RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in Entamoeba Species.

Damien Mornico,C Graham Clark,Mikael Koutero,Jean-Yves Coppée,Chung-Chau Hon,Christian Weber,Marie-Agnes Dillies,Nancy Guillen

doi:10.3390/microorganisms10020396

Abstract

Entamoeba is a genus of Amoebozoa that includes the intestine-colonizing pathogenic species Entamoeba histolytica. To understand the basis of gene regulation in E. histolytica from an evolutionary perspective, we have profiled the transcriptomes of its closely related species E. dispar, E. moshkovskii and E. invadens. Genome-wide identification of transcription start sites (TSS) and polyadenylation sites (PAS) revealed the similarities and differences of their gene regulatory sequences. In particular, we found the widespread initiation of antisense transcription from within the gene coding sequences is a common feature among all Entamoeba species. Interestingly, we observed the enrichment of antisense transcription in genes involved in several processes that are common to species infecting the human intestine, e.g., the metabolism of phospholipids. These results suggest a potentially conserved and compact gene regulatory system in Entamoeba.

Highlights

Entamoeba organisms are endobiotic amoebae colonizing species of animals
Comparing the transcriptomic profiles of genes targeted by natural antisense RNAs (NATs) in E. histolytica to E. dispar and E. moshkovskii, we discovered significant biological processes common to amoebic species infecting the human intestine, with lipid metabolism activities as the most important enriched functions, whereas the comparison with E. invadens highlighted vesicular trafficking and regulation of RNA transcription
E. histolytica strain HM-1: IMSS was cultured in TYI-S-33 medium at 37 ◦ C; E. moshkovskii strain Laredo was cultured in LYI-S-2 medium at room temperature; E. dispar strain SAW760 was cultured in LYI-S-2 medium at 37 ◦ C and

Summary

Introduction

Entamoeba organisms are endobiotic amoebae colonizing species of animals. The persistence of at least seven species of Entamoeba depends on their ability to infect humans, mainly in the intestinal tract, where they divide and encyst [1]. There has been a renewed interest in commensal intestinal amoebae because, being members of the human eukaryome, these microorganisms can be an important component in the establishment and functioning of intestinal homeostasis [2,3]. One of these species is E. histolytica, the etiological agent of amebiasis. E. histolytica varies between the commensal status seen in 90% of infected people and the virulent status that leads to intestinal invasion in the remaining 10% [4].

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