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Showing 1-30 of 117 results for "R4251" within Papers
Michael P Guy et al.
Genes & development, 28(15), 1721-1732 (2014-08-03)
Sequence variation in tRNA genes influences the structure, modification, and stability of tRNA; affects translation fidelity; impacts the activity of numerous isodecoders in metazoans; and leads to human diseases. To comprehensively define the effects of sequence variation on tRNA function
Kevin K Desai et al.
Nucleic acids research, 42(6), 3931-3942 (2014-01-18)
Archease is a 16-kDa protein that is conserved in all three domains of life. In diverse bacteria and archaea, the genes encoding Archease and the tRNA ligase RtcB are localized into an operon. Here we provide a rationale for this
Dan Li et al.
Gene, 545(1), 132-140 (2014-05-02)
The mayfly species Siphluriscus chinensis (Siphluriscidae) has valuable structures useful for phylogeny reconstruction, given its putative basal position within the Ephemeroptera. Here its nearly complete mitochondrial genome is sequenced. We built phylogenetic trees through multiple analytical strategies with some other
Laasya Samhita et al.
Journal of bacteriology, 196(14), 2607-2615 (2014-05-13)
Multiple copies of a gene require enhanced investment on the part of the cell and, as such, call for an explanation. The observation that Escherichia coli has four copies of initiator tRNA (tRNAi) genes, encoding a special tRNA (tRNA(fMet)) required
Jiqiang Ling et al.
Nucleic acids research, 42(1), 499-508 (2013-09-21)
The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic
Jonathan Somme et al.
RNA (New York, N.Y.), 20(8), 1257-1271 (2014-06-22)
The 2'-O-methylation of the nucleoside at position 32 of tRNA is found in organisms belonging to the three domains of life. Unrelated enzymes catalyzing this modification in Bacteria (TrmJ) and Eukarya (Trm7) have already been identified, but until now, no
Crystal E Fagan et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(24), 9716-9721 (2013-05-01)
After four decades of research aimed at understanding tRNA selection on the ribosome, the mechanism by which ribosomal ambiguity (ram) mutations promote miscoding remains unclear. Here, we present two X-ray crystal structures of the Thermus thermophilus 70S ribosome containing 16S
Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress.
Saikia M, Jobava R, Parisien M, et al.
Molecular and Cellular Biology, 34(13), 2450-2463 (2014)
Lucía Otero et al.
RNA (New York, N.Y.), 20(7), 1023-1034 (2014-05-13)
Selenocysteine (Sec) is encoded by an UGA codon with the help of a SECIS element present in selenoprotein mRNAs. SECIS-binding protein (SBP2/SCBP-2) mediates Sec insertion, but the roles of its domains and the impact of its deficiency on Sec insertion
Kevin W Diebel et al.
Gene, 544(1), 8-18 (2014-04-22)
Canonical RNA polymerase III (pol III) type 2 promoters contain a single A and B box and are well documented for their role in tRNA and SINE transcription in eukaryotic cells. The genome of Murid herpesvirus 4 (MuHV-4) contains eight
Multilevel functional and structural defects induced by two pathogenic mitochondrial tRNA mutations.
Meng Wang et al.
The Biochemical journal, 453(3), 455-465 (2013-05-02)
Point mutations in hmtRNAs (human mitochondrial tRNAs) can cause various disorders, such as CPEO (chronic progressive external ophthalmoplegia) and MM (mitochondrial myopathy). Mitochondrial tRNALeu, especially the UUR codon isoacceptor, is recognized as a hot spot for pathogenic mtDNA point mutations.
Steven B Zhang et al.
Radiation research, 180(4), 407-413 (2013-09-26)
This study demonstrates that mice, similar to humans, have a common mitochondrial DNA deletion (3,860 bp) that encodes 5 transfer RNA genes and 5 polypeptide genes that is related to aging, tissue type and radiotoxicity. Our research indicates that the
Li Li et al.
The Journal of biological chemistry, 288(48), 34736-34745 (2013-10-22)
Tryptophanyl-tRNA Synthetase (TrpRS) Urzyme (fragments A and C), a 130-residue construct containing only secondary structures positioning the HIGH and KMSKS active site signatures and the specificity helix, accelerates tRNA(Trp) aminoacylation with ∼10-fold specificity toward tryptophan, relative to structurally related tyrosine.
Robert Kopajtich et al.
American journal of human genetics, 95(6), 708-720 (2014-12-01)
Respiratory chain deficiencies exhibit a wide variety of clinical phenotypes resulting from defective mitochondrial energy production through oxidative phosphorylation. These defects can be caused by either mutations in the mtDNA or mutations in nuclear genes coding for mitochondrial proteins. The
Jean Lehmann et al.
Nucleic acids research, 41(10), 5494-5502 (2013-04-13)
The structure and function of conserved motifs constituting the apex of Stem I in T-box mRNA leaders are investigated. We point out that this apex shares striking similarities with the L1 stalk (helices 76-78) of the ribosome. A sequence and
Jie Zhou et al.
Science (New York, N.Y.), 340(6140), 1236086-1236086 (2013-07-03)
Translocation of messenger and transfer RNA (mRNA and tRNA) through the ribosome is a crucial step in protein synthesis, whose mechanism is not yet understood. The crystal structures of three Thermus ribosome-tRNA-mRNA-EF-G complexes trapped with β,γ-imidoguanosine 5'-triphosphate (GDPNP) or fusidic
Jie Zhou et al.
Science (New York, N.Y.), 345(6201), 1188-1191 (2014-09-06)
Coupled translocation of messenger RNA and transfer RNA (tRNA) through the ribosome, a process catalyzed by elongation factor EF-G, is a crucial step in protein synthesis. The crystal structure of a bacterial translocation complex describes the binding states of two
Manuel Neeb et al.
Journal of medicinal chemistry, 57(13), 5566-5578 (2014-06-25)
Lead optimization focuses on binding-affinity improvement. If a flat structure-activity relationship is detected, usually optimization strategies are abolished as unattractive. Nonetheless, as affinity is composed of an enthalpic and entropic contribution, factorization of both can unravel the complexity of a
Tomasz W Turowski
Gene, 526(1), 23-29 (2013-05-04)
In eukaryotes, three RNA polymerases are responsible for transcription. These complex enzymes show many similarities with one another, such as several common or highly homologue subunits, while some other features, such as transcript length, diversity, processing, and transcription regulation, are
Tanja Kalstrup et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(20), 8272-8277 (2013-05-01)
Atomic-scale models on the gating mechanism of voltage-gated potassium channels (Kv) are based on linear interpolations between static structures of their initial and final state derived from crystallography and molecular dynamics simulations, and, thus, lack dynamic structural information. The lack
Narayana Annaluru et al.
Science (New York, N.Y.), 344(6179), 55-58 (2014-03-29)
Rapid advances in DNA synthesis techniques have made it possible to engineer viruses, biochemical pathways and assemble bacterial genomes. Here, we report the synthesis of a functional 272,871-base pair designer eukaryotic chromosome, synIII, which is based on the 316,617-base pair
Stefan Klumpp et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(42), 16754-16759 (2013-10-02)
Bacterial growth is crucially dependent on protein synthesis and thus on the cellular abundance of ribosomes and related proteins. Here, we show that the slow diffusion of the bulky tRNA complexes in the crowded cytoplasm imposes a physical limit on
Arto Pulk et al.
Science (New York, N.Y.), 340(6140), 1235970-1235970 (2013-07-03)
Protein synthesis by the ribosome requires the translocation of transfer RNAs and messenger RNA by one codon after each peptide bond is formed, a reaction that requires ribosomal subunit rotation and is catalyzed by the guanosine triphosphatase (GTPase) elongation factor
Lorenzo Peverelli et al.
Muscle & nerve, 50(2), 292-295 (2014-04-09)
A 61-year-old woman with a 5-year history of progressive muscle weakness and atrophy had a muscle biopsy characterized by a combination of dystrophic features (necrotic fibers and endomysial fibrosis) and mitochondrial alterations [ragged-red, cytochrome c oxidase (COX)-negative fibers]. Sequencing of
Jin Chen et al.
Nature structural & molecular biology, 20(6), 718-727 (2013-04-30)
During translation elongation, the ribosome compositional factors elongation factor G (EF-G; encoded by fusA) and tRNA alternately bind to the ribosome to direct protein synthesis and regulate the conformation of the ribosome. Here, we use single-molecule fluorescence with zero-mode waveguides
Tamir Tuller et al.
Nucleic acids research, 43(1), 13-28 (2014-12-17)
The codon composition of the coding sequence's (ORF) 5' end first few dozen codons is known to be distinct to that of the rest of the ORF. Various explanations for the unusual codon distribution in this region have been proposed
Sarah McMahon et al.
Carcinogenesis, 35(5), 1046-1054 (2014-01-21)
The presence of mitochondrial DNA (mtDNA) mutations in human cancer has long been recognized, but their functional significance has remained obscure. Debate persists as to whether the mutations help drive the tumor, or are bystander events. Here, we analyze next-generation
Dawid Krokowski et al.
The Journal of biological chemistry, 288(24), 17202-17213 (2013-05-07)
Endoplasmic reticulum (ER) stress-induced responses are associated with the loss of insulin-producing β-cells in type 2 diabetes mellitus. β-Cell survival during ER stress is believed to depend on decreased protein synthesis rates that are mediated via phosphorylation of the translation
Abhishek Chatterjee et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(29), 11803-11808 (2013-07-03)
Here we report the development of a baculovirus-based delivery system that enables the efficient incorporation of unnatural amino acids into proteins in mammalian cells. We have exploited the large cargo-capacity (>30 kb) and stability of the double-stranded DNA genome of
Ulf-Peter Guenther et al.
Nature, 502(7471), 385-388 (2013-09-24)
Nucleic-acid-binding proteins are generally viewed as either specific or nonspecific, depending on characteristics of their binding sites in DNA or RNA. Most studies have focused on specific proteins, which identify cognate sites by binding with highest affinities to regions with
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