Nuclear factors which bind to Dictyostelium discoideum transfer RNA genes

Transfer RNA gene-targeted retrotransposition of Dictyostelium TRE5-A into a chromosomal UMP synthase gene trap

The genome of the eukaryotic microorganism Dictyostelium discoideum hosts a family of seven non-long terminal repeat retrotransposons (TREs) that show remarkable insertion preferences near tRNA genes. We developed an in vivo assay to detect tRNA gene-targeted retrotransposition of endogenous TREs in a reporter strain of D. discoideum. A tRNA gene positioned within an artificial intron was placed into the D. discoideum UMP synthase gene. This construct was inserted into the D. discoideum genome and presented as a landmark for de novo TRE insertions. We show that the tRNA gene-tagged UMP synthase gene was frequently disrupted by de novo insertions of endogenous TRE5-A copies, thus rendering the resulting mutants resistant to 5-fluoroorotic acid selection. Approximately 96% of all isolated 5-FOA-resistant clones contained TRE5-A insertions, whereas the remaining 4% resulted from transposition-independent mutations. The inserted TRE5-As showed complex structural variations and were found about 50 bp upstream of the reporter tRNA gene, similar to previously analysed genomic copies of TRE5-A. No integration by other members of the TRE family was observed. We found that only 51% of the de novo insertions were derived from autonomous TRE5-A.1 copies. The remaining 49% of new insertions were due to TRE5-A.2 elements, which lack the proteins required for reverse transcription and integration, but retain functional promoter sequences.

A nuclear protein factor binds specifically to the 3'-regulatory module of the long-interspersed-nuclear-element-like Dictyostelium repetitive element

The Dictyostelium repetitive element DRE integrates in a position-specific manner upstream of tRNA genes in the Dictyostelium discoideum genome. DRE has structural similarities to the group of long interspersed nuclear elements, whose replication mechanism is poorly understood. The C-module at the 3' end of DRE encodes a regulatory cis-acting sequence that contains an RNA polymerase II promoter. This promoter directs the synthesis of RNAs that are thought to play a critical role in DRE transposition. In this study, we describe the identification of a nuclear protein factor that binds to the C-module in a sequence-specific manner. The C-module-binding factor (CMBF) recognizes three DNA sequence motifs that contain homopolymeric (dT) stretches of variable lengths, but does not bind to a standard RNA polymerase II promoter from D, discoideum. Analysis of highly CMBF-enriched fractions and glycerol gradient sedimentation of CMBF suggest that the factor exists as a monomeric 115-kDa protein. Possible roles of CMBF in DRE transposition are discussed.

Isolation of transcription factor IIIC from Dictyostelium discoideum

Transcription factor IIIC (TFIIIC) binds in a sequence-specific manner to RNA-polymerase-III-transcribed genes (e.g. tRNA genes). It sequesters other transcription factors into the preformed complex, thereby activating transcription by RNA polymerase III. The Dictyostelium discoideum homologue of TFIIIC was highly purified by affinity chromatography based on its tDNA-binding activity. This TFIIIC homologue is a multicomponent factor (molecular mass 380 kDa), which binds to the B-box element of the internal tRNA gene promoter without significant A-box interaction. Partially purified D. discoideum TFIIIC is able to functionally complement a human RNA polymerase III in vitro transcription system depleted of human TFIIIC. We provide evidence that partially purified D. discoideum TFIIIC interacts in vitro with gene-external B-box elements present down-stream of many D. discoideum tRNA genes.