Mobile genetic elements in protozoan parasites

Abstract

Mobile genetic elements, by virtue of their ability to move to new chromosomal locations, are considered important in shaping the evolutionary course of the genome. They are widespread in the biological kingdom. Among the protozoan parasites several types of transposable elements are encountered. The largest variety is seen in the trypanosomatids-Trypanosoma brucei, Trypanosoma cruzi and Crithidia fasciculata. They contain elements that insert site-specifically in the spliced-leader RNA genes, and others that are dispersed in a variety of genomic locations. Giardia lamblia contains three families of transposable elements. Two of these are subtleomeric in location while one is chromosome-internal. Entamoeba histolytica has an abundant retrotransposon dispersed in the genome. Nucleotide sequence analysis of all the elements shows that they are all retrotransposons, and, with the exception of one class of elements in T. cruzi, all of them are non-long-terminal-repeat retrotransposons. Although most copies have accumulated mutations, they can potentially encode reverse transcriptase, endonuclease and nucleic-acid-binding activities. Functionally and phylogenetically they do not belong to a single lineage, showing that retrotransposons were acquired early in the evolution of protozoan parasites. Many of the potentially autonomous elements that encode their own transposition functions have nonautonomous counterparts that probably utilize the functions in trans. In this respect these elements are similar to the mammalian LINEs and SINEs (long and short interspersed DNA elements), showing a common theme in the evolution of retrotransposons. So far there is no report of a DNA transposon in any protozoan parasite. The genome projects that are under way for most of these organisms will help understand the evolution and possible function of these genetic elements.

Comparative Genomic Hybridizations ofEntamoebaStrains Reveal Unique Genetic Fingerprints That Correlate with Virulence

“…Retrotransposons, which are abundant in EH, play a significant role in genome evolution by their ability to move to new chromosomal locations (10,59). Significant numbers of E. histolytica genes are in multiple copies or are members of highly homologous gene family members.…”

Highly abundant pea LTR retrotransposon Ogre is constitutively transcribed and partially spliced

“…Retrotransposons are widespread among eukaryots Bennetzen, 1996;Suoniemi et al, 1998;Kumekawa et al, 1999b; The GenBank accession numbers for the sequences reported here are AY299394 (Ps-phage13), AY299395 (Ps-phage20), AY299396 (Ps-phage22), AY299397 (Ps-cos14), and AY299398 (Ps-cos16). Schmidt, 1999;Arkhipova, 2001;Bhattacharya et al, 2002;Deininger and Batzer, 2002;Wöstemeyer and Kreibich, 2002) and, as a consequence of their replication, they often make up a considerable portion of eukaryotic genomes (SanMiguel et al, 1996;Shirasu et al, 2000;Deininger and Batzer, 2002). In plants, the copy number of elements belonging to individual retrotransposon families vary greatly, from a few up to 10 4 -10 5 copies per haploid genome (1C) (Bennetzen, 1996;Kumar and Bennetzen, 1999;Feschotte et al, 2002).…”

An Entamoeba histolytica LINE/SINE Pair Inserts at Common Target Sites Cleaved by the Restriction Enzyme-Like LINE-Encoded Endonuclease

“…These retrotransposons (also called long interspersed repetitive elements [LINEs]) are considered more primitive than the LTR retrotransposons (13,35). In keeping with this contention, it is interesting that non-LTR elements are found abundantly in parasitic protozoa while there is only one report so far of an LTR element in these organisms (3).…”

“…In addition, short repetitive sequences of about 0.5 kb that are abundantly transcribed have also been identified (10,32,33). These show striking sequence conservation at the 3Ј ends with partner LINEs (3,30,33) and might, therefore, be considered short interspersed repetitive elements (SINEs) (24). Sequence analysis of the LINE EhRLE shows the presence of well-conserved functional domains in the open reading frame.…”

“…Sequence analysis of the LINE EhRLE shows the presence of well-conserved functional domains in the open reading frame. Sequence comparison and phylogeny based on the reverse transcriptase (RT) domain (3,30) places EhRLE closest to the R4 clade (belonging to the R2 group of non-LTR elements) (12,21), which includes the R4 element, which inserts into the 28S rRNA gene of nematodes (6); the Dong element, which inserts into TAA repeats that may be found in the nontranscribed spacer of insect ribososmal DNA and sometimes outside it (36); and Rex6 elements of vertebrates, some of which insert into TAA repeats, while for others the target preferences are not clear (31). In common with the R2 group, EhRLE contains an endonuclease (EN) domain downstream of a centrally located RT domain.…”