Variant antigen genes of Trypanosoma brucei: genomic alteration of a spliced leader orphon and retention of expression-linked copies during differentiation

Two distinct functional spliced leader RNA gene arrays in Leishmania tarentolae are found in several lizard Leishmania species

A second distinct array of spliced leader RNA genes has been found in several Leishmania species particular to lizards. This is the first report of two non-allelic arrays of spliced leader RNA genes within a species cell line. The arrays are identical to each other in their transcribed spliced leader RNA gene sequences, but variable in their non-transcribed spacer sequences. In the two arrays from Leishmania tarentolae UC strain the promoter regions are similar, but not identical, at positions shown previously to be critical for spliced leader RNA transcription. These arrays contain similar numbers of genes and are both transcribed in L. tarentolae in vitro transcription extract as well as in vivo. The -66/-58 regions of both genes, which contain an element of the spliced leader RNA gene promoter, bind proteins likely to be transcription factors in a specific manner. A survey of lizard Leishmania spp. revealed a second spliced leader RNA gene array in three of four species. Phylogenetic analyses of these sequences with each other and with the spliced leader RNA gene sequences of non-lizard Leishmania spp. and their near-relatives showed that the lizard groups are more closely related to each other than to arrays from other Leishmania spp. As the transcripts of the two arrays are identical, they may co-exist to fulfil the substantial requirement for spliced leader RNA production; however, they have the potential for differential usage modulated by their distinct promoter elements. The presence of two distinct spliced leader RNA gene arrays within a single cell type may represent dissociated evolution of two redundant loci, or a previously unsuspected level of control in the post-transcriptional gene expression within some kinetoplastids.

A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata

The tandemly arrayed miniexon genes of the trypanosomatid Crithidia fasciculata are interrupted at specific sites by multiple copies of an inserted element. The element, termed Crithidia retrotransposable element 1 (CRE1), is flanked by 29-base-pair target site duplications and contains a long 3'-terminal poly(dA) stretch. A single 1,140-codon reading frame is similar in sequence to the integrase and reverse transcriptase regions of retroviral pol polyproteins. Cloned lines derived from a stock of C. fasciculata have unique arrangements of CRE1s. In different cloned lines, CRE1s, in association with miniexon genes, are located on multiple chromosomes. By examining the arrangement of CRE1s in subclones, we estimate that the element rearranges at a rate of ca. 1% per generation. These results indicate that the C. fasciculata miniexon locus is the target for a novel retrotransposon.

A rapidly rearranging retrotransposon within the miniexon gene locus of Crithidia fasciculata

The tandemly arrayed miniexon genes of the trypanosomatid Crithidia fasciculata are interrupted at specific sites by multiple copies of an inserted element. The element, termed Crithidia retrotransposable element 1 (CRE1), is flanked by 29-base-pair target site duplications and contains a long 3'-terminal poly(dA) stretch. A single 1,140-codon reading frame is similar in sequence to the integrase and reverse transcriptase regions of retroviral pol polyproteins. Cloned lines derived from a stock of C. fasciculata have unique arrangements of CRE1s. In different cloned lines, CRE1s, in association with miniexon genes, are located on multiple chromosomes. By examining the arrangement of CRE1s in subclones, we estimate that the element rearranges at a rate of ca. 1% per generation. These results indicate that the C. fasciculata miniexon locus is the target for a novel retrotransposon.

Posttranscriptional regulation of cytochrome c expression during the developmental cycle of Trypanosoma brucei

We examined the expression of a nucleus-encoded mitochondrial protein, cytochrome c, during the life cycle of Trypanosoma brucei. The bloodstream forms of T. brucei, the long slender and short stumpy trypanosomes, have inactive mitochondria with no detectable cytochrome-mediated respiration. The insect form of T. brucei, the procyclic trypanosomes, has fully functional mitochondria. Cytochrome c is spectrally undetectable in the bloodstream forms of trypanosomes, but during differentiation to the procyclic form, spectrally detected holo-cytochrome c accumulates rapidly. We have purified T. brucei cytochrome c and raised antibodies that react to both holo- and apo-cytochrome c. In addition, we isolated a partial cDNA to trypanosome cytochrome c. An examination of protein expression and steady-state mRNA levels in T. brucei indicated that bloodstream trypanosomes did not express cytochrome c but maintained significant steady-state levels of cytochrome c mRNA. The results suggest that in T. brucei, cytochrome c is developmentally regulated by a posttranscriptional mechanism which prevents either translation or accumulation of cytochrome c in the bloodstream trypanosomes.

Posttranscriptional regulation of cytochrome c expression during the developmental cycle of Trypanosoma brucei

We examined the expression of a nucleus-encoded mitochondrial protein, cytochrome c, during the life cycle of Trypanosoma brucei. The bloodstream forms of T. brucei, the long slender and short stumpy trypanosomes, have inactive mitochondria with no detectable cytochrome-mediated respiration. The insect form of T. brucei, the procyclic trypanosomes, has fully functional mitochondria. Cytochrome c is spectrally undetectable in the bloodstream forms of trypanosomes, but during differentiation to the procyclic form, spectrally detected holo-cytochrome c accumulates rapidly. We have purified T. brucei cytochrome c and raised antibodies that react to both holo- and apo-cytochrome c. In addition, we isolated a partial cDNA to trypanosome cytochrome c. An examination of protein expression and steady-state mRNA levels in T. brucei indicated that bloodstream trypanosomes did not express cytochrome c but maintained significant steady-state levels of cytochrome c mRNA. The results suggest that in T. brucei, cytochrome c is developmentally regulated by a posttranscriptional mechanism which prevents either translation or accumulation of cytochrome c in the bloodstream trypanosomes.

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.

A 5' spliced leader is added in trans to both alpha- and beta-tubulin transcripts in Trypanosoma brucei

The approximately 15 alpha- and 15 beta-tubulin genes of Trypanosoma brucei are arranged in a tandem array of alternating alpha- and beta-tubulin genes. We have examined the structure of mRNA transcripts from the tubulin gene family and have found at the 5' ends of both alpha- and beta-tubulin messages a 35-nucleotide spliced leader (SL) identical to that identified previously on the 5' ends of variant surface glycoprotein (VSG) mRNAs. No 35-nucleotide SL sequences were encoded in the tubulin intergenic regions; instead, the SL sequence apparently originates from small RNA transcripts encoded at sites that are unlinked to the tubulin genes. The tandem arrangement of the tubulin genes and the presence of the SL at the 5' end of both alpha- and beta-tubulin transcripts establishes that RNA joining between the SL and tubulin mRNA occurs in trans.

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

Images

Calmodulin genes in trypanosomes are tandemly repeated and produce multiple mRNAs with a common 5' leader sequence

In Trypanosoma brucei gambiense, the Ca2+ binding protein calmodulin is encoded by three identical tandemly repeated genes. The transcripts of these genes consist of several RNA species similar in size. A 35-nucleotide spliced leader sequence is present at the 5' end of each mRNA but is not encoded by DNA contiguous to these genes. We have identified two different sites for the fusion of the leader to the mRNA. These results strongly support the idea that a novel, possibly discontinuous, transcription mechanism is used by these parasites.

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.

The IsTat 1.3 VSG multigene family in Trypanosoma brucei: retention of the expression linked copy through multiple antigenic switches

In the IsTaR 1 serodeme of T. brucei the 3 variant surface glycoprotein (VSG) gene family contains about 10 members, one of which has a telomeric location on a minichromosome. The expression linked copy (ELC) of the 3 VSG gene which occurs in an antigenic variant expressing the 3 VSG, also has a telomeric location but unlike the minichromosomal 3 VSG gene has restriction sites upstream from the 5' barren region. This ELC is retained on the same telomere in a subsequent variant that expresses a telomeric 7 VSG ELC and in relapse variants and procyclic forms derived from variant antigenic types (VATs) 3 and 7. The 7 ELC has a restriction map upstream from the 5' barren region that differs from, but is similar to, that of the 3 ELC. These data indicate that the 3 and 7 ELCs are on different telomeres when expressed.

Identification of a small RNA containing the trypanosome spliced leader: a donor of shared 5' sequences of trypanosomatid mRNAs?

The 35 nucleotide spliced leader (SL) sequence is found on the 5' end of numerous trypanosome mRNAs, yet the tandemly organized reiteration units encoding this leader are not detectably linked to any of these structural genes. Here we report the presence of a class of discrete small SL RNA molecules that are derived from the genomic SL reiteration units of Trypanosoma brucei, Trypanosoma cruzi, and Leptomonas collosoma. These small SL RNAs are 135, 105, and 95 nucleotides, respectively, and contain a 5'-terminal SL or SL-like sequence. S1 nuclease analyses demonstrate that these small SL RNAs are transcribed from continuous sequence within the respective SL reiteration units. With the exception of the SL sequence and a concensus donor splice site immediately following it, these small RNAs are not well conserved. We suggest that the small SL RNAs may function as a donor of the SL sequence in an intermolecular process that places the SL at the 5' terminus of many trypanosomatid mRNAs.

Trypanosome mRNAs share a common 5' spliced leader sequence

A 5'-terminal leader sequence of 35 nucleotides was found to be present on multiple trypanosome RNAs. Based on its representation in cDNA libraries, we estimate that many, if not all, trypanosome mRNAs contain this leader. This same leader was originally identified on mRNAs encoding the molecules responsible for antigenic variation, variant surface glycoproteins. Studies of selected cDNAs containing this leader sequence revealed that leader-containing transcripts can be stage-specific, stage-regulated, or constitutive. They can be abundant or rare, and transcribed from single or multigene families. No linkage between the genomic leader sequences and the structural gene exons was observed. Possible mechanisms by which the leader sequences are added to trypanosome mRNAs are discussed.

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

Polymorphism in restriction site cleavage (PstI, SphI, PvuII, HindIII) has been noticed in several occasions in the telomeric sequences harbouring trypanosome variant-specific antigen genes (1, 2, 3). This polymorphism has been further investigated and seems best interpreted as due to partial DNA modification in GC dinucleotides. The actively transcribed telomeric genes do not exhibit such a polymorphism; furthermore, in at least three independent cases, gene inactivation is linked to the appearance of polymorphism. It could thus be hypothesized that DNA modification prevents antigen gene transcription, or vice-versa. We report however that at least some telomeric antigen-specific sequences of the procyclic trypanosomes (in vitro culture form) are not polymorphic, although they do not synthesize any variant-specific antigen mRNA. There is thus no absolute relationship between the absence of polymorphism and antigen gene transcription.

Characterization of the 1.35 kilobase DNA repeat unit containing the conserved 35 nucleotides at the 5'-termini of variable surface glycoprotein mRNAs in Trypanosoma brucei

We have cloned and determined the sequence of the 1.35 kb trypanosome DNA repeat unit that contains the conserved 35 nucleotides found at the 5'-ends of variable surface glycoprotein (VSG) mRNAs and present in many other trypanosome RNAs. Our data indicate that the genomic repeats, estimated by others to be present in 200-250 copies in the haploid genome (18, 21), are structurally very highly conserved but with dispersed point changes. The 1.35 kb repeat unit has an unusual stretch of multiple repetitive elements starting about 100 bp downstream from the 35 nucleotide sequence; in addition there are several potential eukaryotic transcription initiation sites throughout the repeat unit. Genomic mapping studies using portions of the repeat unit as hybridization probes suggest that the entire repeat is conserved at its multiple genomic locations.

Two mechanisms of expression of a predominant variant antigen gene of Trypanosoma brucei

African trypanosomes evade the host immune response by periodically switching their variant surface glycoprotein (VSG) coat. The resulting, serologically distinct variant antigenic types (VATs) appear in a loosely ordered sequence and those arising early in infections are termed predominant VATs. VAT switching reflects the successive transcriptional activation of single VSG genes from a large repertoire. Activation of some VSG genes is accomplished by duplication of a previously silent basic copy (BC) gene and insertion of this expression linked copy (ELC) near a chromosomal telomere where is is expressed. However, other VSG genes, always located near a telomere, use a non-duplication activation ( NDA ) mechanism. We report here that the gene encoding the predominant IsTat 1.A VSG can be activated with or without duplication. Four of six independently derived clones activated the 1.A gene without gene duplication or detectable rearrangement. The other two contained an active 1.A ELC, possibly generated by a gene conversion extending to the end of the telomere. The ability to utilize both NDA and ELC mechanisms of gene activation and perhaps an alternative mechanism for gene duplication may account for the fact that VAT 1.A is the most predominant VAT of the IsTaR 1 serodeme .