Abstract：
:Homing endonuclease genes (HEGs) are mobile DNA elements that are thought to confer no benefit to their host. They encode site-specific DNA endonucleases that perpetuate the element within a species population by homing and disseminate it between species by horizontal transfer. Several yeast species contain the VMA1 HEG that encodes the intein-associated VMA1-derived endonuclease (VDE). The evolutionary state of VDEs from 12 species was assessed by assaying their endonuclease activities. Only two enzymes are active, PI-ZbaI from Zygosaccharomyces bailii and PI-ScaI from Saccharomyces cariocanus. PI-ZbaI cleaves the Z.bailii recognition sequence significantly faster than the Saccharomyces cerevisiae site, which differs at six nucleotide positions. A mutational analysis indicates that PI-ZbaI cleaves the S.cerevisiae substrate poorly due to the absence of a contact that is analogous to one made in PI-SceI between Gln-55 and nucleotides +9/+10. PI-ZbaI cleaves the Z.bailii substrate primarily due to a single base-pair substitution (A/T+5 --> T/A+5). Structural modeling of the PI-ZbaI/DNA complex suggests that Arg-331, which is absent in PI-SceI, contacts T/A+5, and the reduced activity observed in a PI-ZbaI R331A mutant provides evidence for this interaction. These data illustrate that homing endonucleases evolve altered specificity as they adapt to recognize alternative target sites.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Posey KL,Koufopanou V,Burt A,Gimble FSdoi
10.1093/nar/gkh734keywords:
subject
Has Abstractpub_date
2004-07-27 00:00:00pages
3947-56issue
13eissn
0305-1048issn
1362-4962pii
32/13/3947journal_volume
32pub_type
杂志文章abstract：:Biological evolution resulted in a homochiral world in which nucleic acids consist exclusively of d-nucleotides and proteins made by ribosomal translation of l-amino acids. From the perspective of synthetic biology, however, particularly anabolic enzymes that could build the mirror-image counterparts of biological mac...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx079
更新日期：2017-04-20 00:00:00
abstract：:Sox proteins belong to the HMG box superfamily of DNA-binding proteins and are found throughout the animal kingdom. They are involved in the regulation of such diverse developmental processes as germ layer formation, organ development and cell type specifi-cation. Hence, deletion or mutation of Sox proteins often resu...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/27.6.1409
更新日期：1999-03-15 00:00:00
abstract：:The c-myc proto-oncogene encodes a highly unstable mRNA. Stabilized, truncated myc transcripts have been found in several human and murine tumors of hematopoietic origin. Recently, two tumors expressing 3' truncated c-myc mRNAs that were five times more stable than normal myc transcripts, were described. We have tried...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.9.2387
更新日期：1991-05-11 00:00:00
abstract：:Several mono-, di-, tetra-, penta- and nonaribozymes were developed. These multitarget-ribozymes were targeted to cleave HIV-1 env RNA at up to nine different conserved sites. Each multitarget-ribozyme consisted of a chain of up to nine hammerhead motifs, each flanked by a different targeting sequence. The multitarget...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.17.4581
更新日期：1992-09-11 00:00:00
abstract：:Multiplexed tandem PCR (MT-PCR) is a process for highly multiplexed gene expression profiling. In the first step, multiple primer pairs are added to the RNA to be analysed together with reverse transcriptase and Taq DNA polymerase. Following reverse transcription, the multiplexed amplicons are simultaneously amplified...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gni182
更新日期：2005-11-24 00:00:00
abstract：:Genome browsers are widely used for individually exploring various types of genomic data. A handful of genome browsers offer limited tools for collaboration among multiple users. Here, we describe PBrowse, an integrated real-time collaborative genome browser that enables multiple users to simultaneously view and acces...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1358
更新日期：2017-05-19 00:00:00
abstract：:Recurrent chromosome aberrations are an important resource when associating human pathologies to specific genes. However, for technical reasons a large number of chromosome breakpoints are defined only at the level of cytobands and many of the genes involved remain unidentified. We developed a web-based information sy...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki061
更新日期：2005-01-01 00:00:00
abstract：:A study of the activity of deoxyribonucleotide-substituted analogs of the hammerhead domain of RNA catalysis has led to the design of a 14mer oligomer composed entirely of deoxyribonucleotides that promotes the cleavage of an RNA substrate. Characterization of this reaction with sequence variants and mixed DNA/RNA oli...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.20.4092
更新日期：1995-10-25 00:00:00
abstract：:Translational repression (TR) plays an important role in post-transcriptional regulation of gene expression and embryonic development in metazoans. TR also regulates the expression of a subset of the cytoplasmic mRNA population during development of fertilized female gametes of the unicellular malaria parasite, Plasmo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1142
更新日期：2008-03-01 00:00:00
abstract：:The locus DXS269 (P20) defines a deletion hotspot in the distal part of the Duchenne Muscular Dystrophy gene. We have cloned over 90 kilobase-pairs of genomic DNA from this region in overlapping cosmids. The use of whole cosmids as probes in a competitive DNA hybridization analysis proves a fast and convenient method ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.14.5611
更新日期：1989-07-25 00:00:00
abstract：:SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg535
更新日期：2003-07-01 00:00:00
abstract：:HSP90, found in all kingdoms of life, is a major chaperone protein regulating many client proteins. We demonstrated that HSP90α, one of two paralogs duplicated in vertebrates, plays an important role in the biogenesis of fetal PIWI-interacting RNAs (piRNA), which act against the transposon activities, in mouse male ge...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku881
更新日期：2014-10-29 00:00:00
abstract：:Minigenes encoding the peptide Met-Arg-Arg have been used to study the mechanism of toxicity of AGA codons proximal to the start codon or prior to the termination codon in bacteria. The codon sequences of the 'mini-ORFs' employed were initiator, combinations of AGA and CGA, and terminator. Both, AGA and CGA are low-us...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh784
更新日期：2004-08-18 00:00:00
abstract：:Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/27.3.831
更新日期：1999-02-01 00:00:00
abstract：:A small family of DNA sequences is rearranged during the development of the somatic nucleus in Tetrahymena. The family is defined by 266 bp of highly conserved sequence which restriction mapping, hybridization and sequence analysis have shown is shared by a cloned micronuclear fragment and three sequences which consti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.20.8007
更新日期：1986-10-24 00:00:00
abstract：:Engineered nucleases, which incise the genome at predetermined sites, have a number of laboratory and clinical applications. There is, however, a need for better methods for controlled intracellular delivery of nucleases. Here, we demonstrate a method for ligand-mediated delivery of zinc finger nucleases (ZFN) protein...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt710
更新日期：2013-10-01 00:00:00
abstract：:Structured RNA molecules form complex 3D architectures stabilized by multiple interactions involving the nucleotide base, sugar and phosphate moieties. A significant percentage of the bases in structured RNA molecules in the Protein Data Bank (PDB) hydrogen-bond with phosphates of other nucleotides. By extracting and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp468
更新日期：2009-08-01 00:00:00
abstract：:The four Hu [embryonic lethal abnormal vision-like (ELAVL)] protein family members regulate alternative splicing by binding to U-rich sequences surrounding target exons and affecting the interaction of the splicing machinery and/or local chromatin modifications. Each of the Hu proteins contains a divergent N-terminus,...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt166
更新日期：2013-05-01 00:00:00
abstract：:The 0.048502 megabase (Mb), primarily double-stranded DNA of bacteriophage lambda has single-stranded, complementary termini (cohesive ends) that undergo either spontaneous intramolecular joining to form open circular DNA or spontaneous intermolecular joining to form linear, end-to-end oligomeric DNAs (concatemers); c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.11.3047
更新日期：1991-06-11 00:00:00
abstract：:Cells continuously monitor protein synthesis to prevent accumulation of aberrant polypeptides. Insufficient capacity of cellular degradative systems, chaperone shortage or high levels of mistranslation by ribosomes can result in proteotoxic stress and endanger proteostasis. One of the least explored reasons for mistra...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa068
更新日期：2020-04-17 00:00:00
abstract：:Riboswitches are important gene regulatory elements frequently encountered in bacterial mRNAs. The recently discovered nadA riboswitch contains two similar, tandemly arrayed aptamer domains, with the first domain possessing high affinity for nicotinamide adenine dinucleotide (NAD+). The second domain which comprises t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1029
更新日期：2020-12-02 00:00:00
abstract：:Post-translational modifications contribute to the spliceosome dynamics by facilitating the physical rearrangements of the spliceosome. Here, we report USP15, a deubiquitinating enzyme, as a regulator of protein-protein interactions for the spliceosome dynamics. We show that PRP31, a component of U4 snRNP, is modified...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1365
更新日期：2017-05-05 00:00:00
abstract：:By subtractive screening of a library made from mRNA of lipopolysaccharide (LPS)-stimulated mouse B lymphocytes we isolated cDNA-clones encoding the ribosomal protein L7. Human L7 mRNA was cloned from activated T-lymphocytes. Although no specific function of L7 in the translation apparatus is known as yet, it should b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.2.223
更新日期：1993-01-25 00:00:00
abstract：:COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles from given MSAs, constructs local profile-profile alignments and analytically estimates E-values for the detected similarities. Until now, CO...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm293
更新日期：2007-07-01 00:00:00
abstract：:We present the sequences of five additional human U2 pseudogenes which are very similar to the U2.13 pseudogene reported previously [Van Arsdell et al. (1981) Cell 26, 11-17]. All six U2 pseudogenes preserve the 5' end of the mature U2 snRNA sequence, and all six are flanked by nearly perfect direct repeats that diffe...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.3.1463
更新日期：1984-02-10 00:00:00
abstract：:The nucleotide sequence of a T4 tRNA with an anticodon for glycine has been determined using (32)P-labeled material from T4-infected cultures of Escherichiacoli. The sequence is: pGCGGAUAUCGUAUAAUGmGDAUUACCUCAGACUUCCAApsiCUGAUGAUGUGAGTpsiCGAUUCUCAUUAUCCGCUCCA-OH. The 74 nucleotide sequence can be arranged in the class...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.10.1287
更新日期：1974-10-01 00:00:00
abstract：:Genomes undergo changes in organization as a result of gene duplications, chromosomal rearrangements and local mutations, among other mechanisms. In contrast to prokaryotes, in which genes of a common function are often organized in operons and reside contiguously along the genome, most eukaryotes show much weaker clu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku667
更新日期：2014-09-01 00:00:00
abstract：:The budding yeast Saccharomyces cerevisiae is proving to be an useful and accurate model for eukaryotic DNA replication. It contains both DNA polymerase alpha (I) and delta (III). Recently, proliferating cell nuclear antigen (PCNA), which in mammalian cells is an auxiliary subunit of DNA polymerase delta and is essent...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.2.261
更新日期：1990-01-25 00:00:00
abstract：:Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1234
更新日期：2021-01-25 00:00:00
abstract：:Yeast Dna2 helicase/nuclease is essential for DNA replication and assists FEN1 nuclease in processing a subset of Okazaki fragments that have long single-stranded 5' flaps. It is also involved in the maintenance of telomeres. DNA2 is a gene conserved in eukaryotes, and a putative human ortholog of yeast DNA2 (ScDNA2) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl070
更新日期：2006-04-04 00:00:00
