The Trypanosomatid Pr77-hallmark contains a downstream core promoter element essential for transcription activity of the Trypanosoma cruzi L1Tc retrotransposon.

Francisco Macías,Manuel Carlos López,M Carmen Thomas

doi:10.1186/s12864-016-2427-6

Abstract

BackgroundTrypanosomatid genomes are highly colonized by non-LTR retroelements that make up to 5 % of the nuclear genome. These elements are mainly accumulated in the strand switch regions (SSRs) where polycistronic transcription is initiated and have a 77 nt-long sequence - Pr77 - at their 5′ ends. L1Tc is the best represented retrotransposon in the Trypanosoma cruzi genome and is a potentially functional autonomous element that encodes its own retrotransposition machinery. The Pr77 of the T. cruzi L1Tc element activates gene transcription via RNA polymerase II, generating abundant, unspliced transcripts which are translated.ResultsThe present manuscript describes the identification of a downstream core promoter element (DPE) in the L1Tc Pr77 sequence. Just four nucleotides long (CGTG), it covers in Pr77 positions +25 to +28 of the described L1Tc transcription start site. The Pr77-DPE motif is conserved in terms of sequence composition and position in the Pr77 of most trypanosomatid non-LTR retrotransposons, independent of the coding or non-coding capacity of these retroelements. Transcription assays in T. cruzi stable transfectants with vector containing point mutations at 17 locations of the Pr77 nucleotide sequence evidence that the DPE motif is essential for the promoter function of Pr77. Furthermore, the obtained data show that other nucleotides also contributed to the promoter function of Pr77. In addition, the presented results indicate that parasite nuclear proteins specifically bind to different regions of the Pr77 sequence although the strongest binding is to the DPE motif. Moreover, it is shown that the DPE sense single-stranded sequence is being required in DNA-protein recognition of nuclear factors.ConclusionsThe Pr77 sequence present in most of non-LTR retrotransposons of trypanosomatids contains a downstream core promoter element (DPE) which is conserved in terms of nucleotide composition and location. The Pr77-DPE motif is essential for the transcriptional activity of Pr77 although other nucleotides are also involved. DPE has a high affinity binding for nuclear proteins in T. cruzi. The wide retroelement-mediated distribution of Pr77 suggests that it may represent an important tool for regulating gene expression in trypanosomatids.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2427-6) contains supplementary material, which is available to authorized users.

Highlights

Trypanosomatid genomes are highly colonized by non-LTR retroelements that make up to 5 % of the nuclear genome
The Pr77 sequence present in most of non-LTR retrotransposons of trypanosomatids contains a downstream core promoter element (DPE) which is conserved in terms of nucleotide composition and location
Pr77 promoter contains a downstream promoter element In previous work, we reported the presence of an RNA pol II internal promoter involving the first 77 nucleotides (Pr77) of the 5′end of the L1Tc retrotransposon

Summary

Introduction

Trypanosomatid genomes are highly colonized by non-LTR retroelements that make up to 5 % of the nuclear genome. Trypanosoma cruzi is the etiological agent of Chagas disease, a chronic sickness that affects 7 million people worldwide, mostly in Latin America where it was entirely confined it has spread to other continents (http://www.who.int/mediacentre/factsheets/ fs340/en/) This intracellular, protozoan parasite has been extensively studied because of its impact on human health, and because of the interesting molecular characteristics of the family Trypanosomatidae, which shows some unusual features of gene transcription. Trypanosomatid genomes contain versions of the long and short elements known as degenerate ingi/L1Tc-related elements (DIRES) [6] and short interspersed degenerate retrotransposons (SIDERs). These have accumulated a huge number of mutations that have disabled their coding capacity. In the T. brucei genome, some 20 copies of SIDERs have been detected per haploid genome, whereas in Leishmania species there are around 2000 copies per haploid genome [9]

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