The LINEs and SINEs of Entamoeba histolytica: Comparative analysis and genomic distribution

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Abstract

Autonomous non-long terminal repeat retrotransposons are commonly referred to as long interspersed elements (LINEs). Short non-autonomous elements that borrow the LINE machinery are called SINES. The Entamoeba histolytica genome contains three classes of LINEs and SINEs. Together the EhLINEs/SINEs account for about 6% of the genome. The recognizable functional domains in all three EhLINEs included reverse transcriptase and endonuclease. A novel feature was the presence of two types of members—some with a single long ORF (less frequent) and some with two ORFs (more frequent) in both EhLINE1 and 2. The two ORFs were generated by conserved changes leading to stop codon. Computational analysis of the immediate flanking sequences for each element showed that they inserted in AT-rich sequences, with a preponderance of Ts in the upstream site. The elements were very frequently located close to protein-coding genes and other EhLINEs/SINEs. The possible influence of these elements on expression of neighboring genes needs to be determined.

Introduction

Repetitive elements have shaped genomic organization and can influence gene expression (Landry et al., 2001). Repetitive DNA exists to varying extent in the genomes of protozoan parasites (Bhattacharya et al., 2002, Wickstead et al., 2003), including Entamoeba histolytica. This parasite is the causative agent of amoebiasis, a highly prevalent disease in developing countries. It has a 23 Mb genome consisting of 14–17 linear chromosomes and numerous episomes, the most abundant of which is the 24.5 kb ribosomal DNA circle (Bhattacharya et al., 2000, Willhoeft and Tannich, 1999). E. histolytica is not only a clinically important organism but also occupies a unique niche in evolution.

Eukaryotic genomes are home to various types of transposons (Craig, 2002), of which the non-long terminal repeat (LTR) retrotransposons are abundantly found in E. histolytica. Autonomous Non-LTR elements encoding their own retrotransposition machinery are commonly referred to as long interspersed elements (LINEs). Short non-autonomous elements that borrow this machinery for propagation are called short interspersed elements (SINES). LINEs and SINEs profoundly influence the host genome via a multitude of mechanisms (Ostertag and Kazazian, 2001). They may affect gene expression by providing alternative promoters, splicing and polyadenylation sites, and by heterochromatinization. In addition, SINEs can also work as stress sensors in the cell (Kimura et al., 2001). Studies with repetitive DNAs of E. histolytica revealed a 4.8 kb element, part of which had a very close match with reverse transcriptase (RT) of non-LTR retrotransposons (Sharma et al., 2001). Another repetitive and highly transcribed 0.55 kb element was discovered, which lacked an open reading frame (ORF) (Cruz-Reyes et al., 1995, Willhoeft et al., 1999). This element shared a 70 nt sequence at the 3′-end with the 4.8 kb element, and the two were proposed to be a LINE/SINE pair (Bhattacharya et al., 2002, Willhoeft et al., 2002). Analysis of the E. histolytica genome sequence database showed the existence of multiple families of autonomous and non-autonomous non-LTR elements, now designated EhLINEs and EhSINEs (Van Dellen et al., 2002). The discovery of a EhLINE-encoded endonuclease (EN) activity which could nick a natural target site of EhSINE insertion, provided evidence that EhSINE1 could utilize the EhLINE1 machinery for its own transposition (Mandal et al., 2004).

In this article, we report the comparative characterization of three families of LINEs and SINEs in the E. histolytica genome with respect to their sequence organization and genomic distribution.

Section snippets

Identification and assembly of the three families of EhLINEs and EhSINEs

Entamoeba histolytica GSS sequences at NCBI were used for initial element assembly. EhLINE1, 2, and 3 were assembled using standard procedures. IE (AF126955) (Cruz-Reyes et al., 1995) was renamed as EhSINE1 after a consensus sequence was derived from multiple alignment of GSS clones using majority rule. EhSINE2 shares a stretch of ∼70 nt with EhSINE1 at the 5′ end and was thus identified. EhSINE3 was constructed as an E. histolytica homologue for the abundant polyadenylated transcript UEE from

Comparative sequence analysis of EhLINEs and EhSINEs

The E. histolytica genome contains three classes of LINEs (EhLINE1, 2, and 3) and two classes of SINEs (EhSINE1 and 2) with a third class of EhSINE that appears to be present in a single copy. The size and copy number of each element as deduced from the E. histolytica genome sequence submitted with NCBI is shown in Fig. 1. Most copies of each element are truncated at the 5′- or 3′-end or at both ends. Of the full-length copies none was found to contain a complete ORF, due to many point

Discussion

The EhLINEs/SINEs together account for 6% of the E. histolytica genome as deduced from data base analysis. The other types of transposable elements—DNA transposons and LTR-retrotransposons seem to be absent in E. histolytica. Various types of non-LTR retrotransposons are encountered in living organisms. These differ from one another in several ways, including the kind of endonuclease encoded by the element (restriction enzyme-like or apurinic endonuclease), the number of ORFs, the relative

Acknowledgments

This work was supported by a grant from Indian Council of Medical Research (ICMR) and University Grants Commission, India. A.A. B and K.R. are grateful to the Council of Scientific and Industrial Research (CSIR) and ICMR for fellowship, respectively.

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Present address: Centre for Systems Biology, School of Natural Sciences, Institute for Advanced Study, Princeton NJ 08540, USA.

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