Multiple copies of a retroposon interrupt spliced leader RNA genes in the African trypanosome, Trypanosoma gambiense.

Abstract

The 140‐nucleotide spliced leader (SL) RNA, involved in mRNA maturation in the African trypanosomes and in other kinetoplastida, is encoded by a tandem array of spliced leader genes. We show that the 1.4‐kb SL gene repeat unit in Trypanosoma gambiense is organized in tandem arrays confined to two large (minimum size 350‐450 kb) restriction fragments. SL genes in both arrays are interrupted by a total of eight conserved insertion elements. Cleavage of genomic DNA at restriction sites present within the insertion element but not in the SL gene repeat, releases variable numbers of SL genes from the tandem array. Since the insertion element contains a terminal poly(A) track of 36 bases and because a 49‐bp duplication of target DNA has occurred at the integration site, we conclude that it is a retroposon. This retropson is uniquely associated with the SL gene clusters. These retroposons presumably originated from a single insertion event after which their copy number increased, possibly through unequal sister chromatid exchange.

Expression of a retroposon-like sequence upstream of the putative Trypanosoma brucei variant surface glycoprotein gene expression site promoter.

“…3B, asterisks) within this region. The T3 and T5 ESRs are more similar to ingi-3 and human LINE-1 than to the trypanosomatid "siteposons" SLACS, CZAR, and CRE1 (1,9,40) and even less similar to the retrovirus-like LTR elements (Gypsy and copia) and human immunodeficiency virus type 1.…”

Repetitive Elements in Genomes of Parasitic Protozoa

“…The elements SLACS of T. brucei (8) and CZAR of T. cruzi (195) are LINEs that encode proteins with putative RT and restriction enzyme-like endonuclease activities. Along with retroposons of other parasitic Trypanosomatidae-the two distinct CRE retroposon families of Crithidia fasiculata (CRE1 and CRE2 [78,185]) and the LINS1 element of Leptomonas seymouri (21)-these elements are members of an ancient clade of LINEs which are site specific for miniexon (spliced leader) arrays.…”

A new member of a family of site-specific retrotransposons is present in the spliced leader RNA genes of Trypanosoma cruzi.

“…The mechanisms and reasons underlying discontinuous transcription of protein coding genes remain unclear (9). In all trypanosomatid species examined, multiple copies of SL-RNA genes exist in tandem arrays in discrete genomic loci (2,16,22,39,40). It has previously been reported that in the African trypanosome Trypanosoma brucei gambiense, several copies of these SL-RNA genes are interrupted by a 5.5-to 7.0-kb retrotransposon, SLACS (spliced leader-associated conserved sequence) (2, 3) or MAE (miniexon donor RNA gene-associated element) (11).…”

“…In all trypanosomatid species examined, multiple copies of SL-RNA genes exist in tandem arrays in discrete genomic loci (2,16,22,39,40). It has previously been reported that in the African trypanosome Trypanosoma brucei gambiense, several copies of these SL-RNA genes are interrupted by a 5.5-to 7.0-kb retrotransposon, SLACS (spliced leader-associated conserved sequence) (2,3) or MAE (miniexon donor RNA gene-associated element) (11). A similar 4.0-kb element, CRE1, has been described in the distantly related mosquito trypanosomatid Crithidia fasciculata (23).…”

“…Parasites grown to late log phase were concentrated to 5 x 108 cells per ml and then embedded in 0.5% low-melting-point agarose and processed as previously described (2,6 An alternative means of determining copy number of these fragments is described in the text.…”