Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:3.1.30.2 (endonuclease)
18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

All of the fully sequenced iridoviruses have an ORF resembling a putative RNase III gene. However, to the best of our knowledge, functional characterization of the iridovirus-encoded RNase III has not been done. In the present study, we have characterized the putative RNase III of rock bream iridovirus (RBIV), the major cause of mass mortality of cultured rock bream Oplegnathus fasciatus in Korea. RBIV RNase III has a single N-terminal endonuclease domain followed by a C-terminal double-stranded RNA (dsRNA) binding domain. The true presence of the predicted ORF encoding RNase III in RBIV was confirmed by temporal transcription analysis of the ORF in RBIV-infected grunt fin (GF) cells. Comparing the catalytic activity to that of previously reported RNase III proteins, including Escherichia coli RNase III, the present RBIV RNase III had different features in that: (1) the dsRNA substrate was cleaved by the RBIV RNase III at high concentrations of Mg(2+) (5-20 mM) at low salt concentration (50 mM), but the enzyme activity was completely inhibited at 200 mM NaCl (within physiological ranges) irrespective of Mg(2+) concentrations (0.5-20 mM); (2) the substrate dsRNA was cleaved at low concentrations of Mn(2+) (0.5-1 mM) at low salt concentration (50 mM) and was cleaved by increasing Mn(2+) (5-20 mM) at 200 mM salt. These features of RBIV RNase III are similar to E. coli RNase III devoid of the C-terminal dsRBD region. The exact role of the RNase III in RBIV replication is not known, and further studies are needed to elucidate whether the RNase III is involved in the suppression of host RNA interference, which attacks viral mRNAs, or in the processing of viral RNAs for effective replication.
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PMID:Functional characterization of the RNase III gene of rock bream iridovirus. 1864 14

We studied the genomic structure and RNA editing of mitochondrial cox1, cox2, cob and atp9 from the horsetail Equisetum arvense, a representative of an old fern lineage. Editing of cox1, cob and atp9 mRNAs occur only by C-to-U transitions. No changes were found in cox2 transcripts constituting one of the rare examples of unedited mitochondrial mRNA in land plants. From three intervening sequences in cox1, cox1i395 and cox1i624 are group IB introns homologous to the Marchantia polymorpha cox1 introns, and cox1i747 is a group IIA intron different to other introns found in plant mtDNA. The group II intron cox2i373 is very similar to other introns found in cox2 from vascular plants. While cob and atp9 have no introns and display the gene structure found in seed plants, various nucleotide substitutions abolish the only potential ORF, a LAGLIDADG endonuclease present in cox1i395. Thus, E. arvense mitochondria conserve two group I introns from non-vascular plants, probably inherited from a common ancestor with liverworts. Analogous to seed plants, E. arvense has no potential mitochondrial splicing factors encoded in these introns. This is the first report concerning the presence of vertically inherited group I introns in vascular plant mitochondria.
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PMID:The horsetail Equisetum arvense mitochondria share two group I introns with the liverwort Marchantia, acquired a novel group II intron but lost intron-encoded ORFs. 1911 63

We have been studying the functions of PCNA (proliferating-cell nuclear antigen) for the assembly and reassembly of the replisome during replication fork progression. We have identified the functional interactions between PCNA and several proteins involved in DNA replication and repair from Pyrococcus furiosus. We recently reported that the activity of UDG (uracil-DNA glycosylase) in P. furiosus (PfuUDG) is stimulated by PCNA (PfuPCNA) in vitro, and identified an atypical PCNA-binding site, AKTLF, in the PfuUDG protein. To understand further the function of the complex in the BER (base excision repair) process, we investigated the AP (apurinic/apyrimidinic) endonuclease, which can process the BER pathway after uracil removal by UDG. Interestingly, one candidate ORF (open reading frame) for the AP endonuclease was found in the operon containing the gene encoding UDG in the P. furiosus genome. However, this ORF did not exhibit any activity. Instead, we identified the AP endonuclease activity from the other candidate gene products, and designated the protein as PfuAP. We discovered a physical interaction between PfuAP and PfuPCNA, suggesting the formation of a BER complex in one of the repair systems in P. furiosus.
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PMID:Studies on the base excision repair (BER) complex in Pyrococcus furiosus. 1914 6

Neurotropic herpesviruses express viral deoxyuridine triphosphate nucleotidohydrolase (dUTPase) and uracil DNA glycosylase (UDG) enzymes which may reduce uracil misincorporation into viral DNA, particularly in neurons of infected ganglia. The simian varicella virus (SVV) dUTPase (ORF 8) and UDG (ORF 59) share 37.7% and 53.9% amino acid identity, respectively, with varicella-zoster virus (VZV) homologs. Infectious SVV mutants defective in either dUTPase (SVV-dUTPase(-)) or UDG (SVV-UDG(-)) activity or both (SVV-dUTPase(-)/UDG(-)) were constructed using recA assisted restriction endonuclease cleavage (RARE) and a cosmid recombination system. Loss of viral dUTPase and UDG enzymatic activity was confirmed in CV-1 cells infected with the SVV mutants. The SVV-dUTPase(-), SVV-UDG(-), and SVV-dUTPase(-)/UDG(-) mutants replicated as efficiently as wild-type SVV in cell culture. SVV dUTPase and UDG expression was detected in tissues derived from acutely infected animals, but not in tissues derived from latently infected animals. Further studies will evaluate the pathogenesis of SVV dUTPase and UDG mutants and their potential as varicella vaccines.
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PMID:The simian varicella virus uracil DNA glycosylase and dUTPase genes are expressed in vivo, but are non-essential for replication in cell culture. 1920 Apr 45

Homing endonuclease genes are mobile elements that promote their duplication into cognate sites that lack the endonuclease gene [1, 2]. The homing endonuclease initiates this event through site-specific DNA cleavage. Copying of the endonuclease gene follows as a consequence of DNA repair. A genome containing a homing endonuclease gene is subject to self-cleavage. Protection is accomplished through DNA sequence polymorphisms, as is the case in intronless homing of free-standing endonuclease genes [3, 4], or by disruption of the recognition site by a group I intron (or intein) into which the endonuclease ORF is embedded. We describe here a novel free-standing homing endonuclease from cyanobacteriophage S-PM2, which is similar to the DNA resolvase of bacteriophage T4 and is encoded adjacent to an intron-containing psbA gene [5, 6]. The endonuclease makes a specific double-strand cut near the intron insertion site (IIS), its DNA recognition site spans the IIS, and it is unable to cleave intron-containing psbA genes. This interdependence of a free-standing endonuclease gene and a group I intron, which we denote "collaborative homing," has not been reported previously and gives support to a hypothesis of formation of composite mobile introns by independent convergence of an intron and an endonuclease gene on the same target sequence.
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PMID:A free-standing homing endonuclease targets an intron insertion site in the psbA gene of cyanophages. 1920 Jul 28

The DNA polymerase gene of Thermococcus marinus (Tma) contains an intein inserted at the pol-b site that possesses a 1611-bp ORF encoding a 537-amino acid residue. The LAGLIDADG motif, often found in site-specific DNA endonucleases, was detected within the amino acid sequence of the intein. The intein endonuclease, denoted as PI-Tma, was purified as a naturally spliced product from the expression of the complete DNA polymerase gene in Escherichia coli. PI-Tma cleaved intein-less DNA sequences, leaving four-base-long, 3'-hydroxyl overhangs with 5'-phosphate. Nonpalindromic recognition sequences 19 bp long were also identified using partially complementary oligonucleotide pair sequences inserted into the plasmid pET-22b(+). Cleavage by PI-Tma was optimal when present in 50mM glycine-NaOH (pH 10.5), 150mM KCl and 12mM MgCl(2) at 70 degrees C.
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PMID:Characterization of intein homing endonuclease encoded in the DNA polymerase gene of Thermococcus marinus. 1963 5

Retrotransposons including CR1 (chicken repeat 1) elements are important factors in genome evolution. They also mobilize in a genome in a way that makes them useful for phylogenetic analysis and species identification. This study was designed to identify lineages of CR1 elements in the genomes of forensically important oestroid flies and to further characterize one family, Sbul.CR1B. CR1 fragments from several taxa were amplified, cloned, sequenced and analyzed to identify different lineages of elements. A variety of retrotransposon families were recovered that exhibit similarity to known retrotransposon families. A number of these lineages may have given rise to taxon-specific subfamilies that have been recently active in oestroid fly genomes. One element from Sarcophaga bullata was analyzed in detail to reconstruct a partial Open Reading Frame containing both the reverse transcriptase (RT) and endonuclease (EN) domains. These domains were used to identify conserved amino acid regions in the recovered consensus via comparison to known non-LTR retrotransposons. Phylogenetic analysis of the RT domain revealed the recovered ORF in S. bullata compares favorably with previously documented CR1-like elements. This work will serve as the basis for additional analyses targeted at developing a simple, efficient marker system for the identification of forensically important carrion flies.
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PMID:Multiple chicken repeat 1 lineages in the genomes of oestroid flies. 1971 65

Group II introns are both catalytic RNAs and mobile retroelements that move through a process catalyzed by a RNP complex consisting of an intron-encoded protein and the spliced intron lariat RNA. Group II intron-encoded proteins are multifunctional and contain an N-terminal reverse transcriptase domain, followed by a putative RNA-binding domain (domain X) associated with RNA splicing or maturase activity and a C-terminal DNA binding/DNA endonuclease region. The intron-encoded protein encoded by the mobile group II intron RmInt1, which lacks the DNA binding/DNA endonuclease region, has only a short C-terminal extension (C-tail) after a typical domain X, apparently unrelated to the C-terminal regions of other group II intron-encoded proteins. Multiple sequence alignments identified features of the C-terminal portion of the RmInt1 intron-encoded protein that are conserved throughout evolution in the bacterial ORF class D, suggesting a group-specific functionally important protein region. The functional importance of these features was demonstrated by analyses of deletions and mutations affecting conserved amino acid residues. We found that the C-tail of the RmInt1 intron-encoded protein contributes to the maturase function of this reverse transcriptase protein. Furthermore, within the C-terminal region, we identified, in a predicted alpha-helical region and downstream, conserved residues that are specifically required for the insertion of the intron into DNA targets in the orientation that would make it possible to use the nascent leading strand as a primer. These findings suggest that these group II intron intron-encoded proteins may have adapted to function in mobility by different mechanisms to make use of either leading or lagging-oriented targets in the absence of an endonuclease domain.
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PMID:Structural features in the C-terminal region of the Sinorhizobium meliloti RmInt1 group II intron-encoded protein contribute to its maturase and intron DNA-insertion function. 1995 59

This study analyzed 50 varicella zoster virus (VZV) samples collected during 2004 to 2007 from patients with VZV infection, who were treated at the National Center of Communicable Diseases, Ulan-Bator, Mongolia. The method based on amplification of specific DNA fragments of the ORF21, ORF22, and ORF50 genes was used, followed by the sequencing and detection of the status of characteristic point mutations in these fragments. The results indicated that the collected samples belonged to genotypes J (62%), M1 (18%), E1 (12%), E2 (4%), and M2 (4%). Moreover, restriction endonuclease polymorphism in ORF 62 for the cleavage site Smal and Mspl, in ORF 38 and ORF 54 for the cleavage site Pstl and Bgll were analyzed. All the samples were Sma- Msp-. All samples with genotype E were Pst+ Bgl-; all samples with genotype M1 and M2 were Pst+ Bgl+. Out of 31 samples with genotype J, 29 and 2 were Pst+ Bgl+ and Pst+ Bgl+, respectively. The study could identify the genotypes of VZV circulating in Mongolia and confirmed the absence of mutations characteristic for the vaccine strain.
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PMID:[Genotyping of varicella zoster virus strains isolated in Mongolia]. 2126 Sep 96

The retrotransposon known as long interspersed nuclear element-1 (L1) is 6 kb long, although most L1s in mammalian and other eukaryotic cells are truncated. L1 contains two open reading frames, ORF1 and ORF2, that code for an RNA-binding protein and a protein with endonuclease and reverse transcriptase activities, respectively. In this work, we examined the effects of full length L1-ORF2 and ORF2 fragments on green fluorescent protein gene (GFP) expression when inserted into the pEGFP-C1 vector downstream of GFP. All of the ORF2 fragments in sense orientation inhibited GFP expression more than when in antisense orientation, which suggests that small ORF2 fragments contribute to the distinct inhibitory effects of this ORF on gene expression. These results provide the first evidence that different 280-bp fragments have distinct effects on the termination of gene transcription, and that when inserted in the antisense direction, fragment 280-9 (the 3' end fragment of ORF2) induces premature termination of transcription that is consistent with the effect of ORF2.
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PMID:Effects of L1-ORF2 fragments on green fluorescent protein gene expression. 2163 38


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