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Rna helicase

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https://www.readbyqxmd.com/read/29351962/rna-helicases-in-rna-decay
#1
REVIEW
Vanessa Khemici, Patrick Linder
RNA molecules have the tendency to fold into complex structures or to associate with complementary RNAs that exoribonucleases have difficulties processing or degrading. Therefore, degradosomes in bacteria and organelles as well as exosomes in eukaryotes have teamed-up with RNA helicases. Whereas bacterial degradosomes are associated with RNA helicases from the DEAD-box family, the exosomes and mitochondrial degradosome use the help of Ski2-like and Suv3 RNA helicases.
January 19, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29340209/discovery-of-culex-pipiens-associated-tunisia-virus-a-new-ssrna-virus-representing-a-new-insect-associated-virus-family
#2
Diane Bigot, Célestine M Atyame, Mylène Weill, Fabienne Justy, Elisabeth A Herniou, Philippe Gayral
In the global context of arboviral emergence, deep sequencing unlocks the discovery of new mosquito-borne viruses. Mosquitoes of the species Culex pipiens, C. torrentium, and C. hortensis were sampled from 22 locations worldwide for transcriptomic analyses. A virus discovery pipeline was used to analyze the dataset of 0.7 billion reads comprising 22 individual transcriptomes. Two closely related 6.8 kb viral genomes were identified in C. pipiens and named as Culex pipiens associated tunisia virus (CpATV) strains Ayed and Jedaida...
January 2018: Virus Evolution
https://www.readbyqxmd.com/read/29339407/genomic-identification-and-functional-characterization-of-essential-genes-in-caenorhabditis-elegans
#3
Zhaozhao Qin, Robert Johnsen, Shicheng Yu, Jeffrey Shih-Chieh Chu, David Baillie, Nansheng Chen
Using combined genetic mapping, Illumina sequencing, bioinformatics analyses, and experimental validation, we identified 60 essential genes from 104 lethal mutations in two genomic regions of C. elegans totalling approximately 14 Mb on chromosome III(mid) and chromosome V(left). Five of the 60 genes had not previously been shown to have lethal phenotypes by RNA interference depletion. By analyzing the regions around the lethal missense mutations, we identified four putative new protein functional domains. Furthermore, functional characterization of the identified essential genes shows that most are enzymes, including helicases, tRNA synthetases, and kinases in addition to ribosomal proteins...
January 16, 2018: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29336305/inferring-joint-sequence-structural-determinants-of-protein-functional-specificity
#4
Andrew F Neuwald, L Aravind, Stephen F Altschul
Residues responsible for allostery, cooperativity, and other subtle but functionally important interactions remain difficult to detect. To aid such detection, we employ statistical inference based on the assumption that residues distinguishing a protein subgroup from evolutionarily divergent subgroups often constitute an interacting functional network. We identify such networks with the aid of two measures of statistical significance. One measure aids identification of divergent subgroups based on distinguishing residue patterns...
January 16, 2018: ELife
https://www.readbyqxmd.com/read/29329019/salidroside-influences-the-cellular-cross-talk-of-human-fetal-lung-diploid-fibroblasts-a-proteomic-approach
#5
Wenmin Xing, Wenyan Gao, Huili Su, Sanying Wang, Jing Zhang, Genxiang Mao, Jing Yan
Senescence is a complex multiple factor proces, which is still poorly understood. The purpose of this study was to find the proteome of cultured human fetal lung diploid fibroblasts (2BS) of different population doubling (PD), as well as the altered proteome induced by salidroside (SAL) in 2BS cells. Proteins were identified by two-dimensional electrophoresis (2-DE) combining matrix-assisted laser desorption/ionization-time and flight mass spectrometry (MAL DI-TOF/MS). As a result, we found 16 proteins with two-fold variations in senescent cells or after SAL treatment, some being reduced such as reticulocalbin-1, heat shock protein beta-6, elongation factor 1-delta, F-actin-capping protein subunit alpha-1, and chloride intracellular channel 1...
January 5, 2018: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/29328432/a-double-edged-function-of-ddx3-as-an-oncogene-or-tumor-suppressor-in-cancer-progression-review
#6
Yu He, Dan Zhang, Yanfang Yang, Xixi Wang, Xinyu Zhao, Peng Zhang, Hongxia Zhu, Ningzhi Xu, Shufang Liang
DEAD-box RNA helicase 3 (DDX3) is a highly conserved family member of DEAD-box proteins in all eukaryotes from yeasts to human beings. Accumulating studies have confirmed DDX3 has the ability to regulate different steps of RNA metabolism, including RNA splicing, RNA export, transcription and translation initiation. Moreover, DDX3 is involved in many biological processes, such as stress response, cell apoptosis, cell cycle regulation and virus infection. In recent years, DDX3 is getting increasing attention due to its essential roles in cancer progression...
January 9, 2018: Oncology Reports
https://www.readbyqxmd.com/read/29321579/differentiation-potential-of-pluripotent-stem-cells-correlates-to-the-level-of-chd7
#7
Takako Yamamoto, Chiemi Takenaka, Yusuke Yoda, Yasuhiro Oshima, Kenichi Kagawa, Hiroshi Miyajima, Tetsuji Sasaki, Shin Kawamata
Embryonic Stem Cells (ESC) possesses two distinct features; self-renewal and the potential to differentiate. Here we show the differentiation potential and growth rate of ESC correlates positively with the expression level of the gene encoding chromodomain helicase DNA binding protein 7 (CHD7). When ESCs are maintained in feeder-free conditions and single cell seeding, ESC KhES-1 having 4520 copies or more of CHD7 in 5 ng total RNA show differentiation potential, but this is lost when the CHD7 copy number is reduced in KhES-1 to less than 696 by alternative culture conditions...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29315404/interplay-between-rnaseh2-and-mov10-controls-line-1-retrotransposition
#8
Jongsu Choi, Sung-Yeon Hwang, Kwangseog Ahn
Long interspersed nuclear element 1 is an autonomous non-long terminal repeat retrotransposon that comprises ∼17% of the human genome. Its spontaneous retrotransposition and the accumulation of heritable L1 insertions can potentially result in genome instability and sporadic disorders. Moloney leukemia virus 10 homolog (MOV10), a putative RNA helicase, has been implicated in inhibiting L1 replication, although its underlying mechanism of action remains obscure. Moreover, the physiological relevance of MOV10-mediated L1 regulation in human disease has not yet been examined...
January 5, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29314290/oncogene-rna-helicase-ddx6-promotes-the-process-of-c-myc-expression-in-gastric-cancer-cells
#9
Kohei Taniguchi, Ayako Iwatsuki, Nobuhiko Sugito, Haruka Shinohara, Yuki Kuranaga, Yuki Oshikawa, Toshihiro Tajirika, Manabu Futamura, Kazuhiro Yoshida, Kazuhisa Uchiyama, Yukihiro Akao
Human DEAD-box RNA helicase gene DDX6 was cloned from B-cell lymphoma cell line RC-K8. Previously, we reported that DDX6 acts as oncogene in several cancers such as colorectal cancer and hepatocellular carcinoma. However, the detailed mechanism of DDX6 action in carcinogenesis is largely unknown. In this study, we examined the functions of DDX6 in clinical gastric cancer (GC) samples and GC cells. DDX6 protein expression levels of cancer samples were higher than those of the adjacent normal tissues in 25 clinical GC samples (median value: 1...
January 4, 2018: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/29311576/structural-analysis-of-mtexo-mitochondrial-rna-degradosome-reveals-tight-coupling-of-nuclease-and-helicase-components
#10
Michal Razew, Zbigniew Warkocki, Michal Taube, Adam Kolondra, Mariusz Czarnocki-Cieciura, Elzbieta Nowak, Karolina Labedzka-Dmoch, Aleksandra Kawinska, Jakub Piatkowski, Pawel Golik, Maciej Kozak, Andrzej Dziembowski, Marcin Nowotny
Nuclease and helicase activities play pivotal roles in various aspects of RNA processing and degradation. These two activities are often present in multi-subunit complexes from nucleic acid metabolism. In the mitochondrial exoribonuclease complex (mtEXO) both enzymatic activities are tightly coupled making it an excellent minimal system to study helicase-exoribonuclease coordination. mtEXO is composed of Dss1 3'-to-5' exoribonuclease and Suv3 helicase. It is the master regulator of mitochondrial gene expression in yeast...
January 8, 2018: Nature Communications
https://www.readbyqxmd.com/read/29301961/structure-of-a-human-catalytic-step-i-spliceosome
#11
Xiechao Zhan, Chuangye Yan, Xiaofeng Zhang, Jianlin Lei, Yigong Shi
Splicing by the spliceosome involves branching and exon ligation. The branching reaction leads to the formation of the catalytic step I spliceosome (C complex). Here we report the cryo-EM structure of the human C complex at an average resolution of 4.1 Å. Compared to the structure of the S. cerevisiae C complex, the human complex contains 11 additional proteins. The step I splicing factors CCDC49 and CCDC94 (Cwc25 and Yju2 in S. cerevisiae, respectively) closely interact with the DEAH-family ATPase/helicase Prp16 and bridge the gap between Prp16 and the active site RNA elements...
January 4, 2018: Science
https://www.readbyqxmd.com/read/29297844/predominant-role-of-ips-1-over-trif-adaptor-proteins-in-early-innate-immune-response-against-zika-virus-in-mice
#12
Jocelyne Piret, Julie Carbonneau, Chantal Rhéaume, Mariana Baz, Guy Boivin
Toll-like receptors and RNA helicases are involved in the control of RNA virus infection through production of type I interferons (IFNs). To delineate the relative contributions of these signalling pathways in the innate immune response and the control of Zika virus (ZIKV) pathogenesis, the impact of a deficiency in TRIF and/or IPS-1 adaptor proteins was investigated in mice. Mice were infected intravenously with ZIKV and monitored for clinical signs for 14 days. Groups of mice were sacrificed on days 1, 3 and 7 post-infection (p...
January 3, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29288727/characterization-of-the-es-ddx52-involved-in-the-spermatogonial-mitosis-and-spermatid-differentiation-in-chinese-mitten-crab-eriocheir-sinensis
#13
Qing Li, Hongdan Yang, Lin He, Qun Wang
Spermatogenesis involves a series of process including exiting from the mitotic cell cycle, entry into meiosis, completion of complex differentiation programs, and producing spermatozoa. Expression of various genes in an ordered manner, and interactions between various genes and their protein products, primarily controlled at the post-transcriptional level with DEAD-box RNA helicases playing a crucial role in germ cell development, are required for production of fertile sperm. Many members of this family have been deeply studied in spermatogenesis, such as DDX3X, DDX25 and DDX4, but few data are available on DDX52...
December 27, 2017: Gene
https://www.readbyqxmd.com/read/29281624/the-smc5-6-complex-regulates-the-yeast-mph1-helicase-at-rna-dna-hybrid-mediated-dna-damage
#14
Juan Lafuente-Barquero, Sarah Luke-Glaser, Marco Graf, Sonia Silva, Belén Gómez-González, Arianna Lockhart, Michael Lisby, Andrés Aguilera, Brian Luke
RNA-DNA hybrids are naturally occurring obstacles that must be overcome by the DNA replication machinery. In the absence of RNase H enzymes, RNA-DNA hybrids accumulate, resulting in replication stress, DNA damage and compromised genomic integrity. We demonstrate that Mph1, the yeast homolog of Fanconi anemia protein M (FANCM), is required for cell viability in the absence of RNase H enzymes. The integrity of the Mph1 helicase domain is crucial to prevent the accumulation of RNA-DNA hybrids and RNA-DNA hybrid-dependent DNA damage, as determined by Rad52 foci...
December 27, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/29273634/loss-of-the-deubiquitinase-usp36-destabilizes-the-rna-helicase-dhx33-and-causes-preimplantation-lethality-in-mice
#15
Julia M Fraile, Diana Campos-Iglesias, Francisco Rodríguez, Aurora Astudillo, Roser Vilarrasa-Blasi, Nuria Verdaguer-Dot, Miguel A Prado, Joao A Paulo, Steven P Gygi, José I Martín-Subero, José M P Freije, Carlos López-Otín
Deubiquitinases are proteases with a wide functional diversity that profoundly impact multiple biological processes. Among them, the ubiquitin-specific protease 36 (USP36) has been implicated in the regulation of nucleolar activity. However, its functional relevance in vivo has not yet been fully described. Here, we report the generation of an Usp36-deficient mouse model to examine the function of this enzyme. We show that Usp36 depletion is lethal in pre-implantation mouse embryos, where it blocks the transition from morula to blastocyst during embryonic development...
December 22, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29258862/broad-spectrum-antiviral-activity-of-the-eif4a-inhibitor-silvestrol-against-corona-and-picornaviruses
#16
Christin Müller, Falk W Schulte, Kerstin Lange-Grünweller, Wiebke Obermann, Ramakanth Madhugiri, Stephan Pleschka, John Ziebuhr, Roland K Hartmann, Arnold Grünweller
Coronaviruses (CoV) and picornaviruses are plus-strand RNA viruses that use 5' cap-dependent and cap-independent strategies, respectively, for viral mRNA translation initiation. Here, we analyzed the effects of the plant compound silvestrol, a specific inhibitor of the DEAD-box RNA helicase eIF4A, on viral translation using a dual luciferase assay and virus-infected primary cells. Silvestrol was recently shown to have potent antiviral activity in Ebola virus-infected human macrophages. We found that silvestrol is also a potent inhibitor of cap-dependent viral mRNA translation in CoV-infected human embryonic lung fibroblast (MRC-5) cells...
December 16, 2017: Antiviral Research
https://www.readbyqxmd.com/read/29258557/moloney-leukemia-virus-10-mov10-inhibits-the-degradation-of-apobec3g-through-interference-with-the-vif-mediated-ubiquitin-proteasome-pathway
#17
Cancan Chen, Xiaocao Ma, Qifei Hu, Xinghua Li, Feng Huang, Junsong Zhang, Ting Pan, Jinyu Xia, Chao Liu, Hui Zhang
BACKGROUND: MOV10 protein has ATP-dependent 5'-3' RNA helicase activity and belongs to the UPF1p superfamily. It can inhibit human immunodeficiency virus type 1 (HIV-1) replication at multiple stages and interact with apolipoprotein-B-mRNA-editing enzyme catalytic polypeptide-like 3G (APOBEC3G or A3G), a member of the cytidine deaminase family that exerts potent inhibitory effects against HIV-1 infection. However, HIV-1-encoded virion infectivity factor (Vif) protein specifically mediates the degradation of A3G via the ubiquitin-proteasome system (UPS)...
December 19, 2017: Retrovirology
https://www.readbyqxmd.com/read/29237842/human-norovirus-ns3-has-rna-helicase-and-chaperoning-activities
#18
Teng-Feng Li, Myra Hosmillo, Hella Schwanke, Ting Shu, Zhaowei Wang, Lei Yin, Stephen Curry, Ian G Goodfellow, Xi Zhou
RNA remodeling proteins, including RNA helicases and chaperones, act to remodel RNA structures and/or protein-RNA interactions, and are required for all processes involving RNAs. Although many viruses encode RNA helicases and chaperones, their in vitro activities and their roles in infected cells largely remain elusive. Noroviruses are a diverse group of positive-stranded RNA viruses in the family Caliciviridae, and constitute a significant and potentially fatal threat to human health. Here we report that protein NS3 encoded by human norovirus has both ATP-dependent RNA helicase activity that unwinds RNA helices and ATP-independent RNA chaperoning activity that can remodel structured RNAs and facilitate strand-annealing...
December 13, 2017: Journal of Virology
https://www.readbyqxmd.com/read/29236259/identifying-cellular-nonsense-mediated-mrna-decay-nmd-targets-immunoprecipitation-of-phosphorylated-upf1-followed-by-rna-sequencing-p-upf1-rip-seq
#19
Tatsuaki Kurosaki, Mainul Hoque, Lynne E Maquat
Recent progress in the technology of transcriptome-wide high-throughput sequencing has revealed that nonsense-mediated mRNA decay (NMD) targets ~10% of physiologic transcripts for the purpose of tuning gene expression in response to various environmental conditions. Regardless of the eukaryote studied, NMD requires the ATP-dependent RNA helicase upframeshift 1 (UPF1). It was initially thought that cellular NMD targets could be defined by their binding to steady-state UPF1, which is largely hypophosphorylated...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29233693/thermostable-dna-helicase-improves-the-sensitivity-of-digital-pcr
#20
Ryota Hidese, Katsuhiro Kawato, Yukiko Nakura, Ayako Fujiwara, Kiyoshi Yasukawa, Itaru Yanagihara, Shinsuke Fujiwara
DNA/RNA helicases, which catalyze the unwinding of duplex nucleic acids using the energy of ATP hydrolysis, contribute to various biological functions involving DNA or RNA. Euryarchaeota-specific helicase Tk-EshA (superfamily 2) from the hyperthermophilic archaeon Thermococcus kodakarensis has been used to decrease generation of mis-amplified products (noise DNAs) during PCR. In this study, we focused on another type (superfamily 1B) of helicase, Tk-Upf1 (TK0178) from T. kodakarensis, and compared its effectiveness in PCR and digital PCR with that of Tk-EshA...
December 9, 2017: Biochemical and Biophysical Research Communications
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