Transient expression mediated by the Trypanosoma cruzi rRNA promoter

Stage-regulated GFP Expression in Trypanosoma cruzi: applications from host-parasite interactions to drug screening

Trypanosoma cruzi is the etiological agent of Chagas disease, an illness that affects about 10 million people, mostly in South America, for which there is no effective treatment or vaccine. In this context, transgenic parasites expressing reporter genes are interesting tools for investigating parasite biology and host-parasite interactions, with a view to developing new strategies for disease prevention and treatment. We describe here the construction of a stably transfected fluorescent T. cruzi clone in which the GFP gene is integrated into the chromosome carrying the ribosomal cistron in T. cruzi Dm28c. This fluorescent T. cruzi produces detectable amounts of GFP only at replicative stages (epimastigote and amastigote), consistent with the larger amounts of GFP mRNA detected in these forms than in the non replicative trypomastigote stages. The fluorescence signal was also strongly correlated with the total number of parasites in T. cruzi cultures, providing a simple and rapid means of determining the growth inhibitory dose of anti-T.cruzi drugs in epimastigotes, by fluorometric microplate screening, and in amastigotes, by the flow cytometric quantification of T. cruzi-infected Vero cells. This fluorescent T. cruzi clone is, thus, an interesting tool for unbiased detection of the proliferating stages of the parasite, with multiple applications in the genetic analysis of T. cruzi, including analyses of host-parasite interactions, gene expression regulation and drug development.

Footprints of a trypanosomatid RNA world: pre-small subunit rRNA processing by spliced leader addition trans-splicing

The addition of a capped mini-exon [spliced leader (SL)] through trans-splicing is essential for the maturation of RNA polymerase (pol) II-transcribed polycistronic pre-mRNAs in all members of the Trypanosomatidae family. This process is an inter-molecular splicing reaction that follows the same basic rules of cis-splicing reactions. In this study, we demonstrated that mini-exons were added to precursor ribosomal RNA (pre-rRNA) are transcribed by RNA pol I, including the 5' external transcribed spacer (ETS) region. Additionally, we detected the SL-5'ETS molecule using three distinct methods and located the acceptor site between two known 5'ETS rRNA processing sites (A' and A1) in four different trypanosomatids. Moreover, we detected a polyadenylated 5'ETS upstream of the trans-splicing acceptor site, which also occurs in pre-mRNA trans-splicing. After treatment with an indirect trans-splicing inhibitor (sinefungin), we observed SL-5'ETS decay. However, treatment with 5-fluorouracil (a precursor of RNA synthesis that inhibits the degradation of pre-rRNA) led to the accumulation of SL-5'ETS, suggesting that the molecule may play a role in rRNA degradation. The detection of trans-splicing in these molecules may indicate broad RNA-joining properties, regardless of the polymerase used for transcription.

The genome and its implications

Trypanosoma cruzi has a heterogeneous population composed of a pool of strains that circulate in the domestic and sylvatic cycles. Genome sequencing of the clone CL Brener revealed a highly repetitive genome of about 110Mb containing an estimated 22,570 genes. Because of its hybrid nature, sequences representing the two haplotypes have been generated. In addition, a repeat content close to 50% made the assembly of the estimated 41 pairs of chromosomes quite challenging. Similar to other trypanosomatids, the organization of T. cruzi chromosomes was found to be very peculiar, with protein-coding genes organized in long polycistronic transcription units encoding 20 or more proteins in one strand separated by strand switch regions. Another remarkable feature of the T. cruzi genome is the massive expansion of surface protein gene families. Because of the high genetic diversity of the T. cruzi population, sequencing of additional strains and comparative genomic and transcriptome analyses are in progress. Five years after its publication, the genome data have proven to be an essential tool for the study of T. cruzi and increasing efforts to translate this knowledge into the development of new modes of intervention to control Chagas disease are underway.

A high-throughput cloning system for reverse genetics in Trypanosoma cruzi

BACKGROUND

The three trypanosomatids pathogenic to men, Trypanosoma cruzi, Trypanosoma brucei and Leishmania major, are etiological agents of Chagas disease, African sleeping sickness and cutaneous leishmaniasis, respectively. The complete sequencing of these trypanosomatid genomes represented a breakthrough in the understanding of these organisms. Genome sequencing is a step towards solving the parasite biology puzzle, as there are a high percentage of genes encoding proteins without functional annotation. Also, technical limitations in protein expression in heterologous systems reinforce the evident need for the development of a high-throughput reverse genetics platform. Ideally, such platform would lead to efficient cloning and compatibility with various approaches. Thus, we aimed to construct a highly efficient cloning platform compatible with plasmid vectors that are suitable for various approaches.

RESULTS

We constructed a platform with a flexible structure allowing the exchange of various elements, such as promoters, fusion tags, intergenic regions or resistance markers. This platform is based on Gateway® technology, to ensure a fast and efficient cloning system. We obtained plasmid vectors carrying genes for fluorescent proteins (green, cyan or yellow), and sequences for the c-myc epitope, and tandem affinity purification or polyhistidine tags. The vectors were verified by successful subcellular localization of two previously characterized proteins (TcRab7 and PAR 2) and a putative centrin. For the tandem affinity purification tag, the purification of two protein complexes (ribosome and proteasome) was performed.

CONCLUSIONS

We constructed plasmids with an efficient cloning system and suitable for use across various applications, such as protein localization and co-localization, protein partner identification and protein expression. This platform also allows vector customization, as the vectors were constructed to enable easy exchange of its elements. The development of this high-throughput platform is a step closer towards large-scale trypanosome applications and initiatives.

Trypanosoma brucei: a putative RNA polymerase II promoter

RNA polymerase II (pol II) promoters are rare in the African trypanosome Trypanosoma brucei because gene regulation in the parasite is complex and polycistronic. Here, we describe a putative pol II promoter and its structure-function relationship. The promoter has features of an archetypal eukaryotic pol II promoter including putative canonical CCAAT and TATA boxes, and an initiator element. However, the spatial arrangement of these elements is only similar to yeast pol II promoters. Deletion mapping and transcription assays enabled delineation of a minimal promoter that could drive orientation-independent reporter gene expression suggesting that it may be a bidirectional promoter. In vitro transcription in a heterologous nuclear extract revealed that the promoter can be recognized by the basal eukaryotic transcription complex. This suggests that the transcription machinery in the parasite may be very similar to those of other eukaryotes.

Cell culture and animal infection with distinct Trypanosoma cruzi strains expressing red and green fluorescent proteins

Different strains of Trypanosoma cruzi were transfected with an expression vector that allows the integration of green fluorescent protein (GFP) and red fluorescent protein (RFP) genes into the beta-tubulin locus by homologous recombination. The sites of integration of the GFP and RFP markers were determined by pulse-field gel electrophoresis and Southern blot analyses. Cloned cell lines selected from transfected epimastigote populations maintained high levels of fluorescent protein expression even after 6 months of in vitro culture of epimastigotes in the absence of drug selection. Fluorescent trypomastigotes and amastigotes were observed within Vero cells in culture as well as in hearts and diaphragms of infected mice. The infectivity of the GFP- and RFP-expressing parasites in tissue culture cells was comparable to wild type populations. Furthermore, GFP- and RFP-expressing parasites were able to produce similar levels of parasitemia in mice compared with wild type parasites. Cell cultures infected simultaneously with two cloned cell lines from the same parasite strain, each one expressing a distinct fluorescent marker, showed that at least two different parasites are able to infect the same cell. Double-infected cells were also detected when GFP- and RFP-expressing parasites were derived from strains belonging to two distinct T. cruzi lineages. These results show the usefulness of parasites expressing GFP and RFP for the study of various aspects of T. cruzi infection including the mechanisms of cell invasion, genetic exchange among parasites and the differential tissue distribution in animal models of Chagas disease.

RNA polymerase I promoter and splice acceptor site recognition affect gene expression in non-pathogenic Leishmania species

Leishmania (Sauroleishmania) tarentolae has biotechnological potential for use as live vaccine against visceral leishmaniasis and as a system for the over expression of eukaryotic proteins that possess accurate post-translational modifications. For both purposes, new systems for protein expression in this non-pathogenic protozoan are necessary. The ribosomal RNA promoter proved to be a stronger transcription driver since its use yielded increased levels of recombinant protein in organisms of both genera Trypanosoma or Leishmania. We have evaluated heterologous expression systems using vectors with two different polypyrimidine tracts in the splice acceptor site by measuring a reporter gene transcribed from L. tarentolae RNA polymerase I promoter. Our data indicate that the efficiency of chloramphenicol acetyl transferase expression changed drastically with homologous or heterologous sequences, depending on the polypyrimidine tract used in the construct and differences in size and/or distance from the AG dinucleotide. In relation to the promoter sequence the reporter expression was higher in heterologous lizard-infecting species than in the homologous L. tarentolae or in the mammalian-infecting L. (Leishmania) amazonensis.

Diversification of function by different isoforms of conventionally shared RNA polymerase subunits

Eukaryotic nuclei contain three classes of multisubunit DNA-directed RNA polymerase. At the core of each complex is a set of 12 highly conserved subunits of which five--RPB5, RPB6, RPB8, RPB10, and RPB12--are thought to be common to all three polymerase classes. Here, we show that four distantly related eukaryotic lineages (the higher plant and three protistan) have independently expanded their repertoire of RPB5 and RPB6 subunits. Using the protozoan parasite Trypanosoma brucei as a model organism, we demonstrate that these distinct RPB5 and RPB6 subunits localize to discrete subnuclear compartments and form part of different polymerase complexes. We further show that RNA interference-mediated depletion of these discrete subunits abolishes class-specific transcription and hence demonstrates complex specialization and diversification of function by conventionally shared subunit groups.

Evidence supporting a major promoter in the Trypanosoma cruzi rRNA gene

Two clearly separated transcription start points (tsp) have been reported within the Trypanosoma cruzi rDNA (DNA encoding rRNA) gene spacer region. These sites are separated by 270 bp, a distance compatible with the occurrence of two core promoters. To characterize the individual participation of these two elements, a deletion analysis was carried out. Different versions of the promoter regions were assayed in a transient transfection analysis of epimastigotes, using the chloramphenicol acetyl transferase gene (cat) as a reporter. The data indicate that the so-called distal tsp-associated region (relative to the small subunit rRNA 5' terminus coding region) comprises most (80%) if not all of the observed activity. In addition, an associated locus specific repeated element showed a modest upregulating activity, since its presence stimulated the cat reporter gene by about 20%. The data here presented should be valuable in the design of expression vectors for T. cruzi, where the rRNA gene promoter has been an important functional element.

Integration of expression vectors into the ribosomal locus of Trypanosoma cruzi

The expression vectors of the protozoan parasite Trypanosoma cruzi pRIBOTEX and pTREX harbor a ribosomal promoter that improves gene expression and clone selection. Interestingly, the solely presence of this 810 bp long sequence leads to the integration of these vectors into the ribosomal locus, even though circular plasmids are poorly recombinogenic. Initially, it was suggested that a 174 bp long ribosomal-specific repeat element present in the ribosomal promoter region could be responsible for the genetic exchange. On the contrary, we demonstrate that recombination of pTREX occurs within a 86 bp long region located 120 bp downstream the transcription start point (tsp1) of the ribosomal promoter, and it does not depend on the presence of the ribosomal repeat. We also determined that a 291 bp segment encompassing the tsp1 and the 86 bp long recombination region contains all necessary signals to drive transcription and complete recombination into the rRNA locus. Finally, we demonstrate that the integration of pTREX derived plasmids into the nuclear genome occurs within the first 5 h post-transfection, and that non-integrated copies are rapidly degraded.

Protozomics: trypanosomatid parasite genetics comes of age

Trypanosomatid protozoans cause important diseases of humans and their domestic livestock. Various molecular genetic tools are now allowing rapid progress in understanding many of the unique aspects of the molecular and cell biology of these organisms. Diploidy and the lack or difficulty of sexual crossing has been a challenge for forward genetics, but powerful selections and functional complementation have helped to overcome it in Leishmania. RNA interference has been adapted for forward genetics in trypanosomes, in which it is also a powerful tool for reverse genetics. Interestingly, the efficacy of different genetic tools has steered research into different aspects of the biology of these parasites.

Intergenic and external transcribed spacers of ribosomal RNA genes in lizard-infecting Leishmania: molecular structure and phylogenetic relationship to mammal-infecting Leishmania in the subgenus Leishmania (Leishmania)

To establish the relationships of the lizard- and mammal-infecting Leishmania, we characterized the intergenic spacer region of ribosomal RNA genes from L. tarentolae and L. hoogstraali. The organization of these regions is similar to those of other eukaryotes. The intergenic spacer region was approximately 4 kb in L. tarentolae and 5.5 kb in L. hoogstraali. The size difference was due to a greater number of 63-bp repetitive elements in the latter species. This region also contained another element, repeated twice, that had an inverted octanucleotide with the potential to form a stem-loop structure that could be involved in transcription termination or processing events. The ribosomal RNA gene localization showed a distinct pattern with one chromosomal band (2.2 Mb) for L. tarentolae and two (1.5 and 1.3 Mb) for L. hoogstraali. The study also showed sequence differences in the external transcribed region that could be used to distinguish lizard Leishmania from the mammalian Leishmania. The intergenic spacer region structure features found among Leishmania species indicated that lizard and mammalian Leishmania are closely related and support the inclusion of lizard-infecting species into the subgenus Sauroleishmania proposed by Saf'janova in 1982.

Functional domains of the rDNA promoter display a differential recognition in Leishmania

A construct containing the RNA polymerase I promoter of Leishmania (L.) amazonensis, driving the expression of cloramphenicol acetyl transferase reporter gene, was better recognised by heterologous hosts species Leishmania (L.) major and Leishmania (L.) mexicana than by the homologous host L. (L.) amazonensis. The rDNA promoter domains responsible for recognition were functionally mapped. The core domain (-74 to +170) conferred a barely equal recognition on homologous or heterologous cells, slightly favouring to the later. Addition of the upstream domain (-196 to -74) repressed the expression in all cells tested. The third domain, consisting of repeated elements (upstream to -196 in L. (L.) amazonensis), enhanced by about 20 times the core activity of homologous species and by about 40 times the heterologous ones. Gel mobility shift patterns generated by the binding of core sequence of L. (L.) amazonensis to nuclear extracts of the Leishmania species suggested that the rDNA transcriptional machinery is a complex DNA-protein association particular for each species. A model is proposed to explain the mechanism and possible interactions of transcription machinery in the regulation of rDNA expression in phylogenically related organisms.

Trypanosoma cruzi: exogenously regulated gene expression

A regulated expression vector would provide a strong tool for the dissection of gene function in Trypanosoma cruzi. Herein, we establish a system in which genes in T. cruzi expression vectors can be exogenously regulated by tetracycline. We first generated strains of T. cruzi that stably express the repressor of the bacterial tetracycline resistance gene and T7 RNA polymerase. Based on these strains, we developed two T. cruzi expression systems regulated by tetracycline--the first by use of a regulated rRNA promoter and the second by use of a regulated T7 promoter. In the former, we constructed an expression vector in which tetracycline resistance gene operators flank the transcription start point of the T. cruzi rRNA gene promoter. Reporter gene activity from this modified promoter was regulated up to 20-fold in the presence of different concentrations of tetracycline. In the T7 system, tetracycline resistance gene operators flank the transcription start point of the T7 promoter. Reporter gene activity from this modified promoter was regulated up to 150-fold in the presence of different concentrations of tetracycline. Expression in these systems was repressed when tetracycline was removed even after full induction for extended periods in the presence of tetracycline. We are now using these two systems to test protein function in T. cruzi.

Simultaneous stable expression of neomycin phosphotransferase and green fluorescence protein genes in Trypanosoma cruzi

The ribosomal RNA (rRNA) gene promoter was used to construct plasmid vectors that simultaneously express multiple exogenous genes in Trypanosoma cruzi. Vector pBSPANEO expresses neomycin phosphotransferase, and pPAGFPAN expresses both green fluorescent protein and neomycin phosphotransferase from a single promoter. Both vectors require the presence of the rRNA promoter for stable transfection; epimastigotes transfected with pPAGFPAN strongly fluoresced due to green fluorescent protein expression. Intact plasmids were rescued from the T. cruzi-transfected population after >8 mo of culture, indicating stable replication of these vectors. Vectors were integrated into the rRNA locus by homologous recombination and into other loci, presumably by illegitimate recombination. Parasites bearing tandem concatamers of plasmids were also found among the transfectants. Transfectants expressing green fluorescent protein showed a bright green fluorescence distributed throughout the cell. Fluorescence was also detected in amastigotes after infection of mammalian cells with transfected parasites, indicating that the rRNA promoter can drive efficient expression of these reporter genes in multiple life-cycle stages of the parasite. Expression of the heterologous genes was detected after passage in mice or in the insect vector. These vectors will be useful for the genetic dissection of T. cruzi biology and pathogenesis.

PPB1, a putative spliced leader RNA gene transcription factor in Trypanosoma cruzi

In trypanosomatids, the spliced leader RNA, or SL RNA, donates its 5' 39 nucleotides to mature nuclear mRNAs in a process termed trans-splicing. We have previously characterized the SL RNA gene from Trypanosoma cruzi and identified its transcription promoter, including a 14 nt proximal sequence element, or PSE, that binds a putative transcription factor and activates transcription of the gene. Herein, we describe establishment of a yeast one-hybrid system using the 14 nt PSE as bait, and use this system to select T. cruzi cDNAs encoding a putative transcription factor that activates transcription of the SL RNA gene. The cDNA was selected from a normalized library and encodes an approximately 45 kDa putative PSE promoter-binding protein, PPB1. PPB1 in vitro translated or overexpressed in and isolated from transformed E. coli, showed PSE-specific binding activity by electrophoretic mobility shift assays. Finally, overexpression of PPB1 in T. cruzi led to increased expression of the SL RNA gene as well as reporter genes in episomal constructs under the control of the SL RNA gene promoter. These observations suggest that PPB1 is a transcription factor that plays an important role in SL RNA gene expression.

The 28S-18S rDNA intergenic spacer from Crithidia fasciculata: repeated sequences, length heterogeneity, putative processing sites and potential interactions between U3 small nucleolar RNA and the ribosomal RNA precursor

In Crithidia fasciculata, the ribosomal RNA (rRNA) gene repeats range in size from approximately 11 to 12 kb. This length heterogeneity is localized to a region of the intergenic spacer (IGS) that contains tandemly repeated copies of a 19mer sequence. The IGS also contains four copies of an approximately 55 nt repeat that has an internal inverted repeat and is also present in the IGS of Leishmania species. We have mapped the C.fasciculata transcription initiation site as well as two other reverse transcriptase stop sites that may be analogous to the A0 and A' pre-rRNA processing sites within the 5' external transcribed spacer (ETS) of other eukaryotes. Features that could influence processing at these sites include two stretches of conserved primary sequence and three secondary structure elements present in the 5' ETS. We also characterized the C.fasciculata U3 snoRNA, which has the potential for base-pairing with pre-rRNA sequences. Finally, we demonstrate that biosynthesis of large subunit rRNA in both C. fasciculata and Trypanosoma brucei involves 3'-terminal addition of three A residues that are not present in the corresponding DNA sequences.

Colony polymerase chain reaction of stably transfected trypanosoma cruzi grown on solid medium

Tools for the genetic manipulation of Trypanosoma cruzi are largely unavailable, although several vectors for transfection of epimastigotes and expression of foreign or recombinant genes have been developed. We have previously constructed several plasmid vectors in which recombinant genes are expressed in T. cruzi using the rRNA promoter. In this report, we demonstrate that one of these vectors can simultaneously mediate expression of neomycin phosphotransferase and green fluorescent protein when used to stably transfect cultured epimastigotes. These stably transfected epimastigotes can be selected and cloned as unique colonies on solid medium. We describe a simple colony PCR approach to the screening of these T. cruzi colonies for relevant genes. Thus, the methodologies outlined herein provide important new tools for the genetic dissection of this important parasite.

Characterization of the Leishmania donovani ribosomal RNA promoter

The rRNA genes of Leishmania donovani are organized on chromosome 27 as tandem repeats of approximately 12.5-kb units that each contain a promoter, the subunit rRNAs, and approximately 39 copies of a 64-bp species-specific sequence. The transcription initiation site was mapped to 1020 bp upstream of the 18S rRNA gene by RNase protection and primer extension. A 349-bp sequence between the 64-bp repeats and the 18S rRNA gene appears to contain a promoter, since it directs a 60-fold increase in luciferase expression over the no-insert control in transient transfection assays. Stepwise deletion and 10-bp replacement studies identified three domains that affect promoter activity. In strain LSB-51.1, a naturally occurring gene conversion with a portion of the LD1 sequence from chromosome 35 replaced the rRNA genes within one repeat unit, from downstream of the promoter to within the 64-bp repeats. Northern blot analysis of RNA from LSB-51.1 showed large transcripts from the external spacer regions that are not normally transcribed. These results imply that the gene conversion eliminated sequences at or near the 5' terminus of the 64-bp repeats which normally function in transcription termination.

Genetic manipulation of kinetoplastida

During the 1980s, many kinetoplastid genes were cloned and their function inferred from homology with genes from other organisms, location of the corresponding proteins or expression in heterologous systems. Up until 1990, before the availability of DNA transfection methodology, we could not analyze the function of kinetoplastid genes within the organisms themselves. Since then, it has become possible to create and complement mutants, to overexpress foreign proteins in the parasites, to knock out genes and even to switch off essential functions. However, these methods are not equally applicable in all parasites. Here, Christine Clayton highlights the differences and similarities between the most commonly used model organisms, and assesses the relative advantages of different approaches and parasites for different types of investigation.

Control of gene expression in Trypanosomatidae

The study of mechanisms which control gene expression in trypanosomatids has developed at an increasing rate since 1989 when the first successful DNA transfection experiments were reported. Using primarily Trypanosoma brucei as a model, several groups have begun to elucidate the basic control mechanisms and to define the cellular factors involved in mRNA transcription, processing and translation in these parasites. This review focuses on the most recent studies regarding a subset of genes that are expressed differentially during the life cycle of three groups of parasites. In addition to T. brucei, I will address studies on gene regulation in a few species of Leishmania and the results obtained by a much more limited group of laboratories studying gene expression in Trypanosoma cruzi. It is becoming evident that the regulatory strategies chosen by different species of trypanosomatids are not similar, and that for these very successful parasites it is probably advantageous to employ multiple mechanisms simultaneously. In addition, with the increasing numbers of parasite genes that have now been submitted to molecular dissection, it is also becoming evident that, among the various strategies for gene expression control, there is a predominance of regulatory pathways acting at the post-transcriptional level.

pRIBOTEX expression vector: a pTEX derivative for a rapid selection of Trypanosoma cruzi transfectants

To improve the selection phenotype of the expression plasmid pTEX, a Trypanosoma cruzi rDNA (DNA coding for rRNA) gene spacer fragment (806 bp) containing a mapped transcription start point (tsp) was cloned in the vectors pTEX and pTEX-cat, generating the plasmids pRIBOTEX and pRIBOTEX-cat. T. cruzi cultures transiently transfected with pRIBOTEX-cat expressed a chloramphenicol (Cm) acetyltransferase (CAT) activity 16,000-fold greater than the activity observed with the parental vector pTEX-cat. Moreover, T. cruzi cells transformed with pRIBOTEX and pRIBOTEX-cat exhibited logarithmic growth in the presence of Geneticin (G418) 2 weeks earlier than that observed with controls transformed with pTEX. The plasmid copy number in stably transformed trypanosomes was about 50-times higher in cultures transformed with pTEX-cat than in cells transformed with pRIBOTEX or pRIBOTEX-cat. However, the neo RNA steady-state level and the CAT activity observed among the stably transfected cultures showed only modest differences. Finally, it was found that the pRIBOTEX vector was not episomally maintained as pTEX, but integrated into a chromosome indistinguishable from the one encoding rRNA. These features make pRIBOTEX a useful tool for transfection and rapid expression of genes in T. cruzi.

Trypanosoma cruzi strains partition into two groups based on the structure and function of the spliced leader RNA and rRNA gene promoters

We have previously identified a major proximal sequence element (PSE) responsible for transcription of the spliced leader (SL) gene from Trypanosoma cruzi strain CL, and showed that the sequence encompassing this PSE exhibits approximately 30% divergence between two major groups of T. cruzi isolates, but strong conservation within the groups. In this report, we show that the SL RNA gene promoter from the CL strain (group I) is efficiently expressed only in T. cruzi isolates from group I. Similarly, the sequence of the approximately 643 bp promoter region of the T. cruzi rRNA is strongly conserved within, but diverged approximately 20% between, the two groups. Reporter constructs driven by the rRNA promoter sequences from group I strains are strongly expressed after electroporation into other group I strains, but not expressed in group II strains. In contrast, constructs bearing rRNA promoter sequences from group II strains are active in strains from both groups. Phylogenetic analyses performed with both the rRNA and the SL RNA gene promoter sequences yielded similar trees, and these trees strongly reinforce the partitioning of known T. cruzi into two major groups that parallel the observed functional specificity of the promoters. Given the well-documented species specific pattern of both rRNA promoters and PSEs in higher eukaryotes, these results suggest an ancient evolutionary divergence among organisms currently classified as T. cruzi.

The transcription promoter of the spliced leader gene from Trypanosoma cruzi

A putative promoter element responsible for transcription of the spliced leader (SL) gene of Trypanosoma cruzi was identified by overlapping deletion and linker scanning analyses of the upstream flanking sequences using the bacterial chloramphenicol acetyltransferase (CAT) gene as a reporter in transient transfections of cultured epimastigotes. Deletion or substitution of a proximal sequence element (PSE) between positions -53 and -40 relative to the transcription start point eliminated CAT gene expression. Comparison of SL genes from several strains of T. cruzi revealed two alternative sequence patterns for the putative SL PSE, both composed of a short run of purines followed by a run of pyrimidines. Moreover, an examination of these sequences supports the subdivision of T. cruzi isolates into two divergent groups. Double-stranded oligonucleotides containing the sequence of the PSE exhibited specific gel mobility shifts after incubation with T. cruzi nuclear extracts, suggesting that a transcription factor binds this site. Finally, experiments designed to increase the level of CAT expression from the SL promoter suggest that it is not a strong promoter in cultured T. cruzi epimastigotes.

Trypanosoma cruzi rRNA genes: a repeated element from the non-transcribed spacer is locus specific

To determine the occurrence of conserved domains of presumed functional selection, a genomic restriction analysis was carried out in the region surrounding a transcription start point (tsp) from the rRNA cistron in T. cruzi. The transcribed spacer was found highly conserved among several isolates, whereas at 146 bp upstream from the tsp a highly polymorphic pattern was evidenced with a probe that contains sequences of a repetitive element (172 bp). Both genomic and chromosomal hybridizations indicated the linkage of the repetitive element to coding regions of the rRNA cistron. This represents the first example of a repetitive element not interspersed throughout the genome of T. cruzi, and strongly suggests that a functional role is being selected.

The promoter for the ribosomal RNA genes of Leishmania chagasi

A promoter for the rRNA genes of Leishmania chagasi was found to be located about 1 kb upstream of the 18S rRNA coding region and immediately downstream of 64 bp tandem repeats. Its approximate boundaries and corresponding transcription start site were determined by transient transfections and primer extension assays. This promoter for RNA polymerase I has differing activities when transfected into various Leishmania species and no activity in Trypanosoma cruzi. Its sequence has no obvious similarities with other known rRNA promoters in Trypanosomatids. Depending on the species, this promoter can be used to increase expression of a protein from a plasmid in Leishmania by as much as 45-fold over that from a plasmid lacking a promoter.

Structural and functional characterization of the Leishmania amazonensis ribosomal RNA promoter

The promoter region of the ribosomal RNA (rRNA) genes of Leishmania amazonensis was characterised and the transcription start point, defined by primer extension, was shown to be a T residue, 1048 nucleotides upstream of the beginning of the 18S sequence. A repetitive element of 60 bp was identified in the intergenic spacer. This element did not show sequence similarity with the region around the transcription start point. Conserved sequences were found in the external transcribed spacer of L. amazonensis, Trypanosoma cruzi and Crithidia fasciculata rRNA genes, 150 nucleotides downstream of the transcription start point. These sequences might be involved in processing events of the rRNA precursor molecule. The general organisation of the gene resembles the pattern observed for the ribosomal cistron in eukaryotic cells. Constructs containing the L. amazonensis promoter region upstream of the chloramphenicol acetyltransferase (cat) gene were able to drive the expression of the reporter gene in transient transfection experiments. CAT expression could be detected even when no trans-splicing acceptor sequence was added to the constructs, although its presence enhanced 5-fold the level of CAT activity. Species-specificity of the RNA polymerase I promoter activity was also demonstrated since constructs containing the L. amazonensis promoter region were unable to drive CAT expression when transfected into the related trypanosomatids, T. cruzi, C. fasciculata and Endotrypanum schaudini.

Post-transcriptional elements regulating expression of mRNAs from the amastin/tuzin gene cluster of Trypanosoma cruzi

The genome of Trypanosoma cruzi contains tandemly arrayed copies of the gene encoding amastin, an abundant protein on the surface of the amastigote stage of the parasite. The transcription rate of the amastin genes is the same in the different developmental stages, but the steady state level of the 1.4-kilobase amastin mRNA is 50-85 times higher in amastigotes than in epimastigotes or trypomastigotes (1). Here we show that the amastin genes alternate with genes encoding another protein, called tuzin, whose 1.7-kilobase mRNA is much less abundant in amastigotes. The 3'-untranslated region (UTR) of tuzin mRNA is only a few nucleotides in length or even nonexistent, in contrast with the 630-nucleotide 3'-UTR of amastin mRNA. No promoter elements were found upstream or within the amastin/tuzin gene cluster. However, in amastigotes, the protein synthesis inhibitor cycloheximide caused a 3-fold decrease in amastin mRNA and a 7-fold increase in tuzin mRNA. Furthermore, when the amastin 3'-UTR plus its downstream intergenic region were fused behind the luciferase coding region in a chimeric plasmid for transient transfections, luciferase activity increased 7-fold in amastigotes and decreased 5-fold in epimastigotes. Thus, developmental expression of these alternating genes is regulated by different mechanisms.