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Jonathan Rips, Rebecca Meyer-Schuman, Oded Breuer, Reuven Tsabari, Avraham Shaag, Shoshana Revel-Vilk, Shimon Reif, Orly Elpeleg, Anthony Antonellis, Tamar Harel
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes responsible for charging tRNA with cognate amino acids during protein translation. Non-canonical functions are increasingly recognized, and include transcription and translation control and extracellular signaling. Monoallelic mutations in genes encoding several ARSs have been identified in axonal Charcot-Marie-Tooth (CMT2) disease, whereas biallelic mutations in ARS loci have been associated with multi-tissue syndromes, variably involving the central nervous system, lung, and liver...
April 12, 2018: European Journal of Medical Genetics
Wei Rong, Xindong Wang, Xifeng Wang, Sebastien Massart, Zengyan Zhang
Wheat ( Tritium aestivum L.) production is essential for global food security. Infection of barley yellow dwarf virus-GAV (BYDV-GAV) results in wheat showing leaf yellowing and plant dwarfism symptom. To explore the molecular and ultrastructural mechanisms underlying yellow dwarf symptom formation in BYDV-GAV-infected wheat, we investigated the chloroplast ultrastructure via transmission electron microscopy (TEM), examined the contents of the virus, H₂O₂, and chlorophyll in Zhong8601, and studied the comparative transcriptome through microarray analyses in the susceptible wheat line Zhong8601 after virus infection...
April 13, 2018: International Journal of Molecular Sciences
Rebecca E Steiner, Michael Ibba
No abstract text is available yet for this article.
April 13, 2018: Biochemistry
Adeline Pichard-Kostuch, Wenhua Zhang, Dominique Liger, Marie-Claire Daugeron, Juliette Letoquart, Ines Li de la Sierra-Gallay, Patrick Forterre, Bruno Collinet, Herman van Tilbeurgh, Tamara Basta
N6-threonyl-carbamoyl adenosine (t6A) is a universal tRNA modification found at position 37, next to the anticodon, in almost all tRNAs decoding ANN codons (where N = A, U, G or C). t6A stabilizes the codon-anticodon interaction and hence promotes translation fidelity. The first step of the biosynthesis of t6A, the production of threonyl-carbamoyl adenylate (TC-AMP), is catalyzed by the Sua5/TsaC family of enzymes. While TsaC is a single domain protein, Sua5 enzymes are composed of the TsaC-like domain, a linker and an extra domain called SUA5 of unknown function...
April 12, 2018: RNA
Yusuke Terui, Taketo Yoshida, Akihiko Sakamoto, Daisuke Saito, Tairo Oshima, Masahito Kawazoe, Shigeyuki Yokoyama, Kazuei Igarashi, Keiko Kashiwagi
Depurination is accelerated by heat and reactive oxygen species under physiological conditions. We previously reported that polyamines are involved in mitigation of heat shock and oxidative stresses through stimulation of the synthesis of heat shock and antioxidant proteins. This time, we investigated whether polyamines are directly involved in protecting nucleic acids from thermal depurination induced by high temperature. The suppressing efficiencies of depurination of DNA by spermine, caldopentamine and caldohexamine in the presence of 1 mM Mg2+ , were approximately 50%, 60% and 80%, respectively...
April 9, 2018: International Journal of Biochemistry & Cell Biology
Veronika Boczonadi, Kathrin Meyer, Humberto Gonczarowska-Jorge, Helen Griffin, Andreas Roos, Marina Bartsakoulia, Boglarka Bansagi, Giulia Ricci, Fanni Palinkas, René P Zahedi, Francesco Bruni, Brian Kaspar, Hanns Lochmüller, Kym M Boycott, Juliane S Müller, Rita Horvath
The nuclear-encoded glycyl-tRNA synthetase gene (GARS) is essential for protein translation in both cytoplasm and mitochondria. In contrast, different genes encode the mitochondrial and cytosolic forms of most other tRNA synthetases. Dominant GARS mutations were described in inherited neuropathies, while recessive mutations cause severe childhood-onset disorders affecting skeletal muscle and heart. The downstream events explaining tissue-specific phenotype-genotype relations remained unclear. We investigated the mitochondrial function of GARS in human cell lines and in the GarsC210R mouse model...
April 10, 2018: Human Molecular Genetics
Yong Wang, Qi-Yu Zeng, Wen-Qiang Zheng, Quan-Quan Ji, Xiao-Long Zhou, En-Duo Wang
Six pathogenic mutations have been reported in human mitochondrial tRNAThr (hmtRNAThr); however, the pathogenic molecular mechanism remains unclear. Previously, we established an activity assay system for human mitochondrial threonyl-tRNA synthetase (hmThrRS). In the present study, we surveyed the structural and enzymatic effects of pathogenic mutations in hmtRNAThr and then focused on m.15915 G > A (G30A) and m.15923A > G (A38G). The harmful evolutionary gain of non-Watson-Crick base pair A29/C41 caused hmtRNAThr to be highly susceptible to mutations disrupting the G30-C40 base pair in various ways; for example, structural integrity maintenance, modification and aminoacylation of tRNAThr, and editing mischarged tRNAThr...
April 10, 2018: Nucleic Acids Research
Jialu Yu, Jianmei An, Yue Li, Christopher B Boyko
The complete mitochondrial genome sequence of the holoparasitic isopod Gyge ovalis (Shiino, 1939) has been determined. The mitogenome is 14,268 bp in length and contains 34 genes: 13 protein-coding genes, two ribosomal RNA, 19 tRNA and a control region. Three tRNA genes (trnE, trnI and trnS1) are missing. Most of the tRNA genes show secondary structures which derive from the usual cloverleaf pattern except for trnC which is characterised by the loss of the DHU-arm. Compared to the isopod ground pattern and Eurydice pulchra Leach, 1815 (suborder Cymothoida Wägele, 1989), the genome of G...
April 11, 2018: Systematic Parasitology
Dalia Halawani, Valentin Gogonea, Joseph A DiDonato, Vitaliy Pipich, Peng Yao, Arnab China, Celalettin Topbas, Kommireddy Vasu, Abul Arif, Stanley L Hazen, Paul L Fox
Aminoacyl-tRNA synthetases are ubiquitous, evolutionarily conserved enzymes catalyzing the conjugation of amino acids onto cognate tRNAs. During eukaryotic evolution, tRNA synthetases have been the targets of persistent structural modifications. These modifications can be additive, as in the evolutionary acquisition of noncatalytic domains, or subtractive, as in the generation of truncated variants through regulated mechanisms such as proteolytic processing, alternative splicing, or coding region polyadenylation...
April 11, 2018: Journal of Biological Chemistry
Xia Liu, Yuan Li, Hongyuan Yang, Boyang Zhou
The complete chloroplast (cp) genome of Talinum paniculatum (Caryophyllale), a source of pharmaceutical efficacy similar to ginseng, and a widely distributed and planted edible vegetable, were sequenced and analyzed. The cp genome size of T. paniculatum is 156,929 bp, with a pair of inverted repeats (IRs) of 25,751 bp separated by a large single copy (LSC) region of 86,898 bp and a small single copy (SSC) region of 18,529 bp. The genome contains 83 protein-coding genes, 37 transfer RNA (tRNA) genes, eight ribosomal RNA (rRNA) genes and four pseudogenes...
April 9, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Nicola Guzzi, Maciej Cieśla, Phuong Cao Thi Ngoc, Stefan Lang, Sonali Arora, Marios Dimitriou, Kristyna Pimková, Mikael N E Sommarin, Roberto Munita, Michal Lubas, Yiting Lim, Kazuki Okuyama, Shamit Soneji, Göran Karlsson, Jenny Hansson, Göran Jönsson, Anders H Lund, Mikael Sigvardsson, Eva Hellström-Lindberg, Andrew C Hsieh, Cristian Bellodi
Pseudouridylation (Ψ) is the most abundant and widespread type of RNA epigenetic modification in living organisms; however, the biological role of Ψ remains poorly understood. Here, we show that a Ψ-driven posttranscriptional program steers translation control to impact stem cell commitment during early embryogenesis. Mechanistically, the Ψ "writer" PUS7 modifies and activates a novel network of tRNA-derived small fragments (tRFs) targeting the translation initiation complex. PUS7 inactivation in embryonic stem cells impairs tRF-mediated translation regulation, leading to increased protein biosynthesis and defective germ layer specification...
April 4, 2018: Cell
Xili Liang, Chao Sun, Bosheng Chen, Kaiqian Du, Ting Yu, Vijitra Luang-In, Xingmeng Lu, Yongqi Shao
Insects constitute the most abundant and diverse animal class and act as hosts to an extraordinary variety of symbiotic microorganisms. These microbes living inside the insects play critical roles in host biology and are also valuable bioresources. Enterococcus mundtii EMB156, isolated from the larval gut (gut pH >10) of the model organism Bombyx mori (Lepidoptera: Bombycidae), efficiently produces lactic acid, an important metabolite for industrial production of bioplastic materials. E. mundtii EMB156 grows well under alkaline conditions and stably converts various carbon sources into lactic acid, offering advantages in downstream fermentative processes...
April 7, 2018: Applied Microbiology and Biotechnology
Vijaya Bharathi Srinivasan, Govindan Rajamohan
In this study, we present the genome sequence of Serratia marcescens SM03, recovered from a human gut in India. The final assembly consists of 26 scaffolds (4620 coding DNA sequences, 5.08 Mb, 59.6% G + C ratio) and 79 tRNA genes. Analysis identified novel genes associated with lactose utilization, virulence, P-loop GTPases involved in urease production, CFA/I fimbriae apparatus and Yersinia - type CRISPR proteins. Antibiotic susceptibility testing indicated drug tolerant phenotype and inhibition assays demonstrated involvement of extrusion in resistance...
April 5, 2018: Genomics
Lubica Supekova, Claudio Zambaldo, Seihyun Choi, Reyna Lim, Xiaozhou Luo, Stephanie A Kazane, Travis S Young, Peter G Schultz
The noncanonical amino acid p-azidomethyl-l-phenylalanine can be genetically incorporated into proteins in bacteria, and has been used both as a spectroscopic probe and for the selective modification of proteins by alkynes using click chemistry. Here we report identification of Escherichia coli tyrosyl tRNA synthetase mutants that allow incorporation of p-azidomethyl-l-phenylalanine into proteins in yeast. When expressed together with the cognate E. coli tRNACUA Tyr , the new mutant tyrosyl tRNA synthetases directed robust incorporation of p-azidomethyl-l-phenylalanine into a model protein, human superoxide dismutase, in response to the UAG amber nonsense codon...
March 22, 2018: Bioorganic & Medicinal Chemistry Letters
Clarence W Chan, Benjamin R Kiesel, Alfonso Mondragón
RNase P catalyzes the removal of 5' leaders of tRNA precursors and its central catalytic RNA subunit is highly conserved across all domains of life. In eukaryotes, RNase P and RNase MRP, a closely related ribonucleoprotein enzyme, share several of the same protein subunits, contain a similar catalytic RNA core, and exhibit structural features that do not exist in their bacterial or archaeal counterparts. A unique feature of eukaryotic RNase P/MRP is the presence of two relatively long and unpaired internal loops within the P3 region of their RNA subunit bound by a heterodimeric protein complex, Rpp20/Rpp25...
April 3, 2018: Journal of Molecular Biology
Elena Cardaioli, Andrea Mignarri, Teresa Anna Cantisani, Alessandro Malandrini, Claudia Nesti, Anna Rubegni, Niccola Funel, Antonio Federico, Filippo Maria Santorelli, Maria Teresa Dotti
We sequenced the mitochondrial genome from a 40-year-old woman with myoclonus epilepsy, retinitis pigmentosa, leukoencephalopathy and cerebral calcifications. Histological and biochemical features of mitochondrial respiratory chain dysfunction were present. Direct sequencing showed a novel heteroplasmic mutation at nucleotide 5513 in the MT-TW gene that encodes tRNATrp . Restriction Fragment Length Polymorphism analysis confirmed that about 80% of muscle mtDNA harboured the mutation while it was present in minor percentages in mtDNA from other tissues...
April 3, 2018: Biochemical and Biophysical Research Communications
Kristoffer Skovbo Winther, Mohammad Roghanian, Kenn Gerdes
RelA/SpoT homologs (RSHs) are ubiquitous bacterial enzymes that synthesize and hydrolyze (p)ppGpp in response to environmental challenges. Bacteria cannot survive in hosts and produce infection without activating the (p)ppGpp-mediated stringent response, but it is not yet understood how the enzymatic activities of RSHs are controlled. Using UV crosslinking and deep sequencing, we show that Escherichia coli RelA ((p)ppGpp synthetase I) interacts with uncharged tRNA without being activated. Amino acid starvation leads to loading of cognate tRNA⋅RelA complexes at vacant ribosomal A-sites...
April 5, 2018: Molecular Cell
Chew Chieng Yeo
GCN5-related N-acetyltransferase (GNAT) is a huge superfamily of proteins spanning the prokaryotic and eukaryotic domains of life. GNAT proteins usually transfer an acetyl group from acetyl-CoA to a wide variety of substrates ranging from aminoglycoside antibiotics to large macromolecules. Type II toxin-antitoxin (TA) modules are typically bicistronic and widespread in bacterial and archael genomes with diverse cellular functions. Recently, a novel family of type II TA toxins was described which presents a GNAT-fold and functions by acetylating charged tRNA thereby precluding translation...
April 6, 2018: Molecular Microbiology
P Chanphai, H A Tajmir-Riahi
tRNA binding efficacy to folic acid-PAMAM nanoparticles was determined, using multiple spectroscopic methods, thermodynamic analysis and transmission electron microscopy (TEM). The structural analysis showed tRNA binds folic acid-PAMAM through H-bonding, hydrophobic and van der Waals contacts. As PAMAM size increases the binding efficacy and the stability of tRNA conjugates are enhanced. TEM analysis showed major tRNA morphological changes, upon folic acid-PAMAM complexation. Folic acid-PAMAM nanoparticles can transport tRNA in vitro...
April 2, 2018: International Journal of Biological Macromolecules
David Alvarez-Ponce, María Torres-Sánchez, Felix Feyertag, Asmita Kulkarni, Taylen Nappi
DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes three active Dnmts (Dnmt1, Dnmt3a and Dnmt3b), the tRNA methyltransferase Dnmt2, and the regulatory protein Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates...
2018: PloS One
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