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Jason C Grigg et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(18), 7240-7245 (2013-04-17)
The T box leader sequence is an RNA element that controls gene expression by binding directly to a specific tRNA and sensing its aminoacylation state. This interaction controls expression of amino acid-related genes in a negative feedback loop. The T
Paul D Good et al.
Gene, 526(1), 7-15 (2013-05-28)
Transfer RNA (tRNA) genes and other RNA polymerase III transcription units are dispersed in high copy throughout nuclear genomes, and can antagonize RNA polymerase II transcription in their immediate chromosomal locus. Previous work in Saccharomyces cerevisiae found that this local
Min Tan et al.
Nucleic acids research, 41(10), 5513-5523 (2013-04-16)
Faithful translation of the genetic code depends on accurate coupling of amino acids with cognate transfer RNAs (tRNAs) catalyzed by aminoacyl-tRNA synthetases. The fidelity of leucyl-tRNA synthetase (LeuRS) depends mainly on proofreading at the pre- and post-transfer levels. During the
Andreas M Anger et al.
Nature, 497(7447), 80-85 (2013-05-03)
Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here
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
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
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
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
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
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.
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
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
Ling-Ling Zheng et al.
RNA (New York, N.Y.), 19(7), 863-875 (2013-05-25)
Trypanosoma brucei, a pathogen of human and domestic animals, is an early evolved parasitic protozoan with a complex life cycle. Most genes of this parasite are post-transcriptionally regulated. However, the mechanisms and the molecules involved remain largely unknown. We have
Chie Tomikawa et al.
FEBS letters, 587(21), 3575-3580 (2013-10-01)
Thermoplasma acidophilum is a thermo-acidophilic archaeon. We purified tRNA(Leu) (UAG) from T. acidophilum using a solid-phase DNA probe method and determined the RNA sequence after determining via nucleoside analysis and m(7)G-specific aniline cleavage because it has been reported that T.
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
Ewa Skowronek et al.
RNA (New York, N.Y.), 20(1), 115-130 (2013-11-20)
Mature tRNA 3' ends in the yeast Saccharomyces cerevisiae are generated by two pathways: endonucleolytic and exonucleolytic. Although two exonucleases, Rex1 and Rrp6, have been shown to be responsible for the exonucleolytic trimming, the identity of the endonuclease has been
t-RNA fragmentation as an early biomarker of (kidney) injury.
Alexander Holderied et al.
Journal of the American Society of Nephrology : JASN, 25(10), 2145-2147 (2014-05-17)
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
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
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)
Zhongqi Zhang et al.
Biochemistry, 52(45), 8165-8176 (2013-10-17)
A mass spectrometry-based method was developed to measure amino acid substitutions directly in proteins down to a level of 0.001%. When applied to recombinant proteins expressed in Escherichia coli, monoclonal antibodies expressed in mammalian cells, and human serum albumin purified
Silvia Prado et al.
Nucleic acids research, 41(12), 6190-6208 (2013-05-01)
MnmE is a homodimeric multi-domain GTPase involved in tRNA modification. This protein differs from Ras-like GTPases in its low affinity for guanine nucleotides and mechanism of activation, which occurs by a cis, nucleotide- and potassium-dependent dimerization of its G-domains. Moreover
Karri M Haen et al.
Gene, 535(2), 336-344 (2013-11-02)
Three previously studied mitochondrial genomes of glass sponges (phylum Porifera, class Hexactinellida) contained single nucleotide insertions in protein coding genes inferred as sites of +1 translational frameshifting. To investigate the distribution and evolution of these sites and to help elucidate
Bo Zhang et al.
Gene, 533(1), 253-260 (2013-10-08)
To characterize aphid mitochondrial genome (mitogenome) features, we sequenced the complete mitogenome of the Russian wheat aphid, Diuraphis noxia. The 15,784-bp mitogenome with a high A+T content (84.76%) and strong C skew (-0.26) was arranged in the same gene order
Sergei Gaidamakov et al.
Molecular and cellular biology, 34(1), 123-131 (2013-11-06)
La antigen (Sjögren's syndrome antigen B) is a phosphoprotein associated with nascent precursor tRNAs and other RNAs, and it is targeted by autoantibodies in patients with Sjögren's syndrome, systemic lupus erythematosus, and neonatal lupus. Increased levels of La are associated
Enea Salsi et al.
Journal of molecular biology, 427(2), 454-467 (2014-12-03)
Previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor G (EF-G). Here, we follow the movement of domain IV of EF-G relative to domain II of EF-G using ensemble and single-molecule Förster resonance
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.
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
David S Tourigny et al.
Science (New York, N.Y.), 340(6140), 1235490-1235490 (2013-07-03)
A key step of translation by the ribosome is translocation, which involves the movement of messenger RNA (mRNA) and transfer RNA (tRNA) with respect to the ribosome. This allows a new round of protein chain elongation by placing the next
Sarit Edelheit et al.
PLoS genetics, 9(6), e1003602-e1003602 (2013-07-05)
The presence of 5-methylcytidine (m(5)C) in tRNA and rRNA molecules of a wide variety of organisms was first observed more than 40 years ago. However, detection of this modification was limited to specific, abundant, RNA species, due to the usage
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