Abstract
In trypanosomatids, the RNA polymerase I (RNAPI)-dependent promoters controlling the ribosomal RNA (rRNA) genes have been well identified. Although the RNAPI transcription machinery recognizes the DNA conformation instead of the DNA sequence of promoters, no conformational study has been reported for these promoters. Here we present the in silico analysis of the intrinsic DNA curvature of the rRNA gene core promoters in Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major. We found that, in spite of the absence of sequence conservation, these promoters hold conformational properties similar to other eukaryotic rRNA promoters. Our results also indicated that the intrinsic DNA curvature pattern is conserved within the Leishmania genus and also among strains of T. cruzi and T. brucei. Furthermore, we analyzed the impact of point mutations on the intrinsic curvature and their impact on the promoter activity. Furthermore, we found that the core promoters of protein-coding genes transcribed by RNAPI in T. brucei show the same conserved conformational characteristics. Overall, our results indicate that DNA intrinsic curvature of the rRNA gene core promoters is conserved in these ancient eukaryotes and such conserved curvature might be a requirement of RNAPI machinery for transcription of not only rRNA genes but also protein-coding genes.
Highlights
In trypanosomatids, the RNA polymerase I (RNAPI)-dependent promoters controlling the ribosomal RNA genes have been well identified
To further the current understanding of the molecular mechanisms involved in transcription initiation by RNAPI in trypanosomatids, we examined whether the core promoters of Tritryp ribosomal RNA (rRNA) gene share the conformational characteristics conserved in eukaryotes
On the contrary, when we compared the intrinsic curvature of the same core promoter sequences, we found that T. brucei and T. cruzi rRNA promoters showed the conserved eukaryotic DNA structural feature that has been previously described for the corresponding promoters in human [11] (Figure 1A)
Summary
The RNA polymerase I (RNAPI)-dependent promoters controlling the ribosomal RNA (rRNA) genes have been well identified. Individual mRNAs are later generated by 50 trans-splicing, a process that involves the addition of a small conserved RNA called the spliced leader (SL) and the polyadenylation at their 30 ends [8] In this context, regulation of the expression of protein-coding genes in trypanosomatids seems to occur mainly at posttranscriptional levels [6,7]. Signals directing protein recognition at the promoter region are constituted by DNA conformations rather than the primary nucleotide sequences [11,12] For this reason, the conformational structures of the rRNA gene promoters have been examined in several organisms [11,12]. No promoter conformational study has been reported for Tritryps so far
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