Abstract
BackgroundRibosome biogenesis is an energy consuming and stringently controlled process that involves hundreds of trans-acting factors. Small nucleolar RNAs (snoRNAs), important components of ribosome biogenesis are non-coding guide RNAs involved in rRNA processing, nucleotide modifications like 2'-O-ribose methylation, pseudouridylation and possibly gene regulation. snoRNAs are ubiquitous and are diverse in their genomic organization, mechanism of transcription and process of maturation. In vertebrates, most snoRNAs are present in introns of protein coding genes and are processed by exonucleolytic cleavage, while in plants they are transcribed as polycistronic transcripts.ResultsThis is a comprehensive analysis of malaria parasite snoRNA genes and proteins that have a role in ribosomal biogenesis. Computational and experimental approaches have been used to identify several box C/D snoRNAs from different species of Plasmodium and confirm their expression. Our analyses reveal that the gene for endoribonuclease Rnt1 is absent from Plasmodium falciparum genome, which indicates the existence of alternative pre-rRNA processing pathways. The structural features of box C/D snoRNAs are highly conserved in Plasmodium genus; however, unlike other organisms most parasite snoRNAs are present in single copy. The genomic localization of parasite snoRNAs shows mixed patterns of those observed in plants, yeast and vertebrates. We have localized parasite snoRNAs in untranslated regions (UTR) of mRNAs, and this is an unprecedented and novel genetic feature. Akin to mammalian snoRNAs, those in Plasmodium may also behave as mobile genetic elements.ConclusionThis study provides a comprehensive overview on trans-acting genes involved in ribosome biogenesis and also a genetic insight into malaria parasite snoRNA genes.
Highlights
Ribosome biogenesis is an energy consuming and stringently controlled process that involves hundreds of trans-acting factors
Our study reveals the following key features of malaria parasite Small nucleolar RNAs (snoRNAs): (1) structural features of box C/D snoRNA are highly conserved in Plasmodium genus, (2) unlike other organisms, most snoRNAs in malaria parasites are present as a single copy, (3) genomic localization patterns are mixture of those observed in plants, yeast and vertebrates; parasite snoRNAs are present in clusters and introns of a gene (4) we have found snoRNAs in 3'untranslated regions (UTR) of an mRNA, a feature not reported in any organism till date, (5) and we propose that as in mammals, the parasite snoRNAs may behave as mobile genetic elements
Proteins involved in ribosomal biogenesis Considering the unusual gene structure and developmentally regulated transcription of ribosomal RNA in Plasmodium, we have tried to study the process of ribosomal biogenesis in this genus
Summary
Ribosome biogenesis is an energy consuming and stringently controlled process that involves hundreds of trans-acting factors. Small nucleolar RNAs (snoRNAs), important components of ribosome biogenesis are non-coding guide RNAs involved in rRNA processing, nucleotide modifications like 2'-O-ribose methylation, pseudouridylation and possibly gene regulation. SnoRNAs are the small metabolically stable non-coding RNAs present in the nucleoli of cells [8] They play crucial roles in nucleotide modifications, viz methylation and pseudouridylation of various RNAs like rRNA, snRNA, and tRNA. RRNA modification is important for proper functioning of the translation machinery, and deregulation of nucleotide modification can lead to diseases like dyskeratosis congenita [9,10] This disease is caused by point mutations in the human gene encoding dyskerin, responsible for pseudouridylation. In an another case, snoRNA HBII-52 is involved in the regulation of mRNA processing [11]
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