Abstract:
:Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1 HXB2 isolate, simultaneous mutations of the PBS and the A-rich loop (mutant His-AC), but not of the PBS alone (mutant His) allows the virus to stably utilize tRNA(His) as primer. However, mutant His-AC selects additional mutations during cell culture, generating successively His-AC-GAC and His-AC-AT-GAC. Here, we wanted to establish direct relationships between the evolution of these mutants in cell culture, their efficiency in initiating reverse transcription and the structure of the primer/template complexes in vitro. The initiation of reverse transcription of His and His-AC RNAs was dramatically reduced. However, His-AC-GAC RNA, which incorporated three adaptative point mutations, was reverse transcribed more efficiently than the wild type RNA. Incorporation of two additional mutations decreased the efficiency of the initiation of reverse transcription, which remained at the wild type level. Structural probing showed that even though both His-AC and His-AC-GAC RNAs can potentially interact with the anticodon loop of tRNA(His), only the latter template formed a stable interaction. Thus, our results showed that the selection of adaptative mutations by HIV-1 mutants utilizing tRNA(His) as primer was initially dictated by the efficiency of the initiation of reverse transcription, which relied on the existence of a stable interaction between the mutated A-rich loop and the anticodon loop of tRNA(His).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Rigourd M,Goldschmidt V,Brulé F,Morrow CD,Ehresmann B,Ehresmann C,Marquet Rdoi
10.1093/nar/gkg754keywords:
subject
Has Abstractpub_date
2003-10-01 00:00:00pages
5764-75issue
19eissn
0305-1048issn
1362-4962journal_volume
31pub_type
杂志文章abstract::Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By multimerizing the MDB domain of Mbd1, we engineered a poly-MBD protein that displays methyl-CpG-specific binding in vitro with a dissoci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl527
更新日期:2006-08-07 00:00:00
abstract::Aberrant Notch signaling plays a pivotal role in T-cell acute lymphoblastic leukemia (T-ALL) and chronic lymphocytic leukemia (CLL). Amplitude and duration of the Notch response is controlled by ubiquitin-dependent proteasomal degradation of the Notch1 intracellular domain (NICD1), a hallmark of the leukemogenic proce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa088
更新日期:2020-04-17 00:00:00
abstract::Calf lens messenger fractions have been purified on poly(dT)-cellulose. The purified RNA's have been analyzed as nucleosides by a method which can be used on a micro-scale with highly reproduceble results. Both the 10S and 14S lens mRNA contain poly A sequences. The poly A content found in 14S mRNA cannot account for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.245
更新日期:1974-02-01 00:00:00
abstract::Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1232
更新日期:2017-02-17 00:00:00
abstract::Expression of the matrix metalloproteinase (MMP) gene stromelysin-3 ( ST3 ) has been shown to be tightly associated with cell migration and apoptosis inmammals and amphibians. This contrasts with most other MMP genes. We demonstrate here that the Xenopus ST3 gene also has a structure distinct from other MMP genes, wit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.12.3018
更新日期:1998-06-15 00:00:00
abstract::The Metabolic Pathway Collection from EMP is an extraction of data from the larger Enzymes and Metabolic Pathways database (EMP). This extraction has been made publicly available in the hope that others will find it useful for a variety of purposes. The original release in October 1995 contained 1814 distinct pathways...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.37
更新日期:1997-01-01 00:00:00
abstract::Oriented DNA films prepared by the wet-spinning technique have been complexed with several ligands: the anthracycline antibiotic violamycin BI, the dipeptide L-carnosine, and the oligopeptide antibiotic netropsin. The formation of the DNA-ligand complexes is accompanied by dramatic changes of the conformational flexib...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.9165
更新日期:1984-12-11 00:00:00
abstract::MicA is a trans-encoded small non-coding RNA, which downregulates porin-expression in stationary-phase. In this work, we focus on the role of endoribonucleases III and E on Salmonella typhimurium sRNA MicA regulation. RNase III is shown to regulate MicA in a target-coupled way, while RNase E is responsible for the con...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1239
更新日期:2011-04-01 00:00:00
abstract::We have isolated and sequenced a cDNA clone coding for human Retinol Binding Protein. The sequence indicates that Retinol Binding Protein is synthesized as a single polypeptide chain precursor which is then matured to the secreted protein by removal of a leader peptide. Southern and Northern blot analysis suggest that...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.22.7769
更新日期:1983-11-25 00:00:00
abstract::Histone variants play an important role in shaping the mammalian epigenome and their aberrant expression is frequently observed in several types of cancer. However, the mechanisms that mediate their function and the composition of the variant-containing chromatin are still largely unknown. A proteomic interrogation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku303
更新日期:2014-06-01 00:00:00
abstract::Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.3.629
更新日期:1983-02-11 00:00:00
abstract::We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq275
更新日期:2010-07-01 00:00:00
abstract::The structure of eukaryotic chromatin has been investigated by isolating and analyzing the "accessible" DNA fraction of rat liver chromatin. This DNA fraction has been isolated by titrating the chromatin with the protese-resistant D isomer of polylysine to bind the "accessible" DNA sites. After removal of chromosomal ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.5.667
更新日期:1975-05-01 00:00:00
abstract::Human T-cell leukemia virus type 1 (HTLV-1) is the etiological agent of adult T-cell leukemia (ATL). The HTLV-1 basic leucine zipper protein (HBZ) is expressed in all cases of ATL and is directly associated with virus pathogenicity. The two isoforms of the HBZ protein are synthesized from antisense messenger RNAs (mRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky802
更新日期:2018-11-16 00:00:00
abstract::RNA structural complexity and flexibility present a challenge for computational modeling efforts. Experimental information and bioinformatics data can be used as restraints to improve the accuracy of RNA tertiary structure prediction. Regarding utilization of restraints, the fundamental questions are: (i) What is the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz427
更新日期:2019-06-20 00:00:00
abstract::Cultured mammalian cells transduced with the Escherichia coli gene, Ecogpt, synthesize the bacterial enzyme xanthine-guanine phosphoribosyl transferase (XGPT) (1). This paper describes a method for measuring XGPT activity in crude cell extracts by following the conversion of 14C-xanthine (X) to 14C-xanthine monophosph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.8.2921
更新日期:1985-04-25 00:00:00
abstract::The DNA sequence of a 225.4 kilobase segment of the Escherichia coli K-12 genome is described here, from 76.0 to 81.5 minutes on the genetic map. This brings the total of contiguous sequence from the E.coli genome project to 725.1 kb (76.0 to 92.8 minutes). We found 191 putative coding genes (ORFs) of which 72 genes w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.13.2576
更新日期:1994-07-11 00:00:00
abstract::Chemically modified antisense oligonucleotides (ASOs) with phosphorothioate (PS) linkages have been extensively studied as research and therapeutic agents. PS-ASOs can enter the cell and trigger cleavage of complementary RNA by RNase H1 even in the absence of transfection reagent. A number of cell surface proteins hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky145
更新日期:2018-04-20 00:00:00
abstract::The nuclear suppressor allele NSM3 in strain FF1210-6C/170-E22 (E22), which suppresses a mutation of the yeast mitochondrial tRNA(Asp)gene in Saccharomyces cerevisiae, was cloned and identified. To isolate the NSM3 allele, a genomic DNA library using the vector YEp13 was constructed from strain E22. Nine YEp13 recombi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.7.1542
更新日期:2000-04-01 00:00:00
abstract::The InParanoid eukaryotic ortholog database (http://InParanoid.sbc.su.se/) has been updated to version 6 and is now based on 35 species. We collected all available 'complete' eukaryotic proteomes and Escherichia coli, and calculated ortholog groups for all 595 species pairs using the InParanoid program. This resulted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1020
更新日期:2008-01-01 00:00:00
abstract::The Cox protein from bacteriophage P2 forms oligomeric filaments and it has been proposed that DNA can be wound up around these filaments, similar to how histones condense DNA. We here use fluorescence microscopy to study single DNA-Cox complexes in nanofluidic channels and compare how the Cox homologs from phages P2 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw352
更新日期:2016-09-06 00:00:00
abstract::We have compared the properties of the poly(rA).oligo(dT) complex with those of the poly(rU).oligo(dA)n complex. Three main differences were found. First, poly(rA) and oligo(dT)n do not form a complex in concentrations of CsCl exceeding 2 M because the poly(rA) is insoluble in high salt. If the complex is made in low ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.4.1013
更新日期:1976-04-01 00:00:00
abstract::Actin is a major cytoskeletal protein in eukaryotes. Recent studies suggest more diverse functional roles for this protein. Actin mRNA is known to be localized to neuronal synapses and undergoes rapid deadenylation during early developmental stages. However, its 3'-untranslated region (UTR) is not characterized and th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn624
更新日期:2008-11-01 00:00:00
abstract::The yeast protein Rrf1p encoded by the FIL1 nuclear gene bears significant sequence similarity to Escherichia coli ribosome recycling factor (RRF). Here, we call FIL1 Ribosome Recycling Factor of yeast, RRF1. Its gene product, Rrf1p, was localized in mitochondria. Deletion of RRF1 leads to a respiratory incompetent ph...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg449
更新日期:2003-07-15 00:00:00
abstract::Here, we report a webserver for the improved SDM, used for predicting the effects of mutations on protein stability. As a pioneering knowledge-based approach, SDM has been highlighted as the most appropriate method to use in combination with many other approaches. We have updated the environment-specific amino-acid su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx439
更新日期:2017-07-03 00:00:00
abstract::Interactions between proteins bound to distant sites along a DNA molecule require bending and twisting deformations in the intervening DNA. In certain systems, the sterically allowed protein-DNA and protein-protein interactions are hypothesized to produce loops with distinct geometries that may also be thermodynamical...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn389
更新日期:2008-07-01 00:00:00
abstract::ANISEED (www.aniseed.cnrs.fr) is the main model organism database for tunicates, the sister-group of vertebrates. This release gives access to annotated genomes, gene expression patterns, and anatomical descriptions for nine ascidian species. It provides increased integration with external molecular and taxonomy datab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1108
更新日期:2018-01-04 00:00:00
abstract::Optogenetic control of CRISPR-Cas9 systems has significantly improved our ability to perform genome perturbations in living cells with high precision in time and space. As new Cas orthologues with advantageous properties are rapidly being discovered and engineered, the need for straightforward strategies to control th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1198
更新日期:2020-12-16 00:00:00
abstract::The cellular response to DNA double-strand breaks (DSBs) is initiated by the Mre11-Rad50-Xrs2 (MRX) complex that has structural and catalytic functions. MRX association at DSBs is counteracted by Rif2, which is known to interact with Rap1 that binds telomeric DNA through two tandem Myb-like domains. Whether and how Ra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz1203
更新日期:2020-03-18 00:00:00
abstract::Reversion of T type cytoplasmic male sterility (cmsT) to fertility is correlated with sequence changes in a 1.5 kb AvaI fragment. This 1.5 kb AvaI fragment is composed of 5' flanking sequences of ATPase subunit 6, one complete open reading frame (ORF 13) and part of the another (ORF 25). The sequence of the 1.5 kb Ava...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.15.6091
更新日期:1987-08-11 00:00:00