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https://www.readbyqxmd.com/read/27913732/a-hydantoin-isoform-of-cyclic-n6-threonylcarbamoyladenosine-ct6a-is-present-in-trnas
#1
Michal Matuszewski, Jakub Wojciechowski, Kenjyo Miyauchi, Zofia Gdaniec, Wojciech M Wolf, Tsutomu Suzuki, Elzbieta Sochacka
N(6)-Threonylcarbamoyladenosine (t(6)A) and its derivatives are universally conserved modified nucleosides found at position 37, 3' adjacent to the anticodon in tRNAs responsible for ANN codons. These modifications have pleiotropic functions of tRNAs in decoding and protein synthesis. In certain species of bacteria, fungi, plants and protists, t(6)A is further modified to the cyclic t(6)A (ct(6)A) via dehydration catalyzed by TcdA. This additional modification is involved in efficient decoding of tRNA(Lys) Previous work indicated that the chemical structure of ct(6)A is a cyclic active ester with an oxazolone ring...
December 2, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913726/competitive-binding-between-seryl-trna-synthetase-yy1-complex-and-nfkb1-at-the-distal-segment-results-in-differential-regulation-of-human-vegfa-promoter-activity-during-angiogenesis
#2
Chuan-Yang Fu, Po-Chun Wang, Huai-Jen Tsai
Vascular endothelial growth factor (VEGF) plays a pivotal role in angiogenesis. Previous studies focused on transcriptional regulation modulated by proximal upstream cis-regulatory elements (CREs) of the human vegfa promoter. However, we hypothesized that distal upstream CREs may also be involved in controlling vegfa transcription. In this study, we found that the catalytic domain of Seryl-tRNA synthetase (SerRS) interacted with transcription factor Yin Yang 1 (YY1) to form a SerRS/YY1 complex that negatively controls vegfa promoter activity through binding distal CREs at -4654 to -4623 of vegfa Particularly, we demonstrated that the -4654 to -4623 segment, which predominantly controls vegfa promoter activity, is involved in competitive binding between SerRS/YY1 complex and NFKB1...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911835/two-crystal-structures-reveal-design-for-repurposing-the-c-ala-domain-of-human-alars
#3
Litao Sun, Youngzee Song, David Blocquel, Xiang-Lei Yang, Paul Schimmel
The 20 aminoacyl tRNA synthetases (aaRSs) couple each amino acid to their cognate tRNAs. During evolution, 19 aaRSs expanded by acquiring novel noncatalytic appended domains, which are absent from bacteria and many lower eukaryotes but confer extracellular and nuclear functions in higher organisms. AlaRS is the single exception, with an appended C-terminal domain (C-Ala) that is conserved from prokaryotes to humans but with a wide sequence divergence. In human cells, C-Ala is also a splice variant of AlaRS...
November 28, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27911719/transcription-by-rna-polymerase-iii-insights-into-mechanism-and-regulation
#4
REVIEW
Tomasz W Turowski, David Tollervey
The highly abundant, small stable RNAs that are synthesized by RNA polymerase III (RNAPIII) have key functional roles, particularly in the protein synthesis apparatus. Their expression is metabolically demanding, and is therefore coupled to changing demands for protein synthesis during cell growth and division. Here, we review the regulatory mechanisms that control the levels of RNAPIII transcripts and discuss their potential physiological relevance. Recent analyses have revealed differential regulation of tRNA expression at all steps on its biogenesis, with significant deregulation of mature tRNAs in cancer cells...
October 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27908995/complete-genome-sequence-of-bacteroides-ovatus-v975
#5
Udo Wegmann, Alexander Goesmann, Simon R Carding
The complete genome sequence of Bacteroides ovatus V975 was determined. The genome consists of a single circular chromosome of 6,475,296 bp containing five rRNA operons, 68 tRNA genes, and 4,959 coding genes.
December 1, 2016: Genome Announcements
https://www.readbyqxmd.com/read/27908233/procedure-for-purification-of-recombinant-premsk1p-from-e-coli-determines-its-properties-as-a-factor-of-trna-import-into-yeast-mitochondria
#6
E V Smirnova, I V Chicherin, M V Baleva, N S Entelis, I A Tarassov, P A Kamenski
Mitochondrial genomes of many eukaryotic organisms do not code for the full tRNA set necessary for organellar translation. Missing tRNA species are imported from the cytosol. In particular, one out of two cytosolic lysine tRNAs of the yeast Saccharomyces cerevisiae is partially internalized by mitochondria. The key protein factor of this process is the precursor of mitochondrial lysyl-tRNA synthetase, preMsk1p. In this work, we show that recombinant preMsk1p purified from E. coli in native conditions, when used in an in vitro tRNA import system, demonstrates some properties different from those shown by the renatured protein purified from E...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27908230/dna-import-into-mitochondria
#7
REVIEW
Yu M Konstantinov, A Dietrich, F Weber-Lotfi, N Ibrahim, E S Klimenko, V I Tarasenko, T A Bolotova, M V Koulintchenko
In recent decades, it has become evident that the condition for normal functioning of mitochondria in higher eukaryotes is the presence of membrane transport systems of macromolecules (proteins and nucleic acids). Natural competence of the mitochondria in plants, animals, and yeasts to actively uptake DNA may be directly related to horizontal gene transfer into these organelles occurring at much higher rate compared to the nuclear and chloroplast genomes. However, in contrast with import of proteins and tRNAs, little is known about the biological role and molecular mechanism underlying import of DNA into eukaryotic mitochondria...
October 2016: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/27906773/suppression-of-aimp1-protects-cognition-in-alzheimer-s-disease-model-mice-3xtg-ad
#8
Sooah Jang, Jung Ho Lee, Bo Kyung Sohn, Eosu Kim, Sang Gyu Park, Kang Jun Yoon, Minsun Park, Eun Woo Kim, Jihyeon Jeong, Jun-Young Lee, Chul Hoon Kim, Kee Namkoong
Neuroinflammation has been raised as a candidate of unifying pathogenesis and a target of a disease-modifying strategy for Alzheimer's disease (AD). Aminoacyl-tRNA synthetase complex (ARS)-interacting multifunctional protein 1 (AIMP1) is a cytokine that is known to amplify the actions of tumor necrosis factor-α and to be involved in microglial activation and neuronal death. In this respect, AIMP1 could be a plausible target for the treatment of AD. Therefore, we aimed to examine whether anti-AIMP1 antibody could exert therapeutic effects against cognitive impairment using 3xTg-AD mice...
November 30, 2016: Neuroreport
https://www.readbyqxmd.com/read/27906160/mechanistic-insights-into-the-alternative-translation-termination-by-arfa-and-rf2
#9
Chengying Ma, Daisuke Kurita, Ningning Li, Yan Chen, Hyouta Himeno, Ning Gao
During cellular translation of mRNAs by ribosomes, various situations that would result in the pausing or stalling of translation apparatus at elongation and termination steps often occur(1-6). Except for programmed stalling, which is usually utilized by the cells to exert regulatory purposes(5,7,8), ribosomes stalled on mRNAs need to be terminated and recycled to maintain adequate cellular translation capacity(9). A large source of ribosome stalling originates in aberrant mRNAs that lack a stop codon. Transcriptional errors and misprocessing of primary transcripts, as well as undesired mRNA cleavage, all contribute to the formation of non-stop mRNAs...
December 1, 2016: Nature
https://www.readbyqxmd.com/read/27904467/isolation-and-characterization-of-a-bacteriophage-preying-an-antifungal-bacterium
#10
Aryan Rahimi-Midani, Kyoung-Ho Kim, Seon-Woo Lee, Sang Bong Jung, Tae-Jin Choi
Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of 100 ± 5 nm and tail of 200 ± 5 nm, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39...
December 2016: Plant Pathology Journal
https://www.readbyqxmd.com/read/27903914/proteomic-analysis-of-the-human-keops-complex-identifies-c14orf142-as-a-core-subunit-homologous-to-yeast-gon7
#11
Leo C K Wan, Pierre Maisonneuve, Rachel K Szilard, Jean-Philippe Lambert, Timothy F Ng, Noah Manczyk, Hao Huang, Rob Laister, Amy A Caudy, Anne-Claude Gingras, Daniel Durocher, Frank Sicheri
The KEOPS/EKC complex is a tRNA modification complex involved in the biosynthesis of N(6)-threonylcarbamoyladenosine (t(6)A), a universally conserved tRNA modification found on ANN-codon recognizing tRNAs. In archaea and eukaryotes, KEOPS is composed of OSGEP/Kae1, PRPK/Bud32, TPRKB/Cgi121 and LAGE3/Pcc1. In fungi, KEOPS contains an additional subunit, Gon7, whose orthologs outside of fungi, if existent, remain unidentified. In addition to displaying defective t(6)A biosynthesis, Saccharomyces cerevisiae strains harboring KEOPS mutations are compromised for telomere homeostasis, growth and transcriptional co-activation...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903912/the-complex-evolutionary-history-of-aminoacyl-trna-synthetases
#12
Anargyros Chaliotis, Panayotis Vlastaridis, Dimitris Mossialos, Michael Ibba, Hubert D Becker, Constantinos Stathopoulos, Grigorios D Amoutzias
Aminoacyl-tRNA synthetases (AARSs) are a superfamily of enzymes responsible for the faithful translation of the genetic code and have lately become a prominent target for synthetic biologists. Our large-scale analysis of >2500 prokaryotic genomes reveals the complex evolutionary history of these enzymes and their paralogs, in which horizontal gene transfer played an important role. These results show that a widespread belief in the evolutionary stability of this superfamily is misconceived. Although AlaRS, GlyRS, LeuRS, IleRS, ValRS are the most stable members of the family, GluRS, LysRS and CysRS often have paralogs, whereas AsnRS, GlnRS, PylRS and SepRS are often absent from many genomes...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903898/transfer-rna-is-highly-unstable-during-early-amino-acid-starvation-in-escherichia-coli
#13
Sine Lo Svenningsen, Mette Kongstad, Thomas Søndergaard Stenum, Ana J Muñoz-Gómez, Michael A Sørensen
Due to its long half-life compared to messenger RNA, bacterial transfer RNA is known as stable RNA. Here, we show that tRNAs become highly unstable as part of Escherichia coli's response to amino acid starvation. Degradation of the majority of cellular tRNA occurs within twenty minutes of the onset of starvation for each of several amino acids. Both the non-cognate and cognate tRNA for the amino acid that the cell is starving for are degraded, and both charged and uncharged tRNA species are affected. The alarmone ppGpp orchestrates the stringent response to amino acid starvation...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903248/long-term-clinical-course-of-anti-glycyl-trna-synthetase-anti-ej-antibody-related-interstitial-lung-disease-pathologically-proven-by-surgical-lung-biopsy
#14
Hajime Sasano, Eri Hagiwara, Hideya Kitamura, Yasunori Enomoto, Norikazu Matsuo, Tomohisa Baba, Shinichiro Iso, Koji Okudela, Tae Iwasawa, Shinji Sato, Yasuo Suzuki, Tamiko Takemura, Takashi Ogura
BACKGROUND: Anti-glycyl-tRNA synthetase (anti-EJ) antibody is occasionally positive in patients with interstitial lung disease (ILD). We aimed to define the clinical, radiological and pathological features of patients with anti-EJ antibody-positive ILD (EJ-ILD). METHODS: We retrospectively analyzed the medical records of 12 consecutive patients with EJ-ILD who underwent surgical lung biopsy. RESULTS: The median follow-up time was 74 months (range, 17-115 months)...
December 1, 2016: BMC Pulmonary Medicine
https://www.readbyqxmd.com/read/27902925/targeted-inhibition-of-wrn-helicase-replication-stress-and-cancer
#15
REVIEW
Natalie Orlovetskie, Raphael Serruya, Ghada Abboud-Jarrous, Nayef Jarrous
WRN helicase has several roles in genome maintenance, such as replication, base excision repair, recombination, DNA damage response and transcription. These processes are often found upregulated in human cancers, many of which display increased levels of WRN. Therefore, directed inhibition of this RecQ helicase could be beneficial to selective cancer therapy. Inhibition of WRN is feasible by the use of small-molecule inhibitors or application of RNA interference and EGS/RNase P targeting systems. Remarkably, helicase depletion leads to a severe reduction in cell viability due to mitotic catastrophe, which is triggered by replication stress induced by DNA repair failure and fork progression arrest...
November 27, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27902775/determinants-of-trna-recognition-by-the-radical-sam-enzyme-rlmn
#16
Christina M Fitzsimmons, Danica Galonić Fujimori
RlmN, a bacterial radical SAM methylating enzyme, has the unusual ability to modify two distinct types of RNA: 23S rRNA and tRNA. In rRNA, RlmN installs a methyl group at the C2 position of A2503 of 23S rRNA, while in tRNA the modification occurs at nucleotide A37, immediately adjacent to the anticodon triplet. Intriguingly, only a subset of tRNAs that contain an adenosine at position 37 are substrates for RlmN, suggesting that the enzyme carefully probes the highly conserved tRNA fold and sequence features to identify its targets...
2016: PloS One
https://www.readbyqxmd.com/read/27902423/characterization-of-cis-elements-in-the-promoter-of-trz2-encoding-schizosaccharomyces-pombe-mitochondrial-trna-3-end-processing-enzyme
#17
Jinyu Liu, Linting Huang, Yirong Wang, Ying Huang
The endonuclease tRNase Z is responsible for the 3'-end processing of tRNA precursors, which is one of the essential steps in tRNA maturation. The fission yeast Schizosaccharomyces pombe contains two essential tRNase ZL genes (trz1 and trz2) involved in nuclear and mitochondrial tRNA 3'-end processing, respectively. Our previous studies suggest that trz2 is expressed at a very low level. Here we report characterization of the trz2 promoter. Using lacZ as a reporter, we show that the trz2 promoter contains a HomolD box and a very weak diverged TATA element...
November 22, 2016: Microbiology
https://www.readbyqxmd.com/read/27901112/depletion-of-trna-halves-enables-effective-small-rna-sequencing-of-low-input-murine-serum-samples
#18
Alan Van Goethem, Nurten Yigit, Celine Everaert, Myrthala Moreno-Smith, Liselot M Mus, Eveline Barbieri, Frank Speleman, Pieter Mestdagh, Jason Shohet, Tom Van Maerken, Jo Vandesompele
The ongoing ascent of sequencing technologies has enabled researchers to gain unprecedented insights into the RNA content of biological samples. MiRNAs, a class of small non-coding RNAs, play a pivotal role in regulating gene expression. The discovery that miRNAs are stably present in circulation has spiked interest in their potential use as minimally-invasive biomarkers. However, sequencing of blood-derived samples (serum, plasma) is challenging due to the often low RNA concentration, poor RNA quality and the presence of highly abundant RNAs that dominate sequencing libraries...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27899648/genetic-selection-for-mistranslation-rescues-a-defective-co-chaperone-in-yeast
#19
Kyle S Hoffman, Matthew D Berg, Brian H Shilton, Christopher J Brandl, Patrick O'Donoghue
Despite the general requirement for translation fidelity, mistranslation can be an adaptive response. We selected spontaneous second site mutations that suppress the stress sensitivity caused by a Saccharomyces cerevisiae tti2 allele with a Leu to Pro mutation at residue 187, identifying a single nucleotide mutation at the same position (C70U) in four tRNA(Pro)UGG genes. Linkage analysis and suppression by SUF9G3:U70 expressed from a centromeric plasmid confirmed the causative nature of the suppressor mutation...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899625/ym500v3-a-database-for-small-rna-sequencing-in-human-cancer-research
#20
I-Fang Chung, Shing-Jyh Chang, Chen-Yang Chen, Shu-Hsuan Liu, Chia-Yang Li, Chia-Hao Chan, Chuan-Chi Shih, Wei-Chung Cheng
We previously presented the YM500 database, which contains >8000 small RNA sequencing (smRNA-seq) data sets and integrated analysis results for various cancer miRNome studies. In the updated YM500v3 database (http://ngs.ym.edu.tw/ym500/) presented herein, we not only focus on miRNAs but also on other functional small non-coding RNAs (sncRNAs), such as PIWI-interacting RNAs (piRNAs), tRNA-derived fragments (tRFs), small nuclear RNAs (snRNAs) and small nucleolar RNAs (snoRNAs). There is growing knowledge of the role of sncRNAs in gene regulation and tumorigenesis...
November 29, 2016: Nucleic Acids Research
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