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

Differential Metabolic Pathway Analysis of the Proteomes of Leishmania donovani and Leptomonas seymouri

PURPOSE

Although in trypanosomatids, monoxeny (Leptomonas) is ancestral to dixeny (Leishmania), however clinical cases of visceral leishmanisis with Leptomonas co-infection are increasingly being reported from India. Using a proteogenomic approach, a detailed proteome analysis of these two kinetoplastid parasites viz., Leishmania and its sister Leptomonas, to catalog the key proteins associated with and therefore possibly responsible for phenotype changes in Leptomonas evolution and domestication as co-infection with Leishmania is carried out.

EXPERIMENTAL DESIGN

LC-MS/MS is utilized for this proteomic purpose. One Leishmania donovani WHO reference strain and two Leptomonas seymouri isolates, which are originally isolated from clinical cases of kala azar patients with different inherent drug sensitivity viz., responsive and unresponsive, are used in this study.

RESULTS

A network analysis, leveraging protein-protein interaction data helped to find the roles of the proteins in carbon metabolism and biosynthesis of secondary metabolites which is seen to be altered under stress conditions like drug resistance.

CONCLUSIONS AND CLINICAL RELEVANCE

The information provided about the metabolic pathways modulated when contrasting these two phenotypes may lead to the development of new strategies to block parasite differentiation within the host and to also circumvent the problem of drug resistance. This proteomic study also offers new grounds for the investigation of novel hypothetical proteins potentially playing a role in evolutionary biology the knowledge of which is essential for treatment of patients co-infected with these two kinetoplastid parasites.

Amplified fragment length polymorphism (AFLP) analysis is useful for distinguishing Leishmania species of visceral and cutaneous forms

The Leishmania strains belonging to cutaneous leishmaniasis (CL) and visceral leishmaniasis (VL) have been reported to possess close homology in genome profiles. To confirm this on genetic basis an attempt was made to differentiate Leishmania major; Leishmania tropica and Leishmania donovani genetically for the first time using amplified fragment length polymorphism (AFLP)--a high throughput DNA fingerprinting technique. The objective of this research work was to identify DNA markers of CL and VL. Ten combinations of selective primers detect a total of 1487 informative AFLP marker. Percentage of polymorphism was 45.12%. Three hundred and thirty-seven unique AFLP markers were also identified in three species of Leishmania. A clear distinction was revealed between L. major and L. donovani. It was inferred by AFLP analysis that a higher rate of polymorphisms occurred among Leishmania species which indicate the distinguished pattern of the disease cause by Leishmania, i.e. VL and CL. Analysis based on polymorphic AFLP markers revealed considerably high genetic variation among the genome of these species which was sufficient to distinguish between CL and VL.

Leishmania (Viannia) braziliensis transfectants overexpressing the miniexon gene lose virulence in vivo

The miniexon gene has a central role in the processing of polycistronic pre-mRNA of kinetoplastids. It is added to the 5' extremity of each mRNA, supplying the 5'-capped structure to the molecule. Previous studies in Leishmania (Leishmania) major showed that the overexpression of the miniexon array attenuates the virulence of the parasite in in vivo assays. The results presented here extend those findings to Viannia subgenus. Leishmania (Viannia) braziliensis was transfected with a cosmid harboring a tandem array of one hundred miniexon gene copies and then characterized by Northern blot analysis. The overexpression of the exogenous gene was confirmed and its effect on the virulence of L. (V.) braziliensis was investigated in hamsters. In BALB/c mice we could not detect parasites during the course of 15 weeks of infection. In addition, hamsters infected with transfectants overexpressing the miniexon gene exhibited only a minor footpad swelling of late onset and failed to develop progressive lesion, these attenuated parasites could be recovered from the inoculation site 1 year after infection. The persistence of parasites in the host indicates that a stable line overexpressing the miniexon may be tested as live vaccine against leishmaniasis.

Leishmania: sex, lies and karyotype

The exploration of the genome of the tryponosomotid protozoan Leishmania has been difficult until recently owing to a number of obstacles, not least our ignorance of the ploidy and of the number of chromosomes (as in many other protozoa, the latter do not condense during mitosis), the uncertainty of the species concept in these allegedly asexual protozoa and the absence of classical genetic studies. Here, Patrick Bastien, Christine Bloineou and Michel Pages discuss the advances in this field brought about by the advent of molecular biology and its techniques, with on emphasis on ploidy and genetic exchange. In particular, they discuss the data from pulsed field gel electrophoresis (PFGE). When coupled with DNA restriction analysis, PFGE constitutes a powerful tool for the direct examination o f chromosomes of protozoa.

In vivo selection for Leishmania donovani miniexon genes that increase virulence in Leishmania major†

Different species of Leishmania are responsible for the diverse pathologies associated with leishmaniasis including Leishmania donovani which results in fatal visceral infection and Leishmania major which causes non-fatal cutaneous infection. In an attempt to identify genotypic differences between these related Old World Leishmania species which contribute to their distinct phenotypic characteristics, we have introduced a L. donovani cosmid library into L. major to select for L. donovani sequences which may increase L. major virulence in BALB/c mice. Through this approach, we have identified a region of the L. donovani genome which increased virulence in both visceral and cutaneous sites and was divergent from the corresponding region of the L. major genome. When these L. donovani sequences were reintroduced into L. major, they enhanced the overall virulence of L. major, increasing its ability to survive in both visceral and cutaneous sites. The region responsible for increased infection levels was determined to be the miniexon gene array derived from chromosome 36 of L. donovani. Pulse field electrophoresis revealed that L. donovani contained miniexon gene sequences in several chromosome locations as opposed to L. major which contains miniexon gene sequences only in chromosome 2. Because of the requirement for miniexon-derived transcripts in maturation of pre-mRNAs in trypanosomatids, this observation suggests that the increased expression of miniexon genes is associated with increased virulence. As the genome sequence for Leishmania becomes available, the in vivo selection procedure described within will be useful to identify additional species-specific sequences responsible for different pathogenic phenotypes associated with Leishmania infection.

Developmental regulation of heat shock protein 83 in Leishmania. 3' processing and mRNA stability control transcript abundance, and translation id directed by a determinant in the 3'-untranslated region

Developmental gene regulation in trypanosomatids proceeds exclusively by post-transcriptional mechanisms. Stability and abundance of heat shock protein (HSP)70 and HSP83 transcripts in Leishmania increase at mammalian-like temperatures, and their translation is enhanced. Here we report that the 3'-untranslated region (UTR) of HSP83 (886 nucleotides) confers the temperature-dependent pattern of regulation on a chloramphenicol acetyltransferase (CAT) reporter transcript. We also show that the majority of the 3'-UTR sequences are required for increasing mRNA stability during heat shock. Processing of the HSP70 and HSP83 primary transcripts to poly(A)(+) mRNA was more efficient during heat shock; therefore, even when stability at 33 degrees C was reduced by deletions in the 3'-UTR, transcripts still accumulated to comparable and even higher levels. Translation of heat shock transcripts in Leishmania increases dramatically upon temperature elevation. Unlike in other eukaryotes in which the 5'-UTR confers preferential translation on heat shock transcripts, we show that translational control of HSP83 in Leishmania originates from its 3'-UTR. The 5'-UTR alone cannot induce translation during heat shock, but it has a minor contribution when combined with the HSP83 3'-UTR. We identified an element located between positions 201 and 472 of the 3'-UTR which is essential for increasing translation of the CAT-HSP83 reporter RNA at 33-37 degrees C. This region confers preferential translation during heat shock even in transcripts that were less stable. Thus, investigating the traditionally conserved heat shock response reveals that Leishmania parasites use unique pathways for translational control.

Chromosome structure and sequence organization between pathogenic and non-pathogenic Leishmania spp

We have used a chromosome fragmentation strategy based on systematic genomic insertions of the rare cutting yeast I-SceI endonuclease to assess structure and sequence organization of homologous chromosomes between evolutionary divergent pathogenic and non-pathogenic Leishmania species. This method was combined to physical mapping and hybridization studies using a number of specific chromosomal markers as probes. Our studies have concentrated on two different chromosomes of Leishmania major (L. major), L. donovani and L. infantum and of the non-pathogenic species L. tarentolae. Specific chromosome fragmentation events at the level of multiple I-SccI genomic integrations indicated that very similar distances separated internal genomic sequences between homologous chromosomes and that distances from chromosome ends were more variable. The order and orientation of genes along the homologous chromosomes were also conserved between species. With only few exceptions, genome organization between pathogenic and non-pathogenic Leishmania species was found to be highly conserved. Genomic comparison of pathogenic and non-pathogenic species may be useful for depicting regions involved in species-specific related pathologies.

Leishmania (Viannia) guyanensis: a new minicircle class exclusive to this specie isolated from a DNA cosmid library useful for taxonomic purposes

A new minicircle class exclusive to this specie isolated from a DNA cosmid library useful for taxonomic purposes. Experimental Parasitology 94, 143-149. In this paper we describe a new minicircle class exclusive to Leishmania (Viannia) guyanensis. The minicircle class was obtained with the aid of a total DNA cosmid library. The library was screened with an EcoRI fragment isolated from L. (V.) guyanensis (M4147). After screening seven clones were selected which showed strong hybridisation. Clones were digested and hybridised with the same probe. After hybridisation only one clone containing the desired fragment was positive. The fragment sized around 1000 bp was subcloned into pBluescript for sequencing. Sequence analysis using the GCG programme showed no substantial homology with any sequences previously reported, apart from the expected homology with the conserved region of Leishmania kDNA sequences. The probe hybridised strongly only to L. (V.) guyanensis kDNA after medium stringency washing.

The genomic fingerprinting of the coding region of the beta-tubulin gene in Leishmania identification

We have demonstrated the polymorphism of the beta-tubulin gene region in Leishmania and its value in the identification of the parasite. In this work we have shown that the coding region of the gene has sufficient variation to accurately discriminate these parasites at the subgenus level. Nevertheless, intrasubgenus diversity, for particular restriction enzymes, was found in New World Leishmania belonging to the Leishmania subgenus. For instance, differences were found between mexicana and amazonensis strains. A unique pattern at the species level was found in particular species of both subgenera, e.g. L. (L.) major strain P and L. (L.) tropica belonging to the Leishmania subgenus, and L. (V.) panamensis strain LS94 from the Viannia subgenus. Particular endonucleases are diagnostic in Leishmania species discrimination as in the case of PvuII for the mexicana and amazonensis. This variation evidenced in the beta-tubulin gene region of Leishmania also occurred in other Kinetoplastida e.g. Trypanosoma cruzi, Leptomonas spp. and Crithidia spp. Moreover, these organisms showed a different genomic fingerprinting for the beta-tubulin gene among them and also Leishmania. Thus, the polymorphism of the coding region of the beta-tubulin gene can be used as a molecular marker for the identification of Leishmania.

A physical map of the Leishmania major Friedlin genome

An extensive physical map of the Leishmania major Friedlin genome has been assembled by the combination of fingerprint analysis of a shuttle vector cosmid library and probe hybridization. The integrated data obtained for 9004 fingerprinted clones and 974 probes have placed 91.2% of the 33.58-Mb genome into contigs representing each of the 36 chromosomes. This first-generation map has already provided a suitable framework for both high-throughput DNA sequencing and functional studies of the L. major parasite.

Parasite genome analysis. A global map of the Leishmania major genome: prelude to genomic sequencing

In 1994, the World Health Organization (TDR) launched a new strategic initiative in parasite genome analysis, establishing international genome networks for filariae, Schistosoma, Leishmania, Trypanosoma brucei and T. cruzi. For Leishmania, a number of different but complementary approaches have been adopted by members of the Leishmania Genome Network. Our laboratory has been using cosmid clone fingerprinting to produce a physical map of the genome. Progress towards the completion of an integrated physical and biological map of L. major, and the preparations for genomic sequencing, are described.

Unravelling the Leishmania genome

The past few years have been significant advances in our understanding of eukaryotic genomes. In the field of parasitology, this is best exemplified by the application of genome mapping techniques to the study of genome structure and function in the protozoan parasite, Leishmania. Although much is known about the organism and the diseases it causes, molecular genetics has only recently begun to play a major part in elucidating some of the unusual characteristics of this interesting parasite. Mapping of the small (35 Mb) genome and determination of the functional role of genes by the application of in vitro homologous gene targeting techniques are revealing novel avenues for the development of prophylactic measures.

Conservation of low-copy gene loci in Old World leishmanias identifies mechanisms of parasite evolution and diagnostic markers

Genome plasticity has been hypothesized to be a driving force behind parasite speciation. We have evaluated divergence in single and low-copy genes in terms of locus organization, chromosomal localization and gene expression in Leishmania infantum, L. major, L. tropica and three widely divergent geographic isolates of L. donovani. Seventeen genes of low to moderate copy number (1-4 copies/haploid genome) were analyzed to identify restriction fragment length polymorphisms (RFLPs) providing heritable markers distinguishing Old World (OW) leishmanias. These RFLP markers were conserved in parasite isolates from primary infections demonstrating their utility as diagnostic tools. The species designations established by RFLP analysis of field isolates was confirmed by use of monoclonal antibodies. All 17 genes were present in each OW leishmania analyzed except LSIP (A45), which was absent from L. infantum. The 17 genes were found to be distributed among 9 distinct chromosomes. However, in spite of variations in chromosome karyotypes among the various OW leishmanias, individual gene probes localized to a similar sized chromosome from each isolate. These observations coupled with a molecular tree derived from RFLP data suggest that the OW leishmanias comprise a monophyletic lineage, with species associated with cutaneous disease exhibiting the greatest level of divergence. Data from this study supports previous observations that species causing cutaneous and visceral disease have diverged primarily by nucleotide substitutions. Such nucleotide divergence may not only lead to changes in protein function and antigenicity, but may also alter gene regulation programs as exemplified by the finding that the LdI-9-5 and LdE-6-1 genes were expressed only in visceralizing leishmanias.

Genomic variation in Trypanosoma cruzi clonal cultures

Spontaneous changes in restriction DNA profiles and pulsed-field gel electrophoresis (PFGE) patterns, along with a concomitant loss of infectivity, were observed in infective clones of Trypanosoma cruzi strain Y either following a number of passages during the exponential growth phase of after subcloning in liver infusion tryptone (LIT) medium using as the probe a genomic fragment of the parasite (pMYP16), indicating naturally occurring rearrangements of DNA sequences. No variation could be detected when the genomic DNA was probed with conserved T. cruzi tubulin and actin genes. There was no correlation between such rearrangements and the life-cycle forms of the parasites, since trypomastigote forms showed the same karyotype and hybridization patterns as did epimastigote forms. The variations observed could be reverted and infectivity, recovered after inoculation of the parasites in newborn mice.

Identification of differentially expressed Leishmania donovani genes using arbitrarily primed polymerase chain reactions

Arbitrarily primed polymerase chain reactions (AP-PCR) were used to amplify polymorphic DNA fragments from the genomes of a variety of geographic isolates of Leishmania donovani (Ld). From the latter, five polymorphic DNA fragments were cloned and sequence analysis identified 15 unique clones. Northern blot analysis showed that 13 of the 15 clones hybridized to transcribed RNAs isolated from Ld. Eight of these 13 AP-PCR clones specifically hybridized to Ld RNAs that were differentially expressed in promastigote and 'amastigote' cells. Comparative Northern analysis of four differentially expressed AP-PCR clones indicated that two clones, LdS-14-14 and LdI-9-7, were expressed in Ld and several other Leishmania species. However, RNAs corresponding to two other AP-PCR clones, LdE-6-1 and LdI-9-5, were detected only in members of the Ld complex, and not in L. major (Lm) or L. tropica (Lt). Comparative Southern blot analysis of the LdS-14-14 locus revealed numerous restriction-fragment length polymorphisms (RFLP) distinguishing Lm and Lt from the Ld isolates and L. infantum. However, the LdS-14-14 loci were mapped to similar-sized chromosomes observed among all Old World Leishmania species tested, indicating that localized nucleotide divergence, not chromosomal rearrangement, was responsible for altered Southern blot patterns. These results demonstrate that AP-PCR is a very useful method for identifying expressed gene sequences in organisms of relatively low-complexity genomes. Interestingly, the majority of these sequences identified in this study correspond to differentially expressed genes.(ABSTRACT TRUNCATED AT 250 WORDS)

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.

Karyotype analysis of the monogenetic trypanosomatid Leptomonas collosoma

In order to develop a genetic system for the monogenetic trypanosomatids, we have analyzed the molecular karyotype of Leptomonas collosoma based on chromosome separation by clamped homogeneous electric field (CHEF) gel electrophoresis. The chromosome location of 5 RNA coding genes (SL, U6, 5S, 7SL and rRNA) and 2 protein coding genes (for HSP83 and alpha-tubulin) was determined. All of the L. collosoma genes examined were found on at least 2 chromosomes, which differ in size in the range of 100-500 kb, suggesting that the organism is diploid. The weighted sum of L. collosoma chromosomes separated by CHEF analysis was approximately 62 +/- 3 Mb, whereas the genome size determined by FACS was estimated at approx. 80 Mb. This suggests that some of the homologous chromosomes differ in their size. The analysis presented here may facilitate studies on the function of individual genes, and on the genetic stability of this organism.

Expression of heat shock protein 83 in Leishmania is regulated post-transcriptionally

Mechanisms for regulation of heat shock protein (hsp) 83 expression were examined in Leishmania amazonesis. Transcripts of hsp83 accumulated upon temperature elevation; however, in contrast to non-protozoan eukaryotes (i.e. Drosophila, yeast, avian or human cells), no transcriptional activation was observed. The increase in the hsp83 mRNA level evolved from temperature induced variations in mRNA turn-over: the hsp83 transcript was rapidly degraded at normal temperatures, whereas heat shock led to its stabilization. The quick decay of the mRNA at lower temperatures was dependent on active protein synthesis. A similar pattern of regulation was observed for the transfected chloramphenicol acetyltransferase (CAT) gene, which was flanked by sequences from the hsp83 intergenic region (IR), and cloned into the pX transfection vector (pX-ICI). CAT mRNA was abundant at normal temperatures and further accumulated upon temperature elevation. The altered turn-over rates of CAT mRNA at the different temperatures were observed only in the presence of flanking hsp83 IR sequences. The increase in temperature also affected translational regulation of hsps, and synthesis of hsp83 was more efficient at 35 degrees C than at 26 degrees C. However, the effect of translation was transient, and the steady state level of the protein was hardly altered.

Identification, characterisation and genomic cloning of a O-linked N-acetylglucosamine-containing cytoplasmic Leishmania glycoprotein

Antibodies against Leishmania major wheat germ agglutinin-binding glycoproteins were used to select from a genomic lambda gt11 expression library a clone coding for a L. major glycoprotein. The partial DNA sequence indicated the presence of a mosaic of repetitive sequences. Southern blot hybridisation on genomic DNA using the cloned gene as a probe at high stringency suggested a single gene, which was localised to chromosome band 18. Northern blot analysis of L. major mRNA detected a major transcript of 7.5 kb and a minor 4.0-kb transcript. Antibodies affinity-purified on the fusion protein identified a complex of two water-soluble cytoplasmic polypeptides of approximately 96 kDa and 92 kDa in L. major promastigotes and amastigotes. They also recognised polypeptides in other Leishmania species, in Crithidia lucilliae and very weakly in Leptomonas. The apparent molecular weight of these polypeptides, while conserved within each species, varied between species. A peptide map of the two polypeptides from L. major generated an identical pattern suggesting a close relatedness at the protein level. This protein complex was not hydrolysed by N-glycanase and was not affected by tunicamycin, but treatment with anhydrous hydrogen fluoride suggested that it is O-glycosylated. The glycan moiety appears to be N-acetylglucosamine, and N-acetylglucosamine beta-1,4-galactosyltransferase was capable of adding [3H]galactose to it. This was susceptible to beta elimination and beta-galactosidase treatment. Taken together, the data indicates that gp96/92 belongs to the newly described class of cytoplasmic and nuclear glycoproteins containing O-linked N-acetylglucosamine.

A small chromosome of Leishmania (Viannia) braziliensis contains multicopy sequences which are complex specific

Orthogonal Field Alternating Gel Electrophoresis (OFAGE) has been used to show a band of approximately 260 kb which is stained intensely with ethidium bromide in Leishmania (V.) braziliensis stock M2903. This small chromosome (sc-2903), as well as a 50 kb and a 200 kb chromosome seen in L. (L.) mexicana and L. (L.) amazonensis, respectively, are stably maintained and linear. When used as a hybridisation probe, sc-2903 showed homology to large chromosomal DNA bands and to a multiplicity of genomic fragments in all braziliensis stocks tested, indicating either different sequences, different copy numbers or both but no hybridisation to mexicana stocks. It is possible that these sequences are present in all members of the braziliensis complex and are not related to LD1 or any other previously published small chromosome sequences. However, at least one clone isolated from a sc-2903 library recognised genomic DNA of stocks belonging to the braziliensis, mexicana and donovani complexes. Our results suggest that the clone carries sequence(s) that are repeated and shared between stocks of different complexes but with a variable genomic distribution.

Influence of heat shock, drugs, and radiation on karyotype of Leishmania major

Leishmaniasis is one of the important tropical diseases in the world. Although it is not prevalent in Korea, imported cases have been recorded. The karyotype of Leishmania sp. has been observed to be variable by localities or by strains, but the karyotype of a strain is known to be stable. This study was performed to observe if the karyotype of a Leishmania sp. would be changed under some stressful conditions. The karyotype, analyzed by pulsed field gradient gel electrophoresis, was not grossly changed by heat shock, chemotherapeutics, UV illumination, and gamma irradiation. Radiation destroyed the chromosomes mechanically, but subcultured organisms after irradiation showed unaffected karyotype. The present findings suggest that the karyotype of a Leishmania strain is so stable that it is not altered by temporary stimulation with heat, drugs, and radiation.

Field alternation gel electrophoresis--status quo

Since the description of the original technique of field alternation gel electrophoresis (FAGE) about ten years ago there have been significant developments in the area. Between 1983 and early 1987 dramatic improvements in the technique and apparatus resulted in a 500- to 600-fold increase in the functional separation capacity of conventional agarose gel electrophoresis. Details of the improvements in technique and equipment was the subject of an earlier review [H. J. S. Dawkins, J. Chromatogr., 492 (1989) 615]. This review concentrates on the application of FAGE technology. The FAGE technique is no longer restricted to simply separating large DNA fragments. This method is presently being used for electrophoretic karyotyping, long-range genomic mapping, cloning of large DNA fragments into new vectors, the study of pathogenic chromosomal alterations and the structural analysis of chromosomes. The applications of FAGE in molecular biology and genetics is constantly expanding, with the full potential of this technique still to be realised.

Leishmaniases of the New World: current concepts and implications for future research

Recent epidemiologic studies indicate that leishmaniasis in the Americas is far more abundant and of greater public health importance than was previously recognized. The disease in the New World is caused by a number of different parasite species that are capable of producing a wide variety of clinical manifestations. The outcome of leishmanial infection in humans is largely dependent on the immune responsiveness of the host and the virulence of the infecting parasite strain. This article reviews current concepts of the clinical forms, immunology, pathology, laboratory diagnosis, and treatment of the disease as well as aspects of its epidemiology and control. Recommendations for future research on the disease and its control are made.

Expression of a mitochondrial stress protein in the protozoan parasite Leishmania major

The DNA sequence has been determined of a gene from Leishmania major that shares sequence identity with members of the eukaryotic heat shock protein (hsp) 70 gene family. The deduced open reading frame for translation shares a number of features common to hsp70 stress proteins, including conserved amino acids implicated in ATP binding and a putative calmodulin-binding site. In addition, the protein has an N-terminal sequence characteristic of a mitochondrial targeting signal. Specific antibodies to this protein, generated by the use of recombinant fusion peptides, recognise a 65 kDa molecule of pI 6.7. This molecule is constitutively expressed and localises to the mitochondrion in all stages of the parasite life cycle. These features suggest a role for this protein as a molecular chaperone in Leishmania.

Recombinant kinetoplast DNA (kDNA) probe for identifying Leishmania tropica

The paper reports on the construction of a kDNA library with DNA isolated from the WHO reference strain of Leishmania tropica IC-305 and subsequent identification and propagation of recombinant plasmids containing L. tropica kDNA sequences. It also shows that the cloned kDNA sequences can be used as genetic markers in restriction endonuclease, Southern blot transfer, and dot blot hybridisation analysis, to identify L. tropica parasites. When the pL 305-I kDNA probe was used in hybridisation experiments with DNAs from various Leishmania reference strains, species and isolates from different host species and from different geographical locations, hybridisation was detected only with L. tropica, thereby suggesting that the insert in recombinant plasmid 305-I was species-specific. The probe is sensitive to the level of 10(3) parasites in dot blot hybridisation. Additionally, orthogonal field alternation gel electrophoresis (OFAGE) and transverse alternating field electrophoresis (TAFE) were used to characterise Leishmania reference strains and Leishmania species. The molecular karyotypes resolved by these techniques showed significant differences in the profiles of chromosomal sized-DNA molecules among species of Leishmania. The DNA karyotypes of the two reference strains of L. tropica (IC-305 and NLB-067), while similar, were nevertheless distinct.

Dynamics and size polymorphisms of minichromosomes in Leishmania major LV-561 cloned lines

Various lines and cloned lines of Leishmania major of varying degrees of virulence in BALB/c mice possessed size polymorphic multicopy minichromosomes related to previously described LD1/CD1 and 715-class DNAs of Leishmania. The minichromosomes were not necessary for virulence. Two of these DNAs (M180 and M210), coexisting in a single cloned line, showed remarkable dynamics in terms of loss or gain when followed through multiple transfers during in vitro culture and in vivo passage in BALB/c mice. Although there was significant sequence heterogeneity among minichromosomes, M180 sequences were present within large (megabase) and in intermediate (550-760 kb) chromosomes in the L. major lines analysed. M180 related small DNAs were also detected in Leishmania mexicana and Leishmania donovani isolates, suggesting that the generation of these molecules involves a common, probably functional basic mechanism widespread in Leishmania.

The chromosomes of Leishmania

Chromosome size polymorphisms occur in Leishmania such that each strain of a given species has a distinctive molecular karyotype. Despite this variability, the chromosomal similarities among closely related strains of Leishmania are sufficiently characteristic to permit classification of unidentified clinical isolates. Mechanisms generating chromosome size polymorphisms are related to chromosomal evolution. In this review, Geoffrey Lighthall and Suzanne Giannini explain that the chromosomal profiles of members of different species may be diverging from a conserved 'consensus' karyotype at different rates, and present a current understanding of the genomic organization of Leishmania with emphasis on chromosomal elements.

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.

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.

Molecular karyotype and chromosomal localization of genes encoding two major surface glycoproteins, gp63 and gp46/M2, hsp70, and beta-tubulin in cloned strains of several Leishmania species

The molecular karyotypes of several Leishmania isolates (Leishmania amazonensis, Leishmania braziliensis, Leishmania guyanensis, Leishmania panamensis, Leishmania donovani, Leishmania major, Leishmania aethiopica, Leishmania tropica, Leishmania enriettii) have been analyzed by clamped homogeneous electric field (CHEF) gel electrophoresis. The chromosomal localization of genes encoding 2 major surface glycoproteins, gp63 and gp46/M2, heat shock protein 70 (hsp70), and beta-tubulin was determined for cloned isolates of 8 of these Leishmania species. The chromosome size class assignment of hsp70 genes was most conserved in that all species contained a single hybridizing DNA band of approximately 1200 kb. The beta-tubulin gene probe hybridized predominantly to large (1600-1750 kb) chromosome-size DNA and to 1-5 additional bands, the number of which depended on the species. The number and size of DNA bands hybridizing to gp63 or gp46/M2 gene probes were not uniformly conserved among species. In contrast to previous reports of gp63 genes being located on a single chromosome, using various CHEF gel conditions we observed a Leishmania major gp63 gene probe hybridizing to at least 2 chromosomal DNA bands in the New World species and in L. tropica. Gp46/M2 genes were located on 1 band in L. donovani, L. major, and L. aethiopica or 2 bands in L. tropica and L. amazonensis, but surprisingly, do not hybridize to any chromosomal DNA of species in the L. braziliensis complex or in L. enriettii. Whenever both genes were present in a species, gp63 and gp46/M2 genes were located on different chromosomal DNA bands.

18S rRNA sequences of Leishmania enriettii promastigote and amastigote

Dideoxy sequencing with reverse transcriptase and universal primers was used to obtain partial sequences of the 18S rRNAs from the promastigote and amastigote life-cycle stages of L. enriettii. Approximately 1400 nucleotides of sequence from the two stages were compared. Unlike Plasmodium berghei, in which 18S rRNAs from the mosquito stage and the mammalian stage of the life cycle are only 96.5% similar, the amastigote and promastigote rRNAs of L. enriettii are identical. In addition, a comparison of 1425 bases of the L. enriettii promastigote sequence with the published sequence of L. donovani revealed only four differences; the two sequences are 99.8% similar. A likely explanation for this high similarity, considering the 97% similarity between L. donovani and the related genus Crithidia fasciculata, is that the two species are closely related and of comparatively recent origin. The low diversity between the 18S rRNA sequences of Leishmania species is similar to that reported for 13 Tetrahymena species, where similarities ranged from 98.1 to 99.9%, but different from the pattern reported in the genus Naegleria, where divergence was greater.

Eimeria spp. of the domestic fowl: resolution of chromosomes by field inversion gel electrophoresis

The molecular karyotypes of five species of chicken coccidia, viz., Eimeria acervulina, E. brunetti, E. maxima, E. necatrix, and E. tenella, were determined using field inversion gel electrophoresis (FIGE). Each species has a distinctive set of resolvable chromosomes which range from about 1 to greater than 5.7 megabases. We were able to resolve at least 8 chromosomes for E. acervulina, 5 for E. brunetti, 10 for E. maxima, 6 for E. necatrix, and 9 for E. tenella. If the value of 67 megabases for the genomic DNA of E. tenella is accurate, then under the conditions used here only about 60% of its chromosomal complement has been resolved.

Molecular cloning and characterization of the immunologically protective surface glycoprotein GP46/M-2 of Leishmania amazonensis

Immunization of mice with the GP46/M-2 membrane glycoprotein has been demonstrated to elicit protection against infection with the parasitic protozoan Leishmania amazonensis. As this molecule is important for future vaccine studies of leishmaniasis, the gene encoding the GP46/M-2 surface membrane glycoprotein of Leishmania amazonensis has been cloned and sequenced. The protein sequence derived from the DNA sequence data is consistent with the known biochemical and immunochemical properties of the protein and indicates a number of structural areas of interest. A repetitive sequence (24 amino acids repeated four times) occurs within the amino-terminal portion of the molecule and constitutes approximately 22% of the total mature protein. The protease-resistant immunodominant carboxyl-terminal domain of the protein comprises approximately half of the molecule and consists of proline-rich and cysteine-rich areas of sequence; the distribution of cysteine residues is suggestive of metal binding motifs. The sequence predicts a hydrophobic leader peptide, and a putative attachment site for a glycosyl-phosphatidylinositol anchor is indicated at the carboxyl terminus, consistent with the membrane location of the protein. Southern blot analyses also indicate the presence of a GP46/M-2 gene family.

Leishmania major: expression and gene structure of the glycoprotein 63 molecule in virulent and avirulent clones and strains

Two Leishmania membrane glycoconjugates, gp63 and lipophosphoglycan, have been implicated in parasite attachment and uptake into the host macrophage. Moreover, recent data suggest that parasite virulence is associated with high expression of gp63. In this study we have surveyed gp63 gene copy number, in addition to the level of expression of gp63 mRNA and protein in several Leishmania major isolates, as well as virulent and avirulent strains and clones. The highest level of gp63 expression was found in the avirulent cloned line LRC-L119.3G7, which expresses about a 15-fold higher level of gp63 RNA and protein than the virulent cloned line LRC-L137/7/V121, suggesting that large amounts of gp63 are not sufficient for infectivity and do not correlate with virulence. L119.3G7 has eight copies of the gp63 gene compared to five copies in the virulent cloned line V121 and its parental virulent isolate LRC-L137. A series of avirulent clones derived from LRC-L137 also had five copies of the gene, suggesting that gp63 copy number is maintained among closely related parasites. Different virulent isolates of L. major from different geographic regions exhibited six copies of the gp63 gene. The variation in total gene copy number is due to different numbers of the tandemly repeated gp63 isogene in different strains. Our data show that there is wide variability between strains of L. major in the copy number of gp63 genes as well as in the amount of RNA and protein expressed.

Evolution of nuclear DNA and the occurrence of sequences related to new small chromosomal DNAs in the trypanosomatid genus Endotrypanum

Comparisons of nuclear DNA restriction fragment patterns were used to examine the evolutionary relatedness among 17 strains previously identified as Endotrypanum, a trypanosomatid parasite of sloths. Fragments were obtained with 6 restriction enzymes and analyzed by Southern blotting with hybridization probes from three loci. An estimate of the percent nucleotide sequence divergence among strains, delta, was calculated and used to construct molecular evolutionary trees. The 17 isolates fell into four distinct groups, one of which (group D) showed no more relationship to groups A-C than it did to other genera (Leishmania, Crithidia, Leptomonas, Trypanosoma), being too distant to be resolved with this method. These and other data suggest that group D may not actually be Endotrypanum. Molecular karyotype analysis revealed considerable variation among the chromosomes of these strains. One strain (LV88, group B) contained a linear 70-kb chromosome not evident in other isolates. Hybridization probes specific for this chromosome (LV88-70) were developed and revealed that related sequences were present at high levels in group B isolates and low levels in group A isolates, although a complex hybridization pattern was evident. Sequences related to LV88-70 were not present in groups C and D, nor in Leishmania major, showing that this DNA has a disjunct distribution which curiously parallels that of virus-like particles present in these isolates.

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.

Characterization of Leishmania donovani stocks by genomic DNA heterogeneity and molecular karyotype

A hypervariable deoxyribonucleic acid (DNA) probe was isolated by screening a Leishmania donovani genomic DNA library with L. donovani total DNA. The probe was used to characterize L. donovani stocks on the basis of restriction fragment length polymorphisms (RFLPs). The molecular karyotype of the same stocks was examined by orthogonal field alternation gel electrophoresis. On the basis of the observed RFLPs Mediterranean L. donovani infantum and South American L. donovani chagasi stocks were more similar to one another than they were to Indian L. donovani donovani or African L. donovani stocks. This conclusion was also supported by the studies on molecular karyotype. The probe also showed African L. donovani stocks to be heterogeneous in their restriction fragment patterns: the patterns of Indian stocks were, by contrast, relatively homogeneous. Certain L. donovani stocks that appeared to be closely related on the basis of RFLPs and isoenzyme data were markedly different in karyotype, demonstrating the rapidity of chromosome evolution in Leishmania donovani.

The karyotype of Trypanosoma cruzi Dm 28c: comparison with other T. cruzi strains and trypanosomatids

Chromosome-sized DNA molecules from Trypanosoma cruzi clone Dm 28c were analyzed and compared with other T. cruzi strains and monogenetic trypanosomatids by orthogonal field alteration gel electrophoresis. The results showed that T. cruzi Dm 28c displays at least 18 chromosomes ranging from 550 to more than 1500 kb and that in general the trypanosomatids have smaller chromosomes distributed in the size range from 300 to 1500 kb. With the exception of T. cruzi strain G49, there is no evidence of minichromosomes, suggesting they are not widely distributed among different isolates of the parasite. The hybridization of T. cruzi chromosomal Southern blots with probes for T. cruzi-specific genes showed that their location can change from one strain to another, supporting the idea of the plasticity of the parasite genome. Furthermore, the chromosome pattern is strictly conserved during the transformation of T. cruzi Dm 28c epimastigotes to metacyclic trypomastigotes, suggesting that extensive chromosomal rearrangements do not occur during at least part of the life cycle of the parasite.

A family of heat shock protein 70-related genes are expressed in the promastigotes of Leishmania major

We describe the isolation and characterisation of two novel genes of the parasitic protozoan Leishmania major that are related by nucleotide sequence homology to eukaryotic genes encoding 70 Kd. heat shock proteins. The transcription of neither gene is heat-inducible but both are constituitively-expressed throughout the promastigote stage of the parasite life cycle. A third gene shows differential expression between non-infective and infective promastigote stages in the absence of any temperature change. These genes are related by sequence homology to the tandemly-repeated hsp70 genes of trypanosomatids, but are located on different, dispersed chromosomes within the genome of L. major. The open reading frame for translation derived from one of these sequences contains a putative mitochondrial signal peptide at its amino-terminus.

Cloning of a polymorphic DNA fragment from the genome of Leishmania donovani

Recombinant DNA clones, containing highly repetitive DNA sequences, have been isolated from a Leishmania donovani genomic DNA library prepared in the replacement vector lambda gt.WES.lambda B. Two clones, probably telomeric in location, have been characterised and show a restriction fragment size polymorphism. Evidence is presented which suggests that L. donovani is diploid for this cloned genomic locus.

Study of Leishmania mexicana electrokaryotype by clamped homogeneous electric field electrophoresis

In spite of the wide use of electrokaryotypes for Leishmania identification, the number, ploidy and associated functions of the chromosomal bands still remain controversial topics. In the present work, we studied these problems in the pathogenic organism Leishmania mexicana using the clamped homogeneous electric field electrophoresis (CHEF) technique, which allows the separation of uniform chromosomal bands in one run. We arrived at the following general conclusions: (i) a comparative densitometric study using haploid Saccharomyces cerevisiae cells as standard reveals that although L. mexicana is an aneuploid organism, its larger bands are diploid; (ii) a total of 18 chromosomal bands ranging from 3.2 to 0.245 Mbp were resolved. These molecules summed to 1.34 X 10(8) bp, a value within the range of the Leishmania genome; (iii) in hybridisation experiments using different housekeeping gene probes, the majority hybridised with chromosomal band 17 or 18 of L. mexicana, with additional locations for some genes; (iv) the presence of the ubiquitous leishmanial (CA/GT)n sequence in the DNA probes could lead to erroneous gene localisation.

DNA electrophoresis

The migration of a series of supercoiled plasmids ranging in size from 4 to 91 kilobases (kb) has been analyzed by orthogonal-field-alternation gel electrophoresis (OFAGE). These circular DNAs enter OFAGE gels and are resolved over the same region of the gel as linear DNAs from 260 to 2200 kb. Furthermore, a distinct triphasic migration pattern was observed for the supercoiled DNAs. The migration of plasmids between 6 and 20, and 60 and 91 kb is inversely proportional to size, whereas the mobilities of plasmids between 20 and 60 kb increase with size. Unlike linear DNA molecules, the relative mobilities of these plasmids are constant over a broad range of pulse times, from 10 to 120s. Electrophoresis of supercoiled, relaxed, and nicked open circular forms as well as topoisomers of small plasmids shows that the extent of supercoiling has a dramatic effect on plasmid migration on OFAGE. Several practical applications for exploiting the different migration properties of circular and linear DNA molecules on OFAGE are presented.