Possible DNA modification in GC dinucleotides of Trypanosoma brucei telomeric sequences; relationship with antigen gene transcription

Evolutionary aspects of trypanosomes: analysis of genes

The genes for four glycolytic enzymes of Trypanosoma brucei have been analyzed. The proteins encoded by these genes show 38-57% identity with their counterparts in other organisms, whether pro- or eukaryotic. These data are consistent with a phylogenetic tree in which trypanosomes diverged very early from the main branch of the eukaryotic lineage. No definite conclusion can be drawn yet about the evolutionary origin of glycosomes, the microbodies of trypanosomes which contain most enzymes of the glycolytic pathway. A bias could be observed in the codon usage of the glycolytic genes and genes for other housekeeping proteins, indicating that trypanosomes may have selected a nucleotide sequence that enables efficient translation. However, the genes for variant surface glycoproteins (VSGs) do not show such a bias. This lack of preference for special codons is explained by the high evolutionary rate that could be observed for VSG genes.

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

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.

Trypanosoma brucei: the extent of conversion in antigen genes may be related to the DNA coding specificity

The boundaries of gene conversion in variant-specific antigen genes have been determined in six clones of Trypanosoma brucei. In each clone, antigenic switching involved interaction between two telomeric members of the AnTat 1.1 multigene family, which share extensive homology throughout their coding regions. All conversion events occurred by substitution of faithful copies of donor sequences. Conversion endpoints were nonrandomly distributed. In four clones, the 5' conversion limit was near the antigen translation initiation codon, while in three clones, the 3' conversion limit was located at the "hinge" between the two major antigen domains. In one case, two segmental conversions were involved in antigen switching. These observations reveal that antigen gene conversion can occur without generating point mutations, and suggest that postrecombinational selection may impose a limit on the number of possible rearrangements within antigen genes.

Telomeric reciprocal recombination as a possible mechanism for antigenic variation in trypanosomes

In African trypanosomes, antigenic variation is achieved through differential gene activation, with one antigen gene being expressed at a time among a large collection of antigen-specific sequences. Transcription of the antigen gene always takes place in a telomere, but different telomeres can alternatively act as the expression site. Telomeric antigen genes can be expressed without apparent DNA rearrangement, but they can also, like non-telomeric genes, have access to the telomeric expression site through a duplicative transposition mechanism resembling gene conversion. We report here that, as previously suggested, telomeric genes may use another route to be activated. This mechanism of gene activation is by reciprocal crossing-over upstream from the gene, in the so-called 'barren' region. This allows the antigen gene to be placed in the previously activated telomere, while inactivating the formerly expressed gene by recombination into a silent environment. At least for the telomeric antigen gene described here, three possible activation mechanisms coexist.

Two simultaneously active VSG gene transcription units in a single Trypanosoma brucei variant

Trypanosomes can change their surface coat either by slotting a different surface antigen gene copy into an active (telomeric) expression site or by activating a new VSG gene expression site and inactivating the old one. How expression sites are activated or inactivated is not clear. We report an exceptional trypanosome variant in which the inactivation of a surface antigen gene is accompanied by a 30 kb DNA insertion 5' of the gene. Transcription of the region upstream of the insertion continues unaltered and retains the characteristic insensitivity to alpha-amanitin of VSG gene transcription units, showing that the expression site is still active. The expressed VSG gene in this trypanosome variant resides in another telomere. Hence, two VSG gene transcription units can be simultaneously active. This argues against a single mobile activating element controlling VSG gene transcription and favors a stochastic model of telomere activation/inactivation.

Structure and transcription of a telomeric surface antigen gene of Trypanosoma brucei

The gene encoding variant surface glycoprotein 221 in Trypanosoma brucei is located adjacent to a chromosome end and can be activated with or without a concomitant gene duplication. To test whether transcription initiates within the cloned segment of the 221 gene, we analyzed nascent and stable transcripts. We show here that the 221 coding region and 8.5 kilobases of adjacent upstream DNA are transcribed into nascent RNA at a similar rate when gene 221 is activated without duplication. Since only part of this transcribed upstream segment is transferred with the coding region to another telomere upon duplicative activation of gene 221, we infer that initiation of variant surface glycoprotein gene transcription occurs outside the gene segment that moves into an expression site by gene conversion. Our analysis shows that part of the variant surface glycoprotein 221 transcription unit consists of an unusual 3.5-kilobase tandem array of ca. 50 repeat segments and that a rearrangement in this array accompanies the nonduplicative activation of gene 221. A variant surface glycoprotein pseudogene is located within the transcription unit of gene 221, and we discuss models that account for this unusual situation.

Molecular biology of trypanosome antigenic variation

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Inactivation and reactivation of a variant-specific antigen gene in cyclically transmitted Trypanosoma brucei

In Trypanosoma brucei, the activation of the variant-specific antigen gene AnTat 1.1 proceeds by the synthesis of an additional gene copy, the AnTat 1.1 ELC, which is transposed to a new location, the expression site, where it is transcribed. Using the AnTat 1.1 variant to infect flies, we investigated the fate of the AnTat 1.1 ELC during cyclic transmission of T. brucei. We show here that the AnTat 1.1 ELC is conserved in procyclic trypanosomes, obtained either from the midgut of infected Glossina or from cultures, and in metacyclic trypanosomes, although the AnTat 1.1 serotype is not detected among metacyclic antigen types. This same AnTat 1.1 ELC, which is thus silent as the parasite develops in the insect vector, can be reactivated without duplication during the first parasitemia wave following cyclical transmission. This re-expression of the conserved ELC accounts for the early appearance of the 'ingested' antigenic type after passage through the fly.

Structure and transcription of a telomeric surface antigen gene of Trypanosoma brucei

The gene encoding variant surface glycoprotein 221 in Trypanosoma brucei is located adjacent to a chromosome end and can be activated with or without a concomitant gene duplication. To test whether transcription initiates within the cloned segment of the 221 gene, we analyzed nascent and stable transcripts. We show here that the 221 coding region and 8.5 kilobases of adjacent upstream DNA are transcribed into nascent RNA at a similar rate when gene 221 is activated without duplication. Since only part of this transcribed upstream segment is transferred with the coding region to another telomere upon duplicative activation of gene 221, we infer that initiation of variant surface glycoprotein gene transcription occurs outside the gene segment that moves into an expression site by gene conversion. Our analysis shows that part of the variant surface glycoprotein 221 transcription unit consists of an unusual 3.5-kilobase tandem array of ca. 50 repeat segments and that a rearrangement in this array accompanies the nonduplicative activation of gene 221. A variant surface glycoprotein pseudogene is located within the transcription unit of gene 221, and we discuss models that account for this unusual situation.

Selective telomere activation and the control of antigen gene expression in trypanosomes

African trypanosomes escape the immune defence of their mammalian host by changing their antigenic surface coat. Antigenic variation occurs through differential gene activation: only one antigen gene is transcribed at a time, among a large collection of specific sequences. This transcription always takes place in a telomere, but it seems that different telomeres can be used alternatively as the gene expression site. Since the trypanosome genome is made up of numerous chromosomes, it would appear that a highly selective process allows the activation of only one telomere at a time. This process seems linked to the differential inactivation of a peculiar telomeric DNA modification system. Two mechanisms allow antigen genes to be expressed. First, a gene copy can be inserted in the expression site by replacing the formerly expressed gene. This is due to gene conversion, whose extent can vary considerably, according to the degree of homology between the recombining partners. The second mechanism involves the activation of another telomere along with deactivation of the telomere containing the previously expressed gene. This form of activation can occur without apparent DNA rearrangement. The alternate use of these mechanisms leads to rapid changes in the antigen gene repertoire, due to gain and loss of different sequences, and to alteration of their activation rate.

Translocation alters the activation rate of a trypanosome surface antigen gene

We report here the characterization of the gene coding for AnTat 1.13, a very late variable antigen type (VAT) from Trypanosoma b. brucei. This gene is chromosome-internal and it is activated by the duplicative mechanism. Like in another case of late VAT expression (1), its expression-linked copy (ELC) is flanked by "companion" sequences. It was possible to convert the late expression of this VAT into an early one, by changing the location of the gene in the genome. This has been achieved by selecting an AnTat 1.6 clone among heterotypes arising in the AnTat 1.13 cloned population. Indeed, this particular derivation leads to the conservation of the AnTat 1.13 ELC as a new telomeric member of the gene family, and this conserved ELC (or ex-ELC) appears to be preferentially activable. The telomeric position and other factors possibly involved in early or late antigen gene expression are discussed; in this respect, we propose that some antigen genes are rarely activated because their duplicative transposition requires the presence, in the expression site, of "companion" sequences only shared by a limited number of other genes.