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DEAD helicase

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https://www.readbyqxmd.com/read/28526057/recognition-of-a-structural-domain-rwdbd-in-gcn1-proteins-that-interacts-with-the-rwd-domain-containing-proteins
#1
Ramachandran Rakesh, Rangachari Krishnan, Evelyn Sattlegger, Narayanaswamy Srinivasan
The protein Gcn1 (General control non-derepressible 1) is found in virtually all eukaryotes, and is a key component of the general amino acid control signal transduction pathway. This pathway is best known for its importance for cells to sense and overcome amino acid starvation. Gcn1 directly binds to the RWD (RING finger-containing proteins, WD-repeat-containing proteins, and yeast DEAD (DEXD)-like helicases) domain of the protein kinase Gcn2, and this is essential for delivering the starvation signal to Gcn2...
May 19, 2017: Biology Direct
https://www.readbyqxmd.com/read/28520979/the-dead-box-helicase-mss116-plays-distinct-roles-in-mitochondrial-ribogenesis-and-mrna-specific-translation
#2
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/28500788/unraveling-the-importance-of-the-malaria-parasite-helicases
#3
REVIEW
Renu Tuteja
Malaria is a human parasitic disease caused by infection from Plasmodium species, particularly Plasmodium falciparum. Each year millions of people are infected with malaria and large numbers of deaths result due to this deadly infection. P. falciparum contains 14 chromosomes, nearly 5400 genes and a multistage life cycle in humans and mosquitoes. The control of malaria is still a challenge as the parasite is continuously developing resistance to available anti-malarial drugs and the mosquito vector is developing resistance to insecticides...
May 13, 2017: FEBS Journal
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
#4
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/28488947/translation-control-learning-from-viruses-again
#5
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/28475895/slert-regulates-ddx21-rings-associated-with-pol-i-transcription
#6
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/28473661/ddx23-linc00630-hdac1-axis-activates-the-notch-pathway-to-promote-metastasis
#7
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/28468907/gsk-3%C3%A3-homolog-rim11-and-the-histone-deacetylase-complex-ume6-sin3-rpd3-are-involved-in-replication-stress-response-caused-by-defects-in-dna2
#8
Annie Albert Demin, Miju Lee, Chul-Hwan Lee, Yeon-Soo Seo
Lagging strand synthesis is mechanistically far more complicated than leading strand synthesis, since it involves multi-step processes and requires considerably more enzymes and protein factors. Due to this complexity, multiple fail-safe factors are required to ensure successful replication of the lagging strand DNA. We attempted to identify novel factors that are required in the absence of the helicase activity of Dna2, an essential enzyme in Okazaki fragment maturation. In this paper, we identified Rim11, a GSK-3ß kinase homolog, as a multicopy suppressor of dna2 helicase-dead mutant (dna2-K1080E)...
May 3, 2017: Genetics
https://www.readbyqxmd.com/read/28468824/the-dead-box-protein-ddx43-hage-is-a-dual-rna-dna-helicase-and-has-a-k-homology-domain-required-for-full-nucleic-acid-unwinding-activity
#9
Talwar Tanu, Venkatasubramanian Vidhyasagar, Jennifer Qing, Manhong Guo, Ahmad Kariem, Yi Lu, Ravi Shankar Singh, Kiven Erique Lukong, Yuliang Wu
The K-homology (KH) domain is a nucleic acid-binding domain present in many proteins, but has not been reported in helicases. DDX43, also known as HAGE (helicase antigen gene), is a member of the DEAD-box protein family. It contains a helicase core domain in its C-terminus and a potential KH domain in its N-terminus. DDX43 is highly expressed in many tumors, and is therefore considered a potential target for immunotherapy. Despite its potential as a therapeutic target, little is known about its activities. Here, we purified recombinant DDX43 protein to near homogeneity and found that it exists as a monomer in solution...
May 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28456022/cellular-dead-box-rna-helicase-ddx6-modulates-interaction-of-mir-122-with-the-5-untranslated-region-of-hepatitis-c-virus-rna
#10
Jason M Biegel, Eric Henderson, Erica M Cox, Gaston Bonenfant, Rachel Netzband, Samantha Kahn, Rachel Eager, Cara T Pager
Hepatitis C virus (HCV) subverts the cellular DEAD-box RNA helicase DDX6 to promote virus infection. Using polysome gradient analysis and the subgenomic HCV Renilla reporter replicon genome, we determined that DDX6 does not affect HCV translation. Rather expression of the subgenomic HCV Renilla luciferase reporter at late times, as well as labeling of newly synthesized viral RNA with 4-thiouridine showed that DDX6 modulates replication. Because DDX6 is an effector protein of the microRNA pathway, we also investigated its role in miR-122-directed HCV gene expression...
April 26, 2017: Virology
https://www.readbyqxmd.com/read/28455591/mutational-analysis-of-the-rna-helicase-dhh1-in-ste12-expression-and-yeast-mating
#11
Daehee Jung, Jihye Ahn, Boram Rhee, Jinmi Kim
Dhh1 and Dhh1 homologues (RCK/p54/DDX6) are members of the DEAD-box protein family of RNA helicases. These proteins display conserved sequence motifs for ATPase and RNA binding activities. Dhh1 is a component of the P-bodies (processing bodies) of mRNA granules and functions as an mRNA decapping activator in Saccharomyces cerevisiae. Dhh1 also contributes to gene-specific regulation during yeast mating. The dhh1 deletion mutation results in a significant decrease in the expression of Ste12, a mating-specific transcription factor, showing severe mating defects...
May 2017: Journal of Microbiology / the Microbiological Society of Korea
https://www.readbyqxmd.com/read/28450395/binding-of-dead-box-helicase-dhh1-to-the-5-utr-of-ash1-mrna-represses-localized-translation-of-ash1-in-yeast-cells
#12
Qianjun Zhang, Xiuhua Meng, Delin Li, Shaoyin Chen, Jianmin Luo, Linjie Zhu, Robert H Singer, Wei Gu
Local translation of specific mRNAs is regulated by dynamic changes in their subcellular localization, and these changes are due to complex mechanisms controlling cytoplasmic mRNA transport. The budding yeast Saccharomyces cerevisiae is well suited to studying these mechanisms because many of its transcripts are transported from the mother cell to the budding daughter cell. Here, we investigated the translational control of ASH1 mRNA after transport and localization. We show that although ASH1 transcripts were translated after they reached the bud-tip, some mRNAs were bound by the RNA-binding protein Puf6 and were non-polysomal...
April 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28440616/discovery-and-characterization-of-a-eukaryotic-initiation-factor-4a-3-selective-inhibitor-that-suppresses-nonsense-mediated-mrna-decay
#13
Misa Iwatani-Yoshihara, Masahiro Ito, Yoshihiro Ishibashi, Hideyuki Oki, Toshio Tanaka, Daisuke Morishita, Takashi Ito, Hiromichi Kimura, Yasuhiro Imaeda, Samuel Aparicio, Atsushi Nakanishi, Tomohiro Kawamoto
Eukaryotic initiation factor 4A-3 (eIF4A3) is an Asp-Glu-Ala-Asp (DEAD) box-family adenosine triphosphate (ATP)-dependent RNA helicase. Subtypes eIF4A1 and eIF4A2 are required for translation initiation, but eIF4A3 participates in the exon junction complex (EJC) and functions in RNA metabolism including nonsense-mediated RNA decay (NMD). No small molecules for NMD inhibition via selective inhibition of eIF4A3 have been discovered. Here, we identified allosteric eIF4A3 inhibitors from a high-throughput screening campaign...
May 10, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28428796/expression-profiling-coupled-with-in-silico-mapping-identifies-candidate-genes-for-reducing-aflatoxin-accumulation-in-maize
#14
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
#15
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/28411202/characterization-of-the-mammalian-dead-box-protein-ddx5-reveals-functional-conservation-with-s-cerevisiae-ortholog-dbp2-in-transcriptional-control-and-glucose-metabolism
#16
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
#17
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...
May 16, 2017: Oncotarget
https://www.readbyqxmd.com/read/28397605/xenopus-vasa-homolog-xvlg1-is-essential-for-migration-and-survival-of-primordial-germ-cells
#18
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
#19
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/28358513/discovery-of-novel-1-4-diacylpiperazines-as-selective-and-cell-active-eif4a3-inhibitors
#20
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
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