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RNA biogenesis

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https://www.readbyqxmd.com/read/28912690/ring-finger-protein-38-is-a-neuronal-protein-in-the-brain-of-nile-tilapia-oreochromis-niloticus
#1
Kai Lin Cham, Tomoko Soga, Ishwar S Parhar
Really interesting new gene (RING) finger protein is a type of zinc-binding motif found in a large family of functionally distinct proteins. RING finger proteins are involved in diverse cellular processes including apoptosis, DNA repair, cell cycle, signal transduction, tumour suppressor, vesicular transport, and peroxisomal biogenesis. RING finger protein 38 (RNF38) is a member of the family whose functions remain unknown. To gain insight into the putative effects of RNF38 in the central nervous system, we localised its expression...
2017: Frontiers in Neuroanatomy
https://www.readbyqxmd.com/read/28904816/regulation-of-hnrnpa1-by-micrornas-controls-the-mir-18a-k-ras-axis-in-chemotherapy-resistant-ovarian-cancer
#2
Cristian Rodriguez-Aguayo, Paloma Del C Monroig, Roxana S Redis, Emine Bayraktar, Maria I Almeida, Cristina Ivan, Enrique Fuentes-Mattei, Mohammed H Rashed, Arturo Chavez-Reyes, Bulent Ozpolat, Rahul Mitra, Anil K Sood, George A Calin, Gabriel Lopez-Berestein
The regulation of microRNA (miRNA) biogenesis, function and degradation involves a range of mechanisms, including interactions with RNA-binding proteins. The potential contribution of regulatory miRNAs to the expression of these RNA interactor proteins that could control other miRNAs expression is still unclear. Here we demonstrate a regulatory circuit involving oncogenic and tumor-suppressor miRNAs and an RNA-binding protein in a chemotherapy-resistant ovarian cancer model. We identified and characterized miR-15a-5p and miR-25-3p as negative regulators of hnRNPA1 expression, which is required for the processing of miR-18a-3p, an inhibitor of the K-RAS oncogene...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28894177/a-viral-protein-antibiotic-inhibits-lipid-ii-flippase-activity
#3
Karthik R Chamakura, Lok-To Sham, Rebecca M Davis, Lorna Min, Hongbaek Cho, Natividad Ruiz, Thomas G Bernhardt, Ry Young
For bacteriophage infections, the cell walls of bacteria, consisting of a single highly polymeric molecule of peptidoglycan (PG), pose a major problem for the release of progeny virions. Phage lysis proteins that overcome this barrier can point the way to new antibacterial strategies (1) , especially small lytic single-stranded DNA (the microviruses) and RNA phages (the leviviruses) that effect host lysis using a single non-enzymatic protein (2) . Previously, the A2 protein of levivirus Qβ and the E protein of the microvirus ϕX174 were shown to be 'protein antibiotics' that inhibit the MurA and MraY steps of the PG synthesis pathway (2-4) ...
September 11, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28893905/lysine-acetylation-stoichiometry-and-proteomics-analyses-reveal-pathways-regulated-by-sirtuin-1-in-human-cells
#4
Jeovanis Gil, Alberto Ramírez-Torres, Diego Chiappe, Juan Luna-Peñaloza, Francis C Fernandez-Reyes, Bolivar Arcos-Encarnación, Sandra Contreras, Sergio Encarnación-Guevara
Lysine acetylation is a widespread posttranslational modification (PTM) affecting many biological pathways. Recent studies indicate that acetylated lysine residues mainly exhibit low acetylation occupancy, but challenges in sample preparation and analysis make it difficult to confidently assign these numbers, limiting understanding of their biological significance. Here, we tested three common sample preparation methods to determine their suitability for assessing acetylation stoichiometry in three human cell lines, identifying the acetylation occupancy in more than 1,300 proteins from each cell line...
September 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28887445/usb1-controls-u6-snrnp-assembly-through-evolutionarily-divergent-cyclic-phosphodiesterase-activities
#5
Allison L Didychuk, Eric J Montemayor, Tucker J Carrocci, Andrew T DeLaitsch, Stefani E Lucarelli, William M Westler, David A Brow, Aaron A Hoskins, Samuel E Butcher
U6 small nuclear ribonucleoprotein (snRNP) biogenesis is essential for spliceosome assembly, but not well understood. Here, we report structures of the U6 RNA processing enzyme Usb1 from yeast and a substrate analog bound complex from humans. Unlike the human ortholog, we show that yeast Usb1 has cyclic phosphodiesterase activity that leaves a terminal 3' phosphate which prevents overprocessing. Usb1 processing of U6 RNA dramatically alters its affinity for cognate RNA-binding proteins. We reconstitute the post-transcriptional assembly of yeast U6 snRNP in vitro, which occurs through a complex series of handoffs involving 10 proteins (Lhp1, Prp24, Usb1 and Lsm2-8) and anti-cooperative interactions between Prp24 and Lhp1...
September 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/28887370/genome-reprogramming-in-saccharomyces-cerevisiae-upon-nonylphenol-exposure
#6
Ceyhun Bereketoglu, Kazim Yalcin Arga, Serpil Eraslan, Bulent Mertoglu
Bioaccumulative environmental estrogen, nonylphenol (NP; 4-nonylphenol), is widely used as a non-ionic surfactant and can affect human health. Since genomes of Saccharomyces cerevisiae and higher eukaryotes share many structural and functional similarities, we investigated subcellular effects of NP on S. cerevisiae BY4742 cells by analyzing genome-wide transcriptional profiles. We examined effects of low (1 mg/L NP) and high (5 mg/L NP) inhibitory concentration exposures for 120 or 180 min. After 120 and 180 min of 1 mg/L NP exposure, 187 (63 downregulated, 124 upregulated) and 103 genes (56 downregulated, 47 upregulated), respectively, were differentially expressed...
September 8, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28886561/zinc-protects-against-cadmium-induced-toxicity-by-regulating-oxidative-stress-ions-homeostasis-and-protein-synthesis
#7
Jingmei Pan, Xinhe Huang, Yuxing Li, Ming Li, Ning Yao, Zhengdong Zhou, Xueru Li
The widespread environmental toxin cadmium (Cd) is associated with numerous human diseases. The essential trace element zinc (Zn) strongly counteracts Cd-induced toxicity; however, the mechanism is incompletely understood. Here, we conducted RNA sequencing and bioinformatics analyses to determine the global gene expression profiles of yeast cells exposed to Cd or Cd plus Zn. We identified 912 Cd-induced and 627 Cd plus Zn-induced differentially expressed genes (DEGs). Adding Zn during Cd exposure efficiently reversed the expression of 92...
August 21, 2017: Chemosphere
https://www.readbyqxmd.com/read/28886174/development-of-hop-transcriptome-to-support-research-into-host-viroid-interactions
#8
Tine Pokorn, Sebastjan Radišek, Branka Javornik, Nataša Štajner, Jernej Jakše
Viroids, the smallest known pathogens, unable to encode any proteins, can cause severe diseases in their host plants. One of the proposed mechanisms of their pathogenicity includes silencing the host's genes via viroid-derived small RNAs, which are products of the host's immune response to the viroid's double stranded RNA. Humulus lupulus (hop) plants are hosts to several viroids; two of them, HLVd and CBCVd, are interesting models for studying host-viroid interactions, due to the symptomless infection of the former and severe stunting disease caused by the latter...
2017: PloS One
https://www.readbyqxmd.com/read/28886127/genome-wide-mirna-response-to-anacardic-acid-in-breast-cancer-cells
#9
David J Schultz, Penn Muluhngwi, Negin Alizadeh-Rad, Madelyn A Green, Eric C Rouchka, Sabine J Waigel, Carolyn M Klinge
MicroRNAs are biomarkers and potential therapeutic targets for breast cancer. Anacardic acid (AnAc) is a dietary phenolic lipid that inhibits both MCF-7 estrogen receptor α (ERα) positive and MDA-MB-231 triple negative breast cancer (TNBC) cell proliferation with IC50s of 13.5 and 35 μM, respectively. To identify potential mediators of AnAc action in breast cancer, we profiled the genome-wide microRNA transcriptome (microRNAome) in these two cell lines altered by the AnAc 24:1n5 congener. Whole genome expression profiling (RNA-seq) and subsequent network analysis in MetaCore Gene Ontology (GO) algorithm was used to characterize the biological pathways altered by AnAc...
2017: PloS One
https://www.readbyqxmd.com/read/28885715/genome-evolution-is-driven-by-gene-expression-generated-biophysical-constraints-through-rna-directed-genetic-variation-a-hypothesis
#10
REVIEW
Didier Auboeuf
The biogenesis of RNAs and proteins is a threat to the cell. Indeed, the act of transcription and nascent RNAs challenge DNA stability. Both RNAs and nascent proteins can also initiate the formation of toxic aggregates because of their physicochemical properties. In reviewing the literature, I show that co-transcriptional and co-translational biophysical constraints can trigger DNA instability that in turn increases the likelihood that sequences that alleviate the constraints emerge over evolutionary time. These directed genetic variations rely on the biogenesis of small RNAs that are transcribed directly from challenged DNA regions or processed from the transcripts that directly or indirectly generate constraints or aggregates...
September 8, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28883156/structural-insights-into-the-interaction-of-the-nuclear-exosome-helicase-mtr4-with-the-pre-ribosomal-protein-nop53
#11
Sebastian Falk, Jan-Niklas Tants, Jerôme Basquin, Matthias Thoms, Ed Hurt, Michael Sattler, Elena Conti
The nuclear exosome and the associated RNA helicase Mtr4 participate in the processing of several ribonucleoprotein particles (RNP), including the maturation of the large ribosomal subunit (60S). S. cerevisiae Mtr4 interacts directly with Nop53, a ribosomal biogenesis factor present in late pre-60S particles containing precursors of the 5.8S rRNA. The Mtr4-Nop53 interaction plays a pivotal role in the maturation of the 5.8S rRNA, providing a physical link between the nuclear exosome and the pre-60S RNP. An analogous interaction between Mtr4 and another ribosome biogenesis factor, Utp18, directs the exosome to an earlier pre-ribosomal particle...
September 7, 2017: RNA
https://www.readbyqxmd.com/read/28882200/fe-s-cluster-hsp70-chaperones-the-atpase-cycle-and-protein-interactions
#12
Rafal Dutkiewicz, Malgorzata Nowak, Elizabeth A Craig, Jaroslaw Marszalek
Hsp70 chaperones and their obligatory J-protein cochaperones function together in many cellular processes. Via cycles of binding to short stretches of exposed amino acids on substrate proteins, Hsp70/J-protein chaperones not only facilitate protein folding but also drive intracellular protein transport, biogenesis of cellular structures, and disassembly of protein complexes. The biogenesis of iron-sulfur (Fe-S) clusters is one of the critical cellular processes that require Hsp70/J-protein action. Fe-S clusters are ubiquitous cofactors critical for activity of proteins performing diverse functions in, for example, metabolism, RNA/DNA transactions, and environmental sensing...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28880477/exosomes-as-new-players-in-metabolic-organ-cross-talk
#13
REVIEW
Claudiane Guay, Romano Regazzi
Blood glucose homeostasis requires a constant communication between insulin-secreting and insulin-sensitive cells. A wide variety of circulating factors, including hormones, cytokines and chemokines work together to orchestrate the systemic response of metabolic organs to changes in the nutritional state. Failure in the coordination between these organs can lead to a rise in blood glucose levels and to the appearance of metabolic disorders such as diabetes mellitus. Exosomes are small extracellular vesicles (EVs) that are produced via the endosomal pathway and are released from the cells upon fusion of multivesicular bodies with the plasma membrane...
September 2017: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/28880270/circulating-micrornas-in-breast-cancer-novel-diagnostic-and-prognostic-biomarkers
#14
REVIEW
Rimi Hamam, Dana Hamam, Khalid A Alsaleh, Moustapha Kassem, Waleed Zaher, Musaad Alfayez, Abdullah Aldahmash, Nehad M Alajez
Effective management of breast cancer depends on early diagnosis and proper monitoring of patients' response to therapy. However, these goals are difficult to achieve because of the lack of sensitive and specific biomarkers for early detection and for disease monitoring. Accumulating evidence in the past several years has highlighted the potential use of peripheral blood circulating nucleic acids such as DNA, mRNA and micro (mi)RNA in breast cancer diagnosis, prognosis and for monitoring response to anticancer therapy...
September 7, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28879852/type-iii-crispr-cas-system-introduction-and-its-application-for-genetic-manipulations
#15
Tao Liu, Saifu Pan, Yingjun Li, Nan Peng, Qunxin She
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes provide adaptive immunity against invasion of foreign nucleic acids in archaea and bacteria. The system functions in three distinct stages: adaptation, biogenesis, and interference. CRISPR-Cas systems are currently classified into at least five different types, each with a signature protein among which Type III systems exhibit a dual DNA/RNA interference activity. Structures of a few Type III surveillance complexes have been determined: they are composed of several different subunits and exhibit striking architectural similarities to Type I surveillance complexes...
September 7, 2017: Current Issues in Molecular Biology
https://www.readbyqxmd.com/read/28876208/deep-sequencing-uncovers-rice-long-sirnas-and-its-involvement-in-immunity-against-rhizoctonia-solani
#16
Dongdong Niu, Xin Zhang, Xiaoou Song, Zhihui Wang, Yanqiang Li, Lulu Qiao, Zhaoyun Wang, Junzhong Liu, Yiwen Deng, Zuhua He, Donglei Yang, Renyi Liu, Yangli Wang, Hongwei Zhao
Small RNA (sRNA) is a class of non-coding RNA that can silence the expression of target genes. In rice, the majority of characterized sRNAs are within the range of 21 to 24 nucleotide long, whose biogenesis and function are associated with a specific sets of components, such as Dicer-like (OsDCLs) and Argonaute proteins (OsAGOs). Rice sRNAs longer than 24 nt are occasionally reported, with biogenesis and functional mechanism uninvestigated, especially in a context of defense responses against pathogen infection...
September 6, 2017: Phytopathology
https://www.readbyqxmd.com/read/28874570/loquacious-pd-facilitates-drosophila-dicer-2-cleavage-through-interactions-with-the-helicase-domain-and-dsrna
#17
Kyle D Trettin, Niladri K Sinha, Debra M Eckert, Sarah E Apple, Brenda L Bass
Loquacious-PD (Loqs-PD) is required for biogenesis of many endogenous siRNAs in Drosophila In vitro, Loqs-PD enhances the rate of dsRNA cleavage by Dicer-2 and also enables processing of substrates normally refractory to cleavage. Using purified components, and Loqs-PD truncations, we provide a mechanistic basis for Loqs-PD functions. Our studies indicate that the 22 amino acids at the C terminus of Loqs-PD, including an FDF-like motif, directly interact with the Hel2 subdomain of Dicer-2's helicase domain...
September 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28869593/how-type-ii-crispr-cas-establish-immunity-through-cas1-cas2-mediated-spacer-integration
#18
Yibei Xiao, Sherwin Ng, Ki Hyun Nam, Ailong Ke
CRISPR (clustered regularly interspaced short palindromic repeats) and the nearby cas (CRISPR-associated) operon establish an RNA-based adaptive immunity system in prokaryotes(1-5). Molecular memory is created when a short foreign DNA-derived prespacer is integrated into the CRISPR array as a new spacer(6-9). Whereas the RNA-guided CRISPR interference mechanism varies widely among CRISPR-Cas systems, the spacer integration mechanism is essentially identical(7-9). The conserved Cas1 and Cas2 proteins form an integrase complex consisting two distal Cas1 dimers bridged by a Cas2 dimer in the middle(6,10)...
September 4, 2017: Nature
https://www.readbyqxmd.com/read/28866281/integrated-assessment-of-toxic-effects-of-maghemite-%C3%AE-fe2o3-nanoparticles-in-zebrafish
#19
Rolando A R Villacis, José S Filho, Benjamin Piña, Ricardo B Azevedo, Aline Pic-Taylor, Juliana F Mazzeu, Cesar K Grisolia
The increasing use of nanotechnology in the last decade has raised concerns about the impact of nanoparticles in the environment. In particular, the potential harmful effects of iron oxide nanoparticles (IONPs) in aquatic organisms have been poorly addressed. We analyze here the toxic effects induced by IONPs in zebrafish using a combination of classical (genotoxicity, oxidative stress) and molecular (transcriptomic) methodologies. Adult animals were exposed for 96h to five sub-lethal IONP concentrations, ranging from 4...
August 8, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28856519/osppr6-a-pentatricopeptide-repeat-protein-involved-in-editing-and-splicing-chloroplast-rna-is-required-for-chloroplast-biogenesis-in-rice
#20
Jianpeng Tang, Wenwei Zhang, Kai Wen, Gaoming Chen, Juan Sun, Yunlu Tian, Weijie Tang, Jun Yu, Hongzhou An, Tingting Wu, Fei Kong, William Terzaghi, Chunming Wang, Jianmin Wan
OsPPR6, a pentatricopeptide repeat protein involved in editing and splicing chloroplast RNA, is required for chloroplast biogenesis in rice. The chloroplast has its own genetic material and genetic system, but it is also regulated by nuclear-encoded genes. However, little is known about nuclear-plastid regulatory mechanisms underlying early chloroplast biogenesis in rice. In this study, we isolated and characterized a mutant, osppr6, that showed early chloroplast developmental defects leading to albino leaves and seedling death...
August 30, 2017: Plant Molecular Biology
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