Abstract：
:Ribonuclease MRP is an endonuclease, related to RNase P, which functions in eukaryotic pre-rRNA processing. In Saccharomyces cerevisiae, RNase MRP comprises an RNA subunit and ten proteins. To improve our understanding of subunit roles and enzyme architecture, we have examined protein-protein and protein-RNA interactions in vitro, complementing existing yeast two-hybrid data. In total, 31 direct protein-protein interactions were identified, each protein interacting with at least three others. Furthermore, seven proteins self-interact, four strongly, pointing to subunit multiplicity in the holoenzyme. Six protein subunits interact directly with MRP RNA and four with pre-rRNA. A comparative analysis with existing data for the yeast and human RNase P/MRP systems enables confident identification of Pop1p, Pop4p and Rpp1p as subunits that lie at the enzyme core, with probable addition of Pop5p and Pop3p. Rmp1p is confirmed as an integral subunit, presumably associating preferentially with RNase MRP, rather than RNase P, via interactions with Snm1p and MRP RNA. Snm1p and Rmp1p may act together to assist enzyme specificity, though roles in substrate binding are also indicated for Pop4p and Pop6p. The results provide further evidence of a conserved eukaryotic RNase P/MRP architecture and provide a strong basis for studies of enzyme assembly and subunit function.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Aspinall TV,Gordon JM,Bennett HJ,Karahalios P,Bukowski JP,Walker SC,Engelke DR,Avis JMdoi
10.1093/nar/gkm553subject
Has Abstractpub_date
2007-01-01 00:00:00pages
6439-50issue
19eissn
0305-1048issn
1362-4962pii
gkm553journal_volume
35pub_type
杂志文章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 transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks755
更新日期：2012-10-01 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 PAH Mutation Analysis Consortium (81 investigators, 26 countries) is engaged in mutation detection at the human PAH locus. Ascertainment of probands occurs largely through newborn screening for hyperphenylalaninemia. A relational database records allelic variation (disease-producing and polymorphic) at the locus. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.1.127
更新日期：1996-01-01 00:00:00
abstract：:With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh046
更新日期：2004-03-26 00:00:00
abstract：:The reaction of the tetranucleotide, pA-A(2)-A, with 2'(3')-0-(alpha-methoxyethyl)uridine 5'-diphosphate, Mg(2+) ions, and M. luteus polynucleotide phosphorylase followed by mild acid treatment to remove the blocking groups results in a 49% yield of the desired single addition product, pA-A(3)-U, together with smaller...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.12.1665
更新日期：1974-12-01 00:00:00
abstract：:AvrBs3, the founding member of the Xanthomonas transcription-activator-like effectors (TALEs), is translocated into the plant cell where it localizes to the nucleus and acts as transcription factor. The DNA-binding domain of AvrBs3 consists of 17.5 nearly-identical 34 amino acid-repeats. Each repeat specifies binding ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku341
更新日期：2014-06-01 00:00:00
abstract：:We show that in mouse myoblasts the MyoD1 promoter is highly stimulated by MyoD1 expression, suggesting that it is controlled by a positive feedback loop. Using deletion and mutation analyses, we identified the targets for MyoD1 promoter autoregulation as the two proximal E-boxes located close to the MyoD1 core promot...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.12.2234
更新日期：1994-06-25 00:00:00
abstract：:Many genetic manipulations are limited by difficulty in obtaining adequate levels of protein expression. Bioinformatic and experimental studies have identified nucleotide sequence features that may increase expression, however it is difficult to assess the relative influence of these features. Zebrafish embryos are ra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv035
更新日期：2015-04-20 00:00:00
abstract：:Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa826
更新日期：2020-11-04 00:00:00
abstract：:Primase synthesizes decaribonucleotides for priming of lagging and possibly leading strand synthesis at a replication fork. The sites of initiation by purified mouse primase were shown to be highly specific within the SV40 origin of replication. This study further examines the role of the 27-bp inverted repeat in the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.5.1953
更新日期：1989-03-11 00:00:00
abstract：:The web software SIC provides a tool to search for short inverted segments (length 3-5000 bp) in a DNA sequence. The sequence is assumed to follow a Markov model. A statistic which is sensitive to inversion is presented. Searching inverted segments is done by a scanning approach after the user specifies the size of th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg596
更新日期：2003-07-01 00:00:00
abstract：:Active DNA demethylation (ADDM) in mammals occurs via hydroxylation of 5-methylcytosine (5mC) by TET and/or deamination by AID/APOBEC family enzymes. The resulting 5mC derivatives are removed through the base excision repair (BER) pathway. At present, it is unclear how the cell manages to eliminate closely spaced 5mC ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw059
更新日期：2016-05-05 00:00:00
abstract：:A crucial step in analyzing mRNA-Seq data is to accurately and efficiently map hundreds of millions of reads to the reference genome and exon junctions. Here we present OLego, an algorithm specifically designed for de novo mapping of spliced mRNA-Seq reads. OLego adopts a multiple-seed-and-extend scheme, and does not ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt216
更新日期：2013-05-01 00:00:00
abstract：:Clustered damages are formed in DNA by ionising radiation and radiomimetic anticancer agents and are thought to be biologically severe. 7,8-dihydro-8-oxoguanine (8-oxoG), a major DNA damage resulting from oxidative attack, is highly mutagenic leading to a high level of G.C-->T.A transversions if not previously excised...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.5.1107
更新日期：2001-03-01 00:00:00
abstract：:This article describes recent developments of Europe PMC (http://europepmc.org), the leading database for life science literature. Formerly known as UKPMC, the service was rebranded in November 2012 as Europe PMC to reflect the scope of the funding agencies that support it. Several new developments have enriched Europ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1061
更新日期：2015-01-01 00:00:00
abstract：:Nuclei from frozen calf thymus suspended in buffer were analyzed for metal content prior to and after repeated washing. After three such extractions about 0.1 micrograms Zn/mg DNA and 0.025 micrograms Cu/mg DNA remained tightly associated with chromatin. This level of metal was essentially unchanged with subsequent wa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.21.5811
更新日期：1981-11-11 00:00:00
abstract：:Evidence has emerged that repair of clustered DNA lesions may be compromised, possibly leading to the formation of double-strand breaks (DSB) and, thus, to deleterious events. The first repair event occurring at a multiply damaged site (MDS) is of major importance and will largely contribute to the hazardousness of MD...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm190
更新日期：2007-01-01 00:00:00
abstract：:The GWIPS-viz browser (http://gwips.ucc.ie/) is an on-line genome browser which is tailored for exploring ribosome profiling (Ribo-seq) data. Since its publication in 2014, GWIPS-viz provides Ribo-seq data for an additional 14 genomes bringing the current total to 23. The integration of new Ribo-seq data has been auto...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx790
更新日期：2018-01-04 00:00:00
abstract：:Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most importan...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks069
更新日期：2012-06-01 00:00:00
abstract：:As large-scale re-sequencing of genomes reveals many protein mutations, especially in human cancer tissues, prediction of their likely functional impact becomes important practical goal. Here, we introduce a new functional impact score (FIS) for amino acid residue changes using evolutionary conservation patterns. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr407
更新日期：2011-09-01 00:00:00
abstract：:Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is n...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1280
更新日期：2016-01-08 00:00:00
abstract：:A UCSD Pascal program was developed which can analyze nucleic acid dot matrices of up to 9500 X 9500 in size on the Apple II computer. Although matrices of such size consume large amounts of computer memory, this program minimizes these problems by analyzing only small strips of the matrix at a time, and then transfer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.1part2.767
更新日期：1984-01-11 00:00:00
abstract：:RegulonDB, first published 20 years ago, is a comprehensive electronic resource about regulation of transcription initiation of Escherichia coli K-12 with decades of knowledge from classic molecular biology experiments, and recently also from high-throughput genomic methodologies. We curated the literature to keep Reg...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1077
更新日期：2019-01-08 00:00:00
abstract：:A sequence of 89 nucleotides from rabbit beta-globin mRNA has been determined and is shown to code for residues 107 to 137 of the beta-globin protein. In addition, a sequence heterogeneity has been identified within this 89 nucleotide long sequence which corresponds to a known polymorphic variant of rabbit beta-globin...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.7.1811
更新日期：1976-07-01 00:00:00
abstract：:VapD-like virulence-associated proteins have been found in many organisms, but little is known about this protein family including the 3D structure of these proteins. Recently, a relationship between the Cas2 family of ribonucleases associated with the CRISPR system of microbial immunity and VapD was suggested. Here, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1305
更新日期：2012-05-01 00:00:00
abstract：:Alternative splicing is widespread in mammalian gene expression, and variant splice patterns are often specific to different stages of development, particular tissues or a disease state. There is a need to systematically collect data on alternatively spliced exons, introns and splice isoforms, and to annotate this dat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh030
更新日期：2004-01-01 00:00:00
abstract：:Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr750
更新日期：2012-01-01 00:00:00
abstract：:Hepatitis B virus (HBV) replication is initiated by HBV RT binding to the highly conserved encapsidation signal, epsilon, at the 5' end of the RNA pregenome. Epsilon contains an apical stem-loop, whose residues are either totally conserved or show rare non-disruptive mutations. Here we present the structure of the api...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl582
更新日期：2006-01-01 00:00:00
abstract：:Using the quenched flow technique the mechanism of seryl tRNA synthetase action has been investigated with respect to the presteady state kinetics of individual steps. Under conditions where the strong binding sites of the enzyme are nearly saturated and the steady state turnover number is about 1 s-1, rate constants ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/8.17.4021
更新日期：1980-09-11 00:00:00
