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Ribosomal rna

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https://www.readbyqxmd.com/read/29165424/functional-5-utr-mrna-structures-in-eukaryotic-translation-regulation-and-how-to-find-them
#1
REVIEW
Kathrin Leppek, Rhiju Das, Maria Barna
RNA molecules can fold into intricate shapes that can provide an additional layer of control of gene expression beyond that of their sequence. In this Review, we discuss the current mechanistic understanding of structures in 5' untranslated regions (UTRs) of eukaryotic mRNAs and the emerging methodologies used to explore them. These structures may regulate cap-dependent translation initiation through helicase-mediated remodelling of RNA structures and higher-order RNA interactions, as well as cap-independent translation initiation through internal ribosome entry sites (IRESs), mRNA modifications and other specialized translation pathways...
November 22, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/29164646/b-factor-profile-prediction-for-rna-flexibility-using-support-vector-machines
#2
Ivantha Guruge, Ghazaleh Taherzadeh, Jian Zhan, Yaoqi Zhou, Yuedong Yang
Determining the flexibility of structured biomolecules is important for understanding their biological functions. One quantitative measurement of flexibility is the atomic Debye-Waller factor or temperature B-factor. Most existing studies are limited to temperature B-factors of proteins and their prediction. Only one method attempted to predict temperature B-factors of ribosomal RNA. Here, we developed and compared machine-learning techniques in prediction of temperature B-factors of RNAs. The best model based on Support Vector Machines yields Pearson's correction coefficient at 0...
November 21, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/29163430/pdtas-deficiency-affects-resistance-of-mycobacteria-to-ribosome-targeting-antibiotics
#3
Karolina Dadura, Renata Płocińska, Anna Rumijowska-Galewicz, Przemysław Płociński, Anna Żaczek, Bożena Dziadek, Andrzej Zaborowski, Jarosław Dziadek
Two-component regulatory systems (TCSSs) are key regulatory elements responsible for the adaptation of bacteria to environmental stresses. A classical TCSS is typically comprised of a sensory histidine kinase and a corresponding response regulator. Here, we used homologous recombination to construct a Mycobacterium smegmatis mutant defective in the synthesis of cytosolic histidine kinase PdtaS (Msmeg_1918). The resulting ΔpdtaS mutant strain was tested in the Phenotype Microarray screening system, which allowed us to identify aminoglycoside antibiotic sensitivity, tetracyclines antibiotic resistance as well as membrane transport and respiration, as the main processes affected by removal of pdtaS...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29163393/the-5bsl3-2-functional-rna-domain-connects-distant-regions-in-the-hepatitis-c-virus-genome
#4
REVIEW
Cristina Romero-López, Alfredo Berzal-Herranz
Viral genomes are complexly folded entities that carry all the information required for the infective cycle. The nucleotide sequence of the RNA virus genome encodes proteins and functional information contained in discrete, highly conserved structural units. These so-called functional RNA domains play essential roles in the progression of infection, which requires their preservation from one generation to the next. Numerous functional RNA domains exist in the genome of the hepatitis C virus (HCV). Among them, the 5BSL3...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29162882/sublethal-effects-of-imidacloprid-on-targeting-muscle-and-ribosomal-protein-related-genes-in-the-honey-bee-apis-mellifera-l
#5
Yan-Yan Wu, Qi-Hua Luo, Chun-Sheng Hou, Qiang Wang, Ping-Li Dai, Jing Gao, Yong-Jun Liu, Qing-Yun Diao
A sublethal concentration of imidacloprid can cause chronic toxicity in bees and can impact the behavior of honey bees. The nectar- and water-collecting, and climbing abilities of bees are crucial to the survival of the bees and the execution of responsibilities in bee colonies. Besides behavioral impact, data on the molecular mechanisms underlying the toxicity of imidacloprid, especially by the way of RNA-seq at the transcriptomic level, are limited. We treated Apis mellifera L. with sublethal concentrations of imidacloprid (0...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29161847/formulation-of-the-protein-synthesis-rate-with-sequence-information
#6
Wenjun Xia, Jinzhi Lei
Translation is a central biological process by which proteins are synthesized from genetic information contained within mRNAs. Here, we investigate the kinetics of translation at the molecular level by a stochastic simulation model. The model explicitly includes RNA sequences, ribosome dynamics, the tRNA pool and biochemical reactions involved in the translation elongation. The results show that the translation efficiency is mainly limited by the available ribosome number, translation initiation and the translation elongation time...
April 1, 2018: Mathematical Biosciences and Engineering: MBE
https://www.readbyqxmd.com/read/29161481/-eco-epidemiological-aspects-natural-detection-and-molecular-identification-of-leishmania-spp-in-lutzomyia-reburra-lutzomyia-barrettoi-majuscula-and-lutzomyia-trapidoi
#7
Jazzmín Arrivillaga-Henríquez, Sandra Enríquez, Vanessa Romero, Gustavo Echeverría, Jorge Pérez-Barrera, Ana Poveda, Juan-Carlos Navarro, Alon Warburg, Washington Benítez
INTRODUCTION: The province of Pichincha in Ecuador is an endemic area of cutaneous leishmaniasis, where anthropophilic sand flies with natural infection by Leishmania, have been reported as vectors. However, the role in transmission of zoophilic species has not been evaluated. OBJECTIVE: To evaluate natural infection by Leishmania in two zoophilic phlebotomine sand fly species, Lutzomyia reburra and Lu. barrettoi majuscula, and one anthropophilic species, Lu. trapidoi, as well as the endophagy and synanthropism of these species in the northwest of Pichincha...
March 29, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/29161365/genome-scale-analysis-ofescherichia-coliwith-a-comprehensive-prokaryotic-sequence-based-biophysical-model-of-translation-initiation-and-elongation
#8
Gilad Shaham, Tamir Tuller
Translation initiation in prokaryotes is affected by the mRNA folding and interaction of the ribosome binding site with the ribosomal RNA. The elongation rate is affected, among other factors, by the local biophysical properties of the coding regions, the decoding rates of different codons, and the interactions among ribosomes. Currently, there is no comprehensive biophysical model of translation that enables the prediction of mRNA translation dynamics based only on the transcript sequence and while considering all of these fundamental aspects of translation...
November 17, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/29161086/potential-role-of-the-lung-microbiome-in-shaping-asthma-phenotypes
#9
Kian Fan Chung
The introduction of 16s ribosomal RNA sequencing as a nonculture technique has led to the discovery of the presence of microbiota in the lower airways of healthy individuals. These bacterial communities may originate from the mouth and nasopharynx or from the environment by inhalation. The microbial composition of the lower airways may be modulated by dietary factors, antibiotic therapy, and microbial infections, particularly in early life. In addition, circulatory products from gut microbiota may influence the lung microbiota to maintain mucosal immunity...
November 2017: Annals of the American Thoracic Society
https://www.readbyqxmd.com/read/29160852/the-complete-chloroplast-genome-sequences-of-aconitum-pseudolaeve-and-aconitum-longecassidatum-and-development-of-molecular-markers-for-distinguishing-species-in-the-aconitum-subgenus-lycoctonum
#10
Inkyu Park, Sungyu Yang, Goya Choi, Wook Jin Kim, Byeong Cheol Moon
Aconitum pseudolaeve Nakai and Aconitum longecassidatum Nakai, which belong to the Aconitum subgenus Lycoctonum, are distributed in East Asia and Korea. Aconitum species are used in herbal medicine and contain highly toxic components, including aconitine. A. pseudolaeve, an endemic species of Korea, is a commercially valuable material that has been used in the manufacture of cosmetics and perfumes. Although Aconitum species are important plant resources, they have not been extensively studied, and genomic information is limited...
November 21, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29159245/data-on-evolutionary-relationships-of-aeromonas-hydrophila-and-serratia-proteamaculans-that-attach-to-water-tanks
#11
Ogueri Nwaiwu
Here the data on evolutionary relationships of persistent bacteria from water tanks and their close relatives are shown. Curated sequences of the hypervariable region of ribosomal ribonucleic acid (rRNA) obtained from a strain of Aeromonas hydrophila and two strains of Serratia proteamaculans after searches in the GenBank® database were analyzed. The analysis which included 104 other bacteria strains, was carried out using molecular evolutionary genetic analysis (MEGA 7.0) software.
February 2018: Data in Brief
https://www.readbyqxmd.com/read/29158377/evidence-for-rrna-2-o-methylation-plasticity-control-of-intrinsic-translational-capabilities-of-human-ribosomes
#12
Jenny Erales, Virginie Marchand, Baptiste Panthu, Sandra Gillot, Stéphane Belin, Sandra E Ghayad, Maxime Garcia, Florian Laforêts, Virginie Marcel, Agnès Baudin-Baillieu, Pierre Bertin, Yohann Couté, Annie Adrait, Mélanie Meyer, Gabriel Therizols, Marat Yusupov, Olivier Namy, Théophile Ohlmann, Yuri Motorin, Frédéric Catez, Jean-Jacques Diaz
Ribosomal RNAs (rRNAs) are main effectors of messenger RNA (mRNA) decoding, peptide-bond formation, and ribosome dynamics during translation. Ribose 2'-O-methylation (2'-O-Me) is the most abundant rRNA chemical modification, and displays a complex pattern in rRNA. 2'-O-Me was shown to be essential for accurate and efficient protein synthesis in eukaryotic cells. However, whether rRNA 2'-O-Me is an adjustable feature of the human ribosome and a means of regulating ribosome function remains to be determined. Here we challenged rRNA 2'-O-Me globally by inhibiting the rRNA methyl-transferase fibrillarin in human cells...
November 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29158335/a-deconvolution-protocol-for-chip-seq-reveals-analogous-enhancer-structures-on-the-mouse-and-human-ribosomal-rna-genes
#13
Jean-Clement Mars, Marianne Sabourin-Felix, Michel G Tremblay, Tom Moss
The combination of Chromatin Immunoprecipitation and Massively Parallel Sequencing, or ChIP-Seq, has greatly advanced our genome-wide understanding of chromatin and enhancer structures. However, its resolution at any given genetic locus is limited by several factors. In applying ChIP-Seq to the study of the ribosomal RNA genes, we found that a major limitation to resolution was imposed by the underlying variability in sequence coverage that very often dominates the protein-DNA interaction profiles. Here we describe a simple numerical deconvolution approach that in large part corrects for this variability and significantly improves both the resolution and quantitation of protein-DNA interaction maps deduced from ChIP-Seq data...
November 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29156000/structural-rearrangements-in-mrna-upon-its-binding-to-human-80s-ribosomes-revealed-by-epr-spectroscopy
#14
Alexey A Malygin, Dmitri M Graifer, Maria I Meschaninova, Alya G Venyaminova, Ivan O Timofeev, Andrey A Kuzhelev, Olesya A Krumkacheva, Matvey V Fedin, Galina G Karpova, Elena G Bagryanskaya
The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two different types of ribosomal complexes with MR was observed. First, there were stable complexes where MR was fixed in the ribosomal mRNA-binding channel by the codon-anticodon interaction(s) with cognate tRNA(s)...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29150605/global-role-of-the-bacterial-post-transcriptional-regulator-csra-revealed-by-integrated-transcriptomics
#15
Anastasia H Potts, Christopher A Vakulskas, Archana Pannuri, Helen Yakhnin, Paul Babitzke, Tony Romeo
CsrA is a post-transcriptional regulatory protein that is widely distributed among bacteria. This protein influences bacterial lifestyle decisions by binding to the 5' untranslated and/or early coding regions of mRNA targets, causing changes in translation initiation, RNA stability, and/or transcription elongation. Here, we assess the contribution of CsrA to gene expression in Escherichia coli on a global scale. UV crosslinking immunoprecipitation and sequencing (CLIP-seq) identify RNAs that interact directly with CsrA in vivo, while ribosome profiling and RNA-seq uncover the impact of CsrA on translation, RNA abundance, and RNA stability...
November 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/29147024/comparison-of-r-ketamine-and-lanicemine-on-depression-like-phenotype-and-abnormal-composition-of-gut-microbiota-in-a-social-defeat-stress-model
#16
Youge Qu, Chun Yang, Qian Ren, Min Ma, Chao Dong, Kenji Hashimoto
Accumulating evidence suggests a key role of the gut-microbiota-brain axis in the antidepressant actions of certain compounds. Ketamine, an N-methyl-D-aspartate receptor (NMDAR) antagonist, showed rapid and sustained antidepressant effects in treatment-resistant depressed patients. In contrast, another NMDAR antagonist, lanicemine, did not exhibit antidepressant effects in such patients. (R)-ketamine, the (R)-enantiomer of ketamine, has rapid-acting and long-lasting antidepressant effects in rodent models of depression...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146266/endophytism-or-saprophytism-decoding-the-lifestyle-transition-of-the-generalist-fungus-phomopsis-liquidambari
#17
Jun Zhou, Xin Li, Peng-Wei Huang, Chuan-Chao Dai
Filamentous ascomycete Phomopsis sp. are common inhabitants of natural ecosystems and, as saprophytes, are largely responsible for the destructive decay of litterfall, promoting the carbon and nitrogen cycles. Phomopsis liquidambari B3 can establish mutualistic symbiosis with a broad spectrum of crop plants. Colonizing dynamics observations and a growth promotion assay of rice and Arabidopsis thaliana revealed that the B3 colonization strategy is host-adapted and resulted in different growth promotions influenced by N availability...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29146256/isolation-purification-structural-elucidation-and-antimicrobial-activities-of-kocumarin-a-novel-antibiotic-isolated-from-actinobacterium-kocuria-marina-cmg-s2-associated-with-the-brown-seaweed-pelvetia-canaliculata
#18
Bushra Uzair, Farid Menaa, Barkat Ali Khan, Faryal Vali Mohammad, Viqar Uddin Ahmad, Ryad Djeribi, Bouzid Menaa
AIMS: Screening of seaweed-associated bacteria capable of producing antimicrobials. METHODS AND RESULTS: Fifteen microbial strains, associated to the brown seaweed Pelvetia canaliculata (Linnaeus) attached to the rocks of Sonmiani Beach (Karachi, Pakistan), were screened. Crude extract filtrates of CMG S2 strain grew on Zobell marine agar (ZMA) had the most remarkable antimicrobial activity. Based on its phenotypic aspects (e.g. Gram-positive, microccoid form), biochemical characteristics (e...
January 2018: Microbiological Research
https://www.readbyqxmd.com/read/29143818/visualization-of-chemical-modifications-in-the-human-80s-ribosome-structure
#19
S Kundhavai Natchiar, Alexander G Myasnikov, Hanna Kratzat, Isabelle Hazemann, Bruno P Klaholz
Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA...
November 15, 2017: Nature
https://www.readbyqxmd.com/read/29143558/perturbation-of-rna-polymerase-i-transcription-machinery-by-ablation-of-heatr1-triggers-the-rpl5-rpl11-mdm2-p53-ribosome-biogenesis-stress-checkpoint-pathway-in-human-cells
#20
Zsofia Turi, Marketa Senkyrikova, Martin Mistrik, Jiri Bartek, Pavel Moudry
Ribosome biogenesis is an energy consuming process which takes place mainly in the nucleolus. By producing ribosomes to fuel protein synthesis, it is tightly connected with cell growth and cell cycle control. Perturbation of ribosome biogenesis leads to the activation of p53 tumor suppressor protein promoting processes like cell cycle arrest, apoptosis or senescence. This ribosome biogenesis stress pathway activates p53 through sequestration of MDM2 by a subset of ribosomal proteins (RPs), thereby stabilizing p53...
November 16, 2017: Cell Cycle
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