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https://www.readbyqxmd.com/read/28544931/role-for-rif1-interacting-partner-ddx1-in-blm-recruitment-to-dna-double-strand-breaks
#1
Lei Li, Ho-Yin Poon, Matthew R Hildebrandt, Elizabeth A Monckton, Devon R Germain, Richard P Fahlman, Roseline Godbout
Human Rap1-interacting factor 1 (RIF1) is an important player in the repair of DNA double strand breaks (DSBs). RIF1 acts downstream of 53BP1, with well-documented roles in class switch recombination in B-cells and inhibition of end resection initiation in BRCA1-defective cells. Here, we report that DEAD Box 1 (DDX1), a RNA helicase also implicated in DSB repair, interacts with RIF1, with co-localization of DDX1 and RIF1 observed throughout interphase. Recruitment of DDX1 to DSBs is dependent on RIF1, with RIF1 depletion abolishing DDX1-mediated facilitation of homologous recombination at DSBs...
May 13, 2017: DNA Repair
https://www.readbyqxmd.com/read/28542199/specialized-box-c-d-snornps-act-as-antisense-guides-to-target-rna-base-acetylation
#2
Sunny Sharma, Jun Yang, Rob van Nues, Peter Watzinger, Peter Kötter, Denis L J Lafontaine, Sander Granneman, Karl-Dieter Entian
Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 are guided by two orphan box C/D snoRNAs-snR4 and snR45 -not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs...
May 24, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28541562/dna-substrate-recognition-and-processing-by-the-full-length-human-upf1-helicase
#3
Saba Dehghani-Tafti, Cyril M Sanders
UPF1 is a conserved helicase required for nonsense-mediated decay (NMD) regulating mRNA stability in the cytoplasm. Human UPF1 (hUPF1) is also needed for nuclear DNA replication. While loss of NMD is tolerated, loss of hUPF1 induces a DNA damage response and cell cycle arrest. We have analysed nucleic acid (NA) binding and processing by full-length hUPF1. hUPF1 unwinds non-B and B-form DNA and RNA substrates in vitro. Unlike many helicases involved in genome stability no hUPF1 binding to DNA structures stabilized by inter-base-pair hydrogen bonding was observed...
May 24, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28536148/the-lotus-domain-is-a-conserved-dead-box-rna-helicase-regulator-essential-for-the-recruitment-of-vasa-to-the-germ-plasm-and-nuage
#4
Mandy Jeske, Christoph W Müller, Anne Ephrussi
DEAD-box RNA helicases play important roles in a wide range of metabolic processes. Regulatory proteins can stimulate or block the activity of DEAD-box helicases. Here, we show that LOTUS (Limkain, Oskar, and Tudor containing proteins 5 and 7) domains present in the germline proteins Oskar, TDRD5 (Tudor domain-containing 5), and TDRD7 bind and stimulate the germline-specific DEAD-box RNA helicase Vasa. Our crystal structure of the LOTUS domain of Oskar in complex with the C-terminal RecA-like domain of Vasa reveals that the LOTUS domain occupies a surface on a DEAD-box helicase not implicated previously in the regulation of the enzyme's activity...
May 23, 2017: Genes & Development
https://www.readbyqxmd.com/read/28520979/the-dead-box-helicase-mss116-plays-distinct-roles-in-mitochondrial-ribogenesis-and-mrna-specific-translation
#5
Dasmanthie De Silva, Sarah Poliquin, Rui Zeng, Angelica Zamudio-Ochoa, Natalie Marrero, Xochitl Perez-Martinez, Flavia Fontanesi, Antoni Barrientos
Members of the DEAD-box family are often multifunctional proteins involved in several RNA transactions. Among them, yeast Saccharomyces cerevisiae Mss116 participates in mitochondrial intron splicing and, under cold stress, also in mitochondrial transcription elongation. Here, we show that Mss116 interacts with the mitoribosome assembly factor Mrh4, is required for efficient mitoribosome biogenesis, and consequently, maintenance of the overall mitochondrial protein synthesis rate. Additionally, Mss116 is required for efficient COX1 mRNA translation initiation and elongation...
May 18, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28510225/controlling-gene-expression-by-dna-mechanics-emerging-insights-and-challenges
#6
REVIEW
David Levens, Laura Baranello, Fedor Kouzine
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions...
September 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28510218/controlling-gene-expression-by-dna-mechanics-emerging-insights-and-challenges
#7
REVIEW
David Levens, Laura Baranello, Fedor Kouzine
Transcription initiation is a major control point for the precise regulation of gene expression. Our knowledge of this process has been mainly derived from protein-centric studies wherein cis-regulatory DNA sequences play a passive role, mainly in arranging the protein machinery to coalesce at the transcription start sites of genes in a spatial and temporal-specific manner. However, this is a highly dynamic process in which molecular motors such as RNA polymerase II (RNAPII), helicases, and other transcription factors, alter the level of mechanical force in DNA, rather than simply a set of static DNA-protein interactions...
November 2016: Biophysical Reviews
https://www.readbyqxmd.com/read/28500049/metabolic-adaptation-to-nutrients-involves-co-regulation-of-gene-expression-by-the-rna-helicase-dbp2-and-the-cyc8-co-repressor-in-saccharomyces-cerevisiae
#8
Siwen Wang, Zheng Xing, Pete E Pascuzzi, Elizabeth J Tran
Cells fine-tune their metabolic programs according to nutrient availability in order to maintain homeostasis. This is achieved largely through integrating signaling pathways and the gene expression program, allowing cells to adapt to nutritional change. Dbp2, a member of the DEAD-box RNA helicase family in Saccharomyces cerevisiae, has been proposed to integrate gene expression with cellular metabolism. Prior work from our laboratory has reported the necessity of DBP2 in proper gene expression, particularly for genes involved in glucose-dependent regulation...
May 12, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28498893/role-of-dhx33-in-c-myc-induced-cancers
#9
Jijun Fu, Yuchu Liu, Xingshun Wang, Baolei Yuan, Yandong Zhang
Oncogene c-Myc is frequently amplified and activated in human cancers. Deregulation of c-Myc protein has been shown to occur in 30% of all human cancers, especially in hematopoietic malignancies. As a transcription factor, c-Myc has been shown to regulate up to 15% of all human genome genes, controlling diverse cellular activities including cell cycle, ribosome biogenesis, protein synthesis, metabolism, apoptosis and angiogenesis. In this report, we provide evidence that the RNA helicase DHX33 is a critical downstream target of c-Myc...
May 11, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28496438/identification-of-cleavage-sites-recognized-by-the-3c-like-cysteine-protease-within-the-two-polyproteins-of-strawberry-mottle-virus
#10
Krin S Mann, Melanie Walker, Hélène Sanfaçon
Strawberry mottle virus (SMoV, family Secoviridae, order Picornavirales) is one of several viruses found in association with strawberry decline disease in Eastern Canada. The SMoV genome consists of two positive-sense single-stranded RNAs, each encoding one large polyprotein. The RNA1 polyprotein (P1) includes the domains for a putative helicase, a VPg, a 3C-like cysteine protease and an RNA-dependent RNA polymerase at its C-terminus, and one or two protein domains at its N-terminus. The RNA2 polyprotein (P2) is predicted to contain the domains for a movement protein (MP) and one or several coat proteins at its N-terminus, and one or more additional domains for proteins of unknown function at its C-terminus...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28492307/rapid-and-sensitive-quantification-of-micrornas-by-isothermal-helicase-dependent-amplification
#11
Fei Ma, Meng Liu, Bo Tang, Chun-Yang Zhang
Dysregulation of microRNA expression levels is closely associated with a variety of human diseases, and their rapid and sensitive quantification is essential to clinical diagnosis and therapy. Due to their poor sensitivity, conventional quantification methods are unable to detect low abundant microRNAs. Alternatively, nucleic acid amplification approaches have been introduced to improve the detection sensitivity, but most of them involve complicated probe design and time-consuming procedures. Herein, we report a simple, rapid and sensitive fluorescent method for label-free detection of low abundant microRNAs based on isothermal helicase-dependent amplification...
May 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28489911/human-%C3%AE-defensin-2-production-upon-viral-and-bacterial-co-infection-is-attenuated-in-copd
#12
Jason W Arnason, James C Murphy, Cora Kooi, Shahina Wiehler, Suzanne L Traves, Christopher Shelfoon, Barbara Maciejewski, Curtis J Dumonceaux, W Shawn Lewenza, David Proud, Richard Leigh
Viral-bacterial co-infections are associated with severe exacerbations of COPD. Epithelial antimicrobial peptides, including human β-defensin-2 (HBD-2), are integral to innate host defenses. In this study, we examined how co-infection of airway epithelial cells with rhinovirus and Pseudomonas aeruginosa modulates HBD-2 expression, and whether these responses are attenuated by cigarette smoke and in epithelial cells obtained by bronchial brushings from smokers with normal lung function or from COPD patients...
2017: PloS One
https://www.readbyqxmd.com/read/28488947/translation-control-learning-from-viruses-again
#13
Juana Díez, Jennifer Jungfleisch
Viruses are powerful tools to uncover cellular processes. Through viral studies we have recently identified a novel translational control mechanism that involves the DEAD-box helicase Dhh1/DDX6 and RNA folding within coding sequences (CDSs). All Dhh1-dependent mRNAs, viral and cellular ones, (i) contain long and highly structured CDSs, (ii) are directly bound by Dhh1 with a specific pattern, (iii) are activated at the translation initiation step and (iv) express proteins associated with the endoplasmic reticulum...
May 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28488414/a-proteomic-based-investigation-of-potential-copper-responsive-biomarkers-proteins-conceptual-networks-and-metabolic-pathways-featuring-penicillium-janthinellum-from-a%C3%A2-heavy-metal-polluted-ecological-niche
#14
Xin Feng, Jian Xu, Yu Liang, Guo-Li Chen, Xian-Wei Fan, You-Zhi Li
Filamentous fungi-copper (Cu) interactions are very important in the formation of natural ecosystems and the bioremediation of heavy metal pollution. However, important issues at the proteome level remain unclear. We compared six proteomes from Cu-resistant wild-type (WT) Penicillium janthinellum strain GXCR and a Cu-sensitive mutant (EC-6) under 0, 0.5, and 3 mmol/L Cu treatments using iTRAQ. A total of 495 known proteins were identified, and the following conclusions were drawn from the results: Cu tolerance depends on ATP generation and supply, which is relevant to glycolysis pathway activity; oxidative phosphorylation, the TCA cycle, gluconeogenesis, fatty acid synthesis, and metabolism are also affected by Cu; high Cu sensitivity is primarily due to an ATP energy deficit; among ATP generation pathways, Cu-sensitive and Cu-insensitive metabolic steps exist; gluconeogenesis pathway is crucial to the survival of fungi in Cu-containing and sugar-scarce environments; fungi change their proteomes via two routes (from ATP, ATP-dependent RNA helicases (ADRHs), and ribosome biogenesis to proteasomes and from ATP, ADRHs to spliceosomes and/or stress-adapted RNA degradosomes) to cope with changes in Cu concentrations; and unique routes exist through which fungi respond to high environmental Cu...
May 9, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28483922/quantitative-micro-spectroscopic-imaging-reveals-viral-and-cellular-rna-helicase-interactions-in-live-cells
#15
M J Corby, Michael R Stoneman, Gabriel Biener, Joel D Paprocki, Rajesh Kolli, Valerica Raicu, David N Frick
Human cells detect RNA viruses through a set of helicases called RIG-I like receptors (RLRs) that initiate the interferon response via a mitochondrial signaling complex. Many RNA viruses also encode helicases, which sometimes are covalently linked to proteases that cleave signaling proteins. One unresolved question is how RLRs interact with each other and with viral proteins in cells. This study examined the interactions among the hepatitis C virus (HCV) helicase and RLR helicases in live cells with quantitative micro-spectroscopic imaging (Q-MSI), a technique that determines Forster Resonance Energy Transfer (FRET) efficiency and sub-cellular donor and acceptor concentrations...
May 8, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28475895/slert-regulates-ddx21-rings-associated-with-pol-i-transcription
#16
Yu-Hang Xing, Run-Wen Yao, Yang Zhang, Chun-Jie Guo, Shan Jiang, Guang Xu, Rui Dong, Li Yang, Ling-Ling Chen
Dysregulated rRNA synthesis by RNA polymerase I (Pol I) is associated with uncontrolled cell proliferation. Here, we report a box H/ACA small nucleolar RNA (snoRNA)-ended long noncoding RNA (lncRNA) that enhances pre-rRNA transcription (SLERT). SLERT requires box H/ACA snoRNAs at both ends for its biogenesis and translocation to the nucleolus. Deletion of SLERT impairs pre-rRNA transcription and rRNA production, leading to decreased tumorigenesis. Mechanistically, SLERT interacts with DEAD-box RNA helicase DDX21 via a 143-nt non-snoRNA sequence...
May 4, 2017: Cell
https://www.readbyqxmd.com/read/28475736/chd1-regulates-cell-fate-determination-by-activation-of-differentiation-induced-genes
#17
Simon J Baumgart, Zeynab Najafova, Tareq Hossan, Wanhua Xie, Sankari Nagarajan, Vijayalakshmi Kari, Nicholas Ditzel, Moustapha Kassem, Steven A Johnsen
The coordinated temporal and spatial activation of gene expression is essential for proper stem cell differentiation. The Chromodomain Helicase DNA-binding protein 1 (CHD1) is a chromatin remodeler closely associated with transcription and nucleosome turnover downstream of the transcriptional start site (TSS). In this study, we show that CHD1 is required for the induction of osteoblast-specific gene expression, extracellular-matrix mineralization and ectopic bone formation in vivo. Genome-wide occupancy analyses revealed increased CHD1 occupancy around the TSS of differentiation-activated genes...
May 5, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28474797/a-mechanistic-study-of-helicases-with-magnetic-traps
#18
REVIEW
Samar Hodeib, Saurabh Raj, M Manosas, Weiting Zhang, Debjani Bagchi, Bertrand Ducos, Francesca Fiorini, Joanne Kanaan, Hervé Le Hir, Jean-François Allemand, David Bensimon, Vincent Croquette
Helicases are a broad family of enzymes that separate nucleic acid double strand structures (DNA/DNA, DNA/RNA or RNA/RNA) and thus are essential to DNA replication and the maintenance of nucleic acid integrity. We review the picture that has emerged from single molecule studies of the mechanisms of DNA and RNA helicases and their interactions with other proteins. Many features have been uncovered by these studies that were obscured by bulk studies, such as DNA strands switching, mechanical (rather than biochemical) coupling between helicases and polymerases, helicase-induced re-hybridization and stalled fork rescue...
May 5, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28473661/ddx23-linc00630-hdac1-axis-activates-the-notch-pathway-to-promote-metastasis
#19
Guozhang Mao, Hui Jin, Liuguang Wu
Emerging studies demonstrated the roles of long non-coding RNAs (LncRNAs) are being implicated in the progression of many cancers. Here we report the discovery of a critical role for the linc00630 in the development of Non-Small-Cell Lung Cancers (NSCLCs). Screening from the microarray of six paired NSCLCs and adjacent non-tumor tissues, linc00630 showed a significantly higher RNA levels in NSCLCs. With the higher level confirmed in a separate cohort 90 NSCLCs patients, overexpressed of linc00630 also positive associated with tumor size, TNM tumor stage, lymph node status positive and overall patient outcomes...
April 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28472472/human-ddx21-binds-and-unwinds-rna-guanine-quadruplexes
#20
Ewan K S McRae, Evan P Booy, Aniel Moya-Torres, Peyman Ezzati, Jörg Stetefeld, Sean A McKenna
Guanine quadruplexes (G4s) are an important structure of nucleic acids (DNA and RNA) with roles in several cellular processes. RNA G4s require specialized unwinding enzymes, of which only two have been previously identified. We describe the results of a simple and specific mass spectrometry guided method used to screen HEK293T cell lysate for G4 binding proteins. From these results, we validated the RNA helicase protein DDX21. DDX21 is an established RNA helicase, but has not yet been validated as a G4 binding protein...
May 4, 2017: Nucleic Acids Research
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