Genome plasticity in Plasmodium

A Comparative Genomic Study of Attenuated and Virulent Strains of Babesia bigemina

Cattle babesiosis is a socio-economically important tick-borne disease caused by Apicomplexa protozoa of the genus Babesia that are obligate intraerythrocytic parasites. The pathogenicity of Babesia parasites for cattle is determined by the interaction with the host immune system and the presence of the parasite’s virulence genes. A Babesia bigemina strain that has been maintained under a microaerophilic stationary phase in in vitro culture conditions for several years in the laboratory lost virulence for the bovine host and the capacity for being transmitted by the tick vector. In this study, we compared the virulome of the in vitro culture attenuated Babesia bigemina strain (S) and the virulent tick transmitted parental Mexican B. bigemina strain (M). Preliminary results obtained by using the Basic Local Alignment Search Tool (BLAST) showed that out of 27 virulence genes described and analyzed in the B. bigemina virulent tick transmitted strain, only five were fully identified in the attenuated laboratory strain. In all cases, the identity and coverture of the identified genes of the wildtype strain were higher than those of the laboratory strain. This finding is putatively associated with the continuous partial loss of virulence genes in the laboratory strain after several passages of the parasite population under optimal in vitro growth conditions. The loss of virulence factors might be reflected in the absence of symptoms of the disease in cattle inoculated with the attenuated strain despite the presence of infection in the bovine host cells.

Repetitive elements in genomes of parasitic protozoa

Repetitive DNA elements have been a part of the genomic fauna of eukaryotes perhaps since their very beginnings. Millions of years of coevolution have given repeats central roles in chromosome maintenance and genetic modulation. Here we review the genomes of parasitic protozoa in the context of the current understanding of repetitive elements. Particular reference is made to repeats in five medically important species with ongoing or completed genome sequencing projects: Plasmodium falciparum, Leishmania major, Trypanosoma brucei, Trypanosoma cruzi, and Giardia lamblia. These organisms are used to illustrate five thematic classes of repeats with different structures and genomic locations. We discuss how these repeat classes may interact with parasitic life-style and also how they can be used as experimental tools. The story which emerges is one of opportunism and upheaval which have been employed to add genetic diversity and genomic flexibility.

Low-Complexity Regions in Plasmodium falciparum Proteins

Full-sequence data available for Plasmodium falciparumchromosomes 2 and 3 are exploited to perform a statistical analysis of the long tracts of biased amino acid composition that characterize the vast majority of P. falciparum proteins and to make a comparison with similarly defined tracts from other simple eukaryotes. When the relatively minor subset of prevalently hydrophobic segments is discarded from the set of low-complexity segments identified by current segmentation methods in P. falciparum proteins, a good correspondence is found between prevalently hydrophilic low-complexity segments and the species-specific, rapidly diverging insertions detected by multiple-alignment procedures when sequences of bona fide homologs are available. Amino acid preferences are fairly uniform in the set of hydrophilic low-complexity segments identified in the twoP. falciparum chromosomes sequenced, as well as in sequenced genes from Plasmodium berghei, but differ from those observed in Saccharomyces cerevisiae and Dictyostelium discoideum. In the two plasmodial species, amino acid frequencies do not correlate with properties such as hydrophilicity, small volume, or flexibility, which might be expected to characterize residues involved in nonglobular domains but do correlate with A-richness in codons. An effect of phenotypic selection versus neutral drift, however, is suggested by the predominance of asparagine over lysine.

Low-complexity regions in Plasmodium falciparum proteins

Full-sequence data available for Plasmodium falciparum chromosomes 2 and 3 are exploited to perform a statistical analysis of the long tracts of biased amino acid composition that characterize the vast majority of P. falciparum proteins and to make a comparison with similarly defined tracts from other simple eukaryotes. When the relatively minor subset of prevalently hydrophobic segments is discarded from the set of low-complexity segments identified by current segmentation methods in P. falciparum proteins, a good correspondence is found between prevalently hydrophilic low-complexity segments and the species-specific, rapidly diverging insertions detected by multiple-alignment procedures when sequences of bona fide homologs are available. Amino acid preferences are fairly uniform in the set of hydrophilic low-complexity segments identified in the two P. falciparum chromosomes sequenced, as well as in sequenced genes from Plasmodium berghei, but differ from those observed in Saccharomyces cerevisiae and Dictyostelium discoideum. In the two plasmodial species, amino acid frequencies do not correlate with properties such as hydrophilicity, small volume, or flexibility, which might be expected to characterize residues involved in nonglobular domains but do correlate with A-richness in codons. An effect of phenotypic selection versus neutral drift, however, is suggested by the predominance of asparagine over lysine.

The origin of antigenic diversity in Plasmodium falciparum

Most studies of genetic variability of Plasmodium falciparum have focused on protein antigens and the genes that encode them. The consensus is that populations exhibit high levels of genetic polymorphism, most notably the genes encoding surface proteins of the merozoite (Msp1, Msp2) and the sporozoite (Csp). The age and derivation of this variation is a subject that warrants further careful consideration, as discussed here by Stephen Rich, Marcelo Ferreira and Francisco Ayala.

Population structure and recent evolution of Plasmodium falciparum

Plasmodium falciparum is the agent of malignant malaria, one of mankind's most severe maladies. The parasite exhibits antigenic polymorphisms that have been postulated to be ancient. We have proposed that the extant world populations of P. falciparum have derived from one single parasite, a cenancestor, within the last 5, 000-50,000 years. This inference derives from the virtual or complete absence of synonymous nucleotide polymorphisms at genes not involved in immune or drug responses. Seeking to conciliate this claim with extensive antigenic polymorphism, we first note that allele substitutions or polymorphisms can arise very rapidly, even in a single generation, in large populations subject to strong natural selection. Second, new alleles can arise not only by single-nucleotide mutations, but also by duplication/deletion of short simple-repeat DNA sequences, a process several orders of magnitude faster than single-nucleotide mutation. We analyze three antigenic genes known to be extremely polymorphic: Csp, Msp-1, and Msp-2. We identify regions consisting of tandem or proximally repetitive short DNA sequences, including some previously unnoticed. We conclude that the antigenic polymorphisms are consistent with the recent origin of the world populations of P. falciparum inferred from the analysis of nonantigenic genes.

A new look at the challenging world of tandem repeats

Recent research has shown a correlation between some genetic diseases and genomic sequences tandemly repeated a variable and excessive number of times. The excessive number of tandem repeats is usually caused by a progressive expansion, generally considered as purely harmful. We put forward a number of hypotheses: the main one is that the number of repeats has normally a specific significance, and that there exist purposive mechanisms having as a primary function the management of tandem repeats length; such a function is generally useful and only rarely may it become harmful, because of some malfunctioning. These hypotheses are suggested by plausibility arguments, and are supported by a number of recent experimental results. They could provide a simple and unifying explanation of many pathological and non-pathological phenomena replacing many ad hoc assumptions. We finally propose to call the study of the above tandem repeat managing mechanisms 'dynamical genetics'.

Molecular characterization of a Plasmodium chabaudi erythrocyte membrane-associated protein with glutamate-rich tandem repeats

The malarial parasite dramatically affects the structure and function of the erythrocyte membrane by exporting proteins that specifically interact with the host membrane. This report describes the complete sequence and some biochemical properties of a 93-kDa Plasmodium chabaudi chabaudi protein that interacts with the host erythrocyte membrane. Approximately 40% of the deduced protein sequence consists of tandem repeats of 14 amino acids that are rich in glutamic acid residues. Comparison of the repeat sequences from two different P. c. chabaudi strains derived from the same initial isolate revealed an exact duplication of 294 nucleotides suggesting a recent unequal crossing-over event. However, in spite of this potentially high level of intragenic recombination activity, the repeat sequences from P. c. adami are rather conserved suggesting structural or functional constraints on the protein and tandem repeats. The 93-kDa protein exists in an oligomeric form as revealed by gel filtration chromatography and non-denaturing gel electrophoresis. A predominantly alpha-helical predicted secondary structure and a discrepancy between the estimated molecular sizes determined from non-denaturing gel electrophoresis and gel filtration chromatography suggest that the protein is a long rod-shaped or fibrillar, protein. Attributes shared between the 93-kDa protein, some P. falciparum proteins with glutamate-rich tandem repeats, and cytoskeletal proteins suggest that these parasite proteins function as cytoskeletal proteins that possibly stabilize the erythrocyte membrane.

The complete sequence of Plasmodium berghei merozoite surface protein-1 and its inter- and intra-species variability

The complete gene for merozoite surface protein-1 (MSP-1) from Plasmodium berghei has been cloned and sequenced. Comparison of the P. berghei MSP-1 sequence with MSP-1 from other rodent parasites reveals five conserved domains interrupted by four variable blocks. These variable blocks exhibit no sequence homology but do have similar amino acid compositions. Primary proteolytic processing sites are located near the boundaries between the conserved domains and the variable blocks. Sequencing of the variable blocks from several P. berghei isolates shows that the predominant intra-species difference is in the number of tandem repeats. The inter- and intra-species differences suggest that the variable blocks are localized areas with relatively high levels of slipped-strand mispairing, unequal crossing-over, or other intragenic recombination activity. MSP-1 from P. berghei exhibits more repetitiveness than MSP-1 from other species suggesting that P. berghei experiences a higher intrinsic level of events producing variable numbers of tandem repeats or a lower level of events leading to the degeneration of tandem repeats.

Genetic polymorphism and natural selection in the malaria parasite Plasmodium falciparum

We have studied the genetic polymorphism at 10 Plasmodium falciparum loci that are considered potential targets for specific antimalarial vaccines. The polymorphism is unevenly distributed among the loci; loci encoding proteins expressed on the surface of the sporozoite or the merozoite (AMA-1, CSP, LSA-1, MSP-1, MSP-2, and MSP-3) are more polymorphic than those expressed during the sexual stages or inside the parasite (EBA-175, Pfs25, PF48/45, and RAP-1). Comparison of synonymous and nonsynonymous substitutions indicates that natural selection may account for the polymorphism observed at seven of the 10 loci studied. This inference depends on the assumption that synonymous substitutions are neutral, which we test by analyzing codon bias and G+C content in a set of 92 gene loci. We find evidence for an overall trend towards increasing A+T richness, but no evidence for mutation bias. Although the neutrality of synonymous substitutions is not definitely established, this trend towards an A+T rich genome cannot explain the accumulation of substitutions at least in the case of four genes (AMA-1, CSP, LSA-1, and PF48/45) because the Gleft and right arrow C transversions are more frequent than expected. Moreover, the Tajima test manifests positive natural selection for the MSP-1 and, less strongly, MSP-3 polymorphisms; the McDonald-Kreitman test manifests natural selection at LSA-1 and PF48/45. We conclude that there is definite evidence for positive natural selection in the genes encoding AMA-1, CSP, LSA-1, MSP-1, and Pfs48/45. For four other loci, EBA-175, MSP-2, MSP-3, and RAP-1, the evidence is limited. No evidence for natural selection is found for Pfs25.

Sequence diversity and molecular evolution of the merozoite surface antigen 2 of Plasmodium falciparum

Eleven new alleles of the Plasmodium falciparum merozoite surface antigen 2 (MSA2) from Papua New Guinea were analyzed by direct sequencing of polymerase chain reaction (PCR) products. We have used the sequence information to trace the molecular evolution of MSA2. The repeats of ten alleles belonging to the 3D7 allelic family differed considerably in size, nucleotide sequence, and repeat copy number. In the repeat region of these new alleles, codon usage was extremely biased with an exclusive use of NNT codons. Another new allele sequenced belonged to the FC27 family and confirmed the family-specific conserved structure of 96 and 36 bp repeats. In order to assess sequence microheterogeneity within samples defined as the same genotype by restriction fragment length polymorphism (RFLP), we have analyzed single-strand conformation polymorphism (SSCP) of different samples of the most frequent allele (D10 of the FC27 family) in the study population. No sequence heterogeneity could be detected within the repeat region. Based on analysis of the repeat regions in both allelic families, we discuss the hypothesis of a different evolutionary strategy being represented by each of the allelic families. Kew words: Merozoite surface antigen 2 - Nucleotide sequence comparisons - Molecular evolution

The highly immunogenic enolase and Hsp70p are adventitious Candida albicans cell wall proteins

Screening cDNA libraries with polyclonal antibody preparations against Candida albicans yeast or mycelial cell walls resulted in isolation of several positive clones. Some of them encoded enolase; others encoded a protein of the 70 kDa heat-shock protein family (Hsp70p), etc. The presence of these cytosolic proteins in the cell wall of actively growing C. albicans was discovered by analytical (SDS-PAGE and Western blot) and cytological (indirect immunofluorescence) experiments. Supplementation of cell cultures with papulacandin B, an antibiotic that inhibits formation of the beta-glucan skeleton, resulted in the release of enolase to the supernatant fluids; this release was prevented when 0.6 M KCl was present as an osmotic stabilizer. The cell wall of C. albicans incorporated exogenously added proteins (enolase and Escherichia coli and C., albicans cytosolic proteins). The presence in the C. albicans cell wall of enolase, Hsp70p, and probably other intracellular proteins that are highly immunogenic might help the fungal cells to evade the host defences, and consequently could represent a survival mechanism for C. albicans 'in vivo'.