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Open Access Research article

The wide expansion of hepatitis delta virus-like ribozymes throughout trypanosomatid genomes is linked to the spreading of L1Tc/ingi clade mobile elements

Francisco José Sánchez-Luque1, Manuel Carlos López1*, Patricia Eugenia Carreira1, Carlos Alonso2 and María Carmen Thomas1*

Author Affiliations

1 Instituto de Parasitología y Biomedicina “López-Neyra”, CSIC, Parque Tecnológico de Ciencias de la Salud, Av. del Conocimiento s/n, 18016 Granada, Spain

2 Centro de Biología Molecular “Severo Ochoa”, CSIC-UAM, Campus Universidad Autónoma de Madrid, C/Nicolás Cabrera n°1, 28049 Madrid, Spain

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BMC Genomics 2014, 15:340  doi:10.1186/1471-2164-15-340

Published: 6 May 2014

Abstract

Background

Hepatitis Delta Virus (HDV)-like ribozymes have recently been found in many mobile elements in which they take part in a mechanism that releases intermediate RNAs from cellular co-transcripts. L1Tc in Trypanosoma cruzi is one of the elements in which such a ribozyme is located. It lies in the so-called Pr77-hallmark, a conserved region shared by retrotransposons belonging to the trypanosomatid L1Tc/ingi clade. The wide distribution of the Pr77-hallmark detected in trypanosomatid retrotransposons renders the potential catalytic activity of these elements worthy of study: their distribution might contribute to host genetic regulation at the mRNA level. Indeed, in Leishmania spp, the pervasive presence of these HDV-like ribozyme-containing mobile elements in certain 3′-untranslated regions of protein-coding genes has been linked to mRNA downregulation.

Results

Intensive screening of publicly available trypanosomatid genomes, combined with manual folding analyses, allowed the isolation of putatively Pr77-hallmarks with HDV-like ribozyme activity. This work describes the conservation of an HDV-like ribozyme structure in the Pr77 sequence of retrotransposons in a wide range of trypanosomatids, the catalytic function of which is maintained in the majority.

These results are consistent with the previously suggested common phylogenetic origin of the elements that belong to this clade, although in some cases loss of functionality appears to have occurred and/or perhaps molecular domestication by the host.

Conclusions

These HDV-like ribozymes are widely distributed within retrotransposons across trypanosomatid genomes. This type of ribozyme was once thought to be rare in nature, but in fact it would seem to be abundant in trypanosomatid transcripts. It can even form part of the pool of mRNA 3′-untranslated regions, particularly in Leishmania spp. Its putative regulatory role in host genetic expression is discussed.

Keywords:
Retrotransposon; LINE; SINE; HDV-like ribozyme; Pr77; Trypanosoma; Leishmania; L1Tc; SIDER; ingi