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显示 31-60 共 122 条结果 关于 "R8508" 范围 论文
Jenna Friedt et al.
Nucleic acids research, 42(6), 3857-3870 (2013-12-29)
Pseudouridine synthases introduce the most common RNA modification and likely use the same catalytic mechanism. Besides a catalytic aspartate residue, the contributions of other residues for catalysis of pseudouridine formation are poorly understood. Here, we have tested the role of
Zhenhua Shao et al.
Nucleic acids research, 42(1), 509-525 (2013-10-02)
Transfer RNA (tRNA) methylation is necessary for the proper biological function of tRNA. The N(1) methylation of guanine at Position 9 (m(1)G9) of tRNA, which is widely identified in eukaryotes and archaea, was found to be catalyzed by the Trm10
Tatyana V Budkevich et al.
Cell, 158(1), 121-131 (2014-07-06)
The extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. Here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80S ribosome in the posttranslocational state and in
Miao-Miao Chen et al.
Gene, 545(1), 95-101 (2014-05-07)
Mitochondrial genome (mitogenome) can provide information for genomic structure as well as for phylogenetic analysis and evolutionary biology. In this study, we present the complete mitogenome of the atlas moth, Attacus atlas (Lepidoptera: Saturniidae), a well-known silk-producing and ornamental insect
Jun-Feng Gao et al.
Gene, 541(2), 92-100 (2014-03-15)
Bunostomum trigonocephalum and Bunostomum phlebotomum are blood-feeding hookworms of sheep and cattle, causing considerable economic losses to the live stock industries. Studying genetic variability within and among hookworm populations is critical to addressing epidemiological and ecological questions. Mitochondrial (mt) DNA
Structural biology: RNA exerts self-control.
Bhaskar Chetnani et al.
Nature, 500(7462), 279-280 (2013-07-31)
Premal Shah et al.
Cell, 153(7), 1589-1601 (2013-06-26)
Deep sequencing now provides detailed snapshots of ribosome occupancy on mRNAs. We leverage these data to parameterize a computational model of translation, keeping track of every ribosome, tRNA, and mRNA molecule in a yeast cell. We determine the parameter regimes
Jungwook Kim et al.
BMC structural biology, 13, 5-5 (2013-04-27)
Methylaminomethyl modification of uridine or 2-thiouridine (mnm5U34 or mnm5s2U34) at the wobble position of tRNAs specific for glutamate, lysine and arginine are observed in Escherichia coli and allow for specific recognition of codons ending in A or G. In the
Leo C K Wan et al.
Nucleic acids research, 41(12), 6332-6346 (2013-04-27)
The universally conserved Kae1/Qri7/YgjD and Sua5/YrdC protein families have been implicated in growth, telomere homeostasis, transcription and the N6-threonylcarbamoylation (t(6)A) of tRNA, an essential modification required for translational fidelity by the ribosome. In bacteria, YgjD orthologues operate in concert with
Lars V Bock et al.
Nature structural & molecular biology, 20(12), 1390-1396 (2013-11-05)
During protein synthesis, tRNAs move from the ribosome's aminoacyl to peptidyl to exit sites. Here we investigate conformational motions during spontaneous translocation, using molecular dynamics simulations of 13 intermediate-translocation-state models obtained by combining Escherichia coli ribosome crystal structures with cryo-EM
Daniel Castro-Roa et al.
Nature chemical biology, 9(12), 811-817 (2013-10-22)
Fic proteins are ubiquitous in all of the domains of life and have critical roles in multiple cellular processes through AMPylation of (transfer of AMP to) target proteins. Doc from the doc-phd toxin-antitoxin module is a member of the Fic
Keshab Rijal et al.
Gene, 556(1), 35-50 (2014-12-03)
Suppressor tRNAs bear anticodon mutations that allow them to decode premature stop codons in metabolic marker gene mRNAs, that can be used as in vivo reporters of functional tRNA biogenesis. Here, we review key components of a suppressor tRNA system
Alexis J Rovner et al.
Nature, 518(7537), 89-93 (2015-01-22)
Genetically modified organisms (GMOs) are increasingly used in research and industrial systems to produce high-value pharmaceuticals, fuels and chemicals. Genetic isolation and intrinsic biocontainment would provide essential biosafety measures to secure these closed systems and enable safe applications of GMOs
Jungwook Kim et al.
Nature, 498(7452), 123-126 (2013-05-17)
The identification of novel metabolites and the characterization of their biological functions are major challenges in biology. X-ray crystallography can reveal unanticipated ligands that persist through purification and crystallization. These adventitious protein-ligand complexes provide insights into new activities, pathways and
Rushia Turner et al.
RNA (New York, N.Y.), 19(12), 1857-1863 (2013-10-22)
Estimating the reactivity of 2'-hydroxyl groups along an RNA chain of interest aids in the modeling of the folded RNA structure; flexible loops tend to be reactive, whereas duplex regions are generally not. Among the most useful reagents for probing
Cheng-Ye Wang et al.
Zoological science, 30(7), 570-576 (2013-07-09)
The Japanese pine sawyer, Monochamus alternatus Hope, 1842, an important forest pest, mainly occurs in Far East. It is the main vector of pine wood nematode Bursaphelenchus xylophilus, which causes pine wilt disease. We determined the complete mitochondrial genome coding
Md Tauqeer Alam et al.
Gene, 539(1), 44-49 (2014-02-11)
The whale shark (Rhincodon typus) is the largest extant species of fish, belonging to the order Orectolobiformes. It is listed as a "vulnerable" species on the International Union for Conservation of Nature (IUCN)'s Red List of Threatened Species, which makes
Manuel Neeb et al.
Journal of medicinal chemistry, 57(13), 5554-5565 (2014-06-24)
Drug molecules should remain uncharged while traveling through the body and crossing membranes and should only adopt charged state upon protein binding, particularly if charge-assisted interactions can be established in deeply buried binding pockets. Such strategy requires careful pKa design
Ewa Morawiec et al.
Gene, 526(1), 16-22 (2013-05-10)
Maf1 is a negative regulator of RNA polymerase III (Pol III) in yeast. Maf1-depleted cells manifest elevated tRNA transcription and inability to grow on non-fermentable carbon source, such as glycerol. Using genomic microarray approach, we examined the effect of Maf1
Tek N Lamichhane et al.
Molecular and cellular biology, 33(15), 2918-2929 (2013-05-30)
tRNA isopentenyltransferases (Tit1) modify tRNA position 37, adjacent to the anticodon, to N6-isopentenyladenosine (i6A37) in all cells, yet the tRNA subsets selected for modification vary among species, and their relevance to phenotypes is unknown. We examined the function of i6A37
C Grunau et al.
Nucleic acids research, 29(13), E65-E65 (2001-07-04)
Bisulfite genomic sequencing is the method of choice for the generation of methylation maps with single-base resolution. The method is based on the selective deamination of cytosine to uracil by treatment with bisulfite and the sequencing of subsequently generated PCR
Ofer Elhanani et al.
Cell reports, 31(5), 107591-107591 (2020-05-07)
The emerging appreciation of plasticity among pancreatic lineages has created interest in harnessing cellular reprogramming for β cell replacement therapy of diabetes. Current reprogramming methodologies are inefficient, largely because of a limited understanding of the underlying mechanisms. Using an in vitro
Alan Hodgkinson et al.
Science (New York, N.Y.), 344(6182), 413-415 (2014-04-26)
Mutations in the mitochondrial genome are associated with multiple diseases and biological processes; however, little is known about the extent of sequence variation in the mitochondrial transcriptome. By ultra-deeply sequencing mitochondrial RNA (>6000×) from the whole blood of ~1000 individuals
Andreas A H Su et al.
Nucleic acids research, 41(12), 6250-6258 (2013-04-27)
The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA
Timothy M Colussi et al.
Nature, 511(7509), 366-369 (2014-06-10)
RNA is arguably the most functionally diverse biological macromolecule. In some cases a single discrete RNA sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. Such multifunctionality can also be driven or enhanced by the
Miao Chen et al.
Genes & development, 28(9), 959-970 (2014-05-03)
tRNAs are encoded by RNA polymerase III-transcribed genes that reside at seemingly random intervals along the chromosomes of budding yeast. Existing evidence suggests that the genes congregate together at the nucleolus and/or centromeres. In this study, we re-examined spatial and
Martijn J T N Timmermans et al.
Molecular phylogenetics and evolution, 79, 169-178 (2014-06-10)
The backbone phylogeny of Lepidoptera remains unresolved, despite strenuous recent morphological and molecular efforts. Molecular studies have focused on nuclear protein coding genes, sometimes adding a single mitochondrial gene. Recent advances in sequencing technology have, however, made acquisition of entire
Maria Rosa Garcia-Silva et al.
Gene, 538(2), 379-384 (2014-01-28)
The study of small RNAs and Argonaute proteins in eukaryotes that are deficient in functional RNA interference could provide insights into novel functions of small RNAs. In this study we describe small non-coding RNAs bound to a distinctive Argonaute protein
Sichen Shao et al.
Molecular cell, 50(5), 637-648 (2013-05-21)
Quality control of defective mRNAs relies on their translation to detect the lesion. Aberrant proteins are therefore an obligate byproduct of mRNA surveillance and must be degraded to avoid disrupting protein homeostasis. These defective translation products are thought to be
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
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