Dictyostelium mobile elements: strategies to amplify in a compact genome

Abstract

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.

TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs

“…The Dictyostelium non-LTR transposon TRE-5 has also evolved a mechanism to insert upstream of pol III genes. This transposon inserts an average of 48 bp upstream of the pol III transcription start site, and it has been suggested that the integration machinery identifies the upstream boundary of the TFIIIB preinitiation complex and uses it as a platform for adjacent insertion (Beck et al 2002;Winckler et al 2002).…”

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

“…Note that all four TRE3s have similar structures, although the UTR sequences are highly diverged. TRE5-C is not completely assembled, but has most likely AB-modules as 5) UTR (see also Winckler et al, 2002). RNH, RNase H domain; Ï-rec, domain with homology to bacteriophage Ï recombinase; CHROMO, chromatin organizer domain; EN, endonuclease domain; RT, reverse transcriptase domain; HC, domain containing a zinc finger-like histidine/cysteine-rich motif.…”

Protein Interactions Involved in tRNA Gene-Specific Integration of Dictyostelium discoideum Non-Long Terminal Repeat Retrotransposon TRE5-A

“…TRE5-A and TRE5-B are distantly related retrotransposons that probably shared a common ancestor in the evolution of the TREs in the genome of D. discoideum (14). TRE5-B shows the same integration preference as TRE5-A, i.e., 45 to 50 bp upstream of tRNA genes (46). Hence, it was predicted that TRE5-B should use molecular interactions similar to those of TRE5-A to identify integration sites.…”