Genomic distribution of SINEs in Entamoeba histolytica strains: implication for genotyping

Abstract

Background: The major clinical manifestations of Entamoeba histolytica infection include amebic colitis and liver abscess. However the majority of infections remain asymptomatic. Earlier reports have shown that some E. histolytica isolates are more virulent than others, suggesting that virulence may be linked to genotype. Here we have looked at the genomic distribution of the retrotransposable short interspersed nuclear elements EhSINE1 and EhSINE2. Due to their mobile nature, some EhSINE copies may occupy different genomic locations among isolates of E. histolytica possibly affecting adjacent gene expression; this variability in location can be exploited to differentiate strains. Results: We have looked for EhSINE1-and EhSINE2-occupied loci in the genome sequence of Entamoeba histolytica HM-1:IMSS and searched for homologous loci in other strains to determine the insertion status of these elements. A total of 393 EhSINE1 and 119 EhSINE2 loci were analyzed in the available sequenced strains (Rahman, DS4-868, HM1: CA, KU48, KU50, KU27 and MS96-3382. Seventeen loci (13 EhSINE1 and 4 EhSINE2) were identified where a EhSINE1/ EhSINE2 sequence was missing from the corresponding locus of other strains. Most of these loci were unoccupied in more than one strain. Some of the loci were analyzed experimentally for SINE occupancy using DNA from strain Rahman. These data helped to correctly assemble the nucleotide sequence at three loci in Rahman. SINE occupancy was also checked at these three loci in 7 other axenically cultivated E. histolytica strains and 16 clinical isolates. Each locus gave a single, specific amplicon with the primer sets used, making this a suitable method for strain typing. Based on presence/absence of SINE and amplification with locus-specific primers, the 23 strains could be divided into eleven genotypes. The results obtained by our method correlated with the data from other typing methods. We also report a bioinformatic analysis of EhSINE2 copies. Conclusions: Our results reveal several loci with extensive polymorphism of SINE occupancy among different strains of E. histolytica and prove the principle that the genomic distribution of SINEs is a valid method for typing of E. histolytica strains.

Evolutionary genomics and population structure of Entamoeba histolytica

“…Phenotypic characteristic of this parasite is also influenced by their genomic location [37] . Variability in genomic distribution of SINE1 and SINE2 among E. histolytica clinical isolates has been recently studied by Kumari et al [70] . Several loci with extensive polymorphism of SINE occupancy among E. histolytica strains have been identified [70] .…”

Pathogenicity and virulence of Entamoeba histolytica , the agent of amoebiasis

“…To decipher the mechanisms supporting these varying levels of virulence among strains, parasite genotypes have been compared to determine changes in genetic polymorphism (e.g. using polymorphic markers linked to tRNA or interspersed nuclear retrotransposable elements) [ 100–103 ]; data suggest a high genetic diversity in strains of E. histolytica isolated worldwide [ 104 ]; but their link to the outcome of infection is still elusive.…”

llumination On The Structure And Characteristics Of Entamoeba Histolytica Genome.

“…These transposable elements affect the gene expression of nearby or neighboring genes through various mechanisms, including alternative promotor processing, splicing, and others. SINEs are distinguished by being stable across generations, and attempts to insert them into the gene are rare, so genetic analyzes using SINEs are fairly accurate from RFLPs and Microsatellite sites (Kumari et al, 2013).…”