keyword
MENU ▼
Read by QxMD icon Read
search

tRNA Synthetase

keyword
https://www.readbyqxmd.com/read/28439027/biochemical-and-structural-characterization-of-oxygen-sensitive-2-thiouridine-synthesis-catalyzed-by-an-iron-sulfur-protein-ttua
#1
Minghao Chen, Shin-Ichi Asai, Shun Narai, Shusuke Nambu, Naoki Omura, Yuriko Sakaguchi, Tsutomu Suzuki, Masao Ikeda-Saito, Kimitsuna Watanabe, Min Yao, Naoki Shigi, Yoshikazu Tanaka
Two-thiouridine (s(2)U) at position 54 of transfer RNA (tRNA) is a posttranscriptional modification that enables thermophilic bacteria to survive in high-temperature environments. s(2)U is produced by the combined action of two proteins, 2-thiouridine synthetase TtuA and 2-thiouridine synthesis sulfur carrier protein TtuB, which act as a sulfur (S) transfer enzyme and a ubiquitin-like S donor, respectively. Despite the accumulation of biochemical data in vivo, the enzymatic activity by TtuA/TtuB has rarely been observed in vitro, which has hindered examination of the molecular mechanism of S transfer...
April 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28427904/leishmania-donovani-tyrosyl-trna-synthetase-structure-in-complex-with-a-tyrosyl-adenylate-analog-and-comparisons-with-human-and-protozoan-counterparts
#2
Ximena Barros-Álvarez, Keshia M Kerchner, Cho Yeow Koh, Stewart Turley, Els Pardon, Jan Steyaert, Ranae M Ranade, J Robert Gillespie, Zhongsheng Zhang, Christophe L M J Verlinde, Erkang Fan, Frederick S Buckner, Wim G J Hol
The crystal structure of Leishmania donovani tyrosyl-tRNA synthetase (LdTyrRS) in complex with a nanobody and the tyrosyl adenylate analog TyrSA was determined at 2.75 Å resolution. Nanobodies are the variable domains of camelid heavy chain-only antibodies. The nanobody makes numerous crystal contacts and in addition reduces the flexibility of a loop of LdTyrRS. TyrSA is engaged in many interactions with active site residues occupying the tyrosine and adenine binding pockets. The LdTyrRS polypeptide chain consists of two pseudo-monomers, each consisting of two domains...
April 17, 2017: Biochimie
https://www.readbyqxmd.com/read/28422494/genetically-encoded-2-aryl-5-carboxytetrazoles-for-site-selective-protein-photo-cross-linking
#3
Yulin Tian, Marco Paolo Jacinto, Yu Zeng, Zhipeng Yu, Jun Qu, Wenshe R Liu, Qing Lin
The genetically encoded photo-cross-linkers promise to offer a temporally controlled tool to map transient and dynamic protein-protein interaction complexes in living cells. Here we report the synthesis of a panel of 2-aryl-5-carboxytetrazole-lysine analogs (ACTKs) and their site-specific incorporation into proteins via amber codon suppression in Escherichia coli and mammalian cells. Among five ACTKs investigated, N-methylpyrroletetrazole-lysine (mPyTK) was found to give robust and site-selective photo-cross-linking reactivity in E...
April 21, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28420760/novel-lnc-rna-regulated-by-hif-1-inhibits-apoptotic-cell-death-in-the-renal-tubular-epithelial-cells-under-hypoxia
#4
Imari Mimura, Yosuke Hirakawa, Yasuharu Kanki, Natsuki Kushida, Ryo Nakaki, Yutaka Suzuki, Tetsuhiro Tanaka, Hiroyuki Aburatani, Masaomi Nangaku
Chronic tubulointerstitial hypoxia plays an important role as the final common pathway to end-stage renal disease. HIF-1 (hypoxia-inducible factor-1) is a master transcriptional factor under hypoxia, regulating downstream target genes. Genome-wide analysis of HIF-1 binding sites using high-throughput sequencers has clarified various kinds of downstream targets and made it possible to demonstrate the novel roles of HIF-1. Our aim of this study is to identify novel HIF-1 downstream epigenetic targets which may play important roles in the kidney...
April 2017: Physiological Reports
https://www.readbyqxmd.com/read/28419802/programming-post-translational-control-over-the-metabolic-labeling-of-cellular-proteins-with-a-non-canonical-amino-acid
#5
Emily E Thomas, Naresh Pandey, Sarah E Knudsen, Zachary T Ball, Jonathan J Silberg
Transcriptional control can be used to program cells to label proteins with non-canonical amino acids by regulating the expression of orthogonal aminoacyl tRNA synthetases (aaRSs). However, we cannot yet program cells to control labeling in response to aaRS and ligand binding. To identify aaRSs whose activities can be regulated by interactions with ligands, we used a combinatorial approach to discover fragmented variants of Escherichia coli methionyl tRNA synthetase (MetRS) that require fusion to associating proteins for maximal activity...
April 18, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28419689/kinetic-and-structural-changes-in-hsmtphers-induced-by-pathogenic-mutations-in-human-fars2
#6
Ekaterine Kartvelishvili, Dmitry Tworowski, Hilary Vernon, Nina Moor, Jing Wang, Lee-Jun Wong, Zofia Chrzanowska-Lightowlers, Mark Safro
Mutations in the mitochondrial aminoacyl-tRNA synthetases (mtaaRSs) can cause profound clinical presentations, and have manifested as diseases with very selective tissue specificity. To date most of the mtaaRS mutations could be phenotypically recognized, such that clinicians could identify the affected mtaaRS from the symptoms alone. Among the recently reported pathogenic variants are point mutations in FARS2 gene, encoding the human mitochondrial PheRS. Patient symptoms range from spastic paraplegia to fatal infantile Alpers encephalopathy...
April 17, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28414711/the-pimeloyl-coa-synthetase-biow-defines-a-new-fold-for-adenylate-forming-enzymes
#7
Paola Estrada, Miglena Manandhar, Shi-Hui Dong, Jaigeeth Deveryshetty, Vinayak Agarwal, John E Cronan, Satish K Nair
Reactions that activate carboxylates through acyl-adenylate intermediates are found throughout biology and include acyl- and aryl-CoA synthetases and tRNA synthetases. Here we describe the characterization of Aquifex aeolicus BioW, which represents a new protein fold within the superfamily of adenylating enzymes. Substrate-bound structures identified the enzyme active site and elucidated the mechanistic strategy for conjugating CoA to the seven-carbon α,ω-dicarboxylate pimelate, a biotin precursor. Proper position of reactive groups for the two half-reactions is achieved solely through movements of active site residues, as confirmed by site-directed mutational analysis...
April 17, 2017: Nature Chemical Biology
https://www.readbyqxmd.com/read/28405745/lethal-albinic-seedling-encoding-a-threonyl-trna-synthetase-is-involved-in-development-of-plastid-protein-synthesis-system-in-rice
#8
Yuan-Yan Zhang, Yuan-Yuan Hao, Yi-Hua Wang, Chun-Ming Wang, Yun-Long Wang, Wu-Hua Long, Di Wang, Xi Liu, Ling Jiang, Jian-Min Wan
An albinic rice is caused by mutation of threonyl-tRNA synthetase, which is essential for plant development by stabilizing of NEP and PEP gene expressions and chloroplast protein synthesis. Chloroplast biogenesis and development depend on complex genetic mechanisms. Apart from their function in translation, aminoacyl-tRNA synthetases (aaRSs) play additional role in gene expression regulation, RNA splicing, and cytokine activity. However, their detailed functions in plant development are still poorly understood...
April 12, 2017: Plant Cell Reports
https://www.readbyqxmd.com/read/28405378/a-unified-model-of-the-standard-genetic-code
#9
Marco V José, Gabriel S Zamudio, Eberto R Morgado
The Rodin-Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code...
March 2017: Royal Society Open Science
https://www.readbyqxmd.com/read/28397914/improving-target-amino-acid-selectivity-in-a-permissive-aminoacyl-trna-synthetase-through-counter-selection
#10
Itthipol Sungwienwong, Zachary M Hostetler, Robert J Blizzard, Joseph J Porter, Camden M Driggers, Lea Z Mbengi, José A Villegas, Lee C Speight, Jeffery G Saven, John J Perona, Rahul M Kohli, Ryan A Mehl, E James Petersson
The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein dynamics, either alone or as part of a Förster resonance energy transfer (FRET) or photo-induced electron transfer (eT) probe pair. We have previously reported the genetic incorporation of Acd by an aminoacyl tRNA synthetase (RS). However, this RS, developed from a library of permissive RSs, also incorporates N-phenyl-aminophenylalanine (Npf), a trace byproduct of one Acd synthetic route. We have performed negative selections in the presence of Npf and analyzed the selectivity of the resulting AcdRSs by in vivo protein expression and detailed kinetic analyses of the purified RSs...
April 11, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28394346/post-translational-modification-of-hint1-mediates-activation-of-mitf-transcriptional-activity-in-human-melanoma-cells
#11
A Motzik, E Amir, T Erlich, J Wang, B-G Kim, J M Han, J H Kim, H Nechushtan, M Guo, E Razin, S Tshori
Microphthalmia transcription factor (MITF) is a basic helix-loop-helix leucine zipper (bHLH-Zip) DNA-binding protein. This transcription factor plays a crucial role in the physiological and pathological functions of distinct cell types. MITF transcriptional activity is inhibited by the histidine triad nucleotide-binding protein 1 (HINT1) through direct binding. We previously reported that this association is disrupted by the binding of the second messenger Ap4A to HINT1. Ap4A is mainly produced in the mammalian cells by S207-phosphorylated Lysyl-tRNA synthetase...
April 10, 2017: Oncogene
https://www.readbyqxmd.com/read/28393177/difficulty-in-obtaining-the-complete-mrna-coding-sequence-at-5-%C3%A2-region-5-%C3%A2-end-mrna-artifact-causes-consequences-in-biology-and-medicine-and-possible-solutions-for-obtaining-the-actual-amino-acid-sequence-of-proteins-review
#12
Lorenza Vitale, Maria Caracausi, Raffaella Casadei, Maria Chiara Pelleri, Allison Piovesan
The known difficulty in obtaining the actual full length, complete sequence of a messenger RNA (mRNA) may lead to the erroneous determination of its coding sequence at the 5' region (5' end mRNA artifact), and consequently to the wrong assignment of the translation start codon, leading to the inaccurate prediction of the encoded polypeptide at its amino terminus. Among the known human genes whose study was affected by this artifact, we can include disco interacting protein 2 homolog A (DIP2A; KIAA0184), Down syndrome critical region 1 (DSCR1), SON DNA binding protein (SON), trefoil factor 3 (TFF3) and URB1 ribosome biogenesis 1 homolog (URB1; KIAA0539) on chromosome 21, as well as receptor for activated C kinase 1 (RACK1, also known as GNB2L1), glutaminyl‑tRNA synthetase (QARS) and tyrosyl-DNA phosphodiesterase 2 (TDP2) along with another 474 loci, including interleukin 16 (IL16)...
April 6, 2017: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/28393009/a-case-of-anti-aminoacyl-trna-synthetase-ars-antibody-positive-polymyositis-pm-dermatomyositis-dm-associated-interstitial-pneumonia-ip-successfully-controlled-with-bosentan-therapy
#13
Tomoyuki Naito, Yosuke Tanaka, Mitsunori Hino, Akihiko Gemma
A 72-year-old woman was admitted to our hospital and was diagnosed with interstitial pneumonia (IP) associated with amyopathic dermatomyositis (ADM). The patient experienced three acute IP exacerbations in the 7 years that followed, which were each treated and resolved with steroid pulse therapy. The patient was closely examined for respiratory failure with right heart catheterization (RHC), which demonstrated that she had a mean pulmonary artery pressure (mPAP) of 34 mmHg. The patient was thus diagnosed as having pulmonary hypertension (PH) associated with anti-synthetase syndrome (ASS) and was started on bosentan therapy, which led to improvements in mPAP as well as in subjective symptoms over time...
2017: Respiratory Medicine Case Reports
https://www.readbyqxmd.com/read/28383562/vps35-regulates-parkin-substrate-aimp2-toxicity-by-facilitating-lysosomal-clearance-of-aimp2
#14
Seung Pil Yun, Hyojung Kim, Sangwoo Ham, Seung-Hwan Kwon, Gum Hwa Lee, Joo-Ho Shin, Sang Hun Lee, Han Seok Ko, Yunjong Lee
Vacuolar protein sorting-associated protein 35 (VPS35) is involved in retrograde transport of proteins from endosomes to trans-Golgi network. Gene mutations in VPS35 are linked to autosomal dominant late-onset Parkinson's disease (PD). Although the identification of VPS35 mutations has provided novel insight about its interactions with several PD-associated genes including leucine-rich repeat kinase 2 (LRRK2) and α-synuclein, little information is available about the molecular mechanisms of cell death downstream of VPS35 dysfunction...
April 6, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28383180/two-tier-screening-platform-for-directed-evolution-of-aminoacyl-trna-synthetases-with-enhanced-stop-codon-suppression-efficiency
#15
Andrew E Owens, Katherine T Grasso, Christine A Ziegler, Rudi Fasan
Genetic code expansion via amber stop suppression provides a powerful tool for introducing non-proteinogenic functionalities into proteins for a broad range of applications. Here, we report the implementation of a versatile platform for the development of engineered aminoacyl-tRNA synthetases with enhanced efficiency in mediating ncAA incorporation via amber stop codon suppression. This system integrates a white/blue colony screen with a plate-based colorimetric assay, thereby combining high-throughput capabilities with reliable and quantitative measurement of AARS-dependent ncAA incorporation efficiency...
April 6, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28382459/proteomic-studies-on-anti-tumor-agent-ansamitocin-p-3-producer-actinosynnema-pretiosum-in-response-to-ammonium-and-isobutanol
#16
Jinxia Lin, Jian-Jiang Zhong
Our previous work showed that the biosynthesis of ansamitocin P-3 (AP-3), an anti-tumor agent, by Actinosynnema pretiosum was depressed by ammonium but enhanced by isobutanol in the medium. Here we show proteomics analyses on A. pretiosum in different fermentation conditions with and without ammonium or isobutanol using two-dimensional electrophoresis (2-DE), matrix-assisted laser desorption/ionization, and linear ion trap quadrupole mass spectrometry. Pairwise comparison of repetitive 2-DE maps was performed to find differentially expressed spots, and eight proteins were identified as functionally annotated ones...
April 5, 2017: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/28381637/aminoacyl-trna-synthetase-interacting-multifunctional-protein-1-activates-nk-cells-via-macrophages-in-vitro-and-in-vivo
#17
Myun Soo Kim, Ju Han Song, Edward P Cohen, Daeho Cho, Tae Sung Kim
Aminoacyl tRNA synthetase-interacting multifunctional protein 1 (AIMP1) has been reported to have antitumor effects in various tumor models. However, mechanisms by which AIMP1 ameliorates tumorigenesis are not well understood. As NK cells are a major cell type involved in antitumor activities and AIMP1 is known to activate professional APCs, we determined whether AIMP1 induced NK cell activation directly or via these APCs. AIMP1 induced the expression of surface activation markers on murine NK cells in total splenocytes, although AIMP1 did not directly induce these activation markers of NK cells...
April 5, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28380394/synthesis-and-evaluation-of-adenosine-containing-3-arylfuran-2-5h-ones-as-tyrosyl-trna-synthetase-inhibitors
#18
Wei Wei, Qi Liu, Zhen-Zhen Li, Wei-Kang Shi, Xing Fu, Jia Liu, Xuan Zhu, Xiao-Cong Wang, Ning Xu, Teng-Fei Li, Fu-Rui Jiang, Zhu-Ping Xiao, Hai-Liang Zhu
Tyrosyl-tRNA synthetase (TyrRS) is an aminoacyl-tRNA synthetase family protein that possesses an essential role in bacterial protein synthesis. The synthesis, structure-activity relationship, and evolution of a novel series of adenosine-containing 3-arylfuran-2(5H)-ones as TyrRS inhibitors are described. Advanced compound d3 from this series exhibited excellent affinity for TyrRS with IC50 of 0.61 ± 0.04 μM. Bacterial growth inhibition assays demonstrated that d3 showed submicromolar antibacterial potency against Escherichia coli and Pseudomonas aeruginosa, and compared to the marketed antibiotics ciprofloxacin...
March 30, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28371162/protein-crosslinking-by-genetically-encoded-noncanonical-amino-acids-with-reactive-aryl-carbamate-side-chains
#19
Weimin Xuan, Sida Shao, Peter G Schultz
The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions, and improve the pharmacological properties of proteins. We report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that incorporates site-specifically PheK and FPheK into proteins in both E...
April 3, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28369220/a-recurrent-wars-mutation-is-a-novel-cause-of-autosomal-dominant-distal-hereditary-motor-neuropathy
#20
Pei-Chien Tsai, Bing-Wen Soong, Inès Mademan, Yen-Hua Huang, Chia-Rung Liu, Cheng-Tsung Hsiao, Hung-Ta Wu, Tze-Tze Liu, Yo-Tsen Liu, Yen-Ting Tseng, Kon-Ping Lin, Ueng-Cheng Yang, Ki Wha Chung, Byung-Ok Choi, Garth A Nicholson, Marina L Kennerson, Chih-Chiang Chan, Peter De Jonghe, Tzu-Hao Cheng, Yi-Chu Liao, Stephan Züchner, Jonathan Baets, Yi-Chung Lee
Distal hereditary motor neuropathy is a heterogeneous group of inherited neuropathies characterized by distal limb muscle weakness and atrophy. Although at least 15 genes have been implicated in distal hereditary motor neuropathy, the genetic causes remain elusive in many families. To identify an additional causal gene for distal hereditary motor neuropathy, we performed exome sequencing for two affected individuals and two unaffected members in a Taiwanese family with an autosomal dominant distal hereditary motor neuropathy in which mutations in common distal hereditary motor neuropathy-implicated genes had been excluded...
March 22, 2017: Brain: a Journal of Neurology
keyword
keyword
8585
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"