Plasmodium falciparum Prp16 homologue and its role in splicing

Singh, Prashant; Kanodia, Shivani; Dandin, Chethan Jambanna; Vijayraghavan, Usha; Malhotra, Pawan

doi:10.1016/j.bbagrm.2012.08.014

Cited by 12 publications

(6 citation statements)

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“…Similarly, only a small minority – 254 (4.5%) – of genes in P. falciparum have been reported to undergo alternative splicing [30]–[32]. The occurrence of circular RNAs in species in which introns are small and alternative splicing rare argues against earlier suggestions that rare circular RNAs in some metazoans were byproducts of canonical alternative splicing, or arise from errors (mispairing of 3′ and 5′ splice sites) in complex splicing programs which rely on the spliceosome to identify small exons within long pre-mRNAs [3], [18], [33].…”

Section: Discussionmentioning

confidence: 99%

Circular RNA Is Expressed across the Eukaryotic Tree of Life

et al. 2014

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An unexpectedly large fraction of genes in metazoans (human, mouse, zebrafish, worm, fruit fly) express high levels of circularized RNAs containing canonical exons. Here we report that circular RNA isoforms are found in diverse species whose most recent common ancestor existed more than one billion years ago: fungi (Schizosaccharomyces pombe and Saccharomyces cerevisiae), a plant (Arabidopsis thaliana), and protists (Plasmodium falciparum and Dictyostelium discoideum). For all species studied to date, including those in this report, only a small fraction of the theoretically possible circular RNA isoforms from a given gene are actually observed. Unlike metazoans, Arabidopsis, D. discoideum, P. falciparum, S. cerevisiae, and S. pombe have very short introns (∼100 nucleotides or shorter), yet they still produce circular RNAs. A minority of genes in S. pombe and P. falciparum have documented examples of canonical alternative splicing, making it unlikely that all circular RNAs are by-products of alternative splicing or ‘piggyback’ on signals used in alternative RNA processing. In S. pombe, the relative abundance of circular to linear transcript isoforms changed in a gene-specific pattern during nitrogen starvation. Circular RNA may be an ancient, conserved feature of eukaryotic gene expression programs.

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Section: Discussionmentioning

confidence: 99%

Circular RNA Is Expressed across the Eukaryotic Tree of Life

et al. 2014

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“…In addition, proteins involved in the proofreading of the splicing and joining processes such as Prp16, Prp22, and Prp43 were also identified in the Plasmodium genome [ 69 ] (Additional file 1 ). Pfprp16 has been shown to bind RNA and hydrolyze ATP in the presence of helicase associated domain (HA2) [ 70 ].…”

Section: Resultsmentioning

confidence: 99%

A bioinformatic survey of RNA-binding proteins in Plasmodium

et al. 2015

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BackgroundThe malaria parasites in the genus Plasmodium have a very complicated life cycle involving an invertebrate vector and a vertebrate host. RNA-binding proteins (RBPs) are critical factors involved in every aspect of the development of these parasites. However, very few RBPs have been functionally characterized to date in the human parasite Plasmodium falciparum.MethodsUsing different bioinformatic methods and tools we searched P. falciparum genome to list and annotate RBPs. A representative 3D models for each of the RBD domain identified in P. falciparum was created using I-TESSAR and SWISS-MODEL. Microarray and RNAseq data analysis pertaining PfRBPs was performed using MeV software. Finally, Cytoscape was used to create protein-protein interaction network for CITH-Dozi and Caf1-CCR4-Not complexes.ResultsWe report the identification of 189 putative RBP genes belonging to 13 different families in Plasmodium, which comprise 3.5 % of all annotated genes. Almost 90 % (169/189) of these genes belong to six prominent RBP classes, namely RNA recognition motifs, DEAD/H-box RNA helicases, K homology, Zinc finger, Puf and Alba gene families. Interestingly, almost all of the identified RNA-binding helicases and KH genes have cognate homologs in model species, suggesting their evolutionary conservation. Exploration of the existing P. falciparum blood-stage transcriptomes revealed that most RBPs have peak mRNA expression levels early during the intraerythrocytic development cycle, which taper off in later stages. Nearly 27 % of RBPs have elevated expression in gametocytes, while 47 and 24 % have elevated mRNA expression in ookinete and asexual stages. Comparative interactome analyses using human and Plasmodium protein-protein interaction datasets suggest extensive conservation of the PfCITH/PfDOZI and PfCaf1-CCR4-NOT complexes.ConclusionsThe Plasmodium parasites possess a large number of putative RBPs belonging to most of RBP families identified so far, suggesting the presence of extensive post-transcriptional regulation in these parasites. Taken together, in silico identification of these putative RBPs provides a foundation for future functional studies aimed at defining a unique network of post-transcriptional regulation in P. falciparum.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2092-1) contains supplementary material, which is available to authorized users.

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“…Recently, a number of studies have reported the functional characterization of few P. falciparum splicing related proteins; PfSRPK1 and PfPrp16 [38-40]. The present study describes the sequence analysis and molecular architecture of P. falciparum spliceosome core complex.…”

Section: Introductionmentioning

confidence: 94%

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

Hossain

Sharma

Korde

et al. 2013

Malar J

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BackgroundSplicing 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.MethodsPresence 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.ResultsPfSm 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.ConclusionsPlasmodium 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.

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Plasmodium falciparum Prp16 homologue and its role in splicing

Cited by 12 publications

References 44 publications

Circular RNA Is Expressed across the Eukaryotic Tree of Life

Circular RNA Is Expressed across the Eukaryotic Tree of Life

A bioinformatic survey of RNA-binding proteins in Plasmodium

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

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