Physical identification of branched intron side-products of splicing in Trypanosoma brucei

Transcription of protein-coding genes in trypanosomes by RNA polymerase I

In eukaryotes, RNA polymerase (pol) II transcribes the protein-coding genes, whereas RNA pol I transcribes the genes that encode the three RNA species of the ribosome [the ribosomal RNAs (rRNAs)] at the nucleolus. Protozoan parasites of the order Kinetoplastida may represent an exception, because pol I can mediate the expression of exogenously introduced protein-coding genes in these single-cell organisms. A unique molecular mechanism, which leads to pre-mRNA maturation by trans-splicing, facilitates pol I-mediated protein-coding gene expression in trypanosomes. Trans-splicing adds a capped 39-nucleotide mini-exon, or spliced leader transcript, to the 5' end of the main coding exon posttranscriptionally. In other eukaryotes, the addition of a 5' cap, which is essential for mRNA function, occurs exclusively as a result of RNA pol II-mediated transcription. Given the assumption that cap addition represents the limiting factor, trans-splicing may have uncoupled the requirement for RNA pol II-mediated mRNA production. A comparison of the alpha-amanitin sensitivity of transcription in naturally occurring trypanosome protein-coding genes reveals that a unique subset of protein-coding genes-the variant surface glycoprotein (VSG) expression sites and the procyclin or the procyclic acidic repetitive protein (PARP) genes-are transcribed by an RNA polymerase that is resistant to the mushroom toxin alpha-amanitin, a characteristic of transcription by RNA pol I. Promoter analysis and a pharmacological characterization of the RNA polymerase that transcribes these genes have strengthened the proposal that the VSG expression sites and the PARP genes represent naturally occurring protein-coding genes that are transcribed by RNA pol I.

In vitro generation of a circular exon from a linear pre-mRNA transcript

Recent findings have firmly established the existence of circular exons in vivo. We were interested in the possible splicing mechanism by which these unusual mRNA molecules could be created in vitro, though no biological relevance has been attached to their existence as yet. In this report we demonstrate that a modified synthetic linear yeast ACT1 transcript whose sequence begins with the 3'-part of its original intron, is continued by 247 nt of exon sequence and terminates with the 5'-part of its intron will generate a circular exon when introduced to standard in vitro splicing reactions in whole cell splice extracts from Saccharomyces cerevisiae. The formation of a circular exon was found to be independent of specific circular or secondary structures of the pre-mRNA transcript. We hypothesize that circular exons which are found in vivo may be generated from pre-mRNAs which derive from rare events of transcription initiation within an intron.

Analyzing expression of the calmodulin and ubiquitin-fusion genes of Trypanosoma cruzi using simultaneous, independent dual gene replacements

We describe here a strategy for introducing simultaneous, independent gene replacements into the Trypanosoma cruzi chromosome. The goal of this study was to use two linear DNA fragments to simultaneously replace the CalA2 calmodulin and FUS1 ubiquitin-fusion genes with the neomycin resistance (neo(r)) and chloramphenicol acetyltransferase (CAT) genes, respectively. One clone (D6), of thirty G418-resistant clones analyzed, carried the desired dual gene replacement. CDNA sequence analysis indicated that the CAT mRNA was accurately trans-spliced using the previously identified FUS1 mini-exon addition site. However, DNA sequence analysis of the intergenic sequence immediately upstream of the neo(r) gene in clone D6 identified a mutation which altered the pattern of trans-splicing of the neo(r) mRNA. Possible effects of this mutation on 3' splice acceptor site selection are discussed.

Stage-specific differential polyadenylation of mini-exon derived RNA in African trypanosomes

The differentiation of African trypanosomes through several distinct stages in their mammalian host and insect vector correlates with differential expression of some of the parasites' genes. In the search for genes from Trypanosoma brucei brucei involved in switching from the actively dividing long slender to the non-dividing short stumpy bloodstream forms, we have isolated cDNA clones which hybridise specifically to mRNA from short stumpy forms. All clones that were characterised contained similar sequences. Northern blot analysis showed that: (i) RNA transcripts which hybridise to these clones are barely detectable in the poly(A)+ fraction of RNA from long slender bloodstream forms and absent in procyclic culture forms, but are abundant in the poly(A)+ fraction of RNA from short stumpy forms; (ii) the RNA transcripts are abundant in the poly(A)- fraction of RNA from all life cycle stages of the trypanosomes, without significant differences and, (iii) three transcripts of 160, 280 and 400 nucleotides in size are detected in the poly(A)+ fraction of RNA, whereas only a single size-class of transcript of between 140 and 160 nucleotides is detectable in the poly(A)- fraction. Sequence analysis revealed that these clones correspond to mini-exon derived RNA containing a poly(A) tail at their 3' end. The polyadenylation of the transcript is a post-transcriptional event since sequences from genomic DNA could not be amplified in the polymerase chain reaction when mini-exon and oligo(dT) nucleotide sequences were used as primers. The differences in size of the transcripts detected can be accounted for by variations in the poly(A) tail length.

mRNA processing in the Trypanosomatidae

Members of the Trypanosomatidae, which include the African trypanosomes, the American trypanosomes and the leishmanias, cause disease in vast proportions in man and his livestock and are a major detrimental factor to the social and economic well-being of the third world. Current research using the techniques of molecular biology has revealed two unusual types of mRNA processing in these protozoans; these are the addition of a shared leader sequence to the 5' ends of nuclear mRNAs by a mechanism of trans splicing, and the insertion and deletion of specific uridine residues in mitochondrial transcripts by RNA editing. The presence of these two mRNA processing pathways in the Trypanosomatidae has profound consequences for the organization and expression of their genetic information.

A comparison of trans-RNA splicing in trypanosomes and nematodes

Many aspects of the biology of kinetoplastids are unique, so it is surprising that they share with nematodes an unusual post-transcriptional process called trans-splicing. During this process, a small conserved RNA sequence is added to the 5' non-translated ends of transcribed RNAs of protein-encoding genes. Trypanosomes and nematodes are the only organisms to date in which these sequences have been described, and the biological significance of trans-splicing remains a mystery but may be of wider occurrence in invertebrates. In this review, John Donelson and Wenlin Zeng compare the process in nematodes and trypanosomes and speculate on its raison d'être.

Transcription of the heat shock 70 locus in Trypanosoma brucei

The 23-kb heat shock 70 locus of the protozoan parasite Trypanosoma brucei encodes several tightly clustered genes. From 5' to 3', a cognate hsp70 gene (gene 1) (see preceding paper, Lee et al.) is separated from a cluster of five identical hsp70 genes (genes 2-6) by about 6 kb of DNA that encodes several RNAs of unknown function. Polycistronic transcripts could be detected in the tandem array of hsp70 genes 2-6 and the maturation of the hsp70 pre-mRNAs involves addition of mini-exons on at least two different alternate 3' splice acceptor sites. Potential heat shock transcription factor binding sites are present upstream of hsp70 gene 2 and in the intergenic regions of hsp70 genes 2-6, but could not be found upstream of the cognate hsp70 gene 1.

The tubulin gene cluster of Trypanosoma brucei starts with an intact beta-gene and ends with a truncated beta-gene interrupted by a retrotransposon-like sequence

In Trypanosoma brucei the genes coding for alpha- and beta-tubulin are arranged in a single cluster comprising about ten alternating alpha and beta genes. The cluster starts at its 5' end with an intact beta gene. In this area, a 1.1-kb segment upstream of the mini-exon addition site has been sequenced. Several potential transcription signals were seen. The 3' end of the cluster terminates in the middle of a beta gene, making it an inactive truncated pseudogene. The adjoining 1.7-kb sequence shows a high degree of similarity with a retrotransposon-like (RTnL) element previously characterized elsewhere in the trypanosome genome. This is the first report of an RTnL element interrupting a protein-coding gene of T. brucei.

Trans splicing in trypanosomes--archaism or adaptation?

In trypanosomes, a single transcription unit usually covers several protein-coding genes. The primary transcript is cut up by trans-splicing and polyadenylation machineries to generate individual mature mRNAs. All nuclear mRNAs acquire the same capped 39 nucleotide sequence at their 5' end as a consequence of the trans-splicing event. Trans splicing is used in the synthesis of some mRNAs in nematodes and chloroplasts. These unusual systems are clearly related to cis-splicing systems, but it remains an intriguing question whether they are merely exotic offshoots of cis splicing or archaic remnants of cis-splicing progenitors.