Comparison of the expression-linked extra copy (ELC) and basic copy (BC) genes of a trypanosome surface antigen

Predominance of duplicative VSG gene conversion in antigenic variation in African trypanosomes

A number of mechanisms have been described by which African trypanosomes undergo the genetic switches that differentially activate their variant surface glycoprotein genes (VSGs) and bring about antigenic variation. These mechanisms have been observed mainly in trypanosome lines adapted, by rapid syringe passaging, to laboratory conditions. Such "monomorphic" lines, which routinely yield only the proliferative bloodstream form and do not develop through their life cycle, have VSG switch rates up to 4 or 5 orders of magnitude lower than those of nonadapted lines. We have proposed that nonadapted, or pleomorphic, trypanosomes normally have an active VSG switch mechanism, involving gene duplication, that is depressed, or from which a component is absent, in monomorphic lines. We have characterized 88 trypanosome clones from the first two relapse peaks of a single rabbit infection with pleomorphic trypanosomes and shown that they represent 11 different variable antigen types (VATs). The pattern of appearance in the first relapse peak was generally reproducible in three more rabbit infections. Nine of these VATs had activated VSGs by gene duplication, the tenth possibly also had done so, and only one had activated a VSG by the transcriptional switch mechanism that predominates in monomorphic lines. At least 10 of the donor genes have telomeric silent copies, and many reside on minichromosomes. It appears that trypanosome antigenic variation is dominated by one, relatively highly active, mechanism rather than by the plethora of pathways described before.

The relative significance of mechanisms of antigenic variation in African trypanosomes

The large number of genes involved in antigenic variation in African trypanosomes has been the focus of a wide literature that describes an almost bewildering array of mechanisms for their differential activation. To the outsider searching for an underlying strategy for antigenic variation, this can appear as a rather disordered and confusing picture. Here, David Barry argues that an understanding of which mechanisms are significant, which ones are primarily inconsequential and which ones perhaps even arise from overdependence on laboratory models, might be achieved by turning attention to trypanosomes that have not undergone adaptation in laboratory conditions. Application of such an approach has led to a proposal for a main mechanism for antigenic variation.

Genomic organization and context of a trypanosome variant surface glycoprotein gene family

We have defined the genomic organization and genomic context of a Trypanosoma brucei brucei gene family encoding variant surface glycoproteins (VSGs). This gene family is neither tandemly repeated nor closely linked in the genome, and is not located on small or intermediate size chromosomes. Two dispersed repeated sequence elements, RIME-ingi and the upstream repeat sequence, are linked to members of this gene family; however, the upstream repeat sequences are closely linked only to the basic copy. In other isolates of T.b. brucei this gene family appears conserved with some variation; a restriction fragment length polymorphism found among these isolates suggests the hypothesis that VSG genes may occasionally be diploid. A model accounting for both the generation of dispersed families of VSG genes, and for the interstrain variability of VSG genes, is proposed.

Trypanosome variable surface glycoproteins: composite genes and order of expression

Combinatorial processes increase the diversity of variable surface glycoproteins (VSGs) expressed by Trypanosoma equiperdum. We show here that a single telomeric pseudogene provides the 3' portion of three distinct T. equiperdum VSG genes by recombination with different 5' donor pseudogenes. Regions of sequence homology among the pseudogenes determine the sites of recombination in the formation of the expressed copies. This suggests that the recombination between any given basic copy (BC) and the expression-linked copy (ELC) depends on their sharing homology. We present evidence that this is the case and propose that such rules account for the order of expression of the VSGs. These results demonstrate how homologous recombination can generate an ordered sequence of gene expression.

Alternate trans splicing in Trypanosoma equiperdum: implications for splice site selection

We examined the structures of the 5' ends of mRNAs encoding variant surface glycoprotein 78 (VSG-78) and VSG-1(78) in Trypanosoma equiperdum. Several mRNA species were found for each gene, and all contained the 35-base miniexon (or spliced leader) sequence attached at different positions on their 5' ends. Thus, the generation of multiple messages for each VSG occurred by attachment of the miniexon at one of several 3' splice acceptor sites. The frequency with which individual splice sites were used varied from less than 1 to 95% of the RNA produced from a particular gene. We propose that the miniexon RNA and RNA from the VSG genes may interact via base pairing and that this in part specifies the use of particular acceptor sites. Sequences complementary to the miniexon primary transcript, termed the "med-comp site," were found in both genes and in several published sequences. Splice sites were most often used if they were the first site 3' of the med-comp site and contained a high pyrimidine content in the bases preceding the AG acceptor signal.

Alternate trans splicing in Trypanosoma equiperdum: implications for splice site selection

We examined the structures of the 5' ends of mRNAs encoding variant surface glycoprotein 78 (VSG-78) and VSG-1(78) in Trypanosoma equiperdum. Several mRNA species were found for each gene, and all contained the 35-base miniexon (or spliced leader) sequence attached at different positions on their 5' ends. Thus, the generation of multiple messages for each VSG occurred by attachment of the miniexon at one of several 3' splice acceptor sites. The frequency with which individual splice sites were used varied from less than 1 to 95% of the RNA produced from a particular gene. We propose that the miniexon RNA and RNA from the VSG genes may interact via base pairing and that this in part specifies the use of particular acceptor sites. Sequences complementary to the miniexon primary transcript, termed the "med-comp site," were found in both genes and in several published sequences. Splice sites were most often used if they were the first site 3' of the med-comp site and contained a high pyrimidine content in the bases preceding the AG acceptor signal.

The 5' flanking sequence of a Trypanosoma brucei variable surface glycoprotein gene

The mechanism controlling transcription at several telomeric expression sites for variable surface glycoprotein (VSG) genes in Trypanosoma brucei is unknown. Most VSG genes in expression sites have a region 5' of the gene lacking restriction enzyme sites. This 'barren region' is involved in recombination events which replace the VSG gene with a copy of a different, non-telomeric, VSG gene leading to a switch in VSG expression. Alterations in the barren region have been considered as possible modulators of expression of the adjacent VSG gene in other switching events where no gene replacement occurs. The expressed copy of the ILTat 1.3 VSG gene remains in its expression site, on a 160 kilobase (kb) chromosome, in trypanosomes not expressing the ILTat 1.3 VSG. Here we report the complete sequence of the barren region adjacent to this gene, determined both from trypanosomes expressing the gene and from those that are not. The sequence is identical whether or not the ILTat 1.3 VSG gene is expressed. This confirms that alterations in the barren region are not involved in modulation of expression of the gene, as suggested by restriction enzyme mapping. Sequence data from the 5' flanking region of a second telomeric gene copy on an 80 kb minichromosome, and from the ILTat 1.3 expression site after replacement of the ILTat 1.3 gene by another gene from a minichromosome, provide evidence that telomeric VSG genes on minichromosomes are also flanked by long repeat arrays, and that these arrays are involved in inter-telomeric gene replacements as well as replacements by non-telomeric genes.

Molecular biology of trypanosome antigenic variation

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(TAA)n within sequences flanking several intrachromosomal variant surface glycoprotein genes in Trypanosoma brucei

In Trypanosoma brucei telomeric copies of intrachromosomal variant surface glycoprotein (VSG) genes are produced through a gene conversion mechanism and are expressed if the telomere is or becomes transcriptionally activated. We have analyzed a sequence that occurs 1 to 1.5 kb 5' to several intrachromosomal VSG genes. This flanking sequence has three distinct sections: a 5' section containing 5 to 116 TAA or TAA-like tandem repeats; a moderately conserved sequence with an alternating GT characteristic; and a highly conserved 3' sequence that is largely alternating TA. Restriction mapping data and the location of this sequence suggest that it occurs at or near the 5' gene conversion boundary. This sequence, however, is not 5' to all VSG genes. These data suggest that this flanking sequence alone is not sufficient for VSG gene expression but that it may function in gene conversion for many, but not all, VSG genes.

Expression of antigenic regions of a trypanosome variable surface glycoprotein in E. coli using Bal-31 nuclease digestion

We have used the expression of a trypanosome variable surface glycoprotein (VSG) in E. coli to produce VSG serotype-specific antisera which have none of the cross-reacting specificities characteristic of antisera prepared against purified VSGs. This was accomplished by treating restriction fragments of VSG cDNAs with Bal-31 nuclease to facilitate expression of their open reading frames in the E. coli expression vector, pMR100 (4). The resultant VSG-beta-galactosidase fusion proteins possess various antigenic regions of the original VSG. This provides a rapid means for producing VSG-specific antisera for reagent use and has the capability of large scale production of antigen for immunological investigation.