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https://www.readbyqxmd.com/read/28437082/high-efficiency-1-and-2-ribosomal-frameshiftings-revealed-by-force-spectroscopy
#1
Te-Wei Tsai, Haopeng Yang, Heng Yin, Shoujun Xu, Yuhong Wang
Ribosomal frameshifting is a rare but ubiquitous process that is being studied extensively. Meanwhile, frameshifting motifs without any secondary mRNA structures were identified but rarely studied experimentally. We report unambiguous observation of highly efficient "-1" and "-2" frameshiftings on a GA7G slippery mRNA without the downstream secondary structure, using force-induced remnant magnetization spectroscopy combined with unique probing schemes. The result represents the first experimental evidence of multiple frameshifting steps...
April 24, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28422494/genetically-encoded-2-aryl-5-carboxytetrazoles-for-site-selective-protein-photo-cross-linking
#2
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/28421413/substrate-induced-conformational-changes-of-the-tyrocidine-synthetase-1-adenylation-domain-probed-by-intrinsic-trp-fluorescence
#3
Matilda Šprung, Barbara Soldo, Stjepan Orhanović, Viljemka Bučević-Popović
Nonribosomal peptide synthetases (NRPS) are multifunctional proteins that catalyze the synthesis of the peptide products with enormous biological potential. The process of biosynthesis starts with the adenylation (A) domain, which during the catalytic cycle undergoes extensive structural rearrangements. In this paper, we present the first study of the tyrocidine synthetase 1 A-domain (TycA-A) fluorescence properties. The TycA-A protein contains five potentially fluorescent Trp residues at positions 227, 301, 323, 376 and 406...
April 18, 2017: Protein Journal
https://www.readbyqxmd.com/read/28419802/programming-post-translational-control-over-the-metabolic-labeling-of-cellular-proteins-with-a-non-canonical-amino-acid
#4
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
#5
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/28416671/case-for-the-genetic-code-as-a-triplet-of-triplets
#6
Fabienne F V Chevance, Kelly T Hughes
The efficiency of codon translation in vivo is controlled by many factors, including codon context. At a site early in the Salmonella flgM gene, the effects on translation of replacing codons Thr6 and Pro8 of flgM with synonymous alternates produced a 600-fold range in FlgM activity. Synonymous changes at Thr6 and Leu9 resulted in a twofold range in FlgM activity. The level of FlgM activity produced by any codon arrangement was directly proportional to the degree of in vivo ribosome stalling at synonymous codons...
April 17, 2017: Proceedings of the National Academy of Sciences of the United States of America
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
#7
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
#8
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
#9
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/28396658/characterisation-of-aerotolerant-forms-of-a-robust-chicken-colonizing-campylobacter-coli
#10
Peter M O'Kane, Ian F Connerton
Campylobacter contaminated poultry meat is a major source of human foodborne illness. Campylobacter coli strain OR12 is a robust colonizer of chickens that was previously shown to outcompete and displace other Campylobacter strains from the chicken's gastrointestinal tract. This strain is capable of aerobic growth on blood agar. Serial aerobic passage increased this aerotolerance as assessed by quantitative assays for growth and survival on solid media. Aerotolerance was also associated with increased peroxide stress resistance...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28396493/cut-in-translation-ribosome-dependent-mrna-decay
#11
David Lalaouna, Eric Massé
Transcription and translation are two complex mechanisms that are tightly coupled in prokaryotic cells. Even before the completion of transcription, ribosomes attach to the nascent mRNA and initiate protein synthesis. Remarkably, recent publications have indicated an association between translation and decay of certain mRNAs. In this issue of The EMBO Journal, Leroy et al (2017) depicts a fascinating mechanism of mRNA degradation, which involves the ribosome-associated ribonuclease Rae1 in Bacillus subtilis In a translation-dependent manner, Rae1 binds the ribosomal aminoacylation (A)-site and cleaves between specific codons of the targeted mRNA...
April 10, 2017: EMBO Journal
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
#12
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/28386012/giant-viruses-with-an-expanded-complement-of-translation-system-components
#13
Frederik Schulz, Natalya Yutin, Natalia N Ivanova, Davi R Ortega, Tae Kwon Lee, Julia Vierheilig, Holger Daims, Matthias Horn, Michael Wagner, Grant J Jensen, Nikos C Kyrpides, Eugene V Koonin, Tanja Woyke
The discovery of giant viruses blurred the sharp division between viruses and cellular life. Giant virus genomes encode proteins considered as signatures of cellular organisms, particularly translation system components, prompting hypotheses that these viruses derived from a fourth domain of cellular life. Here we report the discovery of a group of giant viruses (Klosneuviruses) in metagenomic data. Compared with other giant viruses, the Klosneuviruses encode an expanded translation machinery, including aminoacyl transfer RNA synthetases with specificities for all 20 amino acids...
April 7, 2017: Science
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/28381637/aminoacyl-trna-synthetase-interacting-multifunctional-protein-1-activates-nk-cells-via-macrophages-in-vitro-and-in-vivo
#16
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
#17
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/28376339/characterization-of-trna-leu-binding-interactions-with-cu-2-and-pb-2-and-their-biological-implications
#18
Aleksandar Dimkovikj, Mallory J Banton, Lance A McDanel, Katelin N Arndt, Katelyn E Unvert, Elizabeth K Thorn, Ana Royo Marco, Rachel A Hellmann-Whitaker
RNA is known to interact with Mg(2+) when assuming higher-ordered tertiary configurations. Structurally, when tRNA molecules interact with Mg(2+), they consistently form a "L-shape" conformation each time they are synthesized. Therefore, if Mg(2+) can induce tertiary structure formation, then binding to alternative cations could produce alternative tertiary configurations. By utilizing circular dichroism and mobility gel-shift assays it was observed that tRNA structure can be altered when in the presence of different divalent cationic species...
March 28, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28369220/a-recurrent-wars-mutation-is-a-novel-cause-of-autosomal-dominant-distal-hereditary-motor-neuropathy
#19
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
https://www.readbyqxmd.com/read/28369041/atat-blocks-translation-initiation-by-n-acetylation-of-the-initiator-trna-fmet
#20
Dukas Jurėnas, Sneha Chatterjee, Albert Konijnenberg, Frank Sobott, Louis Droogmans, Abel Garcia-Pino, Laurence Van Melderen
Toxin-antitoxin (TA) loci are prevalent in bacterial genomes. They are suggested to play a central role in dormancy and persister states. Under normal growth conditions, TA toxins are neutralized by their cognate antitoxins, and under stress conditions, toxins are freed and inhibit essential cellular processes using a variety of mechanisms. Here we characterize ataR-ataT, a novel TA system, from enterohemorrhagic Escherichia coli. We show that the toxin AtaT is a GNAT family enzyme that transfers an acetyl group from acetyl coenzyme A to the amine group of the methionyl aminoacyl moiety of initiator tRNA...
April 3, 2017: Nature Chemical Biology
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