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At least 433 records · Page 24Linked to original sources
PubMed1999

The linear plasmid SCP1 of Streptomyces coelicolor A3(2) possesses a centrally located replication origin and shows significant homology to the transposon Tn4811.

The linear plasmid SCP1 of Streptomyces coelicolor A3(2) is one of the genetically more studied linear streptomycete replicons. Although the genetics of SCP1 and its interaction with the host chromosome have been analyzed for nearly three decades no information exists on its replication. With the help of an ordered cosmid contig for the complete 360-kb element, we have localized a 5439-bp fragment from the central region that confers autonomous replication in Streptomyces lividans. The minimal origin contains two overlapping ORFs which are separated from an AT-rich region which might correspond to the replication start point. ORF1 revealed intensive similarity to a class of DNA-primase/helicases of actinophages and archael plasmids. In addition, we have identified a region in both terminal inverted repeats of SCP1 that shows significant homology to the transposable element Tn4811 located near the ends of the S. lividans 66 chromosome.

Amino Acid Sequence↗
PubMed2000

Telomere sequences attached to nuclearly migrated yeast linear plasmid.

The yeast linear plasmid pCLU1, derived from pGKL1, has terminal proteins (TPs) covalently attached at the 5' ends of inverted terminal repeats (ITRs) and replicates in the cytoplasm, presumably using the TP as a primer for DNA synthesis. In Saccharomyces cerevisiae, under certain conditions, pCLU1 migrated into the nucleus and replicated in either linear or circular form. The linear-form plasmid lacked TPs; instead it carried host-telomere repeats at the ITR ends. The present study showed that (1) the added telomere was primarily composed of the repeated tracts of TGTGTGGGTGTGG, which was complementary to the RNA template of yeast telomerase, (2) the telomeric addition occurred at the very end of the ITRs, and (3) the sequence composition of the added telomeres was diverse among individual plasmids, but symmetrically identical at both ends of each plasmid. A similar mode of telomere addition was also observed in cells defective in the RAD52 gene.

Base Sequence↗
PubMed2001

ISMh2, a novel insertion sequence-like element associated with nifA from Mesorhizobium huakuii.

Sequence analysis of the nifA gene, including its 5' flanking region, of Mesorhizobium huakuii revealed the presence of a novel IS-like element called ISMh2. It is 828 bp in length and possesses two imperfect terminal inverted repeats of 14 bp with only one mismatch. The putative transposase encoded by ISMh2 is composed of 204 amino acids. In comparison with other insertion sequences ISMh2 likely belongs to the IS6 family. Multiple copies of ISMh2 were detected in the genome of M. huakuii 159 by Southern hybridization. RT-PCR analysis showed that nifA and ISMh2 cotranscribed. Attempts to detect the transposition ability of ISMh2 were unsuccessful.

Alphaproteobacteria↗
PubMed1994

Analysis of the complete genome of smallpox variola major virus strain Bangladesh-1975.

We analyzed the 186,102 base pairs (bp) that constitute the entire DNA genome of a highly virulent variola virus isolated from Bangladesh in 1975. The linear, double-stranded molecule has relatively small (725 bp) inverted terminal repeat (ITR) sequences containing three 69-bp direct repeat elements, a 54-bp partial repeat element, and a 105-base telomeric end-loop that can be maximally base-paired to contain 17 mismatches. Proximal to the right-end ITR sequences are another seven 69-bp elements and a 53- and a 27-bp partial element. Sequence analysis showed 187 closely spaced open reading frames specifying putative major proteins containing > or = 65 amino acids. Most of the virus proteins correspond to proteins in current databases, including 150 proteins that have > 90% identity to major gene products encoded by vaccinia virus, the smallpox vaccine. Variola virus has a group of proteins that are truncated compared with vaccinia virus counterparts and a smaller group of proteins that are elongated. The terminal regions encode several novel proteins and variants of other poxvirus proteins that potentially augment variola virus transmissibility and virulence for its only natural host, humans.

Animals↗
PubMed1994

Cowpox virus contains two copies of an early gene encoding a soluble secreted form of the type II TNF receptor.

The inverted terminal repeats of the DNA of cowpox virus (Brighton Red strain) contain the crmB gene, an additional member of a family of viral genes that modify cytokine responses to infection. The crmB gene is transcribed from an early promoter. The primary product is a 355-amino-acid protein containing a signal peptide sequence and three potential N-linked glycosylation sites. The mature gene product is a secreted soluble protein that has an apparent molecular mass of 48 kDa. TNF alpha and TNF beta bind to this protein in a competitive manner, consistent with the sequence of its N-terminal 176 amino acids, which closely resembles the ligand-binding domains of the type II (75-kDa) human TNF receptor. The sequence of the C-terminal 161 amino acids of the CrmB protein is unlike that of human TNF receptors, but overall, the CrmB protein is similar to the T2 proteins of the leporipoxviruses (48% identity) and the predicted product of the G4R/G2R open reading frame of variola virus (85% identity), suggesting that not only the TNF-binding domains but also the C-terminal regions contribute to the functions of these viral proteins. These results show that orthopoxiviruses such as cowpox virus encode secreted forms of TNF receptors that can contribute to the modification of TNF-mediated antiviral processes.

Amino Acid Sequence↗
PubMed1995

Configuration and terminal sequences of the simian varicella virus genome.

The simian varicella virus (SVV) genome is a linear DNA molecule consisting of a unique short (Us) and a unique long (UL) region. The Us is bounded by internal (IR) and terminal inverted repeats and inverts such that virion DNA contains equimolar amounts of two genome isomers. We have sequenced the right and leftward termini and the UL-IR junction region of the SVV genome. A sequence motif common to other herpesviruses, consisting of A and T residues surrounded by G+C-rich regions, was found near the rightward terminus of the SVV genome. Sequence analysis showed no repeats surrounding the UL region of the genome. Nucleic acid hybridization and polymerase chain reaction (PCR) amplification using primers from the right and leftward ends of the SVV genome indicated that the UL region inverts. PCR amplification also showed that, compared with virion DNA, SVV genomes with connected termini are increased in infected cell DNA, suggesting the presence of circular or concatemeric genomic molecules.

Base Sequence↗
PubMed1995

TCl4.7: a novel lepidopteran transposon found in Cydia pomonella granulosis virus.

After the co-infection of larvae of the lepidopteran Cryptophlebia leucotreta with the two baculoviruses C. leucotreta granulosis virus and Cydia pomonella granulosis virus (CIGV and CpGV, respectively), three CpGV mutants and one CIGV mutant carrying insertions of 0.9 to 4.7 kb have been isolated. By cloning, sequencing, and hybridization analysis, one of these insertions was identified as a transposon-like element derived from the C. leucotreta genome. This element, called TCl4.7, was found in the genome of CpGV which naturally replicates in C. pomonella. Sequence analysis suggested that TCl4.7 is 4726 bp in size, flanked by imperfect inverted terminal repeats of 29 bp, and integrated into the target dinucleotide TA. TCl4.7 encompasses an open reading frame sharing homologies to transposase genes of the Tc1-related transposable elements found in Caenorhabditis and in Drosophila species. The open reading frame might represent a pseudogene since it is missing an ATG start codon. The integration site of TCl4.7 is located in a non-protein-coding region of the CpGV genome at m.u. 9.5. In bioassays the TCl4.7-carrying virus and all the other mutants except for one showed LC50 values similar to those of CpGV and CIGV. This is the first report of the horizontal escape of a transposable element during the in vivo infection of lepidopteran larvae by granulosis viruses.

Amino Acid Sequence↗
PubMed1995

Complete nucleotide sequences of 5'- and 3'-noncoding regions of both genome segments of different strains of infectious bursal disease virus.

The terminal sequences of both genomic dsRNA segments of different strains of infectious bursal disease virus were determined. Analysis of the linear sequences revealed in the 5'-noncoding region of both segments the presence of a 32-nucleotide sequence with motifs conserved between segments and serotypes. The 3'-noncoding regions showed a high degree of conservation within segment A or B, but differed between segments. Different inverted terminal repeats were detected in both segments. A sequence of 13 nucleotides found in the 5'-noncoding regions of both segments could function as a binding site for chicken 18 S rRNA. Secondary structure prediction of the different noncoding regions showed a high degree of similarity. Surprisingly, the predicted secondary structure of the 5'-noncoding region of segment A differed between serotypes. A possible influence of these different RNA structures on viral replication is discussed.

Animals↗
PubMed1995

Minimum origin requirements for linear duplex AAV DNA replication in vitro.

We have investigated the minimal requirements for a functional origin of DNA replication in an in vitro assay which requires the adeno-associated virus (AAV) Rep 68/78 protein. When a linear duplex template was used, initiation of one round of DNA replication was achieved when nucleotides 1-56 of the AAV inverted terminal repeat (in the flop orientation) were present at the terminus of the template. A terminal resolution site was not required. Deletion of an additional 11 nucleotides from the terminal repeat blocked the reaction.

DNA Replication↗
PubMed1995

Unclassified poxvirus: characterization and physical mapping of Cotia virus DNA and location of a sequence capable of encoding a thymidine kinase.

DNA from Cotia virus, an unclassified poxvirus, was mapped by overlapping fragment analysis using the restriction endonucleases HindIII, PstI, BamHI, XhoI, SalI, and SmaI. The linear genome was 177 kbp in length and possessed inverted terminal repeats and cross-links. A Cotia virus thymidine kinase (TK) gene was detected and mapped to about 74 kbp from the left end of the genome using degenerate oligonucleotide probes. Nucleotide sequencing of the TK gene revealed an open reading frame (ORF) that encoded a peptide of 178 amino acids. An A/T-rich sequence, TAA AAA TGA ATA AATA, and a transcription termination signal, TTTTTGT, were revealed upstream and just downstream of the ORF, respectively, consistent with the characteristic features of an early poxvirus gene. Cotia virus resembles swinepox virus based on the restriction profiles generated by endonucleases and shares amino acid sequence similarity with orthopox, leporipox, Yaba, and fowlpox viruses.

Amino Acid Sequence↗
PubMed1995

Comparison of the inverted terminal repetition sequences from five porcine adenovirus serotypes.

The nucleotide sequences of the region of inverted terminal repetition from representative strains of all five porcine adenovirus (PAV) serotypes were determined and analyzed. The first 17 nucleotides of this region were identical in PAV-1 to 3 and PAV-5, and 10 bp of identical sequence was found in all the PAVs. The closest relationships were among PAV-1 to 3, which shared more common sequences than the other serotypes. PAV-4 had the longest inverted terminal repeat reported for any adenovirus. The proximal 54-bp AT-rich region was partially conserved and the distal GC-rich region was less well conserved among all five serotypes.

Animals↗
PubMed1995

Analysis of the complete nucleotide sequences of goose and muscovy duck parvoviruses indicates common ancestral origin with adeno-associated virus 2.

The complete nucleotide sequences of two parvoviruses isolated from goose and muscovy duck were determined. The two virus genomes share 81.9% nucleotide sequence identity, indicating that they are closely related. The coding regions are bracketed by inverted terminal repeats containing palindromes. This is similar to the genome organization of human parvoviruses, adeno-associated virus 2, and B19. Amino acid sequence comparison shows that the closest relative of the goose and muscovy duck parvoviruses is adeno-associated virus 2. This is surprising, because the goose and muscovy duck parvoviruses do not require any helper virus for productive replication, suggesting that adeno-associated virus 2 has been derived from a helper-independent ancestor.

Amino Acid Sequence↗
PubMed1996

Characterization of hitchhiker, a transposon insertion frequently associated with baculovirus FP mutants derived upon passage in the TN-368 cell line.

We characterize a new Lepidopteran transposon associated with FP mutations of baculoviruses. This transposon, designated hitchhiker, is 579 bp long with 39-bp imperfect inverted terminal repeats. hitchhiker inserts with extreme specificity for a single trinucleotide target site, TTA, within the 25K gene. This transposon is the most frequently identified insertion in serial passage baculovirus mutants isolated from TN-368 cells.

Amino Acid Sequence↗
PubMed1996

Unique genome arrangement of an ovine adenovirus: identification of new proteins and proteinase cleavage sites.

The completed sequence and genome organization of OAV287, a serologically distinct ovine adenovirus, is described. The genome of 29,544 bp has inverted terminal repeats that are only 46 bp in length. Many OAV genes are identified by their homology with other adenovirus (Ad) sequences but three groups of reading frames show little homology. One group at the left-hand end of the genome probably represents the E1A/E1B regions. Two others, on the complementary strand at the right-hand end of the genome, are tentatively proposed as the E4 and E3 regions. They are separated by approximately 1 kb of A/T-rich sequence of unknown function with E3 being adjacent to the terminus. Structural proteins V and IX of human Ads are absent from the OAV genome but a new, processed, 28-kDa virion polypeptide is encoded on the strand complementary to the proposed E1A region. The coding sequences for two other structural proteins are unidentified. The OAV penton protein lacks the region containing an Arg/Gly/Asp sequence that, in human adenoviruses, is thought to interact with cellular integrins to facilitate virus entry. Analysis of proteins and peptides in purified OAV identified several cleavage sites utilized by the Ad proteinase. Some of these were previously identified in human Ad proteins, but new sites, some of which did not conform to the known specificity of the human Ad proteinase, were also identified. The data emphasize that this ovine virus differs significantly from other known human and animal adenoviruses.

Adenovirus E1 Proteins↗
PubMed1996

Nucleotide sequencing and generation of an infectious clone of adeno-associated virus 3.

We have determined the complete nucleotide sequences of adeno-associated virus 3 (AAV-3) and generated an infectious clone. The single-stranded DNA genome of AAV-3 is 4726 nucleotides in length. The positive strand contains two large open reading frames; the left open reading frame encodes the nonstructural proteins and the right open reading frame encodes the structural proteins. The coding regions are flanked by identical inverted terminal repeat sequences containing palindromes. AAV-3 has little homology with the autonomous parvoviruses or erythroviruses but has 82% overall sequence homology with AAV-2. At the amino acid level there was 88% homology with AAV-2 nonstructural (Rep) proteins and 87% homology with AAV-2 capsid proteins. In addition, AAV-3 differed importantly from AAV-2 in the lack of a typical promoter sequence (TATA box) at p40 and the presence of the consensus sequence for adenovirus-related transcription factor E4F binding within the upstream region of the p5 promoter. These results suggest that AAV-3 not only consists of serologically distinct structural proteins but that viral propagation also may be controlled by different gene regulatory elements at the transcription level. The infectious clone confirmed the sequence and may be useful for developing new vectors for gene therapy.

Amino Acid Sequence↗
PubMed1997

Analysis of 74 kb of DNA located at the right end of the 330-kb chlorella virus PBCV-1 genome.

This report completes a preliminary analysis of the sequence of the 330,740-bp chlorella virus PBCV-1 genome, the largest virus genome to be sequenced to date. The PBCV-1 genome is 57% the size of the genome from the smallest self-replicating organism, Mycoplasma genitalium. Analysis of 74 kb of newly sequenced DNA, from the right terminus of the PBCV-1 genome, revealed 153 open reading frames (ORFs) of 65 codons or longer. Eighty-five of these ORFs, which are evenly distributed on both strands of the DNA, were considered major ORFs. Fifty-nine of the major ORFs were separated by less than 100 bp. The largest intergenic distance was 729 bp, which occurred between two ORFs located in the 2.2-kb inverted terminal repeat region of the PBCV-1 genome. Twenty-seven of the 85 major ORFs resemble proteins in databases, including the large subunit of ribonucleotide diphosphate reductase, ATP-dependent DNA ligase, type II DNA topoisomerase, a helicase, histidine decarboxylase, dCMP deaminase, dUTP pyrophosphatase, proliferating cell nuclear antigen, a transposase, fungal translation elongation factor 3 (EF-3), UDP glucose dehydrogenase, a protein kinase, and an adenine DNA methyltransferase and its corresponding DNA site-specific endonuclease. Seventeen of the 153 ORFs resembled other PBCV-1 ORFs, suggesting that they represent either gene duplications or gene families.

Chlorella↗
PubMed1998

Targeted integration of adeno-associated virus-derived plasmids in transfected human cells.

Adeno-associated virus (AAV) integrates its genomic DNA into a defined region of human chromosome 19 (AAVS1). The specificity of integration is dependent on the presence of the inverted terminal repeats (ITR) and on expression of the rep gene. To develop vectors capable of targeting the insertion of a selected DNA sequence into a specific location of human chromosome, we determined whether the rep gene can mediate site-specific integration when cloned outside of an ITR-flanked transgene cassette. HeLa and Huh-7 cells were transfected with a plasmid containing the rep gene, as well as the green fluorescent protein (GFP) and neomycin (neo) resistance gene inserted between the ITRs of AAV. Southern blot analysis of individual clones detected Rep-mediated site-specific integration of the ITR-flanked DNA in 25% and 12% of the HeLa and Huh-7 clones, respectively. The localization of the GFP-Neo sequence on chromosome 19 also was confirmed by fluorescent in situ hybridization analysis of the transfected HeLa clones. Sequence analysis of the ITR-AAVS1 junction of one of the transfected Huh-7 clones indicated that the insertion of the ITR DNA fragment had occurred at nucleotide 1003. These results have implications for the development of AAV-derived vectors capable of directing the site-specific integration of a gene of interest.

Base Sequence↗
PubMed1999

Genetic variation of chlorella viruses: variable regions localized on the CVK2 genomic DNA.

A physical map of the Chlorella virus CVK2 genomic DNA has been constructed based on a cosmid contig covering the entire genomic region. By using Southern blot analysis with 22 gene probes, the gene arrangement along the genome was compared between CVK2 and PBCV-1, the prototypic member of Phycodnaviridae, whose genomic sequence is now available. The major rearrangements were (1) an insertion of a 20-kbp region around the left end of CVK2 DNA, (2) a duplication of the gene for major capsid protein in CVK2 DNA, (3) deletions/insertions of some open reading frames, and (4) divergence in the terminal inverted repeat sequences. Despite these changes, extensive colinearity was revealed between most of the genes along the CVK2 and PBCV-1 genomes. These data imply that the Chlorella virus genome has an overall high degree of genomic stability, encompassing specific islands of rearrangements.

Amino Acid Sequence↗