Chromosome organization of the protozoan Trypanosoma brucei

Molecular characterization of phosphoribosylpyrophosphate synthetase from Leishmania donovani

The phosphoribosylpyrophosphate synthetase (PRS) enzyme from parasitic protozoa plays a critical role in the acquisition of exogenous purine bases by providing the phosphoribosylpyrophosphate substrate for phosphoribosylation. To characterize a PRS enzyme from parasitic protozoa, the prs gene was isolated from a genomic library of Leishmania donovani DNA. A 1936-bp SalI fragment was sequenced that encompassed an open reading frame of 1113 nucleotides encoding a polypeptide of 371 amino acids and 40 787 Da. After gap alignment, the leishmanial PRS exhibited 40-42% amino acid identity with a variety of mammalian and prokaryotic PRSs. L. donovani PRS also contained an approx. 20-amino acid stretch that was highly homologous to the phosphoribosylpyrophosphate binding domains of mammalian phosphoribosyltransferase enzymes. Two prs-specific transcripts of 2.6 and 2.1 kb were detected by Northern analysis, and Southern blots of genomic DNA implied that the prs locus was not tandemly repeated in the L. donovani genome. PRS activity was detected in L. donovani extracts, and apparent Km values of approx. 30 microM and approx. 1 mM were calculated for ribose-5-phosphate and ATP, respectively. PRS was sensitive to inhibition by AMP and ADP but refractory to IMP, GMP, GTP, CTP, and UTP. The high apparent Km value of the parasite enzyme for ATP and its insensitivity to inhibition by many nucleotides suggested that kinetic differences between the L. donovani and human PRSs could provide an avenue for rational therapeutic manipulation of parasitic disease. The isolation of the L. donovani prs gene now provides an opportunity to genetically dissect the determinants responsible for the function and regulation of this indispensable enzyme of purine and pyrimidine metabolism in a genus of parasitic protozoa.

Molecular variation in trypanosomes

Several species of the genus Trypanosoma cause parasitic diseases of considerable medical and veterinary importance throughout Africa, Asia and the Americas. These parasites exhibit considerable intra-species genetic diversity and variation, which has complicated their taxonomic classification. This diversity and variation can be defined at the level of both the genome and of individual genes. The nuclear genome shows considerable inter- and intra-species plasticity in terms of chromosome number and size (molecular karyotype). The mitochondrial (kDNA) genome also varies considerably between species, especially in terms of minicircle size and organization. There is also considerable intra-specific sequence diversity in minicircles and within the Variable Region of the maxicircle. Restriction enzyme analysis of this diversity has lead to the concept of 'schizodemes'. At the gene level, isoenzyme analysis has proven very useful for strain and isolate identification, with the classification into numerous 'zymodemes'. Considerable antigenic diversity has also been identified in T. cruzi and T. brucei, with the development of 'serodemes' in the latter. In addition to this inter-strain diversity, African trypanosomes (T. brucei, T. congolense, and T. vivax) exhibit the phenomenon of antigenic variation, where individual parasites are able to express any one of hundreds of different copies of the Variant Surface Glycoprotein gene at any particular time. The molecular mechanisms underlying antigenic variation are now understood in considerable detail. The implication of this molecular diversity and variation are discussed in terms of trypanosome taxonomy and disease control.

The glycosomes of the Kinetoplastida

Glycosomes are the microbodies of the organisms belonging to the order of the Kinetoplastida, comprising trypanosomes and leishmanias, both pathogens to man. The organelles sequester a number of glycolytic enzymes that are normally located in the cytosol in other eukaryotic organisms, and share some enzymes with peroxisomes and glyoxysomes of other protists, plants and animals. Proteins enter the glycosome by a mechanism of post-translational translocation which involves in some, but not all, cases a C-terminal oligopeptide sequence.

Stable amplification of a linear extrachromosomal DNA in mycophenolic acid-resistant Leishmania donovani

Pulsed field gel electrophoretic analysis of chromosomes of MPA100 cells, a strain of Leishmania donovani that possesses an approx. 15-fold amplified IMP dehydrogenase (IMPDH) gene copy number, revealed a new 280-kb extrachromosomal DNA, IMPDH-280, that was not present in wild type parental cells. Southern blots of these pulsed field gels revealed that the vast majority of the amplified impdh genes were localized on IMPDH-280. In addition to the 700-kb wild type chromosome, the impdh probe also recognized a 740-kb chromosome in the MPA100 genome. The pulse time-dependent relative mobility of IMPDH-280 in pulsed field gels, the failure of limited gamma-irradiation to generate a new discrete DNA fragment, and the susceptibility of IMPDH-280 to lambda-exonuclease digestion, demonstrated that IMPDH-280 was a linear molecule. IMPDH-280 was also recognized by a telomere probe but not by fragments derived from amplified DNAs found in other drug-resistant Leishmania. IMPDH-280 and the drug resistance phenotype remained stable when MPA100 cells were propagated in the absence of drug for 2 years. The appearance of IMPDH-280 in MPA100 cells represents one of the first examples of an amplification of a linear extrachromosomal DNA element mediating drug resistance in Leishmania and the first instance of a linear DNA amplification that is stable in the absence of selective pressure.

Molecular analysis of the cytosolic and glycosomal glyceraldehyde-3-phosphate dehydrogenase in Leishmania mexicana

Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) activity was detected in two cell compartments of Leishmania mexicana promastigotes. These activities could be attributed to two different isoenzymes, one residing in glycosomes, the other in the cytosol. We have cloned and sequenced the genes for both isoenzymes. The glycosomal enzyme is encoded by two tandemly linked genes of identical sequence and contains features frequently found in glycosomal enzymes: the presence of peptide insertions, a small carboxy-terminal extension with a potential glycosomal targeting signal (-SKM) and an excess of positively charged residues (net charge +7). Only one open reading frame was detected for the cytosolic enzyme. The amino acid sequences of the two proteins are only 55% identical. We discuss some evolutionary aspects of the observed organization of the GAPDH genes in the Trypanosomatidae and the role of the two isoenzymes in the metabolism of these organisms. The possibility to develop GAPDH-specific inhibitors that will be effective against the enzyme of various parasitic members of this family is explored.

Allelic polymorphism of the Trypanosoma brucei polyubiquitin gene

We have characterized a second T. brucei polyubiquitin gene (UbB) that is highly similar in the coding and flanking regions to a previously described T. brucei polyubiquitin gene (UbA). However, UbB differs from UbA in 2 respects: (1) the predicted carboxy-terminal amino acid of UbB is methionine, as opposed to leucine in UbA, and (2) UbB contains approximately 13 ubiquitin repeats, as opposed to approximately 30 repeats in UbA. In Southern blots of intact T. brucei DNA separated by pulsed field gel electrophoresis, the polyubiquitin sequences have been shown to reside on band 19, which may contain 3 chromosomes. Three experiments that target a neomycin-resistance gene to the polyubiquitin locus demonstrate a one-to-one ratio of polyubiquitin 3-flanking sequences, which suggests that UbA and UbB are alleles rather than duplications. Four additional strains of T. brucei and one strain of T. equiperdum show variation in their polyubiquitin gene size, suggesting that this is a common polymorphism.

Trisomy and chromosome size changes in hybrid trypanosomes from a genetic cross between Trypanosoma brucei rhodesiense and T. b. brucei

Further analysis of hybrid clones from an experimental cross of Trypanosoma brucei rhodesiense 058 and T. b. brucei 196 shows 2 of the hybrid clones to have DNA contents about 1.5 times parental values. This represents over 40,000 kb of extra DNA. Comparison of the molecular karyotypes of parental and progeny trypanosomes shows that the bulk of the extra DNA constitutes chromosomes greater than 1 Mb in size, although a small proportion can be accounted for by an increased number of mini-chromosomes. The 2 hybrid clones have 3 alleles at several loci for housekeeping genes as shown by RFLP and isoenzyme analysis. Trisomy of the chromosome carrying phosphoglycerate kinase and tubulin genes and that carrying the phospholipase C gene was demonstrated by analysis of molecular karyotypes. These chromosomes appear prone to substantial size alterations associated with genetic exchange. Our results for one of the hybrid clones are completely consistent with it being triploid and the product of fusion of haploid and diploid nuclei.

Recurrent polymorphisms in small chromosomes of Leishmania tarentolae after nutrient stress or subcloning

Molecular karyotypes of the UC, LEM87 and LEM115 Leishmania tarentolae strains were obtained. All strains had 24-28 chromosomal bands which varied in size between 300 kb and 2.9 Mb. Several recurrent chromosomal polymorphisms occurred in LEM115 after nutrient shock or subcloning. One type of polymorphism involves the truncation of a 365-kb chromosome which contains the miniexon genes. This specific chromosome breakage appears to be induced by the nutrient shock or subcloning process and also occurs spontaneously during routine passage. Another polymorphism is the appearance of a 90-kb minichromosome (115-SNA1) after severe nutrient shock. This appears to be selection of a pre-existing cell type from a mosaic population. The 115-SNA1 minichromosome has sequence homology with a minichromosome in LEM87 cells but shows no homology with any chromosomes in 115wt or other strains. The copy number of 115-SNA1 varies with culture conditions, suggesting a relaxed centromeric control. The nature and origin of this minichromosome is not known.

Loss of the GP46/M-2 surface membrane glycoprotein gene family in the Leishmania braziliensis complex

Immunization with the GP46/M-2 membrane glycoprotein of Leishmania amazonensis has been shown to induce a protective immune response against infection. We have surveyed a variety of trypanosomatid species and genera for the presence and expression of this gene family, information that will be relevant to future vaccine studies against leishmaniasis. Molecular karyotype analysis revealed the presence of GP46/M-2 genes in all members of the Leishmania mexicana complex, Leishmania major, Leishmania donovani, Leishmania tarentolae, and Crithidia fasciculata. In contrast, DNAs from species of the Leishmania braziliensis complex (L. braziliensis, Leishmania guyanensis, and Leishmania panamensis) failed to hybridize to GP46/M-2 probes. Western blot analyses with several polyclonal antisera against the GP46/M-2 protein revealed protein expression in L. major and L. donovani, but not L. panamensis or L. braziliensis. Phylogenetic analysis suggests that a loss of the GP46A gene family occurred following separation of the L. braziliensis complex, prior to speciation events within this complex. These data indicate that GP46/M-2 membrane glycoprotein may not be critical to parasite survival, but may play an ancillary role during the developmental cycle.

Characterization of a candidate gene for GP72, an insect stage-specific antigen of Trypanosoma cruzi

The Trypanosoma cruzi insect stage-specific antigen GP72 was purified from epimastigotes and the amino acid sequences of peptide fragments determined. Oligonucleotides derived from these data were used to amplify and clone a cDNA sequence, which was used to isolate a full-length gene. All the sequenced peptides were encoded within the gene. The characteristics of the encoded 62,600-Da protein, including a potential amino-terminal signal sequence, a hydrophobic carboxy-terminus, and a large number of potential O-glycosylation sites, are consistent with the properties of GP72. No sequence homologies were found in searches of DNA and protein data banks. GP72 is encoded by a single pair of non-telomeric allelic genes.

Molecular cloning and analysis of two tandemly linked genes for pyruvate kinase of Trypanosoma brucei

In Trypanosoma brucei (stock 427) genes encoding the glycolytic enzyme pyruvate kinase are present on two homologous chromosomes. We have cloned and characterized one of the alleles. Two large, tandemly arranged open reading frames were found, each coding for a pyruvate kinase polypeptide of 498 amino acids. The gene sequences differ at 15 positions, resulting in five amino acid substitutions. The calculated molecular masses of the polypeptides are 54,378 Da and 54,363 Da. These values are somewhat smaller than those reported for the subunit molecular mass of the purified protein, which is 57-59 kDa. However, in vitro translation of the DNA region corresponding to the open reading frame, and translation of the RNA in a wheat-germ lysate, yielded a product that comigrated exactly with the native polypeptide in SDS/PAGE. The overall identity between the sequences of the trypanosomal enzyme and the enzymes from other sources is 41-51%. The conserved residues are not equally distributed over the polypeptide. The primary structure of domains A and, to a lesser extent, B, which constitute the active site, are rather well conserved. In contrast, the sequence of domain C, which supposedly is involved in the regulation of the enzyme activity, is much more variable. The cytosolically located pyruvate kinase of T. brucei lacks the specific features found in the majority of the glycolytic enzymes of this organism that are sequestered in a microbody-like organelle, the glycosome. It has neither a relatively high subunit molecular mass, due to unique insertions or terminal extensions, nor a high excess of positively charged amino acids. The polypeptide is shorter than that of most other pyruvate kinases and the calculated net charge is only +3.

Homologous recombination and stable transfection in the parasitic protozoan Trypanosoma brucei

Development of methods for the manipulation of the genomes of parasitic protozoa will lead to enhanced understanding of parasite biology and host-parasite relationships. Efficient gene transfer and targeted integration by homologous recombination were achieved in the parasitic protozoan Trypanosoma brucei, the causative agent of sleeping sickness. An expression vector with the neomycin phosphotransferase gene (neo), under the control of a procyclic acidic repetitive protein (PARP) gene promoter, was targeted into an intergenic region in beta alpha-tubulin-gene tandem array. Sixteen copies of neo were found in a tandem array in one of the transfectants where the PARP promoter controlled alpha-amanitin-resistant transcription of neo, whereas transcription of tubulin genes remained alpha-amanitin-sensitive.