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DEAD helicase

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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
#1
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
#2
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
#3
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
#4
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
#5
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...
January 24, 2018: Nature
https://www.readbyqxmd.com/read/29351962/rna-helicases-in-rna-decay
#6
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/29328432/a-double-edged-function-of-ddx3-as-an-oncogene-or-tumor-suppressor-in-cancer-progression-review
#7
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/29317487/dead-box-helicase-controls-ck1-activity-in-vivo
#8
(no author information available yet)
No abstract text is available yet for this article.
January 9, 2018: Journal of Cell Science
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/29288727/characterization-of-the-es-ddx52-involved-in-the-spermatogonial-mitosis-and-spermatid-differentiation-in-chinese-mitten-crab-eriocheir-sinensis
#10
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/29282651/introgression-generational-expression-and-salinity-tolerance-conferred-by-the-pea-dna-helicase%C3%A2-45-transgene-into-two-commercial-rice-genotypes-br28-and-br47
#11
Sudip Biswas, U S Mahzabin Amin, Sarah Sarker, M Sazzadur Rahman, Ruhul Amin, Rezaul Karim, Narendra Tuteja, Zeba I Seraj
DNA helicase (PDH45) from the pea plant (Pisum sativum) is a member of the DEAD box protein family and plays a vital regulatory role in saline stress tolerance in plants. We previously reported that over-expression of PDH45 gene confers both seedling and reproductive stage salinity tolerance to a Bangladeshi rice landrace, Binnatoa (BA). In this study, transgenic BA-containing PDH45 (♂) was crossed with two different farmer-popular BRRI rice varieties (♀), BR28 and BR47, in a contained net house. F1 plants positive for the transgene and having recipient phenotype were advanced from F1 to F5...
December 27, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29258862/broad-spectrum-antiviral-activity-of-the-eif4a-inhibitor-silvestrol-against-corona-and-picornaviruses
#12
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/29222110/a-ck1-fret-biosensor-reveals-that-ddx3x-is-an-essential-activator-of-ck1%C3%AF%C2%B5
#13
Christine Dolde, Joachim Bischof, Simon Grüter, Anna Montada, Jakob Halekotte, Christian Peifer, Hubert Kalbacher, Ulrich Baumann, Uwe Knippschild, Beat Suter
Casein kinase 1 (CK1) plays central roles in various signal transduction pathways and performs many cellular activities. For a long time CK1 was thought to act independent of modulatory subunits and in a constitutive manner. Recently, DEAD box RNA helicases, in particular DEAD box RNA helicase 3 X-linked (DDX3X), were found to stimulate CK1 activity in vitro In order to observe CK1 activity in living cells and to study its interaction with DDX3X, we developed a CK1-specific FRET biosensor. This tool revealed that DDX3X is indeed required for full CK1 activity in living cells...
December 8, 2017: Journal of Cell Science
https://www.readbyqxmd.com/read/29214235/kinetics-and-thermodynamics-of-dbpa-protein-s-c-terminal-domain-interaction-with-rna
#14
Aliana López de Victoria, Anthony F T Moore, Apostolos G Gittis, Eda Koculi
DbpA is an Escherichia coli DEAD-box RNA helicase implicated in RNA structural isomerization in the peptide bond formation site. In addition to the RecA-like catalytic core conserved in all of the members of DEAD-box family, DbpA contains a structured C-terminal domain, which is responsible for anchoring DbpA to hairpin 92 of 23S ribosomal RNA during the ribosome assembly process. Here, surface plasmon resonance was used to determine the equilibrium dissociation constant and the microscopic rate constants of the DbpA C-terminal domain association and dissociation to a fragment of 23S ribosomal RNA containing hairpin 92...
November 30, 2017: ACS Omega
https://www.readbyqxmd.com/read/29187659/-research-progress-in-dead-box-family-protein-in-cancer
#15
Xiaohong Wen, Shufang Zhang, Ying'ai Zhang
DEAD-box family protein is a kind of ATP dependent RNA helicase, which plays a critical role in RNA metabolism. The DEAD-box family proteins can affect cell proliferation, differentiation, and apoptosis through regulating the expression of oncogenes, tumor suppressor genes and tumor related signaling pathways. It plays the role in promoting or suppressing cancer.
November 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29150525/distinct-rna-unwinding-mechanisms-of-dead-box-and-deah-box-rna-helicase-proteins-in-remodeling-structured-rnas-and-rnps
#16
REVIEW
Benjamin Gilman, Pilar Tijerina, Rick Russell
Structured RNAs and RNA-protein complexes (RNPs) fold through complex pathways that are replete with misfolded traps, and many RNAs and RNPs undergo extensive conformational changes during their functional cycles. These folding steps and conformational transitions are frequently promoted by RNA chaperone proteins, notably by superfamily 2 (SF2) RNA helicase proteins. The two largest families of SF2 helicases, DEAD-box and DEAH-box proteins, share evolutionarily conserved helicase cores, but unwind RNA helices through distinct mechanisms...
November 17, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29146961/identification-of-host-dead-box-rna-helicases-that-regulate-cellular-tropism-of-oncolytic-myxoma-virus-in-human-cancer-cells
#17
Masmudur M Rahman, Eugenie Bagdassarian, Mohamed A M Ali, Grant McFadden
Myxoma virus (MYXV), a Leporipoxvirus, is being developed as an oncolytic virotherapeutic for the treatment of a variety of human cancers. MYXV tropism for human cancer cells is largely mediated by intracellular signaling networks that regulate viral replication or innate antiviral response pathways. Thus, MYXV is fully or partially permissive for the majority of human cancer cells that harbor defects in antiviral signaling, but a minority are nonpermissive because the virus infection aborts before its completion...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29138350/the-dead-box-rna-helicase-rh50-is-a-23s-4-5s-rrna-maturation-factor-that-functionally-overlaps-with-the-plastid-signaling-factor-gun1
#18
Francesca Paieri, Luca Tadini, Nikolay Manavski, Tatjana Kleine, Roberto Ferrari, Pietro Angelo Morandini, Paolo Pesaresi, Jörg Meurer, Dario Leister
DEAD-box RNA helicases (DBRHs) modulate RNA secondary structure, allowing RNA molecules to adopt the conformations required for interaction with their target proteins. RH50 is a chloroplast-located DBRH that co-localizes and is co-expressed with GUN1, a central factor in chloroplast-to-nucleus signaling. When combined with mutations that impair plastid gene expression (prors1-1, prpl11-1, prps1-1, prps21-1, prps17-1 and prpl24-1), rh50 and gun1 mutations evoke similar patterns of epistatic effects. These observations, together with the synergistic growth phenotype of the double mutant rh50-1 gun1-102, suggest that RH50 and GUN1 are functionally related and that this function is associated with plastid gene expression, in particular ribosome functioning...
November 14, 2017: Plant Physiology
https://www.readbyqxmd.com/read/29136196/analysis-of-the-natively-unstructured-rna-protein-recognition-core-in-the-escherichia-coli-rna-degradosome-and-its-interactions-with-regulatory-rna-hfq-complexes
#19
Heather A Bruce, Dijun Du, Dijana Matak-Vinkovic, Katarzyna J Bandyra, R William Broadhurst, Esther Martin, Frank Sobott, Alexander V Shkumatov, Ben F Luisi
The RNA degradosome is a multi-enzyme assembly that plays a central role in the RNA metabolism of Escherichia coli and numerous other bacterial species including pathogens. At the core of the assembly is the endoribonuclease RNase E, one of the largest E. coli proteins and also one that bears the greatest region predicted to be natively unstructured. This extensive unstructured region, situated in the C-terminal half of RNase E, is punctuated with conserved short linear motifs that recruit partner proteins, direct RNA interactions, and enable association with the cytoplasmic membrane...
November 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29127725/a-loss-of-function-homozygous-mutation-in-ddx59-implicates-a-conserved-dead-box-rna-helicase-in-nervous-system-development-and-function
#20
Vincenzo Salpietro, Stephanie Efthymiou, Andreea Manole, Bhawana Maurya, Sarah Wiethoff, Balasubramaniem Ashokkumar, Maria Concetta Cutrupi, Valeria Dipasquale, Sara Manti, Juan A Botia, Mina Ryten, Jana Vandrovcova, Oscar D Bello, Conceicao Bettencourt, Kshitij Mankad, Ashim Mukherjee, Mousumi Mutsuddi, Henry Houlden
We report on a homozygous frameshift deletion in DDX59 (c.185del: p.Phe62fs*13) in a family presenting with oro-facio-digital syndrome phenotype associated to a broad neurological involvement characterized by microcephaly, intellectual disability, epilepsy, and white matter signal abnormalities associated with cortical and sub-cortical ischemic events. DDX59 encodes a DEAD-box RNA helicase and its role in brain function and neurological diseases is unclear. We showed a reduction of mutant cDNA and perturbation of SHH signalling from patient-derived cell lines; furthermore, analysis of human brain gene expression provides evidence that DDX59 is enriched in oligodendrocytes and might act within pathways of leukoencephalopathies associated genes...
November 11, 2017: Human Mutation
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