Transcription of the intergenic regions of the tubulin gene cluster of Trypanosoma brucei: evidence for a polycistronic transcription unit in a eukaryote

A profile of research on the parasitic trypanosomatids and the diseases they cause

The parasitic trypanosomatids cause lethal and debilitating diseases, the leishmaniases, Chagas disease, and the African trypanosomiases, with major impacts on human and animal health. Sustained research has borne fruit by assisting efforts to reduce the burden of disease and by improving our understanding of fundamental molecular and cell biology. But where has the research primarily been conducted, and which research areas have received the most attention? These questions are addressed below using publication and citation data from the past few decades.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

A Global Analysis of Enzyme Compartmentalization to Glycosomes

In kinetoplastids, the first seven steps of glycolysis are compartmentalized into a glycosome along with parts of other metabolic pathways. This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. Much of our understanding of the emergence, evolution, and maintenance of glycosomes is limited to explorations of the dixenous parasites, including the enzymatic contents of the organelle. Our objective was to determine the extent that we could leverage existing studies in model kinetoplastids to determine the composition of glycosomes in species lacking evidence of experimental localization. These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. Our approach initiated with a meta-analysis of existing studies to generate a subset of enzymes with highest evidence of glycosome localization. From this dataset we extracted the best possible glycosome signal peptide identification scheme for in silico identification of glycosomal proteins from any kinetoplastid species. Validation suggested that a high glycosome localization score from our algorithm would be indicative of a glycosomal protein. We found that while metabolic pathways were consistently represented across kinetoplastids, individual proteins within those pathways may not universally exhibit evidence of glycosome localization.

Simplified inducible system for Trypanosoma brucei

Nowadays, most reverse genetics approaches in Trypanosoma brucei, a protozoan parasite of medical and veterinary importance, rely on pre-established cell lines. Consequently, inducible experimentation is reduced to a few laboratory strains. Here we described a new transgene expression system based exclusively on endogenous transcription activities and a minimum set of regulatory components that can easily been adapted to different strains. The pTbFIX vectors are designed to contain the sequence of interest under the control of an inducible rRNA promoter along with a constitutive dicistronic unit encoding a nucleus targeted tetracycline repressor and puromycin resistance genes in a tandem “head-to-tail” configuration. Upon doxycycline induction, the system supports regulatable GFP expression (170 to 400 fold) in both bloodstream and procyclic T. brucei forms. Furthermore we have adapted the pTbFIX plasmid to perform RNAi experimentation. Lethal phenotypes, including α-tubulin and those corresponding to the enolase and clathrin heavy chain genes, were successfully recapitulated in procyclic and bloodstream parasites thus showing the versatility of this new tool.

A functional analysis of TOEFAZ1 uncovers protein domains essential for cytokinesis in Trypanosoma brucei

The parasite Trypanosoma brucei is highly polarized, including a flagellum that is attached along the cell surface by the flagellum attachment zone (FAZ). During cell division, the new FAZ positions the cleavage furrow, which ingresses from the anterior tip of the cell towards the posterior. We recently identified TOEFAZ1 (for 'Tip of the Extending FAZ protein 1') as an essential protein in trypanosome cytokinesis. Here, we analyzed the localization and function of TOEFAZ1 domains by performing overexpression and RNAi complementation experiments. TOEFAZ1 comprises three domains with separable functions: an N-terminal α-helical domain that may be involved in FAZ recruitment, a central intrinsically disordered domain that keeps the morphogenic kinase TbPLK at the new FAZ tip, and a C-terminal zinc finger domain necessary for TOEFAZ1 oligomerization. Both the N-terminal and C-terminal domains are essential for TOEFAZ1 function, but TbPLK retention at the FAZ is not necessary for cytokinesis. The feasibility of alternative cytokinetic pathways that do not employ TOEFAZ1 are also assessed. Our results show that TOEFAZ1 is a multimeric scaffold for recruiting proteins that control the timing and location of cleavage furrow ingression.

Distinct activation mechanisms trigger the trypanocidal activity of DNA damaging prodrugs

Quinone‐based compounds have been exploited to treat infectious diseases and cancer, with such chemicals often functioning as inhibitors of key metabolic pathways or as prodrugs. Here, we screened an aziridinyl 1,4‐benzoquinone (ABQ) library against the causative agents of trypanosomiasis, and cutaneous leishmaniasis, identifying several potent structures that exhibited EC₅₀ values of <100 nM. However, these compounds also displayed significant toxicity towards mammalian cells indicating that they are not suitable therapies for systemic infections. Using anti‐T. brucei ABQs as chemical probes, we demonstrated that these exhibit different trypanocidal modes of action. Many functioned as type I nitroreductase (TbNTR) or cytochrome P450 reductase (TbCPR) dependent prodrugs that, following activation, generate metabolites which promote DNA damage, specifically interstrand crosslinks (ICLs). Trypanosomes lacking TbSNM1, a nuclease that specifically repairs ICLs, are hypersensitive to most ABQ prodrugs, a phenotype exacerbated in cells also engineered to express elevated levels of TbNTR or TbCPR. In contrast, ABQs that contain substituent groups on the biologically active aziridine do not function as TbNTR or TbCPR‐activated prodrugs and do not promote DNA damage. By unravelling how ABQs mediate their activities, features that facilitate the desired anti‐parasitic growth inhibitory effects could be incorporated into new, safer compounds targeting these neglected tropical diseases.

Comparative interactomics provides evidence for functional specialization of the nuclear pore complex

The core architecture of the eukaryotic cell was established well over one billion years ago, and is largely retained in all extant lineages. However, eukaryotic cells also possess lineage-specific features, frequently keyed to specific functional requirements. One quintessential core eukaryotic structure is the nuclear pore complex (NPC), responsible for regulating exchange of macromolecules between the nucleus and cytoplasm as well as acting as a nuclear organizational hub. NPC architecture has been best documented in one eukaryotic supergroup, the Opisthokonts (e.g. Saccharomyces cerevisiae and Homo sapiens), which although compositionally similar, have significant variations in certain NPC subcomplex structures. The variation of NPC structure across other taxa in the eukaryotic kingdom however, remains poorly understood. We explored trypanosomes, highly divergent organisms, and mapped and assigned their NPC proteins to specific substructures to reveal their NPC architecture. We showed that the NPC central structural scaffold is conserved, likely across all eukaryotes, but more peripheral elements can exhibit very significant lineage-specific losses, duplications or other alterations in their components. Amazingly, trypanosomes lack the major components of the mRNA export platform that are asymmetrically localized within yeast and vertebrate NPCs. Concomitant with this, the trypanosome NPC is ALMOST completely symmetric with the nuclear basket being the only major source of asymmetry. We suggest these features point toward a stepwise evolution of the NPC in which a coating scaffold first stabilized the pore after which selective gating emerged and expanded, leading to the addition of peripheral remodeling machineries on the nucleoplasmic and cytoplasmic sides of the pore.

Selective inhibition of RNA polymerase I transcription as a potential approach to treat African trypanosomiasis

Trypanosoma brucei relies on an essential Variant Surface Glycoprotein (VSG) coat for survival in the mammalian bloodstream. High VSG expression within an expression site body (ESB) is mediated by RNA polymerase I (Pol I), which in other eukaryotes exclusively transcribes ribosomal RNA genes (rDNA). As T. brucei is reliant on Pol I for VSG transcription, we investigated Pol I transcription inhibitors for selective anti-trypanosomal activity. The Pol I inhibitors quarfloxin (CX-3543), CX-5461, and BMH-21 are currently under investigation for treating cancer, as rapidly dividing cancer cells are particularly dependent on high levels of Pol I transcription compared with nontransformed cells. In T. brucei all three Pol I inhibitors have IC50 concentrations for cell proliferation in the nanomolar range: quarfloxin (155 nM), CX-5461 (279 nM) or BMH-21 (134 nM) compared with IC50 concentrations in the MCF10A human breast epithelial cell line (4.44 μM, 6.89 μM or 460 nM, respectively). T. brucei was therefore 29-fold more sensitive to quarfloxin, 25-fold more sensitive to CX-5461 and 3.4-fold more sensitive to BMH-21. Cell death in T. brucei was due to rapid inhibition of Pol I transcription, as within 15 minutes treatment with the inhibitors rRNA precursor transcript was reduced 97-98% and VSG precursor transcript 91-94%. Incubation with Pol I transcription inhibitors also resulted in disintegration of the ESB as well as the nucleolus subnuclear structures, within one hour. Rapid ESB loss following the block in Pol I transcription argues that the ESB is a Pol I transcription nucleated structure, similar to the nucleolus. In addition to providing insight into Pol I transcription and ES control, Pol I transcription inhibitors potentially also provide new approaches to treat trypanosomiasis.

Trypanosoma brucei is protected by an essential Variant Surface Glycoprotein (VSG) coat in the mammalian bloodstream. The active VSG gene is transcribed by RNA polymerase I (Pol I), which typically only transcribes rDNA. Pol I transcription inhibitors are under clinical trials for cancer chemotherapy. As T. brucei relies on Pol I for VSG transcription, we investigated its susceptibility to these drugs. We show that quarfloxin (CX-3543), CX-5461, and BMH-21 are effective against T. brucei at nanomolar concentrations. T. brucei death was due to rapid and specific inhibition of Pol I transcription. Incubation with Pol I transcription inhibitors also resulted in disappearance of Pol I subnuclear structures like the nucleolus and the VSG expression site body (ESB). Rapid ESB loss followed the Pol I transcription block, arguing that the ESB is nucleated by Pol I transcription. Pol I transcription inhibitors could therefore potentially function as novel drugs against trypanosomiasis.

DNA repair pathways in trypanosomatids: from DNA repair to drug resistance

All living organisms are continuously faced with endogenous or exogenous stress conditions affecting genome stability. DNA repair pathways act as a defense mechanism, which is essential to maintain DNA integrity. There is much to learn about the regulation and functions of these mechanisms, not only in human cells but also equally in divergent organisms. In trypanosomatids, DNA repair pathways protect the genome against mutations but also act as an adaptive mechanism to promote drug resistance. In this review, we scrutinize the molecular mechanisms and DNA repair pathways which are conserved in trypanosomatids. The recent advances made by the genome consortiums reveal the complete genomic sequences of several pathogens. Therefore, using bioinformatics and genomic sequences, we analyze the conservation of DNA repair proteins and their key protein motifs in trypanosomatids. We thus present a comprehensive view of DNA repair processes in trypanosomatids at the crossroads of DNA repair and drug resistance.

Antigenic variation in African trypanosomes

Studies on Variant Surface Glycoproteins (VSGs) and antigenic variation in the African trypanosome, Trypanosoma brucei, have yielded a remarkable range of novel and important insights. The features first identified in T. brucei extend from unique to conserved-among-trypanosomatids to conserved-among-eukaryotes. Consequently, much of what we now know about trypanosomatid biology and much of the technology available has its origin in studies related to VSGs. T. brucei is now probably the most advanced early branched eukaryote in terms of experimental tractability and can be approached as a pathogen, as a model for studies on fundamental processes, as a model for studies on eukaryotic evolution or often all of the above. In terms of antigenic variation itself, substantial progress has been made in understanding the expression and switching of the VSG coat, while outstanding questions continue to stimulate innovative new approaches. There are large numbers of VSG genes in the genome but only one is expressed at a time, always immediately adjacent to a telomere. DNA repair processes allow a new VSG to be copied into the single transcribed locus. A coordinated transcriptional switch can also allow a new VSG gene to be activated without any detectable change in the DNA sequence, thereby maintaining singular expression, also known as allelic exclusion. I review the story behind VSGs; the genes, their expression and switching, their central role in T. brucei virulence, the discoveries that emerged along the way and the persistent questions relating to allelic exclusion in particular.

Dinoflagellate tandem array gene transcripts are highly conserved and not polycistronic

Dinoflagellates are an important component of the marine biota, but a large genome with high-copy number (up to 5,000) tandem gene arrays has made genomic sequencing problematic. More importantly, little is known about the expression and conservation of these unusual gene arrays. We assembled de novo a gene catalog of 74,655 contigs for the dinoflagellate Lingulodinium polyedrum from RNA-Seq (Illumina) reads. The catalog contains 93% of a Lingulodinium EST dataset deposited in GenBank and 94% of the enzymes in 16 primary metabolic KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways, indicating it is a good representation of the transcriptome. Analysis of the catalog shows a marked underrepresentation of DNA-binding proteins and DNA-binding domains compared with other algae. Despite this, we found no evidence to support the proposal of polycistronic transcription, including a marked underrepresentation of sequences corresponding to the intergenic spacers of two tandem array genes. We also have used RNA-Seq to assess the degree of sequence conservation in tandem array genes and found their transcripts to be highly conserved. Interestingly, some of the sequences in the catalog have only bacterial homologs and are potential candidates for horizontal gene transfer. These presumably were transferred as single-copy genes, and because they are now all GC-rich, any derived from AT-rich contexts must have experienced extensive mutation. Our study not only has provided the most complete dinoflagellate gene catalog known to date, it has also exploited RNA-Seq to address fundamental issues in basic transcription mechanisms and sequence conservation in these algae.

Cell biology of the trypanosome genome

Trypanosomes are a group of protozoan eukaryotes, many of which are major parasites of humans and livestock. The genomes of trypanosomes and their modes of gene expression differ in several important aspects from those of other eukaryotic model organisms. Protein-coding genes are organized in large directional gene clusters on a genome-wide scale, and their polycistronic transcription is not generally regulated at initiation. Transcripts from these polycistrons are processed by global trans-splicing of pre-mRNA. Furthermore, in African trypanosomes, some protein-coding genes are transcribed by a multifunctional RNA polymerase I from a specialized extranucleolar compartment. The primary DNA sequence of the trypanosome genomes and their cellular organization have usually been treated as separate entities. However, it is becoming increasingly clear that in order to understand how a genome functions in a living cell, we will need to unravel how the one-dimensional genomic sequence and its trans-acting factors are arranged in the three-dimensional space of the eukaryotic nucleus. Understanding this cell biology of the genome will be crucial if we are to elucidate the genetic control mechanisms of parasitism. Here, we integrate the concepts of nuclear architecture, deduced largely from studies of yeast and mammalian nuclei, with recent developments in our knowledge of the trypanosome genome, gene expression, and nuclear organization. We also compare this nuclear organization to those in other systems in order to shed light on the evolution of nuclear architecture in eukaryotes.

The evolution of amastin surface glycoproteins in trypanosomatid parasites

Amastin is a transmembrane glycoprotein found on the cell surfaces of trypanosomatid parasites. Encoded by a large, diverse gene family, amastin was initially described from the intracellular, amastigote stage of Trypanosoma cruzi and Leishmania donovani. Genome sequences have subsequently shown that the amastin repertoire is much larger in Leishmania relative to Trypanosoma. However, it is not known when this expansion occurred, whether it is associated with the origins of Leishmania and vertebrate parasitism itself, or prior to this. To examine the timing of amastin diversification, as well as the evolutionary mechanisms regulating gene repertoire and sequence diversity, this study sequenced the genomic regions containing amastin loci from two related insect parasites (Leptomonas seymouri and Crithidia sp.) and estimated a phylogeny for these and other amastin sequences. The phylogeny shows that amastin includes four subfamilies with distinct genomic positions, secondary structures, and evolution, which were already differentiated in the ancestral trypanosomatid. Diversification in Leishmania was initiated from a single ancestral locus on chromosome 34, with rapid derivation of novel loci through transposition and accelerated sequence divergence. This is absent from related organisms showing that diversification occurred after the origin of Leishmania. These results describe a substantial elaboration of amastin repertoire directly associated with the origin of Leishmania, suggesting that some amastin genes evolved novel functions crucial to cell function in leishmanial parasites after the acquisition of a vertebrate host.

Insights into the genome sequence of a free-living Kinetoplastid: Bodo saltans (Kinetoplastida: Euglenozoa)

Background

Bodo saltans is a free-living kinetoplastid and among the closest relatives of the trypanosomatid parasites, which cause such human diseases as African sleeping sickness, leishmaniasis and Chagas disease. A B. saltans genome sequence will provide a free-living comparison with parasitic genomes necessary for comparative analyses of existing and future trypanosomatid genomic resources. Various coding regions were sequenced to provide a preliminary insight into the bodonid genome sequence, relative to trypanosomatid sequences.

Results

0.4 Mbp of B. saltans genome was sequenced from 12 distinct regions and contained 178 coding sequences. As in trypanosomatids, introns were absent and %GC was elevated in coding regions, greatly assisting in gene finding. In the regions studied, roughly 60% of all genes had homologs in trypanosomatids, while 28% were Bodo-specific. Intergenic sequences were typically short, resulting in higher gene density than in trypanosomatids. Although synteny was typically conserved for those genes with trypanosomatid homologs, strict colinearity was rarely observed because gene order was regularly disrupted by Bodo-specific genes.

Conclusion

The B. saltans genome contains both sequences homologous to trypanosomatids and sequences never seen before. Structural similarities suggest that its assembly should be solvable, and, although de novo assembly will be necessary, existing trypanosomatid projects will provide some guide to annotation. A complete genome sequence will provide an effective ancestral model for understanding the shared and derived features of known trypanosomatid genomes, but it will also identify those kinetoplastid genome features lost during the evolution of parasitism.

Improving the prediction of mRNA extremities in the parasitic protozoan Leishmania

Background

Leishmania and other members of the Trypanosomatidae family diverged early on in eukaryotic evolution and consequently display unique cellular properties. Their apparent lack of transcriptional regulation is compensated by complex post-transcriptional control mechanisms, including the processing of polycistronic transcripts by means of coupled trans-splicing and polyadenylation. Trans-splicing signals are often U-rich polypyrimidine (poly(Y)) tracts, which precede AG splice acceptor sites. However, as opposed to higher eukaryotes there is no consensus polyadenylation signal in trypanosomatid mRNAs.

Results

We refined a previously reported method to target 5' splice junctions by incorporating the pyrimidine content of query sequences into a scoring function. We also investigated a novel approach for predicting polyadenylation (poly(A)) sites in-silico, by comparing query sequences to polyadenylated expressed sequence tags (ESTs) using position-specific scanning matrices (PSSMs). An additional analysis of the distribution of putative splice junction to poly(A) distances helped to increase prediction rates by limiting the scanning range. These methods were able to simplify splice junction prediction without loss of precision and to increase polyadenylation site prediction from 22% to 47% within 100 nucleotides.

Conclusion

We propose a simplified trans-splicing prediction tool and a novel poly(A) prediction tool based on comparative sequence analysis. We discuss the impact of certain regions surrounding the poly(A) sites on prediction rates and contemplate correlating biological mechanisms. This work aims to sharpen the identification of potentially functional untranslated regions (UTRs) in a large-scale, comparative genomics framework.

Identification and analysis of internal promoters in Caenorhabditis elegans operons

The current Caenorhabditis elegans genomic annotation has many genes organized in operons. Using directionally stitched promoterGFP methodology, we have conducted the largest survey to date on the regulatory regions of annotated C. elegans operons and identified 65, over 25% of those studied, with internal promoters. We have termed these operons "hybrid operons." GFP expression patterns driven from internal promoters differ in tissue specificity from expression of operon promoters, and serial analysis of gene expression data reveals that there is a lack of expression correlation between genes in many hybrid operons. The average length of intergenic regions with putative promoter activity in hybrid operons is larger than previous estimates for operons as a whole. Genes with internal promoters are more commonly involved in gene duplications and have a significantly lower incidence of alternative splicing than genes without internal promoters, although we have observed almost all trans-splicing patterns in these two distinct groups. Finally, internal promoter constructs are able to rescue lethal knockout phenotypes, demonstrating their necessity in gene regulation and survival. Our work suggests that hybrid operons are common in the C. elegans genome and that internal promoters influence not only gene organization and expression but also operon evolution.

In vivo translation and stability of trans-spliced mRNAs in nematode embryos

Spliced leader trans-splicing adds a short exon, the spliced leader (SL), to pre-mRNAs to generate 5' ends of mRNAs. Addition of the SL in metazoa also adds a new cap to the mRNA, a trimethylguanosine (m(3)(2,2,7)GpppN) (TMG) that replaces the typical eukaryotic monomethylguanosine (m7GpppN)(m7G) cap. Both trans-spliced (m3(2,2,7)GpppN-SL-RNA) and not trans-spliced (m7GpppN-RNA) mRNAs are present in the same cells. Previous studies using cell-free systems to compare the overall translation of trans-spliced versus non-trans-spliced RNAs led to different conclusions. Here, we examine the contribution of m3(2,2,7)GpppG-cap and SL sequence and other RNA elements to in vivo mRNA translation and stability in nematode embryos. Although 70-90% of all nematode mRNAs have a TMG-cap, the TMG cap does not support translation as well as an m7G-cap. However, when the TMG cap and SL are present together, they synergistically interact and translation is enhanced, indicating both trans-spliced elements are necessary to promote efficient translation. The SL by itself does not act as a cap-independent enhancer of translation. The poly(A)-tail synergistically interacts with the mRNA cap enhancing translation and plays a greater role in facilitating translation of TMG-SL mRNAs. In general, recipient mRNA sequences between the SL and AUG and the 3' UTR do not significantly contribute to the translation of trans-spliced mRNAs. Overall, the combination of TMG cap and SL contribute to mRNA translation and stability in a manner typical of a eukaryotic m7G-cap and 5' UTRs, but they do not differentially enhance mRNA translation or stability compared to RNAs without the trans-spliced elements.

Tandem gene arrays in Trypanosoma brucei: comparative phylogenomic analysis of duplicate sequence variation

Background

The genome sequence of the protistan parasite Trypanosoma brucei contains many tandem gene arrays. Gene duplicates are created through tandem duplication and are expressed through polycistronic transcription, suggesting that the primary purpose of long, tandem arrays is to increase gene dosage in an environment where individual gene promoters are absent. This report presents the first account of the tandem gene arrays in the T. brucei genome, employing several related genome sequences to establish how variation is created and removed.

Results

A systematic survey of tandem gene arrays showed that substantial sequence variation existed across the genome; variation from different regions of an array often produced inconsistent phylogenetic affinities. Phylogenetic relationships of gene duplicates were consistent with concerted evolution being a widespread homogenising force. However, tandem duplicates were not usually identical; therefore, any homogenising effect was coincident with divergence among duplicates. Allelic gene conversion was detected using various criteria and was apparently able to both remove and introduce sequence variation. Tandem arrays containing structural heterogeneity demonstrated how sequence homogenisation and differentiation can occur within a single locus.

Conclusion

The use of multiple genome sequences in a comparative analysis of tandem gene arrays identified substantial sequence variation among gene duplicates. The distribution of sequence variation is determined by a dynamic balance of conservative and innovative evolutionary forces. Gene trees from various species showed that intraspecific duplicates evolve in concert, perhaps through frequent gene conversion, although this does not prevent sequence divergence, especially where structural heterogeneity physically separates a duplicate from its neighbours. In describing dynamics of sequence variation that have consequences beyond gene dosage, this survey provides a basis for uncovering the hidden functionality within tandem gene arrays in trypanosomatids.

Evolution of tubulin gene arrays in Trypanosomatid parasites: genomic restructuring in Leishmania

BACKGROUND

alpha- and beta-tubulin are fundamental components of the eukaryotic cytoskeleton and cell division machinery. While overall tubulin expression is carefully controlled, most eukaryotes express multiple tubulin genes in specific regulatory or developmental contexts. The genomes of the human parasites Trypanosoma brucei and Leishmania major reveal that these unicellular kinetoplastids possess arrays of tandem-duplicated tubulin genes, but with differences in organisation. While L. major possesses monotypic alpha and beta arrays in trans, an array of alternating alpha- and beta tubulin genes occurs in T. brucei. Polycistronic transcription in these organisms makes the chromosomal arrangement of tubulin genes important with respect to gene expression.

RESULTS

We investigated the genomic architecture of tubulin tandem arrays among these parasites, establishing which character state is derived, and the timing of character transition. Tubulin loci in T. brucei and L. major were compared to examine the relationship between the two character states. Intergenic regions between tubulin genes were sequenced from several trypanosomatids and related, non-parasitic bodonids to identify the ancestral state. Evidence of alternating arrays was found among non-parasitic kinetoplastids and all Trypanosoma spp.; monotypic arrays were confirmed in all Leishmania spp. and close relatives.

CONCLUSION

Alternating and monotypic tubulin arrays were found to be mutually exclusive through comparison of genome sequences. The presence of alternating gene arrays in non-parasitic kinetoplastids confirmed that separate, monotypic arrays are the derived state and evolved through genomic restructuring in the lineage leading to Leishmania. This fundamental reorganisation accounted for the dissimilar genomic architectures of T. brucei and L. major tubulin repertoires.

Life-cycle and growth-phase-dependent regulation of the ubiquitin genes of Trypanosoma cruzi

BACKGROUND

Trypanosoma cruzi, the causative agent of Chagas disease, exhibits a complex life cycle that is accompanied by the stage-specific gene expression. At the molecular level, very little is known about gene regulation in trypanosomes. Complex gene organizations coupled with polycistronic transcription units make the analysis of regulated gene expression difficult in trypanosomes. The ubiquitin genes of T. cruzi are a good example of this complexity. They are organized as a single cluster containing five ubiquitin fusion (FUS) and five polyubiquitin (PUB) genes that are polycistronically transcribed but expressed differently in response to developmental and environmental changes.

METHODS

Gene replacements were used to study FUS and PUB gene expression at different stages of growth and at different points in the life cycle of T. cruzi.

RESULTS

Based on the levels of reporter gene expression, it was determined that FUS1 expression was downregulated as the parasites approached stationary phase, whereas PUB12.5 polyubiquitin gene expression increased. Conversely, FUS1 expression increases when epimastigotes and amastigotes differentiate into trypomastigotes, whereas the expression of PUB12.5 decreases when epimastigotes differentiate into amastigotes and trypomastigotes.

CONCLUSIONS

Although the level of CAT activity in logarithmic growing epimastigotes is six- to seven-fold higher when the gene was expressed from the FUS1 locus than when expressed from the PUB12.5 locus, the rate of transcription from the two loci was the same implying that post-transcriptional mechanisms play a dominant role in the regulation of gene expression.

Transcription in kinetoplastid protozoa: why be normal?

Transcription in the kinetoplastid protozoa shows substantial variation from the paradigms of eukaryotic gene expression, including polycistronic transcription, a paucity of RNA polymerase (RNAP) II promoters, no qualitative regulated transcription initiation for most protein-coding genes, transcription of some protein-coding genes by RNAP I, an exclusive subnuclear location for VSG transcription, the dependence of small nuclear RNA gene transcription on an upstream tRNA gene, and the synthesis of mitochondrial tRNAs in the nucleus. Here, we present a broad overview of what is known about transcription in the kinetoplastids and what has yet to be determined.

Alternative splicing of LYT1 transcripts in Trypanosoma cruzi

As a result of alternative trans splicing, three distinct LYT1 mRNAs are produced in Trypanosoma cruzi, two encoding the full-length LYT1 protein and the third encoding a truncated LYT1 protein lacking a possible signal sequence. Analysis of the three mRNAs in different developmental forms of the parasite revealed that the alternative processing events were regulated differently during the parasite life cycle.

Uniform distribution of transcription complexes over the entire Leishmania donovani clpB (hsp 100) gene locus

We have analyzed the RNA polymerase density on the Leishmania donovani clpB gene locus. Our results show an even distribution of RNA polymerase over the clpB locus indicating an undiscriminative transcription. We conclude that, unlike the hsp70 genes, the clpB gene is not transcribed individually, but rather as part of a larger, polycistronic transcription unit.

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.

Transcription of the Leishmania major Hsp70-I gene locus does not proceed through the noncoding region

Primary transcripts in kinetoplastid protozoa are generally assumed to be multicistronic. We have analyzed the transcription in the gene locus which encodes the 70-kDa heat shock protein by using nuclear run-on analysis. We find that RNA synthesis in the Hsp70-I gene locus either is terminated or pauses within the intergenic region approximately 250 nt downstream of the polyadenylation site. We therefore propose a discontinuous mode of transcription in the Hsp70 genes of Leishmania major.

gamma-tubulin in trypanosomes: molecular characterisation and localisation to multiple and diverse microtubule organising centres

A genomic clone from Trypanosoma brucei, which contains a full length gamma-tubulin gene, was isolated using degenerate oligonucleotide primers. The sequence of this clone predicts a protein of 447 amino acids having a high degree of homology with gamma-tubulins from human and Xenopus laevis (67.2% amino acid identity) and only 57.7% identity with the Plasmodium falciparum gamma-tubulin. Northern blot analysis of poly(A)+ selected RNA from a procyclic culture detects a major transcript of approximately 2.2 kb plus a minor transcript of approximately 3.6 kb. A fusion protein comprising almost the full length gamma-tubulin gene product (amino acids 8–447) plus an amino-terminal histidine tag has been expressed and purified from Escherichia coli and used to raise a polyclonal antibody. Immunofluorescence, using this antibody, shows classical centrosomal localisation in mammalian cells. In T. brucei gamma-tubulin is present in the basal bodies which subtend the flagellum and also at the anterior tip of the cell body where many minus ends of microtubules are located. Furthermore the antibody reveals a small subset of the sub-pellicular microtubules and a discrete dot within the nucleus which alters form with progression through the mitotic cycle. Evidence is also presented for discrete punctate staining within the microtubules of the cell body which may represent the presence of gamma-tubulin on the ends of individual microtubules. Our results indicate that gamma-tubulin is associated with diverse microtubule organising centres and structures in trypanosomes.

An RNA polymerase II promoter in the hsp70 locus of Trypanosoma brucei

To study of structure of RNA polymerase (pol) II transcription units a nd the influence of temperature on the regulation of gene expression in Trypanosoma brucei, and hsp70 intergenic region promoter was characterized. In T. brucei, the hsp70 locus contains, from 5' to 3', a cognate hsp70-related gene (gene 1) which is separated by about 6 kb of DNA from a cluster of five identical hsp70 genes (genes 2 to 6). Transcription proceeds on the entire 23-kb locus, and polycistronic transcription occurs in hsp70 genes 2 to 6. Transcription of hsp70 genes 2 to 6 is only moderately sensitive to UV irradiation, indicating that it cannot be driven by a single far-upstream promoter, which suggests that promoters could be located in the region close to the hsp70 coding region. Transient transformations demonstrated that sequences located upstream of hsp70 gene 2 and in the intergenic region between hsp70 genes 2 and 3 are able to direct transcription of the reporter gene, the chloramphenicol acetyltransferase (CAT) gene. The plasmid DNA driven by the hsp70 intergenic region promoter gave CAT activity approximately 85-fold above to background level. This is equivalent to approximately 1% of that derived from a CAT plasmid driven by the procyclic acidic repetitive protein gene promoter, which is controlled by RNA pol I. The hsp70 intergenic region promoter can drive alpha-amanitin-sensitive transcription at an internal position of the chromosome as well as an episome, suggesting that it is controlled by RNA pol II. However, this hsp70 intergenic region promoter, along with the 3' splice site and the 5' untranslated region of the hsp70 genes that controls the transcription of the reporter gene, cannot up-regulate the expression of the reporter gene during heat shock. This result is consistent with the previous observation that expression of the hsp70 genes in T. brucei is mainly controlled at the posttranscriptional level.

Mechanisms of stage-regulated gene expression in kinetoplastida

During their life cycle, trypanosomatid parasites of mammals encounter substantially different environments in their hosts and insect vectors, to which they must adapt by undergoing a series of differentiation processes. At the molecular level, these processes must be the direct result of an elaborate series of changes in stage-regulated expression of a wide range of gene products. How are these changes accomplished? In this review, Sheila Graham discusses some recent advances in understanding the mechanisms of gene expression in trypanosomatids, and examines some clues to some intriguingly complex means of regulating life cycle stage-specific gene expression.

A foreign transcription unit in the inactivated VSG gene expression site of the procyclic form of Trypanosoma brucei and formation of large episomes in stably transformed trypanosomes

Transcription of the variant surface glycoprotein (VSG) gene expression site (ES) in Trypanosoma brucei is inactivated upon differentiation from the bloodstream form to the insect-adapted, procyclic form. This paper demonstrates that a foreign transcription unit, containing a procyclic acidic repetitive protein (PARP) gene promoter driving a neomycin phosphotransferase (neo) gene, can be fully active once integrated at the lingering, transcriptionally inactive VSG ES of procyclic trypanosomes. Following targeting into the ES two types of transformants were identified. Type one transformants were generated by integration of the PARP-neo gene into the region downstream of the long 70-bp repeat array of the silent telomeric ES encoding VSG gene 118. alpha-amanitin-resistant transcription at the neo locus proceeded from the PARP promoter to approximately 2.5 kb downstream of the integration site and terminated in front of the VSG 118 gene. Type two transformants contained variously sized large episomes (ranging from 135 kb to 500 kb), consisting of tandemly linked input plasmids. Transcription of the neo gene in the episomes was also resistant to alpha-amanitin. The presence of large amounts of the active episomal PARP promoter did not significantly affect the transcription of most RNA polymerase II transcribed genes, but resulted in a significant and equal reduction of the transcriptional efficiency of the endogenous PARP genes and VSG gene promoter sequences. This observation suggests that transcription of the PARP gene and the VSG gene expression sites in insect form trypanosomes may share a common transcriptional machinery.

Alternative splicing within and between alleles of the ATPase gene 1 locus of Trypanosoma brucei

The P-type ATPase gene TBA1 of Trypanosoma brucei belongs to a polycistronic transcription unit. We analyzed the structure and expression of a 4-kb region located immediately downstream from TBA1. This region is unique and contains two large open reading frames transcribed into stable mRNAs. These putative genes, termed ADG1 and ADG2, can respectively encode a 24-kDa and a 81-kDa protein. The intergenic spacings between the polyadenylation sites and the next 3' splice acceptor sites are very short: 148 bp between TBA1 and ADG1, and 127 bp between ADG1 and ADG2. Transcripts from each of the two ADG1 alleles can be detected, indicating that both homologs are transcribed. These transcripts are differentially spliced due to a single base difference which destroys in one homolog the AG acceptor site present in the other. In the 'mutant' allele an alternative downstream splice acceptor site is used. Despite its sequence conservation in both alleles, this splice site is only used in the allele lacking the upstream AG acceptor site. The major population of ADG1 transcripts exhibit a long 5'-untranslated extension and no 3'-terminal tail, but a minor population shows a smaller 5'-untranslated region due alternative splicing closer to the initiation codon of the gene. The steady-state amounts of transcripts from individual genes in this region are differentially stage-regulated.

Using simultaneous, tandem gene replacements to study expression of the multicopy ubiquitin-fusion (FUS) gene family of Trypanosoma cruzi

Many genes in trypanosomes exist as members of multicopy gene families. Due to this fact it is frequently difficult to determine if specific members of a gene family are expressed. We describe here a strategy for simultaneous tandem gene replacement in T. cruzi which leads to the replacement of the gene of interest by a silent reporter gene, the expression of which can be assayed in stable transformants. To determine if the FUS1 gene (one of 5 copies of the ubiquitin-fusion, FUS, gene family) was expressed, stable G418-resistant transformants were isolated in which the tandemly arrayed CUB2.65 and FUS1 genes were precisely replaced by the neomycin phosphotransferase (neo(r)) and chloramphenicol acetyltransferase (CAT) genes, respectively. All stable clones carrying the tandem gene replacements were shown to express the CAT activity indicating that FUS1 is expressed in mid-log epimastigotes. Northern blot analysis of parasites carrying the tandem gene replacements indicated that at least one other member of the FUS gene family is expressed and that there were no apparent polar effects on the expression of genes downstream of the replacement events. These experiments have demonstrated the utility of tandem gene replacements as a means of inserting a nonselected reporter gene into the chromosome, facilitating the molecular genetic analysis of the expression of multicopy gene families.

Differential regulation of two distinct families of glucose transporter genes in Trypanosoma brucei

A tandemly arranged multigene family encoding putative hexose transporters in Trypanosoma brucei has been characterized. It is composed of two 80% homologous groups of genes called THT1 (six copies) and THT2 (five copies). When Xenopus oocytes are microinjected with in vitro-transcribed RNA from a THT1 gene, they express a glucose transporter with properties similar to those of the trypanosome bloodstream-form protein(s). This THT1-encoded transport system for glucose differs from the human erythrocyte-type glucose transporter by its moderate sensitivity to cytochalasin B and its capacity to transport D-fructose. These properties suggest that the trypanosomal transporter may be a good target for antitrypanosomal drugs. mRNA analysis revealed that expression of these genes was life cycle stage dependent. Bloodstream forms express 40-fold more THT1 than THT2. In contrast, procyclic trypanosomes express no detectable THT1 but demonstrate glucose-dependent expression of THT2.

Differential regulation of two distinct families of glucose transporter genes in Trypanosoma brucei

A tandemly arranged multigene family encoding putative hexose transporters in Trypanosoma brucei has been characterized. It is composed of two 80% homologous groups of genes called THT1 (six copies) and THT2 (five copies). When Xenopus oocytes are microinjected with in vitro-transcribed RNA from a THT1 gene, they express a glucose transporter with properties similar to those of the trypanosome bloodstream-form protein(s). This THT1-encoded transport system for glucose differs from the human erythrocyte-type glucose transporter by its moderate sensitivity to cytochalasin B and its capacity to transport D-fructose. These properties suggest that the trypanosomal transporter may be a good target for antitrypanosomal drugs. mRNA analysis revealed that expression of these genes was life cycle stage dependent. Bloodstream forms express 40-fold more THT1 than THT2. In contrast, procyclic trypanosomes express no detectable THT1 but demonstrate glucose-dependent expression of THT2.

Evolution of the retrotransposons TRS/ingi and of the tubulin genes in trypanosomes

The African trypanosomes have genomes of high plasticity, as demonstrated for instance by their ability to shuffle their genes around, coding for variant-specific surface glycoproteins (VSGs). Another indication of their genome plasticity is the presence of multiple retro-elements. The retrotransposon-like element TRS/ingi is present in many copies in the genome of trypanosomes. One particular derivative of TRS/ingi, called TUBIS, had previously been found to interrupt a tubulin gene in a particular strain of T. brucei. Here both TRS/ingi and TUBIS were studied by hybridizing genomic DNA of various strains and species of trypanosomes with suitable probes in order to elucidate the evolution of this family of retro-elements. The TSR/ingi elements are highly repeated and have very long open reading frames, while TUBIS clearly is a truncated, inactivated form of this element, found in only one particular chromosomal location. Both elements were shown to be present in several strains and species of the subgenus Trypanozoon, in particular in T. brucei brucei, T. gambiense, T. rhodesiense, T. equiperdum and T. evansi. They could not be detected in species of other subgenera, in particular in T. congolense and T. cruzi. These findings suggest that the retrotransposon TRS/ingi was acquired by trypanosomes only after divergence of present day subgenera. The TUBIS element was found in exactly the same chromosomal location (at the 3' end of the tubulin gene cluster) in many different strains and species of the subgenus Trypanozoon. This shows that the element was transposed to this location before speciation of the subgenus. Although, TRS/ingi is unlikely to be involved directly in VSG switching, it may have contributed to the genome plasticity of trypanosomes.

Gene expression in Leishmania: analysis of essential 5' DNA sequences

A major unanswered question in Kinetoplastida parasites is the mechanism of regulating gene expression. Using a transfection system, we have previously shown that the intergenic region of the alpha-tubulin gene of Leishmania enriettii contained sequences required for gene expression. The goal of the work reported here was to determine whether the Leishmania-derived sequences were providing transcriptional control signals or functioning at a post-transcriptional level, most likely in trans-splicing. The chloramphenicol acetyltransferase (cat) gene was used as the reporter gene and was stably introduced into L. enriettii as part of an extrachromosomal element by transfection. We show here that the production of cat mRNA was dramatically dependent on the presence of the intergenic region 5' to the cat gene. The intergenic region could be substituted by a smaller fragment (222 base pairs) that contained the trans-splice acceptor site and an adjacent polypyrimidine tract. This native fragment could be replaced by a synthetic polypyrimidine tract containing an AG site. The native and the synthetic fragments had unidirectional activity. No effect on transcription of the cat gene by the wild-type fragment or the synthetic polypyrimidine was detected. The results indicate that both regions contain signals that affect RNA stability, probably sequences involved in trans-splicing.

Structure and transcription of a P-ATPase gene from Trypanosoma brucei

A putative ATPase gene was cloned from Trypanosoma brucei genomic DNA. The length of the gene open reading frame is 3,033 bp, predicting a protein of about 110 kDa. The sequence of this protein shares 10 blocks of homology with other eukaryotic ATPases, including the putative phosphorylation site characteristic of P-ATPases. Its hydropathy profile reveals 8-10 potential membrane-spanning regions. While the amino acid sequence of the T. brucei ATPase shows only 25% overall homology with its counterpart from the related kinetoplastid protozoan Leishmania donovani, 49% sequence conservation is found when compared with the calcium-ATPase from rabbit sarcoplasmic reticulum. This gene is present in only one copy, localized in the large chromosome fraction. It is transcribed at a similar level in procyclic and bloodstream forms, as a 4.3-kb mRNA. Run-on assays suggest continuous transcription of the gene and flanking sequences over at least 10 kb, by a RNA polymerase sensitive to alpha-amanitin. Transcription inhibition by UV irradiation suggests that the ATPase gene is more than 4 kb downstream from its promoter.

Stable integrative transformation of Trypanosoma brucei that occurs exclusively by homologous recombination

A calmodulin-neomycin-resistance fusion gene was introduced into Trypanosoma brucei by electroporation, and stably transformed cell lines were obtained. In all of the transformants, the fusion gene had integrated into the host genome at the cognate locus, evidently by homologous recombination within flanking calmodulin DNA. This unusual observation distinguishes trypanosomes as the only eukaryote other than yeast known to undergo gene targeting in essentially 100% of the stable transformants. It should now be possible to systematically manipulate the trypanosome genome, directing predetermined mutations to virtually any chromosomal locus.

Transient activity assays of the Trypanosoma brucei variant surface glycoprotein gene promoter: control of gene expression at the posttranscriptional level

The putative promoter of the variant surface glycoprotein (VSG) gene of Trypanosoma brucei was cloned into a plasmid containing the chloramphenicol acetyltransferase (CAT) gene. After electroporation into trypanosomes, this construct directed the expression of the CAT reporter gene. The essential region for promoter activity was found to reside within 88 bp upstream of the putative transcription start site. Transcription of the CAT construct occurred at approximately the same level in both bloodstream and procyclic forms and was resistant to alpha-amanitin. However, CAT expression appeared to be modulated in the two forms of the parasite. Sequences 3' to the gene seemed to be important in this respect, as CAT activity in bloodstream forms was readily detectable only when the 3' region of a VSG cDNA was placed downstream of the CAT gene. Two separate VSG gene promoter sequences, both cloned from T. brucei AnTat 1.3A, were equally able to direct CAT expression, which suggests that there are a number of potential VSG gene promoters in the genome, although usually only one expression site is fully active at any one time.

Transient activity assays of the Trypanosoma brucei variant surface glycoprotein gene promoter: control of gene expression at the posttranscriptional level

The putative promoter of the variant surface glycoprotein (VSG) gene of Trypanosoma brucei was cloned into a plasmid containing the chloramphenicol acetyltransferase (CAT) gene. After electroporation into trypanosomes, this construct directed the expression of the CAT reporter gene. The essential region for promoter activity was found to reside within 88 bp upstream of the putative transcription start site. Transcription of the CAT construct occurred at approximately the same level in both bloodstream and procyclic forms and was resistant to alpha-amanitin. However, CAT expression appeared to be modulated in the two forms of the parasite. Sequences 3' to the gene seemed to be important in this respect, as CAT activity in bloodstream forms was readily detectable only when the 3' region of a VSG cDNA was placed downstream of the CAT gene. Two separate VSG gene promoter sequences, both cloned from T. brucei AnTat 1.3A, were equally able to direct CAT expression, which suggests that there are a number of potential VSG gene promoters in the genome, although usually only one expression site is fully active at any one time.

Differential expression of a family of putative adenylate/guanylate cyclase genes in Trypanosoma brucei

The expression site for the variant surface glycoprotein (VSG) gene of Trypanosoma brucei contains several genes of unknown function (ESAGs, for expression site-associated genes). Among these, ESAG 4 shows homology to eukaryotic adenylate/guanylate cyclase genes, in the region encoding the presumptive enzyme catalytic domain. This gene belongs to a family of related sequences, and hybridizes to the genomic DNA of other trypanosomatids, such as Trypanosoma congolense, Trypanosoma vivax and Trypanosoma mega. While ESAG 4 is transcribed only in bloodstream forms by a RNA polymerase resistant to alpha-amanitin, at least three other members of this family are transcribed in both bloodstream and procyclic forms, by a RNA polymerase sensitive to the drug. These genes encode different putative transmembrane proteins showing high sequence conservation in the region corresponding to the adenylate/guanylate cyclase catalytic domain.

The Trypanosoma brucei protein phosphatase gene: polycistronic transcription with the RNA polymerase II largest subunit gene

We have previously described the trypanosomal gene encoding the largest subunit of RNA polymerase II (RNAP II) and found that two almost identical genes are encoded within the Trypanosoma brucei genome. Here we show by Southern analyses that the 5' breakpoint between both loci is located approximately 7.5 kb upstream of the RNAP II genes. Northern analyses revealed that the 5' duplicated segment contains at least four other genes, which are transcribed in both bloodstream and procyclic trypanosomes. The gene located immediately upstream of the RNAP II gene in both loci was characterized by sequence analyses. The deduced amino acid sequences show a high degree of similarity to the catalytic subunit of protein phosphatase class 1 (PP1) genes. S1 mapping provided strong evidence in support of the fact that the PP1 and RNAP II genes belong to a single transcription unit.

The new trypanosomatid genetics

The recent development of transfection systems for trypanosomatids has removed a major obstacle to research and provides an important tool for the biochemist, immunologist and molecular biologist. Obtaining expression of a foreign gene in a trypanosomatid has been difficult. In this review, Vivian Bellofatto describes the problems and pitfalls of the process and final successes achieved.

Linkage of the calmodulin and ubiquitin loci in Trypanosoma cruzi

We describe here the organization of the calmodulin genes of Trypanosoma cruzi and their linkage to the ubiquitin gene family. The nucleotide sequence of the CalA2 gene has been determined and is 85% homologous to the protein coding sequence of the calmodulin genes of the African trypanosome, Trypanosoma brucei. The proteins encoded by CalA2 and the T. brucei genes contain a single mismatch out of a total of 149 amino acids. The genome of T. cruzi contains eight calmodulin genes present at two distinct loci (2.8 and 2.65) each of which is linked to downstream ubiquitin genes. Within each locus two calmodulin gene families have been defined, CalA and CalB. Each calmodulin locus consist of alternating tandem arrays of the CalA and CalB genes. Both 2.8 and 2.65 calmodulin loci and their respective downstream ubiquitin genes share the same DNA coding strand. Transcription of the calmodulin genes in the epimastigote stage of T. cruzi results in the generation of two stable mRNAs of 1.6Kb and 1.1Kb.

Identification and characterisation of a Leishmania donovani antigen belonging to the 70-kDa heat-shock protein family

A Leishmania donovani promastigote cDNA library was screened with serum obtained from a patient infected with visceral leishmaniasis. Sequence analysis of a clone obtained from this library revealed that the 600-bp insert corresponded to the carboxy-terminal region of an antigen related to the 70-kDa heat-shock protein family. The full-length sequence of the corresponding gene (1959 nucleotides) was determined after isolation of genomic clones. Genes encoding the antigen are present on a single chromosome as a series of approximately twelve 3.7-kb direct tandem repeats. The antigen can be identified as a 70-kDa heat-shock cognate protein by virtue of its molecular mass, sequence and constitutive expression during heat shock. It is expressed at all stages of the parasite life-cycle. Antibodies against the lambda gt11 fusion protein were detected in more than 50% of serum samples obtained from patients with visceral leishmaniasis, but were not detected in sera from patients with cutaneous leishmaniasis or Chagas' disease.

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.