Abstract：
:In many viruses and transposons, expression of some genes requires alternative reading of the genetic code, also called recoding. Such events depend on specific mRNA sequences and can lead to read through of an in-frame stop codon or to +1 or -1 frameshifting. Here, we addressed the issue of conservation of recoding rules between the yeast Saccharomyces cerevisiae and mammalian cells by establishing a versatile vector that can be used to study recoding in both species. We first assessed this vector by analysing the site of +1 frameshift of the Ty1 transposon. Two sequences from higher organisms were then tested in both yeast and mammalian cells: the gag-pol junction of human immunodeficiency virus type 1 (HIV-1) (a site of -1 frameshift), and the stop codon region of the replicase cistron from the tobacco mosaic virus (a site of UAG read through). We show that both sequences direct a high level of recoding in yeast. Furthermore, different mutations of the target sequences have similar effects on recoding in yeast and in mouse cells. Most notably, a strong decrease of frameshifting was observed in the absence of the HIV-1 stem-loop stimulatory signal. Taken together, these data suggest that mechanisms of some recoding events are conserved between lower and higher eukaryotes, thus allowing the use of S. cerevisiae as a model system to study recoding on target sequences from higher organisms.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Stahl G,Bidou L,Rousset JP,Cassan Mdoi
10.1093/nar/23.9.1557subject
Has Abstractpub_date
1995-05-11 00:00:00pages
1557-60issue
9eissn
0305-1048issn
1362-4962pii
4w0237journal_volume
23pub_type
杂志文章abstract：:The hydroxyl radical is a powerful oxidant that generates DNA lesions including the stereoisomeric R and S 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG) pairs that have been detected in cellular DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the human ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku162
更新日期：2014-04-01 00:00:00
abstract：:The mitochondrial DNA of Neurospora crassa has a heterogeneous intramolecular base distribution. A contiguous piece, representing at least 30% of the total genome, has a G+C content that is 6% lower than the overall G+C content of the DNA. The genes for both ribosomal RNAs are contained in the remaining, relatively G+...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.1.129
更新日期：1977-01-01 00:00:00
abstract：:An open reading frame upstream from nifHDK operon of Klebsiella pneumoniae had been described. The orientation of this open reading frame is opposite to that of nifHDK and sequence homology was found between the open reading frame promoter and the promoter of nifHDK operon. A recombinant plasmid carrying the promoter ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.12.4241
更新日期：1983-06-25 00:00:00
abstract：:A mutant at the carboxyl end of the terminal protein, p3, of phage phi 29 DNA has been constructed by inserting an containing the stop translation codon TGA in the three possible reading frames, immediately downstream of a phage phi 29 DNA fragment coding for all but the last five amino acids of protein p3. The activ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.21.7397
更新日期：1983-11-11 00:00:00
abstract：:Motif3D is a web-based protein structure viewer designed to allow sequence motifs, and in particular those contained in the fingerprints of the PRINTS database, to be visualised on three-dimensional (3D) structures. Additional functionality is provided for the rhodopsin-like G protein-coupled receptors, enabling finge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg534
更新日期：2003-07-01 00:00:00
abstract：:The properties of the interaction of 5-fluorocytosine-containing DNA with the EcoRII methyltransferase were studied. The DNA used was either a polymer synthesized in vitro, or a 20-mer containing one CCA/TGG sequence. The DNA could be methylated by the enzyme. In the process the enzyme formed a tight binding adduct wi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.12.3241
更新日期：1992-06-25 00:00:00
abstract：:From a sarkosyl-insoluble outer membrane fraction prepared from the Helicobacter pylori strain ATCC 43504, 19 proteins could be sequenced N-terminally by Edman degradation. Oligonucleotides were deduced and used for screening of a genomic library. From the isolated genes, five code for different members of a H.pylori ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.16.3325
更新日期：1999-08-15 00:00:00
abstract：:The bHLH transcription factor MyoD, the prototypical master regulator of differentiation, directs a complex program of gene expression during skeletal myogenesis. The up-regulation of the cdk inhibitor p57kip2 plays a critical role in coordinating differentiation and growth arrest during muscle development, as well as...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks619
更新日期：2012-09-01 00:00:00
abstract：:Starting from a crude E. coli extract, two activities which specifically protect highly repetitive bacterial DNA sequences (called PU for Palindromic Unit or REP for Repetitive Extragenic Palindromic sequence) against a digestion with Exonuclease III have been purified. We show that one of these activities is due to t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.13.3941
更新日期：1990-07-11 00:00:00
abstract：:Given that greater than 90% of the human genome is expressed, it is logical to assume that post-transcriptional regulatory mechanisms must be the primary means of controlling the flow of information from mRNA to protein. This report describes a robust approach that includes in silico, in vitro and in cellulo experimen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq557
更新日期：2010-11-01 00:00:00
abstract：:We present a simple and highly accurate computational method for operon prediction, based on intergenic distances and functional relationships between the protein products of contiguous genes, as defined by STRING database (Jensen,L.J., Kuhn,M., Stark,M., Chaffron,S., Creevey,C., Muller,J., Doerks,T., Julien,P., Roth,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq254
更新日期：2010-07-01 00:00:00
abstract：:A dnaB-like protein from P. aeruginosa was purified to near homogeneity using as an assay the immunoprecipitation by E. coli dnaB antiserum in a solid-phase. In the chromatographic characteristics including the affinity to immobilized ATP the dnaB-like protein of P. aeruginosa is similar to the dnaB protein of E. coli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.2.385
更新日期：1987-01-26 00:00:00
abstract：:Nuclear receptors for the thyroid hormone and vitamin A and D cooperate with the retinoid X receptor (RXR) in activating the transcription. Although the hormone response elements for these receptors have been proposed in which spacing of the direct repeated motifs determine the specificity (so called 3-4-5 rule), vita...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.15.2902
更新日期：1994-08-11 00:00:00
abstract：:We have reported previously (1) two unexpected consequences of the microinjection into fertilized mouse eggs of a recombinant plasmid designated p12B1, carrying a 343 bp insert of non-repetitive mouse DNA. Injected at very low concentrations, this plasmid could be established as an extrachromosomal genetic element. Wh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.25.7243
更新日期：1991-12-01 00:00:00
abstract：:SynergyFinder (https://synergyfinder.fimm.fi) is a stand-alone web-application for interactive analysis and visualization of drug combination screening data. Since its first release in 2017, SynergyFinder has become a widely used web-tool both for the discovery of novel synergistic drug combinations in pre-clinical mo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa216
更新日期：2020-07-02 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv561
更新日期：2015-07-01 00:00:00
abstract：:A series of plasmids were constructed in which a promoter was introduced into a lac-based operon fusion vector. A perfectly symmetrical oligonucleotide of 22-bp corresponding to an idealized binding site for cAMP receptor protein (CRP) of E. coli was chemically synthesized. The synthetic CRP site was placed between th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.15.7315
更新日期：1988-08-11 00:00:00
abstract：:Adenosine to inosine editing of mRNA from the human 5-HT2C receptor gene (HTR2C) occurs at five exonic positions (A-E) in a stable stem-loop that includes the normal 5' splice site of intron 5 and is flanked by two alternative splice sites. Using in vitro editing, we identified a novel editing site (F) located in the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh536
更新日期：2004-04-15 00:00:00
abstract：:ATP-dependent type I topoisomerases from extremely thermophilic archaebacteria--reverse gyrases--drive positive supercoiling of DNA. We showed that reverse gyrase from Desulfurococcus amylolyticus breaks the DNA at specific sites and covalently binds to the 5' end. In 30 out of 31 sites located in pBR322 DNA fragments...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.9.2801
更新日期：1990-05-11 00:00:00
abstract：:The nucleotide sequence of the 5S ribosomal RNA of Streptococcus cremoris has been determined. The sequence is 5' (sequence in text) 3'. Comparison of the S. cremoris 5S RNA sequence to an updated prokaryotic generalized 5S RNA structural model shows that this 5S RNA contains some unusual structural features. These fe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.21.7569
更新日期：1983-11-11 00:00:00
abstract：:We have isolated and sequenced the complete murine I-E alpha immune response gene of the H-2db haplotype. The I-E alpha d gene consists of 5300 basepairs and is organized into five or possibly six exons that correspond to different domains of the alpha chain. The amino acid sequence deduced from the I-E alpha gene sho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.15.5055
更新日期：1983-08-11 00:00:00
abstract：:The MyHits web site (http://myhits.isb-sib.ch) is an integrated service dedicated to the analysis of protein sequences. Since its first description in 2004, both the user interface and the back end of the server were improved. A number of tools (e.g. MAFFT, Jacop, Dotlet, Jalview, ESTScan) were added or updated to imp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm352
更新日期：2007-07-01 00:00:00
abstract：:Mariner transposition is a complex reaction that involves three recombination sites and six strand breaking and joining reactions. This requires precise spatial and temporal coordination between the different components to ensure a productive outcome and minimize genomic instability. We have investigated how the cleav...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku172
更新日期：2014-05-01 00:00:00
abstract：:Riboswitch RNAs fold into complex tertiary structures upon binding to their cognate ligand. Ligand recognition is accomplished by key residues in the binding pocket. In addition, it often crucially depends on the stability of peripheral structural elements. The ligand-bound complex of the guanine-sensing riboswitch fr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr664
更新日期：2011-12-01 00:00:00
abstract：:The cloned 18 S ribosomal RNA gene from Saccharomyces cerevisiae have been sequenced, using the Maxam-Gilbert procedure. From this data the complete sequence of 1789 nucleotides of the 18 S RNA was deduced. Extensive homology with many eucaryotic as well as E. coli ribosomal small subunit rRNA (S-rRNA) has been observ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.23.5779
更新日期：1980-12-11 00:00:00
abstract：:Proper expression of the genes of the human beta-globin gene locus requires the associated locus control region (LCR). Structurally, the LCR is defined by the presence of four domains of erythroid-specific chromatin structure. These domains, which have been characterized as DNase I hypersensitive sites (HSs), comprise...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.24.5684
更新日期：1998-12-15 00:00:00
abstract：:A novel cytoplasmic gene expression system has been developed. This system differs from other expression systems in that it relies on the co-delivery of plasmid DNA and T7 RNA polymerase (RNAP) during transfection. The plasmid contains a T7 RNAP gene driven by the T7 promoter (T7 autogene) and a functional/reporter ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.11.2114
更新日期：1994-06-11 00:00:00
abstract：:Human immunodeficiency virus type 2 (HIV-2) reverse transcription is initiated from cellular tRNA(Lys3) partially annealed to the RNA viral genome at the primer binding site (PBS). This annealing involves interactions between two highly structured RNA molecules. In contrast to HIV-1, in which the reverse transcription...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.13.2757
更新日期：2001-07-01 00:00:00
abstract：:PRINTS is a database of protein family 'fingerprints' offering a diagnostic resource for newly-determined sequences. By contrast with PROSITE, which uses single consensus expressions to characterise particular families, PRINTS exploits groups of motifs to build characteristic signatures. These signatures offer improve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.1.304
更新日期：1998-01-01 00:00:00
abstract：:Chromatin assembly factor 1 (CAF-1) is a histone H3-H4 chaperone that deposits newly synthesized histone (H3-H4)2 tetramers during replication-coupled nucleosome assembly. However, how CAF-1 functions in this process is not yet well understood. Here, we report the crystal structure of C terminus of Cac1 (Cac1C), a sub...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw106
更新日期：2016-06-20 00:00:00
