Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.26.4 (RNase H)
 2,751 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We have investigated the use of oligodeoxycytidylic acid [oligo(dC)] as a primer for the initiation of DNA synthesis by the avian retrovirus reverse transcriptase in vitro, employing the viral RNA genome as template. The addition of oligo(dC)(12-18) to viral 35S RNA results in a stimulation of DNA synthesis by the viral RNA-directed DNA polymerase comparable to that observed when oligo(dT) is employed as a primer. Under similar conditions neither oligo(dA)(12-18) nor oligo(dG)(12-18) was active as primer for transcription of the avian retrovirus genome. Several different approaches have been employed to localize the oligo(dC)(12-18) binding site on the viral genome, including isolation of poly(A)-containing fragments, competition hybridization, and RNase H hydrolysis. These analyses indicate that oligo(dC)(12-18) binds to a site approximately 2,000 to 3,000 nucleotides from the 3' terminus of the genome of transforming strains of avian sarcoma viruses and approximately 700 to 1,000 nucleotides from the 3' terminus of nontransforming avian retroviruses. Therefore, the major site of initiation of DNA synthesis by oligo(dC)(12-18) appears to be in the vicinity of the 3' end of the env gene and the 5' end of the src gene, although the presence of minor initiation sites located elsewhere on the viral genome cannot be excluded by these data. Characterization of oligonucleotides after pancreatic RNase hydrolysis and poly(C)-Sepharose chromatography of viral RNA directly demonstrates the presence of oligoguanylic acid residues in the avian sarcoma virus genome. DNA sequences transcribed from the oligo(dC) primer appear to be conserved in all of the avian leukosis-sarcoma viruses tested. The use of oligo(dC) as a tool for the production of specific complementary DNA probes is discussed.
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PMID:Initiation of DNA synthesis by the avian retrovirus reverse transcriptase in vitro: nature and location of the oligodeoxycytidylic acid primer binding site. 9 Jan 58

We have determined the DNA structure of the Ulysses transposable element of Drosophila virilis and found that this transposon is 10,653 bp and is flanked by two unusually large direct repeats 2136 bp long. Ulysses shows the characteristic organization of LTR-containing retrotransposons, with matrix and capsid protein domains encoded in the first open reading frame. In addition, Ulysses contains protease, reverse transcriptase, RNase H and integrase domains encoded in the second open reading frame. Ulysses lacks a third open reading frame present in some retrotransposons that could encode an env-like protein. A dendrogram analysis based on multiple alignments of the protease, reverse transcriptase, RNase H, integrase and tRNA primer binding site of all known Drosophila LTR-containing retrotransposon sequences establishes a phylogenetic relationship of Ulysses to other retrotransposons and suggests that Ulysses belongs to a new family of this type of elements.
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PMID:Ulysses transposable element of Drosophila shows high structural similarities to functional domains of retroviruses. 131 87

We have determined the nucleotide sequence of the Drosophila retrotransposon 1731. 1731 is 4648 bp long and is flanked by 336 bp terminal repeats (LTRs) previously described as being reminiscent of provirus LTRs. The 1731 genome consists of two long open reading frames (ORFs 1 and 2) which slightly overlap each other. The ORF 1 and 2 present similarities with retroviral gag and pol genes respectively as shown by computer analysis. The pol gene exhibits several enzymatic activities in the following order: protease, endonuclease and reverse transcriptase. It is possible that 1731 also encompasses a ribonuclease H activity located between the endonuclease and reverse transcriptase domains. Moreover, comparison of the 1731 pol gene with the pol region of copia shows similarities extending over the protease, endonuclease and reverse transcriptase domains. We show that codon usage in the two retrotransposons is different. Finally, no ORF able to encode an env gene is detected in 1731.
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PMID:Primary structure and functional organization of Drosophila 1731 retrotransposon. 245 22

We determined the complete nucleotide sequence of the intracisternal A-particle gene, IAP-H18, cloned from the normal Syrian hamster liver DNA. IAP-H18 was 7,951 base pairs in length with two identical long terminal repeats of 376 base pairs at both ends. On the coding strand, imperfect open reading frames corresponding to gag and pol of the retrovirus genome were observed, whereas many stop codons were present in the region corresponding to env. The putative H18 gag gene (809 amino acids) had a sequence homologous to the N-terminal half of the mouse mammary tumor virus gag gene and locally to the Rous sarcoma virus gag gene. The putative H18 pol gene (900 residues) was homologous to the Rous sarcoma virus pol gene almost throughout the entire region. Two conserved regions among the retrovirus pol genes have been reported. One presumably corresponds to the DNA polymerase and the RNase H domain, and the other corresponds to the DNA endonuclease domain of the multifunctional protein pol. By the comparison of the deduced amino acid sequences of the putative endonuclease domain of six representative oncovirus genomes, a phylogenetic tree of the oncovirus genomes was constructed, and the intracisternal A-particle (type A) genome was found to be more closely related to the mouse mammary tumor virus (type B) and squirrel monkey retrovirus (type D) genomes.
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PMID:Nucleotide sequence of the Syrian hamster intracisternal A-particle gene: close evolutionary relationship of type A particle gene to types B and D oncovirus genes. 299 63

We have isolated and characterized a new human endogenous provirus, which is closely related to the human retrovirus S71, but unlike S71 has a full-length pol gene. Two degenerate oligonucleotide primers based on highly conserved motifs within the active sites of two retroviral proteins (the protease and reverse transcriptase) were designed and used for PCR. An amplified product of 847 bp in length, which showed significant homology to protease and reverse transcriptase of several retroviruses, was used for high stringency hybridization with a human genomic library. The MuLV-related endogenous retrovirus sequence, designated HC2, was isolated and completely sequenced. HC2 is a provirus with complete gag and pol genes and a 3' LTR; the 5' LTR and env gene are missing. The gag and pol genes appear complete, since they contain sequences homologous to the matrix protein, capsid protein, and nucleocapsid protein of gag and to the protease, reverse transcriptase, tether, RNase H, and integrase of pol. Phylogenetic analysis suggests that although HC2 and S71 are MuLV-related retroviruses, their characters are quite distinct, being placed outside of a clade containing most of the previously characterized MuLV-related retroviruses such as GaLV, FeLV, BaEV, and SSV/SSAV.
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PMID:Human endogenous retrovirus HC2 is a new member of the S71 retroviral subgroup with a full-length pol gene. 894 25

Cytotoxic T lymphocytes (CTL) play an important role in the control of human immunodeficiency virus (HIV) infection. CTL responses have been demonstrated for most of the HIV gene products, predominantly gag, pol, and env-encoded proteins, and also for the regulatory proteins Nef, Tat, Vif, or Rev. The HIV-1 reverse transcriptase (RT), which derives from expression of the pol gene, is an important target of cellular immune responses in infected individuals. More than 40 different peptides containing RT-specific CTL epitopes have been identified. The most conserved and frequently detected are located in the 'fingers' and 'palm' subdomains of the enzyme, but other epitopes have been found in the 'thumb' and 'connection' subdomains as well as in the RNase H domain. Studies on the sequence variability and functional role of amino acids forming CTL epitopes are relevant for addressing important questions relative to viral escape from immmune control and the future design of anti-AIDS vaccines.
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PMID:Cytotoxic T-lymphocyte responses to HIV-1 reverse transcriptase (review). 1018 85

The Osvaldo retrotransposon has shown a high transposition rate in some strains of Drosophila buzzatii and in hybrids between D. buzzatii and its sibling D. koepferae. In order to understand the molecular basis of this phenomenon, we developed a procedure to clone a recently transposed copy with the aim of characterizing an active, full- length Osvaldo element. The complete nucleotide sequence of Osvaldo, obtained from a recent insertion site, was determined. Osvaldo is 9,045 bp long and is composed of a central coding region flanked by identical long terminal repeats (LTRs) of 1,196 bp each. Sequences homologous to the polypurine tract and tRNA-primer-binding site of retroviruses are located adjacent to the 3' and 5' LTRs, respectively. The internal region of Osvaldo contains three long open reading frames (ORFs 1, 2, and 3), comparable in size and location to gag, pol, and env retroviral genes. The conceptual translation of Osvaldo ORF1 exhibits sequence homology to HIV1 and SIV capsid (p24) and nucleocapsid (p7) mature proteins. ORF2 encodes the putative protease (PR), reverse transcriptase/ribonuclease H (RT/RH), integrase (IN), and a significant portion of the surface envelope (ENV) protein that is interrupted by a putative intron. A third ORF encodes the remaining part of the ENV protein. The predicted 62-kDa ENV protein shares several general features with membrane glycoproteins, including a potential signal peptide, a transmembrane domain near the C-terminus that could function as a membrane anchor, four consensus N-linked glycosylation motifs, and, finally, a potential protease cleavage site. The phylogenetic relationships of Osvaldo are explored, and they suggest that Osvaldo may constitute a new family of retroviruses in insects, distantly related to the previously described group of gypsy retroviruses.
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PMID:The retrotransposon Osvaldo from Drosophila buzzatii displays all structural features of a functional retrovirus. 1040 8

We have determined the nucleotide sequence of the 6868 bp full-size retrotransposon termed 'Tv1'. Tv1 was isolated from the DNA fraction of extracellular virus-like particles of Drosophila virilis culture cells. Tv1 has the typical structure for a gypsy-group retrotransposon. The Tv1 element was found to be flanked by 453 bp long terminal direct repeats identical to each other. The central part of the element contains three long open reading frames which resemble the gag, pol and env genes of retroviruses. ORF2 includes conservative motifs of protease, reverse transcriptase, RNase H and integrase in the order characteristic for the gypsy-group retrotransposons. Although most copies of Tv1 are located in pericentromeric heterochromatin, the amplification of this family demonstrated in the cell culture and site polymorphism observed in different Drosophila strains suggest functional activity of the Tv1 element.
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PMID:Gypsy group retrotransposon Tv1 from Drosophila virilis. 1057 Oct 49

SIRE-1 is a multi-copy, Ty1-copia-like retroelement family found in the genome of Glycine max. A sequenced SIRE-1 genomic copy has an uninterrupted ORF that can be translated into a gag-pol polyprotein, followed by an unprecedented second ORF whose conceptual translation yielded a theoretical protein predicted to possess many of the same secondary structural elements found in mammalian retroviral envelope proteins. Similar, but clearly pseudogenic, envelope-like sequences were recovered from conceptual translations of 10 Arabidopsis GenBank accessions. All were associated with identifiable Ty1-copia-like retroelements. Phylogenetic analysis of the adjacent ribonuclease H regions from these sequences and three similarly endowed elements, two from maize and one from tomato, indicate that the 14 elements constitute a monophyletic group distinct from several closely related plant Ty1-copia-like elements in which pol is immediately followed by a downstream LTR. The conservation of identifiable env-like gene features suggests that these plant elements are endogenous retroviruses whose ancestors were acquired from animal vectors. The finding that the env and env-less retroelements identified in this study form distinct lineages does not support the hypothesis that horizontal transmission of retrotransposons is sponsored by ancestral infectious retroviruses that subsequently lost all traces of env genes.
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PMID:Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes. 1095 1

The wild mouse species most closely related to the common laboratory strains contain proviral env genes of the xenotropic/polytropic subgroup of mouse leukemia viruses (MLVs). To determine if the polytropic proviruses of Mus spretus contain functional genes, we inoculated neonates with Moloney MLV (MoMLV) or amphotropic MLV (A-MLV) and screened for viral recombinants with altered host ranges. Thymus and spleen cells from MoMLV-inoculated mice were plated on Mus dunni cells and mink cells, since these cells do not support the replication of MoMLV, and cells from A-MLV-inoculated mice were plated on ferret cells. All MoMLV-inoculated mice produced ecotropic viruses that resembled their MoMLV progenitor, although some isolates, unlike MoMLV, grew to high titers in M. dunni cells. All of the MoMLV-inoculated mice also produced nonecotropic virus that was infectious for mink cells. Sequencing of three MoMLV- and two A-MLV-derived nonecotropic recombinants confirmed that these viruses contained substantial substitutions that included the regions of env encoding the surface (SU) protein and the 5' end of the transmembrane (TM) protein. The 5' recombination breakpoint for one of the A-MLV recombinants was identified in RNase H. The M. spretus-derived env substitutions were nearly identical to the corresponding regions in prototypical laboratory mouse polytropic proviruses, but the wild mouse infectious viruses had a more restricted host range. The M. spretus proviruses contributing to these recombinants were also sequenced. The seven sequenced proviruses were 99% identical to one another and to the recombinants; only two of the seven had obvious fatal defects. We conclude that the M. spretus proviruses are likely to be recent germ line acquisitions and that they contain functional genes that can contribute to the production of replication-competent virus.
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PMID:Characterization of recombinant nonecotropic murine leukemia viruses from the wild mouse species Mus spretus. 1461 Jan 99


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