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Showing 1-30 of 122 results for "r8508" within Papers
Eikan Mishima et al.
Journal of the American Society of Nephrology : JASN, 25(10), 2316-2326 (2014-05-17)
Tissue damage by oxidative stress is a key pathogenic mechanism in various diseases, including AKI and CKD. Thus, early detection of oxidative tissue damage is important. Using a tRNA-specific modified nucleoside 1-methyladenosine (m1A) antibody, we show that oxidative stress induces
Thomas D Grant et al.
Journal of molecular biology, 425(14), 2480-2493 (2013-04-16)
Eukaryotic glutaminyl-tRNA synthetase (GlnRS) contains an appended N-terminal domain (NTD) whose precise function is unknown. Although GlnRS structures from two prokaryotic species are known, no eukaryotic GlnRS structure has been reported. Here we present the first crystallographic structure of yeast
Eleni Kyriakou et al.
Gene, 540(1), 78-85 (2014-02-25)
Species of the genus Mytilus carry two mitochondrial genomes in obligatory coexistence; one transmitted though the eggs (the F type) and one through the sperm (the M type). We have studied the 3' and 5' ends of rRNA and tRNA
David J F Ramrath et al.
Proceedings of the National Academy of Sciences of the United States of America, 110(52), 20964-20969 (2013-12-11)
During protein synthesis, coupled translocation of messenger RNAs (mRNA) and transfer RNAs (tRNA) through the ribosome takes place following formation of each peptide bond. The reaction is facilitated by large-scale conformational changes within the ribosomal complex and catalyzed by elongtion
Jingyan Wu et al.
Genes & development, 28(14), 1556-1561 (2014-07-18)
In eukaryotes and archaea, tRNA splicing generates free intron molecules. Although ∼ 600,000 introns are produced per generation in yeast, they are barely detectable in cells, indicating efficient turnover of introns. Through a genome-wide search for genes involved in tRNA
Matthieu G Gagnon et al.
Science (New York, N.Y.), 345(6197), 684-687 (2014-08-12)
Elongation factor 4 (EF4/LepA) is a highly conserved guanosine triphosphatase translation factor. It was shown to promote back-translocation of tRNAs on posttranslocational ribosome complexes and to compete with elongation factor G for interaction with pretranslocational ribosomes, inhibiting the elongation phase
Tobias W Giessen et al.
Biochemistry, 52(24), 4274-4283 (2013-05-28)
A large number of bioactive natural products containing a 2,5-diketopiperazine (DKP) moiety have been isolated from various microbial sources. Especially tryptophan-containing cyclic dipeptides (CDPs) show great structural and functional diversity, while little is known about their biosynthetic pathways. Here, we
Richard J Maraia et al.
RNA (New York, N.Y.), 20(7), 977-984 (2014-06-18)
Whole-genome and functional analyses suggest a wealth of secondary or auxiliary genetic information (AGI) within the redundancy component of the genetic code. Although there are multiple aspects of biased codon use, we focus on two types of auxiliary information: codon-specific
Daniel W Thomson et al.
Nucleic acids research, 43(1), 470-481 (2014-12-03)
High-throughput sequencing reveals an abundance of microRNA-sized fragments derived from larger non-coding RNAs. Roles for these small RNAs in gene silencing are suggested by their co-precipitation with Argonaute, the microRNA effector protein, though the extent to which they suppress gene
Keiichiro Hiratsu et al.
Molecular genetics and genomics : MGG, 288(12), 707-715 (2013-10-25)
The factors maintaining genomic integrity, which have been studied in detail in other species, have yet to be investigated in plants. Recent progress in gene-silencing technology has made it possible to produce transgenic plants with loss-of-function phenotypes for the effective
Karen Yap et al.
Molecular cell, 72(3), 525-540 (2018-10-16)
Functions of many long noncoding RNAs (lncRNAs) depend on their ability to interact with multiple copies of specific RNA-binding proteins (RBPs). Here, we devised a workflow combining bioinformatics and experimental validation steps to systematically identify RNAs capable of multivalent RBP
Shuxian Liu et al.
Gene, 547(1), 136-144 (2014-06-27)
The complete mitochondrial genome (mitogenome) of a female flightless geometrid moth Apocheima cinerarius was found to be 15,722 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region.
Takamasa Hirano et al.
RNA (New York, N.Y.), 20(8), 1223-1237 (2014-06-11)
Small RNAs mediate gene silencing by binding Argonaute/Piwi proteins to regulate target RNAs. Here, we describe small RNA profiling of the adult testes of Callithrix jacchus, the common marmoset. The most abundant class of small RNAs in the adult testis
Kai-Jun Zhang et al.
Gene, 533(1), 100-109 (2013-10-15)
The white-backed planthopper (WBPH), Sogatella furcifera (Horváth), is one of the most destructive pests of rice crops in many Asian countries. Using long-PCR and shotgun library methods, we sequenced the entire mitochondrial genomes (mt-genomes) of two WBPH individuals. Total lengths
Paul Ryvkin et al.
RNA (New York, N.Y.), 19(12), 1684-1692 (2013-10-24)
RNA is often altered post-transcriptionally by the covalent modification of particular nucleotides; these modifications are known to modulate the structure and activity of their host RNAs. The recent discovery that an RNA methyl-6 adenosine demethylase (FTO) is a risk gene
Jinwei Zhang et al.
Nature, 500(7462), 363-366 (2013-07-31)
In Gram-positive bacteria, T-box riboswitches regulate the expression of aminoacyl-tRNA synthetases and other proteins in response to fluctuating transfer RNA aminoacylation levels under various nutritional states. T-boxes reside in the 5'-untranslated regions of the messenger RNAs they regulate, and consist
Kaihang Wang et al.
Nature chemistry, 6(5), 393-403 (2014-04-24)
The ability to introduce different biophysical probes into defined positions in target proteins will provide powerful approaches for interrogating protein structure, function and dynamics. However, methods for site-specifically incorporating multiple distinct unnatural amino acids are hampered by their low efficiency.
Cem Albayrak et al.
Nucleic acids research, 41(11), 5949-5963 (2013-04-17)
We describe a new cell-free protein synthesis (CFPS) method for site-specific incorporation of non-natural amino acids (nnAAs) into proteins in which the orthogonal tRNA (o-tRNA) and the modified protein (i.e. the protein containing the nnAA) are produced simultaneously. Using this
Xiangyun Wu et al.
Gene, 533(1), 439-446 (2013-10-03)
In contrast to the extreme conservation of nuclear-encoded tRNAs, organization of the mitochondrial (mt) tRNA gene family in invertebrates is highly dynamic and rapidly evolving. While gene duplication and loss, gene isomerism, recruitment, and rearrangements have occurred sporadically in several
Fu-Jung Lin et al.
PLoS genetics, 9(5), e1003516-e1003516 (2013-05-30)
Mouse Ikbkap gene encodes IKAP--one of the core subunits of Elongator--and is thought to be involved in transcription. However, the biological function of IKAP, particularly within the context of an animal model, remains poorly characterized. We used a loss-of-function approach
Małgorzata Cieśla et al.
Biochimica et biophysica acta, 1843(6), 1103-1110 (2014-03-01)
Yeast Fba1 (fructose 1,6-bisphosphate aldolase) is a glycolytic enzyme essential for viability. The overproduction of Fba1 enables overcoming of a severe growth defect caused by a missense mutation rpc128-1007 in a gene encoding the C128 protein, the second largest subunit
Yang Zhou et al.
Nucleic acids research, 41(11), 5669-5678 (2013-04-23)
The conserved pre-mRNA retention and splicing (RES) complex, which in yeast consists of Bud13p, Snu17p and Pml1p, is thought to promote nuclear retention of unspliced pre-mRNAs and enhance splicing of a subset of transcripts. Here, we find that the absence
Wei Wan et al.
Biochimica et biophysica acta, 1844(6), 1059-1070 (2014-03-19)
The genetic incorporation of the 22nd proteinogenic amino acid, pyrrolysine (Pyl) at amber codon is achieved by the action of pyrrolysyl-tRNA synthetase (PylRS) together with its cognate tRNA(Pyl). Unlike most aminoacyl-tRNA synthetases, PylRS displays high substrate side chain promiscuity, low
T Winckler
Die Pharmazie, 68(7), 467-473 (2013-08-09)
Almost 25 years ago, Theo Dingermann published the discovery of a new mobile genetic element in the unicellular microbe Dictyostelium discoideum in the journal Science. An interesting property of this new molecular parasite, the Dictyostelium Repetitive Element (DRE), was that
Hervé Seligmann et al.
Gene, 542(2), 248-257 (2014-02-25)
Mitochondrial light strand DNA replication is initiated at light strand replication origins (OLs), short stem-loop hairpins formed by the heavy strand DNA. OL-like secondary structures are also formed by heavy strand DNA templating for the five tRNAs adjacent to OLs
Beatriz A Castilho et al.
Biochimica et biophysica acta, 1843(9), 1948-1968 (2014-04-16)
The protein kinase Gcn2 is present in virtually all eukaryotes and is of increasing interest due to its involvement in a large array of crucial biological processes. Some of these are universally conserved from yeast to humans, such as coping
Fang Zhao et al.
Dong wu xue yan jiu = Zoological research, 34(E4-5), E109-E119 (2013-10-12)
The Riodinidae is one of the lepidopteran butterfly families. This study describes the complete mitochondrial genome of the butterfly species Abisara fylloides, the first mitochondrial genome of the Riodinidae family. The results show that the entire mitochondrial genome of A.
Igor Cestari et al.
Molecular and cellular biology, 33(24), 4872-4888 (2013-10-16)
The genes for all cytoplasmic and potentially all mitochondrial aminoacyl-tRNA synthetases (aaRSs) were identified, and all those tested by RNA interference were found to be essential for the growth of Trypanosoma brucei. Some of these enzymes were localized to the
Djemel Hamdane et al.
Biochemistry, 52(49), 8949-8956 (2013-11-16)
TrmFO is a tRNA methyltransferase that uses methylenetetrahydrofolate (CH2THF) and flavin adenine dinucleotide hydroquinone as cofactors. We have recently shown that TrmFO from Bacillus subtilis stabilizes a TrmFO-CH2-FADH adduct and an ill-defined neutral flavin radical. The adduct contains a unique
Yonatan Savir et al.
Cell, 153(2), 471-479 (2013-04-16)
The ribosome is a complex molecular machine that, in order to synthesize proteins, has to decode mRNAs by pairing their codons with matching tRNAs. Decoding is a major determinant of fitness and requires accurate and fast selection of correct tRNAs
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