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O N Danilevskaya

Publications and source records attributed to O N Danilevskaya.

At least 19 recordsLinked to original sources
PubMed1999

The two Drosophila telomeric transposable elements have very different patterns of transcription.

The transposable elements HeT-A and TART constitute the telomeres of Drosophila chromosomes. Both are non-long terminal repeat (LTR) retrotransposons, sharing the remarkable property of transposing only to chromosome ends. In addition, strong sequence similarity of their gag proteins indicates that these coding regions share a common ancestor. These findings led to the assumption that HeT-A and TART are closely related. However, we now find that these elements produce quite different sets of transcripts. HeT-A produces only sense-strand transcripts of the full-length element, whereas TART produces both sense and antisense full-length RNAs, with antisense transcripts in more than 10-fold excess over sense RNA. In addition, features of TART sequence organization resemble those of a subclass of non-LTR elements characterized by unequal terminal repeats. Thus, the ancestral gag sequence appears to have become incorporated in two different types of elements, possibly with different functions in the telomere. HeT-A transcripts are found in both nuclear and cytoplasmic cell fractions, consistent with roles as both mRNA and transposition template. In contrast, both sense and antisense TART transcripts are almost entirely concentrated in nuclear fractions. Also, TART open reading frame 2 probes detect a cytoplasmic mRNA for reverse transcriptase (RT), with no similarity to TART sequence 5' or 3' of the RT coding region. This RNA could be a processed TART transcript or the product of a "free-standing" RT gene. Either origin would be novel. The distinctive transcription patterns of both HeT-A and TART are conserved in Drosophila yakuba, despite significant sequence divergence. The conservation argues that these sets of transcripts are important to the function(s) of HeT-A and TART.

Animals↗
PubMed1998

Unusual features of the Drosophila melanogaster telomere transposable element HeT-A are conserved in Drosophila yakuba telomere elements.

HeT-A was the first transposable element shown to have a bona fide role in chromosome structure, maintenance of telomeres in Drosophila melanogaster. HeT-A has hallmarks of non-long-terminal-repeat (non-LTR) retrotransposable elements but also has several unique features. We have now isolated HeT-A elements from Drosophila yakuba, showing that the retrotransposon mechanism of telomere maintenance predates the separation of D. melanogaster and D. yakuba (5-15 million years ago). HeT-A elements from the two species show significant sequence divergence, yet unusual features seen in HeT-Amel are conserved in HeT-Ayak. In both species, HeT-A elements are found in head-to-tail tandem arrays in telomeric heterochromatin. In both species, nearly half of the HeT-A sequence is noncoding and shows a distinctive imperfect repeat pattern of A-rich segments. Neither element encodes reverse transcriptase. The HeT-Amel promoter appears to be intermediate between the promoters of non-LTR and of LTR retrotransposons. The HeT-Ayak promoter shows similar features. HeT-Amel has a frameshift within the coding region. HeT-Ayak does not require a frameshift but shows conservation of the polypeptide sequence of the frameshifted product of D. melanogaster.

Animals↗
PubMed1998

Conserved subfamilies of the Drosophila HeT-A telomere-specific retrotransposon.

HeT-A, a major component of Drosophila telomeres, is the first retrotransposon proposed to have a vital cellular function. Unlike most retrotransposons, more than half of its genome is noncoding. The 3' end contains > 2.5 kb of noncoding sequence. Copies of HeT-A differ by insertions or deletions and multiple nucleotide changes, which initially led us to conclude that HeT-A noncoding sequences are very fluid. However, we can now report, on the basis of new sequences and further analyses, that most of these differences are due to the existence of a small number of conserved sequence subfamilies, not to extensive sequence change during each transposition event. The high level of sequence conservation within subfamilies suggests that they arise from a small number of replicatively active elements. All HeT-A subfamilies show preservation of two intriguing features. First, segments of extremely A-rich sequence form a distinctive pattern within the 3' noncoding region. Second, there is a strong strand bias of nucleotide composition: The DNA strand running 5' to 3' toward the middle of the chromosome is unusually rich in adenine and unusually poor in guanine. Although not faced with the constraints of coding sequences, the HeT-A 3' noncoding sequence appears to be under other evolutionary constraints, possibly reflecting its roles in the telomeres.

Animals↗
PubMed1997

Promoting in tandem: the promoter for telomere transposon HeT-A and implications for the evolution of retroviral LTRs.

HeT-A elements are non-long terminal repeat (non-LTR) retrotransposons found in head-to-tail arrays on Drosophila chromosome ends, where they form telomeres. We report that HeT-A promoter activity is located in the 3' end of the element, unlike the 5' location seen for other non-LTR retrotransposons. In HeT-A arrays the 3' sequence of one element directs transcription of its downstream neighbor. Because the upstream promoter has the same sequence as the 3' end of the transcribed element, the HeT-A promoter is effectively equivalent to a 5' LTR in both structure and function. Retroviruses and LTR retrotransposons have their promoters and transcription initiation sites in their 5' LTRs. Thus HeT-A appears to have the structure of an evolutionary intermediate between non-LTR and LTR retrotransposons.

Animals↗
PubMed1997

Evolutionary links between telomeres and transposable elements.

Transposable elements are abundant in the genomes of higher organisms but are usually thought to affect cells only incidentally, by transposing in or near a gene and influencing its expression. Telomeres of Drosophila chromosomes are maintained by two non-LTR retrotransposons, HeT-A and TART. These are the first transposable elements with identified roles in chromosome structure. We suggest that these elements may be evolutionarily related to telomerase; in both cases an enzyme extends the end of a chromosome by adding DNA copied from an RNA template. The evolution of transposable elements from chromosomal replication mechanisms may have occurred multiple times, although in other organisms the new products have not replaced the endogenous telomerase, as they have in Drosophila. This is somewhat reminiscent of the oncogenes that have arisen from cellular genes. Perhaps the viruses that carry oncogenes have also arisen from cellular genetic systems.

Amino Acid Sequence↗
PubMed1996

The gag coding region of the Drosophila telomeric retrotransposon, HeT-A, has an internal frame shift and a length polymorphic region.

A major component of Drosophila telomeres is the retrotransposon HeT-A, which is clearly related to other retrotransposons and retroviruses. This retrotransposon is distinguished by its exclusively telomeric location, and by the fact that, unlike other retrotransposons, it does not encode its own reverse transcriptase. HeT-A coding sequences diverge significantly, even between elements within the same genome. Such rapid divergence has been noted previously in studies of gag genes from other retroelements. Sequence comparisons indicate that the entire HeT-A coding region codes for gag protein, with regions of similarity to other insect retrotransposon gag proteins found throughout the open reading frame (ORF). Similarity is most striking in the zinc knuckle region, a region characteristic of gag genes of most replication-competent retroelements. We identify a subgroup of insect non-LTR retrotransposons with three zinc knuckles of the form: (1) CX2CX4HX4C, (2) CX2CX3HX4C, (3) CX2CX3HX6C. The first and third knuckles are invariant, but the second shows some differences between members of this subgroup. This subgroup includes HeT-A and a second Drosophila telomeric retrotransposon, TART. Unlike other gag regions, HeT-A requires a -1 frameshift for complete translation. Such frameshifts are common between the gag and pol sequences of retroviruses but have not before been seen within a gag sequence. The frameshift allows HeT-A to encode two polypeptides; this mechanism may substitute for the post-translational cleavage that creates multiple gag polypeptides in retroviruses. D. melanogaster HeT-A coding sequences have a polymorphic region with insertions/deletions of 1-31 codons and many nucleotide changes. None of these changes interrupt the open reading frame, arguing that only elements with translatable ORFs can be incorporated into the chromosomes. Perhaps HeT-A translation products act in cis to target the RNA to chromosome ends.

Amino Acid Sequence↗
PubMed1996

Drosophila telomeres: new views on chromosome evolution.

In Drosophila, chromosome ends (telomeres) are composed of telomere-specific transposable elements (the retroposons HeT-A and TART). These elements are a bona fide part of the cellular machinery yet have many of the hallmarks of retrotransposable elements and retroviruses, raising the possibility that parasitic transposable elements and viruses might have evolved from mechanisms that the cell uses to maintain its chromosomes. It is striking that Drosophila, the model organism for many discoveries in genetics, development and molecular biology (including the classical concept of telomeres), should prove to have chromosome ends different from the generally accepted model. Studies of these telomere-specific retrotransposable elements raise questions about conventional wisdom concerning not only telomeres, but also transposable elements and heterochromatin.

Animals↗
PubMed1994

Drosophila telomere transposon HeT-A produces a transcript with tightly bound protein.

Telomeres from Drosophila appear to be very different from those of other organisms. A transposable element, HeT-A, plays a major role in forming telomeres and may be the sole structural element, since telomerase-generated repeats are not found. The structure of the HeT-A element, deduced from cloned fragments of DNA, suggests that transposition of the element is mediated by a polyadenylylated RNA intermediate. We now report analyses of HeT-A transcripts. The major RNA is of the appropriate size and strandedness to serve as a transposition intermediate. This RNA is found in cultured cells and in intact flies and is unusual in that it is associated with protein after treatments that apparently remove all protein from other RNAs.

Animals↗
PubMed1992

A repetitive DNA element, associated with telomeric sequences in Drosophila melanogaster, contains open reading frames.

He-T sequences are a complex repetitive family of DNA sequences in Drosophila that are associated with telomeric regions, pericentromeric heterochromatin, and the Y chromosome. A component of the He-T family containing open reading frames (ORFs) is described. These ORF-containing elements within the He-T family are designated T-elements, since hybridization in situ with the polytene salivary gland chromosomes results in detectable signal exclusively at the chromosome tips. One T-element that has been sequenced includes ORFs of 1,428 and 1,614 bp. The ORFs are overlapping but one nucleotide out of frame with respect to each other. The longer ORF contains cysteine-histidine motifs strongly resembling nucleic acid binding domains of gag-like proteins, and the overall organization of the T-element ORFs is reminiscent of LINE elements. The T-elements are transcribed and appear to be conserved in Drosophila species related to D. melanogaster. The results suggest that T-elements may play a role in the structure and/or function of telomeres.

Amino Acid Sequence↗
PubMed1992

An eclectic DNA structure adopted by human telomeric sequence under superhelical stress and low pH.

We have found, with the aid of 2-D gel electrophoresis, that double-stranded human telomeric repeat, (T2AG3)12.(C3TA2)12, being cloned within a plasmid, forms a protonated superhelically-induced structure. Experiments on chemical and enzymatic probing also indicate that the human telomeric repeats adopt an unusual structure. We have proposed an eclectic model for this structure in which four different elements coexist: a non-orthodox intramolecular triplex stabilized by the canonical protonated C.G*C+ base-triads and highly enriched by noncanonical base-triads; the intramolecular quadruplex formed by a portion of the G-rich strand; the single-stranded region encompassing a portion of the G-rich strand and, probably, the (C,A)-hairpin formed by a portion of the C-rich strand.

Base Sequence↗
PubMed1991

He-T family DNA sequences in the Y chromosome of Drosophila melanogaster share homology with the X-linked stellate genes.

The genome of Drosophila melanogaster contains a class of repetitive DNA sequences called the He-T family, which is unusual in being confined to telomeric and heterochromatic regions. The specific He-T fragment designated Dm665 was cloned in yeast by selection for an autonomously replicating sequence (ARS). Dm665 contains a restriction fragment length polymorphism (RFLP) that is specific to males and thus derives from the Y chromosome. Deletion mapping using X-Y translocations indicates that sequences homologous to Dm665 occur in at least one major cluster in each arm of the Y chromosome. Among 20 yeast artificial chromosome (YAC) clones containing Drosophila sequences homologous with Dm665, four clones derive from defined regions of the long arm of the Y and two from the short arm. The sequence of Dm665 is 2443 bp long, consists of 59% A + T, and contains no significant open reading frames or direct or inverted repeats. However, Dm665 contains a region of 650 bp that shares homology with portions of the X-linked locus Stellate.

Animals↗
PubMed1989

An unusual DNA structure detected in a telomeric sequence under superhelical stress and at low pH.

Telomeric sequences of DNA, which are found at the ends of linear chromosomes, have been attracting attention as potential sites for the formation of unusual DNA structures. They consist of (GnTm) or (GnATm) motifs (n greater than or equal to m) and, in the single-stranded state, form hairpins stabilized by non-canonical G.G pairs. In the duplex state and under superhelical stress they exhibit hypersensitivity to SI nuclease which by analogy with homopurine-homopyrimidine sequences may reflect the formation of an unusual structure. To determine whether this is the case we have inserted into a plasmid the Tetrahymena telomeric motif (G4T2).(A2C4) and probed it by two-dimensional gel electrophoresis, chemical modification and oligonucleotide binding. Our data demonstrate that, under superhelical stress and at low pH, the insert does indeed adopt a novel DNA conformation. We have concluded that in this structure the C-rich strand forms a hairpin stabilized by non-Watson-Crick base pairs C.C+ and A.A+, whereas the G-rich strand remains unstructured. We term this new DNA structure the (C,A)-hairpin.

DNA↗
PubMed1988

An ARS element from Drosophila melanogaster telomeres contains the yeast ARS core and bent replication enhancer.

We have sequenced the 0.7-kb-long fragment of Drosophila DNA which ensures the autonomous replication of plasmids in yeast. Deletion mapping has shown the ARS element to consist of at least two domains: the core having the consensus 11-bp sequence TAAATATAAAT and the enhancer which is no more than 90 bp long and is located at the 3'-end of the A-rich core strand. Neither domain per se ensures plasmid replication in yeast. A comparison of the enhancer sequence with the sequences of 14 different ARS elements failed to reveal significant homology areas. Most probably the ARS flanks that are adjacent to the core and act as enhancer do not carry any consensus. They may determine a peculiar structural feature of DNA (for example bends) which are necessary for the protein-ARS interaction.

Animals↗
PubMed1984

Mutation to rifampicin resistance at the beginning of the RNA polymerase beta subunit gene in Escherichia coli.

The unusual recombinant plasmid pRC19 carrying the N-terminal fragment of the Escherichia coli RNA polymerase rpoB gene was found to specify high level rifampicin resistance of E. coli cells. Sequence analysis of this plasmid revealed one substitution only: transversion G----T, leading to amino acid substitution Val146----Phe. This mutational change marks the second domain of the beta subunit involved in rifampicin binding.

Base Sequence↗
PubMed1982

Decreased degradation of beta beta' RNA polymerase subunits and abnormal proteins in a mutant E. coli.

An opr24 mutation decreasing the degradation of RNA polymerase beta beta' subunits was found among the Ts+ revertants of Ts strain carrying an rpoC1 mutation which stimulates overproduction of these polypeptides. The opr24 mutation is allele-non-specific, for it decreases the degradation of the mutant beta and beta' subunits, the amber-fragment of the beta subunit and the non-mutant beta' subunit. Moreover, opr24 reduces the proteolysis of abnormal proteins containing canavanine. The opr24 mutation maps between 17 and 21 min on the E. coli genetic map. The results demonstrate that a slow proteolysis rate in the bacterial cell can suppress conditional lethal mutations. In addition, the slower degradation and the ensuing accumulation of beta beta' subunits does not effect the rate of the beta beta' subunit synthesis.

Bacterial Proteins↗
PubMed1981

Primary structure of Escherichia coli RNA polymerase nucleotide substitution in the beta subunit gene of the rifampicin resistant rpoB255 mutant.

The transducing phage lambda dsupM814 and the plasmid pIB1830 containing the wild-type rpoB gene have been constructed and the primary structure of the gene's central fragment has been established. In contrast with the wild-type, the gene of the rpoB255 mutant, whose primary structure has been published, was found to contain an A.T. leads to T.A. transversion entailing the substitution of a valine residue for the aspartic acid residue (516) of the wild-type beta subunit.

Base Sequence↗
PubMed1980

Curing of Escherichia coli K12 plasmids by coumermycin.

Low concentrations of the antibiotic coumermycin A1, the inhibitor of bacterial DNA gyrase, effectively eliminate pBR322, pMB9 and other ColE 1 related plasmids from E. coli K12 strains. The curing action of antibiotic seems to result from the plasmid degradation and not just from the inhibition of replication.

Aminocoumarins↗