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https://www.readbyqxmd.com/read/29927035/swapping-interface-contacts-in-the-homodimeric-trna-guanine-transglycosylase-an-option-for-functional-regulation
#1
Frederik Rainer Ehrmann, Jorna Kalim, Toni Pfaffeneder, Bruno Bernet, Christoph Hohn, Elisabeth Schäfer, Thomas Botzanowski, Sarah Cianférani Cianférani, Andreas Heine, Klaus Reuter, François Diederich, Gerhard Klebe
The enzyme tRNA guanine transglycosylase, a target to fight Shigellosis, recognizes tRNA only as a homodimer and performs full nucleobase exchange at the wobble position. Active-site inhibitors block the enzyme function by competitively replacing tRNA. In solution, the wild-type homodimer dissociates only marginally, whereas mutated variants show substantial monomerization in solution. Surprisingly, one inhibitor transforms of the protein into a twisted state, whereby one monomer unit rotates by approximately 130°...
June 21, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29925958/publisher-correction-ankrd16-prevents-neuron-loss-caused-by-an-editing-defective-trna-synthetase
#2
My-Nuong Vo, Markus Terrey, Jeong Woong Lee, Bappaditya Roy, James J Moresco, Litao Sun, Hongjun Fu, Qi Liu, Thomas G Weber, John R Yates, Kurt Fredrick, Paul Schimmel, Susan L Ackerman
In the Fig. 3b western blot of this Article, 'Myc-AlaRS' in row one should have been 'Myc-AAD Aars', 'AlaRS' in row two should have been 'Aars' and 'ANKRD16' in row four should have been 'Ankrd16'. In Fig. 4f, 'ANKRD16' and 'ANKRD16(3xR)' should have been 'Ankrd16' and 'Ankrd163xR ; and in Fig. 3c the position of the molecular mass markers had shifted. These figures have been corrected online, and see Supplementary Information to the accompanying Amendment for the original figure.
June 20, 2018: Nature
https://www.readbyqxmd.com/read/29925953/codon-specific-translation-reprogramming-promotes-resistance-to-targeted-therapy
#3
Francesca Rapino, Sylvain Delaunay, Florian Rambow, Zhaoli Zhou, Lars Tharun, Pascal De Tullio, Olga Sin, Kateryna Shostak, Sebastian Schmitz, Jolanda Piepers, Bart Ghesquière, Latifa Karim, Benoit Charloteaux, Diane Jamart, Alexandra Florin, Charles Lambert, Andrée Rorive, Guy Jerusalem, Eleonora Leucci, Michael Dewaele, Marc Vooijs, Sebastian A Leidel, Michel Georges, Marianne Voz, Bernard Peers, Reinhard Büttner, Jean-Christophe Marine, Alain Chariot, Pierre Close
Reprogramming of mRNA translation has a key role in cancer development and drug resistance 1 . However, the molecular mechanisms that are involved in this process remain poorly understood. Wobble tRNA modifications are required for specific codon decoding during translation2,3 . Here we show, in humans, that the enzymes that catalyse modifications of wobble uridine 34 (U34 ) tRNA (U34 enzymes) are key players of the protein synthesis rewiring that is induced by the transformation driven by the BRAF V600E oncogene and by resistance to targeted therapy in melanoma...
June 20, 2018: Nature
https://www.readbyqxmd.com/read/29925295/a-case-report-pharmacology-and-resistance-patterns-of-three-generations-of-alk-inhibitors-in-metastatic-inflammatory-myofibroblastic-sarcoma
#4
Barbara M Parker, John V Parker, Anastasios Lymperopoulos, Vijay Konda
Background Little exists currently in research about the mechanisms of resistance of ALK inhibitors in inflammatory myofibroblastic sarcoma. It is known, however, that ALK gene rearrangements are common in inflammatory myofibroblastic tumors, similar to non-small cell lung cancer. In roughly 50% of inflammatory myofibroblastic tumors, gene rearrangement has been found to occur on chromosome 2 at band 2p23. In non-small cell lung cancer, it has been shown that about a third of patients who progress on the first generation ALK inhibitor, crizotinib develops mutations in the ALK kinase domain...
January 1, 2018: Journal of Oncology Pharmacy Practice
https://www.readbyqxmd.com/read/29923643/functional-plasticity-of-antibacterial-endou-toxins
#5
Karolina Michalska, Dinh Quan Nhan, Julia L E Willett, Lucy M Stols, William H Eschenfeldt, Allison M Jones, Josephine Y Nguyen, Sanna Koskiniemi, David A Low, Celia W Goulding, Andrzej Joachimiak, Christopher S Hayes
Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily...
June 20, 2018: Molecular Microbiology
https://www.readbyqxmd.com/read/29921582/rpp29-regulates-histone-h3-3-chromatin-assembly-through-transcriptional-mechanisms
#6
Prashanth Krishna Shastrula, Peder J Lund, Benjamin A Garcia, Susan M Janicki
The histone H3 variant, H3.3, is a highly conserved and dynamic regulator of chromatin organization.  Therefore, fully elucidating its nucleosome incorporation mechanisms is essential to understanding its functions in epigenetic inheritance.  We previously identified the RNase P protein subunit, Rpp29, as a repressor of H3.3 chromatin assembly.  Here, we use a biochemical assay to show that Rpp29 interacts with H3.3 through a sequence element in its own N-terminus, and we identify a novel interaction with histone H2B at an adjacent site...
June 19, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29920503/prognosis-of-interstitial-lung-disease-associated-with-anti-aminoacyl-trna-synthetase-antibodies-look-in-the-middle
#7
Vasilios Tzilas, Argyris Tzouvelekis, Evangelos Bouros, Demosthenes Bouros
No abstract text is available yet for this article.
June 19, 2018: Respiration; International Review of Thoracic Diseases
https://www.readbyqxmd.com/read/29916024/lost-in-translation-evidence-for-protein-synthesis-deficits-in-als-ftd-and-related-neurodegenerative-diseases
#8
Erik M Lehmkuhl, Daniela C Zarnescu
Cells utilize a complex network of proteins to regulate translation, involving post-transcriptional processing of RNA and assembly of the ribosomal unit. Although the complexity provides robust regulation of proteostasis, it also offers several opportunities for translational dysregulation, as has been observed in many neurodegenerative disorders. Defective mRNA localization, mRNA sequatration, inhibited ribogenesis, mutant tRNA synthetases, and translation of hexanucleotide expansions have all been associated with neurodegenerative disease...
2018: Advances in Neurobiology
https://www.readbyqxmd.com/read/29915213/the-genotypic-and-phenotypic-spectrum-of-pars2-related-infantile-onset-encephalopathy
#9
Xiaomeng Yin, Beisha Tang, Xiao Mao, Jinxin Peng, Sheng Zeng, Yaqin Wang, Hong Jiang, Nan Li
Mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are a family of enzymes that play critical roles in protein biosynthesis. Mutations in mt-aaRSs are associated with various diseases. As a member of the mt-aaRS family, PARS2 encoding prolyl-tRNA synthetase 2 was recently shown to be associated with Alpers syndrome and certain infantile-onset neurodegenerative disorders in four patients. Here, we present two patients in a pedigree with early developmental delay, epileptic spasms, delayed myelination combined with cerebellar white matter abnormalities, and progressive cortical atrophy...
June 18, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29915081/error-prone-protein-synthesis-in-parasites-with-the-smallest-eukaryotic-genome
#10
Sergey V Melnikov, Keith D Rivera, Denis Ostapenko, Arthur Makarenko, Neil D Sanscrainte, James J Becnel, Mark J Solomon, Catherine Texier, Darryl J Pappin, Dieter Söll
Microsporidia are parasitic fungi-like organisms that invade the interior of living cells and cause chronic disorders in a broad range of animals, including humans. These pathogens have the tiniest known genomes among eukaryotic species, for which they serve as a model for exploring the phenomenon of genome reduction in obligate intracellular parasites. Here we report a case study to show an apparent effect of overall genome reduction on the primary structure and activity of aminoacyl-tRNA synthetases, indispensable cellular proteins required for protein synthesis...
June 18, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29914801/genomic-characterization-of-methylotrophy-of-oharaeibacter-diazotrophicus-strain-sm30-t
#11
Haoxin Lv, Akio Tani
Oharaeibacter diazotrophicus strain SM30T , isolated from rice rhizosphere, is an aerobic, facultative lanthanide (Ln3+ )-utilizing methylotroph and diazotroph that belongs to the Methylocystaceae family. In this research, the complete genome sequence of strain SM30T was determined, and its methylotrophy modules were characterized. The genome consists of one chromosome and two plasmids, comprising a total of 5,004,097 bp, and the GC content was 71.6 mol%. A total of 4497 CDSs, 67 tRNA, and 9 rRNA were encoded...
June 15, 2018: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/29914378/the-mitochondrial-genomes-of-sarcoptiform-mites-are-any-transfer-rna-genes-really-lost
#12
Xiao-Feng Xue, Wei Deng, Shao-Xuan Qu, Xiao-Yue Hong, Renfu Shao
BACKGROUND: Mitochondrial (mt) genomes of animals typically contain 37 genes for 13 proteins, two ribosomal RNA (rRNA) genes and 22 transfer RNA (tRNA) genes. In sarcoptiform mites, the entire set of mt tRNA genes is present in Aleuroglyphus ovatus, Caloglyphus berlesei, Dermatophagoides farinae, D. pteronyssinus, Histiostoma blomquisti and Psoroptes cuniculi. Loss of 16 mt tRNA genes, however, was reported in Steganacarus magnus; loss of 2-3 tRNA genes was reported in Tyrophagus longior, T...
June 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29910077/endogenous-stochastic-decoding-of-the-cug-codon-by-competing-ser-and-leu-trnas-in-ascoidea-asiatica
#13
Stefanie Mühlhausen, Hans Dieter Schmitt, Kuan-Ting Pan, Uwe Plessmann, Henning Urlaub, Laurence D Hurst, Martin Kollmar
Although the "universal" genetic code is now known not to be universal, and stop codons can have multiple meanings, one regularity remains, namely that for a given sense codon there is a unique translation. Examining CUG usage in yeasts that have transferred CUG away from leucine, we here report the first example of dual coding: Ascoidea asiatica stochastically encodes CUG as both serine and leucine in approximately equal proportions. This is deleterious, as evidenced by CUG codons being rare, never at conserved serine or leucine residues, and predominantly in lowly expressed genes...
June 9, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29908293/reversible-rna-modification-n-1-methyladenosine-m-1-a-in-mrna-and-trna
#14
REVIEW
Chi Zhang, Guifang Jia
More than 100 modifications have been found in RNA. Analogous to epigenetic DNA methylation, epitranscriptomic modifications can be written, read, and erased by a complex network of proteins. Apart from N6 -methyladenosine (m6 A), N1 -methyladenosine (m1 A) has been found as a reversible modification in tRNA and mRNA. m1 A occurs at positions 9, 14, and 58 of tRNA, with m1 A58 being critical for tRNA stability. Other than the hundreds of m1 A sites in mRNA and long non-coding RNA transcripts, transcriptome-wide mapping of m1 A also identifies > 20 m1 A sites in mitochondrial genes...
June 13, 2018: Genomics, Proteomics & Bioinformatics
https://www.readbyqxmd.com/read/29908270/complete-mitochondrial-genome-of-parasesarma-affine-brachyura-sesarmidae-gene-rearrangements-in-sesarmidae-and-phylogenetic-analysis-of-the-brachyura
#15
Zhengfei Wang, Ziqian Wang, Xuejia Shi, Qiong Wu, Yitao Tao, Huayun Guo, Chenyao Ji, Yuze Bai
In this study, the complete mitochondrial DNA (mtDNA) sequence of the crab Parasesarma affine is determined, characterized and compared with other decapod crustaceans. The P. affine mitochondrial genome (mitogenome) is 15,638 bp in size, and contains 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes and a control region (CR). Then, 23 of the 37 genes are encoded by the heavy (+) strand while 14 are encoded by the light (-) strand. All PCGs are initiated by ATN codons and 4 of the 13 PCGs harbored the incomplete termination codon by T or TA...
June 13, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29908208/nucleic-acids-binding-strategies-of-small-molecules-lessons-from-alkaloids
#16
Anirban Basu, Gopinatha Suresh Kumar
BACKGROUND: Nucleic acids are now important targets for therapeutic intervention. Alkaloids are an important class of molecules that have myriad therapeutic utility. Isoquinoline and benzophenanthridine alkaloids exhibit multiple pharmacological activities which are often related to their strong nucleic acid binding abilities. Therefore, a review of their interaction aspects with varying nucleic acid structures is essential for rational design and development as therapeutic agents. SCOPE OF THE REVIEW: This work reviews the interaction of various therapeutically important isoquinoline and benzophenanthridine alkaloids with nucleic acids...
June 13, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29906204/context-specific-action-of-ribosomal-antibiotics
#17
Nora Vázquez-Laslop, Alexander S Mankin
The ribosome is a major antibiotic target. Many types of inhibitors can stop cells from growing by binding at functional centers of the ribosome and interfering with its ability to synthesize proteins. These antibiotics were usually viewed as general protein synthesis inhibitors, which indiscriminately stop translation at every codon of every mRNA, preventing the ribosome from making any protein. However, at each step of the translation cycle, the ribosome interacts with multiple ligands (mRNAs, tRNA substrates, translation factors, etc...
June 15, 2018: Annual Review of Microbiology
https://www.readbyqxmd.com/read/29904057/characterization-and-phylogenetic-analysis-of-the-complete-mitochondrial-genome-of-the-medicinal-fungus-laetiporus-sulphureus
#18
Qiang Li, Mei Yang, Cheng Chen, Chuan Xiong, Xin Jin, Zhigang Pu, Wenli Huang
The medicinal fungus Laetiporus sulphureus is widely distributed worldwide. To screen for molecular markers potentially useful for phylogenetic analyses of this species and related species, the mitochondrial genome of L. sulphureus was sequenced and assembled. The complete circular mitochondrial genome was 101,111 bp long, and contained 38 protein-coding genes (PCGs), 2 rRNA genes, and 25 tRNA genes. Our BLAST search aligned about 6.1 kb between the mitochondrial and nuclear genomes of L. sulphureus, indicative of possible gene transfer events...
June 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29901762/3-end-labeling-of-nucleic-acids-by-a-polymerase-ribozyme
#19
Biswajit Samanta, David P Horning, Gerald F Joyce
A polymerase ribozyme can be used to label the 3' end of RNA or DNA molecules by incorporating a variety of functionalized nucleotide analogs. Guided by a complementary template, the ribozyme adds a single nucleotide that may contain a fluorophore, biotin, azide or alkyne moiety, thus enabling the detection and/or capture of selectively labeled materials. Employing a variety of commercially available nucleotide analogs, efficient labeling was demonstrated for model RNAs and DNAs, human microRNAs and natural tRNA...
June 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29900970/the-association-of-anti-aminoacyl-transfer-ribonucleic-acid-synthetase-antibodies-in-patients-with-rheumatoid-arthritis-and-interstitial-lung-disease
#20
Masakazu Matsushita, Naoto Tamura, Michihiro Ogasawara, Kurisu Tada, Ken Yamaji, Yoshinari Takasaki
Objectives: This study aims to analyze the distribution and clinicopathological characteristics of anti-aminoacyl-transfer ribonucleic acid (tRNA) synthetase (ARS) antibodies in rheumatoid arthritis patients. Patients and methods: We retrospectively studied the anti-ARS antibody levels in 228 RA patients' (44 males, 184 females; mean age 62.9±14.0 years; range 23 to 88 years) sera from their medical charts. We determined the association with anti-cyclic citrullinated peptide antibody levels, interstitial lung disease (ILD), rheumatoid factor, and methotrexate or biological disease modifying antirheumatic drug treatments...
March 2018: Archives of Rheumatology
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