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https://www.readbyqxmd.com/read/28801462/protein-glutaminylation-is-a-yeast-specific-posttranslational-modification-of-elongation-factor-1a
#1
Thomas Jank, Yury Belyi, Christophe Wirth, Sabine Rospert, Zehan Hu, Jörn Dengjel, Tina Tzivelekidis, Gregers Rom Andersen, Carola Hunte, Andreas Schlosser, Klaus Aktories
Ribosomal translation factors are fundamental for protein synthesis and highly conserved in all kingdoms of life. The essential eukaryotic elongation factor 1A (eEF1A), delivers aminoacyl tRNAs to the A-site of the translating 80S ribosome. Several studies have revealed that eEF1A is posttranslationally modified. Using MS analysis, site-directed mutagenesis, and X-ray structural data analysis of Saccharomyces cerevisiae eEF1A, we identified a posttranslational modification in which the alpha amino group of mono-L-glutamine is covalently linked to the side chain of glutamate 45 in eEF1A...
August 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28801221/the-aminoacyl-trna-synthetases-had-only-a-marginal-role-in-the-origin-of-the-organization-of-the-genetic-code-evidence-in-favor-of-the-coevolution-theory
#2
Massimo Di Giulio
The coevolution theory of the origin of the genetic code suggests that the organization of the genetic code coevolved with the biosynthetic relationships between amino acids. The mechanism that allowed this coevolution was based on tRNA-like molecules on which - this theory - would postulate the biosynthetic transformations between amino acids to have occurred. This mechanism makes a prediction on how the role conducted by the aminoacyl-tRNA synthetases (ARSs), in the origin of the genetic code, should have been...
August 9, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28797100/mapping-the-contact-surfaces-in-the-lamin-a-aimp3-complex-by-hydrogen-deuterium-exchange-ft-icr-mass-spectrometry
#3
Yeqing Tao, Pengfei Fang, Sunghoon Kim, Min Guo, Nicolas L Young, Alan G Marshall
Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear...
2017: PloS One
https://www.readbyqxmd.com/read/28768811/conformational-and-chemical-selection-by-a-trans-acting-editing-domain
#4
Eric M Danhart, Marina Bakhtina, William A Cantara, Alexandra B Kuzmishin, Xiao Ma, Brianne L Sanford, Marija Košutić, Yuki Goto, Hiroaki Suga, Kotaro Nakanishi, Ronald Micura, Mark P Foster, Karin Musier-Forsyth
Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNA(Pro), the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNA(Pro) and mischarged Ala-tRNA(Ala) is unclear...
August 15, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28764927/d-tyrosyl-trna-deacylase-a-new-function
#5
Richard Calendar
d-Aminoacyl-tRNA deacylase (DTD) hydrolyzes d-amino acids mistakenly attached to tRNAs and, thus, has been implicated in perpetuating protein homochirality. Fifty years after the discovery of DTD, it has now been shown that its function extends beyond 'chiral proofreading' because it also eliminates glycine that has been erroneously coupled to tRNA(Ala).
July 29, 2017: Trends in Biochemical Sciences
https://www.readbyqxmd.com/read/28751745/translational-roles-of-the-c75-2-oh-in-an-in-vitro-trna-transcript-at-the-ribosomal-a-p-and-e-sites
#6
Jinfan Wang, Anthony C Forster
Aminoacyl-tRNAs containing a deoxy substitution in the penultimate nucleotide (C75 2'OH → 2'H) have been widely used in translation for incorporation of unnatural amino acids (AAs). However, this supposedly innocuous modification surprisingly increased peptidyl-tRNA(Ala)ugc drop off in biochemical assays of successive incorporations. Here we predict the function of this tRNA 2'OH in the ribosomal A, P and E sites using recent co-crystal structures of ribosomes and tRNA substrates and test these structure-function models by systematic kinetics analyses...
July 27, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28745585/maturation-of-selected-human-mitochondrial-trnas-requires-deadenylation
#7
Sarah F Pearce, Joanna Rorbach, Lindsey Van Haute, Aaron R D'Souza, Pedro Rebelo-Guiomar, Christopher A Powell, Ian Brierley, Andrew E Firth, Michal Minczuk
Human mitochondria contain a genome (mtDNA) that encodes essential subunits of the oxidative phosphorylation system. Expression of mtDNA entails multi-step maturation of precursor RNA. In other systems, the RNA life cycle involves surveillance mechanisms, however, the details of RNA quality control have not been extensively characterised in human mitochondria. Using a mitochondrial ribosome profiling and mitochondrial poly(A)-tail RNA sequencing (MPAT-Seq) assay, we identify the poly(A)-specific exoribonuclease PDE12 as a major factor for the quality control of mitochondrial non-coding RNAs...
July 26, 2017: ELife
https://www.readbyqxmd.com/read/28743072/molecular-modeling-and-molecular-dynamics-simulation-study-of-archaeal-leucyl-trna-synthetase-in-complex-with-different-mischarged-trna-in-editing-conformation
#8
A V Rayevsky, M Sharifi, M A Tukalo
Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA(Leu) was modeled wherever tRNA's acceptor stem was oriented directly into the editing site...
July 18, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28741290/biochemical-characterization-of-lysine-acetylation-of-tyrosyl-trna-synthetase-in-escherichia-coli
#9
Sumana Venkat, Caroline Gregory, Qinglei Gan, Chenguang Fan
Aminoacyl-tRNA synthetases (AARSs) play essential roles in protein synthesis. As a member of the AARS family, the tyrosyl-tRNA synthetase (TyrRS) in Escherichia coli has been shown to be acetylated at multiple lysine residues by proteomic studies. However, these putative acetylation targets have not been biochemically characterized yet. In this study, we applied the genetic code expansion strategy to site-specifically incorporate Nε-acetyl-L-lysine into selected positions of TyrRS for in vitro characterization...
July 24, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28737471/quality-control-by-trans-editing-factor-prevents-global-mistranslation-of-non-protein-amino-acid-%C3%AE-aminobutyrate
#10
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/28723566/genome-wide-rnai-screen-for-fat-regulatory-genes-in-c-%C3%A2-elegans-identifies-a-proteostasis-ampk-axis-critical-for-starvation-survival
#11
Christopher M Webster, Elizabeth C Pino, Christopher E Carr, Lianfeng Wu, Ben Zhou, Lucydalila Cedillo, Michael C Kacergis, Sean P Curran, Alexander A Soukas
Organisms must execute metabolic defenses to survive nutrient deprivation. We performed a genome-wide RNAi screen in Caenorhabditis elegans to identify fat regulatory genes indispensable for starvation resistance. Here, we show that opposing proteostasis pathways are principal determinants of starvation survival. Reduced function of cytoplasmic aminoacyl tRNA synthetases (ARS genes) increases fat mass and extends starvation survival, whereas reduced proteasomal function reduces fat and starvation survival. These opposing pathways converge on AMP-activated protein kinase (AMPK) as the critical effector of starvation defenses...
July 18, 2017: Cell Reports
https://www.readbyqxmd.com/read/28716624/recent-advances-in-mitochondrial-aminoacyl-trna-synthetases-and-disease
#12
REVIEW
Marie Sissler, Ligia Elena González-Serrano, Eric Westhof
Dysfunctions in mitochondria - the powerhouses of the cell - lead to several human pathologies. Because mitochondria integrate nuclear and mitochondrial genetic systems, they are richly intertwined with cellular activities. The nucleus-encoded mitochondrial aminoacyl-tRNA synthetases (mt-aaRSs) are key components of the mitochondrial translation apparatus. Mutations in these enzymes predominantly affect the central nervous system (CNS) but also target other organs. Comparable mutations in mt-aaRSs can lead to vastly diverse diseases, occurring at different stages in life, and within different tissues; this represents a confounding issue...
July 14, 2017: Trends in Molecular Medicine
https://www.readbyqxmd.com/read/28716262/new-genetic-causes-for-complex-hereditary-spastic-paraplegia
#13
Paulo Victor Sgobbi de Souza, Thiago Bortholin, Renan Braido Dias, Marco Antônio Troccoli Chieia, Stênio Burlin, Fernando George Monteiro Naylor, Wladimir Bocca Vieira de Rezende Pinto, Acary Souza Bulle Oliveira
INTRODUCTION: Hereditary Spastic Paraplegia (HSP) represents a complex and heterogeneous group of rare neurodegenerative disorders that share a common clinical feature of weakness and lower limb spasticity that can occur alone or in combination with a constellation of other neurological or systemic signs and symptoms. Although the core clinical feature of weakness and lower limb spasticity is virtually universal, the genetic heterogeneity is almost uncountable with more than 70 genetic forms described so far...
August 15, 2017: Journal of the Neurological Sciences
https://www.readbyqxmd.com/read/28708455/functionality-of-trnas-encoded-in-a-mobile-genetic-element-from-an-acidophilic-bacterium
#14
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/28698277/deep-sea-hydrothermal-vent-viruses-compensate-for-microbial-metabolism-in-virus-host-interactions
#15
Tianliang He, Hongyun Li, Xiaobo Zhang
Viruses are believed to be responsible for the mortality of host organisms. However, some recent investigations reveal that viruses may be essential for host survival. To date, it remains unclear whether viruses are beneficial or harmful to their hosts. To reveal the roles of viruses in the virus-host interactions, viromes and microbiomes of sediment samples from three deep-sea hydrothermal vents were explored in this study. To exclude the influence of exogenous DNAs on viromes, the virus particles were purified with nuclease (DNase I and RNase A) treatments and cesium chloride density gradient centrifugation...
July 11, 2017: MBio
https://www.readbyqxmd.com/read/28688370/whole-transcriptome-rnaseq-analysis-of-oenococcus-oeni-reveals-distinct-intra-specific-expression-patterns-during-malolactic-fermentation-including-genes-involved-in-diacetyl-metabolism
#16
Peter R Sternes, Peter J Costello, Paul J Chambers, Eveline J Bartowsky, Anthony R Borneman
We report the first whole transcriptome RNAseq analysis of the wine-associated lactic acid bacterium Oenococcus oeni using a combination of reference-based mapping and de novo transcript assembly in three distinct strains during malolactic fermentation in Cabernet Sauvignon wine. Two of the strains (AWRIB551 and AWRIB552) exhibited similar transcriptomes relative to the third strain (AWRIB419) which was dissimilar by comparison. Significant intra-specific variation for genes related to glycolysis/gluconeogenesis, purine metabolism, aminoacyl-tRNA biosynthesis, ABC transporters and phosphotransferase systems was observed...
June 28, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28679533/a-hypertension-associated-mitochondrial-dna-mutation-alters-the-tertiary-interaction-and-function-of-trnaleu-uur
#17
Mi Zhou, Meng Wang, Ling Xue, Zhi Lin, Qiufen He, Wenwen Shi, Yaru Chen, Xiaofen Jin, Haiying Li, Pingping Jiang, Min-Xin Guan
Several mitochondrial tRNA mutations have been associated with hypertension, but their pathophysiology remains poorly understood. In this report, we identified a novel homoplasmic 3253T>C mutation in the mitochondrial tRNALeu(UUR) gene in a Han Chinese family with maternally inherited hypertension. The m.3253T>C mutation affected a highly conserved uridine at position 22 at the D-stem of tRNALeu(UUR), introducing a G-C base pairing (G13-C22) at the D-stem and a tertiary base pairing (C22-G46) between the D-stem and the variable loop...
July 5, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28675565/compound-heterozygosity-for-loss-of-function-gars-variants-results-in-a-multisystem-developmental-syndrome-that-includes-severe-growth-retardation
#18
Stephanie N Oprescu, Xenia Chepa-Lotrea, Ryuichi Takase, Gretchen Golas, Thomas C Markello, David R Adams, Camilo Toro, Andrea L Gropman, Ya-Ming Hou, May Christine V Malicdan, William A Gahl, Cynthia J Tifft, Anthony Antonellis
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in myriad dominant and recessive disease phenotypes. Glycyl-tRNA synthetase (GARS) is a bifunctional ARS that charges tRNA(Gly) in the cytoplasm and mitochondria. GARS variants have been associated with dominant Charcot-Marie-Tooth disease but have not been convincingly implicated in recessive phenotypes. Here, we describe a patient from the NIH Undiagnosed Diseases Program with a multisystem, developmental phenotype...
July 4, 2017: Human Mutation
https://www.readbyqxmd.com/read/28660466/identity-elements-of-trna-as-derived-from-information-analysis
#19
Gabriel S Zamudio, Marco V José
The decipherment of the tRNA's operational code, known as the identity problem, requires the location of the sites in the tRNA structure that are involved in their correct recognition by the corresponding aminoacyl-tRNA synthetase. In this work, we determine the identity elements of each tRNA isoacceptor by means of the variation of information measure from information theory. We show that all isoacceptors exhibit sites associated with some bases of the anticodon. These sites form clusters that are scattered along the tRNA structure...
June 28, 2017: Origins of Life and Evolution of the Biosphere
https://www.readbyqxmd.com/read/28650581/deficiency-of-wars2-encoding-mitochondrial-tryptophanyl-trna-synthetase-causes-severe-infantile-onset-leukoencephalopathy
#20
Benjamin E Theisen, Anastasia Rumyantseva, Julie S Cohen, Wendy A Alcaraz, Deepali N Shinde, Sha Tang, Siddarth Srivastava, Jonathan Pevsner, Aleksandra Trifunovic, Ali Fatemi
Pathogenic variants in the mitochondrial aminoacyl tRNA synthetases lead to deficiencies in mitochondrial protein synthesis and are associated with a broad range of clinical presentations usually with early onset and inherited in an autosomal recessive manner. Of the 19 mitochondrial aminoacyl tRNA synthetases, WARS2, encoding mitochondrial tryptophanyl tRNA synthetase, was as of late the only one that had not been associated with disease in humans. A case of a family with pathogenic variants in WARS2 that caused mainly intellectual disability, speech impairment, aggressiveness, and athetosis was recently reported...
June 26, 2017: American Journal of Medical Genetics. Part A
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