Bioinformatic analysis of Entamoeba histolytica SINE1 elements

Derek M Huntley,Sarah A Butcher,John P Ackers,Ioannis Pandis

doi:10.1186/1471-2164-11-321

Derek M Huntley, Sarah A Butcher + Show 2 more

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https://doi.org/10.1186/1471-2164-11-321

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Abstract

BackgroundInvasive amoebiasis, caused by infection with the human parasite Entamoeba histolytica remains a major cause of morbidity and mortality in some less-developed countries. Genetically E. histolytica exhibits a number of unusual features including having approximately 20% of its genome comprised of repetitive elements. These include a number of families of SINEs - non-autonomous elements which can, however, move with the help of partner LINEs. In many eukaryotes SINE mobility has had a profound effect on gene expression; in this study we concentrated on one such element - EhSINE1, looking in particular for evidence of recent transposition.ResultsEhSINE1s were detected in the newly reassembled E. histolytica genome by searching with a Hidden Markov Model developed to encapsulate the key features of this element; 393 were detected. Examination of their sequences revealed that some had an internal structure showing one to four 26-27 nt repeats. Members of the different classes differ in a number of ways and in particular those with two internal repeats show the properties expected of fairly recently transposed SINEs - they are the most homogeneous in length and sequence, they have the longest (i.e. the least decayed) target site duplications and are the most likely to show evidence (in a cDNA library) of active transcription. Furthermore we were able to identify 15 EhSINE1s (6 pairs and one triplet) which appeared to be identical or very nearly so but inserted into different sites in the genome; these provide good evidence that if mobility has now ceased it has only done so very recently.ConclusionsOf the many families of repetitive elements present in the genome of E. histolytica we have examined in detail just one - EhSINE1. We have shown that there is evidence for waves of transposition at different points in the past and no evidence that mobility has entirely ceased. There are many aspects of the biology of this parasite which are not understood, in particular why it is pathogenic while the closely related species E. dispar is not, the great genetic diversity found amongst patient isolates and the fact, which may be related, that only a small proportion of those infected develop clinical invasive amoebiasis. Mobile genetic elements, with their ability to alter gene expression may well be important in unravelling these puzzles.

Highlights

Invasive amoebiasis, caused by infection with the human parasite Entamoeba histolytica remains a major cause of morbidity and mortality in some less-developed countries
By using a Hidden Markov Model to search the newly assembled E. histolytica genome we have identified 393 copies of a SINE element - EhSINE1; this number is in reasonable agreement with that found by Lorenzi et al and with older hybridisation data
Our working hypothesis was that newly transposed EhSINE1s would be identical in sequence to the parent copy and would have -recognisable TSDs, but that over time these similarities would decay, providing a rough measure of time since transposition

Summary

Introduction

Invasive amoebiasis, caused by infection with the human parasite Entamoeba histolytica remains a major cause of morbidity and mortality in some less-developed countries. SINE elements (Short INterspersed repetitive Elements) are non-autonomous and are thought to use the enzymatic machinery of matching LINEs (Autonomous Non Long-TerminalRepeat retroposons [Long INterspersed repetitive Element]) - in this case EhLINE1 [11]) for their transposition [12]. This transposition mechanism results in the formation of flanking short direct repeats of the target site (Target Site Duplications, TSDs). Most EhSINE1s described so far are about 500-600 bp in length; this range is largely due to variable numbers of internal 26-27 bp repeats; the 5' and 3' terminal regions are normally well conserved. (For reviews of E. histolytica LINEs and SINEs see [9] and [10])

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