Size-fractionation of the small chromosomes of Trypanozoon and Nannomonas trypanosomes by pulsed field gradient gel electrophoresis

Single nucleotide polymorphisms and copy-number variations in the Trypanosoma brucei repeat (TBR) sequence can be used to enhance amplification and genotyping of Trypanozoon strains

The Trypanosoma brucei repeat (TBR) is a tandem repeat sequence present on the Trypanozoon minichromosomes. Here, we report that the TBR sequence is not as homogenous as previously believed. BLAST analysis of the available T. brucei genomes reveals various TBR sequences of 177 bp and 176 bp in length, which can be sorted into two TBR groups based on a few key single nucleotide polymorphisms. Conventional and quantitative PCR with primers matched to consensus sequences that target either TBR group show substantial copy-number variations in the TBR repertoire within a collection of 77 Trypanozoon strains. We developed the qTBR, a novel PCR consisting of three primers and two probes, to simultaneously amplify target sequences from each of the two TBR groups into one single qPCR reaction. This dual probe setup offers increased analytical sensitivity for the molecular detection of all Trypanozoon taxa, in particular for T.b. gambiense and T. evansi, when compared to existing TBR PCRs. By combining the qTBR with 18S rDNA amplification as an internal standard, the relative copy-number of each TBR target sequence can be calculated and plotted, allowing for further classification of strains into TBR genotypes associated with East, West or Central Africa. Thus, the qTBR takes advantage of the single-nucleotide polymorphisms and copy number variations in the TBR sequences to enhance amplification and genotyping of all Trypanozoon strains, making it a promising tool for prevalence studies of African trypanosomiasis in both humans and animals.

Barcoding in trypanosomes

Trypanosomes (genus Trypanosoma) are parasites of humans, and wild and domestic mammals, in which they cause several economically and socially important diseases, including sleeping sickness in Africa and Chagas disease in the Americas. Despite the development of numerous molecular diagnostics and increasing awareness of the importance of these neglected parasites, there is currently no universal genetic barcoding marker available for trypanosomes. In this review we provide an overview of the methods used for trypanosome detection and identification, discuss the potential application of different barcoding techniques and examine the requirements of the 'ideal' trypanosome genetic barcode. In addition, we explore potential alternative genetic markers for barcoding Trypanosoma species, including an analysis of phylogenetically informative nucleotide changes along the length of the 18S rRNA gene.

Rediscovery of Trypanosoma (Pycnomonas) suis, a tsetse-transmitted trypanosome closely related to T. brucei

The African tsetse-transmitted trypanosomes are considered to be a well-known group of parasitic protozoa, but in 2008 a novel and distinctive trypanosome related to Trypanosoma brucei was discovered among tsetse isolates from Msubugwe in Tanzania. The host range, distribution and potential pathogenicity of this new trypanosome remain to be elucidated; such studies would be facilitated by a sensitive and specific identification method. Here, we identified two highly repetitive elements in the genome of the new trypanosome: a 177 bp repeat, which was located predominantly on the highly abundant minichromosomes, and a 138 bp repeat, which was widely dispersed in the genome. A PCR test based on each repeat was specific for the new trypanosome and sensitive to <0.1 trypanosome equivalent. These PCR tests were used to identify trypanosomes in archival pig blood smears from the 1950's, confirming the identity of the Msubugwe trypanosome as Trypanosoma (Pycnomonas) suis. We also present data on the molecular karyotype and spliced leader (SL, miniexon) repeat of the new trypanosome, both of which distinguish T. suis from other, better-known African tsetse-transmitted trypanosomes. The rediscovery of T. suis opens new lines of research into the evolution and biology of the African trypanosomes.

Development of real time PCR to study experimental mixed infections of T. congolense Savannah and T. b. brucei in Glossina morsitans morsitans

Tsetse flies are able to acquire mixed infections naturally or experimentally either simultaneously or sequentially. Traditionally, natural infection rates in tsetse flies are estimated by microscopic examination of different parts of the fly after dissection, together with the isolation of the parasite in vivo. However, until the advent of molecular techniques it was difficult to speciate trypanosomes infections and to quantify trypanosome numbers within tsetse flies. Although more expensive, qPCR allows the quantification of DNA and is less time consuming due to real time visualization and validation of the results. The current study evaluated the application of qPCR to quantify the infection load of tsetse flies with T. b. brucei and T. congolense savannah and to study the possibility of competition between the two species. The results revealed that the two qPCR reactions are of acceptable efficiency (99.1% and 95.6%, respectively), sensitivity and specificity and can be used for quantification of infection load with trypanosomes in experimentally infected Glossina morsitans morsitans. The mixed infection of laboratory Glossina species and quantification of the infection suggests the possibility that a form of competition exists between the isolates of T. b. brucei and T. congolense savannah that we used when they co-exist in the fly midgut.

Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427

Trypanosoma brucei evades the adaptive immune response through the expression of antigenically distinct Variant Surface Glycoprotein (VSG) coats. To understand the progression and mechanisms of VSG switching, and to identify the VSGs expressed in populations of trypanosomes, it is desirable to predetermine the available repertoire of VSG genes (the 'VSGnome'). To date, the catalog of VSG genes present in any strain is far from complete and the majority of current information regarding VSGs is derived from the TREU927 strain that is not commonly used as an experimental model. We have assembled, annotated and analyzed 2563 distinct and previously unsequenced genes encoding complete and partial VSGs of the widely used Lister 427 strain of T. brucei. Around 80% of the VSGnome consists of incomplete genes or pseudogenes. Read-depth analysis demonstrated that most VSGs exist as single copies, but 360 exist as two or more indistinguishable copies. The assembled regions include five functional metacyclic VSG expression sites. One third of minichromosome sub-telomeres contain a VSG (64-67 VSGs on ∼96 minichromosomes), of which 85% appear to be functionally competent. The minichromosomal repertoire is very dynamic, differing among clones of the same strain. Few VSGs are unique along their entire length: frequent recombination events are likely to have shaped (and to continue to shape) the repertoire. In spite of their low sequence conservation and short window of expression, VSGs show evidence of purifying selection, with ∼40% of non-synonymous mutations being removed from the population. VSGs show a strong codon-usage bias that is distinct from that of any other group of trypanosome genes. VSG sequences are generally very divergent between Lister 427 and TREU927 strains of T. brucei, but those that are highly similar are not found in 'protected' genomic environments, but may reflect genetic exchange among populations.

Nuclear architecture, genome and chromatin organisation in Trypanosoma brucei

The nucleus of the human pathogen Trypanosoma brucei not only has unusual chromosomal composition, characterised by the presence of megabase, intermediate and minichromosomes, but also chromosome and gene organisation that is unique amongst eukaryotes. Here I provide an overview of current knowledge of nuclear structure, chromatin organisation and chromosome dynamics during interphase and mitosis. New technologies such as chromatin immunoprecipitation, in combination with new generation sequencing and proteomic analysis of subnuclear fractions, have led to novel insights into the organisation of the nucleus and chromatin. In particular, we are beginning to understand how universal mechanisms of chromatin modifications and nuclear position effects are deployed for parasite-specific functions and are centrally involved in genomic organisation and transcriptional regulation. These advances also have a major impact on progress in understanding the molecular basis of antigenic variation.

Fly transmission and mating of Trypanosoma brucei brucei strain 427

Like yeast, Trypanosoma brucei is a model organism and has a published genome sequence. Although T. b. brucei strain 427 is used for studies of trypanosome molecular biology, particularly antigenic variation, in many labs worldwide, this strain was not selected for the genome sequencing project as it is monomorphic and unable to complete development in the insect vector. Instead, the fly transmissible, mating competent strain TREU 927 was used for the genome project, but is not as easily grown or genetically manipulable as strain 427; furthermore, recent findings have spread concern on the potential human infectivity of TREU 927. Here we show that a 40-year-old cryopreserved line of strain 427, Variant 3, is fly transmissible and also able to undergo genetic exchange with another strain of T. b. brucei. Comparison of Variant 3 with lab isolates of 427 shows that all have variant surface glycoprotein genes 117, 121 and 221, and identical alleles for 3 microsatellite loci. Therefore, despite some differences in molecular karyotype, there is no doubt that Variant 3 is an ancestral line of present day 427 lab isolates. Since Variant 3 grows fast both as bloodstream forms and procyclics and is readily genetically manipulable, it may prove useful where a fly transmissible version of 427 is required.

Will the real Trypanosoma b. gambiense please stand up

Controversy has surrounded the differentiation of Trypanosoma brucei gambiense from T. b. rhodesiense (causative agents of Gambian and Rhodesian sleeping sickness, respectively) almost from the moment they were named. In the light of recent findings from biochemical and immunological characterization studies, Wendy Gibson reviews the status of T. b. gambiense to see if there is now a consensus concerning its identity.

Species concepts for trypanosomes: from morphological to molecular definitions?

The way species and subspecies names are applied in African trypanosomes of subgenera Trypanozoon and Nannomonas is reviewed in the light of data from molecular taxonomy. In subgenus Trypanozoon the taxonomic importance of pathogenicity, host range and distribution appear to have been inflated relative to actual levels of genetic divergence. The opposite is true for subgenus Nannomonas, where current taxonomic usage badly underrepresents genetic diversity. Data from molecular characterisation studies are revealing a growing number of genotypes, which may represent distinct taxa. Unfortunately few of these genotypes are yet supported by sufficient biological data to be recognized taxonomically. But we may be missing fundamental epidemiological information, because of our inability to distinguish these trypanosomes in host blood morphologically or in tsetse by their developmental cycle. Molecular taxonomy has led the way in identifying these new genotypes and now offers the key to elucidating the biology of these organisms.

Epidemiology and diagnosis of African trypanosomiasis using DNA probes

The accurate identification of trypanosome species has been a challenging problem in the epidemiology of African trypanosomiasis, both human and animal. The last 10 years have seen great progress through the application of deoxyribonucleic acid (DNA) probe technology, although this has also revealed greater complexity than supposed. While a single repetitive DNA probe can identify all members of the subgenus Trypanosoma (Trypanozoon), including the human pathogens T. brucei gambiense and T. b. rhodesiense as well as the non-tsetse-transmitted trypanosomes T. evansi and T. equiperdum, at least 6 probes are needed to distinguish members of the subgenus Nannomonas, in which only 2 species, T. congolense and T. simiae, were previously recognized. Similarly, the subgenus Duttonella appears to consist of more than one species. Use of this battery of DNA probes to identify the trypanosomes carried by tsetse flies in the field has yielded some surprises about the accuracy (or inaccuracy) of previous identification methods. An unexpectedly high prevalence of mixed infections has been found in all the field studies carried out so far. The large number of infections that remain unidentified by the available probes suggests the existence of other, as yet unknown, trypanosome species. Limited use of the polymerase chain reaction has been made for diagnosis of human and animal trypanosomiasis, due to its high cost.

A novel GFP approach for the analysis of genetic exchange in trypanosomes allowing the in situ detection of mating events

Trypanosoma brucei undergoes genetic exchange in its insect vector by an unknown mechanism. To visualize the production of hybrids in the fly, a tetracycline (Tet)-inducible expression system was adapted. One parental trypanosome clone was transfected with the gene encoding Green Fluorescent Protein (GFP) under control of the Tet repressor in trans; transfection with these constructs also introduced genes for resistance to hygromycin and phleomycin, respectively. An experimental cross with a second parental clone carrying a gene for geneticin resistance produced fluorescent hybrids with both hygromycin and geneticin resistance. These results are consistent with the meiotic segregation and reassortment of the GFP and repressor genes. Fluorescent hybrids were visible in the salivary glands of the fly, but not the midgut, confirming that genetic exchange occurs among the trypanosome life cycle stages present in (or possibly en route to) the salivary glands. In conclusion, the experimental design has successfully produced fluorescent hybrids which can be observed directly in the salivary glands of the fly, and it has been shown that the recombinant genotypes were most probably the result of meiosis.

Molecular characterization of field isolates of human pathogenic trypanosomes

The accurate identification of each of the three subspecies of Trypanosoma brucei remains a challenging problem in the epidemiology of sleeping sickness. Advances in molecular characterization have revealed a much greater degree of heterogeneity within the species than previously supposed. Only group 1 T. b. gambiense stands out as a separate entity, defined by several molecular markers. T. b. rhodesiense is generally too similar to sympatric T. b. brucei strains to be distinguished from them by any particular molecular markers. Nevertheless, characterization of trypanosome isolates from humans and other animals has allowed the identification of potential reservoir hosts of T. b. rhodesiense. The recent discovery of a gene for human serum resistance may provide a useful marker for T. b. rhodesiense in the future. There have been few attempts to find associations between genetic markers and other biological characters, except human infectivity. However, virulence or fly transmissibility have been correlated with molecular markers in some instances.

Diversity and dynamics of the minichromosomal karyotype in Trypanosoma brucei

The genome of African trypanosomes contains a large number of minichromosomes. Their only proposed role is in the expansion of the parasites' repertoire of telomeric variant surface glycoprotein (VSG) genes as minichromosomes carry silent VSG gene copies in telomeric locations. Despite their importance as VSG gene donors, little is known about the actual composition of the minichromosomal karyotype and the stability of its inheritance. In this study we show, by using high-resolution pulsed-field electrophoresis, that a non-clonal trypanosome population contains an extremely diverse pattern of minichromosomes, which can be resolved into less complex clone-specific karyotypes by non-selective cloning. We show that the minichromosome patterns of such clones are stable over at least 360 generations. Furthermore, using DNA markers for specific minichromosomes, we demonstrate the mitotic stability of these minichromosomes within the population over a period of more than 5 years. Length variation is observed for an individual minichromosome and is most likely caused by a continuous telomeric growth of approximately 6 bp per telomere per cell division. This steady telomeric growth, counteracted by stochastic large losses of telomeric sequences is the most likely cause of minichromosome karyotype heterogeneity within a population.

Genetic exchange in the trypanosomatidae

The only trypanosomatid so far proved to undergo genetic exchange is Trypanosoma brucei, for which hybrid production after co-transmission of different parental strains through the tsetse fly vector has been demonstrated experimentally. Analogous mating experiments have been attempted with other Trypanosoma and Leishmania species, so far without success. However, natural Leishmania hybrids, with a combination of the molecular characters of two sympatric species, have been described amongst both New and Old World isolates. Typical homozygotic and heterozygotic banding patterns for isoenzyme and deoxyribonucleic acid markers have also been demonstrated amongst naturally-occurring T. cruzi isolates. The mechanism of genetic exchange in T. brucei remains unclear, although it appears to be a true sexual process involving meiosis. However, no haploid stage has been observed, and intermediates in the process are still a matter for conjecture. The frequency of sex in trypanosomes in nature is also a matter for speculation and controversy, with conflicting results arising from population genetics analysis. Experimental findings for T. brucei are discussed in the first section of this review, together with laboratory evidence of genetic exchange in other species. The second section covers population genetics analysis of the large body of data from field isolates of Leishmania and Trypanosoma species. The final discussion attempts to put the evidence from experimental and population genetics into its biological context.

Nuclear and genome organization of Trypanosoma brucei

In this article, Klaus Ersfeld, Sara Melville and Keith Gull review current understanding of the structural organization of the nucleus of Trypanosoma brucei, and summarize recent data pertinent to the organization of its genome. Until recently, the cell biology of the trypanosome nucleus and issues of DNA organization and gene expression have often been treated as separate themes. However, recent work emphasizes the need for a more holistic approach to understanding these aspects of the biology of this parasite.

Segregation of minichromosomes in trypanosomes: implications for mitotic mechanisms

In addition to 11 pairs of housekeeping chromosomes, the genome of Trypanosoma brucei contains approximately 100 minichromosomes that are probably involved in the ability of the parasite to evade the host's immune response. This minichromosomal population is segregated on the mitotic spindle. How this is achieved provides insight into potential segregation mechanisms for small DNA molecules in eukaryotic microorganisms.

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.

Parasite genome analysis. Genome research in Trypanosoma brucei: chromosome size polymorphism and its relevance to genome mapping and analysis

Before the development of pulsed field gel electrophoresis (PFGE), little was known of the chromosomal organization of Trypanosoma brucei. This technique first revealed that the nuclear genome was subdivided into distinct size classes of chromosomes, subsequently shown to have disparate genetic roles in the life cycle of the parasite. PFGE also facilitated the determination of chromosome ploidy and the observation that apparent homologues often differed significantly in size within and between isolates. While the biological reasons underlying this plasticity may prove very interesting, nevertheless it could pose real problems for the global analysis of the T. brucei genome. Therefore, before undertaking large scale physical mapping, it is necessary to determine the number and size of chromosomes in the reference stock; to compare these to the chromosomes of other stocks to determine the relative sizes of homologues; and to investigate the deoxyribonucleic acid content of the size of polymorphic regions in order to assess how these may affect the execution of a physical mapping programme.

Wide variation in DNA content among isolates of Trypanosoma brucei ssp

The DNA contents of 18 Trypanosoma brucei ssp. stocks were compared using flow cytometry, karyotype analysis and quantitation of repetitive DNA by Southern blotting and hybridisation. The DNA contents of Type 1 T. b. gambiense stocks were lower than those of non-gambiense stocks, but both groups showed a wide range of variation in DNA content. Amongst T. b. gambiense stocks. Mabia at the lower end of the range had 14% less DNA than Dal 972 at the top of the range. Similarly, amongst non-gambiense stocks. 117R at the lower end of the range had 14% less DNA than LM55 at the top of the range. The T. b. gambiense stock Mabia had 29% less DNA than non-gambiense stock LM55. The DNA content of Type II T. b. gambiense stocks had minichromosomes albeit fewer than non-gambiense stocks. This result was verified by hybridisation with probes for satellite DNA and a telomere-specific repeat. Hybridisation with the probe for the beta-tubulin genes also revealed an apparent reduction of gene copy number T. b. gambiense relative to non-gambiense stocks. In conclusion, there is a wide range of variation in genome size in T. brucei ssp., with T. b. gambiense stocks at the lower end of the range. The reduction in genome size correlates with loss of repeated genes and non-coding sequences in T. b. gambiense stocks, and is not continued to chromosomes of a particular size.

Detection of Trypanosoma brucei spp. in human blood by a nonradioactive branched DNA-based technique

We have developed a nonradioactive branched DNA (bDNA)-based assay for the diagnosis of the African trypanosomiases in simple buffy coat preparations of human blood. Two repetitive DNA sequences specific to the Trypanosoma brucei complex were chosen as targets of the bDNA assay, a technique which amplifies the signal from a target molecule rather than the target itself. Comparable sensitivities were observed with cloned target sequences, purified T. brucei DNA, procyclic trypanosomes, and bloodstream trypomastigotes. The results of bDNA analysis of human blood samples from Côte d'Ivoire (n = 50) showed excellent agreement with those of buffy coat microscopy. The bDNA technology offers certain advantages over alternative molecular biological techniques, including the simplicity of sample preparation and of the procedure itself, the stability of the reagents, the ability to process large numbers of samples simultaneously, and freedom from crosscontamination artifacts. We have successfully applied the bDNA technique to the detection of T. brucei in clinical samples from regions where T. brucei infection is endemic; to our knowledge, this is the first report of the molecular detection of T. brucei in human blood.

Artificial linear mini-chromosomes for Trypanosoma brucei

We have constructed artificial linear mini- chromosomes for the parasitic protozoan Trypanosoma brucei. These chromosomes exist at approx. 2 copies per cell, are indefinitely stable under selection but are lost from 50% of the transformed population in approx. 7 generations when grown in the absence of selective pressure. Consistent with results obtained earlier with natural chromosomes in T.brucei, the telomeres on these artificial chromosomes grow, adding approx. 1- 1.5 telomeric repeats per generation. The activity of a procyclic acidic repetitive protein (parp) gene promoter on these elements is unaffected by its proximity to a telomere, implying the lack of a telomere-proximal position effect (TPE) in procyclic trypanosomes. Among other things, these autonomously replicating dispensable genetic elements will provide a defined system for the study of nuclear DNA replication, karyotypic plasticity and other aspects of chromosomal behavior in this ancient eukaryotic lineage.

The P-glycoprotein-related gene family in Leishmania

P-glycoprotein gene amplification has been described in several drug-resistant parasitic protozoa. The first P-glycoprotein related gene described in Leishmania was ltpgpA, a gene frequently amplified in arsenite resistant Leishmania. Hybridization experiments indicated that ltpgpA was part of a gene family. In addition to ltpgpA, four novel genes were cloned that are present in two loci: ltpgpB and ltpgpC tandemly linked to ltpgpA on a 800-kb chromosome; and ltpgpD and ltpgpE closely linked on a chromosome ranging from 950 kb to 1400 kb, depending on the Leishmania species. Another P-glycoprotein gene, homologous to the more recently described ldmdr1, was linked to ltpgpD and ltpgpE. Nucleotide sequencing of ltpgpB and ltpgpE revealed that the Leishmania P-glycoprotein-related genes have diverged considerably from the main branch of P-glycoproteins and are more homologous to the recently described multidrug resistance-associated protein found in multidrug-resistant human lung cancer cell lines. Cross-resistance studies and gene transfection experiments indicated that under the conditions tested only ltpgpA and ldmdr1 are involved in resistance to arsenite and antimonials or hydrophobic drugs such as vinblastine respectively.

Cloning and expression of the dihydrofolate reductase-thymidylate synthase gene from Trypanosoma cruzi

We have cloned, sequenced and expressed the Trypanosoma cruzi gene encoding the bifunctional protein dihydrofolate reductase-thymidylate synthase (DHFR-TS). The strategy followed for the isolation of positive clones from a genomic library was based on the construction of a probe by the amplification of highly conserved sequences of the TS domain by the polymerase chain reaction. Translation of the open reading frame of 1563 bp yields a polypeptide of 521 amino acids with a molecular mass of 58829 Da. For heterologous expression of T. cruzi DHFR-TS in Escherichia coli, the entire coding sequence was amplified by polymerase chain reaction and cloned into the plasmid vector pKK223.3. The presence of catalytically active DHFR-TS was demonstrated by complementation of the Thy- E. coli strain chi 2913 and the DHFR- Thy- E. coli strain PA414. The gene is expressed as an active protein which constitutes approximately 2% of the total cell soluble protein. Recombinant bifunctional enzyme and the DHFR domain have been purified by methotrexate-Sepharose chromatography to yield 1-2 mg of active DHFR-TS per litre of culture. Southern and electrophoretic analyses using the coding sequence as probe indicated that the T. cruzi enzyme is encoded by a single copy gene which maps to two bands of approximately 990 kb and 1047 kb. It appears that T. cruzi is diploid for the DHFR-TS gene which is located on two different-sized homologous chromosomes.

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.

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.

Molecular karyotype analysis in Leishmania

The advent of pulsed field electrophoresis has allowed a direct approach to the karyotype of Leishmania. The molecular karyotype thus obtained is a stable characteristic of a given strain, although minor modifications may occur during in vitro maintenance. Between 20 and 28 chromosomal bands can be resolved depending on the strain, ranging in size from approximately 250 to 2600 kb. The technique has revealed a striking degree of polymorphism in the size and number of the chromosomal bands between different strains, and this seems independent of the category (species, zymodeme, population) to which the strains belong. It appears that only certain strains originating from the same geographic area may share extensive similarities. This polymorphism can largely be accounted for by chromosome size variations, which can involve up to 25% of the chromosome length. As a result, homologous chromosomes can exist in versions of markedly different size within the same strain. When this occurs with several different chromosomes, the interpretation of PFE patterns appears difficult without prior identification of the size-variable chromosomes and of the chromosome homologies. DNA deletions and amplifications have been shown to account for some of these size modifications, but other mechanisms are probably involved; nevertheless, interchromosomal exchange does not seem to play a major role in these polymorphisms. These chromosomal rearrangements, yet in an early stage of characterization, exhibit two relevant features: they seem (1) to affect essentially the subtelomeric regions and (2) to occur in a recurrent nonrandom manner. Chromosomal rearrangements sharing the same characteristics have been identified in yeast and other protozoa such as Trypanosoma and Plasmodium. The significance of this hypervariability for the biology of the parasite remains unknown, but it can be expected that such mechanisms have been maintained for some purpose; genes specifically located near chromosome ends might benefit from rapid sequence change, alternating activation, or polymorphism of expression. The chromosomal plasticity could represent a general mode of mutation in these parasites, in parallel with genetic exchange which may be uncommon in nature. The molecular characterization of these rearrangements, the identification of each chromosome with the help of physical restriction maps and linkage maps, and the collation of such data on a number of strains and species should allow a significant progress in the understanding of the genetics of Leishmania, in particular as regards ploidy, generation of phenotypic diversity, and genome evolution. Finally, like other models, this is susceptible to improve our knowledge of DNA-DNA interactions and of the chromosome functional structure and dynamics.

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.

The Trypanosoma brucei DNA polymerase alpha core subunit gene is developmentally regulated and linked to a constitutively expressed open reading frame

As an initial step towards the characterization of replicative DNA polymerases of trypanosomes, we have cloned, sequenced and examined the expression of the Trypanosoma (Trypanozoon) brucei brucei gene that encodes the DNA polymerase alpha catalytic core (pol alpha). The protein sequence contains the six conserved regions that have been recognized previously in eukaryotic and viral replicative DNA polymerases. In addition, we have identified a seventh region which appears to be conserved primarily in alpha-type DNA polymerases. The T.brucei DNA pol alpha core N-terminus is 123 and 129 amino acids smaller than that of the human and yeast homologue, respectively. The gene is separated by 386 bp from an upstream open reading frame (ORF) of 442 codons. Stable transcripts of the upstream sequence are detected in both dividing and non-dividing forms, while pol alpha transcripts are detected principally in dividing forms. Allelic copies of the T.brucei pol alpha region exhibit restriction site polymorphisms; one such sequence polymorphism affects the amino acid sequence of the T.brucei DNA pol alpha core. The T.brucei pol alpha region cross-hybridizes weakly with that of T.(Nannomonas) congolense and T.(Duttonella) vivax.

Long-range restriction maps of size-variable homologous chromosomes in Leishmania infantum

In order to clarify the interpretation of molecular karyotype polymorphisms in Leishmania, the three smallest chromosomes from five cloned strains of Leishmania infantum were identified by chromosome-specific anonymous DNA probes. The presence in the same clone of homologous chromosomes of a different size was demonstrated. The chromosome size polymorphism appeared even more dramatic, with size variations affecting up to 20% of the chromosome, and the two smallest bands in one strain being equivalent to six bands in another strain. Long-range restriction maps of five different-sized homologues of chromosome I showed the size-variation to be located to a terminal fragment in 4 out of 5 cases, and to a central fragment in one. The size-variable sequence was present on at least three other chromosomes as determined by hybridisation analysis. This suggests an instability of the subtelomeric regions such as that in Plasmodium falciparum. Lastly, the finding of several pairs of distinct-sized homologous chromosomes, together with other studies, strongly suggest that Leishmania is diploid in at least part of its chromosomal complement.

Identification and chromosomal locations of a family of cytochrome P-450 genes for pisatin detoxification in the fungus Nectria haematococca

The ability to detoxify the phytoalexin, pisatin, an antimicrobial compound produced by pea (Pisum sativum L.), is one requirement for pathogenicity of the fungus Nectria haematococca on this plant. Detoxification is mediated by a cytochrome P-450, pisatin demethylase, encoded by any one of six Pda genes, which differ with respect to the inducibility and level of pisatin demethylase activity they confer, and which are associated with different levels of virulence on pea. A previously cloned Pda gene (PdaT9) was used in this study to characterize further the known genes and to identify additional members of the Pda family in this fungus by Southern analysis. DNA from all isolates which demethylate pisatin (Pda+ isolates) hybridized to PdaT9, while only one Pda- isolate possessed DNA homologous to the probe. Hybridization intensity and, in some cases, restriction fragment size, were correlated with enzyme inducibility. XhoI/BamHI restricted DNA from reference strains with a single active Pda allele had only one fragment with homology to PdaT9; no homology attributable to alleles associated with the Pda- phenotype was found. Homology to this probe was also limited to one or two restriction fragments in most of the 31 field isolates examined. Some unusual progeny from laboratory crosses that failed to inherit demethylase activity also lost the single restriction fragment homologous to PdaT9. At the chromosome level, N. haematococca is highly variable, each isolate having a unique electrophoretic karyotype. In most instances, PdaT9 hybridized to one or two chromosomes containing 1.6-2 million bases of DNA, while many Pda- isolates lacked chromosomes in this size class. The results from this study of the Pda family support the hypothesis that deletion of large amounts of genomic DNA is one mechanism that reduces the frequency of Pda genes in N. haematococca, while simultaneously increasing its karyotypic variation.

Genetic exchange in Trypanosoma brucei brucei: variable chromosomal location of housekeeping genes in different trypanosome stocks

A Trypanosoma brucei brucei clone from West Africa was crossed with another T. b. brucei clone from the East African kiboko group. This group is defined by characteristic isoenzyme patterns and kinetoplast DNA maxicircle polymorphisms, and is associated with a wild animal-tsetse transmission cycle. Three types of clone were isolated from the cross, 2 of which were hybrid. The hybrids were heterozygotic at 7 loci where the parents were homozygotic and the hybrids also had molecular karyotypes different from those of both parents. Both molecular karyotypes had an extra non-parental band, which was shown to have a different origin in the 2 sets of clones by Southern analysis with various housekeeping gene probes. This analysis also revealed that although the GPI and PGK genes reside on the same chromosome in parent J10, they are on different chromosomes in parent 196. Hybridisation of PFG blots carrying a variety of other trypanosome stocks confirmed that the GPI gene is not always in the same linkage group as the PGK gene cluster. Given that genetic exchange in trypanosomes involves meiosis, such differences in gene linkage will give rise to progeny with incorrect gene dosage, i.e., certain crosses will be partially infertile. This incipient speciation may explain why natural populations of T. brucei spp. are observed not to be in a randomly mating equilibrium.

The molecular epidemiology of parasites

The explosion of new techniques, made available by the rapid advance in molecular biology, has provided a battery of novel approaches and technology which can be applied to more practical issues such as the epidemiology of parasites. In this review, we discuss the ways in which this new field of molecular epidemiology has contributed to and corroborated our existing knowledge of parasite epidemiology. Similar epidemiological questions can be asked about many different types of parasites and, using detailed examples such as the African trypanosomes and the Leishmania parasites, we discuss the techniques and the methodologies that have been or could be employed to solve many of these epidemiological problems.

DNA fingerprinting of the human intestinal parasite Giardia intestinalis with hypervariable minisatellite sequences

Individual isolates of the Giardia duodenalis group of protozoan intestinal parasites were identified by DNA fingerprinting with hypervariable minisatellite sequences. A morphologically identical parasite is found in some forty different animal species. Although the species name intestinalis is reserved for the human isolates, electrophoretic karyotyping suggests that most duodenalis isolates fall into the same species grouping. Distinction based upon morphology, restriction endonuclease cleavage of genomic DNA or isoenzyme analysis has not been adequate to identify individual strains. The successful use of hypervariable sequences in the identification of individual human genomes encouraged us to examine the use of these same sequences for the possible identification of parasite isolates. We initially use as a fingerprinting probe the genome of the bacteriophage M13, which has repeated sequences recognising homologous hypervariable sequences in the human genome. The M13 probe recognises a weakly homologous set of hypervariable sequences in Giardia. The number of informative bands is comparable to those seen in mammals, since the lower molecular weight bands are also useful. There is considerable divergence in the sequences of individual Giardia minisatellites. Some cloned Giardia hypervariable sequences are more homologous to M13 than they are to each other. Similar results were observed with the hypervariable repeat sequences 3' to the human alpha-globin gene when they were used as a probe to distinguish Giardia isolates. The poly(dA-dC).poly(dG-dT) probe which recognises frequent TG tracts in a number of organisms also detects a few variable bands amidst a hybridisation background in the Giardia genome. Thus Giardia isolates which could not be distinguished by restriction endonuclease cleavage, antibody typing or isoenzyme analysis have been identified by DNA fingerprinting procedures. Detailed analysis of strain movement, resurgence, variation, host range and drug resistance is now possible. Similar families of sequences may be widespread in lower eukaryotes and useful for generating individual specific fingerprints. A procedure for detecting individual parasites is also presented. Since Giardia is regarded as the most ancient eukaryote before the occurrence of symbiosis with purple non-sulphur bacteria to generate mitochondria, the identification of hypervariable sequences in the Giardia genome should also aid in understanding the mechanism of generation and evolution of these sequences.

Chromosomal localization of seven cloned antigen genes provides evidence of diploidy and further demonstration of karyotype variability in Trypanosoma cruzi

The karyotype of Trypanosoma cruzi was studied by pulsed field gel electrophoresis (PFGE) in conditions that allowed 20-25 chromosome bands to be detected. However, several of these bands were present in non-equimolar amounts, suggesting that the total chromosome number is considerably higher. The patterns obtained with the different cloned and uncloned strains were unique, suggesting that the karyotype of T. cruzi is highly variable. The chromosomal localizations of seven cloned genes were determined by Southern blotting of PFGE-separated chromosomes. Three of the clones gave rise to similar patterns and mapped on a chromosome or a family of chromosomes larger than 1.6 Mb. Two clones mapped on either single or pairs of chromosomes, which in some cases differed considerably in size between the different strains tested, suggesting that extensive chromosome rearrangements occur in T. cruzi. Another clone hybridized to several chromosomes in most strains and probably represents a family of genes. Lastly, one clone hybridized to nearly all chromosomes. Many of the clones hybridized to pairs of restriction fragments in the different strains, suggesting that they are allelic. For one of the clones it was possible to provide further evidence for the allelic nature of the fragments by establishing detailed restriction maps around them and by showing that the two fragments in a pair hybridized to chromosomes which differed slightly in size. Taken together, the results infer that the genome of T. cruzi epimastigotes is diploid.

Molecular karyotype of Entamoeba histolytica and Entamoeba invadens

We report the size-fractionation of Entamoeba histolytica and E. invadens deoxyribonucleic acid (DNA) by pulsed field gradient electrophoresis. Using 3 different electrophoretic conditions, we were able to resolve 6 to 9 bands between 300 and 2000 kilobases (kb), distributed in 16-22 large and up to 31 small chromosomes for E. histolytica DNA. For E. invadens, 4 to 5 bands between 300 and over 2000 kb were resolved and discriminated in 4 large and 6 small chromosomes. A ribosomal probe from Trypanosoma brucei hybridized with a 1100 kb band in E. histolytica strain HM1:IMSS and with a 1000 kb band in clone A of strain HM1:IMSS. Both cell lines also showed hybridization at the origin. The ribosomal probe hybridized only at the origin of the E. invadens DNA lane. A triosephosphate isomerase DNA probe from T. brucei hybridized only with a 2000 kb band in E. invadens, indicating that banding patterns are chromosomal bands and ruling out the possibility of DNA degradation.

Specific probes for Trypanosoma (Trypanozoon) evansi based on kinetoplast DNA minicircles

Trypanosoma evansi is difficult to distinguish from other members of subgenus Trypanozoon, save for its inability to develop cyclically in the tsetse fly and its characteristic kinetoplast DNA (kDNA). We have used cloned kDNA minicircle fragments as specific probes to distinguish T. evansi from other trypanosomes of subgenus Trypanozoon. Two probes were required, each specific for one of the subgroups of T. evansi previously described. Probe A reacted only with the major isoenzyme group of T. evansi stocks, which have minicircle type A and occur in South America, Kenya, Sudan, Nigeria and Kuwait. The probe did not hybridise with various Trypanosoma brucei spp. stocks, Trypanosoma vivax, Trypanosoma congolense or Trypanosoma simiae, nor with trypanosomes of the minor isoenzyme group of T. evansi stocks found in Kenya with type B minicircles. Probe B was specific for the latter. The probes were sensitive down to a level of 100 trypanosomes in a dot blot. These probes thus provide a simple means of distinguishing T. evansi from T. brucei spp. using comparatively few trypanosomes and without resort to tsetse transmission experiments.

Extensive homologies between Leishmania donovani chromosomes of markedly different size

The smallest chromosome (230 kb) of the HU3 stock of Leishmania donovani was purified from an orthogonal field alternation (OFAGE) gel, digested with PstI and cloned into the plasmid pUC13. When used to probe Southern blots of OFAGE gels, the cloned sequences recognised one or more large chromosomes in all L. donovani stocks and a small chromosome in HU3 and two additional L. donovani stocks (Khartoum and DD8). These probes recognised a single band on Southern blots of restricted genomic DNA regardless of their homologies to only large or large and small chromosomes. Analysis of lambda EMBL3 genomic clones selected with the same probes suggested that at least 30 kb of DNA was common to large and small chromosomes. Most of the cloned sequences were mapped to the same 50-kb SfiI fragment present in both chromosomes. These data indicate that two or more L. donovani chromosomes of markedly different size on OFAGE gels are extensively homologous.

Chromosomes of Blastocystis hominis

Three stocks of Blastocystis hominis were adapted to monophasic culture in minimal essential medium (MEM) and the chromosomes of these stocks separated by field inversion gel electrophoresis (FIGE). Ten-twelve chromosomes were distinguished in the electrophoretic karyotype of these three stocks over the range 200 kilobase pairs to greater than 1 megabase pairs. The karyotype of each stock was different. Three DNA probes, B10, B30 and B31, derived from the Netsky stock isolated in America were used as chromosome markers. Probe B10 hybridized to chromosomes of the same size in two of the stocks, one of which was isolated in the U.S.A. and the other in Queensland. B30 and B31 hybridized to a similar number of chromosomes of different sizes in these two stocks. The third stock, from Australia, did not hybridize at all with probes B10 and B30 and only weakly with probe B31.

Analysis of a genetic cross between Trypanosoma brucei rhodesiense and T. b. brucei

Two trypanosome clones, representing East and West African homozygotes at 2 isoenzyme loci (T. b. rhodesiense MHOM/ZM/74/58 [CLONE B] and T. b. brucei MSUS/CI/78/TSW 196 [CLONE A]), were cotransmitted through tsetse flies and the resulting trypanosome populations checked for the presence of non-parental karyotypes by pulsed-field gel electrophoresis. Ten clones isolated from these populations proved to have 5 different recombinant genotypes by analysis of nuclear and kinetoplast DNA (kDNA) polymorphisms. It is inferred that genetic exchange occurred between the 2 trypanosome clones in the fly, as previously reported for 2 other T. brucei spp. clones by Jenni and colleagues. For the most part, the hybrid clones shared many characteristics with both parents and their genotypes were consistent with segregation and reassortment of parental alleles. The least amount of genetic material exchanged was kDNA alone. Regarding the mechanism of genetic exchange, several hybrid clones had identical and unique nuclear DNA polymorphisms, but different kDNA type. Assuming that the same reassortment of nuclear markers is unlikely to occur by chance, these clones most probably arose from a predecessor carrying both types of kDNA.

Glucosephosphate isomerase from Trypanosoma brucei. Cloning and characterization of the gene and analysis of the enzyme

In Trypanosoma brucei the enzyme glucose-6-phosphate isomerase, like most other enzymes of the glycolytic pathway, resides in a microbody-like organelle, the glycosome. Here we report a detailed study of this enzyme, involving a determination of its kinetic properties and the cloning and sequence analysis of its gene. The gene codes for a polypeptide of 606 amino acids, with a calculated Mr of 67280. The protein predicted from the gene sequence has 54-58% positional identity with its yeast and mammalian counterparts. Compared to those other glucose-6-phosphate isomerases the trypanosomal enzyme contains an additional 38-49 amino acids in its N-terminal domain, as well as a number of small insertions and deletions. The additional amino acids are responsible for the 5-kDa-larger subunit mass of the T. brucei enzyme, as measured by gel electrophoresis. The glucose-6-phosphate isomerase of the trypanosome has no excess of positive residues and, consequently, no high isoelectric point, in contrast to the other glycolytic enzymes that are present in the glycosome. However, similar to other glycosomal proteins analyzed so far, specific clusters of positive residues can be recognized in the primary structure. Comparison of the kinetic properties of the T. brucei glucose-6-phosphate isomerase with those of the yeast and rabbit muscle enzymes did not reveal major differences. The three enzymes have very similar pH profiles. The affinity for the substrate fructose 6-phosphate (Km = 0.122 mM) and the inhibition constant for the competitive inhibitor gluconate 6-phosphate (Ki = 0.14 mM) are in the same range as those of the similar enzymes. The Km shows the same strong dependence on salt as the rabbit muscle enzyme, although somewhat less than the yeast glucose-6-phosphate isomerase. The trypanocidal drug suramin inhibits the T. brucei and yeast enzymes to the same extent (Ki = 0.29 and 0.36 mM, respectively), but it had no effect on the rabbit muscle enzyme. Agaricic acid, a potent inhibitor of various glycosomal enzymes of T. brucei, has also a strong, irreversible effect on glucose-6-phosphate isomerase, while leaving the yeast and mammalian enzymes relatively unaffected.

Geographic variation in Giardia karyotypes

Chromosomes of 41 stocks of Giardia duodenalis derived from humans and 14 stocks from other animal species were analysed by field inversion gel electrophoresis (FIGE). These stocks have two predominant karyotypes as judged by FIGE which appear to fit a geographic distribution. Under FIGE conditions used to optimize the detection of size variation in Giardia chromosomes, five or six major chromosomes could be identified. Most of the stocks derived from North America have three major chromosomes smaller than 800 kb while most of the Australian stocks have four. A few exceptions, and minor variations, of these karyotypes were observed. It was estimated that not all of the DNA entered the gel, the remainder being trapped conformations or very large chromosomes. Karyotypes of Giardia stocks from different animal hosts and human sources within a geographical region are similar.

Trypanosoma brucei contains two RNA polymerase II largest subunit genes with an altered C-terminal domain

We have identified and cloned four trypanosomal RNA polymerase largest subunit genes. Here, we present the molecular analysis of two genes, Trp4.8 and Trp5.9. The sequence of these genes shows that they are almost identical to each other and indicates that they encode the largest subunit of RNA polymerase II. Both genes contain a C-terminal extension that is clearly distinct from that of other eukaryotic RNA polymerase II genes, because it lacks the common tandemly repeated heptapeptide sequence and is rich in acidic amino acids. It shares many potential phosphorylation sites, however, with the C-terminal extension of other eukaryotic RNA polymerase II large subunits. The presence of two RNA polymerase II loci suggests that a fourth RNA polymerase could be formed. Interestingly, the fourth gene is only found in species exhibiting antigenic variation.

Origins and organization of genetic diversity in natural populations of Trypanosoma brucei

Experimental work has established that a sexual process can occur in African trypanosomes (Jenni, Marti, Schweizer, Betschart, Le Page, Wells, Tait, Paindavoine, Pays & Steinert, 1986; Paindavoine, Zampetti-Bosseler, Pays, Schweizer, Guyaux, Jenni & Steinert, 1986; Tait, personal communication). However, the role of the process in natural populations of trypanosomes is poorly understood. This paper considers what information can be gained from analyses of isoenzyme polymorphism. A cladistic approach is used to help determine whether trypanosome diversity could have been produced by mutation alone. When applied to three East African populations of Trypanosoma brucei it provides evidence that some diversity has arisen through a sexual process; this explains the variation observed within a locality and can account for the evolution of differences between localities. However, the extent to which genetic exchange currently operates is less clear. Analysis of genotype frequencies indicates that agreements with Hardy-Weinberg expectations can be obtained even if genetic exchange exerted no influence over genotype frequencies. Moreover, analysis of joint locus frequencies reveals disequilibrium between loci and that trypanosome populations may be lacking several genotype combinations. Thus, genetic exchange may not occur sufficiently frequently, or in such a way as to break up associations between loci. The relevance of these observations to the evolution of strain differences within T. brucei is discussed.

The timing and frequency of hybrid formation in African trypanosomes during cyclical transmission

The frequency of hybrid formation between two Trypanosoma brucei clones during cyclical transmission through Glossina morsitans centralis was analyzed. In two independent experiments, teneral G. m. centralis were infected with an equal mixture of two T. brucei clones showing different homozygous isoenzyme patterns for isocitrate dehydrogenase (ICD; E.C.1.1.1.42) and alkaline phosphatase (AP; E.C. 3.1.3.1). Trypanosomes were cyclically transmitted to mice from 23 infective flies and the subsequent bloodstream-form populations were characterized by isoenzyme electrophoresis. Heterozygous patterns for ICD and AP indicated that hybrid formation occurred in at least 9 of the 23 vectors. There was further evidence that extrusion of hybrid parasites with saliva from a single fly was not necessarily continuous but could alter over time with the occurrence of either or both of the homozygous parental clones.

The genome and the antigen gene repertoire of Trypanosoma brucei gambiense are smaller than those of T. b. brucei

The amount of nuclear DNA of Trypanosoma brucei gambiense is only 70% of that of T. b. brucei. The difference is partially due to depletion of 50-150 kb mini-chromosomes in T. b. gambiense, as well as a reduction in the content of some repetitive DNA families. Quantitation of 'barren' DNA regions characteristic of the 5' environment of telomeric antigen genes confirms that the T. b. gambiense genome contains fewer chromosome ends, and thus most probably fewer telomeric antigen genes, than T. b. brucei. The extent of the antigen gene repertoire of the two subspecies has been estimated by hybridization with probes specific for the conserved 3' region of antigen genes. It appears that the repertoire of the gambiense subspecies is only about 50% of that of T. b. brucei. These observations are discussed with regard to the stability of the T. b. gambiense repertoire.

Molecular karyotype of five species of Leishmania and analysis of gene locations and chromosomal rearrangements

The molecular karyotypes of five species of Leishmania were studied by pulsed field gradient gel electrophoresis (PFGGE) of chromosome-sized DNA bands. Each species exhibits a unique pattern of 22-28 bands in the size range approximately 200-2200 kb whereas strains of one species exhibit similar karyotypes. Analysis of the behaviour of kinetoplast DNA during PFGGE showed that minicircle DNA remains confined to the gel slot but a proportion of the maxicircle DNA fractionates as a low molecular weight band below band 1. The band location of genes for alpha and beta tubulin, the 5' spliced leader sequence (5'SL), heat shock proteins 70 (hsp 70) and 83 (hsp 83) and thymidylate synthase-dihydrofolate reductase (TS-DHFR) were analysed. Housekeeping genes are not clustered in Leishmania but are found on at least 7 bands in L. major. The hsp 83 gene is linked to the tandemly repeated beta tubulin allele on band 21 in L. major. Among different species, the location of the unlinked hsp 83 and hsp 70 genes is conserved whereas the TS-DHFR and 5'SL sequences are found on bands of varying size. The 5'SL gene may be rearranged in L. enriettii and two 5'SL loci were identified in L. donovani and L. tropica. The conservation of loci in strains of L. major suggests that the chromosomal genetic linkage map should be a reliable marker for identifying unknown isolates of Leishmania. Sequences on one band in L. mexicana sp. were shared among several bands and distributed on homologous and non-homologous bands in other species showing that DNA sequences are rearranged during speciation in Leishmania.

Chromosome size polymorphisms of Leishmania donovani

A minimum of 22 chromosomes were found in all Leishmania donovani stocks examined by orthogonal field alternation gel electrophoresis (OFAGE). Chromosome sizes ranged from approximately 270 to 4000 kb. Certain chromosomes were polymorphic in size between stocks and chromosomes present in some stocks had no apparent equivalent in others. Specific polymorphisms were useful in distinguishing the subspecies L. d. donovani, L. d. infantum and L. d. chagasi and African L. donovani stocks but there were karotypic differences within these taxa. Radiolabelled DNA derived from whole chromosomes was hybridised to OFAGE Southern blots. Chromosome 1 of L. d. donovani was homologous to two larger chromosomes in all stocks. Chromosome 2 of certain L. d. chagasi and L. d. infantum stocks was homologous to both chromosomes 2 and 3 of L. d. donovani: this suggested that translocation between chromosomes may have contributed to the size polymorphisms. The smallest chromosome seen (270 kb) was unique to the African stock HU3. It was not homologous to small chromosomes in L. d. donovani, L. d. infantum or L. d. chagasi. The small chromosome did hybridise to two small chromosomes in another African stock, Khartoum, and to a large chromosome present in all stocks. The beta-tubulin gene was mapped to chromosomes 21/22, 13 and 7 with strongest hybridisation to 21/22. alpha-Tubulin was mapped to chromosomes 9. The alpha- and beta-tubulin arrangement was highly conserved.

DNA contents and molecular karyotypes of hybrid Trypanosoma brucei

We have used restriction fragment length polymorphism markers to characterise parental and hybrid trypanosome stocks. Unexpected differences in the intensities of Southern hybridisation banding patterns led us to suspect that the hybrid organisms contained more DNA than the parental stocks. This has been confirmed using flow cytofluorimetry (FCF). Hybrids contained significantly more DNA than the parents, both as procyclic organisms (1.5 fold) and as bloodstream forms (1.5-1.6 fold). The DNA contents of both forms were stable through prolonged culture (procyclics), or serial passage (bloodstream forms), although limited data indicated that falls in DNA content could occur in bloodstream forms. FCF analysis of purified nuclei revealed that the increased DNA content of hybrids could be wholly ascribed to nuclear DNA. Our methods are able to detect hybrid organisms with elevated DNA contents in uncloned isolates following cyclical mixed transmission. We have used alternating field electrophoresis techniques to investigate whether the inheritance by the hybrids of the smaller chromosomes could account for their elevated DNA contents. Hybrids lacked the single 500 kb chromosome from one of the parents but appeared to have virtually double the amount of minichromosomes. However, this increase could only account for about 20% of the additional DNA. We are unable at present to distinguish between models for hybrid formation based on the fusion of predominantly diploid cells, and models in which the diploid chromosomes participate in conventional meiosis.

Kinetoplast DNA of Trypanosoma evansi

We show here that the kinetoplast DNA (kDNA) networks from six Trypanosoma evansi strains differ from those of T. brucei by their lack of maxi-circles and absence of mini-circle sequence heterogeneity. The lack of maxi-circles is sufficient to account for the inability of T. evansi to multiply in tsetse flies, since this requires functional mitochondria containing maxi-circle gene products. Judged by restriction enzyme analysis, five of the six T. evansi strains contain mini-circles that differ less than 4% in sequence. This type A mini-circle is found in strains from East Africa, West Africa and South America. Another strain from East Africa contains a very different mini-circle (type B), which shows about the same degree of hybridization to type A mini-circles as to a mini-circle from T. brucei. We propose that the pronounced sequence heterogeneity of the mini-circles of T. brucei has arisen by recombination of strains that had diverged for long periods of time in reproductive isolation. We further propose that the homogeneous mini-circles of T. evansi (and T. equiperdum) reflect the inability of species to mate. This proposal implies that mini-circle heterogeneity indicates (infrequent) genetic exchange and that all kinetoplastid flagellates with heterogeneous mini-circles exchange DNA.

Variation of G-rich mitochondrial transcripts among stocks of Trypanosoma brucei

We have compared maxicircle transcripts from eight stocks of subspecies of Trypanosoma brucei. Transcripts from the rRNA and protein genes have a constant size among stocks and exhibit only minor variation in abundance. In contrast, four of the G+C rich sequences encode multiple transcripts that very markedly in size or abundance. Maxicircle nucleotide sequence comparison of three stocks shows very limited sequence divergence suggesting that sequence divergence may not explain the transcript variability. These results suggest that the G-rich transcripts do not encode proteins and that their variability among stocks may result from posttranscriptional processing events.