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DEAD helicase

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https://www.readbyqxmd.com/read/29653436/a-chloroplast-targeted-cabbage-dead-box-rna-helicase-brrh22-confers-abiotic-stress-tolerance-to-transgenic-arabidopsis-plants-by-affecting-translation-of-chloroplast-transcripts
#1
Ghazala Nawaz, Kwanuk Lee, Su Jung Park, Yeon-Ok Kim, Hunseung Kang
Although the roles of many DEAD-box RNA helicases (RHs) have been determined in the nucleus as well as in cytoplasm during stress responses, the importance of chloroplast-targeted DEAD-box RHs in stress response remains largely unknown. In this study, we determined the function of BrRH22, a chloroplast-targeted DEAD-box RH in cabbage (Brassica rapa), in abiotic stress responses. The expression of BrRH22 was markedly increased by drought, heat, salt, or cold stress and by ABA treatment, but was largely decreased by UV stress...
April 7, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29642538/ddx5-rna-helicases-emerging-roles-in-viral-infection
#2
REVIEW
Wenyu Cheng, Guohua Chen, Huaijie Jia, Xiaobing He, Zhizhong Jing
Asp-Glu-Ala-Asp (DEAD)-box polypeptide 5 (DDX5), also called p68, is a prototypical member of the large ATP-dependent RNA helicases family and is known to participate in all aspects of RNA metabolism ranging from transcription to translation, RNA decay, and miRNA processing. The roles of DDX5 in cell cycle regulation, tumorigenesis, apoptosis, cancer development, adipogenesis, Wnt-β-catenin signaling, and viral infection have been established. Several RNA viruses have been reported to hijack DDX5 to facilitate various steps of their replication cycles...
April 9, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29622601/dual-role-of-the-rna-helicase-ddx5-in-post-transcriptional-regulation-of-myelin-basic-protein-in-oligodendrocytes
#3
Peter Hoch-Kraft, Robin White, Stefan Tenzer, Eva-Maria Krämer-Albers, Jacqueline Trotter, Constantin Gonsior
In the central nervous system, oligodendroglial expression of Myelin Basic Protein (MBP) is crucial for the assembly and structure of the myelin sheath. MBP synthesis is tightly regulated in space and time, particularly on the post-transcriptional level. We have identified the DEAD-box RNA helicase DDX5 (alias p68) in a complex with Mbp mRNA in oligodendroglial cells. Expression of DDX5 is highest in progenitor cells and immature oligodendrocytes, where it localizes to heterogeneous populations of cytoplasmic ribonucleoprotein (RNP) complexes associated with Mbp mRNA in the cell body and processes...
April 5, 2018: Journal of Cell Science
https://www.readbyqxmd.com/read/29621707/identification-of-cd-responsive-rna-helicase-genes-and-expression-of-a-putative-bnrh-24-mediated-by-mir158-in-canola-brassica-napus
#4
Xian Duo Zhang, Jia Yun Sun, Yuan Yuan You, Jian Bo Song, Zhi Min Yang
RNA helicases play crucial roles in RNA splicing, transport, editing and degradation, protein translation initiation and siRNA-mediated gene silencing. However, knowledge about their functionality in rapeseed (Brassica napus) is rare. In the study, we identified and annotated 271 RNA helicase genes from B. napus using bioinformatics and high-throughput RNA-sequencing (RNA-seq). Three subfamilies DEAD-box, DEAH-box, or DExD/H-box have been identified. One hundred and ninety-five RNA helicases were confirmed by RNA-seq and 49 were identified to differentially respond to cadmium (Cd) stress (> 1...
April 2, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29588407/the-sole-dead-box-rna-helicase-of-the-gastric-pathogen-helicobacter-pylori-is-essential-for-colonization
#5
Lamya El Mortaji, Sylvie Aubert, Eloïse Galtier, Christine Schmitt, Karine Anger, Yulia Redko, Yves Quentin, Hilde De Reuse
Present 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 the Helicobacter genus, including the major gastric pathogen H. pylori , is among the exceptions, as it encodes a sole DEAD-box RNA helicase...
March 27, 2018: MBio
https://www.readbyqxmd.com/read/29584632/inhibition-of-zika-virus-replication-by-silvestrol
#6
Fabian Elgner, Catarina Sabino, Michael Basic, Daniela Ploen, Arnold Grünweller, Eberhard Hildt
The Zika virus (ZIKV) outbreak in 2016 in South America with specific pathogenic outcomes highlighted the need for new antiviral substances with broad-spectrum activities to react quickly to unexpected outbreaks of emerging viral pathogens. Very recently, the natural compound silvestrol isolated from the plant Aglaia foveolata was found to have very potent antiviral effects against the (-)-strand RNA-virus Ebola virus as well as against Corona- and Picornaviruses with a (+)-strand RNA-genome. This antiviral activity is based on the impaired translation of viral RNA by the inhibition of the DEAD-box RNA helicase eukaryotic initiation factor-4A (eIF4A) which is required to unwind structured 5´-untranslated regions (5'-UTRs) of several proto-oncogenes and thereby facilitate their translation...
March 27, 2018: Viruses
https://www.readbyqxmd.com/read/29574779/a-dead-box-rna-helicase-rh8-is-critical-for-regulation-of-aba-signaling-and-the-drought-stress-response-via-inhibition-of-pp2ca-activity
#7
Woonhee Baek, Chae Woo Lim, Sung Chul Lee
Abscisic acid (ABA) is major plant hormone involved in regulating abiotic stress responses. Several studies have established that an ABA-signaling transduction pathway-from ABA perception to response-functions in plant cells. The group A PP2Cs constitute core components of ABA signaling, and they negatively regulate ABA signaling and stress responses. Recent studies have identified and functionally analyzed regulators of PP2C activity; however, the precise regulatory mechanisms remain unclear. In the present study, we used a yeast two-hybrid (Y2H) screening analysis to identify the DEAD-box RNA helicase RH8, which interacted with PP2CA in the nucleus...
March 25, 2018: Plant, Cell & Environment
https://www.readbyqxmd.com/read/29535419/dead-box-helicase-27-promotes-colorectal-cancer-growth-and-metastasis-and-predicts-poor-survival-in-crc-patients
#8
Jieting Tang, Huarong Chen, Chi-Chun Wong, Dabin Liu, Tong Li, Xiaohong Wang, Jiafu Ji, Joseph Jy Sung, Jing-Yuan Fang, Jun Yu
Copy number alterations (CNAs) are crucial for colorectal cancer (CRC) development. In this study, DEAD box polypeptide 27 (DDX27) was identified to be highly amplified in both TCGA CRC (474/615) and primary CRC (47/103), which was positively correlated with its mRNA overexpression. High DDX27 mRNA (N = 199) and protein expression (N = 260) predicted poor survival in CRC patients. Ectopic expression of DDX27 increased CRC cells proliferation, migration and invasion, but suppressed apoptosis. Conversely, silencing of DDX27 exerted opposite effects in vitro and significantly inhibited murine xenograft tumor growth and lung metastasis in vivo...
March 14, 2018: Oncogene
https://www.readbyqxmd.com/read/29523774/the-multiple-lives-of-dead-box-rna-helicase-dp103-ddx20-gemin3
#9
REVIEW
Frank Curmi, Ruben J Cauchi
Gemin3, also known as DDX20 or DP103, is a DEAD-box RNA helicase which is involved in more than one cellular process. Though RNA unwinding has been determined in vitro , it is surprisingly not required for all of its activities in cellular metabolism. Gemin3 is an essential gene, present in Amoeba and Metazoa. The highly conserved N-terminus hosts the helicase core, formed of the helicase- and DEAD-domains, which, based on crystal structure determination, have key roles in RNA binding. The C-terminus of Gemin3 is highly divergent between species and serves as the interaction site for several accessory factors that could recruit Gemin3 to its target substrates and/or modulate its function...
March 9, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29522752/rna-helicase-ddx5-participates-in-oxldl-induced-macrophage-scavenger-receptor-1-expression-by-suppressing-mrna-degradation
#10
Wenting Zhao, Zhen Wang, Zewei Sun, Yuxian He, Dongdong Jian, Xiaotong Hu, Wang Zhang, Liangrong Zheng
The DEAD box protein DDX5, an ATP-dependent RNA helicase, plays an important role in transcriptional regulation and is associated with solid tumors and leukemia. However, its role in oxLDL-induced lipid uptake in macrophages remains unclear. In this study, we detected the expression of DDX5 mRNA and protein in oxidized low-density lipoprotein (oxLDL)-treated human primary macrophages that were induced from monocytes isolated from human peripheral blood with or without several chemical inhibitors using quantitative real-time PCR (qRT-PCR) or Western blotting...
March 6, 2018: Experimental Cell Research
https://www.readbyqxmd.com/read/29520635/computational-analysis-of-high-risk-snps-in-human-dby-gene-responsible-for-male-infertility-a-functional-and-structural-impact
#11
Mili Nailwal, Jenabhai B Chauhan
BACKGROUND: DEAD-box helicase 3, Y-linked (DBY) is a candidate gene of the AZF region which is involved in spermatogenesis process. Mutations in the DBY gene may disrupt the spermatogenesis and lead to infertility in men. Identification of functionally neutral mutation from the disease-causing mutation is the biggest challenge in human genetic variation analysis. Owing to the importance of DBY in male infertility, functional analysis was carried out to reveal the association between genetic mutation and phenotypic variation through various in silico approaches...
March 8, 2018: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/29518074/rna-helicase-ddx27-regulates-skeletal-muscle-growth-and-regeneration-by-modulation-of-translational-processes
#12
Alexis H Bennett, Marie-Francoise O'Donohue, Stacey R Gundry, Aye T Chan, Jeffrey Widrick, Isabelle Draper, Anirban Chakraborty, Yi Zhou, Leonard I Zon, Pierre-Emmanuel Gleizes, Alan H Beggs, Vandana A Gupta
Gene expression in a tissue-specific context depends on the combined efforts of epigenetic, transcriptional and post-transcriptional processes that lead to the production of specific proteins that are important determinants of cellular identity. Ribosomes are a central component of the protein biosynthesis machinery in cells; however, their regulatory roles in the translational control of gene expression in skeletal muscle remain to be defined. In a genetic screen to identify critical regulators of myogenesis, we identified a DEAD-Box RNA helicase, DDX27, that is required for skeletal muscle growth and regeneration...
March 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29514904/the-experimental-analysis-of-mimivirus-translation-initiation-factor-4a-reveals-its-importance-for-viral-proteins-translation-during-infection-of-acanthamoeba-polyphaga
#13
Meriem Bekliz, Said Azza, Hervé Seligmann, Philippe Decloquement, Didier Raoult, Bernard La Scola
Acanthamoeba polyphaga mimivirus is the first giant virus ever described, with a 1.2-Mb genome which encodes 979 proteins including central components of the translation apparatus. One of these proteins, R458, was predicted to initiate translation, although its specific role remains unknown.We silenced the R458 gene using siRNA and compared viral fitness and protein expression in silenced versus wild-type mimivirus. Silencing decreased growth rate but viral particle production at the end of the viral cycle was unaffected...
March 7, 2018: Journal of Virology
https://www.readbyqxmd.com/read/29510985/molecular-architecture-of-lsm14-interactions-involved-in-the-assembly-of-mrna-silencing-complexes
#14
Tobias Brandmann, Hana Fakim, Zoya Padamsi, Ji-Young Youn, Anne-Claude Gingras, Marc R Fabian, Martin Jinek
The LSM domain-containing protein LSM14/Rap55 plays a role in mRNA decapping, translational repression, and RNA granule (P-body) assembly. How LSM14 interacts with the mRNA silencing machinery, including the eIF4E-binding protein 4E-T and the DEAD-box helicase DDX6, is poorly understood. Here we report the crystal structure of the LSM domain of LSM14 bound to a highly conserved C-terminal fragment of 4E-T. The 4E-T C-terminus forms a bi-partite motif that wraps around the N-terminal LSM domain of LSM14. We also determined the crystal structure of LSM14 bound to the C-terminal RecA-like domain of DDX6...
March 6, 2018: EMBO Journal
https://www.readbyqxmd.com/read/29471489/the-h-subunit-of-the-restriction-endonuclease-cgli-contains-a-prototype-dead-z1-helicase-like-motor
#15
Paulius Toliusis, Giedre Tamulaitiene, Rokas Grigaitis, Donata Tuminauskaite, Arunas Silanskas, Elena Manakova, Ceslovas Venclovas, Mark D Szczelkun, Virginijus Siksnys, Mindaugas Zaremba
CglI is a restriction endonuclease from Corynebacterium glutamicum that forms a complex between: two R-subunits that have site specific-recognition and nuclease domains; and two H-subunits, with Superfamily 2 helicase-like DEAD domains, and uncharacterized Z1 and C-terminal domains. ATP hydrolysis by the H-subunits catalyses dsDNA translocation that is necessary for long-range movement along DNA that activates nuclease activity. Here, we provide biochemical and molecular modelling evidence that shows that Z1 has a fold distantly-related to RecA, and that the DEAD-Z1 domains together form an ATP binding interface and are the prototype of a previously undescribed monomeric helicase-like motor...
February 20, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29454090/characterization-of-vasa-homolog-in-a-neotropical-catfish-jundi%C3%A3-rhamdia-quelen-molecular-cloning-and-expression-analysis-during-embryonic-and-larval-development
#16
Juliana M B Ricci, Emanuel R M Martinez, Arno J Butzge, Lucas B Doretto, Marcos A Oliveira, Robie Allan Bombardelli, Jan Bogerd, Rafael H Nóbrega
We have characterized the full-length vasa cDNA from Jundiá, Rhamdia quelen (Heptapteridae, Siluriformes). vasa encodes a member of the DEAD-box protein family of ATP-dependent RNA helicases. This protein is highly conserved among different organisms and its role is associated with RNA metabolism. In the majority of the investigated species, vasa is restricted to the germ cell lineage and its expression has been used to study germline development in many organisms, including fish. The deduced R. quelen vasa amino acid sequence displayed high similarity with Vasa protein sequences from other organisms, and did not cluster with PL10 or P68 DEAD-box protein subfamilies...
February 14, 2018: Gene
https://www.readbyqxmd.com/read/29408876/cloning-and-expression-analysis-of-the-dead-box-rna-helicase-oslaf-1-in-ovomermis-sinensis
#17
Siying Tao, Zhenlong Jiao, Guigui Wen, Lihong Zhang, Guoxiu Wang
Ovomermis sinensis is a potentially-valuable nematode for controlling insect pests. The parasitic stage of the nematode absorbs nutrients in its host's hemolymph to maintain its growth development and then kills the host when it emerges. At present, little known about its reproductive development, particularly the responsible molecular mechanism. More detailed research on the genes of reproductive development will not only help us understand the mechanisms underlying sex differentiation in the nematode, but would also be valuable for successfully cultivating them in vitro and using them for biocontrol...
2018: PloS One
https://www.readbyqxmd.com/read/29373715/positive-sense-rna-viruses-reveal-the-complexity-and-dynamics-of-the-cellular-and-viral-epitranscriptomes-during-infection
#18
Will McIntyre, Rachel Netzband, Gaston Bonenfant, Jason M Biegel, Clare Miller, Gabriele Fuchs, Eric Henderson, Manoj Arra, Mario Canki, Daniele Fabris, Cara T Pager
More than 140 post-transcriptional modifications (PTMs) are known to decorate cellular RNAs, but their incidence, identity and significance in viral RNA are still largely unknown. We have developed an agnostic analytical approach to comprehensively survey PTMs on viral and cellular RNAs. Specifically, we used mass spectrometry to analyze PTMs on total RNA isolated from cells infected with Zika virus, Dengue virus, hepatitis C virus (HCV), poliovirus and human immunodeficiency virus type 1. All five RNA viruses significantly altered global PTM landscapes...
January 24, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29364893/sequence-determinants-of-protein-phase-behavior-from-a-coarse-grained-model
#19
Gregory L Dignon, Wenwei Zheng, Young C Kim, Robert B Best, Jeetain Mittal
Membraneless organelles important to intracellular compartmentalization have recently been shown to comprise assemblies of proteins which undergo liquid-liquid phase separation (LLPS). However, many proteins involved in this phase separation are at least partially disordered. The molecular mechanism and the sequence determinants of this process are challenging to determine experimentally owing to the disordered nature of the assemblies, motivating the use of theoretical and simulation methods. This work advances a computational framework for conducting simulations of LLPS with residue-level detail, and allows for the determination of phase diagrams and coexistence densities of proteins in the two phases...
January 2018: PLoS Computational Biology
https://www.readbyqxmd.com/read/29364875/tissue-selective-effects-of-nucleolar-stress-and-rdna-damage-in-developmental-disorders
#20
Eliezer Calo, Bo Gu, Margot E Bowen, Fardin Aryan, Antoine Zalc, Jialiang Liang, Ryan A Flynn, Tomek Swigut, Howard Y Chang, Laura D Attardi, Joanna Wysocka
Many craniofacial disorders are caused by heterozygous mutations in general regulators of housekeeping cellular functions such as transcription or ribosome biogenesis. Although it is understood that many of these malformations are a consequence of defects in cranial neural crest cells, a cell type that gives rise to most of the facial structures during embryogenesis, the mechanism underlying cell-type selectivity of these defects remains largely unknown. By exploring molecular functions of DDX21, a DEAD-box RNA helicase involved in control of both RNA polymerase (Pol) I- and II-dependent transcriptional arms of ribosome biogenesis, we uncovered a previously unappreciated mechanism linking nucleolar dysfunction, ribosomal DNA (rDNA) damage, and craniofacial malformations...
February 1, 2018: Nature
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