Structure and transcription of the actin gene of Trypanosoma brucei

Sequences and proteins that influence mRNA processing in Trypanosoma brucei: Evolutionary conservation of SR-domain and PTB protein functions

BACKGROUND

Spliced leader trans splicing is the addition of a short, capped sequence to the 5' end of mRNAs. It is widespread in eukaryotic evolution, but factors that influence trans splicing acceptor site choice have been little investigated. In Kinetoplastids, all protein-coding mRNAs are 5' trans spliced. A polypyrimidine tract is usually found upstream of the AG splice acceptor, but there is no branch point consensus; moreover, splicing dictates polyadenylation of the preceding mRNA, which is a validated drug target.

METHODOLOGY AND PRINCIPAL FINDINGS

We here describe a trans splicing reporter system that can be used for studies and screens concerning the roles of sequences and proteins in processing site choice and efficiency. Splicing was poor with poly(U) tracts less than 9 nt long, and was influenced by an intergenic region secondary structure. A screen for signals resulted in selection of sequences that were on average 45% U and 35% C. Tethering of either the splicing factor SF1, or the cleavage and polyadenylation factor CPSF3 within the intron stimulated processing in the correct positions, while tethering of two possible homologues of Opisthokont PTB inhibited processing. In contrast, tethering of SR-domain proteins RBSR1, RBSR2, or TSR1 or its interaction partner TSR1IP, promoted use of alternative signals upstream of the tethering sites. RBSR1 interacts predominantly with proteins implicated in splicing, whereas the interactome of RBSR2 is more diverse.

CONCLUSIONS

Our selectable constructs are suitable for screens of both sequences, and proteins that affect mRNA processing in T. brucei. Our results suggest that the functions of PTB and SR-domain proteins in splice site definition may already have been present in the last eukaryotic common ancestor.

Emerging Functions of Actins and Actin Binding Proteins in Trypanosomatids

Actin is the major protein constituent of the cytoskeleton that performs wide range of cellular functions. It exists in monomeric and filamentous forms, dynamics of which is regulated by a large repertoire of actin binding proteins. However, not much was known about existence of these proteins in trypanosomatids, till the genome sequence data of three important organisms of this class, viz. Trypanosoma brucei, Trypanosoma cruzi and Leishmania major, became available. Here, we have reviewed most of the findings reported to date on the intracellular distribution, structure and functions of these proteins and based on them, we have hypothesized some of their functions. The major findings are as follows: (1) All the three organisms encode at least a set of ten actin binding proteins (profilin, twinfilin, ADF/cofilin, CAP/srv2, CAPz, coronin, two myosins, two formins) and one isoform of actin, except that T. cruzi encodes for three formins and several myosins along with four actins. (2) Actin 1 and a few actin binding proteins (ADF/cofilin, profilin, twinfilin, coronin and myosin13 in L. donovani; ADF/cofilin, profilin and myosin1 in T. brucei; profilin and myosin-F in T.cruzi) have been identified and characterized. (3) In all the three organisms, actin cytoskeleton has been shown to regulate endocytosis and intracellular trafficking. (4) Leishmania actin1 has been the most characterized protein among trypanosomatid actins. (5) This protein is localized to the cytoplasm as well as in the flagellum, nucleus and kinetoplast, and in vitro, it binds to DNA and displays scDNA relaxing and kDNA nicking activities. (6) The pure protein prefers to form bundles instead of thin filaments, and does not bind DNase1 or phalloidin. (7) Myosin13, myosin1 and myosin-F regulate endocytosis and intracellular trafficking, respectively, in Leishmania, T. brucei and T. cruzi. (8) Actin-dependent myosin13 motor is involved in dynamics and assembly of Leishmania flagellum. (9) Leishmania twinfilin localizes mostly to the nucleolus and coordinates karyokinesis by effecting splindle elongation and DNA synthesis. (10) Leishmania coronin binds and promotes actin filament formation and exists in tetrameric form rather than trimeric form, like other coronins. (11) Trypanosomatid profilins are essential for survival of all the three parasites.

Trypanosoma cruzi: multiple actin isovariants are observed along different developmental stages

The expression and biological role of actin during the Trypanosoma cruzi life cycle remains largely unknown. Polyclonal antibodies against a recombinant T. cruzi actin protein were used to confirm its expression in epimastigotes, trypomastigotes, and amastigotes. Although the overall levels of expression were similar, clear differences in the subcellular distribution of actin among the developmental stages were identified. The existence of five actin variants in each developmental stage with distinct patterns of expression were uncovered by immunoblotting of protein extracts separated 2D-SDS gels. The isoelectric points of the actin variants in epimastigotes ranged from 4.45 to 4.9, whereas they ranged from 4.9 to 5.24 in trypomastigotes and amastigotes. To determine if the actin variants found could represent previously unidentified actins, we performed a genomic survey of the T.cruzi GeneDB database and found 12 independent loci encoding for a diverse group of actins and actin-like proteins that are conserved among trypanosomatids.

Selection of reference genes for mRNA quantification in Trypanosoma brucei

Internal normalization is an established procedure that is necessary for accurate and reliable quantification of differentially regulated mRNAs. The profound changes of gene expression in parasitic life cycles pose a particular challenge on selection of appropriate reference genes for normalization, most importantly when using quantitative real time PCR (qPCR). Here we use the ranking algorithm implemented in the geNorm application to identify suitable Trypanosoma brucei reference genes for comparisons between the bloodstream and procyclic developmental stages and for analysis of mRNA induction by environmental conditions. For these conditions, the TERT gene is a good choice for valid normalization of qPCR and is clearly superior to some other reference genes reported in the literature. For comparison of other conditions, the ranking algorithm is recommended to verify a reliable and valid normalization that is instrumental to quantitative analysis of gene expression.

Roles of a Trypanosoma brucei 5'->3' exoribonuclease homolog in mRNA degradation

The genome of the kinetoplastid parasite Trypanosoma brucei encodes four homologs of the Saccharomyces cerevisiae 5'-->3' exoribonucleases Xrn1p and Xrn2p/Rat1p, XRNA, XRNB, XRNC, and XRND. In S. cerevisiae, Xrn1p is a cytosolic enzyme involved in degradation of mRNA, whereas Xrn2p is involved in RNA processing in the nucleus. Trypanosome XRND was found in the nucleus, XRNB and XRNC were found in the cytoplasm, and XRNA appeared to be in both compartments. XRND and XRNA were essential for parasite growth. Depletion of XRNA increased the abundances of highly unstable developmentally regulated mRNAs, perhaps by delaying a deadenylation-independent decay pathway. Degradation of more stable or unregulated mRNAs was not affected by XRNA depletion although a slight decrease in average poly(A) tail length was observed. We conclude that in trypanosomes 5'-->3' exonuclease activity is important in degradation of highly unstable, regulated mRNAs, but that for other mRNAs another step is more important in determining the decay rate.

A novel homologue of coronin colocalizes with actin in filament-like structures in Leishmania

The presence of actin in Leishmania has recently been demonstrated, but the functional form of this protein (filamentous actin) has not yet been identified. We report here that the putative coronin homologue identified in the Leishmania genome is invariably associated with the filament-like structures of actin in Leishmania promastigotes. The occurrence of filamentous structures is significantly increased upon overexpression of Leishmania coronin as its GFP fusion product in Leishmania cells. However, expression of Leishmania actin or coronin alone in mammalian cells does not result in formation of any filament-like structures of Leishmania actin or association of Leishmania coronin with mammalian filamentous actin, but coexpression of both the proteins in these cells leads to formation of filamentous structures containing Leishmania actin and coronin. The high specificity of Leishmania coronin for Leishmania actin could be attributed to its unique structure as it differs from other coronins not only in the unique region but also in the actin-binding site and leucine zipper motif. These results taken together indicate that Leishmania contains a novel form of coronin which colocalizes with actin in filament-like structures in these cells.

Trypanosoma cruzi: allelic comparisons of the actin genes and analysis of their transcripts

Two allelic genomic fragments containing actin genes from Trypanosoma cruzi were isolated and characterized. One allele comprises two complete tandem repeats of a sequence encoding an actin gene. In the other, only one actin gene is found. Each one of these three gene copies encode for a complete and identical potential protein of 376 amino acids which is 93% similar with its homolog from Trypanosoma brucei. Northern hybridizations of both total and polysomal RNA from epimastigotes demonstrated the presence of an actin polyadenylated mRNA of about 1.6 kb. Actin transcripts processing sites were determined by 5(')- and 3(')-RACE. The obtained sequence data demonstrates that actin genes from both alleles are expressed. The stability of actin mRNA was found to be similar to the one exhibited by the ribosomal protein S4 mRNA as an internal reference. A time course analysis of cultured epimastigotes showed a novel behaviour in which actin mRNA steady state concentration peaks during the transition from the logarithmic to the stationary phase of growth.

Two pathways of homologous recombination in Trypanosoma brucei

African trypanosomes are unicellular parasites that use DNA recombination to evade the mammalian immune response. They do this in a process called antigenic variation, in which the parasites periodically switch the expression of VSG genes that encode distinct Variant Surface Glycoprotein coats. Recombination is used to move new VSG genes into specialised bloodstream VSG transcription sites. Genetic and molecular evidence has suggested that antigenic variation uses homologous recombination, but the detailed reaction pathways are not understood. In this study, we examine the recombination pathways used by trypanosomes to integrate transformed DNA into their genome, and show that they possess at least two pathways of homologous recombination. The primary mechanism is dependent upon RAD51, but a subsidiary pathway exists that is RAD51-independent. Both pathways contribute to antigenic variation. We show that the RAD51-independent pathway is capable of recombining DNA substrates with very short lengths of sequence homology and in some cases aberrant recombination reactions can be detected using such microhomologies.

Genetic variants of the TbAT1 adenosine transporter from African trypanosomes in relapse infections following melarsoprol therapy

We have analyzed the TbAT1 gene, which codes for the P2 adenosine transporter, from Trypanosoma brucei field isolates to investigate a possible link between the presence of mutations in this gene and melarsoprol treatment failure. Of 65 T. b. gambiense isolates analyzed from a focus in north-western Uganda with high treatment failure rates following melarsoprol therapy, 38 had a mutated TbAT1. Unexpectedly, all individual isolates contained the same set of nine mutations in their TbAT1 genes. Of these, five point mutations resulted in amino acid substitutions, one resulted in the deletion of an entire codon, and three were silent point mutations. Eight of these mutations had previously been reported in a laboratory-derived Cymelarsan-resistant T. b. brucei clone. Identical sets of mutations were also found in a drug-resistant T.b.rhodesiense isolate from south-eastern Uganda and in a T.b.gambiense isolate from a relapsing patient from northern Angola. A deletion of the TbAT1 gene was found in a single T. b. gambiense isolate from a relapsing patient from northern Angola. The data presented demonstrate the surprising finding that trypanosomes from individual relapse patients of one area, as well as from geographically distant localities, contain an identical set of point mutations in the transporter gene TbAT1. They further demonstrate that many isolates from relapse patients contained the wild-type TbAT1 genes, suggesting that melarsoprol refractoriness is not solely due to a mutational inactivation of TbAT1.

TcRho1, a farnesylated Rho family homologue from Trypanosoma cruzi: cloning, trans-splicing, and prenylation studies

Rho GTPases are members of the Ras superfamily and are involved in signal transduction pathways, including maintenance of cell morphology and motility, cell cycle progression, and transcription activation. We report the molecular identification in trypanosomatids (Trypanosoma cruzi) of the first member of the Rho family. The cloned Rho protein, TcRho1, shares approximately 40% homology with other members of the Rho family. Southern blot analysis revealed that TcRHO1 is a single copy gene per haploid genome, and Northern blot assays showed a transcript of 1200 nucleotides in length. Mapping the 5'-untranslated region of TcRHO1 transcripts revealed at least five different transcripts derived from differential trans-splicing. Three of the five transcripts contain the trans-splicing site within the coding region of the TcRHO1 gene. TcRho1 also contains the C-terminal sequence CQLF (CAAX motif), which is predicted to direct post-translation prenylation of the cysteine residue. A synthetic peptide containing this C-terminal motif, when tested against Q-Sepharose chromatography fractions from T. cruzi cytosol, was shown to be efficiently farnesylated, but not geranylgeranylated, despite the fact that the CAAX motif with X = Phe specifies geranylgeranylation by mammalian protein geranylgeranyltransferase I. Furthermore, immunoblot analyses of epimastigote protein with anti-S-farnesylcysteine methyl ester and anti-TcRho1 antisera strongly suggested that TcRho1 is farnesylated in vivo. The farnesylation of proteins such as Rho GTPases could be the basis for the selective cytotoxic action of protein farnesyltransferase inhibitors on trypanosomatids versus mammalian cells.

The VSG expression sites of Trypanosoma brucei: multipurpose tools for the adaptation of the parasite to mammalian hosts

The variant surface glycoprotein (VSG) genes of Trypanosoma brucei are transcribed in telomeric loci termed VSG expression sites (ESs). Despite permanent initiation of transcription in most if not all of these multiple loci, RNA elongation is abortive except in bloodstream forms where full transcription up to the VSG occurs only in a single ES at a time. The ESs active in bloodstream forms are polycistronic and contain several genes in addition to the VSG, named ES-associated genes (ESAGs). So far 12 ESAGs have been identified, some of which are present only in some ESs. Most of these genes encode surface proteins and this list includes different glycosyl phosphatidyl inositol (GPI)-anchored proteins such as the heterodimeric receptor for the host transferrin (ESAG7/6), integral membrane proteins such as the receptor-like transmembrane adenylyl cyclase (ESAG4) and a surface transporter (ESAG10). An interesting exception is ESAG8, which may encode a cell cycle regulator involved in the differentiation of long slender into short stumpy bloodstream forms. Several ESAGs belong to multigene families including pseudogenes and members transcribed out of the ESs, named genes related to ESAGs (GRESAGs). However, some ESAGs (7, 6 and 8) appear to be restricted to the ESs. Most of these genes can be deleted from the active ES without apparently affecting the phenotype of bloodstream form trypanosomes, probably either due to the expression of ESAGs from 'inactive' ESs (ESAG7/6) or due to the expression of GRESAGs (in particular, GRESAGs4 and GRESAGs1). At least three ESAGs (ESAG7, ESAG6 and SRA) share the evolutionary origin of VSGs. The presence of these latter genes in ESs may confer an increased capacity of the parasite for adaptation to various mammalian hosts, as suggested in the case of ESAG7/6 and proven for SRA, which allows T. brucei to infect humans. Similarly, the existence of a collection of slightly different ESAG4s in the multiple ESs might provide the parasite with adenylyl cyclase isoforms that may regulate growth in response to different environmental conditions. The high transcription rate and high recombination level that prevail in VSG ESs may have favored the generation and/or recruitment in these sites of genes whose hyper-evolution allows adaptation to a larger variety of hosts.

A receptor-like flagellar pocket glycoprotein specific to Trypanosoma brucei gambiense

Trypanosoma brucei gambiense and T. b. rhodesiense are protozoan parasites causing sleeping sickness in humans due to their resistance to lysis by normal human serum (NHS). Based on the observation that the resistance gene of T. b. rhodesiense encodes a truncated form of the variant specific glycoprotein (VSG), we cloned a similar gene in T. b. gambiense using reverse transcription-linked polymerase chain reaction with VSG-specific primers. This gene, termed TgsGP for T. gambiense-specific glycoprotein, was found to be specific to T. b. gambiense. It is located close to a telomere and is transcribed by a pol II RNA polymerase, only at the bloodstream stage of the parasite development. TgsGP encodes a 47-kDa protein consisting of a N-terminal VSG domain presumably provided with a glycosylphosphatidylinositol (GPI) anchor sequence, similar to the pESAG6 subunit of the trypanosomal transferrin receptor. TgsGP is located in the flagellar pocket, and contains the linear N-linked polyacetyllactosamine characteristic of the endocytotic machinery of T. brucei. These observations strongly suggest that TgsGP is a T. b. gambiense specific receptor. Since stable expression of this protein in T. b. brucei did not confer resistance to NHS, TgsGP may either need another factor to achieve this purpose or fulfils another function linked to adaptation of the parasite to man.

Targeting of cytoskeletal proteins to the flagellum of Trypanosoma brucei

The eukaryotic flagellum represents one of the most complex macromolecular structures found in any organism and contains more than 250 proteins. Due to the relative ease of genetic manipulation the flagellum of Trypanosoma brucei has emerged as an accessible model system to study the morphogenesis and dynamics of this organelle. We have recently started to characterise the mechanisms by which components of the cytoskeletal fraction of the flagellum, such as the axoneme, the paraflagellar rod and the flagellar attachment zone, are targeted by proteins synthesised in the cytoplasm and assembled. Here, we present the identification of a novel actin-related protein as a component of the axoneme. We show that this protein shares the tripeptid motif histidine-leucine-alanine (HLA) with one of the major proteins of the paraflagellar rod, PFRA. Building on previous work from this lab which showed that a deletion comprising this motif abolished targeting of PFRA to the flagellum we demonstrate in this study that the deletion of the tripeptid motif is sufficient to achieve mistargeting both of the PFRA and the actin-related protein. We propose that this motif represents an essential part of a flagellar targeting machinery in trypanosomes and possibly in other flagellated organisms.

The molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock 427

We present the molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock 427, clone 221a. This cloned stock is most commonly used in research laboratories in genetic manipulation experiments and in studies of antigenic variation. Using 116 previously characterised chromosome-specific markers, we identify 11 diploid pairs of megabase chromosomes and detect no loss of synteny in EST and gene marker distribution between this stock and the genome project reference stock TREU 927/4. Nevertheless, the chromosomes of 427 are all larger than their homologues in 927, except chromosomes IIa and IXa. The greatest size variation is seen in chromosome I, the smallest of which is 1.1 Mb (927-Ia) and the largest 3.6 Mb (427-Ib). The total nuclear DNA content of both stocks has been estimated by comparison of the mobility of T. brucei and yeast chromosomes. Trypanosomes of stock 427 contain approximately 16.5 Mb more megabase chromosomal DNA than those of stock 927. We have detected the presence of bloodstream-form expression-site-associated sequences on eight or more megabase chromosomes. These sequences are not found on the same chromosomes in each stock. We have determined the chromosomal band location of nine characterised variant surface glycoprotein genes, including the currently expressed VSG 221. Our results demonstrate both the stability of the T. brucei genome, as illustrated by the conservation of syntenic groups of genes in the two stocks, and the polymorphic nature of the genomic regions involved in antigenic variation. We propose that the chromosomes of stock 427 be numbered to correspond to their homologues in the genome project reference stock TREU 927/4.

Molecular cloning of profilin from Tetrahymena thermophila

The actin-binding protein profilin was isolated from Tetrahymena thermophila by affinity chromatography, and the peptide sequence was determined for part of the protein. The cDNA sequence was obtained by using the peptide sequence, reverse transcription-PCR and 5' and 3' RACE. The cDNA coded for a profilin of 16680Da, which made it among the largest known profilins, and it had a predicted isoelectric point of 8.27. The deduced amino acid sequence was divergent from other profilins, having more than 26% identity only with profilin from Tetrahymena pyriformis. The sequence contained insertions that are also present in profilins from Tetrahymena pyriformis and Trypanosoma brucei. There appeared to be only a single profilin gene and one transcript from this gene.

Transcription of the kinetoplastid spliced leader RNA gene

In recent years, much has been learned about the cis-elements controlling transcription of the kinetoplastid spliced leader (SL) RNA gene. The SL RNA gene contains the first 39 nucleotides that are trans-spliced on to all nuclear-derived mRNAs in these organisms. Transcription initiation is determined by two precisely spaced upstream elements and transcription termination is directed by the downstream poly-T tract, although the RNA polymerase responsible for SL RNA synthesis is still questioned. In this article, David Campbell, Nancy Sturm and Michael Yu review the field of kinetoplastid SL RNA gene transcription, address past proposals in light of current data and discuss some of the differences that appear in the literature.

The cytoskeleton of trypanosomatid parasites

Species of the trypanosomatid parasite genera Trypanosoma and Leishmania exhibit a particular range of cell shapes that are defined by their internal cytoskeletons. The cytoskeleton is characterized by a subpellicular corset of microtubules that are cross-linked to each other and to the plasma membrane. Trypanosomatid cells possess an extremely precise organization of microtubules and filaments, with some of their organelles, such as the mitochondria, kinetoplasts, basal bodies, and flagella, present as single copies in each cell. The duplication of these structures and changes in their position during life cycle differentiations provide markers and insight into events involved in determining cell form and division. We have a rapidly increasing catalog of these structures, their molecular cytology, and their ontogeny. The current sophistication of available molecular genetic techniques for use in these organisms has allowed a new functional analysis of the cytoskeleton, including functions that are intrinsic to the proliferation and pathogenicity of these parasites.

The cytostome of Trypanosoma cruzi epimastigotes is associated with the flagellar complex

Okuda, K., Esteva, M., Segura, E. L., and Bijovsky, A. T. 1999. The cytostome of Trypanosoma cruzi epimastigotes is associated with the flagellar complex. Experimental Parasitology 92, 223-231. Proliferative forms of Trypanosoma cruzi, amastigotes and epimastigotes, have a cytostome, a specialized structure formed by an invagination of the flagellar pocket's membrane surrounded by microtubules and frequently followed by a row of vesicles. All this assemblage penetrates deeply into the cytoplasm overpassing the nucleus. This structure, together with the flagellar pocket, appears to play an important role in the nutrition of the parasite. We demonstrated that the monoclonal antibody 2C4, made-up against isolated flagellar complex of T. cruzi epimastigotes, recognizes a protein doublet of 76 and 87 kDa in total epimastigotes homogenate. The 76-kDa polypeptide is enriched in the detergent-soluble fraction whereas the 87-kDa polypeptide is highly represented in the insoluble fractions and the purified flagella. Immuno-fluorescence assays show the antigen as a small spot at the flagellar pocket region. Immunogold labeling of ultrathin sections of epimastigote forms reveals gold particles at the opening of flagellar pocket, concentrated in the cytostome region. Immunocytochemistry of epimastigote whole-mount cytoskeletons reveals the labeling on an array of three to four microtubules that appears attached to flagellum, running in the direction of the nucleus. Ultrastructural observations have shown that the posterior region of isolated flagella, corresponding to the level of the flagellar pocket, possesses a microtubular structure compatible with that from the cytostome. The relationship between the cytostome, an endocytic organelle, and the flagellum is here described for the first time.

Actin gene sequence from Euglena gracilis

The full length coding sequence of the Euglena gracilis actin gene was determined by RT-PCR of Euglena gracilis mRNA. Conserved regions in the actin amino acid sequence were used as guides for the synthesis of degenerate primers. Sequence was obtained for 1,238 nucleotides, of which 1,131 were coding for 377 amino acids. Sequence comparisons showed a similarity with other actins of 56% to 80%. Even though most of the actin amino acid sequence was conserved, some regions showed high divergence, i.e. the DNase I-binding loop at the N-terminal region. The construction of a phylogenetic tree based on actin sequences from different organisms placed Euglena gracilis in a cluster with Trypanosoma brucei and Leishmania major.

Trypanosoma brucei TBRGG1, a mitochondrial oligo(U)-binding protein that co-localizes with an in vitro RNA editing activity

We report the characterization of a Trypanosoma brucei 75-kDa protein of the RGG (Arg-Gly-Gly) type, termed TBRGG1. Dicistronic and monocistronic transcripts of the TBRGG1 gene were produced by both alternative splicing and polyadenylation. TBRGG1 was found in two or three forms that differ in their electrophoretic mobility on SDS-polyacrylamide gel electrophoresis gels, one of which was more abundant in the procyclic form of the parasite. TBRGG1 was localized to the mitochondrion and appeared to be more abundant in bloodstream intermediate and stumpy forms in which the mitochondrion reactivates and during the procyclic stage, which possesses a fully functional mitochondrion. This protein was characterized to display oligo(U) binding characteristics and was found to co-localize with an in vitro RNA editing activity in a sedimentation analysis. TBRGG1 most likely corresponds to the 83-kDa oligo(U)-binding protein previously identified by UV cross-linking of guide RNA to mitochondrial lysates (Leegwater, P., Speijer, D., and Benne, R. (1995) Eur. J. Biochem. 227, 780-786).

The molecular karyotype of the megabase chromosomes of Trypanosoma brucei and the assignment of chromosome markers

We present the molecular karyotype of the megabase chromosomes of Trypanosoma brucei stock TREU927/4 (927). We have identified 11 diploid chromosomes ranging in size from 1 to 5.2 Mb approximately and pairs of homologues differ in size by up to 15%. A total of 401 cDNA probes were hybridised to T. brucei stock 927 chromosomes and 168 chromosome-specific markers were defined. Most of these markers were hybridised to the separated chromosomal DNA of two other cloned field isolates and four F1 progeny clones from a laboratory cross. The chromosomes vary in size by up to two and a half times between stocks and the DNA content of the 11 pairs of homologues varies by up to 33% in different stocks. Stock 927 contains the smallest chromosomes and the least nuclear genomic DNA. Nevertheless, all 11 syntenic groups of cDNA probes are maintained in all stocks. In the F1 hybrids only we have identified one extra PFG band to which none of our probes hybridise. We have shown that probes thought to be specific for the bloodstream-form variant surface glycoprotein expression sites hybridise to different chromosomes in different stocks and may hybridise to either one or both of a homologous pair of chromosomes. We have also determined the chromosomal location of the ribosomal RNA gene arrays.

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.

Identification of a profilin homologue in Trypanosoma brucei by complementation screening

Using genetic complementation in Saccharomyces cerevisiae, we have isolated a Trypanosoma brucei gene encoding profilin. Overexpression of trypanosome profilin suppresses defects that are associated with the loss of the C-terminal domain of the adenylyl cyclase-associated protein in S. cerevisiae. Similarly, the T. brucei gene complements a profilin-deletion mutant of S. cerevisiae. The full-length cDNA clone isolated contains an open reading frame of 150 amino acids, with a predicted molecular mass of 16.1 kDa. The gene appears to be present at single copy and is expressed at approximately equal levels in both mammalian and insect forms of the parasite.

Polysomal, procyclin mRNAs accumulate in bloodstream forms of monomorphic and pleomorphic trypanosomes treated with protein synthesis inhibitors

The major surface antigen of insect stage (procyclic and epimastigote form) Trypanosoma brucei is termed procyclin or procyclic acidic repetitive protein (PARP). Procyclin/PARP is not expressed in bloodstream form parasites, which are coated instead with the variant surface glycoprotein (VSG). Although procyclin/PARP protein is not present and the mRNA is barely detectable, procyclin/PARP genes are transcribed at this life cycle stage. We examined the mechanism for down-regulation of procyclin/PARP expression in bloodstream trypanosomes by using protein synthesis inhibitors to effect accumulation of procyclin/PARP transcripts. We show that the accumulation is not due to increased transcription of procyclin/PARP genes. Further, transcripts which accumulate under these conditions are of mature size, polyadenylated and polysome-associated indicating that normally, in bloodstream trypanosomes, down-regulation of procyclin/PARP expression is exerted either during transcript processing or at the level of mRNA stability. A comparison of the inhibitor-induced accumulation of procyclin/PARP transcripts in bloodstream forms of monomorphic and pleomorphic cell lines of trypanosome stock EATRO 795 shows that accumulation occurs with similar kinetics in both cell lines.

Families of adenylate cyclase genes in Trypanosoma brucei

Four genes for adenylate cyclase have been characterized in Trypanosoma brucei. One of them, esag 4 (for expression site associated gene 4) is present in different VSG (variant surface glycoprotein) gene expression sites and, thus, is only expressed in the bloodstream form of the parasite. The others, termed gresag 4.1, 4.2 and 4.3 (for genes related to esag 4) are expressed in both bloodstream and procyclic forms. In addition, we cloned a esag 4-related gene from T. congolense. Here we characterize the genomic organization of gresag 4.1 and 4.3. While gresag 4.3 is unique, gresag 4.1 exists as a multigenic family of at least nine members located on a 3-Mb chromosome. Six of them are clustered in a region of 300 kb, three copies being tandemly linked. The determination of the nucleotide sequence of a conserved 1.6 kb PstI fragment demonstrated the presence of two separate subgroups in this family. This gene arrangement is present in different isolates of T.b. brucei/rhodesiense/gambiense. Several gresag 4.1 copies are transcribed in both bloodstream and procyclic forms.

The PARP promoter of Trypanosoma brucei is developmentally regulated in a chromosomal context

African trypanosomes are extracellular protozoan parasites that are transmitted from one mammalian host to the next by tsetse flies. Bloodstream forms express variant surface glycoprotein (VSG); the tsetse fly (procyclic) forms express instead the procyclic acidic repetitive protein (PARP). PARP mRNA is abundant in procyclic forms and almost undetectable in blood-stream forms. Post-transcriptional mechanisms are mainly responsible for PARP mRNA regulation but results of nuclear run-on experiments suggested that transcription might also be regulated. We measured the activity of genomically-integrated PARP, VSG and rRNA promoters in permanently-transformed blood-stream and procyclic form trypanosomes, using reporter gene constructs that showed no post-transcriptional regulation. When the constructs were integrated in the rRNA non-transcribed spacer, the ribosomal RNA and VSG promoters were not developmentally regulated, but integration at the PARP locus reduced rRNA promoter activity in bloodstream forms. PARP promoter activity was 5-fold down-regulated in bloodstream forms when integrated at either site. Regulation was probably at the level of transcriptional initiation, but elongation through plasmid vector sequences was also reduced.

Post-transcriptional control of hsp70 mRNA in Trypanosoma brucei

The control of hsp70 mRNA levels was investigated using transgenic bloodstream and procyclic trypanosomes. Heat shock of procyclic and bloodstream trypanosomes caused no significant change in overall protein synthesis, but led to a 2-3-fold increase in the relative hsp70 mRNA level in bloodstream trypanosomes. Incubation of procyclic trypanosomes at 35 degrees C for up to 18 h increased the level of hsp70 mRNA only marginally. The expression of actin and hsp70 mRNAs was markedly reduced in late log phase procyclic trypanosomes but PARP mRNA levels remained constant. Measurements of phleomycin-binding-protein RNAs bearing 3'- and 5'-untranslated regions from the actin, PARP or hsp70 loci indicated that both the heat-shock and cell-density effects were mediated by the untranslated regions. No significant promoter activity was detected in the different hsp70 locus intergenic regions in transient assays.

Isolation, characterization and chromosomal mapping of an actin gene from the primitive red alga Cyanidioschyzon merolae

Based on the results of cytological studies, it has been assumed that Cyanidioschyzon merolae does not contain actin genes. However, Southern hybridization of C. merolae cell-nuclear DNA with a yeast actin-gene probe has been suggested the presence of an actin gene in the C. merolae genome. In the present study, an actin gene was isolated from a C. merolae genomic library using a yeast actin-gene probe. The C. merolae actin gene has no intron. The predicted actin is composed of 377 amino acids and has an estimated molecular mass of 42 003 Da. Southern hybridization indicated that the C. merolae genome contains only one actin gene. This gene is transcribed at a size of 2.4 kb. When Southern hybridization was performed with C. merolae chromosomes separated by pulsed-field gel electrophoresis, a band appeared on unseparated chromosomes XI and XII. A phylogenetic tree based on known eucaryote actin-gene sequences revealed that C. merolae diverged after the division of Protozoa, but before the division of Fungi, Animalia and Chlorophyta.

The 3'-untranslated regions from the Trypanosoma brucei phosphoglycerate kinase-encoding genes mediate developmental regulation

The phosphoglycerate kinase (PGK)-encoding genes of Trypanosoma brucei are transcribed in a polycistronic fashion, but the mRNAs encoding the three PGK isozymes show differing developmental regulation. We demonstrate here that the 3'-untranslated regions of the major cytoplasmic and glycosomal PGK isozymes are capable of conferring the anticipated types of regulation on a transfected reporter gene.

Structural features and phylogeny of the actin gene of Chondrus crispus (Gigartinales, Rhodophyta)

We have characterized the cDNA and genomic sequences that encode actin from the multicellular red alga Chondrus crispus. Southern-blot analysis indicates that the C. crispus actin gene (ChAc) is present as a single copy. Northern analysis shows that, like the GapA gene, the actin gene is well expressed in gametophytes but weakly in protoplasts. Compared to actin genes of animals, fungi, green plants and oomycetes, that of C. crispus displays a higher evolutionary rate and does not show any of the amino-acid signatures characteristic of the other lineages. As previously described for GapA, ChAc is interrupted by a single intron at the beginning of the coding region. The site of initiation of transcription was characterized by RNAse protection. The promoter region displays a CAAT box but lacks a canonical TATA motif. Other noticeable features, such as a high content of pyrimidines as well as a 14-nt motif found in both the 5'-untranslated region and the intron, were observed.

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.

The interaction of Trypanosoma congolense with endothelial cells

Factors which affect adhesion of cultured Trypanosoma congolense bloodstream forms to mammalian feeder cells have been examined. Using an in vitro binding assay, the initial events following interaction of trypanosomes with bovine aorta endothelial (BAE) cells were monitored by both light- and electron microscopy. Metabolic inhibitors and other biochemicals were incubated with either cells or parasites, to test whether any inhibited the process. Our findings suggest that adhesion of the parasites is an active process requiring metabolic energy from the trypanosomes, but not from endothelial cells. We also provide data suggesting that T. congolense bloodstream forms possess a lectin-like domain, localized at distinct sites on their flagellar surface, which interacts with specific carbohydrate receptors, most likely sialic acid residues, on the endothelial cell plasma membrane. We also suggest that the cytoskeletal protein actin is probably involved in this interaction.

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.

Cloning and sequencing of the Leishmania major actin-encoding gene

We report the cloning and characterization of the genomic sequence of the actin (Act)-encoding gene (act) from Leishmania major. Restriction maps of two genomic clones, as well as genomic Southern analysis strongly suggest that the act of L. major is a single-copy gene. A single 1.6-kb transcript is detected in Northern blots. The deduced amino-acid sequence shows 68-89% identity with Act sequences from other eukaryotes.

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.

Abrupt RNA changes precede the first cell division during the differentiation of Trypanosoma brucei bloodstream forms into procyclic forms in vitro

We have monitored the timing of DNA and RNA synthesis during the synchronous differentiation of Trypanosoma brucei bloodstream forms into procyclic forms in vitro. Both are triggered after a lag period of 4 h and reach a first peak after 9 h. The division of the kinetoplast precedes that of the nucleus by about 4 h. The first cell divisions are observed after 10 h, and the cell number is doubled after 20 h. The total RNA content per cell increases sharply between 4 and 10 h, then progressively decreases as cell division progresses. The increase in RNA content cannot be due solely to accumulation of rRNA since it is also observed for mRNAs such as actin. The VSG mRNA has almost disappeared within 2 h, while the procyclin mRNA accumulates soon after the triggering of differentiation, with a strong peak between 4 and 6 h. At this moment, the amount of procyclin mRNA per cell is at least 20-fold higher than in established procyclic culture forms. The loss of the VSG and the appearance of procyclic-specific proteins essentially occur before the first cell division. These observations contrast with the progressive transition observed when monomorphic slender forms are induced to transform under the same conditions.

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.

A Drosophila homologue of the Schizosaccharomyces pombe act2 gene

Diverse proteins that are 35% to 55% identical to actins have been discovered recently in yeasts, nematodes, and vertebrates. In order to study these proteins systematically and relate their functions to those of conventional actins, we are isolating the corresponding genes from the genetically tractable eukaryote, Drosophila melanogaster. Here we report the isolation and partial characterization of a Drosophila homologue of the Schizosaccharomyces pombe act2 gene. Degenerate oligonucleotide primers specifying peptides that are highly conserved within the actin protein superfamily were used in conjunction with polymerase chain reaction (PCR) to amplify a portion of the Drosophila gene that we have named actr66B. The corresponding full-length cDNA sequence encodes a protein of 418 residues that is 65% identical to the product of the S. pombe act2 gene, 80% identical to the bovine act2 homologue, but only 48% identical to the principal Drosophila cytoplasmic actin encoded by the Act5C actin gene. Alignment of the yeast, bovine, and Drosophila actin-related proteins shows that they have four peptide insertions, relative to conventional actins, three of which are well placed to modify actin polymerization and one that is likely to perturb the binding of myosin. Locations of two of the five actr66B introns are conserved between Drosophila and yeast genes, further attesting that they evolved from a common ancestor and are likely to encode proteins having similar functions. We demonstrate that the Drosophila gene is located on the left arm of chromosome 3, within subdivision 66B. Finally, we show by RNA blot-hybridization that the gene is expressed at low levels, relative to conventional nonmuscle actin, in all developmental stages. From these and other observations we infer that the actr66B protein is a minor component of all cells, perhaps serving to modify the polymerization, structure, and dynamic behavior of actin filaments.

A chimeric actin carrying N-terminal portion of Tetrahymena actin does not bind to DNase I

A chimeric actin gene was constructed from Tetrahymena actin sequence corresponding to residues 1-83 and Dictyostelium actin sequence corresponding to residues 84-375, and the gene was expressed in Dictyostelium cells. Using DNase I-affinity column, we revealed that the product of the chimeric actin gene was not retained in the column whereas intrinsic actin was retained. In conjunction with our previous data that Tetrahymena actin does not interact with DNase I [Hirono, M., Kumagai, Y., Numata, O., & Watanabe Y. (1989) Proc. Natl. Acad. Sci. U.S. 86, 75-79], we suggest that the binding site of DNase I in an ubiquitous actin is located in N-terminal region (residues 1-83).

Molecular phylogenetic analysis of actin genic regions from Achlya bisexualis (Oomycota) and Costaria costata (Chromophyta)

Actin genic regions were isolated and characterized from the heterokont-flagellated protists, Achlya bisexualis (Oomycota) and Costaria costata (Chromophyta). Restriction enzyme and cloning experiments suggested that the genes are present in a single copy and sequence determinations revealed the existence of two introns in the C. costata actin genic region. Phylogenetic analyses of actin genic regions using distance matrix and maximum parsimony methods confirmed the close evolutionary relationship of A. bisexualis and C. costata suggested by ribosomal DNA (rDNA) sequence comparisons and reproductive cell ultrastructure. The higher fungi, green plants, and animals were seen as monophyletic groups; however, a precise order of branching for these assemblages could not be determined. Phylogentic frameworks inferred from comparisons of rRNAs were used to assess rates of evolution in actin genic regions of diverse eukaryotes. Actin genic regions had nonuniform rates of nucleotide substitution in different lineages. Comparison of rates of actin and rDNA sequence divergence indicated that actin genic regions evolve 2.0 and 5.3 times faster in higher fungi and flowering plants, respectively, than their rDNA sequences. Conversely, animal actins evolve at approximately one-fifth the rate of their rDNA sequences.

High homology between variant surface glycoprotein gene expression sites of Trypanosoma brucei and Trypanosoma gambiense

The AnTat 11.17 variant surface glycoprotein (VSG) is synthesized in both metacyclic and bloodstream forms of Trypanosoma gambiense. We have characterized the AnTat 11.17 gene, and analyzed its expression site (ES) in the bloodstream form by Southern and Northern blotting with probes from the Trypanosoma brucei AnTat 1.3A VSG ES, and by run-on transcription. The AnTat 11.17 ES is located at the end of a 700-kb chromosome. It appears to contain all the genes (ESAGs, for Expression Site-Associated Genes) present in the AnTat 1.3A VSG ES, with the possible exception of ESAG 1. Limited nucleotide sequence analysis of ESAG cDNAs from the AnTat 11.17 ES shows considerable conservation with ESAGs of T. brucei. The transcription promoter of the AnTat 11.17 VSG ES, localized by virtue of the specific accumulation of promoter-proximal transcripts which occurs following UV irradiation, was found to be at the same relative position to the first ESAG (ESAG 7) as in AnTat 1.3A.

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.

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.