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tRNA Synthetase

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https://www.readbyqxmd.com/read/28924459/genetic-code-optimization-for-cotranslational-protein-folding-codon-directional-asymmetry-correlates-with-antiparallel-betasheets-trna-synthetase-classes
#1
Hervé Seligmann, Ganesh Warthi
A new codon property, codon directional asymmetry in nucleotide content (CDA), reveals a biologically meaningful genetic code dimension: palindromic codons (first and last nucleotides identical, codon structure XZX) are symmetric (CDA = 0), codons with structures ZXX/XXZ are 5'/3' asymmetric (CDA = - 1/1; CDA = - 0.5/0.5 if Z and X are both purines or both pyrimidines, assigning negative/positive (-/+) signs is an arbitrary convention). Negative/positive CDAs associate with (a) Fujimoto's tetrahedral codon stereo-table; (b) tRNA synthetase class I/II (aminoacylate the 2'/3' hydroxyl group of the tRNA's last ribose, respectively); and (c) high/low antiparallel (not parallel) betasheet conformation parameters...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28918092/growth-rate-dependent-regulation-of-trna-level-and-charging-in-bacillus-licheniformis
#2
Iolanda Ferro, Klaus Liebeton, Zoya Ignatova
Cellular growth crucially depends on protein synthesis and the abundance of translational components. Among them, aminoacyl-tRNAs play a central role in biosynthesis and shape the kinetics of mRNA translation, thus influencing protein production. Here, we used microarray-based approaches to determine the charging levels and tRNA abundance of Bacillus licheniformis. We observed an interesting cross-talk among tRNA expression, charging pattern and growth rate. For a large subset of tRNAs, we found a co-regulated and augmented expression at high growth rate...
September 13, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28912467/highly-chromophoric-cy5-methionine-for-n-terminal-fluorescent-tagging-of-proteins-in-eukaryotic-translation-systems
#3
Jung Min Kim, Baik Lin Seong
Despite significant advances on fluorescent labeling of target proteins to study their structural dynamics and function, there has been need for labeling with high quantum yield ensuring high sensitivity and selectivity without sacrificing the biological function of the protein. Here as a technical advancement over non-canonical amino acid incorporation, we provided a conceptual design of the N-terminal fluorescent tagging of proteins. Cy5-labeled methionine (Cy5-Met) was chemically synthesized, and then the purified Cy5-Met was coupled with synthetic human initiator tRNA by methionine tRNA synthetase...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28910573/an-alternative-conformation-of-human-trprs-suggests-a-role-of-zinc-in-activating-non-enzymatic-function
#4
Xiaoling Xu, Huihao Zhou, Quansheng Zhou, Fei Hong, My-Nuong Vo, Wanqiang Niu, Zhiguo Wang, Xiaolin Xiong, Kanaha Nakamura, Keisuke Wakasugi, Paul Schimmel, Xiang-Lei Yang
Tryptophanyl-tRNA synthetase (TrpRS) in vertebrates contains a N-terminal extension in front of the catalytic core. Proteolytic removal of the N-terminal 93 amino acids gives rise to T2-TrpRS, which has potent anti-angiogenic activity mediated through its extracellular interaction with VE-cadherin. Zinc has been shown to have anti-angiogenic effects and can bind to human TrpRS. However, the connection between zinc and the anti-angiogenic function of TrpRS has not been explored. Here we report that zinc binding can induce structural relaxation in human TrpRS to facilitate the proteolytic generation of a T2-TrpRS-like fragment...
September 14, 2017: RNA Biology
https://www.readbyqxmd.com/read/28905880/mutations-in-rars-cause-a-hypomyelination-disorder-akin-to-pelizaeus-merzbacher-disease
#5
Michael Nafisinia, Nara Sobreira, Lisa Riley, Wendy Gold, Birgit Uhlenberg, Claudia Weiß, Corinne Boehm, Kristina Prelog, Robert Ouvrier, John Christodoulou
Pelizaeus-Merzbacher disease (PMD) is a rare Mendelian disorder characterised by central nervous system hypomyelination. PMD typically manifests in infancy or early childhood and is caused by mutations in proteolipid protein-1 (PLP1). However, variants in several other genes including gap junction protein gamma 2 (GJC2) can also cause a similar phenotype and are referred to PMD-like disease (PMLD). Whole-exome sequencing in two siblings presenting with clinical symptoms of PMD revealed a homozygous variant in the arginyl-tRNA synthetase (RARS) gene: NM_002887...
October 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28905057/a-water-mediated-and-substrate-assisted-aminoacylation-mechanism-in-the-discriminating-aminoacyl-trna-synthetase-glnrs-and-non-discriminating-glurs
#6
Mohamed M Aboelnga, John J Hayward, James W Gauld
Glutaminyl-tRNA synthetase (GlnRS) catalyzes the aminoacylation of glutamine to the corresponding tRNA(Gln). However, most bacteria and all archaea lack GlnRS and thus an indirect noncanonical aminoacylation is required. With the assistance of a non-discriminating version of Glutamyl-tRNA synthetases (ND-GluRS) the tRNA(Gln) is misaminoacylated by glutamate. In this study, we have computationally investigated the aminoacylation mechanism in GlnRS and ND-GluRS employing Molecular Dynamics (MD) simulations, Quantum Mechanics (QM) cluster and Quantum Mechanics/Molecular Mechanics (QM/MM) calculations...
September 14, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28902227/a-genetically-encoded-cyclobutene-probe-for-labelling-of-live-cells
#7
K Liu, B Enns, B Evans, N Wang, X Shang, W Sittiwong, P H Dussault, J Guo
We have identified an aminoacyl-tRNA synthetase/tRNA pair for the efficient and site-specific incorporation of a cyclobutene-containing amino acid into proteins in response to an amber nonsense codon. Fast and fluorescent labeling of purified proteins and intact proteins in live cells was demonstrated using the inverse electron demand Diels-Alder reaction with a tetrazine.
September 13, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28887846/mutations-in-kars-cause-early-onset-hearing-loss-and-leukoencepha-lopathy-potential-pathogenic-mechanism
#8
Xiao-Long Zhou, Long-Xia He, Li-Jia Yu, Yong Wang, Xi-Jin Wang, En-Duo Wang, Tao Yang
Leukoencephalopathies are a broad class of common neurologic deterioration for which the etiology remain unsolved in many cases. In a Chinese Han family segregated with sensorineural hearing loss and leukoencephalopathy, candidate pathogenic variants were identified by targeted next-generation sequencing of 144 genes associated with deafness and 108 genes with leukoencephalopathy. Novel compound heterozygous mutations p.R477H and p.P505S were identified in KARS, which encodes lysyl-tRNA synthetase (LysRS), as the only candidate causative variants...
September 8, 2017: Human Mutation
https://www.readbyqxmd.com/read/28882589/visualization-of-leucyl-trna-synthetase-in-lysosome-depending-on-leucine-sensor
#9
Hyosun Choi, Jung Bae Son, Jooyoun Kang, Jiwoong Kwon, Jong Hyun Kim, Minkyo Jung, Seong Keun Kim, Sunghoon Kim, Ji Young Mun
Leucyl-tRNA synthetase (LRS) plays major roles in providing leucine-tRNA and activating mechanistic target of rapamycin complex 1 (mTORC1) through intracellular leucine sensing. mTORC1 activated by amino acids affects the influence on physiology functions including cell proliferation, protein synthesis and autophagy in various organisms. Biochemical results demonstrating leucine sensing have been published, but visual results are lacking. Therefore, we observed the location of LRS with and without leucine using stimulated emission depletion (STED) microscopy one of the super-resolution microscopy and transmission electron microscopy (TEM)...
September 4, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28875178/genetic-validation-of-leishmania-donovani-lysyl-trna-synthetase-shows-that-it-is-indispensable-for-parasite-growth-and-infectivity
#10
Sanya Chadha, N Arjunreddy Mallampudi, Debendra K Mohapatra, Rentala Madhubala
Leishmania donovani is a protozoan parasite that causes visceral leishmaniasis. Increasing resistance and severe side effects of existing drugs have led to the need to identify new chemotherapeutic targets. Aminoacyl-tRNA synthetases (aaRSs) are ubiquitous and are required for protein synthesis. aaRSs are known drug targets for bacterial and fungal pathogens. Here, we have characterized and evaluated the essentiality of L. donovani lysyl-tRNA synthetase (LdLysRS). Two different coding sequences for lysyl-tRNA synthetases are annotated in the Leishmania genome database...
July 2017: MSphere
https://www.readbyqxmd.com/read/28871595/role-of-immune-microenvironment-in-gastrointestinal-stromal-tumors
#11
Andrew M Blakely, Andres Matoso, Pallavi A Patil, Ross Taliano, Jason T Machan, Thomas J Miner, Kara A Lombardo, Murray B Resnick, Li-Juan Wang
INTRODUCTION: The immune microenvironment is a prognostic factor for various malignancies. The significance of key players of this immune microenvironment including tumor-infiltrating lymphocytes and expression of programmed death-ligand 1 (PD-L1), indoleamine-2,3-dioxygenase (IDO), and tryptophanyl-tRNA synthetase (WARS) in gastrointestinal stromal tumors (GISTs) is largely unknown. METHODS: Tissue microarrays were constructed from pathology files, 1996-2016. Immunohistochemistry for PD-L1, IDO, WARS was correlated with tumor size, mitoses, and outcomes...
September 4, 2017: Histopathology
https://www.readbyqxmd.com/read/28867614/targeting-prolyl-trna-synthetase-to-accelerate-drug-discovery-against-malaria-leishmaniasis-toxoplasmosis-cryptosporidiosis-and-coccidiosis
#12
Vitul Jain, Manickam Yogavel, Haruhisa Kikuchi, Yoshiteru Oshima, Norimitsu Hariguchi, Makoto Matsumoto, Preeti Goel, Bastien Touquet, Rajiv S Jumani, Fabienne Tacchini-Cottier, Karl Harlos, Christopher D Huston, Mohamed-Ali Hakimi, Amit Sharma
Developing anti-parasitic lead compounds that act on key vulnerabilities are necessary for new anti-infectives. Malaria, leishmaniasis, toxoplasmosis, cryptosporidiosis and coccidiosis together kill >500,000 humans annually. Their causative parasites Plasmodium, Leishmania, Toxoplasma, Cryptosporidium and Eimeria display high conservation in many housekeeping genes, suggesting that these parasites can be attacked by targeting invariant essential proteins. Here, we describe selective and potent inhibition of prolyl-tRNA synthetases (PRSs) from the above parasites using a series of quinazolinone-scaffold compounds...
August 24, 2017: Structure
https://www.readbyqxmd.com/read/28860303/conservation-of-trna-mimicry-in-the-5-untranslated-region-of-distinct-hiv-1-subtypes
#13
Roopa Comandur, Erik D Olson, Karin Musier-Forsyth
Human tRNA(Lys3) serves as the primer for reverse transcription in human immunodeficiency virus type-1 (HIV-1) and anneals to the complementary primer binding site (PBS) in the genome. All tRNA(Lys) isoacceptors interact with human lysyl-tRNA synthetase (hLysRS) and are selectively packaged into virions. tRNA(Lys3) must be released from hLysRS in order to anneal to the PBS and this process is proposed to be facilitated by the interaction of hLysRS with a tRNA-like element (TLE) first identified in the HIV-1 5'-untranslated region (5'-UTR) of the subtype B NL4-3 virus...
August 31, 2017: RNA
https://www.readbyqxmd.com/read/28853922/origin-and-evolution-of-the-universal-genetic-code
#14
Eugene V Koonin, Artem S Novozhilov
The standard genetic code (SGC) is virtually universal among extant life forms. Although many deviations from the universal code exist, particularly in organelles and prokaryotes with small genomes, they are limited in scope and obviously secondary. The universality of the code likely results from the combination of a frozen accident, i.e., the deleterious effect of codon reassignment in the SGC, and the inhibitory effect of changes in the code on horizontal gene transfer. The structure of the SGC is nonrandom and ensures high robustness of the code to mutational and translational errors...
August 30, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28837402/trna-pyl-structure-function-and-applications
#15
Jeffery M Tharp, Andreas Ehnbom, Wenshe R Liu
Pyrrolysine is the 22(nd) proteinogenic amino acid encoded into proteins in response to amber (TAG) codons in a small number of archaea and bacteria. The incorporation of pyrrolysine is facilitated by a specialized aminoacyl-tRNA synthetase (PylRS) and its cognate tRNA (tRNA(Pyl)). The secondary structure of tRNA(Pyl) contains a number of unique features not found in canonical tRNAs. Numerous studies have demonstrated that the PylRS/tRNA(Pyl) pair from archaea is orthogonal in E. coli and eukaryotic hosts, which has led to the widespread use of this pair for the genetic incorporation of non-canonical amino acids...
August 24, 2017: RNA Biology
https://www.readbyqxmd.com/read/28836574/translational-fidelity-and-mistranslation-in-the-cellular-response-to-stress
#16
REVIEW
Kyle Mohler, Michael Ibba
Faithful translation of mRNA into the corresponding polypeptide is a complex multistep process, requiring accurate amino acid selection, transfer RNA (tRNA) charging and mRNA decoding on the ribosome. Key players in this process are aminoacyl-tRNA synthetases (aaRSs), which not only catalyse the attachment of cognate amino acids to their respective tRNAs, but also selectively hydrolyse incorrectly activated non-cognate amino acids and/or misaminoacylated tRNAs. This aaRS proofreading provides quality control checkpoints that exclude non-cognate amino acids during translation, and in so doing helps to prevent the formation of an aberrant proteome...
August 24, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28835631/neuropilin-1-sequestration-by-neuropathogenic-mutant-glycyl-trna-synthetase-is-permissive-to-vascular-homeostasis
#17
James N Sleigh, Adriana Gómez-Martín, Na Wei, Ge Bai, Xiang-Lei Yang, Giampietro Schiavo
The mechanism by which dominantly inherited mutations in the housekeeping gene GARS, which encodes glycyl-tRNA synthetase (GlyRS), mediate selective peripheral nerve toxicity resulting in Charcot-Marie-Tooth disease type 2D (CMT2D) is still largely unresolved. The transmembrane receptor protein neuropilin 1 (Nrp1) was recently identified as an aberrant extracellular binding partner of mutant GlyRS. Formation of the Nrp1/mutant GlyRS complex antagonises Nrp1 interaction with one of its main natural ligands, vascular endothelial growth factor-A (VEGF-A), contributing to neurodegeneration...
August 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28828732/coding-of-class-i-and-ii-aminoacyl-trna-synthetases
#18
Charles W Carter
The aminoacyl-tRNA synthetases and their cognate transfer RNAs translate the universal genetic code. The twenty canonical amino acids are sufficiently diverse to create a selective advantage for dividing amino acid activation between two distinct, apparently unrelated superfamilies of synthetases, Class I amino acids being generally larger and less polar, Class II amino acids smaller and more polar. Biochemical, bioinformatic, and protein engineering experiments support the hypothesis that the two Classes descended from opposite strands of the same ancestral gene...
August 22, 2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28820624/retinopathy-and-optic-atrophy-expanding-the-phenotypic-spectrum-of-pathogenic-variants-in-the-aars2-gene
#19
Jason H Peragallo, Stephanie Keller, Marjo S van der Knaap, Bruno P Soares, Suma P Shankar
BACKGROUND: Optic atrophy may be the sequela of optic nerve injury due to any insult, including isolated and syndromic genetic diseases. Alanyl-tRNA synthetase 2 (AARS2) pathogenic variants have been reported to cause leukodystrophy with ovarian failure, and cardiomyopathy (#615889) as well as combined oxidative phosphorylation deficiency-8 (#614096). We report a young child who presented with decreased vision due to optic atrophy and was found to harbor missense variants in the AARS2 gene expanding the phenotypic expression of the AARS2 gene...
August 18, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28814526/hiv-1-exploits-dynamic-multi-aminoacyl-trna-synthetase-complex-to-enhance-viral-replication
#20
Alice A Duchon, Corine St-Gelais, Nathan Titkemeier, Joshua Hatterschide, Li Wu, Karin Musier-Forsyth
A hallmark of retroviruses such as human immunodeficiency virus type 1 (HIV-1) is reverse transcription of genomic RNA to DNA, a process that is primed by cellular tRNAs. HIV-1 recruits human tRNA(Lys3) to serve as the reverse transcription primer via an interaction between lysyl-tRNA synthetase (LysRS) and the HIV-1 Gag polyprotein. LysRS is normally sequestered in a multi-aminoacyl-tRNA synthetase complex (MSC). Previous studies demonstrated that components of the MSC can be mobilized in response to certain cellular stimuli, but how LysRS is redirected from the MSC to viral particles for packaging is unknown...
August 16, 2017: Journal of Virology
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