Tdd-3, a tRNA gene-associated poly(A) retrotransposon  from Dictyostelium discoideum

Winckler, Thomas; Tschepke, C.; Hostos, Eugenio L. de; Jendretzke, A.; Dingermann, Theo

doi:10.1007/s004380050694

Cited by 7 publications

(13 citation statements)

References 28 publications

(49 reference statements)

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“…This suggested that both elements evolved from a common ancestor capable of inserting downstream of tRNA genes. In a more recent study [65] the full-length 5.2-kb DNA sequence of Tdd-3 was obtained. Tdd-3 elements encode two overlapping ORFs flanked by nonredundant UTRs.…”

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

“…3). Tdd-3 elements appear to be transcribed into full-length RNAs during vegetative growth of D. discoideum [65], a prerequisite for transposition. The promoter regulating the transcription of Tdd-3 RNAs is located within the first 360 bp at the 5% end of the Tdd-3 element (T.W., unpublished results).…”

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

“…All Tdd-3 clones isolated so far are inserted downstream of tRNA genes. Of 14 Tdd-3 clones, 11 were inserted 80-100 bp downstream of the B boxes of the corresponding tRNA genes [65]. Three Tdd-3 elements were inserted about 130 bp downstream of a B box and 70-90 bp of an exB box, respectively.…”

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

“…all isolated RED clones are inserted downstream of tRNA genes (T.W., unpublished data). RED elements encode all protein domains found in Tdd-3, and their deduced protein sequences are highly homologous [65]. About 30 RED copies are identified on Southern blots probed with 3% ends of RED, and many 5%-truncated RED copies were isolated in screenings aimed at determining the full-length RED sequence.…”

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

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Retrotransposable elements in the Dictyostelium discoideum genome

Winckler¹

1998

Cellular and Molecular Life Sciences (CMLS)

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Repetitive DNA is a major component of any living cell. In eukaryotes retrotransposable elements make up several percent of the genome size, and consequently, retroelements are often identified in experiments aimed at establishing physical maps and whole genome sequences. In this review, recent progress in the characterization of retrotransposable elements in the genome of the eukaryotic microorganism Dictyostelium discoideum is summarized with a focus on retroelements which integrate near transfer RNA genes with intriguing position specificity.

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Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

Section: Tdd-3 and Red Elementsmentioning

confidence: 99%

See 2 more Smart Citations

Retrotransposable elements in the Dictyostelium discoideum genome

Winckler¹

1998

Cellular and Molecular Life Sciences (CMLS)

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“…50 bp upstream of tRNA genes (Table 1). TRE3-A was the first non-LTR retrotransposon found to insert specifically downstream of D. discoideum tRNA genes (Winckler et al, 1998). The Dictyostelium genome project discovered three more TRE3-A-related elements, named TRE3-B, TRE3-C, and TRE3-D (Table 1; Glöckner et al, 2001).…”

Section: Discoideum Non-ltr Retrotransposonsmentioning

confidence: 99%

Transfer RNA gene-targeted integration: an adaptation of retrotransposable elements to survive in the compact <i>Dictyostelium discoideum</i> genome

Winckler

Szafranski²,

Glöckner³

2005

Cytogenet Genome Res

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Almost every organism carries along a multitude of molecular parasites known as transposable elements (TEs). TEs influence their host genomes in many ways by expanding genome size and complexity, rearranging genomic DNA, mutagenizing host genes, and altering transcription levels of nearby genes. The eukaryotic microorganism Dictyostelium discoideum is attractive for the study of fundamental biological phenomena such as intercellular communication, formation of multicellularity, cell differentiation, and morphogenesis. D. discoideum has a highly compacted, haploid genome with less than 1 kb of genomic DNA separating coding regions. Nevertheless, the D. discoideum genome is loaded with 10% of TEs that managed to settle and survive in this inhospitable environment. In depth analysis of D. discoideum genome project data has provided intriguing insights into the evolutionary challenges that mobile elements face when they invade compact genomes. Two different mechanisms are used by D. discoideum TEs to avoid disruption of host genes upon retrotransposition. Several TEs have invented the specific targeting of tRNA gene-flanking regions as a means to avoid integration into coding regions. These elements have been dispersed on all chromosomes, closely following the distribution of tRNA genes. By contrast, TEs that lack bona fide integration specificities show a strong bias to nested integration, thus forming large TE clusters at certain chromosomal loci that are hardly resolved by bioinformatics approaches. We summarize our current view of D. discoideum TEs and present new data from the analysis of the complete sequences of D. discoideum chromosomes 1 and 2, which comprise more than one third of the total genome.

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Dictyostelium mobile elements: strategies to amplify in a compact genome

Winckler

Dingermann

Glöckner³

2002

Cellular and Molecular Life Sciences (CMLS)

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Dictyostelium discoideum is a eukaryotic microorganism that is attractive for the study of fundamental biological phenomena such as cell-cell communication, formation of multicellularity, cell differentiation and morphogenesis. Large-scale sequencing of the D. discoideum genome has provided new insights into evolutionary strategies evolved by transposable elements (TEs) to settle in compact microbial genomes and to maintain active populations over evolutionary time. The high gene density (about 1 gene/2.6 kb) of the D. discoideum genome leaves limited space for selfish molecular invaders to move and amplify without causing deleterious mutations that eradicate their host. Targeting of transfer RNA (tRNA) gene loci appears to be a generally successful strategy for TEs residing in compact genomes to insert away from coding regions. In D. discoideum, tRNA gene-targeted retrotransposition has evolved independently at least three times by both non-long terminal repeat (LTR) retrotransposons and retrovirus-like LTR retrotransposons. Unlike the nonspecifically inserting D. discoideum TEs, which have a strong tendency to insert into preexisting TE copies and form large and complex clusters near the ends of chromosomes, the tRNA gene-targeted retrotransposons have managed to occupy 75% of the tRNA gene loci spread on chromosome 2 and represent 80% of the TEs recognized on the assembled central 6.5-Mb part of chromosome 2. In this review we update the available information about D. discoideum TEs which emerges both from previous work and current large-scale genome sequencing, with special emphasis on the fact that tRNA genes are principal determinants of retrotransposon insertions into the D. discoideum genome.

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Tdd-3, a tRNA gene-associated poly(A) retrotransposon from Dictyostelium discoideum

Cited by 7 publications

References 28 publications

Retrotransposable elements in the Dictyostelium discoideum genome

Retrotransposable elements in the Dictyostelium discoideum genome

Transfer RNA gene-targeted integration: an adaptation of retrotransposable elements to survive in the compact <i>Dictyostelium discoideum</i> genome

Dictyostelium mobile elements: strategies to amplify in a compact genome

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