Synthesis of small nuclear ribonucleoprotein particles by the malarial parasite Plasmodium falciparum

The RNA structurome in the asexual blood stages of malaria pathogen plasmodium falciparum

Plasmodium falciparum is a deadly human pathogen responsible for the devastating disease called malaria. In this study, we measured the differential accumulation of RNA secondary structures in coding and non-coding transcripts from the asexual developmental cycle in P. falciparum in human red blood cells. Our comprehensive analysis that combined high-throughput nuclease mapping of RNA structures by duplex RNA-seq, SHAPE-directed RNA structure validation, immunoaffinity purification and characterization of antisense RNAs collectively measured differentially base-paired RNA regions throughout the parasite's asexual RBC cycle. Our mapping data not only aligned to a diverse pool of RNAs with known structures but also enabled us to identify new structural RNA regions in the malaria genome. On average, approximately 71% of the genes with secondary structures are found to be protein coding mRNAs. The mapping pattern of these base-paired RNAs corresponded to all regions of mRNAs, including the 5' UTR, CDS and 3' UTR as well as the start and stop codons. Histone family genes which are known to form secondary structures in their mRNAs and transcripts from genes which are important for transcriptional and post-transcriptional control, such as the unique plant-like transcription factor family, ApiAP2, DNA-/RNA-binding protein, Alba3 and proteins important for RBC invasion and malaria cytoadherence also showed strong accumulation of duplex RNA reads in various asexual stages in P. falciparum. Intriguingly, our study determined stage-specific, dynamic relationships between mRNA structural contents and translation efficiency in P. falciparum asexual blood stages, suggesting an essential role of RNA structural changes in malaria gene expression programs.

Organization of Plasmodium falciparum spliceosomal core complex and role of arginine methylation in its assembly

BACKGROUND

Splicing and alternate splicing are the two key biological processes that result in the generation of diverse transcript and protein isoforms in Plasmodium falciparum as well as in other eukaryotic organisms. Not much is known about the organization of splicing machinery and mechanisms in human malaria parasite. Present study reports the organization and assembly of Plasmodium spliceosome Sm core complex.

METHODS

Presence of all the seven Plasmodium Sm-like proteins in the intra-erythrocytic stages was assessed based on the protein(s) expression analysis using immuno-localization and western blotting. Localization/co-localization studies were performed by immunofluorescence analysis on thin parasite smear using laser scanning confocal microscope. Interaction studies were carried out using yeast two-hybrid analysis and validated by in vitro pull-down assays. PfPRMT5 (arginine methyl transferase) and PfSmD1 interaction analysis was performed by pull-down assays and the interacting proteins were identified by MALDI-TOF spectrometry.

RESULTS

PfSm proteins are expressed at asexual blood stages of the parasite and show nucleo-cytoplasmic localization. Protein-protein interaction studies showed that PfSm proteins form a heptameric complex, typical of spliceosome core complex as shown in humans. Interaction of PfSMN (survival of motor neuron, tudor domain containing protein) or PfTu-TSN (Tudor domain of Tudor Staphylococcal nuclease) with PfSmD1 proteins was found to be methylation dependent. Co-localization by immunofluorescence and co-immunoprecipitation studies suggested an association between PfPRMT5 and PfSmD1, indicating the role of arginine methylation in assembly of Plasmodium spliceosome complex.

CONCLUSIONS

Plasmodium Sm-like proteins form a heptameric ring-like structure, although the arrangement of PfSm proteins slightly differs from human splicing machinery. The data shows the interaction of PfSMN with PfSmD1 and this interaction is found to be methylation dependent. PfPRMT5 probably exists as a part of methylosome complex that may function in the cytoplasmic assembly of Sm proteins at asexual blood stages of P. falciparum.

Plasmodium falciparum spliceosomal RNAs: 3' and 5' end processing

The major spliceosomal small nuclear ribonucleoproteins (snRNPs) consist of snRNA (U1, U2, U4 or U5) and several proteins which can be unique or common to each snRNP particle. The common proteins are known as Sm proteins; they are crucial for RNP assembly and nuclear import of spliceosomal RNPs. This paper reports detecting the interaction between Plasmodium falciparum snRNAs and Sm proteins, and the usual 5' trimethylated caps on the snRNAs, by immunoprecipitation with specific antibodies. Furthermore, an unusual poly(A) tail was detected on these non-coding RNAs.

5' and 3' end modifications of spliceosomal RNAs in Plasmodium falciparum

5' caps provide recognition sequences for the nuclear import of snRNAs. The 5' and 3' ends of snRNAs were studied in Plasmodium falciparum with a modified adapter ligation method, which showed that 5' ends of U1, U2, U4, U5 and U6 snRNAs are capped. In P. falciparum, the 3' ends of U1, U2, U4 and U5 snRNAs have free hydroxyl groups whereas U6 snRNA has a blocked 3' end. An immunoprecipitation assay for trimethyl guanosine caps shows that the cap structures of parasite U1-U5 snRNAs are hypermethylated while U6 snRNA may be gamma-mono-methylated. Bioinformatics analysis of proteins involved in hypermethylation and trafficking of snRNAs indicates that the methyltransferase TGS1 is present in the P. falciparum genome. PfTGS1 is larger than its orthologs and may have transmembrane domains in the C-terminus. Surprisingly, the snRNA trafficking protein Snurportin is absent from the P. falciparum genome suggesting that reminiscent of yeast, parasite snRNAs may be retained in the nucleus.

Tudor domain proteins in protozoan parasites and characterization of Plasmodium falciparum tudor staphylococcal nuclease

RNA-binding proteins play key roles in post-transcriptional regulation of gene expression. In eukaryotic cells, a multitude of RNA-binding proteins with several RNA-binding domains/motifs have been described. Here, we show the existence of two Tudor domain containing proteins, a survival of motor neuron (SMN)-like protein and a Staphylococcus aureus nuclease homologue referred to as TSN, in Plasmodium and other protozoan parasites. Activity analysis shows that Plasmodium falciparum TSN (PfTSN) possesses nuclease activity and Tudor domain is the RNA-binding domain. A specific inhibitor of micrococcal nucleases, 3',5'-deoxythymidine bisphosphate (pdTp) inhibits the nuclease as well as RNA-binding activities of the protein. PfTSN shows a predominant nuclear localization. Treatment of P. falciparum with pdTp, inhibited in vitro growth of both chloroquine-sensitive and chloroquine-resistant strains of P. falciparum, while a four fold concentration of pdTp did not have any significant effect on the mammalian cell line, Huh-7D12. Altogether, these results suggest that PfTSN is an essential enzyme in the parasite's life cycle.

Mosquito homolog of the La autoantigen binds to Sindbis virus RNA

We have isolated a 50-kDa mosquito protein that binds with high affinity to a riboprobe representing the 3' end of the minus strand of Sindbis virus RNA. The isolated protein has been used to obtain cDNA clones encoding this protein that have been sequenced and used to express the protein in large amounts. Sequence comparisons make clear that this protein is the mosquito homolog of the La autoantigen. The N-terminal half of the protein shares considerable sequence identity with the human La protein, the rat La protein, and the recently identified Drosophila melanogaster homolog. There is one stretch of 100 amino acids in the N-terminal domain in which 48 residues are identical in all four proteins. In contrast, the C-terminal domain of the mosquito protein shares little identity with any of the other three proteins. We have also shown that the mosquito protein, the human protein, and a putative chicken homolog of the La protein cross-react immunologically and, thus, all share antigenic epitopes. The mosquito La protein is primarily nuclear in location, but significant amounts are present in the cytoplasm, as is the case for the La proteins of other species. The equilibrium constant for the binding of the expressed mosquito La protein to the Sindbis virus riboprobe is 15.4 nM, and thus the affinity of binding is high enough to be physiologically relevant. Furthermore, the conservation of this protein in the animal kingdom may be significant, because Sindbis virus utilizes mosquitoes, birds, and mammals as hosts. We propose that the interactions we observe between the La protein and toes, birds, and mammals as hosts. We propose that the interactions we observe between the La protein and a putative promoter in the Sindbis virus genome are significant for Sindbis virus RNA replication.

La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth

The human autoantigen La is a 50-kDa protein which binds to the 3' termini of virtually all nascent polymerase III transcripts. Experiments with mammalian transcription extracts have led to the proposal that the La protein is required for multiple rounds of transcription by RNA polymerase III (E. Gottlieb and J. A. Steitz, EMBO J. 8:851-861, 1989; R. J. Maraia, D. J. Kenan, and J. D. Keene, Mol. Cell. Biol. 14:2147-2158, 1994). Although La protein homologs have been identified in a variety of vertebrate species, the protein has not been identified in invertebrates. In order to begin a genetic analysis of La protein function, we have characterized homologs of the La protein in the fruit fly Drosophila melanogaster and the yeast Saccharomyces cerevisiae. We show that both the Drosophila and yeast La proteins are bound to precursors of polymerase III RNAs in vivo. The Drosophila and yeast proteins resemble the human La protein in their biochemical properties, as both proteins can be partially purified from cells by a procedure previously devised to purify the human protein. Similarly to vertebrate La proteins, the Drosophila and yeast homologs preferentially bind RNAs that terminate with a 3' hydroxyl. Despite the fact that the La protein is conserved between humans and Saccharomyces cerevisiae, yeast cells containing a null allele of the gene encoding the La protein are viable, suggesting that another protein(s) plays a functionally redundant role.

La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth

The human autoantigen La is a 50-kDa protein which binds to the 3' termini of virtually all nascent polymerase III transcripts. Experiments with mammalian transcription extracts have led to the proposal that the La protein is required for multiple rounds of transcription by RNA polymerase III (E. Gottlieb and J. A. Steitz, EMBO J. 8:851-861, 1989; R. J. Maraia, D. J. Kenan, and J. D. Keene, Mol. Cell. Biol. 14:2147-2158, 1994). Although La protein homologs have been identified in a variety of vertebrate species, the protein has not been identified in invertebrates. In order to begin a genetic analysis of La protein function, we have characterized homologs of the La protein in the fruit fly Drosophila melanogaster and the yeast Saccharomyces cerevisiae. We show that both the Drosophila and yeast La proteins are bound to precursors of polymerase III RNAs in vivo. The Drosophila and yeast proteins resemble the human La protein in their biochemical properties, as both proteins can be partially purified from cells by a procedure previously devised to purify the human protein. Similarly to vertebrate La proteins, the Drosophila and yeast homologs preferentially bind RNAs that terminate with a 3' hydroxyl. Despite the fact that the La protein is conserved between humans and Saccharomyces cerevisiae, yeast cells containing a null allele of the gene encoding the La protein are viable, suggesting that another protein(s) plays a functionally redundant role.

Recently characterised autoantibodies and their clinical significance

Multisystem autoimmune diseases such as systemic lupus erythematosus (SLE), primary Sjögren's syndrome (SS), scleroderma and polymyositis are characterised by the presence of antinuclear antibodies (ANAs). Immunoblotting and cDNA cloning studies reveal that the autoantigens of the multisystem autoimmune diseases are important proteins involved in nucleic acid metabolism, including tRNA charging, intron splicing, DNA uncoiling, and RNA polymerase co-factors. Each specific syndrome associates with a restricted variety of ANAs, e.g. anti-La with primary SS, anti-Sm with SLE, anti-synthetase enzymes with myositis, anti-topoisomerase 1 (Scl 70) with scleroderma, and anti-centromere with CREST. Precise characterisation of an ANA provides valuable diagnostic and prognostic information, and should be performed when an ANA is detected.

An immunological determinant of RNase P protein is conserved between Escherichia coli and humans

RNase P, an enzyme with RNA and protein subunits, cleaves tRNA precursor molecules to form the 5' termini of mature tRNAs in both prokaryotes and eukaryotes. Rabbit antibodies made against the protein subunit, C5 protein, of Escherichia coli RNase P bound RNase P protein from E. coli and Bacillus subtilis in immunoblots and solid-phase immunoassays. These rabbit anti-C5 antibodies also bound a protein (Mr approximately 40,000) in preparations of RNase P from human (HeLa) cells and depleted the enzymatic activity from preparations of RNase P from both human and E. coli cells. Finally, rabbit anti-C5 antibodies immunoprecipitated from crude extracts of human cells a ribonucleoprotein complex containing H1 RNA, the putative RNA component of human RNase P. These results show that an antigenic determinant is shared by C5 protein from E. coli RNase P and a protein component of RNase P from human cells.

Analysis of autoantibody specificities in selected systemic lupus erythematosus (SLE) sera

In order to design effective diagnostics for lupus, the heterogeneity in patient response must be understood. This heterogeneity in the anti-Sm and anti-U1-RNP response was examined via a frequency analysis of autoantibody fine specificities. Thus, 275 sera were studied by immunoprecipitation, immunoblotting, and immunodiffusion, and the frequency of occurrence of different autoantibodies to individual snRNP polypeptides and to other HeLa cell polypeptides was determined. The sera were found to contain autoantibodies reactive with denatured as well as native forms of HeLa-cell polypeptides. The common occurrence of several novel antibody fine specificities was noted, such as anti-p45 (different from anti-La/SS-B), anti-p105, and anti-p115. Another group of autoantibodies that is apparently not disease associated was observed in both lupus and normal sera.

The RNA binding protein La influences both the accuracy and the efficiency of RNA polymerase III transcription in vitro

The autoantigen La binds the U-rich 3' ends of all nascent RNA polymerase III transcripts. Here, we demonstrate that this abundant nuclear phosphoprotein not only binds these RNAs but appears to be required for their synthesis. HeLa cell extracts immunochemically depleted of La by either patient or mouse monoclonal antibodies lose greater than 99% of their transcription activity on class III genes. The few transcripts synthesized in the absence of La have fewer uridylate residues at their 3' ends than those made in its presence. Reconstitution of La-depleted extracts with biochemically purified HeLa La protein stimulates transcription levels and completely restores transcript length. A model coupling transcription levels to the action of La at the RNA polymerase III termination signal is presented.

Additional low-abundance human small nuclear ribonucleoproteins: U11, U12, etc

Two-dimensional gel fractionation has revealed the existence of a number (greater than or equal to 8) of additional species of HeLa cell small RNAs that have 5' trimethylguanosine cap structures and are bound by proteins containing Sm epitopes. Therefore, these low-abundance (10(3)-10(4) per cell) RNAs belong to the Sm class of small nuclear ribonucleoproteins (snRNPs), whose best-known members are the four highly abundant (approximately 10(6) per cell) particles required for pre-mRNA splicing. The complexity of Sm snRNPs in mammalian cells is thus not greatly different from that previously established for lower eukaryotes. Two of the new RNAs, designated U11 (131 nucleotides) and U12 (150 nucleotides), have been sequenced. The U11 and U12 snRNPs have been characterized further by examining their nuclease sensitivity and their possible interactions with other snRNPs. Potential roles for the low-abundance snRNPs in aspects of pre-mRNA processing are discussed.