A Novel Chimeric Gene, siren, With Retroposed Promoter Sequence in the Drosophila bipectinata Complex (original) (raw)
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[Analysis of the suffix short retroelement copies and the encoded protein domain of Drosophila]
Genetika, 2002
To analyze the copies of the suffix short retro-element, its homologs were sought in nucleic acid sequence databases of the Drosophila melanogaster genome. The search yielded several conserved (near identical in sequence) copies, which are indicative of recent suffix transposition, and numerous divergent copies, which suggest ancient suffix transposition. Analysis of the short suffix ORF revealed a conserved protein domain, which was also found as the eighth C-terminal domain in reverse transcriptases of certain long interspersed elements (LINEs). The suffix-encoded polypeptide proved to be homologous to DNA- and RNA-recognizing domains.
The EMBO Journal
Academy of Sciences of the USSR, 117984 Moscow, USSR Communicated by G.P.Georgiev The mobile element jockey is similar in structural organization and coding potential to the LINEs of various organisms. It is transcribed at different stages of Drosophila ontogenesis. The Drosophila LINE family includes active transposable elements. Current models for the mechanism of transposition involve reverse transcription of an RNA intermediate and utilization of elementencoded proteins. As demonstrated here, a 2.23 kb DNA fragment from the region ofjockey encoding the putative reverse transcriptase was stably introduced into an expression system under inducible control of the Escherichia coli lac regulatory elements. We describe the expression of the 92 kDa protein and identify this polypeptide alone as the authentic jockey reverse transcriptase based on some of its physical and enzymic properties. The jockey polymerase demonstrates RNA and DNA-directed DNA polymerase activities but lacks detectable RNase H, has a temperature optimum at 260C, requires Mg2+ or Mn2+ as a cofactor and is inactivated by sulphydryl reagent. The enzyme prefers poly(rC) and poly(rA) as template and 'activated' DNA is not effective.
Evidence for retrotranscription of protein-coding genes in the Drosophila subobscura genome
Journal of Molecular Evolution, 1992
Evidence is provided for the presence of retrosequences (also named retroposons) arising from Adh in the Drosophila subobscura genome. Restriction analysis and primary structure of two different retrosequence-containing clones, $812 and S135, are reported. The fact that these retrosequences lack introns and a recognizable promoter strongly supports their retrotranscriptional origin. Adjacent to the two retrosequences analyzed, a middle repetitive DNA element has been found which bears no clear similarity to any sequence reported to date in the GenBank/EMBL Data Library. A comparative analysis of these retrosequences with the functional Adh gene of D. subobscura is presented. In addition, a model concerning the origin, functionality, and propagation of these genome elements is discussed.
1731, a new retrotransposon with hormone modulated expression
Nucleic acids research, 1986
We report here the characterisation of 1731, a new copia-like element of Drosophila melanogaster. 1731 was first isolated in a screening for ecdysterone modulated genes. This element is about 4.6 Kb long and is flanked by two long terminal repeats (LTRs) 336 base pairs in length. The whole 1731 element is transcribed into polyA+ RNAs, and these transcripts decrease rapidly upon hormonal treatment. 1731 is moderately repeated in the fly genome and slightly amplified in Kc/cells where extrachromosomal circular forms are found. The LTRs were sequenced in one cloned copy of 1731 and show a structural organisation similar to that of several other copia-like elements and retroviral proviruses. Small nucleotide stretches, similar to those found in Mouse Mammary Tumor Virus LTRs and known to be important in its regulation by a steroid hormone, occur in 1731 LTRs.
Primary structure and functional organization of Drosophila 1731 retrotransposon
Nucleic Acids Research, 1988
We have determined the nucleotide sequence of the Drosophila retrotransposon 1 731. 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, endnuclease and reverse transcriptase domains. We show that codon usep in the two retrotransposons is different. Finally, no ORF able to encode an env gene is detected in 1 731.
Genome biology, 2000
Non-long terminal repeat (non-LTR) retrotransposons are eukaryotic mobile genetic elements that transpose by reverse transcription of an RNA intermediate. We have performed a systematic search for sequences matching the characteristic reverse transcriptase domain of non-LTR retrotransposons in the sequenced regions of the Drosophila melanogaster genome. In addition to previously characterized BS, Doc, F, G, I and Jockey elements, we have identified new non-LTR retrotransposons: Waldo, You and JuanDm. Waldo elements are related to mosquito RTI elements. You to the Drosophila I factor, and JuanDm to mosquito Juan-A and Juan-C. Interestingly, all JuanDm elements are highly homogeneous in sequence, suggesting that they are recent components of the Drosophila genome. The genome of D. melanogaster contains at least ten families of non-site-specific non-LTR retrotransposons representing three distinct clades. Many of these families contain potentially active members. Fine evolutionary anal...
PLoS ONE, 2011
Transposition of two retroelements (Ulysses and Penelope) mobilized in the course of hybrid dysgenesis in Drosophila virilis has been investigated by in situ hybridization on polytene chromosomes in two D. virilis strains of different cytotypes routinely used to get dysgenic progeny. The analysis has been repeatedly performed over the last two decades, and has revealed transpositions of Penelope in one of the strains, while, in the other strain, the LTR-containing element Ulysses was found to be transpositionally active. The gypsy retroelement, which has been previously shown to be transpositionally inactive in D. virilis strains, was also included in the analysis. Whole mount is situ hybridization with the ovaries revealed different subcellular distribution of the transposable elements transcripts in the strains studied. Ulysses transpositions occur only in the strain where antisense piRNAs homologous to this TE are virtually absent and the ping-pong amplification loop apparently does not take place. On the other hand small RNAs homologous to Penelope found in the other strain, belong predominantly to the siRNA category (21nt), and consist of sense and antisense species observed in approximately equal proportion. The number of Penelope copies in the latter strain has significantly increased during the last decades, probably because Penelope-derived siRNAs are not maternally inherited, while the low level of Penelope-piRNAs, which are faithfully transmitted from mother to the embryo, is not sufficient to silence this element completely. Therefore, we speculate that intrastrain transposition of the three retroelements studied is controlled predominantly at the post-transcriptional level.
Identification of Waldo-A and Waldo-B, Two Closely Related Non-LTR Retrotransposons in Drosophila
Molecular Biology and Evolution, 2001
We have identified two novel, closely related subfamilies of non-long-terminal-repeat (non-LTR) retrotransposons in Drosophila melanogaster, the Waldo-A and Waldo-B subfamilies, that are in the same lineage as site-specific LTR retrotransposons of the R1 clade. Both contain potentially active copies with two large open reading frames, having coding capacities for a nucleoprotein as well as endonuclease and reverse transcriptase activities. Many copies are truncated at the 5Ј end, and most are surrounded by target site duplications of variable lengths. Elements of both subfamilies have a nonrandom distribution in the genome, often being inserted within or very close to (CA) n arrays. At the DNA level, the longest elements of Waldo-A and Waldo-B are 69% identical on their entire length, except for the 5Ј untranslated regions, which have a mosaic organization, suggesting that one arose from the other following new promoter acquisition. This event occurred before the speciation of the D. melanogaster subgroup of species, since both Waldo-A and Waldo-B coexist in other species of this subgroup.
Molecular Biology and Evolution, 1997
genes, and pseudogenes originated by retrotranscription are frequent components of vertebrate genomes, but they have only occasionally been described in invertebrates. In Drosophila, very few retrosequences have been reported, among them those of alcohol dehydrogenase (Adh) and phosphoglyceromutase (Pglym). Although 52 Adh gene sequences are available for comparison, Adh retrosequences have been described only in the sibling species D. teissieri and D. yakuba (melunoguster subgroup) and in D. subobscuru (obscuru subgroup). Here, we report the presence of Adh retrosequences in two closely related species of D. subobscuru: D. mudeirensis and D. guunche. Extensive sequence comparisons with their functional paralogs suggest separate retrotranscriptional events: one in the melunoguster subgroup in the ancestor of D. teissieri and D. yukubu, and the other in the obscuru subgroup before the radiation of the lineages leading to D. subobscuru, D. mudeirensis, and D. guunche. In the former, the Adh retrotranscript originated a new expressed gene, named jingwei. However, in the obscuru Adh retrosequences, retention of codon bias and higher K, than K, values, both distinctive evolutionary features supporting functionality, have to be considered together with a frameshift, premature stop codons, and other nucleotide substitutions, which, added to the lack of the original promoter elements, suggest that they are pseudogenes.