Chromosomes of malaria parasites

Quantitative characterization of hemozoin in Plasmodium berghei and vivax

The incidence and global distribution of chloroquine resistant (CR) Plasmodium vivax infection has increased since emerging in 1989. The mechanism of resistance in CR P. vivax has not been defined. The resistance likely relates to the formation and disposition of hemozoin as chloroquine's primary mechanism of action involves disruption of hemozoin formation. CR P. berghei strains, like CR P. vivax strains, are confined to reticulocyte host cells and reportedly they do not accumulate appreciable intraerythrocytic hemozoin. Reports comparing hemozoin production between P. vivax strains and CR to chloroquine sensitive (CS) P. berghei are absent. Here we compare in vivo patterns of hemozoin formation and distribution in blood, spleen and liver tissue of male Swiss mice infected with CS or CR P. berghei not treated with chloroquine and CR P. berghei also treated with chloroquine. Light microscopy, laser desorption mass spectrometry and a colorimetric hemozoin assay detect trace hemozoin in the blood of CR P. berghei infected mice but significant hemozoin accumulation in liver and spleen tissue. Field emission in lens scanning electron microscopy reveals CR P. berghei hemozoin crystals are morphologically smaller but similar to those formed by CS parasites. CR P. berghei produces approximately five-fold less total hemozoin than CS strain. Lipid analysis of CS and CR P. berghei sucrose gradient purified bloodstage hemozoin indicates a similar lipid environment around the isolated hemozoin, predominately monopalmitic glycerol and monostearic glycerol. In contrast to CR and CS P. berghei, colorimetric hemozoin analysis of P. vivax strains indicates similar amounts of hemozoin are produced despite differing chloroquine sensitivities. These results suggest CR P. berghei forms significant hemozoin which accumulates in liver and spleen tissues and that the P. vivax chloroquine resistance mechanism differs from P. berghei.

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Chloroquine resistant Plasmodium berghei release measurable hemozoin into tissues with blood hemozoin 100 times less per parasite while total in all tissues is only 5 times less than chloroquine sensitive.

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Chloroquine resistant P. bergheihemozoin crystals are morphologically smaller but similar to those formed by chloroquine sensitive parasites.

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Chloroquine resistance in P. vivax is distinct from P. berghei even though both infect reticulocytes.

The landscape of inherited and de novo copy number variants in a Plasmodium falciparum genetic cross

BACKGROUND

Copy number is a major source of genome variation with important evolutionary implications. Consequently, it is essential to determine copy number variant (CNV) behavior, distributions and frequencies across genomes to understand their origins in both evolutionary and generational time frames. We use comparative genomic hybridization (CGH) microarray and the resolution provided by a segregating population of cloned progeny lines of the malaria parasite, Plasmodium falciparum, to identify and analyze the inheritance of 170 genome-wide CNVs.

RESULTS

We describe CNVs in progeny clones derived from both Mendelian (i.e. inherited) and non-Mendelian mechanisms. Forty-five CNVs were present in the parent lines and segregated in the progeny population. Furthermore, extensive variation that did not conform to strict Mendelian inheritance patterns was observed. 124 CNVs were called in one or more progeny but in neither parent: we observed CNVs in more than one progeny clone that were not identified in either parent, located more frequently in the telomeric-subtelomeric regions of chromosomes and singleton de novo CNVs distributed evenly throughout the genome. Linkage analysis of CNVs revealed dynamic copy number fluctuations and suggested mechanisms that could have generated them. Five of 12 previously identified expression quantitative trait loci (eQTL) hotspots coincide with CNVs, demonstrating the potential for broad influence of CNV on the transcriptional program and phenotypic variation.

CONCLUSIONS

CNVs are a significant source of segregating and de novo genome variation involving hundreds of genes. Examination of progeny genome segments provides a framework to assess the extent and possible origins of CNVs. This segregating genetic system reveals the breadth, distribution and dynamics of CNVs in a surprisingly plastic parasite genome, providing a new perspective on the sources of diversity in parasite populations.

Monitoring of in vitro susceptibilities and molecular markers of resistance of Plasmodium falciparum isolates from Thai-Myanmar border to chloroquine, quinine, mefloquine and artesunate

Malaria is one of the major causes of morbidity and mortality worldwide. The major factor which has aggravated the situation is the emergence of multidrug resistant Plasmodium falciparum malaria. To successfully deal with the problem, thorough understanding of the molecular bases for reduced parasite sensitivity to existing antimalarial drugs is of considerable importance. The objective of this work was to broaden the insight into the molecular mechanisms of resistance of P. falciparum to quinoline-containing antimalarials and artemisinin derivatives. Polymorphisms of the candidate genes pfmdr1 and pfcrt were investigated in relation to the susceptibility (in vitro sensitivity) of P. falciparum isolates to chloroquine (CQ), mefloquine (MQ), quinine (QN) and the artemisinin derivative - artesunate (AS). A total of 26 P. falciparum isolates were successful cultured. In vitro sensitivity results indicate the increase in susceptibility of P. falciparum strains in Thailand to CQ, while the susceptibility to MQ and QN was markedly declined. The pattern of cross-resistance was observed between MQ vs QN vs AS. Only one point mutation in the pfmdr1 gene, i.e., N86Y was observed with low prevalence of 7.7% (2/26). In contrast, the mutations at positions 76T, 220S, 271E, 326S, 356T and 371I in the pfcrt gene were identified in almost all isolates (25 isolates, 96.2%). The association between polymorphisms of the pfmdr1 and susceptibility of the parasite to MQ and QN was observed (increased susceptibilities to MQ and QN in isolates with mutations). Moreover, the correlation between pfmdr1 gene amplification and susceptibility of the parasite to MQ, QN and AS was observed (decreased susceptibilities to MQ, QN and AS in isolates with increased pfmdr1 copy number).

Karyotype variability in KP1(+) and KP1(-) strains of Trypanosoma rangeli isolated in Brazil and Colombia

In the present study, the molecular karyotypes of 12 KP1(+) and KP1(-) Trypanosoma rangeli strains were determined and 10 different molecular markers were hybridized to the chromosomes of the parasite, including seven obtained from T. rangeli [ubiquitin hydrolase (UH), a predicted serine/threonine protein kinase (STK), hexose transporter, hypothetical protein, three anonymous sequences] and three from Trypanosoma cruzi [ubiquitin-conjugating enzyme E2 (UBE2), ribosomal RNA methyltransferase (rRNAmtr), proteasome non-ATPase regulatory subunit 6 (PSMD6)]. Despite intraspecific variation, analysis of the karyotype profiles permitted the division of the T. rangeli strains into two groups coinciding with the KP1(+) and KP1(-) genotypes. Southern blot hybridization showed that, except for the hexose transporter probe, all other probes produced distinct patterns able to differentiate the KP1(+) and KP1(-) genotypes. The UH, STK and An-1A04 probes exclusively hybridized to the chromosomes of KP1(+) strains and can be used as markers of this group. In addition, the UBE2, rRNAmtr and PSMD6 markers, which are present in a conserved region in all trypanosomatid species sequenced so far, co-hybridized to the same T. rangeli chromosomal bands, suggesting the occurrence of gene synteny in these species. The finding of distinct molecular karyotypes in KP1(+) and KP1(-) strains of T. rangeli is noteworthy and might be used as a new approach to the study of genetic variability in this parasite. Together with the Southern blot hybridization results, these findings demonstrate that differences at the kDNA level might be associated with variations in nuclear DNA.

The ABC transporter genes of Plasmodium falciparum and drug resistance

The seminal observations that (a) chloroquine-resistant Plasmodium falciparum strains accumulate less drug than more sensitive parasites, and (b) chloroquine resistance could be modulated in vitro by the classic multidrug-resistance (MDR) modulator verapamil, suggested not only that parasite resistance to multiple drugs may be similar to the MDR phenotype described in mammalian cancer cells, but that homologous proteins may be involved. These findings prompted search for MDR-like genes in the parasite. To date, three full-length ABC transporter genes have been isolated from P. falciparum: two P-glycoprotein-like homologues, pfmdr1 and pfmdr2, and a homologue of the yeast GCN20 gene, pfgcn20.

The malaria-infected red blood cell: structural and functional changes

The asexual stage of malaria parasites of the genus Plasmodium invade red blood cells of various species including humans. After parasite invasion, red blood cells progressively acquire a new set of properties and are converted into more typical, although still simpler, eukaryotic cells by the appearance of new structures in the red blood cell cytoplasm, and new proteins at the red blood cell membrane skeleton. The red blood cell undergoes striking morphological alterations and its rheological properties are considerably altered, manifesting as red blood cells with increased membrane rigidity, reduced deformability and increased adhesiveness for a number of other cells including the vascular endothelium. Elucidation of the structural changes in the red blood cell induced by parasite invasion and maturation and an understanding of the accompanying functional alterations have the ability to considerably extend our knowledge of structure-function relationships in the normal red blood cell. Furthermore, interference with these interactions may lead to previously unsuspected means of reducing parasite virulence and may lead to the development of novel antimalarial therapeutics.

Newly identified repeat sequences, derived from human chromosome 21qter, are also localized in the subtelomeric region of particular chromosomes and 2q13, and are conserved in the chimpanzee genome

Subtelomeric regions have been a target of structural and functional studies of human chromosomes. Markers having a defined structure are especially useful to such studies. Here, we report 93 bp tandem repeat sequences found in the subtelomeric region of human chromosome 21q. They were also detected in the telomeric region of several other chromosomes. Interestingly, the repeat was also found in the 2q13 region which is known to be a position of chromosomal fusion, a major difference between the human and chimpanzee karyotypes. To the best of our knowledge, this repetitive sequence is a new member of human subtelomeric interspersed repeats.

Optical Mapping of Plasmodium falciparum Chromosome 2

Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered restriction maps from ensembles of individual DNA molecules. DNA molecules were bound to derivatized glass surfaces, cleaved with NheI or BamHI, and imaged by digital fluorescence microscopy. Large pieces of the chromosome containing ordered DNA restriction fragments were mapped. Maps were assembled from 50 molecules producing an average contig depth of 15 molecules and high-resolution restriction maps covering the entire chromosome. Chromosome 2 was found to be 976 kb by optical mapping withNheI, and 946 kb with BamHI, which compares closely to the published size of 947 kb from large-scale sequencing. The maps were used to further verify assemblies from the plasmid library used for sequencing. Maps generated in silico from the sequence data were compared to the optical mapping data, and good correspondence was found. Such high-resolution restriction maps may become an indispensable resource for large-scale genome sequencing projects.

Establishing the Cryptosporidium parvum karyotype by NotI and SfiI restriction analysis and Southern hybridization

The molecular karyotype of the coccidian parasite Cryptosporidium parvum has proven difficult to study because chromosomes of similar sizes migrate together when submitted to pulsed-field gel electrophoresis (PFGE). In the present work, the karyotype was studied by restriction of chromosome-sized DNA with the rare-cutting enzymes NotI and SfiI, followed by PFGE separation of the restriction fragments and Southern hybridization. These experiments showed that the C. parvum karyotype is formed by eight chromosomes, ranging in size from approximately 0.95 to 1.45 million base pairs (Mbp), accounting for a genome size of 9.6Mbp. As a first step towards the construction of a physical map of the C. parvum genome, a total of 20 probes, including 16 genes and the ribosomal DNA (rDNA) sequence, was mapped to intact chromosomes and to their restriction fragments. In this way, all chromosomes, but one, were identified by specific markers. A comparison of mapping data of homologous genes from different species belonging to the phylum Apicomplexa showed differences in the distribution of rDNA sequences and in the chromosomal localization of alpha- and beta-tubulin genes. The variation in genome size among these parasites is also discussed.

Short-sequence DNA repeats in prokaryotic genomes

Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10(-4) per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant.

Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley

The wheat genome is large, hexaploid, and contains a high amount of repetitive sequences. In order to isolate agronomically important genes from wheat by map-based cloning, a simpler model of the genome must be used for identifying candidate genes. The objective of this study was to comparatively map the genomic regions of two wheat leaf rust disease resistance loci, Lr1 and Lr10, in the putative model genomes of rice and barley. Two probes cosegregating with the Lr1 gene on chromosome 5DL of wheat were studied. The rice sequences corresponding to the two probes were isolated and mapped. The two probes mapped to two different rice chromosomes, indicating that the organization of the region orthologous to Lr1 is different in rice and wheat. In contrast, synteny was conserved between wheat and barley in this chromosomal region. The Lrk10 gene cosegregated with Lr10 on chromosome 1AS in wheat. The rice gene corresponding to Lrk10 was mapped on rice chromosome 1, where it occurred in many copies. This region on rice chromosome 1 corresponds to the distal part of the group 3S chromosomes in Triticeae. The synteny is conserved between rice chromosome 1 and the Triticeae group 3S chromosomes up to the telomere of the chromosomes. On group 3S chromosomes, we found a gene that is partially homologous to Lrk10. We conclude that in the genomic regions studied, there is limited and only partially useful synteny between wheat and rice. Therefore, barley should also be considered as a model genome for isolating the Lr1 and Lr10 genes from wheat.

Separation and mapping of chromosomes of parasitic protozoa

Many protozoan parasites represent an important group of human pathogens. Pulsed Field Gradient Gel Electrophoresis (PFGE) analysis has been an important tool for fundamental genetic studies of parasites like Trypanosoma, Leishmania, Giardia or the human malaria parasite Plasmodium falciparum. We present PFGE conditions allowing a high resolution separation of chromosomes ranging from 500 to 4000 kb within a two day electrophoresis run. In addition, we present conditions for separating large chromosomes (2000-6000 kb) within 36 hr. We demonstrate that the application of two dimensional PFGE (2D-PFGE) technique to parasite karyotypes is a very useful method for the analysis of dispersed gene families and comparative studies of the intrachromosomal genome organization.

Biological parameters and molecular markers of clone CL Brener--the reference organism of the Trypanosoma cruzi genome project

Clone CL Brener is the reference organism used in the Trypanosoma cruzi Genome Project. Some biological parameters of CL Brener were determined: (a) the doubling time of epimastigote forms cultured in liver infusion-tryptose (LIT) medium at 28 degrees C is 58 +/- 13 hr; (b) differentiation of epimastigotes to metacyclic trypomastigotes is obtained by incubation in LIT-20% Grace's medium; (c) trypomastigotes infect mammalian cultured cells and perform the complete intracellular cycle at 33 and 37 degrees C; (d) blood forms are highly infective to mice; (e) blood forms are susceptible to nifurtimox and benznidazole. The molecular typing of CL Brener has been determined: (a) isoenzymatic profiles are characteristic of zymodeme ZB; (b) PCR amplification of a 24S alpha ribosomal RNA sequence indicates it belongs to T. cruzi lineage 1; (c) schizodeme, randomly amplified polymorphic DNA (RAPD) and DNA fingerprinting analyses were performed.

Construction and characterization of a Plasmodium vivax genomic library in yeast artificial chromosomes

Here we describe the construction of a representative YAC library for the human malarial parasite Plasmodium vivax. As P. vivax cannot be maintained continuously under laboratory conditions, the P. vivax DNA necessary for the library construction was isolated from a single human patient presenting himself with vivax malaria to a local hospital in the Brazilian Amazon. Thus, this YAC library is the first of its kind to be generated from patient-derived material. The YAC library consists of 560 clones with an average insert size of 180 kb. Of 9 published P. vivax genes, 8 were found to be present in the library. In addition, 12 P. vivax telomeric YAC clones were identified.

The DNA structures at the ends of eukaryotic chromosomes

The sequence organisation of the telomeric regions is extremely similar for all eukaryotes examined to date. Subtelomeric areas may contain large sequence arrays of middle repetitive, complex elements that sometimes have similarities to retrotransposons. In between and within these complex sequences are short, satellite-like repeats. These areas contain very few genes and are thought to be organised into a heterochromatin-like domain. The terminal regions almost invariably consist of short, direct repeats. These repeats usually contain clusters of 2-4 G residues and the strand that contains these clusters (the G strand) always forms the extreme 3'-end of the chromosome. Thus, most telomeric repeats are clearly related to each other which in turn suggests a common evolutionary origin. A number of different structures can be formed by single-stranded telomeric G strand repeats and, as has been suggested recently, by the G strand. Since the main mechanism for the maintenance of telomeric repeats predicts the occurrence of single-stranded extensions of the G strand, the propensity of G-rich DNA to fold into alternative DNA structures may have implications for telomere biology.

Current status of the Plasmodium falciparum genome project

The Plasmodium falciparum Genome Project is a collaborative effort by many laboratories that will provide detailed molecular information about the parasite, which may be used for developing practical control measures. Initial goals are to prepare an electronically indexed clone bank containing partially sequenced clones representing up to 80% of the parasite's genes and to prepare an ordered set of overlapping clones spanning each of the parasite's 14 chromosomes. Currently, clones of genomic DNA, prepared as yeast artificial chromosomes, are arranged into contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than contigs covering approximately 70% of the genome of parasite clone 3D7, gene sequence tags are available from more than 20% of the parasite's genes, and approximately 5% of the parasite's genes are tentatively identified from similarity searches of entries in the international sequence databases. A total of > 0.5 Mb of P. falciparum sequence tag data is available. The gene sequence tags are presently being used to complete YAC contig assembly and localize the cloned genes to positions on the physical map in preparation for sequencing the genome. Routes of access to project information and services are described.

Karyotype variability in Trypanosoma cruzi

Like many other protozoam parasites, Trypanosoma cruzi (the causative agent of Chagas disease) has a plastic genome. Chromosome size polymorphisms occur in different strains of T. cruzi as well as among clones originating from the same strain, Despite this polymorphism, major interchromosomal rearrangements appear to be rare since several linkage groups of chromosomal markers are well conserved among different T. cruzi strains. In addition, some correlation has been found between karyotype variability and classification by multilocus enzyme electrophoresis. In this review, Jan Henriksson, Lena Aslund and Ulf Petterson discuss the genomic variability and suggest that amplication of repetitive sequences or members of gene families make a major contribution to the chromosomal size variation

Mapping variation in chromosome homologues of different Giardia strains

A landmark physical map of the 2-Mb chromosome of the Giardia duodenalis cloned line WB-1B, constructed using randomly cloned, chromosome specific markers, was used to compare the organisation and map order of the equivalent chromosome in other strains. A representative marker from each of the 13 NotI segments of the 2-Mb chromosome was hybridized to NotI cleavages of whole chromosomes of the other strains. Two strains, one isolated from a human, and one from a cat, had the same chromosome hybridization patterns as WB-1B. A strain isolated from a sheep, had one NotI chromosome 5 segment larger than WB-1B. Two additional strains isolated from a calf and a human had significantly different NotI cleavage patterns from the previous strains and shared no similar-sized chromosome NotI segment from their 2Mb chromosome homologues and only one in common with WB-1B. In one strain, two markers from the same WB-1B NotI segment did not hybridize suggesting deletion events have occurred. The order of some NotI segments within the 2Mb chromosome homologue was maintained, as determined from partial NotI chromosome cleavages, while in the most divergent of strains internal chromosome rearrangements and deletions were evident. All but one of the 2Mb WB-1B chromosome markers examined hybridized to a single chromosome band in all strains. Thus, while Giardia chromosomes vary in size, copy number and organisation, some linkage of markers is apparently maintained in isolates from disparate hosts and localities. We have therefore generated a genetic analysis system for Giardia with landmark maps using representative markers to replace the paucity of classical genetic markers and mutants. This approach is being extended to the complete genome.

DNA organization and polymorphism of a wild-type Drosophila telomere region

Telomeres at the ends of linear chromosomes of eukaryotes protect the chromosome termini from degradation and fusion. While telomeric replication/elongation mechanisms have been studied extensively, the functions of subterminal sequences are less well understood. In general, subterminal regions can be quite polymorphic, varying in size from organism to organism, and differing among chromosomes within an organism. The subterminal regions of Drosophila melanogaster are not well characterized today, and it is not known which and how many different components they contain. Here we present the molecular characterization of DNA components and their organization in the subterminal region of the left arm of chromosome 2 of the Oregon RC wild-type strain of D. melanogaster, including a minisatellite with a 457bp repeat length. Two distinct polymorphic arrangements at 2L were found and analyzed, supporting the Drosophila telomere elongation model by retrotransposition. The high incidence of terminal chromosome deficiencies occurring in natural Drosophila populations is discussed in view of the telomere structure at 2L.

A polymorphic minisatellite sequence in the subtelomeric regions of chromosomes I and V in Leishmania infantum

A minisatellite DNA sequence is described for the first time in Leishmania infantum. It is borne by four chromosomes and consists of an 81-bp repeat unit organised in several clusters. On chromosomes I and V of L. infantum, the clusters are tightly located in the size-variable subtelomeric regions. The organisation of this sequence may be related to that of the subtelomeric interspersed repeat sequences identified in the human genome. The sequencing of seven repeat units, some subcloned from the same cluster, allowed the definition of a consensus sequence of 81 bp, particularly G/C rich (73%). Two subfamilies were clearly defined: one exhibits a 91-95% homology with the consensus sequence; the second one comprises two monomers sharing a 91% homology but only 77% homology with the consensus sequence. The two types of monomers can be found in the same cluster. These data suggest interactions between monomers and a possible role of this sequence in the instability of these regions. Finally, restriction fragment length polymorphisms were revealed by this sequence among various strains of L. infantum. Besides allowing the detection of recombination events in the unstable regions of the chromosomes, this new marker may become a useful tool in the study of the parasite population dynamics in leishmaniasis foci.

Rice-barley synteny and its application to saturation mapping of the barley Rpg1 region

In order to facilitate the map-based cloning of the barley stem rust resistance gene Rpg1, we have demonstrated a high degree of synteny at a micro level between the telomeric region of barley chromosome 1P and rice chromosome 6. We have also developed and applied a simple and efficient method for selecting useful probes from large insert genomic YAC and cosmid clones. The gene order within the most terminal 6.5 cM of barley chromosome 1P was compared with the most terminal 2.7 cM of rice chromosome 6. Nine rice probes, previously mapped in rice or isolated from YAC or cosmid clones from this region, were mapped in barley. All, except one, were in synteny with the rice gene order. The exception, probe Y617R, was duplicated in barley. One copy was located on a different chromosome and the other in a non-syntenic position on barley chromosome 1P. The barley probes from this region could not be mapped to rice, but two of them were inferred to be in a syntenic location based on their position on a rice YAC. This work demonstrates the utility of applying the results of genetic and physical mapping of the small genome cereal rice to map-based cloning of interesting genes from large genome relatives.

Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes

Plasmodium falciparum expresses on the host erythrocyte surface clonally variant antigens and ligands that mediate adherence to endothelial receptors. Both are central to pathogenesis, since they allow chronicity of infection and lead to concentration of infected erythrocytes in cerebral vessels. Here we show that expression of variant antigenic determinants is correlated with expression of individual members of a large, multigene family named var. Each var gene contains copies of a motif that has been previously shown to bind diverse host receptors; expression of a specific var gene correlated with binding to ICAM-1. Thus, our findings are consistent with the involvement of var genes in antigenic variation and binding to endothelium.

A family of complex tandem DNA repeats in the telomeres of Chironomus pallidivittatus

A family of 340-bp tandem telomere-associated DNA repeats is present in 50- to 200-kb blocks in seven of the eight paired chromosome ends in Chironomus pallidivittatus. It consists of four main subfamilies, differing from each other by small clusters of mutations. This differentiation may reflect different functional roles for the repeats. Here we find that one subfamily, D3, is consistently localized most peripherally and extends close to the ends of the chromosomes, as shown by its sensitivity to the exonuclease Bal 31. The amounts of D3 are highly variable between individuals. The repeat characteristic for D3 forms a segment with pronounced dyad symmetry, which in single-strand form would give rise to a hairpin. Evidence from an interspecies comparison suggests that a similar structure is the result of selective forces. Another subfamily, M1, is present more proximally in a subgroup of telomeres characterized by a special kind of repeat variability. Thus, a complex block with three kinds of subfamilies may occupy different M1 telomeres depending on the stock of animals. We conclude that subfamilies are differentially distributed between and within telomeres and are likely to serve different functions.

A family of complex tandem DNA repeats in the telomeres of Chironomus pallidivittatus

A family of 340-bp tandem telomere-associated DNA repeats is present in 50- to 200-kb blocks in seven of the eight paired chromosome ends in Chironomus pallidivittatus. It consists of four main subfamilies, differing from each other by small clusters of mutations. This differentiation may reflect different functional roles for the repeats. Here we find that one subfamily, D3, is consistently localized most peripherally and extends close to the ends of the chromosomes, as shown by its sensitivity to the exonuclease Bal 31. The amounts of D3 are highly variable between individuals. The repeat characteristic for D3 forms a segment with pronounced dyad symmetry, which in single-strand form would give rise to a hairpin. Evidence from an interspecies comparison suggests that a similar structure is the result of selective forces. Another subfamily, M1, is present more proximally in a subgroup of telomeres characterized by a special kind of repeat variability. Thus, a complex block with three kinds of subfamilies may occupy different M1 telomeres depending on the stock of animals. We conclude that subfamilies are differentially distributed between and within telomeres and are likely to serve different functions.

Subtelomeric chromosome instability in Plasmodium falciparum: short telomere-like sequence motifs found frequently at healed chromosome breakpoints

The stability of chromosome ends of the human malaria parasite P. falciparum was analysed using a polymerase chain reaction (PCR) assay that detects potential chromosome breaks that have been healed by the addition of telomere repeats. The data show that the Pf332 and Pf87 genes located in subtelomeric positions of chromosomes 3 and 11, respectively, represent fragile sites. Breakpoints were observed in different regions of these genes. In the broken genes, the DNA sequences preceding the telomere addition sites generally have complementarity to the predicted RNA template of a P. falciparum telomerase ribonucleoprotein enzyme complex. We propose a model for the creation of new telomeres in P. falciparum adjacent to broken ends containing short telomere-like sequence motifs.

Establishing a physical map of chromosome No. 4 of Plasmodium falciparum

We isolated a panel of 20 DNA probes that hybridize specifically to chromosome No. 4 of Plasmodium falciparum and used them to construct a restriction map of chromosome No. 4 in the FCR3 strain. These probes were partially sequenced and had an insert size range of 70-310 bp (average 160 bp) and a GC content range of 19-53% (average 35%). Three probes were identical to previously described P. falciparum sequences. Two probes were homologous to an 18-bp repetitive sequence in a previously cloned P. falciparum gene but were not homologous to other parts of the gene. One probe sequence is a homologue of the heat shock protein, DnaJ. The location of these probes and four previously cloned probes on chromosome No. 4 were determined by using eight restriction enzymes that recognize 6-bp sites containing only G or C and 10 restriction enzymes that recognize 6-bp sites containing four G or C and two A or T. The locations of the probes were well distributed along the chromosome. Three probes were located at two sites and two probes were found at at least four sites on chromosome No. 4. Maps of chromosome No. 4 of the FCR3 strain, and three laboratory-selected, pyrimethamine-resistant derivative strains were constructed. Two of the strains, FCR3-D81 and FCR3-D85, each had two polymorphic forms of chromosome No. 4. Each of those polymorphic chromosomes had a duplicated part of the center of the chromosome making the cell diploid for the genetic material in that region. Those chromosomes also had an amplification and probable intrachromosomal translocation of a 50-kb fragment of chromosome No. 4. One strain derived from FCR3-D7, FCR3-D7-1 contained 20 copies of a tandemly amplified fragment carrying the dihydrofolate reductase-thymidylate synthase gene and an amplification of an unrelated part of the chromosome.

The polymorphic subtelomeric regions of Plasmodium falciparum chromosomes contain arrays of repetitive sequence elements

The human malaria parasite Plasmodium falciparum exhibits a high degree of chromosomal polymorphism, which may contribute to its ability to evade host defenses. The analysis of parasite chromosomes has revealed that these polymorphisms are confined to the subtelomeric regions, which are transcriptionally silent and contain repetitive sequence elements. Several subtelomeric repetitive elements have been isolated and mapped by using P. falciparum yeast artificial chromosome (YAC) clones. Structural analysis of parasite telomeric and subtelomeric YAC clones demonstrated that these repetitive elements are conserved between P. falciparum chromosome ends. We suggest that these subtelomeric elements promote chromosome pairing in P. falciparum and facilitate meiotic recombination and gene conversion between telomere-proximal genes.

Organization of chromosomes in Plasmodium falciparum: A model for generating karyotypic diversity

Chromosomes of the human malaria parasite, Plasmodium falciparum, are compartmentalized into conserved and polymorphic domains. The conserved domains are transcribed and localized within the central region o f a chromosome, whereas the polymorphic domains are transcriptionally silent and situated at chromosome ends. Unlike the central chromosomal domains, chromosome ends contain repetitive sequence elements. In this review, Michael Lonzer, Derik de Bruin, Samuel Wertheimer and Jeffrey Ravetch propose that the chromosome ends play a functional role in generating genetic diversity by promoting meiotic and mitotic recombination and chromosomal rearrangement events.

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.

Electrophoretic karyotype and chromosome assignments for a pathogenic and a nonpathogenic strain of Entamoeba histolytica

The electrophoretic karyotypes of a pathogenic and a nonpathogenic strain of Entamoeba histolytica were determined by pulsed-field gel electrophoresis. A number of previously isolated genes were assigned to specific chromosomal bands. Significant differences between the chromosomal patterns of these strains as well as in the assignment of most genes were found.

Characterization of Megatrypanum trypanosomes from European Cervidae

Megatrypanum trypanosomes have been isolated from a number of different European Cervidae, but on the basis of morphology it has not been possible to define the species to which these isolates belong. We isolated Trypanosoma (Megatrypanum) theileri from 10 cattle, and Megatrypanum trypanosomes from 11 fallow deer (Cervus dama), 9 red deer (Cervus elaphus), and 4 roe deer (Capreolus capreolus) by blood culture on a biphasic medium (NNN agar slopes). Trypanosomes were propagated in Schneider's Drosophila medium and characterized by isoenzyme analysis and molecular karyotyping. Isocitrate dehydrogenase and phosphoglucomutase were visualized after starch gel electrophoresis of trypanosome lysates. By cluster analysis of this data all isolates from deer were clearly separated from the T.(M.) theileri isolates from cattle. Isolates from roe deer were different not only from T. (M.) theileri but also from the other deer isolates. Isolates from fallow deer and red deer were grouped together. Thus, there are probably at least two different species of Megatrypanum trypanosomes in the three Cervidae. One parasitizing roe deer, the other, apparently less host specific species, infecting red deer and fallow deer. Separation of the chromosomes of Megatrypanum trypanosomes by pulsed-field gradient gel electrophoresis (PFGE) showed that each isolate contained a large number (> 18) of chromosomes ranging in size from 300 to > 2200 kb. The molecular karyotypes were similar for all isolates, although no isolate was identical to another.

Characterisation of the gene encoding an unusually divergent TATA-binding protein (TBP) from the extremely A+T-rich human malaria parasite Plasmodium falciparum

The intergenic regions of the human malaria parasite, Plasmodium falciparum, are extreme in their base composition, averaging approx. 90% A + T. As a first step to investigating whether transcription in this organism follows conventional models based largely on yeast, we have isolated and characterised the gene (TBP) encoding its TATA-binding protein (TBP). The gene is present as a single copy on chromosome 5 and is expressed as a 1.8-kb mRNA encoding a protein of 228 amino acids (aa) (26 164 Da). The inferred protein product has a bipartite structure consisting of a 45-aa species-specific N-terminal domain and a 183-aa C-terminal domain. In the latter, the malarial protein contains two directly repeated, but imperfectly homologous regions, each approx. 78 aa in length, together with a highly basic region located between them. These features are characteristic of all TBPs studied to date. Moreover, hydropathy plots suggest that the overall folding of this C-terminal domain is very similar to that of other TBPs. However, TBP from P. falciparum is much less closely related at the primary sequence level to the archetypal yeast homologue than are all other characterised TBPs (42% identity, compared to 76-93%, respectively). Despite this divergence of the primary sequence, most residues known to be involved in DNA binding are conserved. Those instances where sequence variation at generally conserved residues is observed may reflect functional differences that could ultimately be exploited by selective chemotherapy.

Pfl I-I and Pf332: Two giant proteins synthesized in erythrocytes infected with Plasmodium falciparum

Although the malaria parasite develops within erythrocytes, it has to modify the surrounding red blood cell membrane for its intracellular survival and maturation. These changes include the translocation of proteins across the parasite and the parasitophorous vacuole membranes to the host membrane. In this review, Denise Mattei, Katherine Hinterberg and Artur Scherf focus on two distinct giant parasite molecules of unprecedented size (approximately one MDa), called Pf332 and PflI-I, that are synthesized and exported into the cytoplasm of the host cell in the asexual and sexual blood stages of Plasmodium falciparum, respectively. The corresponding genes are located in genetically unstable subtelomeric chromosome regions.

Molecular analysis of Plasmodium falciparum hexokinase

Hexokinase, a key glycolytic enzyme, is involved in the initial phosphorylation reaction of imported glucose and specific blocking of this activity may therefore arrest the development of malaria parasites. We describe here the cloning of a single copy hexokinase gene of Plasmodium falciparum (PfHK) from cDNA or genomic DNA libraries. The deduced amino acid sequence of PfHK has 26% identity with human hexokinase I and its predicted molecular mass assigns it as an invertebrate type isoenzyme of hexokinase. A single 1.5-kb exon is translated from a 3-kb mRNA in asexual stages of the parasite. In contrast to aldolase and GPI, the gene for this glycolytic enzyme is located on chromosome 8. Poly- and monoclonal antibodies against recombinant PfHK support our cloning results at the protein level as they detect a protein of the predicted size and isoelectric point by Western blotting in parasite protein samples. Moreover, polyclonal rabbit IgG against recombinant PfHK partially inhibits the hexokinase activity of a P. falciparum lysate which provides direct proof that the gene cloned encodes hexokinase of the parasite.

Code domains in tandem repetitive DNA sequence structures

Traditionally, many people doing research in molecular biology attribute coding properties to a given DNA sequence if this sequence contains an open reading frame for translation into a sequence of amino acids. This protein coding capability of DNA was detected about 30 years ago. The underlying genetic code is highly conserved and present in every biological species studied so far. Today, it is obvious that DNA has a much larger coding potential for other important tasks. Apart from coding for specific RNA molecules such as rRNA, snRNA and tRNA molecules, specific structural and sequence patterns of the DNA chain itself express distinct codes for the regulation and expression of its genetic activity. A chromatin code has been defined for phasing of the histone-octamer protein complex in the nucleosome. A translation frame code has been shown to exist that determines correct triplet counting at the ribosome during protein synthesis. A loop code seems to organize the single stranded interaction of the nascent RNA chain with proteins during the splicing process, and a splicing code phases successive 5' and 3' splicing sites. Most of these DNA codes are not exclusively based on the primary DNA sequence itself, but also seem to include specific features of the corresponding higher order structures. Based on the view that these various DNA codes are genetically instructive for specific molecular interactions or processes, important in the nucleus during interphase and during cell division, the coding capability of tandem repetitive DNA sequences has recently been reconsidered.

Towards a high-resolution map of the Plasmodium falciparum genome

Until recently very little was known about the genome of Plasmodium falciparum. The situation has changed considerably with the advent of pulsed field gradient electrophoresis and yeast artificial chromosome technologies. It should now be possible to generate a high-resolution map within a few years. Here, Tony Triglia, Thomas Wellems and David Kemp review current knowledge.

Cloning and characterization of chromosome breakpoints of Plasmodium falciparum: breakage and new telomere formation occurs frequently and randomly in subtelomeric genes

We analysed the genetic stability of two subtelomeric genes of the human malaria parasite Plasmodium falciparum. A PCR based assay, using a telomere and a target-gene specific primer was used to detect potential chromosome rearrangements. We show that chromosome breakage and the formation of new telomeres occur frequently in the two genes coding for histidine rich proteins (HRP I and HRP II) in laboratory isolates, but remains undetectable in clinical parasite isolates. This finding suggests an essential role of these genes in vivo and that chromosome breakage is rather an accidental process than a programmed chromosome fragmentation. Cloning and sequencing of 8 chromosome breakpoints of the HRP II gene from one parasite isolate shows that the breakage occurs within a broad region in which new telomere formation appear to take place at random sites. Furthermore, this analysis revealed no obvious sequence similarities of sites of telomere addition. Finally, we show that an irregular pattern of heterogeneous telomere repeats is added at each broken end and that each healed chromosome contains a distinct pattern of repeats. We discuss a model for telomere formation in P. falciparum.

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.

A Plasmodium falciparum blood stage antigen highly homologous to the glycophorin binding protein GBP

We have isolated a gene coding for a protein highly homologous to an antigen known as the glycophorin binding protein (GBP) which was therefore called GBPH. The gene consists of 2 exons interrupted by an intron located at a position corresponding to that of the GBP gene. The deduced amino acid sequence of GBPH comprises 427 residues and is characterized by a signal sequence and by an extended repeat region consisting of 8 units of 40 amino acid residues. The comparison of the amino acid sequences of GBPH and GBP reveals an identity of 69%. Antisera raised against a GBPH fragment that carries part of the repetitive region cross-react with GBP (105 kDa) and additionally detect some bands between 40 and 70 kDa, one of which may correspond to GBPH. The genes coding for GBP and GBPH are located on chromosomes 10 and 14, respectively. The GBP gene is transcribed as a highly abundant 6.5 kb mRNA in the blood-stage form, whereas Northern blot analysis using a GBPH specific probe detects 2 less abundant mRNAs of 2.3 kb and 2.7 kb. Southern blot analysis of P. falciparum DNA identifies a third member of the GBP gene family.

7H8/6, a multicopy DNA probe for distinguishing isolates of Plasmodium falciparum

A method using DNA fingerprinting to distinguish Plasmodium falciparum isolates has been developed using a clone, 7H8/6, isolated by screening a genomic expression library of the Malayan Camp strain with a monoclonal antibody. Unlike other P. falciparum DNA probes that contain internally repetitive sequences, this probe contains a single full-length open reading frame and lacks any repetitive sequences. Chromosome mapping located the hybridizing sequences to most chromosomes. 7H8/6 sequences are located at sites near the subtelomeric regions, although they are further from the telomeres than the subtelomeric repetitive sequences rep20. The probe gave multiple polymorphic bands on Southern blots of genomic DNA allowing all unrelated isolates tested to be readily distinguished. Hybridization patterns of parent and progeny from the genetic cross of two P. falciparum clones showed that most bands were inherited independently and no new bands were generated during the cross. This probe is useful for distinguishing isolates of P. falciparum and also for analyzing relationships between closely related isolates.

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.

Genetic mapping of the chloroquine-resistance locus on Plasmodium falciparum chromosome 7

The resurgence of malaria in recent decades has been accompanied by the worldwide spread of resistance to chloroquine, a drug once uncontested as the first-line antimalarial agent because of its efficacy and low toxicity. Chloroquine-resistant strains of Plasmodium falciparum counter the drug by expelling it rapidly via an unknown mechanism. In the absence of explicit biochemical knowledge of this efflux mechanism, reverse genetics provides a powerful approach to the molecular basis of chloroquine resistance. Here we report genetic linkage analysis in which 85 restriction fragment length polymorphism markers were used to examine inheritance of the 14 P. falciparum chromosomes in a laboratory cross between a chloroquine-resistant and a chloroquine-sensitive parasite. Inheritance data from 16 independent recombinant progeny show that the rapid efflux, chloroquine-resistant phenotype is governed by a single locus within an approximately 400-kilobase region of chromosome 7. Identification and characterization of genes within this region should lead to an understanding of the chloroquine-resistance mechanism.

Large fragments of Plasmodium falciparum DNA can be stable when cloned in yeast artificial chromosomes

A major problem in cloning large segments of Plasmodium falciparum DNA is the instability of this very A + T-rich DNA in Escherichia coli. We have therefore investigated whether P. falciparum DNA segments over 100 kb in size cloned in the yeast Saccharomyces cerevisiae as yeast artificial chromosomes (YACs) are stable. An analysis of EcoRI fragments adding up to 230 kb, or nearly 1% of the P. falciparum genome, showed that sequences cloned as YACs were indistinguishable from the DNA in the P. falciparum genome, showing neither deletions nor rearrangements. Over 400 YACs have been obtained so far with an average insert size between 110 and 130 kb. Screening the YACs with single-copy probes suggested that most sequences should be represented in a library of less than 10(3) YACs. Hence YACs provide an approach to cloning large segments of P. falciparum DNA.

Polymorphism of the TRAP gene of Plasmodium falciparum

Natural sequence variation of the thrombospondin related anonymous protein (TRAP) gene of Plasmodium falciparum has been investigated by DNA analysis following the polymerase chain reaction amplification, and this shows the gene to be highly polymorphic. The region containing the sequence motif Trp-Ser-Pro-Cys-Ser-Val-Thr-Cys-Gly (WSPCSVTCG), common to TRAP, the circumsporozoite protein, properdin, and thrombospondin, was invariant. Elsewhere in the molecule, over 50 amino acid substitutions are described including the insertion of an in-frame, small-variable tandemly repeating motif between amino acid residues 352 and 353. Only one silent mutation was observed. Most nucleotide changes that occur in the first two codon positions result in conservative amino acid changes. Restriction fragment length polymorphism (RFLP) analysis was used to examine inheritance of TRAP in a cross between the HB3 and 3D7 clones of P. falciparum. Out of nine progeny examined, four possessed the HB3 gene and five the 3D7 gene. The TRAP gene hybridized to chromosome 13. Previous work has shown that a subtelomeric region of chromosome 13 from the 3D7 parent (marked by the HRP-III gene) was favoured strongly in this cross. The TRAP gene, however, is over 1 Mb away from this subtelomeric region and exhibits no such linkage because of chromosome crossovers. Five geographically separate isolates shared the same TRAP sequence as well as the same variant of the Th2R/Th3R region from the circumsporozoite protein. The correlation between independent markers in these isolates suggests that they have a common provenance.