Abstract：
:Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision repair (BER) glycosylase endonuclease III, for which functional homologs have been identified and characterized in Escherichia coli, yeast and humans. So far, little is known about how hyperthermophilic Archaea cope with such pyrimidine damage. Here we report characterization of an endonuclease III homolog, PaNth, from the hyperthermophilic archaeon Pyrobaculum aerophilum, whose optimal growth temperature is 100 degrees C. The predicted product of 223 amino acids shares significant sequence homology with several [4Fe-4S]-containing DNA N:-glycosylases including E.coli endonuclease III (EcNth). The histidine-tagged recombinant protein was expressed in E.coli and purified. Under optimal conditions of 80-160 mM NaCl and 70 degrees C, PaNth displays DNA glycosylase/ss-lyase activity with the modified pyrimidine base 5,6-dihydrothymine (DHT). This activity is enhanced when DHT is paired with G. Our data, showing the structural and functional similarity between PaNth and EcNth, suggests that BER of modified pyrimidines may be a conserved repair mechanism in Archaea. Conserved amino acid residues are identified for five subfamilies of endonuclease III/UV endonuclease homologs clustered by phylogenetic analysis.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yang H,Phan IT,Fitz-Gibbon S,Shivji MK,Wood RD,Clendenin WM,Hyman EC,Miller JHdoi
10.1093/nar/29.3.604keywords:
subject
Has Abstractpub_date
2001-02-01 00:00:00pages
604-13issue
3eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract：:The pDd56 mRNA sequence is highly enriched in prestalk over prespore cells and is inducible by DIF, the putative Dictyostelium stalk-specific morphogen. We show that the pDd56 gene is composed of forty one copies of a twenty four amino acid, cysteine rich repeat. This is highly homologus to a repeat which we have prev...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.18.7463
更新日期：1987-09-25 00:00:00
abstract：:Mouse DNA contains two equally abundant, homologous subfamilies of MspI 3.6 and 5 kb repeated fragments. The first subfamily corresponds to the previously described (1) Bam 4 kb repeats, the second one to Bam repeated fragments of higher molecular weight. These subfamilies account for the vast majority of long Bam rep...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.3.1593
更新日期：1984-02-10 00:00:00
abstract：:Toscana virus (TOSV) is an arthropod-borne human pathogen responsible for seasonal outbreaks of fever and meningoencephalitis in the Mediterranean basin. TOSV is a segmented negative-strand RNA virus (sNSV) that belongs to the genus phlebovirus (family Phenuiviridae, order Bunyavirales), encompassing other important h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz838
更新日期：2019-11-18 00:00:00
abstract：:The (cytosine-5) DNA methyltransferase M.HhaI causes its target cytosine base to be flipped completely out of the DNA helix upon binding. We have investigated the effects of replacing the target cytosine by other, mismatched bases, including adenine, guanine, thymine and uracil. We find that M.HhaI binds more tightly ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.8.1388
更新日期：1995-04-25 00:00:00
abstract：:Soil salinity is a significant threat to sustainable agricultural production worldwide. Plants must adjust their developmental and physiological processes to cope with salt stress. Although the capacity for adaptation ultimately depends on the genome, the exceptional versatility in gene regulation provided by the spli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1229
更新日期：2018-02-28 00:00:00
abstract：:Maintaining genome integrity is important for cells and damaged DNA triggers autoimmunity. Previous studies have reported that Three-prime repair exonuclease 1(TREX1), an endogenous DNA exonuclease, prevents immune activation by depleting damaged DNA, thus preventing the development of certain autoimmune diseases. Con...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx178
更新日期：2017-05-05 00:00:00
abstract：:Exposure of pyrimidines of DNA to ionizing radiation under aerobic conditions or oxidizing agents results in attack on the 5,6 double bond of the pyrimidine ring or on the exocyclic 5-methyl group. The primary product of oxidation of the 5,6 double bond of thymine is thymine glycol, while oxidation of the 5-methyl gro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.16.3239
更新日期：1995-08-25 00:00:00
abstract：:As protein-protein interactions are crucial in most biological processes, it is valuable to understand how and where protein pairs interact. We developed a web server HOMCOS (Homology Modeling of Complex Structure, http://biunit.naist.jp/homcos) to predict interacting protein pairs and interacting sites by homology mo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn218
更新日期：2008-07-01 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：: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：:The multiprotein complexes involved in active dis-ruption of chromatin structure, homologous to yeast SWI/SNF complex, have been described for human and Drosophila cells. In all SWI/SNF-class complexes characterised so far, one of the key components is the SNF5-type protein. Here we describe the isolation of a plant (...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.11.2393
更新日期：1999-06-01 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：:Enzymes of intermediary metabolism are often reported to have moonlighting functions as RNA-binding proteins and have regulatory roles beyond their primary activities. Human serine hydroxymethyltransferase (SHMT) is essential for the one-carbon metabolism, which sustains growth and proliferation in normal and tumour c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz129
更新日期：2019-05-07 00:00:00
abstract：:Although mobility of the phylogenetically widespread group I introns appears to be mechanistically similar, the phage T4 intron-encoded endonucleases that promote mobility of the td and sunY introns are different from their eukaryotic counterparts. Most notably, they cleave at a distance from the intron insertion site...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.13.3763
更新日期：1990-07-11 00:00:00
abstract：:The editing function of aminoacyl-tRNA synthetases (aaRSs) is indispensible for formation of the correct aminoacyl-tRNAs. Editing deficiency may lead to growth inhibition and the pathogenesis of various diseases. Herein, we confirmed that norvaline (Nva) but not isoleucine or valine is the major threat to the editing ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx487
更新日期：2017-07-07 00:00:00
abstract：:R spider is a web-based tool for the analysis of a gene list using the systematic knowledge of core pathways and reactions in human biology accumulated in the Reactome and KEGG databases. R spider implements a network-based statistical framework, which provides a global understanding of gene relations in the supplied ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq482
更新日期：2010-07-01 00:00:00
abstract：:The products of the RAG-1 and RAG-2 genes are essential for the recombination of the DNA encoding the antigen receptors of the developing immune system. Little is known of the specific role these genes play. We have explored the sequences encoding mouse RAG-1 by deleting large parts of the gene and by introducing loca...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.24.5644
更新日期：1993-12-11 00:00:00
abstract：:Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa793
更新日期：2021-01-08 00:00:00
abstract：:Cellular RNAs that do not function as messenger RNAs (mRNAs), transfer RNAs (tRNAs) or ribosomal RNAs (rRNAs) comprise a diverse class of molecules that are commonly referred to as non-protein-coding RNAs (ncRNAs). These molecules have been known for quite a while, but their importance was not fully appreciated until ...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkj469
更新日期：2006-01-25 00:00:00
abstract：:A simple and efficient gene replacement method, based on the recombination and repair activities of the cell, was developed. The method permits the targeted construction of markerless deletions, insertions and point mutations in the Escherichia coli chromosome. A suicide plasmid, carrying the mutant allele and the rec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.22.4409
更新日期：1999-11-15 00:00:00
abstract：:Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the alpha- and beta-subunits, respectively, are not in a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1079
更新日期：2010-03-01 00:00:00
abstract：:We developed a sensitive 32P-postlabeling method for the detection of bifunctional intrastrand crosslinks d(Pt-GpG) and d(Pt-ApG) in DNA in vitro and in vivo. After enzymatic digestion of DNA the positively charged platinum adducts were purified from unplatinated products, using strong cation exchange chromatography. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.8.1300
更新日期：1995-04-25 00:00:00
abstract：:The human beta-globin LCR plays a key role in the transcriptional regulation of the beta-globin locus and comprises four erythroid specific DNase I hypersensitive sites, designated 5'HS1-4. We have now isolated genomic clones containing 5'HS3 and 5'HS4 of the mouse beta-globin LCR. 5'HS3 and 5'HS4 are located 15 kb an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.21.5797
更新日期：1992-11-11 00:00:00
abstract：:We describe here the cloning, characterization and expression in E. coli of the gene coding for a DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). This enzyme methylates completely and exclusively CpG sequences. The Spiroplasma gene was transcribed in E. coli using its own promoter. Translation of the entire me...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.5.1145
更新日期：1990-03-11 00:00:00
abstract：:Escherichia coli seryl-tRNA synthetase (SerRS) is a homo-dimeric class II aminoacyl-tRNA synthetase. Each subunit is composed of two distinct domains: the N-terminal domain is a 60 A long, arm-like coiled coil structure built up of two antiparallel alpha-helices, whereas the C-terminal domain, the catalytic core, is a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.7.1113
更新日期：1995-04-11 00:00:00
abstract：:The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.15.3155
更新日期：1994-08-11 00:00:00
abstract：:The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPre...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq318
更新日期：2010-07-01 00:00:00
abstract：:Gene Ontology (GO) is the most widely accepted attempt to construct a unified and structured vocabulary for the description of genes and their products in any organism. Annotation by GO terms is performed in most of the current genome projects, which besides generality has the advantage of being very convenient for co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg582
更新日期：2003-07-01 00:00:00
abstract：:E. coli C6 rel- met- cys- was cultured in a fully supplemented medium and in media lacking cysteine or methionine. tRNA isolated from the three cultures containted, respectively, a normal complement of modified nucleosides; a deficiency in thiolated nucleosides and a deficiency in methylated nucleosides. Both sulfur-d...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/2.5.691
更新日期：1975-05-01 00:00:00
abstract：:In Trypanosoma brucei the genes are organised into long polycistronic transcription units and only three promoters for protein-encoding genes and a single terminator have been characterised. These promoters recruit a polI-like RNA polymerase for the transcription units encoding the two major stage-specific antigens of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.2.597
更新日期：2000-01-15 00:00:00
