Abstract:
:Lateral ribosomal stalk is responsible for binding and recruiting translation factors during protein synthesis. The eukaryotic stalk consists of one P0 protein with two copies of P1•P2 heterodimers to form a P0(P1•P2)₂ pentameric P-complex. Here, we have solved the structure of full-length P1•P2 by nuclear magnetic resonance spectroscopy. P1 and P2 dimerize via their helical N-terminal domains, whereas the C-terminal tails of P1•P2 are unstructured and can extend up to ∼125 Å away from the dimerization domains. (15)N relaxation study reveals that the C-terminal tails are flexible, having a much faster internal mobility than the N-terminal domains. Replacement of prokaryotic L10(L7/L12)₄/L11 by eukaryotic P0(P1•P2)₂/eL12 rendered Escherichia coli ribosome, which is insensitive to trichosanthin (TCS), susceptible to depurination by TCS and the C-terminal tail was found to be responsible for this depurination. Truncation and insertion studies showed that depurination of hybrid ribosome is dependent on the length of the proline-alanine rich hinge region within the C-terminal tail. All together, we propose a model that recruitment of TCS to the sarcin-ricin loop required the flexible C-terminal tail, and the proline-alanine rich hinge region lengthens this C-terminal tail, allowing the tail to sweep around the ribosome to recruit TCS.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Lee KM,Yusa K,Chu LO,Yu CW,Oono M,Miyoshi T,Ito K,Shaw PC,Wong KB,Uchiumi Tdoi
10.1093/nar/gkt636subject
Has Abstractpub_date
2013-10-01 00:00:00pages
8776-87issue
18eissn
0305-1048issn
1362-4962pii
gkt636journal_volume
41pub_type
杂志文章abstract::Proteins engage in highly selective interactions with their macromolecular partners. Sequence variants that alter protein binding affinity may cause significant perturbations or complete abolishment of function, potentially leading to diseases. There exists a persistent need to develop a mechanistic understanding of i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw374
更新日期:2016-07-08 00:00:00
abstract::Bacteriophage T4 Dda helicase has recently been shown to be active as a monomer for unwinding of short duplex oligonucleotides and for displacing streptavidin from 3'-biotinylated oligonucleotides. However, its activity for streptavidin displacement and DNA unwinding has been shown to increase as the number of Dda mol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl369
更新日期:2006-05-31 00:00:00
abstract::Bacillus subtilis OhrR is a dimeric repressor that senses organic peroxides and regulates the expression of the OhrA peroxiredoxin. Derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1052
更新日期:2009-03-01 00:00:00
abstract::Cadmium (Cd2+) is a known carcinogen that inactivates the DNA mismatch repair (MMR) pathway. In this study, we have tested the effect of Cd2+ exposure on the enzymatic activity of the mismatch binding complex MSH2-MSH6. Our results indicate that Cd2+ is highly inhibitory to the ATP binding and hydrolysis activities of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki291
更新日期:2005-03-03 00:00:00
abstract::Chinese hamster genomic DNA sequences from the region downstream of the dihydrofolate reductase (DHFR) gene reported to contain a chromosomal origin of bidirectional DNA replication (OBR-1) were tested for their ability to support autonomous DNA replication in human cells. A 13.3 kilobase fragment containing OBR-1 and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.22.5971
更新日期:1992-11-25 00:00:00
abstract::In most cells, transcriptionally inactive heterochromatin is preferentially localized in the nuclear periphery and transcriptionally active euchromatin is localized in the nuclear interior. Different cell types display characteristic chromatin distribution patterns, which change dramatically during cell differentiatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz123
更新日期:2019-05-21 00:00:00
abstract::Starting from a synthetic E. coli promoter with the consensus sequences at -35 and -10 regions, a sequence CAT frequently occurred in the RNA start points of natural promoters was introduced in the downstream of the consensus sequences, and the sequences around the RNA start points as well as the relative positions of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.11.4085
更新日期:1985-06-11 00:00:00
abstract::The promoter region of the mouse CCAAT-Enhancer Binding Protein (C/EBP alpha) gene is capable of directing high levels of expression of reporter constructs in various cell lines, albeit even in cells that do not express their endogenous C/EBP alpha gene. To understand the molecular mechanisms underlying this ubiquitou...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.8.1735
更新日期:1993-04-25 00:00:00
abstract::Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the uniq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1237
更新日期:2014-02-01 00:00:00
abstract::In eukaryotes, exposure to stress conditions causes a shift from cap-dependent to cap-independent translation. In trypanosomatids, environmental switches are the driving force of a developmental program of gene expression, but it is yet unclear how their translation machinery copes with their constantly changing envir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr555
更新日期:2011-10-01 00:00:00
abstract::Extracellular and intracellular barriers typically prevent non-viral gene vectors from having an effective transfection efficiency. Formulation of a gene delivery vehicle that can overcome the barriers is a key step for successful tissue regeneration. We have developed a novel core-shelled DNA nanoparticle by invoking...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni171
更新日期:2005-11-03 00:00:00
abstract::We have constructed simple test-plasmids to study transcriptional enhancers in yeast. In this paper the reporter-gene is a plasmid borne deletion-substitution derivative (his-del4) of the Saccharomyces cerevisiae HIS3 gene in which the native promoter has been replaced by a dormant, susceptible pseudopromoter. We inve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.18.8847
更新日期:1988-09-26 00:00:00
abstract::African trypanosomes are extracellular protozoan parasites that are transmitted from one mammalian host to the next by tsetse flies. Bloodstream forms express variant surface glycoprotein (VSG); the tsetse fly (procyclic) forms express instead the procyclic acidic repetitive protein (PARP). PARP mRNA is abundant in pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.7.1202
更新日期:1996-04-01 00:00:00
abstract::The goal of the present study is to identify genes that respond to iron availability. Suppression subtraction hybridization (SSH) was used to generate cDNA libraries from iron loaded and control human astrocytoma cells (SW1088). The cDNA libraries were screened with antisense cDNA probes obtained from mRNA isolated fr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.8.1802
更新日期:2000-04-15 00:00:00
abstract::Purified 15 S globin mRNA-protein (mRNP) complexes obtained by EDTA dissociation of duck reticulocytes polyribosomes were digested with the calcium dependant Staphylococcus aureus nuclease (EC 3. 1. 4. 7.). 25% of the globin mRNA sequences were resistant to extensive nuclease digestion as determined by TCA precipitati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.8.2787
更新日期:1979-06-25 00:00:00
abstract::The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks994
更新日期:2013-01-01 00:00:00
abstract::Quantitative real-time PCR (qPCR) is the method of choice for specific and sensitive quantification of nucleic acids. However, data validation is still a major issue, partially due to the complex effect of PCR inhibition on the results. If undetected PCR inhibition may severely impair the accuracy and sensitivity of r...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr778
更新日期:2012-02-01 00:00:00
abstract::The tissue specificity of mitochondrial tRNA mutations remains largely elusive. In this study, we demonstrated the deleterious effects of tRNAThr 15927G>A mutation that contributed to pathogenesis of coronary artery disease. The m.15927G>A mutation abolished the highly conserved base-pairing (28C-42G) of anticodon ste...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky1241
更新日期:2019-02-28 00:00:00
abstract::Recent evidence indicates a link between Parkinson's Disease (PD) and the expression of a-synuclein (SNCA) isoforms with different 3' untranslated regions (3'UTRs). Yet, the post-transcriptional mechanisms regulating SNCA expression are unknown. Using a large-scale in vitro /in silico screening we identified RNA-bindi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1048
更新日期:2017-12-15 00:00:00
abstract::The recent publication of the Caenorhabditis elegans cisRED database has provided an extensive catalog of upstream elements that are conserved between nematode genomes. We have performed a secondary analysis to determine which subsequences of the cisRED motifs are found in multiple locations throughout the C. elegans ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq003
更新日期:2010-05-01 00:00:00
abstract::Transcription factors (TFs) and miRNAs are the most important dynamic regulators in the control of gene expression in multicellular organisms. These regulatory elements play crucial roles in development, cell cycling and cell signaling, and they have also been associated with many diseases. The Regulatory Network Anal...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks573
更新日期:2012-07-01 00:00:00
abstract::Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.24.5609
更新日期:1998-12-15 00:00:00
abstract::Understanding the normal state of human tissue transcriptome profiles is essential for recognizing tissue disease states and identifying disease markers. Recently, the Human Protein Atlas and the FANTOM5 consortium have each published extensive transcriptome data for human samples using Illumina-sequenced RNA-Seq and ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv608
更新日期:2015-08-18 00:00:00
abstract::Chemically modified siRNAs are expected to have resistance toward nuclease degradation and good thermal stability in duplex formation for in vivo applications. We have recently found that 2'-OMe-4'-thioRNA, a hybrid chemical modification based on 2'-OMeRNA and 4'-thioRNA, has high hybridization affinity for complement...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks204
更新日期:2012-07-01 00:00:00
abstract::The replication control circuit of the FII plasmids R1, R100 and R6-5 involves a small untranslated RNA molecule of about 93 nucleotides. This RNA, designated CopA RNA in plasmid R1, acts in vivo as a post-transcriptional inhibitor of the expression of the RepA protein whose synthesis is required for each round of pla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2523
更新日期:1986-03-25 00:00:00
abstract::DNA primases recognize single-stranded DNA (ssDNA) sequences to synthesize RNA primers during lagging-strand replication. Arabidopsis thaliana encodes an ortholog of the DNA primase-helicase from bacteriophage T7, dubbed AtTwinkle, that localizes in chloroplasts and mitochondria. Herein, we report that AtTwinkle synth...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx745
更新日期:2017-10-13 00:00:00
abstract::Well defined biomacromolecular patterns such as binding sites, catalytic sites, specific protein or nucleic acid sequences, etc. precisely modulate many important biological phenomena. We introduce PatternQuery, a web-based application designed for detection and fast extraction of such patterns. The application uses a...
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::The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1154
更新日期:2018-01-04 00:00:00
abstract::The NCBI Taxonomy database (http://www.ncbi.nlm.nih.gov/taxonomy) is the standard nomenclature and classification repository for the International Nucleotide Sequence Database Collaboration (INSDC), comprising the GenBank, ENA (EMBL) and DDBJ databases. It includes organism names and taxonomic lineages for each of the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1178
更新日期:2012-01-01 00:00:00
abstract::An R-loop is a DNA:RNA hybrid formed during transcription when a DNA duplex is invaded by a nascent RNA transcript. R-loops accumulate in nucleoli during RNA polymerase I (RNAP I) transcription. Here, we report that mammalian RNase H1 enriches in nucleoli and co-localizes with R-loops in cultured human cells. Co-migra...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx710
更新日期:2017-10-13 00:00:00