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https://www.readbyqxmd.com/read/29156229/indirect-trna-aminoacylation-during-accurate-translation-and-phenotypic-mistranslation
#1
REVIEW
Udumbara M Rathnayake, Whitney N Wood, Tamara L Hendrickson
The fact that most bacteria do not contain a full set of aminoacyl-tRNA synthetases (aaRS) is often underappreciated. In the absence of asparaginyl-tRNA and/or glutaminyl-tRNA synthetase (AsnRS and GlnRS), Asn-tRNA(Asn) and/or Gln-tRNA(Gln) are produced by an indirect tRNA aminoacylation pathway that relies on misacylation of these two tRNAs by two different misacylating aaRSs, followed by transamidation by an amidotransferase (GatCAB in bacteria). This review highlights the central importance of indirect tRNA aminoacylation to accurate protein translation, mechanistic peculiarities that appear to be unique to this system, and the newly recognized connection between indirect tRNA aminoacylation and mistranslation as a strategy used by bacteria to respond to environmental stressors like antibiotics...
November 15, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29156000/structural-rearrangements-in-mrna-upon-its-binding-to-human-80s-ribosomes-revealed-by-epr-spectroscopy
#2
Alexey A Malygin, Dmitri M Graifer, Maria I Meschaninova, Alya G Venyaminova, Ivan O Timofeev, Andrey A Kuzhelev, Olesya A Krumkacheva, Matvey V Fedin, Galina G Karpova, Elena G Bagryanskaya
The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two different types of ribosomal complexes with MR was observed. First, there were stable complexes where MR was fixed in the ribosomal mRNA-binding channel by the codon-anticodon interaction(s) with cognate tRNA(s)...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155943/logical-engineering-of-d-arm-and-t-stem-of-trna-that-enhances-d-amino-acid-incorporation
#3
Takayuki Katoh, Yoshihiko Iwane, Hiroaki Suga
A bacterial translation factor EF-P alleviates ribosomal stalling caused by polyproline sequence by accelerating Pro-Pro formation. EF-P recognizes a specific D-arm motif found in tRNAPro isoacceptors, 9-nt D-loop closed by a stable D-stem sequence, for Pro-selective peptidyl-transfer acceleration. It is also known that the T-stem sequence on aminoacyl-tRNAs modulates strength of the interaction with EF-Tu, giving enhanced incorporation of non-proteinogenic amino acids such as some N-methyl amino acids. Based on the above knowledge, we logically engineered tRNA's D-arm and T-stem sequences to investigate a series of tRNAs for the improvement of consecutive incorporation of d-amino acids and an α, α-disubstituted amino acid...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155070/cytosolic-aminoacyl-trna-synthetases-unanticipated-relocations-for-unexpected-functions
#4
Nathaniel Yakobov, Sylvain Debard, Frédéric Fischer, Bruno Senger, Hubert Dominique Becker
Prokaryotic and eukaryotic cytosolic aminoacyl-tRNA synthetases (aaRSs) are essentially known for their conventional function of generating the full set of aminoacyl-tRNA species that are needed to incorporate each organism's repertoire of genetically-encoded amino acids during ribosomal translation of messenger RNAs. However, bacterial and eukaryotic cytosolic aaRSs have been shown to exhibit other essential nonconventional functions. Here we review all the subcellular compartments that prokaryotic and eukaryotic cytosolic aaRSs can reach to exert either a conventional or nontranslational role...
November 15, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29147923/anti-aminoacyl-trna-synthetase-related-myositis-and-dermatomyositis-clues-for-differential-diagnosis-on-muscle-biopsy
#5
Bruna Cerbelli, Annalinda Pisano, Serena Colafrancesco, Maria Gemma Pignataro, Marco Biffoni, Silvia Berni, Antonia De Luca, Valeria Riccieri, Roberta Priori, Guido Valesini, Giulia d'Amati, Carla Giordano
Anti-synthetase syndrome is an autoimmune disease characterized by autoantibodies toward amino acyl-tRNA synthetases (ARS), anti-Jo 1 being the most commonly detected. Muscle damage develops in up to 90% of ARS-positive patients, characterized by a necrotizing myositis restricted to the perifascicular region. This topographic distribution of muscle damage may lead to a misdiagnosis of dermatomyositis (DM) at muscle biopsy. We compared morphological, immunohistochemical, and histoenzymatic features of muscle from ARS-positive patients (n = 11) with those of DM (n = 7) providing clues for their differential diagnosis...
November 16, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29137650/recessive-vars2-mutation-underlies-a-novel-syndrome-with-epilepsy-mental-retardation-short-stature-growth-hormone-deficiency-and-hypogonadism
#6
Abdulaziz Alsemari, Banan Al-Younes, Ewa Goljan, Dyala Jaroudi, Faisal BinHumaid, Brian F Meyer, Stefan T Arold, Dorota Monies
BACKGROUND: Most mitochondrial and cytoplasmic aminoacyl-tRNA synthetases (aaRSs) are encoded by nuclear genes. Syndromic disorders resulting from mutation of aaRSs genes display significant phenotypic heterogeneity. We expand aaRSs-related phenotypes through characterization of the clinical and molecular basis of a novel autosomal-recessive syndrome manifesting severe mental retardation, ataxia, speech impairment, epilepsy, short stature, microcephaly, hypogonadism, and growth hormone deficiency...
November 14, 2017: Human Genomics
https://www.readbyqxmd.com/read/29137381/gene-expression-and-molecular-pathway-activation-signatures-of-mycn-amplified-neuroblastomas
#7
Ivan Petrov, Maria Suntsova, Elena Ilnitskaya, Sergey Roumiantsev, Maxim Sorokin, Andrew Garazha, Pavel Spirin, Timofey Lebedev, Nurshat Gaifullin, Sergey Larin, Olga Kovalchuk, Dmitry Konovalov, Vladimir Prassolov, Alexander Roumiantsev, Anton Buzdin
Neuroblastoma is a pediatric cancer arising from sympathetic nervous system. Remarkable heterogeneity in outcomes is one of its widely known features. One of the traits strongly associated with the unfavorable subtype is the amplification of oncogene MYCN. Here, we performed cross-platform biomarker detection by comparing gene expression and pathway activation patterns from the two literature reports and from our experimental dataset, combining profiles for the 761 neuroblastoma patients with known MYCN amplification status...
October 13, 2017: Oncotarget
https://www.readbyqxmd.com/read/29126765/new-insights-into-the-phenotype-of-fars2-deficiency
#8
Elise Vantroys, Austin Larson, Marisa Friederich, Kaz Knight, Michael A Swanson, Christopher A Powell, Joél Smet, Sarah Vergult, Boel De Paepe, Sara Seneca, Herbert Roeyers, Björn Menten, Michal Minczuk, Arnaud Vanlander, Johan Van Hove, Rudy Van Coster
Mutations in FARS2 are known to cause dysfunction of mitochondrial translation due to deficient aminoacylation of the mitochondrial phenylalanine tRNA. Here, we report three novel mutations in FARS2 found in two patients in a compound heterozygous state. The missense mutation c.1082C>T (p.Pro361Leu) was detected in both patients. The mutations c.461C>T (p.Ala154Val) and c.521_523delTGG (p.Val174del) were each detected in one patient. We report abnormal in vitro aminoacylation assays as a functional validation of the molecular genetic findings...
October 12, 2017: Molecular Genetics and Metabolism
https://www.readbyqxmd.com/read/29122587/the-splicing-code
#9
REVIEW
Marco Baralle, Francisco Ernesto Baralle
This issue dedicated to the code of life tackles very challenging and open questions in Biology. The genetic code, brilliantly uncovered over 50 years ago is an example of a univocal biological code. In fact, except for very few and marginal variations, it is the same from bacteria to man, the RNA stretch: 5' GUGUUC 3' reads as the dipeptide: Val-Phe in bacteria, in yeast, in Arabidopsis, in zebra fish, in mouse and in human. A degree of ambiguity is possible if mutations are introduced in the tRNAs in a way that the anticodon reads one amino acid but the aminoacyl-transferase attaches a different one onto the tRNA...
November 6, 2017: Bio Systems
https://www.readbyqxmd.com/read/29120675/utility-of-adenosine-monophosphate-detection-system-for-monitoring-the-activities-of-diverse-enzyme-reactions
#10
Subhanjan Mondal, Kevin Hsiao, Said A Goueli
Adenosine monophosphate (AMP) is a key cellular metabolite regulating energy homeostasis and signal transduction. AMP is also a product of various enzymatic reactions, many of which are dysregulated during disease conditions. Thus, monitoring the activities of these enzymes is a primary goal for developing modulators for these enzymes. In this study, we demonstrate the versatility of an enzyme-coupled assay that quantifies the amount of AMP produced by any enzymatic reaction regardless of its substrates. We successfully implemented it to enzyme reactions that use adenosine triphosphate (ATP) as a substrate (aminoacyl tRNA synthetase and DNA ligase) by an elaborate strategy of removing residual ATP and converting AMP produced into ATP; so it can be detected using luciferase/luciferin and generating light...
October 2017: Assay and Drug Development Technologies
https://www.readbyqxmd.com/read/29120065/biallelic-mutations-in-mitochondrial-tryptophanyl-trna-synthetase-cause-levodopa-rresponsive-infantile-onset-parkinsonism
#11
E A Burke, S J Frucht, K Thompson, L A Wolfe, T Yokoyama, M Bertoni, Y Huang, M Sincan, D R Adams, R W Taylor, W A Gahl, C Toro, M C V Malicdan
Mitochondrial aminoacyl-tRNA synthetases (mtARSs) are essential, ubiquitously expressed enzymes that covalently attach amino acids to their corresponding tRNA molecules during translation of mitochondrial genes. Deleterious variants in the mtARS genes cause a diverse array of phenotypes, many of which involve the nervous system. Moreover, distinct mutations in mtARSs often cause different clinical manifestations. Recently, the gene encoding mitochondrial tryptophanyl tRNA synthetase (WARS2) was reported to cause two different neurological phenotypes, a form of autosomal recessive intellectual disability and a syndrome of severe infantile-onset leukoencephalopathy...
November 9, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/29111345/aminoacyl-trna-quality-control-provides-a-speedy-solution-to-discriminate-right-from-wrong
#12
Paul Kelly, Michael Ibba
No abstract text is available yet for this article.
October 27, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29111343/kinetic-origin-of-substrate-specificity-in-post-transfer-editing-by-leucyl-trna-synthetase
#13
Morana Dulic, Nevena Cvetesic, Igor Zivkovic, Andrés Palencia, Stephen Cusack, Branimir Bertosa, Ita Gruic-Sovulj
The intrinsic editing capacities of aminoacyl-tRNA synthetases ensure a high-fidelity translation of the amino acids that possess effective non-cognate aminoacylation surrogates. The dominant error-correction pathway comprises deacylation of misaminoacylated tRNA within the aminoacyl-tRNA synthetase editing site. To assess the origin of specificity of Escherichia coli leucyl-tRNA synthetase (LeuRS) against the cognate aminoacylation product in editing, we followed binding and catalysis independently using cognate leucyl- and non-cognate norvalyl-tRNA(Leu) and their non-hydrolyzable analogues...
October 27, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/29107333/granzyme-b-disrupts-central-metabolism-and-protein-synthesis-in-bacteria-to-promote-an-immune-cell-death-program
#14
Farokh Dotiwala, Sumit Sen Santara, Andres Ariel Binker-Cosen, Bo Li, Sriram Chandrasekaran, Judy Lieberman
Human cytotoxic lymphocytes kill intracellular microbes. The cytotoxic granule granzyme proteases released by cytotoxic lymphocytes trigger oxidative bacterial death by disrupting electron transport, generating superoxide anion and inactivating bacterial oxidative defenses. However, they also cause non-oxidative cell death because anaerobic bacteria are also killed. Here, we use differential proteomics to identify granzyme B substrates in three unrelated bacteria: Escherichia coli, Listeria monocytogenes, and Mycobacteria tuberculosis...
November 16, 2017: Cell
https://www.readbyqxmd.com/read/29106828/expanding-the-scope-of-single-and-double-noncanonical-amino-acid-mutagenesis-in-mammalian-cells-using-orthogonal-polyspecific-leucyl-trna-synthetases
#15
Yunan Zheng, Raja Mukherjee, Melissa A Chin, Peter Igo, Martin J Gilgenast, Abhishek Chatterjee
Engineered aminoacyl-tRNA synthetase/tRNA pairs that enable site-specific incorporation of noncanonical amino acids (ncAAs) into proteins in living cells have emerged as powerful tools in chemical biology. The Escherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair is a promising candidate for ncAA mutagenesis in mammalian cells, but it has been engineered to charge only a limited set of ncAAs so far. Here we show that two highly polyspecific EcLeuRS mutants can efficiently charge a large array of useful ncAAs into proteins expressed in mammalian cells, while discriminating against the 20 canonical amino acids...
November 15, 2017: Biochemistry
https://www.readbyqxmd.com/read/29101229/-almg-responsible-for-polymyxin-resistance-in-pandemic-v-cholerae-is-a-glycyl-transferase-distantly-related-to-lipid-a-late-acyltransferases
#16
Jeremy C Henderson, Carmen M Herrera, M Stephen Trent
Cationic antimicrobial peptides (CAMPs), such as polymyxins are used as a last-line defense in treatment of many bacterial infections. However, some bacteria have developed resistance mechanisms to survive these compounds. Current pandemic O1 Vibrio cholerae biotype El Tor is resistant to polymyxins, whereas previous pandemic strain of the classical biotype is polymyxin sensitive. The almEFG operon found in El Tor V. cholerae confers >100-fold resistance to antimicrobial peptides through aminoacylation of lipopolysaccharide (LPS), expected to decrease the negatively charged surface of the V...
November 3, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29093389/the-onset-of-eosinophilic-pneumonia-preceding-anti-synthetase-syndrome
#17
Yoshimasa Hachisu, Yasuhiko Koga, Noriaki Sunaga, Chiharu Kashiwagi, Yuri Sawada, Yasuyuki Saito, Yusuke Tsukagoshi, Norimitsu Kasahara, Reiko Sakurai, Hiroaki Tsurumaki, Masakiyo Yatomi, Kyoichi Kaira, Akihiro Ono, Toshitaka Maeno, Takeshi Hisada
A 66-year-old man had been treated with prednisolone for eosinophilic pneumonia for 8 years. His slowly progressing cough and dyspnea were accompanied by elevated levels of fibrotic serological markers and an increased reticular shadow on chest computed tomography images. The patient had recently tested positive for anti-EJ antibodies, a type of anti-aminoacyl-tRNA synthetase antibody; therefore, we diagnosed him with an exacerbation of interstitial pneumonia due to anti-synthetase syndrome (ASS). He was treated with tacrolimus and an increased prednisolone dosage...
November 1, 2017: Internal Medicine
https://www.readbyqxmd.com/read/29081953/defining-the-current-scope-and-limitations-of-dual-noncanonical-amino-acid-mutagenesis-in-mammalian-cells
#18
Yunan Zheng, Partha Sarathi Addy, Raja Mukherjee, Abhishek Chatterjee
The ability to site-specifically incorporate two distinct noncanonical amino acids (ncAAs) into the proteome of a mammalian cell with high fidelity and efficiency will have many enabling applications. It would require the use of two different engineered aminoacyl-tRNA synthetase (aaRS)/tRNA pairs, each suppressing a distinct nonsense codon, and which cross-react neither with each other, nor with their counterparts from the host cell. Three different aaRS/tRNA pairs have been developed so far to expand the genetic code of mammalian cells, which can be potentially combined in three unique ways to drive site-specific incorporation of two distinct ncAAs...
October 1, 2017: Chemical Science
https://www.readbyqxmd.com/read/29077934/interdependence-reflexivity-fidelity-impedance-matching-and-the-evolution-of-genetic-coding
#19
Charles W Carter, Peter R Wills
Genetic coding is generally thought to have required ribozymes whose functions were taken over by polypeptide aminoacyl-tRNA synthetases (aaRS). Two discoveries about aaRS and their interactions with tRNA substrates now furnish a unifying rationale for the opposite conclusion: that the key processes of the Central Dogma of molecular biology emerged simultaneously and naturally from simple origins in a peptide•RNA partnership, eliminating the epistemological utility of a prior RNA world. First, the two aaRS classes likely arose from opposite strands of the same ancestral gene, implying a simple genetic alphabet...
October 24, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29058197/site-directed-unnatural-amino-acid-mutagenesis-to-investigate-potassium-channel-pharmacology-in-xenopus-laevis-oocytes
#20
Robin Y Kim, Harley T Kurata
Unnatural amino acid mutagenesis is a useful tool enabling detailed investigation of ion channel structure-function relationships and pharmacology. Methods have been developed to apply this technique to different heterologous systems for electrophysiological studies, with each system offering unique advantages and limitations. Synthesis of aminoacylated-tRNA followed by injection into Xenopus laevis oocytes is beneficial because it allows for the incorporation of a wide range of unnatural sidechains, including amino acids with subtle structural differences...
2018: Methods in Molecular Biology
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