Protein stability regulates the expression of cytochrome c during the developmental cycle of Trypanosoma brucei

Insights on a putative aminoacyl-tRNA-protein transferase of Leishmania major

The N-end rule pathway leads to regulated proteolysis as an adaptive response to external stress and is ubiquitous from bacteria to mammals. In this study, we investigated a gene coding for a putative core enzyme of this post-translational regulatory pathway in Leishmania major, which may be crucial during cytodifferentiation and the environment adaptive responses of the parasite. Leucyl, phenylalanyl-tRNA protein transferase and arginyl-tRNA protein transferase are key components of this pathway in E. coli and eukaryotes, respectively. They catalyze the specific conjugation of leucine, phenylalanine or arginine to proteins containing exposed N-terminal amino acid residues, which are recognized by the machinery for the targeted proteolysis. Here, we characterized a conserved hypothetical protein coded by the LmjF.21.0725 gene in L. major. In silico analysis suggests that the LmjF.21.0725 protein is highly conserved among species of Leishmania and might belong to the Acyl CoA-N-acyltransferases (NAT) superfamily of proteins. Immunofluorescence cell imaging indicates that the cytosolic localization of the studied protein and the endogenous levels of the protein in promastigotes are barely detectable by western blotting assay. The knockout of the two alleles of LmjF.21.0725 by homologous recombination was only possible in the heterozygous transfectant expressing LmjF.21.0725 as a transgene from a plasmid. Moreover, the kinetics of loss of the plasmid in the absence of drug pressure suggests that maintenance of the gene is essential for promastigote survival. Here, evidence is provided that this putative aminoacyl tRNA-protein transferase is essential for parasite survival. The enzyme activity and corresponding post-translational regulatory pathway are yet to be investigated.

High-throughput Methods for Dissection of Trypanosome Gene Regulatory Networks

From synthesis to decay, mRNA associates with RNA-binding proteins (RBPs) establishing dynamic ribonucleoprotein particles (RNPs). Understanding the composition and function of RNPs is fundamental to understanding how eukaryotic mRNAs are controlled. This is especially relevant for trypanosomes and related kinetoplastid parasites, which mostly rely on post-transcriptional mechanisms to control gene expression. Crucial for trypanosome differentiation, development, or even response to heat shock, RBPs are known to be essential modulators of diverse molecular processes. The recent application of large-scale quantitative methods, such as Next-Generation Sequencing (NGS) and quantitative mass spectrometry, has revealed new exciting features about the parasite RNA-related metabolism. Novel proteins carrying RNA-binding activity, including many proteins without RNA-related ontology were discovered setting a necessary groundwork to get in insights into RNA biology.

Conclusion: This review aims to give the reader an understanding of current trypanosome RNP research, highlighting the progress made using high-throughput approaches.

Integrative analysis of the Trypanosoma brucei gene expression cascade predicts differential regulation of mRNA processing and unusual control of ribosomal protein expression

Background

Trypanosoma brucei is a unicellular parasite which multiplies in mammals (bloodstream form) and Tsetse flies (procyclic form). Trypanosome RNA polymerase II transcription is polycistronic, individual mRNAs being excised by trans splicing and polyadenylation. We previously made detailed measurements of mRNA half-lives in bloodstream and procyclic forms, and developed a mathematical model of gene expression for bloodstream forms. At the whole transcriptome level, many bloodstream-form mRNAs were less abundant than was predicted by the model.

Results

We refined the published mathematical model and extended it to the procyclic form. We used the model, together with known mRNA half-lives, to predict the abundances of individual mRNAs, assuming rapid, unregulated mRNA processing; then we compared the results with measured mRNA abundances. Remarkably, the abundances of most mRNAs in procyclic forms are predicted quite well by the model, being largely explained by variations in mRNA decay rates and length. In bloodstream forms substantially more mRNAs are less abundant than predicted. We list mRNAs that are likely to show particularly slow or inefficient processing, either in both forms or with developmental regulation. We also measured ribosome occupancies of all mRNAs in trypanosomes grown in the same conditions as were used to measure mRNA turnover. In procyclic forms there was a weak positive correlation between ribosome density and mRNA half-life, suggesting cross-talk between translation and mRNA decay; ribosome density was related to the proportion of the mRNA on polysomes, indicating control of translation initiation. Ribosomal protein mRNAs in procyclics appeared to be exceptionally rapidly processed but poorly translated.

Conclusions

Levels of mRNAs in procyclic form trypanosomes are determined mainly by length and mRNA decay, with some control of precursor processing. In bloodstream forms variations in nuclear events play a larger role in transcriptome regulation, suggesting aquisition of new control mechanisms during adaptation to mammalian parasitism.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2624-3) contains supplementary material, which is available to authorized users.

Targeting the substrate preference of a type I nitroreductase to develop antitrypanosomal quinone-based prodrugs

Nitroheterocyclic prodrugs are used to treat infections caused by Trypanosoma cruzi and Trypanosoma brucei. A key component in selectivity involves a specific activation step mediated by a protein homologous with type I nitroreductases, enzymes found predominantly in prokaryotes. Using data from determinations based on flavin cofactor, oxygen-insensitive activity, substrate range, and inhibition profiles, we demonstrate that NTRs from T. cruzi and T. brucei display many characteristics of their bacterial counterparts. Intriguingly, both enzymes preferentially use NADH and quinones as the electron donor and acceptor, respectively, suggesting that they may function as NADH:ubiquinone oxidoreductases in the parasite mitochondrion. We exploited this preference to determine the trypanocidal activity of a library of aziridinyl benzoquinones against bloodstream-form T. brucei. Biochemical screens using recombinant NTR demonstrated that several quinones were effective substrates for the parasite enzyme, having K(cat)/K(m) values 2 orders of magnitude greater than those of nifurtimox and benznidazole. In tests against T. brucei, antiparasitic activity mirrored the biochemical data, with the most potent compounds generally being preferred enzyme substrates. Trypanocidal activity was shown to be NTR dependent, as parasites with elevated levels of this enzyme were hypersensitive to the aziridinyl agent. By unraveling the biochemical characteristics exhibited by the trypanosomal NTRs, we have shown that quinone-based compounds represent a class of trypanocidal compound.

Regulated expression of an essential allosteric activator of polyamine biosynthesis in African trypanosomes

Trypanosoma brucei is the causative agent of African sleeping sickness. The polyamine biosynthetic pathway has the distinction of being the target of the only clinically proven anti-trypanosomal drug with a known mechanism of action. Polyamines are essential for cell growth, and their metabolism is extensively regulated. However, trypanosomatids appear to lack the regulatory control mechanisms described in other eukaryotic cells. In T. brucei, S-adenosylmethionine decarboxylase (AdoMetDC) and ornithine decarboxylase (ODC) are required for the synthesis of polyamines and also for the unique redox-cofactor trypanothione. Further, trypanosomatid AdoMetDC is activated by heterodimer formation with a catalytically dead homolog termed prozyme, found only in these species. To study polyamine regulation in T. brucei, we generated inducible AdoMetDC RNAi and prozyme conditional knockouts in the mammalian blood form stage. Depletion of either protein led to a reduction in spermidine and trypanothione and to parasite death, demonstrating that prozyme activation of AdoMetDC is essential. Under typical growth conditions, prozyme concentration is limiting in comparison to AdoMetDC. However, both prozyme and ODC protein levels were significantly increased relative to stable transcript levels by knockdown of AdoMetDC or its chemical inhibition. Changes in protein stability do not appear to account for the increased steady-state protein levels, as both enzymes are stable in the presence of cycloheximide. These observations suggest that prozyme and ODC are translationally regulated in response to perturbations in the pathway. In conclusion, we describe the first evidence for regulation of polyamine biosynthesis in T. brucei and we demonstrate that the unique regulatory subunit of AdoMetDC is a key component of this regulation. The data support ODC and AdoMetDC as the key control points in the pathway and the likely rate-limiting steps in polyamine biosynthesis.

Post-transcriptional regulation of gene expression in trypanosomes and leishmanias

Gene expression in Kinetoplastids is very unusual in that the open reading frames are arranged in long polycistronic arrays, monocistronic mRNAs being created by post-transcriptional processing. Thus the regulation of gene expression is post-transcriptional. We here discuss recent results concerning the enzymes required for mRNA degradation, and components of the translation initiation machinery, and how both are regulated.

Characterization and developmentally regulated localization of the mitochondrial carrier protein homologue MCP6 from Trypanosoma brucei

Proteins of the mitochondrial carrier family (MCF) are located mainly in the inner mitochondrial membrane and mediate the transport of a large range of metabolic intermediates. The genome of Trypanosoma brucei harbors 29 genes encoding different MCF proteins. We describe here the characterization of MCP6, a novel T. brucei MCF protein. Sequence comparison and phylogenetic reconstruction revealed that MCP6 is closely related to different mitochondrial ADP/ATP and calcium-dependent solute carriers, including the ATP-Mg/Pi carrier of Homo sapiens. However, MCP6 lacks essential amino acids and sequence motifs conserved in these metabolite transporters, and functional reconstitution and transport assays with E. coli suggested that this protein indeed does not function as an ADP/ATP or ATP-Mg/Pi carrier. The subcellular localization of MCP6 is developmentally regulated: in bloodstream-form trypanosomes, the protein is predominantly glycosomal, whereas in the procyclic form, it is found mainly in the mitochondria. Depletion of MCP6 in procyclic trypanosomes resulted in growth inhibition, an increased cell size, aberrant numbers of nuclei and kinetoplasts, and abnormal kinetoplast morphology, suggesting that depletion of MCP6 inhibits division of the kinetoplast.

The RACK1 homologue from Trypanosoma brucei is required for the onset and progression of cytokinesis

The receptor for activated C kinase 1 (RACK1) is a conserved scaffold protein that helps regulate a range of cell activities including cell growth, shape, and protein translation. We report that a homologue of RACK1 is required for cytokinesis in pathogenic Trypanosoma brucei. The protein, referred to as TRACK, is comprised of WD repeat elements and can complement cpc2 null mutants of Schizosaccharomyces pombe. TRACK is expressed throughout the trypanosome life cycle and is distributed predominantly in a perinuclear region and the cytoplasm but not along the endoplasmic reticulum, mitochondrion, or cleavage furrow of dividing cells. When tetracycline-inducible RNA interference (RNAi) is used to deplete the cellular content of TRACK, the cells remain metabolically active, but growth is inhibited. In bloodstream forms, growth arrest is due to a delay in the onset of cytokinesis. By contrast, procyclic forms are able to initiate cytokinesis in the absence of TRACK but arrest midway through cell cleavage. The RNAi cells undergo multiple rounds of partial cytokinesis and accumulate nuclei and cytoplasmic extensions with attached flagella. The TRACK RNAi construct is also inducible within infected mice. Under these conditions parasites are eliminated from peripheral blood within 3 days post-infection. Taken as a whole, these data indicate that trypanosomes utilize a RACK1 homologue to regulate the final stages of mitosis. Moreover, disrupting the interaction between TRACK and its partners might be targeted in the design of novel therapies.

Import and assembly of Neurospora crassa Tom40 into mitochondria of Trypanosoma brucei in vivo

The TOM complex (translocase of the mitochondrial outer membrane) is a dynamic, multisubunit protein complex. Tom40 is the major component of the complex and forms the preprotein conducting pore. To determine if a heterologous Tom40 could be properly targeted and assembled into the Trypanosoma brucei mitochondrial outer membrane, an ectopic copy of a gene encoding Neurospora crassa Tom40 (NcTom40) was expressed in procyclic trypanosomes from a tetracycline regulated procyclic acidic repetitive protein promoter. The level of NcTom40 expression was found to be maximal within 20-26 h of induction with tetracycline. Immunoblot analysis of subcellular fractions showed that NcTom40 was enriched in the mitochondrial fraction. Alkali extraction of isolated mitochondria revealed that NcTom40 was assembled as an integral membrane protein and limited proteolysis demonstrated that it was present in the outer membrane of the mitochondria. These data demonstrate that a heterologous mitochondrial protein containing internal targeting information can be correctly targeted to T. brucei mitochondria. Following blue native gel electrophoresis, the NcTom40 protein was found in a 370 kDa complex which may contain T. brucei Tom components. A 16 kDa protein was coimmunoprecipitated from T. brucei mitochondria containing NcTom40 using antisera developed against the N. crassa protein. The 16 kDa protein may represent a component of the T. brucei TOM complex that associates with NcTom40.

Stage-specific translational efficiency and protein stability regulate the developmental expression of p37, an RNA binding protein from Trypanosoma brucei

We have previously characterized two novel RNA binding proteins, p34 and p37, from Trypanosoma brucei. Their sequences do not show significant homology to other proteins but are highly homologous to one another. The p34 and p37 proteins are developmentally regulated, with p34 the predominant protein in the procyclic stage and p37 nearly exclusively expressed in the bloodstream cells. In vivo metabolic labeling of procyclic cells showed that p34 and p37 were differentially translated, with levels of p34 approximately fourfold higher than p37. The newly synthesized p34 and p37 exhibited differential stability in the procyclic stage. In vitro analysis confirmed this observation and further suggested that this differential stability may be due to a trypsin-like cysteine protease activity in procyclic extracts that selectively degraded the p37 protein. Taken together, these results indicate that the developmental regulation of the T. brucei RNA binding protein, p37, occurs at both translational and post-translational levels.

Trypanosome alternative oxidase is regulated post-transcriptionally at the level of RNA stability

In the bloodstream form of African trypanosomes, trypanosome alternative oxidase (TAO), the non-cytochrome ubiquinol:oxidoreductase, is the only terminal oxidase of the mitochondrial electron transport system. TAO is developmentally regulated during mitochondrial biogenesis in this parasite. During in vitro differentiation of Trypanosoma brucei from the bloodstream to the procyclic form, the overall rate of oxygen consumption decreased about 80%. The mode of respiration changed over a 2- to 3-wk period from a cyanide-insensitive, SHAM-sensitive pathway to a predominantly cyanide-sensitive pathway. The TAO protein level gradually decreased to the level present in the procyclic forms during this 3-wk period. However, within the first week of differentiation, the TAO transcript level decreased about 90% and then in the following weeks it reached the level present in the established procyclic form, that is about 20% of that in bloodstream forms. Like other trypanosomatid genes TAO transcript synthesis remains unaltered in fully differentiated bloodstream and procyclic trypanosomes. The half-life of the TAO mRNA was about 3.2 h in the procyclic trypanosomes, whereas the TAO transcript level remained unaltered even after 4 h of incubation with actinomycin D in bloodstream forms. Inhibition of protein synthesis resulted in about a four-fold accumulation of the TAO transcript in the procyclic trypanosomes, comparable to the level present in the bloodstream forms. Thus, TAO is regulated at the level of mRNA stability and de novo protein synthesis is required for the reduction of the TAO mRNA pool in the procyclic form.

Unique aspects of mitochondrial biogenesis in trypanosomatids

Mitochondrial biogenesis consists of the sum of all processes required for the formation of the mitochondrial membranes as well as the soluble compartments they contain. Furthermore, it includes the replication of the mitochondrial genome and correct segregation of the organelles during cell division. Mitochondrial proteins come from two sources, a limited but essential set of inner membrane proteins is encoded by the mitochondrial genome, whereas the large majority (90-95%) is derived from nucleus-encoded genes and are posttranslationally imported into the organelle. Trypanosomatids belong to the earliest diverging branches of the eukaryotic evolutionary tree which have mitochondria. This is reflected in the organisation of their mitochondrial DNA that consists of a network of two classes of topologically interlocked circular DNA molecules as well as many unique features in their mitochondrial biogenesis. The proteins encoded on the mitochondrial genome are conventional for a mitochondrial genome, their expression, however, involves a complex series of processes. Many genes represent incomplete open reading frames and their primary transcripts have to remodelled by RNA editing to convert them into translatable mRNAs. RNA editing is mediated by small mitochondria-encoded transcripts, the guide RNAs, and is in that form specific for trypanosomatids and closely related organisms. Mitochondrial translation is also unconventional. No tRNA genes are encoded on the mitochondrial genome. Instead, mitochondrial protein synthesis functions exclusively with imported cytosolic, eukaryotic-type tRNAs. The composition of mitochondrial ribosomes is also unusual in that they contain the smallest known rRNAs. They are about 30% shorter than the already much reduced rRNAs in human mitochondria. Furthermore, the topological organisation of the mitochondrial genome requires an elaborate replication machinery involving topoisomerases. Finally, some trypanosomatids have life cycle stages exhibiting very different mitochondrial activities and can therefore serve as a model system for the regulation of mitochondrial biogenesis.

Non-equilibrium proteins

There exist no methodical studies concerning non-equilibrium systems in cellular biology. This paper is an attempt to partially fill this shortcoming. We have undertaken an extensive data-mining operation in the existing scientific literature to find scattered information about non-equilibrium subcellular systems, in particular concerning fast proteins, i.e. those with short turnover half-time. We have advanced the hypothesis that functionality in fast proteins emerges as a consequence of their intrinsic physical instability that arises due to conformational strains resulting from co-translational folding (the interdependence between chain elongation and chain folding during biosynthesis on ribosomes). Such intrinsic physical instability, a kind of conformon (Klonowski-Klonowska conformon, according to Ji, (Molecular Theories of Cell Life and Death, Rutgers University Press, New Brunswick, 1991)) is probably the most important feature determining functionality and timing in these proteins. If our hypothesis is true, the turnover half-time of fast proteins should be positively correlated with their molecular weight, and some experimental results (Ames et al., J. Neurochem. 35 (1980) 131) indeed demonstrated such a correlation. Once the native structure (and function) of a fast protein macromolecule is lost, it may not be recovered--denaturation of such proteins will always be irreversible; therefore, we searched for information on irreversible denaturation. Only simulation and modeling of protein co-translational folding may answer the questions concerning fast proteins (Ruggiero and Sacile, Med. Biol. Eng. Comp. 37 (Suppl. 1) (1999) 363). Non-equilibrium structures may also be built up of protein subunits, even if each one taken by itself is in thermodynamic equilibrium (oligomeric proteins; sub-cellular sol-gel dissipative network structures).

Cytochrome oxidase subunit VI of Trypanosoma brucei is imported without a cleaved presequence and is developmentally regulated at both RNA and protein levels

Mitochondrial respiration in the African trypanosome undergoes dramatic developmental stage regulation. This requires co-ordinated control of components encoded by both the nuclear genome and the kinetoplast, the unusual mitochondrial genome of these parasites. As a model for understanding the co-ordination of these genomes, we have examined the regulation and mitochondrial import of a nuclear-encoded component of the cytochrome oxidase complex, cytochrome oxidase subunit VI (COXVI). By generating transgenic trypanosomes expressing intact or mutant forms of this protein, we demonstrate that COXVI is not imported using a conventional cleaved presequence and show that sequences at the N-terminus of the protein are necessary for correct mitochondrial sorting. Analyses of endogenous and transgenic COXVI mRNA and protein expression in parasites undergoing developmental stage differentiation demonstrates a temporal order of control involving regulation in the abundance of, first, mRNA and then protein. This represents the first dissection of the regulation and import of a nuclear-encoded protein into the cytochrome oxidase complex in these organisms, which were among the earliest eukaryotes to possess a mitochondrion.

Import of a constitutively expressed protein into mitochondria from procyclic and bloodstream forms of Trypanosoma brucei

Trypanosoma brucei developmentally regulates mitochondrial function during its life cycle. Numerous nuclear encoded mitochondrial proteins undergo posttranslational regulation in a developmental fashion, but exactly how that regulation is achieved is unclear. We are interested in mitochondrial import as a potential regulatory step for nuclear encoded mitochondrial proteins. Previously, an in vitro import system was developed for the procyclic lifestage. We report here the development of an in vitro import system for bloodstream trypanosomes using a crude mitochondrial preparation. NADH dehydrogenase subunit K (NdhK) is a nuclear encoded mitochondrial protein that is constitutively expressed in bloodstream and procyclic trypanosomes. We examined the import of NdhK into procylic and bloodstream mitochondria in vitro. In both lifestages import of NdhK requires a membrane potential across the inner mitochondrial membrane, mitochondrial matrix ATP, and is time dependent. The precursor protein is processed by a matrix associated metalloprotease in a single cleavage step to mature protein.

A developmentally regulated aconitase related to iron-regulatory protein-1 is localized in the cytoplasm and in the mitochondrion of Trypanosoma brucei

Mitochondrial energy metabolism and Krebs cycle activities are developmentally regulated in the life cycle of the protozoan parasite Trypanosoma brucei. Here we report cloning of a T. brucei aconitase gene that is closely related to mammalian iron-regulatory protein 1 (IRP-1) and plant aconitases. Kinetic analysis of purified recombinant TbACO expressed in Escherichia coli resulted in a K(m) (isocitrate) of 3 +/- 0.4 mM, similar to aconitases of other organisms. This was unexpected since an arginine conserved in the aconitase protein family and crucial for substrate positioning in the catalytic center and for activity of pig mitochondrial aconitase (Zheng, L., Kennedy, M. C., Beinert, H., and Zalkin, H. (1992) J. Biol. Chem. 267, 7895-7903) is substituted by leucine in the TbACO sequence. Expression of the 98-kDa TbACO was shown to be lowest in the slender bloodstream stage of the parasite, 8-fold elevated in the stumpy stage, and increased a further 4-fold in the procyclic stage. The differential expression of TbACO protein contrasted with only minor changes in TbACO mRNA, indicating translational or post-translational mechanisms of regulation. Whereas animal cells express two distinct compartmentalized aconitases, mitochondrial aconitase and cytoplasmic aconitase/IRP-1, TbACO accounts for total aconitase activity in trypanosomes. By cell fractionation and immunofluorescence microscopy, we show that native as well as a transfected epitope-tagged TbACO localizes in both the mitochondrion (30%) and in the cytoplasm (70%). Together with phylogenetic reconstructions of the aconitase family, this suggests that animal IRPs have evolved from a multicompartmentalized ancestral aconitase. The possible functions of a cytoplasmic aconitase in trypanosomes are discussed.

Changes in polysome profiles accompany trypanosome development

Development of the protozoan pathogen Trypanosoma brucei involves regulated changes in parasite structure, biochemistry, and the cell cycle. The transition of slender blood forms into stumpy bloodforms includes cell cycle arrest and a decrease in protein synthesis. The next stage in the development cycle, the procyclic form, shows increased protein synthesis and proliferates. To address the mechanism of the cyclical changes in protein synthesis, we examined two parameters: polyadenylation of mRNA and ribosome loading. We developed a method for analytical polyribosome analysis in T. brucei which provided excellent results with regard to reproducibility, yield of mRNA densely loaded with ribosomes, and separation of mRNA associated with different numbers of polyribosomes. Use of this technique allowed us to determine that the polysome profiles of the different developmental stages are distinctly different, with higher ribosome loading in the proliferating stages. The lengths of the poly(A) tails on the total population of RNA from the different developmental stages showed no significant variation. These data indicate that changes in polysome loading of mRNAs accompany development, and that they do not reflect bulk changes in polyadenylation. We speculate that developmental changes in translation reflect reduced translational initiation.

Developmental regulation of two nuclear RNA binding proteins, p34 and p37, from Trypanosoma brucei

We have previously reported the purification of two closely related nucleic acid binding proteins, p34 and p37, from Trypanosoma brucei and the cloning and sequencing of the two genes encoding these two proteins. The predicted primary structures of the two proteins are nearly identical with one major and several minor differences. Three sequence motifs have been identified in both proteins: an N-terminal alanine, proline, and lysine rich domain, one and a half internal consensus RNA binding domains, and a C-terminal KKDX repeat region. p34 and p37 bind preferentially to heterogeneous RNA as compared with other nucleic acids. Here, we report the developmental regulation of the expression of these two highly related proteins and their intracellular localization in T. brucei. The results indicate that these two RNA binding proteins are differently regulated through the Trypanosoma brucei life cycle. The steady state level of p34 transcript and protein are highest in the procyclic form. In bloodstream form, however, the p34 message is readily detectable, while the protein is not detectable. The p37 transcript level is nearly as high as that for p34 in procyclic form, while the p37 protein level is low. In bloodstream form p37 protein does correlate with the relative abundance of the steady state mRNA level. The two proteins have been localized to the nucleus by immunofluorescent confocal microscopy and subcellular fractionation.

In vitro import of the Rieske iron-sulfur protein by trypanosome mitochondria

Most of the proteins present in the mitochondrion are imported to that location from the cytosol. While this process has been studied extensively in fungal and mammalian systems, little work has been done in other eukaryotic organisms. We are particularly interested in the Trypanosoma brucei system because this organism developmentally regulates mitochondrial function during its life cycle and because one of the imported proteins lacks a conventional targeting sequence. We report here the development of an in vitro import system using crude trypanosome mitochondria and a nuclear encoded, mitochondrial protein. Import of the Rieske iron-sulfur protein subunit of the cytochrome c reductase complex requires a membrane potential, ATP, and a protein component on the mitochondrial surface. The precursor protein is sequentially processed to the mature form in two steps by peptidases that require divalent metal ions for activity. As in other eukaryotic systems, the first processing event occurs inside the inner membrane and is probably catalyzed by a matrix-processing protease. Surprisingly, the second processing activity is located outside the inner membrane. Both processing steps require ATP but are independent of a membrane potential. We suggest that the trypanosome iron-sulfur protein is imported along a "conservative sorting pathway" but that the assembly mechanism of the reductase complex may be unique to trypanosomes.

Purification and characterization of proteasomes from Trypanosoma brucei

Proteasomes are multisubunit proteases that exist universally among eukaryotes. They have multiple proteolytic activities, and are believed to have important roles in regulating cell cycle, selective intracellular proteolysis, and antigen presentation. To determine the possible role that proteasomes may play in controlling the life cycle of African trypanosomes, we have isolated proteasomes from the bloodstream and the insect (procyclic) forms of Trypanosoma brucei by DEAE-cellulose chromatography and glycerol gradient fractionation in the presence of ATP. No 26 S proteasome homologs was identified in T. brucei under these experimental conditions. The proteasomes isolated from these two forms of T. brucei are very similar to the rat blood cell 20 S proteasome in their general appearance under the electron microscope. The profile of trypanosome proteasome subunits in sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) has eight visible protein bands with molecular weights ranging from 23 to 34 kDa, and cross-reacted very poorly with the anti-human 20 S proteasome antibodies on immunoblots. Two-dimensional gel electrophoresis of the parasite proteasomes shows a similar number of major subunits with pI's ranging from 4.5 to 7. Using a variety of fluorogenic peptides as substrates, the trypanosome proteasomes exhibited unusually high trypsin-like, but somewhat lower chymotrypsin-like activities, as compared to the rat 20 S proteasome. These proteolytic activities were, however, insensitive to phenylmethylsulfonyl fluoride (PMSF), tosyl-phenylalanine chloromethylketone (TPCK), tosyl-lysine chloromethylketone (TLCK) and trans-epoxy succinyl-L-leucylamido-(4 guanidino) butane (E-64), but the trypsin-like activity of trypanosome proteasomes was inhibited by leupeptin, an aldehyde known to inhibit the trypsin-like activity of mammalian proteasomes, thus ruling out possible contamination by other serine or cysteine proteases. Some quantitative differences in the substrate specificities between the proteasomes from bloodstream and procyclic forms were indicated, which may play a role in determining the differential protein turnovers at two different stages of development of T. brucei.

Stage-regulated expression of cruzipain, the major cysteine protease of Trypanosoma cruzi is independent of the level of RNA1

The genes that encode cruzipain, the major cysteine protease of Trypanosoma cruzi are known to be arranged in tandem arrays. To gain a detailed insight into how these arrays are organised at the chromosomal level we have isolated clones from a cosmid library constructed with DNA from the X10.6 strain. In this strain we found that cruzipain is encoded by two allelic clusters composed of approximately 14 and 23 tandemly repeated genes which are located on homologous chromosomes of 650 and 670 kb. With the exception of the 3'-proximal genes, the cruzipain genes were all of identical or very similar sequence. An unusual feature of the 3'-proximal genes is that they lack the sequences that encode the 130 amino acid carboxyl terminal extension which is characteristic of cruzipain. Both gene clusters are situated in a similar chromosomal environment and are flanked by sequences which have the potential to form Z-DNA. In other eukaryotes, these motifs have been associated with recombinational hotspots and have been demonstrated to enhance gene conversion. The cruzipain genes are transcribed to produce a 1.8-kb transcript which is present at the same steady-state level in each of the parasite life cycle stages. However, protein levels and activity are 4-5-times higher in the insect epimastigote stage than in the trypomastigote and amastigote stages. By implication developmental regulation of cruzipain expression occurs predominantly at the translational and/or post-translational levels.

Cloning by functional complementation in Trypanosoma brucei

A procyclic Trypanosoma brucei double-knockout mutant lacking the ornithine decarboxylase (ODC) gene was transfected with a T. brucei genomic library in the expression vector pTSO-HYG4, which utilizes the PARP promoter and replicates extrachromosomally by virtue of a minicircle origin of replication. Transfectants which grew in the absence of exogenous putrescine, the product of the ODC-catalyzed reaction, were obtained at a frequency of 1.6 x 10(-7) and shown to restore ODC protein synthesis and enzymatic activity. Restriction enzyme patterns and Southern blot analysis of plasmids recovered from these cells and propagated in E. coli showed that the inserts contained a single copy of the T. brucei ODC gene. These results demonstrate for the first time the feasibility of identifying novel T. brucei genes by direct complementation of mutant T. brucei cell lines.

Protein trafficking in kinetoplastid protozoa

The kinetoplastid protozoa infect hosts ranging from invertebrates to plants and mammals, causing diseases of medical and economic importance. They are the earliest-branching organisms in eucaryotic evolution to have either mitochondria or peroxisome-like microbodies. Investigation of their protein trafficking enables us to identify characteristics that have been conserved throughout eucaryotic evolution and also reveals how far variations, or alternative mechanisms, are possible. Protein trafficking in kinetoplastids is in many respects similar to that in higher eucaryotes, including mammals and yeasts. Differences in signal sequence specificities exist, however, for all subcellular locations so far examined in detail--microbodies, mitochondria, and endoplasmic reticulum--with signals being more degenerate, or shorter, than those of their higher eucaryotic counterparts. Some components of the normal array of trafficking mechanisms may be missing in most (if not all) kinetoplastids: examples are clathrin-coated vesicles, recycling receptors, and mannose 6-phosphate-mediated lysosomal targeting. Other aspects and structures are unique to the kinetoplastids or are as yet unexplained. Some of these peculiarities may eventually prove to be weak points that can be used as targets for chemotherapy; others may turn out to be much more widespread than currently suspected.

Control of gene expression in trypanosomes

Trypanosomes are protozoan agents of major parasitic diseases such as Chagas' disease in South America and sleeping sickness of humans and nagana disease of cattle in Africa. They are transmitted to mammalian hosts by specific insect vectors. Their life cycle consists of a succession of differentiation and growth phases requiring regulated gene expression to adapt to the changing extracellular environment. Typical of such stage-specific expression is that of the major surface antigens of Trypanosoma brucei, procyclin in the procyclic (insect) form and the variant surface glycoprotein (VSG) in the bloodstream (mammalian) form. In trypanosomes, the regulation of gene expression is effected mainly at posttranscriptional levels, since primary transcription of most of the genes occurs in long polycistronic units and is constitutive. The transcripts are processed by transsplicing and polyadenylation under the influence of intergenic polypyrimidine tracts. These events show some developmental regulation. Untranslated sequences of the mRNAs seem to play a prominent role in the stage-specific control of individual gene expression, through a modulation of mRNA abundance. The VSG and procyclin transcription units exhibit particular features that are probably related to the need for a high level of expression. The promoters and RNA polymerase driving the expression of these units resemble those of the ribosomal genes. Their mutually exclusive expression is ensured by controls operating at several levels, including RNA elongation. Antigenic variation in the bloodstream is achieved through DNA rearrangements or alternative activation of the telomeric VSG gene expression sites. Recent discoveries, such as the existence of a novel nucleotide in telomeric DNA and the generation of point mutations in VSG genes, have shed new light on the mechanisms and consequences of antigenic variation.

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.

Rat antizyme inhibits the activity but does not promote the degradation of mouse ornithine decarboxylase in Trypanosoma brucei

Ornithine decarboxylase (ODC) of African trypanosomes is an important target for anti-trypanosomal chemotherapy because of its remarkable stability in vivo. The in vivo activity and stability of mammalian ODC are regulated by polyamines. Polyamines induce antizyme, which inactivates ODC by tight association and promotes degradation of ODC by the mammalian 26 S proteasome. Here we found, in contrast to mammalian cells, that polyamines caused no reduction of ODC activity in Trypanosoma brucei. Mouse ODC expressed in T. brucei was also unaffected by exogenous polyamines, suggesting that a mammalian antizyme equivalent may be absent in T. brucei. The rat antizyme expressed in T. brucei was found capable of inhibiting mouse ODC activity by the formation of rat antizyme-mouse ODC complex. However, complex formation did not lead to degradation of mouse ODC in T. brucei. Further in vitro experiments suggested the presence of an inhibitory factor(s) in trypanosome, which interferes with the degradation of mouse ODC. We also demonstrated the presence of proteasomes in T. brucei. But the mobility of the trypanosomal proteasome on native gel is different from that of the mammalian proteasome. Thus, the absence of antizyme, the presence of inhibitory factor(s), and the differences between trypanosomal and mammalian proteasome may account for the stability of mouse ODC in T. brucei cells.

Developmental regulation of Trypanosoma brucei cytochrome c reductase during bloodstream to procyclic differentiation

The bloodstream forms of the protozoan parasite Trypanosoma brucei lack spectrally detectable cytochromes and satisfy energy requirements mainly by glycolysis. When infected blood is ingested by the tse-tse fly vector, the bloodstream form cells differentiate to procyclic forms that have fully functional mitochondria. Procyclic cells have cyanide-sensitive, cytochrome-mediated electron transport and the full complement of TCA cycle enzymes. The developmental regulation of the cytochrome c reductase complex was examined at the RNA and protein levels. RNase T1 protection studies and Northern blot analyses demonstrated that bloodstream and procyclic form cells constitutively expressed the genes for two nuclear encoded cytochrome c reductase subunits, cytochrome c1 and subunit 4. Polyadenylated transcripts of both genes were present in bloodstream form cells at up to 20% of the procyclic cell levels. These levels were significantly up-regulated sometime after the onset of differentiation to the procyclic form. Despite the presence of subunit mRNAs in bloodstream form cells, subunit proteins were not detected until the cells had been allowed to differentiate in vitro for 6 h. Procyclic cell levels of subunit proteins and holocytochromes were reached by 48 h. Our results suggest that cytochrome c reductase is developmentally regulated at multiple levels, some involving post-transcriptional mechanisms.

Dihydrolipoamide dehydrogenase in the trypanosoma subgenus, trypanozoon

The enzyme dihydrolipoamide dehydrogenase has been discovered and characterised in four salivarian trypanosomes of the subgenus trypanozoon: Trypanosoma brucei brucei, T. b. gambiense, T. b. rhodesiense, and Trypanosoma evansi. The three T. brucei species, which have insect procyclic forms biochemically distinct from their mammalian bloodstream forms, express dihydrolipoamide dehydrogenase in both cell types, but have higher levels in the procyclic forms. Determination of Michaelis constants for the enzyme from each of the three T. brucei species did not reveal any significant kinetic differences between the bloodstream and procyclic enzymes. On Western blots, antibodies raised against dihydrolipoamide dehydrogenase from the stereorarian trypanosome, Trypanosoma cruzi, cross-react strongly with the dihydrolipoamide dehydrogenase from all three T. brucei species; by this method, the relative molecular masses of their dihydrolipoamide dehydrogenases are indistinguishable. Dihydrolipoamide dehydrogenase was purified from both the bloodstream and the procyclic forms of T. b. brucei, and the N-terminal have been sequenced. These sequences are identical to the derived protein sequence of the cloned gene (Else et al., Eur. J. Biochem. 212 (1993) 423-429), but have a nine amino acid N-terminal truncation, giving an N-terminus equivalent to that of T. cruzi dihydrolipoamide dehydrogenase. The T. b. brucei dihydrolipoamide dehydrogenase gene has been expressed in Escherichia coli and the resultant protein purified; its N-terminus is processed in a similar fashion to that in the trypanosome, but with reduced specificity.

Developmental regulation of mitochondrial biogenesis in Trypanosoma brucei

The metabolism of Trypanosoma brucei undergoes a significant change as the parasite differentiates from the mammalian bloodstream form to the form found in the tse-tse fly vector. Because the mitochondria of bloodstream form cells lack cytochromes and several key citric acid cycle enzymes, the metabolism of these cells is mostly limited to glycolysis. The reducing equivalents generated by this process are passed to oxygen by a plant-like alternative oxidase. As cells differentiate to the insect form, they begin to oxidatively metabolize proline. The mitochondria of insect form cells contain functional, cytochrome-mediated electron transport chains and have complete complements of citric acid cycle enzymes. Although the characterization is far from complete, the nuclear and mitochondrial genes involved in the expression of these mitochondrial functions appear to be developmentally regulated at posttranscriptional and posttranslational levels. This review outlines some of the molecular processes that are associated with the developmental regulation of mitochondrial biogenesis and suggests some possible mechanisms of regulation.

A possible role for the 3'-untranslated region in developmental regulation in Trypanosoma brucei

A series of Trypanosoma brucei transfection vectors was constructed in which transcription of the luciferase gene was driven by the procyclic acidic repetitive protein (procyclin) promoter. The untranslated regions surrounding the luciferase gene were derived from the actin, fructose bisphosphate aldolase, or PARP loci. Trans-splicing of the resulting transcripts occurred as expected, but the site of 3' polyadenylation was upstream of the position anticipated. The nature of the 3'-untranslated region was crucial to the level of expression in bloodstream forms.