Cryptosporidium parvum: the many secrets of a small genome

Molecular characterization of bovine Cryptosporidium isolated from diarrheic calves in the Sudan

Cryptosporidiosis is a common protozoan infection causing morbidity and mortality in young cattle and may be zoonotically transmitted to humans. So far, there is no data available on the presence of Cryptosporidium spp. in the Sudan. The aim of this study was to isolate, identify, and genotype Cryptosporidium oocysts sampled from diarrheic calves housed at different farms in three different municipalities in Khartoum State (Khartoum, Khartoum North, Omdurman). A total of 149 fecal samples were evaluated microscopically for the presence of Cryptosporidium oocysts using the modified Ziehl-Neelsen staining method and 87 (58.3%) samples tested positive. Positive and negative samples were further analyzed by nested PCR targeting the SSU rRNA region. Positive samples were subjected to restriction enzyme analysis of PCR amplicons (PCR-RFLP). Nested PCR identified Cryptosporidium DNA in 53 samples (35.5%); restriction digestion of the PCR products revealed the presence of C. parvum (73.5%), C. ryanae (13.2%), C. andersoni (7.5%), and C. bovis (1.8%). Species distribution was clearly related to age with C. parvum being the predominant species in dysenteric pre-weaned calves. Sequencing of three genes (SSU rRNA, COWP, and GP60) for three C. parvum isolates originating from the three different municipalities showed that all belong to C. parvum subtype family IId. Based on data obtained by GP60, sequencing the two C. parvum isolates from Khartoum and Omdurman represent subtype IIdA18G1, whereas oocysts isolated in Khartoum North belong to subtype IIdA19G1. The observed genotypes are zoonotic and thus C. parvum in calves is potentially a health risk to humans in Khartoum State, Sudan. To the best of our knowledge, this is the first reported attempt to characterize Cryptosporidium isolated from cattle in the Sudan.

Genotyping of Cryptosporidium spp. in environmental water in Turkey

This research was undertaken to study the molecular detection and characterization of Cryptosporidium spp. in environmental water sources at Samsun and Giresun Provinces of The Black Sea in Turkey. Two-hundred forty and one-hundred eighty environmental samples were collected from a total of twenty and twenty-five sampling sites of Giresun and Samsun Provinces. One hundred twenty untreated drinking water samples were also detected for Cryptosporidium spp. in both investigated areas. 101 (%42), 92 (%38.3) of 240 and 74 (41.1%), 70 (38.8%) of 180 environmental samples have been found positive for Cryptosporidium spp. by Loop mediated isothermal amplification (LAMP) targeting the S-adenosyl-L-methionine synthetase (SAM) gene and nested PCR targeting small subunit (SSU)rRNA gene in Samsun and Giresun Provinces, respectively. Of the tested untreated drinking water samples collected from the investigated area, one sample was positive for Cryptosporidium spp. Six and twelve samples were clearly sequenced for the Cryptosporidium (SSU)rRNA gene among the highest positive samples selected from each of the twenty and twenty-five sampling sites of Giresun and Samsun Provinces, respectively. Genetic characterization of Cryptosporidium isolates from water samples represented Cryptosporidium bovis for five samples, Cryptosporidium parvum for six samples and one sample for Cryptosporidium felis in Samsun Province, where C. parvum for five samples and C. bovis for one sample were sequenced in Giresun Province. According to accessible information sources, this is the first research about genotyping of Cryptosporidium spp. in water samples collected from Samsun and Giresun Provinces of Turkey.

Genome-wide upstream motif analysis of Cryptosporidium parvum genes clustered by expression profile

Background

There are very few molecular genetic tools available to study the apicomplexan parasite Cryptosporidium parvum. The organism is not amenable to continuous in vitro cultivation or transfection, and purification of intracellular developmental stages in sufficient numbers for most downstream molecular applications is difficult and expensive since animal hosts are required. As such, very little is known about gene regulation in C. parvum.

Results

We have clustered whole-genome gene expression profiles generated from a previous study of seven post-infection time points of 3,281 genes to identify genes that show similar expression patterns throughout the first 72 hours of in vitro epithelial cell culture. We used the algorithms MEME, AlignACE and FIRE to identify conserved, overrepresented DNA motifs in the upstream promoter region of genes with similar expression profiles. The most overrepresented motifs were E2F (5′-TGGCGCCA-3′); G-box (5′-G.GGGG-3′); a well-documented ApiAP2 binding motif (5′-TGCAT-3′), and an unknown motif (5′-[A/C] AACTA-3′). We generated a recombinant C. parvum DNA-binding protein domain from a putative ApiAP2 transcription factor [CryptoDB: cgd8_810] and determined its binding specificity using protein-binding microarrays. We demonstrate that cgd8_810 can putatively bind the overrepresented G-box motif, implicating this ApiAP2 in the regulation of many gene clusters.

Conclusion

Several DNA motifs were identified in the upstream sequences of gene clusters that might serve as potential cis-regulatory elements. These motifs, in concert with protein DNA binding site data, establish for the first time the beginnings of a global C. parvum gene regulatory map that will contribute to our understanding of the development of this zoonotic parasite.

Genotyping of Cryptosporidium parvum isolates in bovine population in Kolkata and characterization of new bovine genotypes

Cryptosporidium infection may have adverse effect in health and production potential of cattle herd. The exact profile of Cryptosporidium infection in bovine population of India in general, particularly from Kolkata is scarce. We here report systematic investigation of clinical and genetic profiling of promiscuous Cryptosporidium infection in selected representative cattle farms from Kolkata as well as some surrounding local areas. The current study was conducted in the period of October to September, 2000-2001 with 149 diarrhoeic and non-diarrhoeic cattle of different age groups from two Government cattle farms, Harringhata Cattle Unit and Kalyani State Livestock Farm and animals raised by local farmers. Among these 149 samples, diarrhoea was recorded in 79 cases (53%) and non-diarrhoeic in 70 (46.9%). Out of 149 faecal samples screened microscopically, 32.9% from diarrhoeic faecal samples and 7.1% from healthy faecal samples revealed the presence of oocysts. Cryptosporidium genus was confirmed by DNA typing with nested PCR. The PCR-RFLP analysis was carried out for genotype identification. In course of PCR-RFLP, unique band patterns were obtained in two of our samples. The unusual RFLP products were characterized by DNA sequencing and homology analysis with other reported variants. This is the first report of identification and characterization of such a variant from the area of present investigation. Further study will be required to understand the phylogenetic origin and functional significance in virulence and morbidity of this genotype.

Peculiar behavior of distinct chromosomal DNA elements during and after development in the dicyemid mesozoan Dicyema japonicum

The dicyemid mesozoans are obligate parasites that inhabit the cephalopod renal appendage. Dicyemids have a simple body, consisting of approximately 30 cells: one long cylindrical axial cell contains intracellular stem cells (called axoblast), from which embryos are derived, and is surrounded by some 30 peripheral somatic cells. Somatic cells divide at most eight times in their life span, and never divide after differentiation. During early somatic cell development, numerous unique DNA sequences are first amplified and then eliminated, in the form of extrachromosomal circular DNA, leading to genome reduction. In this study we demonstrate that the remaining sequences, single-copy genes and repetitive sequences, have very different fates. Single-copy genes, such as beta-tubulin, are initially amplified, presumably via endoreduplication, but subsequently decrease in copy number through development, suggesting that the whole genome is initially amplified and then the amplified DNAs are simply diluted in successive cell divisions, with little DNA replication. In contrast, repetitive sequences are maintained even in terminally differentiated somatic cell nuclei. Considering the increasing intensity of in-situ hybridization, incorporation of BrdU, and a general correlation between nuclear content and cell size, those repetitive sequences must be selectively endoreplicated in the peripheral cell nucleus, concomitant with the increase of cell size. The biological significance of this mechanism is discussed as a unique dicyemid adaptation to parasitism.

Identification of putative cis-regulatory elements in Cryptosporidium parvum by de novo pattern finding

Background

Cryptosporidium parvum is a unicellular eukaryote in the phylum Apicomplexa. It is an obligate intracellular parasite that causes diarrhea and is a significant AIDS-related pathogen. Cryptosporidium parvum is not amenable to long-term laboratory cultivation or classical molecular genetic analysis. The parasite exhibits a complex life cycle, a broad host range, and fundamental mechanisms of gene regulation remain unknown. We have used data from the recently sequenced genome of this organism to uncover clues about gene regulation in C. parvum. We have applied two pattern finding algorithms MEME and AlignACE to identify conserved, over-represented motifs in the 5' upstream regions of genes in C. parvum. To support our findings, we have established comparative real-time -PCR expression profiles for the groups of genes examined computationally.

Results

We find that groups of genes that share a function or belong to a common pathway share upstream motifs. Different motifs are conserved upstream of different groups of genes. Comparative real-time PCR studies show co-expression of genes within each group (in sub-sets) during the life cycle of the parasite, suggesting co-regulation of these genes may be driven by the use of conserved upstream motifs.

Conclusion

This is one of the first attempts to characterize cis-regulatory elements in the absence of any previously characterized elements and with very limited expression data (seven genes only). Using de novo pattern finding algorithms, we have identified specific DNA motifs that are conserved upstream of genes belonging to the same metabolic pathway or gene family. We have demonstrated the co-expression of these genes (often in subsets) using comparative real-time-PCR experiments thus establishing evidence for these conserved motifs as putative cis-regulatory elements. Given the lack of prior information concerning expression patterns and organization of promoters in C. parvum we present one of the first investigations of gene regulation in this important human pathogen.

Comparative genomics of microsporidia

Microsporidia have been known for some time to possess among the smallest genomes of any eukaryote. There is now a completely sequenced microsporidian genome, as well as several other large-scale sequencing efforts, so the nature of these genomes is becoming apparent. This paper reviews some of the characteristics of microsporidian genomes in general, and some of the recent discoveries made through comparative genomic analyses. In general, microsporidian genomes are both reduced and compacted. Reduction takes place through gene loss, which is understandable in obligate intracellular parasites that rely on their host for many metabolites. Compaction is a more complex process, and is as yet not fully understood. It is clear from genomes surveyed thus far that the remaining genes are tightly packed and that there is little non-coding sequence, resulting in some extraordinary arrangements, including overlapping genes. Compaction also seems to affect certain aspects of genome evolution, like the frequency of rearrangements. The force behind this compaction is not known, and is especially interesting in light of the fact that surveys of genomes that are significantly different in size yield similar complements of protein-coding genes. There are some interesting exceptions, including catalase, photolyase and some mitochondrial proteins, but the rarity of these raises an interesting question as to what accounts for the significant differences seen in the genome sizes among microsporidia.

Protozoan genomes: gene identification and annotation

The draft sequence of several complete protozoan genomes is now available and genome projects are ongoing for a number of other species. Different strategies are being implemented to identify and annotate protein coding and RNA genes in these genomes, as well as study their genomic architecture. Since the genomes vary greatly in size, GC-content, nucleotide composition, and degree of repetitiveness, genome structure is often a factor in choosing the methodology utilised for annotation. In addition, the approach taken is dictated, to a greater or lesser extent, by the particular reasons for carrying out genome-wide analyses and the level of funding available for projects. Nevertheless, these projects have provided a plethora of material that will aid in understanding the biology and evolution of these parasites, as well as identifying new targets that can be used to design urgently required drug treatments for the diseases they cause.

The sensitivity of PCR detection of Cryptosporidium oocysts in fecal samples using two DNA extraction methods

BACKGROUND

The implementation of cost-effective intervention strategies for zoonotic protozoa relies on the development of sensitive and accurate diagnostic methods. We carried out a study to evaluate the accuracy of a PCR method for the detection of Cryptosporidium spp. oocysts in fecal samples from cattle.

METHODS

Fecal samples were spiked with different numbers of oocysts and the limit of detection of the method was determined. Two methods of DNA extraction were assessed: glass beads and freeze-thawing using liquid nitrogen. A nested PCR approach was developed targeting the Cryptosporidium SSU rRNA and TRAP-C2 genes. Agreement between the diagnosis of Cryptosporidium spp. at the SSU rRNA and TRAP-C2 loci was quantified using the kappa-coefficient.

RESULTS

Compared with the freeze-thawing method, the glass beads method was found to be a better way of extracting DNA from Cryptosporidium oocysts (sensitivities were 83 and 100%, respectively). The limits of detection for glass beads and freeze-thaw were low, 1 and 10 oocyst/g fecal samples, respectively. Forty-six percent of the field samples previously classified as negative for Cryptosporidium parvum by the flotation-concentration and enzyme-linked immunosorbent assay methods showed DNA with the PCR protocol.

CONCLUSION

Primers for SSU rRNA are more successful in producing an amplification than primers for the TRAP-C2 gene which makes the former PCR protocol the approach of choice for detecting Cryptosporidium parvum oocysts in field samples.

Mitochondrial-type iron-sulfur cluster biosynthesis genes (IscS and IscU) in the apicomplexan Cryptosporidium parvum

Several reports have indicated that the iron-sulfur cluster [Fe-S] assembly machinery in most eukaryotes is confined to the mitochondria and chloroplasts. The best-characterized and most highly conserved [Fe-S] assembly proteins are a pyridoxal-5'-phosphate-dependent cysteine desulfurase (IscS), and IscU, a protein functioning as a scaffold for the assembly of [Fe-S] prior to their incorporation into apoproteins. In this work, genes encoding IscS and IscU homologues have been isolated and characterized from the apicomplexan parasite Cryptosporidium parvum, an opportunistic pathogen in AIDS patients, for which no effective treatment is available. Primary sequence analysis (CpIscS and CpIscU) and phylogenetic studies (CpIscS) indicate that both genes are most closely related to mitochondrial homologues from other organisms. Moreover, the N-terminal signal sequences of CpIscS and CpIscU predicted in silico specifically target green fluorescent protein to the mitochondrial network of the yeast Saccharomyces cerevisiae. Overall, these findings suggest that the previously identified mitochondrial relict of C. parvum may have been retained by the parasite as an intracellular site for [Fe-S] assembly.

Utility of the Cryptosporidium oocyst wall protein (COWP) gene in a nested PCR approach for detection infection in cattle

A preliminary molecular epidemiological study was carried out to investigate the utility of the Cryptosporidium oocyst wall protein (COWP) gene in the detection of Cryptosporidium oocysts in fecal samples. A nested polymerase chain reaction (PCR) approach using COWP gene primers was adopted for this purpose. Fecal samples were spiked with each of 1, 10, and 100 oocysts of C. parvum, four samples for each number, and the DNA was extracted from each sample using a glassbead method. The presence of oocysts was determined using the nested PCR with COWP gene primers, and the limit of detection of oocysts by the PCR was determined. The limit of detection was 100 oocysts spiked in 1 ml of fecal material (50% sold material) (four positives/four samples tested). Seventy-five percent of DNA extracted samples spiked with 1 and 10 oocysts was positive by the PCR (three positives/four samples tested). Based on this, small sample size using the COWP gene primers with a nested PCR analysis could reliably identify infected animals rather conveniently and accurately.

Characterization of Cryptosporidium spp.--recent developments and future needs

Cryptosporidia, widely distributed protozoan parasites of vertebrates have recently attracted increasing interest due to several serious waterborne outbreaks, the life-threatening nature of infection in immunocompromised patients, and the realization of economic losses caused by these pathogens in livestock. Genetic polymorphism within Cryptosporidium spp. is being detected at a continuously growing rate, owing to the widespread use of modern molecular techniques. The aim of this paper is to review the current status of taxonomy, genotyping, molecular phylogeny, and characterization of cryptosporidia, and to highlight the need for polyphasic typing, i.e. an integrated approach comprising standardized morphologic, biologic, and molecular methods for describing Cryptosporidium species and isolates, and for establishing "virtual" reference strains.

Epidemiology of Cryptosporidium spp. and Giardia duodenalis on a dairy farm

Prevalences of Cryptosporidium spp. and Giardia duodenalis in relation to age and season were investigated on a dairy farm in The Netherlands over the course of 1year. The whole herd was sampled five times, whereas calves younger than about 2 months were sampled every 2-3 weeks. Associations between diarrhoea and presence of one or more pathogens (Cryptosporidium spp., G. duodenalis, rotavirus) were investigated. Potential transmission routes of Cryptosporidium spp. were evaluated and positive samples of Cryptosporidium spp. and G. duodenalis were identified to genotype level by PCR microsatellite identification and fingerprinting. Shedding of Cryptosporidium spp. was found in all age categories but peaked in calves 1-3 weeks old (39.1%). Herd prevalence of shedding for Cryptosporidium spp. varied from 2.4% in June to 22.2% in December. Shedding of G. duodenalis was found in all age categories but peaked in animals 4-5 months old (54.5%). Herd prevalence of shedding for G. duodenalis varied from 0.8% in June to 15.5% in February. Cryptosporidium spp. and rotavirus appeared to be significantly associated with diarrhoea in calves. Microsatellite analysis showed two different subtypes (C3 and C1) of Cryptosporidium parvum calf strains. Two genotypes of G. duodenalis were found, one positive by A lineage specific PCR and thus closely related to human genotypes and one genotype, which was negative by A and B lineage specific PCR. The results indicate that cow-to-calf and indirect calf-to-calf transmission both are important routes for acquiring infection with Cryptosporidium spp.

Synonymous codon usage in Cryptosporidium parvum: identification of two distinct trends among genes

The usage of alternative synonymous codons in the apicomplexan Cryptosporidium parvum has been investigated. A data set of 54 genes was analysed. Overall, A- and U-ending codons predominate, as expected in an A+T-rich genome. Two trends of codon usage variation among genes were identified using correspondence analysis. The primary trend is in the extent of usage of a subset of presumably translationally optimal codons, that are used at significantly higher frequencies in genes expected to be expressed at high levels. Fifteen of the 18 codons identified as optimal are more G+C-rich than the otherwise common codons, so that codon selection associated with translation opposes the general mutation bias. Among 40 genes with lower frequencies of these optimal codons, a secondary trend in G+C content was identified. In these genes, G+C content at synonymously variable third positions of codons is correlated with that in 5' and 3' flanking sequences, indicative of regional variation in G+C content, perhaps reflecting regional variation in mutational biases.

Toxoplasma gondii homologue of plasmodium apical membrane antigen 1 is involved in invasion of host cells

Proteins with constitutive or transient localization on the surface of Apicomplexa parasites are of particular interest for their potential role in the invasion of host cells. We describe the identification and characterization of TgAMA1, the Toxoplasma gondii homolog of the Plasmodium apical membrane antigen 1 (AMA1), which has been shown to elicit a protective immune response against merozoites dependent on the correct pairing of its numerous disulfide bonds. TgAMA1 shows between 19% (Plasmodium berghei) and 26% (Plasmodium yoelii) overall identity to the different Plasmodium AMA1 homologs and has a conserved arrangement of 16 cysteine residues and a putative transmembrane domain, indicating a similar architecture. The single-copy TgAMA1 gene is interrupted by seven introns and is transcribed into an mRNA of approximately 3.3 kb. The TgAMA1 protein is produced during intracellular tachyzoite replication and initially localizes to the micronemes, as determined by immunofluorescence assay and immunoelectron microscopy. Upon release of mature tachyzoites, TgAMA1 is found distributed predominantly on the apical end of the parasite surface. A approximately 54-kDa cleavage product of the large ectodomain is continuously released into the medium by extracellular parasites. Mouse antiserum against recombinant TgAMA1 blocked invasion of new host cells by approximately 40%. This and our inability to produce a viable TgAMA1 knock-out mutant indicate that this phylogenetically conserved protein fulfills a key function in the invasion of host cells by extracellular T. gondii tachyzoites.

The plastid in Apicomplexa: what use is it?

An extrachromosomal genome of between 27 and 35 kb has been described in several apicomplexan parasites including Plasmodium falciparum and Toxoplasma gondii. Examination of sequence data proved the genomes to be a remnant plastid genome, from which all genes encoding photosynthetic functions had been lost. Localisation studies had shown that the genome was located within a multi-walled organelle, anterior to the nucleus. This organelle had been previously described in ultrastructural studies of several genera of apicomplexa, but no function had been attributed to it. This invited review describes the evolution of knowledge on the apicomplexan plastid, then discusses current research findings on the likely role of the plastid in the Apicomplexa. How the plastid may be used to effect better drug treatments for apicomplexan diseases, and its potential as a marker for investigating phylogenetic relationships among the Apicomplexa, are discussed.