Abstract:
:Mobile introns and inteins self-propagate by 'homing', a gene conversion process initiated by site-specific homing endonucleases. The VMA intein, which encodes the PI-SceI endonuclease in Saccharomyces cerevisiae, is present in several different yeast strains. Surprisingly, a wild wine yeast (DH1-1A) contains not only the intein(+) allele, but also an inteinless allele that has not undergone gene conversion. To elucidate how these two alleles co-exist, we characterized the endonuclease encoded by the DH1-1A intein(+) allele and the target site in the intein(-) allele. Sequence analysis reveals seven mutations in the 31 bp recognition sequence, none of which occurs at positions that are individually critical for activity. However, binding and cleavage of the sequence by PI-SceI is reduced 10-fold compared to the S.cerevisiae target. The PI-SceI analog encoded by the DH1-1A intein(+) allele contains 11 mutations at residues in the endonuclease and protein splicing domains. None affects protein splicing, but one, a R417Q substitution, accounts for most of the decrease in DNA cleavage and DNA binding activity of the DH1-1A protein. Loss of activity in the DH1-1A endonuclease and target site provides one explanation for co-existence of the intein(+) and intein(-) alleles.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gimble FSdoi
10.1093/nar/29.20.4215keywords:
subject
Has Abstractpub_date
2001-10-15 00:00:00pages
4215-23issue
20eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract::The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki113
更新日期:2005-01-01 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
abstract::The compilation of 5S rRNA and 5S rRNA gene nucleotide sequences as of 30 September 1996, contains a total of 1661 primary structures of 5S rRNAs or their genes, which is an increase of 928 new sequence entries over the last compilation. It covers sequences from 54 archaea, 449 eubacteria, 34 plastids, nine mitochondr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.96
更新日期:1997-01-01 00:00:00
abstract::Human Hepatitis B Virus (HBV) RNAs contain a cis -acting sequence, the post-transcriptional regulatory element (HPRE), which facilitates the cytoplasmic localization of intronless transcripts. Our previous studies have shown that the HPRE is composed of at least two independent sub-elements, HPREalpha and HPREbeta, wh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.4818
更新日期:1998-11-01 00:00:00
abstract::The Superimposé webserver performs structural similarity searches with a preference towards 3D structure-based methods. Similarities can be detected between small molecules (e.g. drugs), parts of large structures (e.g. binding sites of proteins) and entire proteins. For this purpose, a number of algorithms were implem...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkn285
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abstract::Two enzymatic pathways are involved in the inhibitory effects of double-stranded (ds)RNA on protein synthesis in cell extracts derived from interferon-treated human fibroblasts or HeLa cells, an oligonucleotide polymerase that synthesizes (2'-5')An from ATP and a protein kinase that phosphorylates the alpha subunit of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.19.4939
更新日期:1981-10-10 00:00:00
abstract::The enzyme endonuclease V nicks uracil-containing DNA at the second or third phosphodiester bond 3' to uracil sites. I applied the enzyme to random fragmentation of DNA to revise the complex DNA shuffling protocol. The merit of using endonuclease V is that cleavage occurs at random sites and the length of the fragment...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf139
更新日期:2002-12-15 00:00:00
abstract::Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.21.9933
更新日期:1988-11-11 00:00:00
abstract::Organisms growing at elevated temperatures face the challenge of maintaining the integrity of their genetic materials. Archaea possess unique chromatin proteins for gene organization and information processing. We present the solution structure of Sso7c4 from Sulfolobus solfataricus, which has a homodimeric DNA-bindin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr283
更新日期:2011-08-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz555
更新日期:2019-08-22 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.20.6383
更新日期:1982-10-25 00:00:00
abstract::Using a bio-oligo pull-down DNA-binding assay we investigated the binding capacity of endogenous, DNA damage-induced p53 in human diploid fibroblasts to several p53-responsive elements (REs) present in p53-regulated genes. During the course of p53 accumulation, we observed a decrease in p53 binding to the GADD45 but n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.11.2340
更新日期:2002-06-01 00:00:00
abstract::KU is a heterodimer, consisting of approximately 70 and approximately 80 kDa subunits (KU70 and KU80, respectively), which is involved in a variety of nuclear functions. We generated tbKU80-deficient trypanosomes to explore the potential role of the tbKU complex in telomere maintenance and transcriptional regulation o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh991
更新日期:2004-12-15 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::We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An eff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.17.8603
更新日期:1988-09-12 00:00:00
abstract::Smad proteins transduce signals from transforming growth factor-beta (TGF-beta) receptors and regulate transcription of target genes. TGF-beta is implicated in the regulation of the smooth muscle cell specific gene SM22alpha, but little is known about how Smads are involved in SM22alpha gene transcription. In this rep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg224
更新日期:2003-02-15 00:00:00
abstract::Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.3039
更新日期:1988-04-11 00:00:00
abstract::We describe the structure (3840 bp) of a novel Euglena gracilis chloroplast ribosomal protein operon that encodes the five genes rpl16-rpl14-rpl5-rps8-rpl36. The gene organization resembles the spc and the 3'-end of the S10 ribosomal protein operons of E. coli. The rpl5 is a new chloroplast gene not previously reporte...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.19.7591
更新日期:1989-10-11 00:00:00
abstract::Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic dist...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh815
更新日期:2004-09-07 00:00:00
abstract::The intrinsic stiffness of DNA limits its ability to be bent and twisted over short lengths, but such deformations are required for gene regulation. One classic paradigm is DNA looping in the regulation of the Escherichia coli lac operon. Lac repressor protein binds simultaneously to two operator sequences flanking th...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2007-01-01 00:00:00
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journal_title:Nucleic acids research
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更新日期:2004-11-23 00:00:00
abstract::Chicken-erythrocyte inner histone tetramer has been complexed with several natural and synthetic DNA duplexes by salt-gradient dialysis at various protein/DNA ratios. The resulting complexes, in low-ionic-strength buffer, have been examined by electron microscopy, circular dichroism, and thermal denaturation. Electron...
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更新日期:1978-10-01 00:00:00
abstract::By means of a combination of ion-exchange and sequence-specific affinity chromatography techniques, we have purified to homogeneity two protein complexes binding in a human DNA region (B48) previously recognized to contain a DNA replication origin. The DNA sequence used for the protein purification (B48 binding site) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.14.3257
更新日期:1993-07-11 00:00:00
abstract::An updated compilation of 300 E. coli mRNA promoter sequences is presented. For each sequence the most recent relevant paper was checked, to verify the location of the transcriptional start position as identified experimentally. We comment on the reliability of the sequence databanks and analyze the conservation of kn...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.7.1507
更新日期:1993-04-11 00:00:00
abstract::Mutant AraC proteins were selected for their ability to induce but not to repress, or their ability to repress but not to induce the araBAD operon. One such unusual mutant is able to bind to the araI site with an affinity only two to three-fold weaker than the wild type AraC protein, but the mutant protein was shown, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.14.5019
更新日期:1985-07-25 00:00:00
abstract::The 16S ribosomal RNA mutation database (16SMDB) provides a list of mutated positions in 16S ribosomal RNA from Escherichia coli and the identity of each alteration. Information provided for each mutation includes: (i) a brief description of the phenotype(s) associated with each mutation; (ii) whether a mutant phenoty...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.166
更新日期:1996-01-01 00:00:00
abstract::5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx473
更新日期:2017-06-20 00:00:00
abstract::Late SV40 16S and 19S mRNAs were found to contain an average of three m6A residues per mRNA molecule. The methylated residues of both the viral and cellular mRNAs occur in two sequences; Gpm6ApC and (Ap)nm6ApC, where n = 1-4. More than 60% of the m6A residues in SV40 16S and 19S mRNAs occur in Gpm6ApC even though ther...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1979-06-25 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn647
更新日期:2008-12-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh085
更新日期:2004-06-17 00:00:00