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https://www.readbyqxmd.com/read/28428796/expression-profiling-coupled-with-in-silico-mapping-identifies-candidate-genes-for-reducing-aflatoxin-accumulation-in-maize
#1
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/28426938/high-throughput-screening-to-identify-inhibitors-of-dead-box-helicase-ddx41
#2
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/28414160/paraquat-induces-extrinsic-pathway-of-apoptosis-in-a549-cells-by-induction-of-dr5-and-repression-of-anti-apoptotic-proteins-ddx3-and-gsk3-expression
#3
Sasiphen Hathaichoti, Daranee Visitnonthachai, Pronrumpa Ngamsiri, Apichaya Niyomchan, Oyu Tsogtbayar, Churaibhon Wisessaowapak, Piyajit Watcharasit, Jutamaad Satayavivad
Paraquat (PQ) is a bipyridyl derivative herbicide known to cause lung toxicity partly through induction of apoptosis. Here we demonstrated that PQ caused apoptosis in A549 cells. PQ increased cleavage of caspase-8 and Bid, indicating caspase-8 activation and truncated Bid, the two key mediators of extrinsic apoptosis. Additionally, PQ treatment caused an increase in DR5 (death receptor-5) and caspase-8 interaction, indicating formation of DISC (death-inducing signaling complex). These results indicate that PQ induces apoptosis through extrinsic pathway in A549 cells...
April 14, 2017: Toxicology in Vitro: An International Journal Published in Association with BIBRA
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
#4
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/28402257/-dead-box-rna-helicase-3-modulates-nf-%C3%AE%C2%BAb-signal-pathway-by-controlling-the-phosphorylation-of-pp2a-c-subunit
#5
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/28397605/xenopus-vasa-homolog-xvlg1-is-essential-for-migration-and-survival-of-primordial-germ-cells
#6
Kazumi Shimaoka, Yoshiko Mukumoto, Yoko Tanigawa, Tohru Komiya
Xenopus vasa-like gene 1 (XVLG1), a DEAD-Box Helicase 4 (DDX4) gene identified as a vertebrate vasa homologue, is required for the formation of primordial germ cells (PGCs). However, it remains to be clarified when and how XVLG1 functions in the formation of the germ cells. To gain a better understanding of the molecular mechanisms underlying XVLG1 during PGC development, we injected XVLG1 morpholino oligos into germ-plasm containing blastomeres of 32-cell stage of Xenopus embryos, and traced cell fates of the injected blastomere-derived PGCs...
April 2017: Zoological Science
https://www.readbyqxmd.com/read/28396352/association-of-the-cold-shock-dead-box-rna-helicase-rhle-to-the-rna-degradosome-in-caulobacter-crescentus
#7
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/28388421/dead-box-rna-binding-protein-ddx5-not-a-black-box-during-reprogramming
#8
Christian M Nefzger, Jose M Polo
The role of RNA binding proteins (RBPs) during nuclear reprogramming is poorly characterized. In this issue of Cell Stem Cell,Li et al. (2017) show that DEAD-box RBP DDX5 acts as a reprogramming roadblock and give important mechanistic insights into the establishment of pluripotency by characterizing the intricate downstream events.
April 6, 2017: Cell Stem Cell
https://www.readbyqxmd.com/read/28379444/a-dead-box-protein-acts-through-rna-to-promote-hiv-1-rev-rre-assembly
#9
Rajan Lamichhane, John A Hammond, Raymond F Pauszek, Rae M Anderson, Ingemar Pedron, Edwin van der Schans, James R Williamson, David P Millar
The HIV-1 Rev protein activates nuclear export of unspliced and partially spliced viral RNA transcripts, which encode the viral genome and the genes encoding viral structural proteins, by binding to and oligomerizing on the Rev Response Element (RRE). The human DEAD-box protein 1 (DDX1) enhances the RNA export activity of Rev through an unknown mechanism. Using a single-molecule assembly assay and various DDX1 mutants, we show that DDX1 acts through the RRE RNA to specifically accelerate the nucleation step of the Rev-RRE assembly process...
March 31, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28358513/discovery-of-novel-1-4-diacylpiperazines-as-selective-and-cell-active-eif4a3-inhibitors
#10
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/28348086/the-dead-box-rna-helicase-ddx41-is-a-novel-repressor-of-p21-waf1-cip1-translation
#11
Dominik Peters, Claudia Radine, Alina Reese, Wilfried Budach, Dennis Sohn, Reiner U Jänicke
The cyclin-dependent kinase inhibitor p21 is an important player in stress pathways exhibiting both tumor-suppressive and oncogenic functions. Thus, expression of p21 has to be tightly controlled, which is achieved by numerous mechanisms at the transcriptional, translational and post-translational level. Performing immunoprecipitations of bromouridine (BrU)-labeled p21 mRNAs that had been incubated before with cytoplasmic extracts of untreated HCT116 colon carcinoma cells, we identified the DEAD-box RNA helicase DDX41 as a novel regulator of p21 expression...
March 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28339678/ddx4-egfp-transgenic-rat-model-for-the-study-of-germline-development-and-spermatogenesis-%C3%A2
#12
Kathrin Gassei, Yi Sheng, Adetunji Fayomi, Payal Mital, Meena Sukhwani, Chih-Cheng Lin, Karen A Peters, Andrew Althouse, Hanna Valli, Kyle E Orwig
Spermatogonial stem cells (SSC) are essential for spermatogenesis and male fertility. In addition, these adult tissue stem cells can be used as vehicles for germline modification in animal models and may have application for treating male infertility. To facilitate the investigation of SSCs and germ lineage development in rats, we generated a DEAD-box helicase 4 (DDX4) (VASA) promoter-enhanced green fluorescent protein (EGFP) reporter transgenic rat. Quantitative real-time polymerase chain reaction and immunofluorescence confirmed that EGFP was expressed in the germ cells of the ovaries and testes and was absent in somatic cells and tissues...
March 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/28337468/comparative-analysis-data-of-sf1-and-sf2-helicases-from-three-domains-of-life
#13
Wafi Chaar, Hiba Ibrahim, Juliana Kozah, Hala Chamieh
SF1 and SF2 helicases are important molecular motors that use the energy of ATP to unwind nucleic acids or nucleic-acid protein complexes. They are ubiquitous enzymes and found in almost all organisms sequenced to date. This article provides a comparative analysis for SF1 and SF2 helicase families from three domains of life archaea, human, bacteria. Seven families are conserved in these three representatives and includes Upf1-like, UvrD-like, Rad3-like, DEAD-box, RecQ-like. Snf2 and Ski2-like. The data highlight conservation of the helicase core motifs for each of these families...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28288365/dexd-h-box-rna-helicase-genes-are-differentially-expressed-between-males-and-females-during-the-critical-period-of-male-sex-differentiation-in-channel-catfish
#14
Changxu Tian, Suxu Tan, Lisui Bao, Qifan Zeng, Shikai Liu, Yujia Yang, Xiaoxiao Zhong, Zhanjiang Liu
DExD/H-box RNA helicases are motor proteins participating in nearly all aspects of cellular processes, especially in RNA metabolism. In this study, a total of 54 DExD/H-box RNA helicase genes including 37 DDX (DEAD-box) and 17 DHX (DEAH-box) genes were characterized in channel catfish (Ictalurus punctatus), and annotated through phylogenetic and syntenic analyses. All the catfish RNA helicases contained conserved helicase signature motifs, demonstrating that the RNA helicase gene family was highly conserved...
March 1, 2017: Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics
https://www.readbyqxmd.com/read/28238534/structural-insights-into-a-unique-dimeric-dead-box-helicase-csha-that-promotes-rna-decay
#15
Jennifer Huen, Chia-Liang Lin, Bagher Golzarroshan, Wan-Li Yi, Wei-Zen Yang, Hanna S Yuan
CshA is a dimeric DEAD-box helicase that cooperates with ribonucleases for mRNA turnover. The molecular mechanism for how a dimeric DEAD-box helicase aids in RNA decay remains unknown. Here, we report the crystal structure and small-angle X-ray scattering solution structure of the CshA from Geobacillus stearothermophilus. In contrast to typical monomeric DEAD-box helicases, CshA is exclusively a dimeric protein with the RecA-like domains of each protomer forming a V-shaped structure. We show that the C-terminal domains protruding outward from the tip of the V-shaped structure is critical for mediating strong RNA binding and is crucial for efficient RNA-dependent ATP hydrolysis...
March 7, 2017: Structure
https://www.readbyqxmd.com/read/28216671/dual-mechanisms-regulate-the-nucleocytoplasmic-localization-of-human-ddx6
#16
Jo-Hsi Huang, Wei-Chi Ku, Yen-Chun Chen, Yi-Ling Chang, Chia-Ying Chu
DDX6 is a conserved DEAD-box protein (DBP) that plays central roles in cytoplasmic RNA regulation, including processing body (P-body) assembly, mRNA decapping, and translational repression. Beyond its cytoplasmic functions, DDX6 may also have nuclear functions because its orthologues are known to localize to nuclei in several biological contexts. However, it is unclear whether DDX6 is generally present in human cell nuclei, and the molecular mechanism underlying DDX6 subcellular distribution remains elusive...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28212935/dissecting-biochemical-peculiarities-of-the-atpase-activity-of-tcsub2-a-component-of-the-mrna-export-pathway-in-trypanosoma-cruzi
#17
Ize de Aguiar Bittencourt, Mariana Serpeloni, Priscila Mazzochi Hiraiwa, Tatiana de Arruda Campos Brasil de Souza, Andréa Rodrigues Ávila
The RNA helicase DEAD-box protein Sub2 (yeast)/UAP56 (mammals) is conserved across eukaryotes and is essential for mRNA export in trypanosomes. Despite the high conservation of Sub2 in lower eukaryotes such as Trypanosoma cruzi, the low conservation of other mRNA export factors raises questions regarding whether the mode of action of TcSub2 is similar to that of orthologs from other eukaryotes. Mutation of the conserved K87 residue of TcSub2 abolishes ATPase activity, showing that its ATPase domain is functional...
May 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28191733/a-novel-dynamic-expression-of-vasa-in-male-germ-cells-during-spermatogenesis-in-the-chinese-soft-shell-turtle-pelidiscus-sinensis
#18
Wei Li, Piaoyi Zhang, Xuling Wu, Xinping Zhu, Hongyan Xu
vasa gene encodes a highly conserved DEAD-box RNA helicase, required for germ cell development across animal kingdom. Vasa mutations cause male infertility in mammals. It has been widely used as a biomarker for studying animal fertility or manipulating germ cells in organisms. However, in reptilians, the functions of vasa gene involved in germ cell differentiation are largely unclear; this hampers the development of biological techniques and the improvement of the productivity in these species. Here a vasa cDNA was isolated in Chinese soft-shell turtle and it predicts a protein of 691 amino acid residues, which is 72%, 69%, 58%, 59%, and 54-56% identical to its homolog from mouse, platypus, frog, chicken, and fish, respectively, and named as PsVasa...
February 13, 2017: Journal of Experimental Zoology. Part B, Molecular and Developmental Evolution
https://www.readbyqxmd.com/read/28153748/a-dead-box-helicase-mediates-an-rna-structural-transition-in-the-hiv-1-rev-response-element
#19
John A Hammond, Rajan Lamichhane, David P Millar, James R Williamson
Nuclear export of partially spliced or unspliced HIV-1 RNA transcripts requires binding of the viral protein regulator of expression of virion (Rev) to the Rev response element (RRE) and subsequent oligomerization in a cooperative manner. Cellular DEAD-box helicase DEAD-box protein 1 (DDX1) plays a role in HIV replication, interacting with and affecting Rev-containing HIV transcripts in vivo, interacting directly with the RRE and Rev in vitro, and promoting Rev oligomerization in vitro. Binding of DDX1 results in enhancement of Rev oligomerization on the RRE that is correlated with an RNA structural change within the RRE that persists even after dissociation of DDX1...
March 10, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28148788/the-atp-dependent-rna-helicase-ddx3x-modulates-herpes-simplex-virus-1-gene-expression
#20
Bita Khadivjam, Camille Stegen, Marc-Aurèle Hogue-Racine, Nabil El Bilali, Katinka Döhner, Beate Sodeik, Roger Lippé
The human protein DDX3X is a DEAD box ATP-dependent RNA helicase that regulates transcription, mRNA maturation, and mRNA export and translation. DDX3X concomitantly modulates the replication of several RNA viruses and promotes innate immunity. We previously showed that herpes simplex virus 1 (HSV-1), a human DNA virus, incorporates DDX3X into its mature particles and that DDX3X is required for optimal HSV-1 infectivity. Here, we show that viral gene expression, replication, and propagation depend on optimal DDX3X protein levels...
April 15, 2017: Journal of Virology
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