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RNA Biology

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https://www.readbyqxmd.com/read/28812932/celebrating-wobble-decoding-half-a-century-and-still-much-is-new
#1
Paul F Agris, Emily R Eruysal, Amithi Narendran, Ville Y P Väre, Sweta Vangaveti, Srivathsan V Ranganathan
A simple post-transcriptional modification of tRNA, deamination of adenosine to inosine at the first, or wobble, position of the anticodon, inspired Francis Crick's Wobble Hypothesis 50 years ago. Many more naturally-occurring modifications have been elucidated and continue to be discovered. The post-transcriptional modifications of tRNA's anticodon domain are the most diverse and chemically complex of any RNA modifications. Their contribution with regards to chemistry, structure and dynamics reveal individual and combined effects on tRNA function in recognition of cognate and wobble codons...
August 16, 2017: RNA Biology
https://www.readbyqxmd.com/read/28805544/rna-silencing-in-plant-symbiotic-bacteria-insights-from-a-protein-centric-view
#2
José I Jiménez-Zurdo, Marta Robledo
Extensive work in model enterobacteria has evidenced that the RNA chaperone Hfq and several endoribonucleases, such as RNase E or RNase III, serve pivotal roles in small RNA-mediated post-transcriptional silencing of gene expression. Characterization of these protein hubs commonly provide global functional and mechanistic insights into complex sRNA regulatory networks. The legume endosymbiont Sinorhizobium meliloti is a non-classical model bacterium with a very complex lifestyle in which riboregulation is expected to play important adaptive functions...
August 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28805496/natural-antisense-transcripts-drive-a-regulatory-cascade-controlling-c-myc-transcription
#3
Sara Napoli, Valentina Piccinelli, Sarah Mapelli, Giuseppina Pisignano, Carlo V Catapano
Cis-natural antisense transcripts (cis-NATs) are long noncoding RNAs transcribed from the opposite strand and overlapping coding and noncoding genes on the sense strand. cis-NATs are widely present in the human genome and can be involved in multiple mechanisms of gene regulation. Here, we describe the presence of cis-NATs in the 3' distal region of the c-MYC locus and investigate their impact on transcriptional regulation of this key oncogene in human cancers. We found that cis-NATs are produced as consequence of the activation of cryptic transcription initiation sites in the 3' distal region downstream of the c-MYC 3'UTR...
August 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28795877/editorial-rna-modifications-what-to-read-first
#4
Mark Helm
No abstract text is available yet for this article.
August 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28786741/human-mitochondrial-ribosomes-can-switch-structural-trnas-but-when-and-why
#5
Zofia Chrzanowska-Lightowlers, Joanna Rorbach, Michal Minczuk
High resolution cryoEM of mammalian mitoribosomes revealed the unexpected presence of mitochondrially encoded tRNA as a structural component of mitochondrial large ribosomal subunit (mt-LSU). Our previously published data identified that only mitochondrial (mt-) tRNA(Phe) and mt-tRNA(Val) can be incorporated into mammalian mt-LSU and within an organism there is no evidence of tissue specific variation. When mt-tRNA(Val) is limiting, human mitoribosomes can integrate mt-tRNA(Phe) instead to generate a translationally competent monosome...
August 8, 2017: RNA Biology
https://www.readbyqxmd.com/read/28783426/characterization-of-the-pirna-pathway-during-development-of-the-sea-anemone-nematostella-vectensis
#6
Daniela Praher, Bob Zimmermann, Grigory Genikhovich, Yaara Columbus-Shenkar, Vengamanaidu Modepalli, Reuven Aharoni, Yehu Moran, Ulrich Technau
PIWI-interacting RNAs (piRNAs) and associated proteins comprise a conserved pathway for silencing transposons in metazoan germlines. piRNA pathway components are also expressed in multipotent somatic stem cells in various organisms. piRNA functions have been extensively explored in bilaterian model systems, however, comprehensive studies in non-bilaterian phyla remain limited. Here we investigate the piRNA pathway during the development of Nematostella vectensis, a well-established model system belonging to Cnidaria, the sister group to Bilateria...
August 7, 2017: RNA Biology
https://www.readbyqxmd.com/read/28745933/does-eif3-promote-reinitiation-after-translation-of-short-upstream-orfs-also-in-mammalian-cells
#7
Vladislava Hronová, Mahabub Pasha Mohammad, Susan Wagner, Josef Pánek, Stanislava Gunišová, Jakub Zeman, Kristýna Poncová, Leoš Shivaya Valášek
Reinitiation after translation of short upstream ORFs (uORFs) represents one of the means of regulation of gene expression on the mRNA-specific level in response to changing environmental conditions. Over the years it has been shown - mainly in budding yeast - that its efficiency depends on cis-acting features occurring in sequences flanking reinitiation-permissive uORFs, the nature of their coding sequences, as well as protein factors acting in trans. We earlier demonstrated that the first two uORFs from the reinitiation-regulated yeast GCN4 mRNA leader carry specific structural elements in their 5' sequences that interact with the translation initiation factor eIF3 to prevent full ribosomal recycling post their translation...
July 26, 2017: RNA Biology
https://www.readbyqxmd.com/read/28737471/quality-control-by-trans-editing-factor-prevents-global-mistranslation-of-non-protein-amino-acid-%C3%AE-aminobutyrate
#8
Jo Marie Bacusmo, Alexandra B Kuzmishin, William A Cantara, Yuki Goto, Hiroaki Suga, Karin Musier-Forsyth
Accuracy in protein biosynthesis is maintained through multiple pathways, with a critical checkpoint occurring at the tRNA aminoacylation step catalyzed by aminoacyl-tRNA synthetases (ARSs). In addition to the editing functions inherent to some synthetases, single-domain trans-editing factors, which are structurally homologous to ARS editing domains, have evolved as alternative mechanisms to correct mistakes in aminoacyl-tRNA synthesis. To date, ARS-like trans-editing domains have been shown to act on specific tRNAs that are mischarged with genetically encoded amino acids...
July 24, 2017: RNA Biology
https://www.readbyqxmd.com/read/28726545/the-t-6-a-modification-acts-as-a-positive-determinant-for-the-anticodon-nuclease-prrc-and-is-distinctively-nonessential-in-streptococcus-mutans
#9
Jo Marie Bacusmo, Silvia S Orsini, Jennifer Hu, Michael DeMott, Patrick C Thiaville, Ameer Elfarash, Mellie June Paulines, Diego Rojas-Benítez, Birthe Meineke, Chris Deutsch, Dirk Iwata-Reuyl, Patrick A Limbach, Peter C Dedon, Kelly C Rice, Stewart Shuman, Valérie de Crécy-Lagard
Endoribonuclease toxins (ribotoxins) are produced by bacteria and fungi to respond to stress, eliminate non-self competitor species, or interdict virus infection. PrrC is a bacterial ribotoxin that targets and cleaves tRNA(Lys)UUU in the anticodon loop. In vitro studies suggested that the post-transcriptional modification threonylcarbamoyl adenosine (t(6)A) is required for PrrC activity but this prediction had never been validated in vivo. Here, by using t(6)A-deficient yeast derivatives, it is shown that t(6)A is a positive determinant for PrrC proteins from various bacterial species...
July 20, 2017: RNA Biology
https://www.readbyqxmd.com/read/28722545/trna-engineering-for-manipulating-genetic-code
#10
Takayuki Katoh, Yoshihiko Iwane, Hiroaki Suga
In ribosomal translation, only 20 kinds of proteinogenic amino acids (pAAs), namely 19 l-amino acids and glycine, are exclusively incorporated into polypeptide chain. To overcome this limitation, various methods to introduce non-proteinogenic amino acids (npAAs) other than the 20 pAAs have been developed to date. However, the repertoire of amino acids that can be simultaneously introduced is still limited. Moreover, the efficiency of npAA incorporation is not always sufficient depending on their structures...
July 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28722509/adaptation-of-mrna-structure-to-control-protein-folding
#11
Guilhem Faure, Aleksey Y Ogurtsov, Svetlana A Shabalina, Eugene V Koonin
Comparison of mRNA and protein structures shows that highly structured mRNAs typically encode compact protein domains suggesting that mRNA structure controls protein folding. This function is apparently performed by distinct structural elements in the mRNA, which implies 'fine tuning' of mRNA structure under selection for optimal protein folding. We find that, during evolution, changes in the mRNA folding energy follow amino acid replacements, reinforcing the notion of an intimate connection between the structures of a mRNA and the protein it encodes, and the double encoding of protein sequence and folding in the mRNA...
July 19, 2017: RNA Biology
https://www.readbyqxmd.com/read/28708455/functionality-of-trnas-encoded-in-a-mobile-genetic-element-from-an-acidophilic-bacterium
#12
Pamela Alamos, Mario Tello, Paula Bustamante, Fernanda Gutiérrez, Amir Shmaryahu, Juan Maldonado, Gloria Levicán, Omar Orellana
The genome of the acidophilic, bioleaching bacterium Acidithiobacillus ferrooxidans, strain ATCC 23270, contains 95 predicted tRNA genes. Thirty-six of these genes (all 20 species) are clustered within an actively excising integrative-conjugative element (ICEAfe1). We speculated that these tRNA genes might have a role in adapting the bacterial tRNA pool to the codon usage of ICEAfe1 genes. To answer this question, we carried out theoretical calculations of the global tRNA adaptation index to the entire A. ferrooxidans genome with and without the ICEAfe1 encoded tRNA genes...
July 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28708448/quick-or-quality-how-mrna-escapes-nuclear-quality-control-during-stress
#13
Gesa Zander, Heike Krebber
Understanding the mechanisms for mRNA production under normal conditions and in response to cytotoxic stresses has been subject of numerous studies for several decades. The shutdown of canonical mRNA transcription, export and translation is required to have enough free resources for the immediate production of heat shock proteins that act as chaperones to sustain cellular processes. In recent work we uncovered a simple mechanism, in which the export block of regular mRNAs and a fast export of heat shock mRNAs is achieved by deactivation of the nuclear mRNA quality control mediated by the guard-protein...
July 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28692405/6s-rna-in-rhodobacter-sphaeroides-6s-rna-and-prna-transcript-levels-peak-in-late-exponential-phase-and-gene-deletion-causes-a-high-salt-stress-phenotype
#14
Daria Elkina, Lennart Weber, Marcus Lechner, Olga Burenina, Andrea Weisert, Elena Kubareva, Roland K Hartmann, Gabriele Klug
The function of 6S RNA, a global regulator of transcription, was studied in the photosynthetic α-proteobacterium Rhodobacter sphaeroides. The cellular levels of R. sphaeroides 6S RNA peak toward the transition to stationary phase and strongly decrease during extended stationary phase. The synthesis of so-called product RNA transcripts (mainly 12-16-mers) on 6S RNA as template by RNA polymerase was found to be highest in late exponential phase. Product RNA ≥ 13-mers are expected to trigger the dissociation of 6S RNA:RNA polymerase complexes...
July 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28692404/one-step-hot-formamide-extraction-of-rna-from-saccharomyces-cerevisiae
#15
Daniel Shedlovskiy, Natalia Shcherbik, Dimitri G Pestov
Current methods for isolating RNA from budding yeast require lengthy and laborious steps such as freezing and heating with phenol, homogenization with glass beads, or enzymatic digestion of the cell wall. Here, extraction with a solution of formamide and EDTA was adapted to isolate RNA from whole yeast cells through a rapid and easily scalable procedure that does not require mechanical cell lysis, phenol, or enzymes. RNA extracted with formamide-EDTA can be directly loaded on gels for electrophoretic analysis without alcohol precipitation...
July 10, 2017: RNA Biology
https://www.readbyqxmd.com/read/28665784/the-evidence-for-a-microrna-product-of-human-drosha-gene
#16
Peter Mechtler, Sydney Johnson, Hannah Slabodkin, Amir B Cohanim, Leonid Brodsky, Eugene S Kandel
MicroRNAs are short RNA molecules that regulate function and stability of a large subset of eukaryotic mRNAs. In the main pathway of microRNA biogenesis, a short "hairpin" is excised from a primary transcript by ribonuclease DROSHA, followed by additional nucleolytic processing by DICER and inclusion of the mature microRNA into the RNA-induced silencing complex. We report that a microRNA-like molecule is encoded by human DROSHA gene within a predicted stem-loop element of the respective transcript. This putative mature microRNA is complementary to DROSHA transcript variant 1 and can attenuate expression of the corresponding protein...
June 30, 2017: RNA Biology
https://www.readbyqxmd.com/read/28665778/drna-seq-transcriptional-profiling-of-the-fk506-biosynthetic-gene-cluster-in-streptomyces-tsukubaensis-nrrl18488-and-general-analysis-of-the-transcriptome
#17
Judith S Bauer, Sven Fillinger, Konrad Förstner, Alexander Herbig, Adam C Jones, Katrin Flinspach, Cynthia Sharma, Harald Gross, Kay Nieselt, Alexander K Apel
FK506 (tacrolimus) is a valuable immunosuppressant produced by several Streptomyces strains. In the genome of the wild type producer Streptomyces tsukubaensis NRRL18488, FK506 biosynthesis is encoded by a gene cluster that spans 83.5 (kb). A whole transcriptome differential shotgun sequencing (dRNA-seq) of S. tsukubaensis was performed to analyze transcription at 2 different time points; before and during active FK506 production. In total, 8,914 transcription start sites were identified in either condition, which enabled precise determination of the 5'-UTR length of the corresponding transcripts as well as the identification of 2 consensus sequence motifs in the promoter regions...
June 30, 2017: RNA Biology
https://www.readbyqxmd.com/read/28665774/new-drb-complexes-for-new-drb-functions-in-plants
#18
Thomas Montavon, Yerim Kwon, Aude Zimmermann, Fabrice Michel, Patrice Dunoyer
Double-stranded RNA binding (DRB) proteins are generally considered as promoting cofactors of Dicer or Dicer-like (DCL) proteins that ensure efficient and precise production of small RNAs, the sequence-specificity guide of RNA silencing processes in both plants and animals. However, the characterization of a new clade of DRB proteins in Arabidopsis has recently challenged this view by showing that DRBs can also act as potent inhibitors of DCL processing. This is achieved through sequestration of a specific class of small RNA precursors, the endogenous inverted-repeat (endoIR) dsRNAs, thereby selectively preventing production of their associated small RNAs, the endoIR-siRNAs...
June 30, 2017: RNA Biology
https://www.readbyqxmd.com/read/28662365/a-compensatory-mutagenesis-study-of-a-conserved-hairpin-in-the-m-gene-segment-of-influenza-a-virus-shows-its-role-in-virus-replication
#19
M I Spronken, C E van de Sandt, E P de Jongh, O Vuong, S van der Vliet, T M Bestebroer, R C L Olsthoorn, G F Rimmelzwaan, R A M Fouchier, A P Gultyaev
RNA structures are increasingly recognized to be of importance during influenza A virus replication. Here, we investigated a predicted conserved hairpin in the M gene segment (nt 967-994) within the region of the vRNA 5' packaging signal. The existence of this RNA structure and its possible role in virus replication was investigated using a compensatory mutagenesis approach. Mutations were introduced in the hairpin stem, based on natural variation. Virus replication properties were studied for the mutant viruses with disrupted and restored RNA structures...
June 29, 2017: RNA Biology
https://www.readbyqxmd.com/read/28640690/a-new-layer-of-rrna-regulation-by-small-interference-rnas-and-the-nuclear-rnai-pathway
#20
Xufei Zhou, Xiangyang Chen, Yun Wang, Xuezhu Feng, Shouhong Guang
Ribosome biogenesis drives cell growth and proliferation, but mechanisms that modulate this process remain poorly understood. For a long time, small ribosomal RNA sequences have been widely treated as non-specific degradation products and neglected as garbage sequences. Recently, we identified a new class of antisense ribosomal siRNAs (risiRNAs) that downregulate pre-rRNA through the nuclear RNAi pathway in C. elegans. risiRNAs exhibit sequence characteristics similar to 22G RNA while complement to 18S and 26S rRNA...
June 22, 2017: RNA Biology
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