Domain function and predicted structure of three heterodimeric endonuclease subunits of RNA editing catalytic complexes in Trypanosoma brucei.

Each of the three similar RNA Editing Catalytic Complexes (RECCs) that perform gRNA-directed uridine insertion and deletion during Trypanosoma brucei mitochondrial (mt) mRNA editing has a distinct endonuclease activity that requires two related RNase III proteins, with only one competent for catalysis. We identified multiple loss-of-function mutations in the RNase III and other motifs of the non-catalytic KREPB6, KREPB7, and KREPB8 components by random mutagenesis and screening. These mutations had various effects on growth, editing, and both the abundances and RECC associations of these RNase III protein pairs in bloodstream form (BF) and procyclic form (PF) cells. Protein structure modelling predicted that the Zinc Finger (ZnF) of each paired RNase III protein contacts RNA positioned at the heterodimeric active site which is flanked by helices of a novel RNase III-Associated Motif (RAM). The results indicate that the protein domains of the non-catalytic subunits function together in RECC integrity, substrate binding, and editing site recognition during the multistep RNA editing process. Additionally, several mutants display distinct functional consequences in different life cycle stages. These results highlight the complementary roles of protein pairs and three RECCs within the complicated T. brucei mRNA editing machinery that matures mt mRNAs differentially between developmental stages.

Rapid test for the evaluation of the activity of the prodrug hydroxymethylnitrofurazone in the processing of Trypanosoma cruzi messenger RNAs.

No fully effective treatment has been developed since the discovery of Chagas' disease by Carlos Chagas in 1909. Since drug-resistant Trypanosoma cruzi strains are occurring and the current therapy is effectiveness in the acute phase but with various adverse side effects, more studies are needed to characterize the susceptibility of T. cruzi to new drugs. Many natural and/or synthetic substances showing trypanocidal activity have been used, even though they are not likely to be turned into clinically approved drugs. Originally, drug screening was performed using natural products, with only limited knowledge of the molecular mechanism involved in the development of diseases. Trans-splicing, which is unusual RNA processing reaction and occurs in nematodes and trypanosomes, implies the processing of polycistronic transcription units into individual mRNAs; a short transcript spliced leader (SL RNA) is trans-spliced to the acceptor pre-mRNA, giving origin to the mature mRNA. In the present study, permeable cells of T. cruzi epimastigote forms (Y, BOL and NCS strains) were treated to evaluate the interference of two drugs (hydroxymethylnitrofurazone - NFOH-121 and nitrofurazone) in the trans-splicing reaction using silver-stained PAGE analysis. Both drugs induced a significant reduction in RNA processing at concentrations from 5 to 12.5 microM. These data agreed with the biological findings, since the number of parasites decreased, especially with NFOH-121. This proposed methodology allows a rapid and cost-effective screening strategy for detecting drug interference in the trans-splicing mechanism of T. cruzi.

Subcellular localization and light-regulated expression of protoporphyrinogen IX oxidase and ferrochelatase in Chlamydomonas reinhardtii.

Protoporphyrinogen IX oxidase (PPO) catalyzes the last common step in chlorophyll and heme synthesis, and ferrochelatase (FeC) catalyzes the last step of the heme synthesis pathway. In plants, each of these two enzymes is encoded by two or more genes, and the enzymes have been reported to be located in the chloroplasts or in the mitochondria. We report that in the green alga Chlamydomonas reinhardtii, PPO and FeC are each encoded by a single gene. Phylogenetic analysis indicates that C. reinhardtii PPO and FeC are most closely related to plant counterparts that are located only in chloroplasts. Immunoblotting results suggest that C. reinhardtii PPO and FeC are targeted exclusively to the chloroplast, where they are associated with membranes. These results indicate that cellular needs for heme in this photosynthetic eukaryote can be met by heme that is synthesized in the chloroplast. It is proposed that the multiplicity of genes for PPO and FeC in higher plants could be related to differential expression in differently developing tissues rather than to targeting of different gene products to different organelles. The FeC content is higher in C. reinhardtii cells growing in continuous light than in cells growing in the dark, whereas the content of PPO does not significantly differ in light- and dark-grown cells. In cells synchronized to a light/dark cycle, the level of neither enzyme varied significantly with the phase of the cycle. These results indicate that heme synthesis is not directly regulated by the levels of PPO and FeC in C. reinhardtii.

Cloning and characterization of the 82 kDa tyrosine-rich sexual stage glycoprotein, GAM82, and its role in oocyst wall formation in the apicomplexan parasite, Eimeria maxima.

The sexual (macrogamete/macrogametocyte) stage antigen, GAM82, in the apicomplexan parasite Eimeria maxima, has an apparent molecular mass of 82 kDa, and has been implicated in protective immunity against coccidiosis in poultry. The gene encoding this protein, gam82, was cloned and sequenced. It is a single-copy, intronless gene, which localizes to a 2145 bp transcript, and is first detected at 130 h post-infection. The gene predicts two distinct domains rich in the residues tyrosine and serine, amino acids that have been implicated in oocyst wall formation in other Eimeria spp., and in the extraorganismic sclerotization of structural proteins throughout the animal kingdom. A high number of small amino acids, predominantly alanine and proline, were detected in the intervening sequence between these two domains. The inference that GAM82 is involved in oocyst wall formation in Eimeria was confirmed when it was shown that a specific antibody to a recombinant version of GAM82 recognized the wall forming bodies in macrogametes, and the walls of oocysts in E. maxima. A closer biochemical analysis of the role of GAM82 in oocyst wall formation by sodium dodecyl sulfate polyacrylamide gel electrophoresis and immunoblotting showed that the antibodies to the recombinant version of GAM82 recognized an 82 kDa protein in macrogametocyte extracts, and a 30 kDa protein in unsporulated and sporulated oocyst extracts, as well as in purified oocyst wall fragments. Together, these findings indicate that the 82 kDa macrogametocyte antigen, GAM82, is a tyrosine and serine rich precursor protein that is proteolytically processed during development to give rise to a 30 kDa protein, that is incorporated into the oocyst wall. In addition, these findings provide evidence that the oocyst wall of Eimeria species is composed of a family of tyrosine rich proteins, that arise from precursor proteins found in the wall forming bodies of macrogametes.

Cloning and characterization of a novel serine/threonine protein phosphatase type 5 from Trypanosoma brucei.

Reversible protein phosphorylation is essential for the regulation of numerous cellular functions and differentiation. The haemo-flagellated parasitic protozoan Trypanosoma brucei, the causative agent for African trypanosomiasis undergoes various stages of cellular differentiation during its digenetic life cycle. A complete cDNA of a unique serine/threonine phosphatase type five (TbPP5) was cloned and characterized from T. brucei. TbPP5 contains an open reading frame of 1416 bp that encodes a protein of about 53 kDa and exists as a single copy gene in the T. brucei genome. The deduced amino acid sequence showed 45-48% overall identity and 60-65% similarity with protein phosphatase 5's (PP5) from different species. Analysis of the primary sequence revealed that TbPP5 contains three TPR motifs at the N-terminal region (amino acid residues 7-107) while the phosphatase catalytic domain occurs in the C-terminal region (amino acid residues 210-410). A TbPP5 cDNA hybridized with a transcript of 2.5 kb which is present at similar levels in the procyclic and the bloodstream forms. However, the level of expression of the TbPP5 protein (52 kDa) detected by an antibody developed against a recombinant protein produced in E. coli was about 2-fold higher in the procyclic than the bloodstream form. The TbPP5 transcript level gradually decreased in cells grown in the logarithmic phase to the stationary phase in culture. Moreover, 18 h serum starvation of the procyclic forms decreased the level of the specific transcript about 3-fold suggesting that this protein may play a role during the active growth phase of the organism. The recombinant protein showed phosphatase activity which was stimulated about 2.6-fold by arachidonic acid with half-maximal activity at 75 microM. Indirect immuno-fluorescence of permeabilized cells revealed that the protein is localized in the cytosol and the nucleus This is the first report for the identification of a type 5 serine/threonine protein phosphatase in an ancient eukaryote such as T. brucei.

Cysteine biosynthesis in Chlamydomonas reinhardtii. Molecular cloning and regulation of O-acetylserine(thiol)lyase.

A cDNA, Cys1ACr, encoding an isoform of O-acetylserine(thiol) lyase has been isolated from Chlamydomonas reinhardtii, using a PCR-based approach. The inclusion of dimethylsulfoxide in the PCR reaction has been demonstrated to be essential for the correct amplification of C. reinhardtii templates with complex secondary structures caused by a high G + C content. The deduced amino acid sequence exhibited highest similarity with plant O-acetylserine(thiol)lyase isoforms, indicating that the C. reinhardtii enzyme was structurally more similar to higher plant O-acetylserine(thiol)lyase than to the corresponding prokaryotic enzymes. The N-terminal extension present in Cys1ACr showed several characteristics of an organellar transit peptide, with a length typical for C. reinhardtii. Southern blot analysis suggested that the C. reinhardtii genome may contain a single copy of the organellar O-acetylserine(thiol)lyase gene. O-acetylserine(thiol)lyase activity was strongly induced by sulfur-deficient conditions (up to sevenfold the level observed in a sulfur-repleted cell culture) and required the presence of a nitrogen source. Northern blot analysis showed a different pattern of regulation of Cys1ACr to that observed at the activity level. To obtain an increase of transcript abundance a longer period of sulfur limitation was required, reaching a maximum level of approximately threefold Cys1ACr mRNA when compared with the level of a sulfate-grown culture.

TcDJ1, a putative mitochondrial DnaJ protein in Trypanosoma cruzi.

A full length cDNA encoding a novel Trypanosoma cruzi DnaJ protein was cloned and characterized. The 324 amino acid protein encoded by the cDNA (TcDJ1) displays a characteristics J-domain, but lacks the Gly-Phe and zinc finger regions present in some other DnaJ proteins. Relative to four other T. cruzi DnaJ proteins, TcDJ1 has an amino terminal extension containing basic and hydroxylated resides characteristic of mitochondrial import peptides. A T. cruzi transfectant expressing epitope-tagged TcDJ1 was generated and subcellular fractions were produced. Western blot analysis revealed that the protein has a molecular mass of 29 kDa and is found in the mitochondrial fraction. The expression of TcDJ1 is developmentally regulated since the levels of both mRNA and protein are much higher in epimastigotes (replicative form) than in metacyclic trypomastigotes (infective form). Thus it may participate in mitochondrial biosynthetic processes in this organism.

Accurate modification of the trypanosome spliced leader cap structure in a homologous cell-free system.

During RNA maturation in trypanosomatid protozoa, trans-splicing transfers the spliced leader (SL) sequence and its cap from the SL RNA to the 5' end of all mRNAs. In Trypanosoma brucei and Crithidia fasciculata the SL RNA has an unusual cap structure with four methylated nucleotides following the 7-methylguanosine residue (cap 4). Since modification of the 5' end of the SL RNA is a pre-requisite for trans-splicing activity in T. brucei, we have begun to characterize the enzyme(s) involved in this process. Here we report the development of a T. brucei cell-free system for modification of the cap of the SL RNA. Analysis of the nucleotide composition of the in vitro generated cap structure by two-dimensional thin layer chromatography established that the in vitro reaction is accurate. Cap 4 formation requires the SL RNA to be in a ribonucleoprotein particle and can be inhibited by annealing a complementary 2'-O-methyl RNA oligonucleotide to nucleotides 7-18 of the SL RNA. Methylation of the 5' end of the SL RNA is also required for trans-splicing in T. cruzi and Leishmania amazonensis and cell-free extracts from C. fasciculata and L. amazonensis are capable of modifying the cap structure on the T. brucei SL ribonucleoprotein particle.

A possible role for the guide RNA U-tail as a specificity determinant in formation of guide RNA-messenger RNA chimeras in mitochondrial extracts of Crithidia fasciculata.

Chimeric g(uide) RNA:pre-mRNA molecules are potential intermediates of the RNA editing process in kinetoplastid mitochondria. We have studied the characteristics of chimeric molecules formed in mitochondrial extracts of the insect trypanosomatid Crithidia fasciculata which had been supplied with synthetic NADH dehydrogenase (ND) subunit-7 gRNA and pre-mRNA variants. The ability of a gRNA to participate in chimera formation in this system depends on the possibility of base pairing with the pre-mRNA via the anchor sequence, but not on the presence of a U-tail or a full-length informational part. Chimeras formed with a specific gRNA:pre-mRNA pair displayed a large variation in length, due to variably sized 3' end truncations of the gRNA moieties and variation in the sites in the pre-mRNA to which the gRNAs were attached. Surprisingly, the presence of a U-tail in the gRNA for a large part determined the specificity of the linkage. In 60% of the cases gRNAs possessing a U-tail of at least one residue were attached to an editing site, whereas 75% of the gRNAs without Us were attached to non-editing sites. Furthermore, the chimera forming activity was greatly stimulated by the addition of ATP but not by AMP-CPP, an ATP-analogue with a non-hydrolyzable alpha-beta phosphate bond. This suggests the involvement in the chimera formation of an RNA ligase.

Three Tetrahymena tRNA(Gln) isoacceptors as tools for studying unorthodox codon recognition and codon context effects during protein synthesis in vitro.

Three glutamine tRNA isoacceptors are known in Tetrahymena thermophila. One of these has the anticodon UmUG which reads the two normal glutamine codons CAA and CAG, whereas the two others with CUA and UmUA anticodons recognize UAG and UAA, respectively, which serve as termination codons in other organisms. We have employed these tRNA(Gln)-isoacceptors as tools for studying unconventional base interactions in a mRNA- and tRNA-dependent wheat germ extract. We demonstrate here (i) that tRNA(Gln)UmUG suppresses the UAA as well as the UAG stop codon, involving a single G:U wobble pair at the third anticodon position and two simultaneous wobble base pairings at the first and third position, respectively, and (ii) that tRNA(Gln)CUA, in addition to its cognate codon UAG, reads the UAA stop codon which necessitates a C:A mispairing in the first anticodon position. These unorthodox base interactions take place in a codon context which favours readthrough in tobacco mosaic virus (TMV) or tobacco rattle virus (TRV) RNA, but are not observed in a context that terminates zein and globin protein synthesis. Furthermore, our data reveal that wobble or mispairing in the middle position of anticodon-codon interactions is precluded in either context. The suppressor activities of tRNAs(Gln) are compared with those of other known naturally occurring suppressor tRNAs, i.e., tRNA(Tyr)G psi A and tRNA(Trp)CmCA. Our results indicate that a 'leaky' context is neither restricted to a single stop codon nor to a distinct tRNA species.