawei Song, Qing Xia, Kaimeng Huang, Na He, Wangfang Ping, Jiayu Chen, Zhongzhou Yang, Jiao Li, Mingze Yao, Xiaotao Dong, Jicheng Zhao, Chunhui Hou, Miguel A Esteban, Shaorong Gao, Duanqing Pei, Andrew P Hutchins, Hongjie Yao
No abstract text is available yet for this article.
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28378460/chlorosis-caused-by-two-recessively-interacting-genes-reveals-a-role-of-rna-helicase-in-hybrid-breakdown-in-arabidopsis-thaliana
#16
Björn Plötner, Markus Nurmi, Axel Fischer, Mutsumi Watanabe, Korbinian Schneeberger, Svante Holm, Neha Vaid, Mark Aurel Schöttler, Dirk Walther, Rainer Hoefgen, Detlef Weigel, Roosa A E Laitinen
Hybrids often differ in fitness from their parents. They may be superior, translating into hybrid vigour or heterosis, but they may also be markedly inferior, because of hybrid weakness or incompatibility. The underlying genetic causes for the latter can often be traced back to genes that evolve rapidly because of sexual or host-pathogen conflicts. Hybrid weakness may manifest itself only in later generations, in a phenomenon called hybrid breakdown. We have characterized a case of hybrid breakdown among two Arabidopsis thaliana accessions, Shahdara (Sha, Tajikistan) and Lövvik-5 (Lov-5, Northern Sweden)...
April 4, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28377575/the-role-of-lon-mediated-proteolysis-in-the-dynamics-of-mitochondrial-nucleic-acid-protein-complexes
#17
Nina Kunová, Gabriela Ondrovičová, Jacob A Bauer, Jana Bellová, Ľuboš Ambro, Lucia Martináková, Veronika Kotrasová, Eva Kutejová, Vladimír Pevala
Mitochondrial nucleoids consist of several different groups of proteins, many of which are involved in essential cellular processes such as the replication, repair and transcription of the mitochondrial genome. The eukaryotic, ATP-dependent protease Lon is found within the central nucleoid region, though little is presently known about its role there. Aside from its association with mitochondrial nucleoids, human Lon also specifically interacts with RNA. Recently, Lon was shown to regulate TFAM, the most abundant mtDNA structural factor in human mitochondria...
April 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28360888/the-absence-of-the-transcription-factor-yrr1p-identified-from-comparative-genome-profiling-increased-vanillin-tolerance-due-to-enhancements-of-abc-transporters-expressing-rrna-processing-and-ribosome-biogenesis-in-saccharomyces-cerevisiae
#18
Xinning Wang, Zhenzhen Liang, Jin Hou, Yu Shen, Xiaoming Bao
Enhancing the tolerance of Saccharomyces cerevisiae to inhibitors derived from lignocellulose is conducive to producing biofuel and chemicals using abundant lignocellulosic materials. Vanillin is a major type of phenolic inhibitor in lignocellulose hydrolysates for S. cerevisiae. In the present work, the factors beneficial to vanillin resistance in yeast were identified from the vanillin-resistant strain EMV-8, which was derived from strain NAN-27 by adaptive evolution. We found 450 SNPs and 44 genes with InDels in the vanillin-tolerant strain EMV-8 by comparing the genome sequences of EMV-8 and NAN-27...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28358513/discovery-of-novel-1-4-diacylpiperazines-as-selective-and-cell-active-eif4a3-inhibitors
#19
Masahiro Ito, Toshio Tanaka, Douglas R Cary, Misa Iwatani-Yoshihara, Yusuke Kamada, Tomohiro Kawamoto, Samuel Aparicio, Atsushi Nakanishi, Yasuhiro Imaeda
Eukaryotic initiation factor 4A3 (eIF4A3), a member of the DEAD-box RNA helicase family, is one of the core components of the exon junction complex (EJC). The EJC is known to be involved in a variety of RNA metabolic processes typified by nonsense-mediated RNA decay (NMD). In order to identify molecular probes to investigate the functions and therapeutic relevance of eIF4A3, a search for selective eIF4A3 inhibitors was conducted. Through the chemical optimization of 1,4-diacylpiperazine derivatives identified via high-throughput screening (HTS), we discovered the first reported selective eIF4A3 inhibitor 53a exhibiting cellular NMD inhibitory activity...
April 11, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28355211/transcriptome-wide-analysis-of-alternative-routes-for-rna-substrates-into-the-exosome-complex
#20
Clémentine Delan-Forino, Claudia Schneider, David Tollervey
The RNA exosome complex functions in both the accurate processing and rapid degradation of many classes of RNA. Functional and structural analyses indicate that RNA can either be threaded through the central channel of the exosome or more directly access the active sites of the ribonucleases Rrp44 and Rrp6, but it was unclear how many substrates follow each pathway in vivo. We used CRAC (UV crosslinking and analysis of cDNA) in growing cells to identify transcriptome-wide interactions of RNAs with the major nuclear exosome-cofactor Mtr4 and with individual exosome subunits (Rrp6, Csl4, Rrp41 and Rrp44) along the threaded RNA path...
March 2017: PLoS Genetics
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