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https://www.readbyqxmd.com/read/28614360/comparative-genomics-of-cryptococcus-neoformans-var-grubii-associated-with-meningitis-in-hiv-infected-and-uninfected-patients-in-vietnam
#1
Jeremy N Day, Seet Qihui, Lam Tuan Thanh, Phan Hai Trieu, Anh Duong Van, Nha Hoang Thu, Tran Thi Hong Chau, Nguyen P H Lan, Nguyen Van Vinh Chau, Philip M Ashton, Guy E Thwaites, Maciej F Boni, Marcel Wolbers, Niranjan Nagarajan, Patrick B O Tan, Stephen Baker
The vast burden of cryptococcal meningitis occurs in immunosuppressed patients, driven by HIV, and is caused by Cryptococcus neoformans var. grubii. We previously reported cryptococcal meningitis in Vietnam arising atypically in HIV uninfected, apparently immunocompetent patients, caused by a single amplified fragment length polymorphism (AFLP) cluster of C. neoformans var. grubii (VNIγ). This variant was less common in HIV infected individuals; it remains unclear why this lineage is associated with apparently immunocompetent patients...
June 14, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28610761/comparative-proteomic-analysis-provides-insight-into-the-biological-role-of-protein-phosphatase-inhibitor-2-from-arabidopsis
#2
Nagib Ahsan, Mingjie Chen, Fernanda Salvato, Rashaun S Wilson, R Shyama Prasad Rao, Jay J Thelen
Protein phosphatase inhibitor-2 (PPI-2) is a conserved eukaryotic effector protein that inhibits type one protein phosphatases (TOPP). A transfer-DNA knockdown of AtPPI-2 resulted in stunted growth in both vegetative and reproductive phases of Arabidopsis development. At the cellular level, AtPPI-2 knockdown had 35 to 40% smaller cells in developing roots and leaves. This developmental phenotype was rescued by transgenic expression of the AtPPI-2 cDNA behind a constitutive promoter. Comparative proteomics of developing leaves of wild type (WT) and AtPPI-2 mutant revealed reduced levels of proteins associated with chloroplast development, ribosome biogenesis, transport, and cell cycle regulation processes...
June 10, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28602976/sting-signaling-in-tumorigenesis-and-cancer-therapy-a-friend-or-foe
#3
Liangmei He, Xiaomei Xiao, Xi Yang, Zixiang Zhang, Wu Longhuo, Zhiping Liu
Stimulator of interferon genes (STING) is a DNA sensor and an important cytoplasmic adaptor for other DNA sensors, such as Z-DNA binding protein 1 (DAI), DEAD-box helicase 41 (DDX41), and interferon-γ-inducible protein 16 (IFI16). The activation of STING signaling leads to the production of type I interferons and some other pro-inflammatory cytokines, and is critical for host defense against viral infection. Recent accumulating evidences suggest that STING is also involved in tumor development. However, the role of STING signaling in tumorigenesis is complicated, and a comprehensive review is still lacking...
June 7, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28596782/chloroplast-or-mitochondria-targeted-dead-box-rna-helicases-play-essential-roles-in-organellar-rna-metabolism-and-abiotic-stress-responses
#4
REVIEW
Ghazala Nawaz, Hunseung Kang
The yields and productivity of crops are greatly diminished by various abiotic stresses, including drought, cold, heat, and high salinity. Chloroplasts and mitochondria are cellular organelles that can sense diverse environmental stimuli and alter gene expression to cope with adverse environmental stresses. Organellar gene expression is mainly regulated at posttranscriptional levels, including RNA processing, intron splicing, RNA editing, RNA turnover, and translational control, during which a variety of nucleus-encoded RNA-binding proteins (RBPs) are targeted to chloroplasts or mitochondria where they play essential roles in organellar RNA metabolism...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28559293/a-conserved-metal-binding-motif-in-the-bacillus-subtilis-competence-protein-comfa-enhances-transformation
#5
Scott S Chilton, Tanya G Falbel, Susan Hromada, Briana M Burton
Genetic competence is a process in which cells are able to take up DNA from their environment, resulting in horizontal gene transfer, a major mechanism for generating diversity in bacteria. Many bacteria carry homologs of the central DNA uptake machinery that has been well characterized in Bacillus subtilis It has been postulated that the B. subtilis competence helicase ComFA belongs to the DEAD-box family of helicases/translocases. Here, we make a series of mutants to analyze conserved amino acid motifs in several regions of B...
May 30, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28559278/the-p90-ribosomal-s6-kinase-ubr5-pathway-controls-toll-like-receptor-signaling-via-mirna-induced-translational-inhibition-of-tnf-receptor-associated-factor-3
#6
Jin Hwa Cho, Sung Ah Kim, Yeon-Soo Seo, Sung Goo Park, Byoung Chul Park, Jeong-Hoon Kim, Sunhong Kim
MicroRNAs (miRNAs) are small, noncoding RNAs that post-transcriptionally regulate gene expression. For example, miRNAs repress gene expression by recruiting the miRNA-induced silencing complex (miRISC), a ribonucleoprotein complex that contains miRNA-engaged Argonaute (Ago) and the scaffold protein GW182. Recently, ubiquitin protein ligase E3 component N-recognin 5 (UBR5) has been identified as a component of miRISC. UBR5 directly interacts with GW182 proteins and participates in miRNA silencing by recruiting downstream effectors, such as the translation regulator DEAD-box helicase 6 (DDX6) and transducer of ERBB2...
May 30, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28557706/downregulation-of-p68-rna-helicase-ddx5-activates-a-survival-pathway-involving-mtor-and-mdm2-signals
#7
M Kokolo, M Bach-Elias
The DEAD box p68 RNA helicase (DDX5) is required to manipulate RNA structures implicated in mRNA/rRNA processing and transcript export, and acts as a co-activator for a range of transcription factors. Previous research has indicated that p68 RNA helicase may also be important in tumour development. Wild-type HeLa and stable HeLa (clone 13) cell cultures containing RNAi-mediated depletion of p68 RNA helicase induced by doxycycline (DOX) were used to study how the p68 RNA helicase affects the mTOR cell signalling pathway...
2017: Folia Biologica (Praha)
https://www.readbyqxmd.com/read/28550373/black-carp-vasa-identifies-embryonic-and-gonadal-germ-cells
#8
Ting Xue, Miao Yu, Qihua Pan, Yizhou Wang, Jian Fang, Lingyu Li, Yu Deng, Kai Chen, Qian Wang, Tiansheng Chen
Identification of molecular markers is an essential step in the study of germ cells. Vasa is an RNA helicase and a well-known germ cell marker that plays a crucial role in germ cell development. Here, we identified the Vasa homolog termed Mpvasa as the first germ cell marker in black carp (Mylopharyngodon piceus). First, a 2819-bp full-length Mpvasa complementary DNA (cDNA) was cloned by PCR using degenerated primers of conserved sequences and gene-specific primers. The Mpvasa cDNA sequence encodes a 637-amino acid protein that contains eight conserved characteristic motifs of the DEAD box protein family, and shares high identity to grass carp (81%) and zebrafish (74%) vasa homologs...
May 26, 2017: Development Genes and Evolution
https://www.readbyqxmd.com/read/28544931/role-for-rif1-interacting-partner-ddx1-in-blm-recruitment-to-dna-double-strand-breaks
#9
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/28536148/the-lotus-domain-is-a-conserved-dead-box-rna-helicase-regulator-essential-for-the-recruitment-of-vasa-to-the-germ-plasm-and-nuage
#10
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 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28520979/the-dead-box-helicase-mss116-plays-distinct-roles-in-mitochondrial-ribogenesis-and-mrna-specific-translation
#11
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/28500049/metabolic-adaptation-to-nutrients-involves-co-regulation-of-gene-expression-by-the-rna-helicase-dbp2-and-the-cyc8-co-repressor-in-saccharomyces-cerevisiae
#12
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
#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/28475895/slert-regulates-ddx21-rings-associated-with-pol-i-transcription
#14
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
#15
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...
June 13, 2017: Oncotarget
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
#16
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
#17
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
#18
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-untranslated-region-of-ash1-mrna-represses-localized-translation-of-ash1-in-yeast-cells
#19
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...
June 9, 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
#20
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
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