The trypanosome spliced leader small RNA gene family: stage-specific modification of one of several similar dispersed genes

Abstract

Diverse mRNAs of Trypanosoma brucei possess the same 5' terminal 35 nucleotides, termed the spliced leader (SL), which appears to be derived from a separate 135 nucleotide transcript. This small SL RNA is encoded within a 1.4 kb unit of DNA which is tandemly reiterated in the genome. In addition, there are at least 4 orphon elements containing SL sequences dispersed from the tandem array. Here we show that during the trypanosome life cycle one of the SL orphons undergoes a stage-specific modification that prevents cleavage of an EcoRV site and we further demonstrate that although only one orphon is modified, three of the SL orphons are flanked by very similar sequences. Each of these contains SL reiteration units including the non-transcribed spacer DNA, suggesting that they did not originate through an RNA intermediate. In addition no evidence of direct repeats at the junction of 1.4 kb and non-1.4 kb DNA was observed. Finally, a phylogenetic survey indicates that while many trypanosomatid species possess similarly organized SL-like sequences, only the SL orphons of closely related subspecies of the T. brucei -T. evansi complex share similar flanking regions.

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

“…Multiple SLACS sequences inserted into the SL gene cluster are also present in T. rhodesiense on an -600-kb XbaI fragment. The flanking DNA sequence of one of the SLcontaining fragments isolated from the IsTaR serodeme of T. brucei is in agreement with our results (Parsons et al, 1986). This non-SL sequence is also found to be associated with the other SL fragments in the IsTaR serodeme, suggesting the conservation of the retroposon.…”

“…The flanking DNA sequence of one of the SLcontaining fragments isolated from the IsTaR serodeme of T. brucei is in agreement with our results (Parsons et al, 1986). For instance, in the T brucei serotype expressing glycoprotein (VSG) 117, we find 17 SLACS-related DNA fragments, all of which are present on an -600-kb XbaI fragment (unpublished observations).…”

“…However, small fragments containing the SL gene are also found. These small fragments have been referred to as the SL gene orphons and these fragments vary in size and number among different T. brucei isolates (Nelson et al, 1983;Parsons et al, 1984Parsons et al, , 1986.…”

The structure and transcription of an element interspersed between tandem arrays of mini-exon donor RNA genes inTrypanosoma brucei

“…A small proportion of the medRNA genes occur in shorter tandem arrays termed orphons (14). The 3' and 5' flanking regions of one of these orphons have been characterised and are conserved between medRNA gene arrays (15). The junction between the 3' end of the orphon medRNA gene array and the surrounding DNA occured just 20 bp 3' of a mini-exon (in the sense of transcription) (15).…”

“…The 3' and 5' flanking regions of one of these orphons have been characterised and are conserved between medRNA gene arrays (15). The junction between the 3' end of the orphon medRNA gene array and the surrounding DNA occured just 20 bp 3' of a mini-exon (in the sense of transcription) (15). Consequently there are at least two sequences, the orphon flanking sequence and the medRNA gene sequence, found close to the 3' end of the mini-exon.…”