The ribosomal genes of Plasmodium

Emerging nucleic acid-based tests for point-of-care detection of malaria

Malaria remains a serious disease in the developing world. There is a growing consensus that new diagnostics are needed in low-resource settings. The ideal malaria diagnostic should be able to speciate; measure parasitemia; low-cost, quick, and simple to use; and capable of detecting low-level infections. A promising development are nucleic acid tests (NATs) for the diagnosis of malaria, which are well suited for point-of-care use because of their ability to detect low-level infections and speciate, and because they have high sensitivity and specificity. The greatest barrier to NAT use in the past has been its relatively high cost, and the amount of infrastructure required in the form of equipment, stable power, and reagent storage. This review describes recent developments to decrease the cost and run time, and increase the ease of use of NAT while maintaining their high sensitivity and specificity and low limit of detection at the point-of-care.

Structural RNAs of known and unknown function identified in malaria parasites by comparative genomics and RNA analysis

As the genomes of more eukaryotic pathogens are sequenced, understanding how molecular differences between parasite and host might be exploited to provide new therapies has become a major focus. Central to cell function are RNA-containing complexes involved in gene expression, such as the ribosome, the spliceosome, snoRNAs, RNase P, and telomerase, among others. In this article we identify by comparative genomics and validate by RNA analysis numerous previously unknown structural RNAs encoded by the Plasmodium falciparum genome, including the telomerase RNA, U3, 31 snoRNAs, as well as previously predicted spliceosomal snRNAs, SRP RNA, MRP RNA, and RNAse P RNA. Furthermore, we identify six new RNA coding genes of unknown function. To investigate the relationships of the RNA coding genes to other genomic features in related parasites, we developed a genome browser for P. falciparum (http://areslab.ucsc.edu/cgi-bin/hgGateway). Additional experiments provide evidence supporting the prediction that snoRNAs guide methylation of a specific position on U4 snRNA, as well as predicting an snRNA promoter element particular to Plasmodium sp. These findings should allow detailed structural comparisons between the RNA components of the gene expression machinery of the parasite and its vertebrate hosts.

A single-step, PCR-based method for the detection and differentiation of Plasmodium vivax and P. falciparum

The ability to detect and differentiate between Plasmodium falciparum and P. vivax is of great importance for the routine laboratory diagnosis of malaria, donor-blood screening and epidemiological studies. Most PCR-based methods for the discrimination of these two species require nested protocols or an additional hybridization reaction, leading to high labour costs and long turn-around times. A simple, time-effective and yet sensitive and specific technique, based on a multiplex PCR, has now been developed for the simultaneous detection and differentiation of P. falciparum and P. vivax in blood samples. Compared with the 'gold standard' of microscopy, this method had a sensitivity and specificity of 100%, with a detection limit of just one P. falciparum or three P. vivax parasites/microl blood.

Analysis of intergenic spacer transcripts suggests 'read-around' transcription of the extrachromosomal circular rDNA in Euglena gracilis

We report here the sequence of the 1743 bp intergenic spacer (IGS) that separates the 3'-end of the large subunit ribosomal RNA (rRNA) gene from the 5'-end of the small subunit (SSU) rRNA gene in the circular, extrachromosomal ribosomal DNA (rDNA) of Euglena gracilis. The IGS contains a 277 nt stretch of sequence that is related to a sequence found in ITS 1, an internal transcribed spacer between the SSU and 5.8S rRNA genes. Primer extension analysis of IGS transcripts identified three abundant reverse transcriptase stops that may be analogous to the transcription initiation site (TIS) and two processing sites (A' and A0) that are found in this region in other eukaryotes. Features that could influence processing at these sites include an imperfect palindrome near site A0 and a sequence near site A' that could potentially base pair with U3 small nucleolar RNA. Our identification of the TIS (verified by mung bean nuclease analysis) is considered tentative because we also detected low-abundance transcripts upstream of this site throughout the entire IGS. This result suggests the possibility of 'read-around' transcription, i.e. transcription that proceeds multiple times around the rDNA circle without termination.

Scant parasitemia in BALB/c mice with congenital malaria infection

Balb/c mice were examined to determine whether or not they transmitted rodent malaria, Plasmodium berghei, to their fetuses. On the 15th day of pregnancy, mice were inoculated with approximately 3 x 10(6) P. berghei-infected erythrocytes by peritoneal injection. The blood from 27 adult females and 196 neonates was examined using a sensitive polymerase chain reaction (PCR) method with a detection level of approximately 1 parasite/microl blood. The average parasitemia of females at delivery was 8.1%, ranging from nondetectable to 37.1%. In 12 females, nested PCR established the presence of blood parasite DNA. Malaria parasites were microscopically confirmed in 2 of the 12 neonates. Maternal parasitemia at the time of delivery was not correlated with the incidence of vertical infection (6.1%), which was higher in this study than that found in previous studies. Although the combination of balb/c mice and P. berghei has not been used to examine vertical transmission of malaria, our report showed that this model may be used for this purpose.

Distinct types of rRNA operons exist in the genome of the actinomycete Thermomonospora chromogena and evidence for horizontal transfer of an entire rRNA operon

We describe here the presence of two distinct types of rRNA operons in the genome of a thermophilic actinomycete Thermomonospora chromogena. The genome of T. chromogena contains six rRNA operons (rrn), of which four complete and two incomplete ones were cloned and sequenced. Comparative analysis revealed that the operon rrnB exhibits high levels of sequence variations to the other five nearly identical ones throughout the entire length of the operon. The coding sequences for the 16S and 23S rRNA genes differ by approximately 6 and 10%, respectively, between the two types of operons. Normal functionality of rrnB is concluded on the basis of the nonrandom distribution of nucleotide substitutions, the presence of compensating nucleotide covariations, the preservation of secondary and tertiary rRNA structures, and the detection of correctly processed rRNAs in the cell. Comparative sequence analysis also revealed a close evolutionary relationship between rrnB operon of T. chromogena and rrnA operon of another thermophilic actinomycete Thermobispora bispora. We propose that T. chromogena acquired rrnB operon from T. bispora or a related organism via horizontal gene transfer.

Detection of Plasmodium ovale malaria parasites by species-specific 18S rRNA gene amplification

A polymerase chain reaction (PCR) assay was developed for the specific detection of Plasmodium ovale, one of the four malaria parasites that infect humans. On the basis of sequence variation of the Plasmodium 18S ribosomal RNA (rRNA) gene, oligonucleotide primers for PCR were designed to amplify various fragments of the P. ovale gene. Using a recombinant plasmid with the complete P. ovale 18S rRNA gene as target, 59 primer combinations were tested so that at least one of the pairs was species-specific while the other primer was either genus conserved or P. ovale species-specific. Three primer pairs yielding DNA fragments at stringent conditions were further tested against genomic DNA of four human malaria species. This approach yielded P. ovale species-specific primer pairs that may be useful for further field testing.

Regulation and trafficking of three distinct 18 S ribosomal RNAs during development of the malaria parasite

The human malaria parasite Plasmodium vivax has been shown to regulate the transcription of two distinct 18 RNAs during development. Here we show a third and distinctive type of ribosome that is present shortly after zygote formation, a transcriptional pattern of ribosome types that relates closely to the developmental state of the parasite and a phenomenon that separates ribosomal types at a critical phase of maturation. The A-type ribosome is predominantly found in infected erythrocytes of the vertebrate and the mosquito blood meal. Transcripts from the A gene are replaced by transcripts from another locus, the O gene, shortly after fertilization and increase in number as the parasite develops on the mosquito midgut. Transcripts from another locus, the S gene, begins as the oocyst form of the parasite matures. RNA transcripts from the S gene are preferentially included in sporozoites that bud off from the oocyst and migrate to the salivary gland while the O gene transcripts are left within the oocyst. Although all three genes are typically eukaryotic in structure, the O gene transcript, described here, varies from the other two in core regions of the rRNA that are involved in mRNA decoding and translational termination. We now can correlate developmental progression of the parasite with changes in regions of rRNA sequence that are broadly conserved, where sequence alterations have been related to function in other systems and whose effects can be studied outside of Plasmodium. This should allow assessment of the role of translational control in parasite development.

The actinomycete Thermobispora bispora contains two distinct types of transcriptionally active 16S rRNA genes

Here we present the first description of the presence of two distinct types of 16S rRNA genes in the genome of a (eu)bacterium, Thermobispora bispora. We cloned and determined the nucleotide sequences of all four rRNA operons of T. bispora. Sequence comparisons revealed that the genome of T. bispora contains two distinct types of 16S rRNA genes, each type consisting of two identical or nearly identical copies, and three identical copies of the 23S RNA gene. The nucleotide sequences of the two types of 16S rRNA genes differ at 98 nucleotide positions (6.4% of total nucleotides) together with six regions of deletion-insertions. None of the base substitutions or insertion-deletions corresponds to any of the approximately 600 evolutionarily invariable or rarely variable nucleotides, indicating that both genes are functional. Both types of 16S rRNA genes are transcribed and processed as determined by Northern (RNA) hybridization and reverse transcriptase-mediated PCR.

Blood and sporozoite stage-specific small subunit ribosomal RNA-encoding genes of the human malaria parasite Plasmodium vivax

Malaria parasites, unlike other eukaryotes, have developmentally controlled distinct small subunit ribosomal RNA (SSUrRNA)-encoding genes (SSUrDNA), sporozoite stage-specific C and blood stage-specific A genes. This report describes characterization of the C and A forms of SSUrDNA from the human malaria parasite Plasmodium vivax. We have aligned and compared these sequences with the reported SSUrDNA sequences of other human malaria parasites to identify the regions with potential for diagnostic probes. The comparison revealed the presence of seven conserved regions (> or = 90% similarity), four highly variable regions (< 60% similarity) and three semiconserved regions. The analysis also revealed that the A and C genes of P. vivax share more similarity with each other, as compared to the A and C genes of P. falciparum. Comparison of the SSUrDNA of human, monkey and rodent malaria parasites revealed that the A genes share more similarity with each other than the C genes share with each other.

Evidence for two single copy units in Theileria parva ribosomal RNA genes

Bacteriophage clones containing ribosomal RNA genes of Theileria parva were isolated from genomic DNA libraries. Physical mapping studies revealed 2 ribosomal DNA units, which were distinguishable by restriction enzyme site polymorphisms in flanking sequences. The cloned ribosomal DNA units were mapped to 2 separate T. parva chromosomes. Analysis of sequences contained in lambda EMBL3 recombinants, together with Southern blot analysis of genomic DNA and data on the copy number of the rRNA genes, suggested that the rDNA units were not tandemly repeated. This organisation of ribosomal transcription units is similar to that described for other genera of apicomplexan protozoa, but 2 rDNA units, each containing single copies of the rRNA coding genes, would be the lowest copy number described for any eukaryote in which amplification of rRNA genes is not known to occur. EcoRI restriction fragment length polymorphisms, which were revealed using rRNA gene probes, separated T. parva stocks into 2 categories. Nucleotide sequence analysis of polymerase chain reaction-amplified internal transcribed spacer DNA revealed 2 different ITS sequences derived from rDNA transcription units within the genome of a cloned T. parva parasite. Polymorphism was also observed between ITS sequences amplified from the DNA of different T. parva stocks. A synthetic oligonucleotide derived from T. parva Uganda ribosomal ITS DNA sequences hybridised to DNA from the T. parva Uganda stock, but not to the DNA of the T. parva Muguga stock. This oligonucleotide is potentially useful as a marker for the T. parva Uganda stock.

Transition of Plasmodium vivax ribosome types corresponds to sporozoite differentiation in the mosquito

Two distinct small subunit ribosomal RNA (SSUrRNA) genes were amplified from the genomic DNA of Plasmodium vivax. Comparison of the two coding sequences reveals an overall divergence of 14.5% and most differences are clustered into the regions known to diverge rapidly in all eukaryotic SSUrRNAs. Oligonucleotides complementary to unique sequences of each gene have been used to distinguish the transcripts expressed either at schizogony in human blood (A gene) or at sporogony in the mosquito (C gene). These oligonucleotides were also used to monitor turnover of ribosomes during parasite development in mosquitoes. Transcripts of the A gene were predominant in the infected human blood and engorged mosquitoes but disappeared within 24 h after feeding. Expression of the C gene in mosquitoes was not detected until day 6 after the blood meal. A period of rapid accumulation of the C type rRNA from day 6 to day 8 corresponds to differentiation of individual sporozoites within the oocyst. Possible functional implications relating to the timing of this transition are discussed.

Molecular characterization of the largest subunit of Plasmodium falciparum RNA polymerase I

Plasmodium species possess developmentally regulated ribosomal RNA (rRNA) genes. This report describes the expression and gene structure of the largest subunit of P. falciparum RNA polymerase I (RNAPI), which is responsible for the synthesis of rRNA. The RNAPI largest subunit gene was present as a single copy gene on chromosome 9. Three exons encode the 2910-amino acid RNAPI polypeptide (340 140 Da). A comparison of Plasmodium, Trypanosoma, and Saccharomyces cerevisiae nuclear RNAP largest subunits identified conserved amino acid positions and class-specific amino acid positions. Novel amino acid insertions were found between RNAPI conserved regions A and B (region A'), D and DE1 (region D'), DE2 and E (region DE2'), and F and G (region F'). Leucine zipper domains were found within regions D', DE2, and DE2'. A novel serine-rich repeat domain, a domain with homology to the C-terminal domain of eukaryotic upstream binding factor (UBF), and 4 highly conserved casein kinase II (CKII) Ser/Thr phosphorylation motifs were found within a 127-amino acid sub-region of enlarged region F'. The novel RNAPI serine-rich repeat contained a conserved motif, Ser-X3-Ser, which was also identified in the serine-rich repeat domains of the P. falciparum RNAPII and RNAPIII largest subunits, as well as within a highly homologous serine-rich repeat from trophozoite antigen R45. The results of this molecular analysis indicate that phosphorylation and dephosphorylation mechanisms regulate the activity of P. falciparum RNAPI.

Babesia bovis, Babesia bigemina, Babesia canis, Babesia microti and Babesia rodhaini: comparison of ribosomal RNA gene organization

The three ribosomal DNA (rDNA) units have been cloned from an Australian isolate of Babesia bigemina. The organization of the units is very similar to that reported for a Mexican isolate of B. bigemina. In Babesia canis four rDNA units have been identified. Both Babesia rodhaini and Babesia microti contain two different rDNA units. A small number of different rDNA units appears to be a common feature of this group of Protozoa. Restriction enzyme analysis of the rDNA units form these species and B. bovis suggests that the genus Babesia as currently defined does indeed include two distinct groups of organisms namely, B. bovis, B. bigemina and B. canis and B. rodhaini and B. microti.

Physical and genetic mapping of cloned ribosomal DNA from Toxoplasma gondii: primary and secondary structure of the 5S gene

The ribosomal DNA (rDNA encoding rRNA) of the obligately intracellular protozoan parasite, Toxoplasma gondii, was identified, cloned, physically mapped, its copy number determined, and the 5S gene sequenced. Using total RNA as a probe, a collection of recombinant lambda phages containing copies of rDNA were isolated from a lambda 2001 tachyzoite genomic library. Northern gel hybridization confirmed specific homology of the 7.5-kb rDNA unit, subcloned into pTZ18R, to T. gondii rRNA. The mapped rDNA found in pTOX1 contained small ribosomal subunit (SS; 18S)- and large ribosomal subunit (LS; 26S)-encoding genes localized using intragenic heterologous probes from the conserved sequences of the SS (18S) and LS (28S) Xenopus laevis genes. the physical mapping data, together with partial digestion experiments and Southern gel hybridization, confirmed a 7.5-kb rDNA unit arranged in a simple head-to-tail fashion that is tandemly repeated. We estimated the rDNA repeat copy number in T. gondii to be 110 copies per haploid tachyzoite genome. Parts of the SS gene and the complete 5S gene were sequenced. The 5S gene was found to be within the rDNA locus, a rare occurrence found only in some fungi and protozoa. Secondary-structure analysis revealed an organization remarkably similar to the 5S RNA of eukaryotes.

18S rRNA sequences of Leishmania enriettii promastigote and amastigote

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

Characterization of the gene encoding the largest subunit of Plasmodium falciparum RNA polymerase III

We report here the isolation, sequence analysis, structure, and expression of the gene encoding the largest subunit of RNA polymerase III (RPIII) from Plasmodium falciparum. The P. falciparum RPIII gene consists of 5 exons and 4 introns, is expressed in all of the asexual erythrocytic stages of the parasite as a 8.5-kb mRNA, and is present in a single copy on chromosome 13. The predicted 2339 amino acid residue RPIII subunit contained 5 regions that were conserved between different eukaryotic RPIII subunits, and 4 variable regions that separated the conserved regions. Three of the variable regions were greatly enlarged in comparison to the corresponding variable regions in other RPIII subunits. Variable region C' represented nearly one-third of the P. falciparum RPIII subunit (750 amino acid residues), included a unique repeated decapeptide sequence, and had some homology with yeast DNA topoisomerase II. Noteworthy amino acid sequences and structures were identified in both the conserved regions and in the enlarged variable regions, and their possible role(s) as domains that regulate RPIII enzyme activity is discussed.

The evolution of plasmodial stage-specific rRNA genes is dominated by gene conversion

Plasmodium species exhibit the unprecedented situation of distinct, stage-specific rRNA sequences. We present an analysis of two pairs of sequences of the small rRNA subunit (Plasmodium falciparum and Plasmodium berghei) and show that these genes do not evolve independently and that in fact their evolution is dominated by gene conversion. This analysis also shows that no extensive stage-specific sequences are conserved in the two species, thus rendering unlikely that the existence of stage-specific rRNA genes results from a requirement for distinct rRNA types.

The structure and role of RNA polymerases in Plasmodium

During the past few years the characterization of several Plasmodium falciparum RNA polymerase subunits has revealed potentially significant differences between the corresponding subunits of the host and parasite enzymes(1-3). The largest subunits of P. falciparum RNA polymerase II and III contain enlarged variable domains that separate conserved domains in these subunits. The partially characterized beta and beta '-like subunits of an organellar P. falciparum RNA polymerase also appear to be distinct from the host RNA polymerases. In this review David Bzik discusses the structure and role of RNA polymerases in Plasmodium.

Cloning and characterization of the rRNA genes and flanking regions from Babesia bovis: use of the genes as strain discriminating probes

Three sets of rRNA genes (units 1S-3S) have been identified in Babesia bovis (Samford isolate). All three units are present in the same, probably single, copy number. The rRNA genes and flanking regions have been analysed by cloning, restriction mapping and DNA hybridization. The units are approximately 7 kb in length and have essentially identical restriction maps. In contrast the flanking regions exhibit significant restriction site differences. However, the regions upstream of all three units are related and sequences similar to part of the region upstream of units 1S and 3S are present in multiple copies in the genome. The downstream regions appear to be unrelated, but downstream from unit 1S is a region of at least 7 kb similar to a second region not closely linked to the rDNA units. The restriction enzyme site polymorphisms in the flanking regions of the equivalent units in different isolates allow ready discrimination among six different isolates of B. bovis.

Heterogeneity and expression of the Plasmodium falciparum 5.8S ribosomal RNA genes

The number and expression of some of the large ribosomal RNA (rRNA) gene classes present in the human malaria parasite Plasmodium falciparum was determined. Southern blot analyses, using the 5.8S rRNA coding region as a marker, indicate that the P. falciparum genome contains at least 5 distinct subclasses of large rRNA genes. Dideoxy sequencing of the 5.8S rRNA domain and Northern blot analyses demonstrate that only one subclass is transcribed during the parasite's asexual erythrocytic life cycle.

Nuclear rDNA in Euglena gracilis: paucity of chromosomal units and replication of extrachromosomal units

Copy number of chromosomal rDNA units was investigated in two Euglena gracilis wild-type strains. It was established by dot blot analysis that these strains possess about four integrated units per haploid genome. This is the first example of a photosynthetic cell with only a few chromosomal ribosomal genes. In addition to these units, Euglena has 800 to 4000 extrachromosomal rDNA units. Electron microscopy revealed that these free rDNA circles bear a replication origin, and intermediates of replication show a D-loop structure.

The three 5S rRNA genes from the human malaria parasite Plasmodium falciparum are linked

5S rRNA and rDNA from Plasmodium falciparum have been characterized. The 5S rRNA transcripts isolated from erythrocytic stage parasites are composed of three distinct subclasses, 117-119 nucleotides in length, which are identical in sequence with the exception of one or two additional uridine residues at the 3' terminus. Southern blot analysis of genomic DNA identified three 5S rRNA gene classes which are clustered within 1.5 kb of DNA. Cloning and sequence analyses of the 5S rDNA revealed identical coding regions surrounded by divergent extremely A+T rich flanking sequences (greater than 90%). Typical PolIII termination signals (6-8) T residues abut each coding region. Copy number analysis indicates that P. falciparum contains only three 5S rRNA genes, the lowest number reported for any organism.

Ribosomal RNA and the major lines of evolution: a perspective

Does the "universal tree" based on small-subunit ribosomal RNA sequences show the phylogenetic relationship of all modern organisms? The answer is "yes" only if all these rRNAs are orthologous. Herein I argue that the major rRNA lineages (e.g. eubacterial, one or more archaebacterial and eukaryotic nucleocytoplasmic) probably arose from a divergent population of rRNAs in the progenote, antedating the universal common ancestral organism. Thus the major lineages of rRNA are probably not orthologous, but paralogous. The extrapolated date for the origin of the common ancestral small-subunit rRNA (3.6-4.7 x 10(9) years ago) is consistent with major rRNA lineages being paralogous. This perspective on the early evolution of genes and organisms rationalizes the presence of unexpected ribosomal characters in microsporidia, and bears on xenogenous and endogenous theories of the origin of the organelles in eukaryotes.