Characterization of natural antisense transcripts arisen from the locus encoding Toxoplasma gondii ubiquitin-like protease.

Natural antisense transcripts (NATs) are non-protein coding RNAs that could play an important role in regulating the expression of their counterpart protein encoding sense transcript. Although NATs are widespread in most eukaryotic genomes, very little is known about their functions. This study focuses on gaining a better understanding of the function of NATs in Toxoplasma gondii, a pathogenic unicellular eukaryote. Previously, we characterized the gene encoding the first committed enzyme in sumoylation, named ubiquitin-like protease 1 (TgUlp1), and showed that the expression of TgUlp1 is vital to the life cycle of T. gondii. Interestingly, the locus of TgUlp1 also transcribes a NAT species. Using a dual luciferase assay, we identified the promoter of TgUlp1 NAT to be located within the 3'-region of its counterpart coding sequence. While TgUlp1 mRNA level was detected at a lower level throughout the life cycle of T. gondii, its NAT level was upregulated when the parasite converts from actively replicating tachyzoite form to slowly growing bradyzoite form. To investigate the effect of TgUlp1 NAT on the expression of its counterpart mRNA, we used a reporter system bearing TgUlp1 mRNA sequences and showed that the single-stranded TgUlp1 NAT and its in vitro RNase III processed products have the ability to lower the expression of the reporter system. Using a transgenic Dicer-knockout (TgDicer-KO) strain, we showed that TgDicer is required for the function of TgUlp1 NAT in vivo. The findings strongly suggest that the RNA interference pathway is necessary for the function of TgUlp1 NAT.