Genome-wide analysis of small nucleolar RNAs ofLeishmania majorreveals a rich repertoire of RNAs involved in modification and processing of rRNA

Abstract

(2015) Genome-wide analysis of small nucleolar RNAs of Leishmaniamajor reveals a rich repertoire of RNAs involved in modification and processing of rRNA, RNA Biology, 12:11, 1222-1255, DOI: 10.1080/15476286.2015 Trypanosomatids are protozoan parasites and the causative agent of infamous infectious diseases. These organisms regulate their gene expression mainly at the post-transcriptional level and possess characteristic RNA processing mechanisms. In this study, we analyzed the complete repertoire of Leishmania major small nucleolar (snoRNA) RNAs by performing RNA-seq analysis on RNAs that were affinity-purified using the C/D snoRNA core protein, SNU13, and the H/ ACA core protein, NHP2. This study revealed a large collection of C/D and H/ACA snoRNAs, organized in gene clusters generally containing both snoRNA types. Abundant snoRNAs were identified and predicted to guide trypanosomespecific rRNA cleavages. The repertoire of snoRNAs was compared to that of the closely related Trypanosoma brucei, and 80% of both C/D and H/ACA molecules were found to have functional homologues. The comparative analyses elucidated how snoRNAs evolved to generate molecules with analogous functions in both species. Interestingly, H/ACA RNAs have great flexibility in their ability to guide modifications, and several of the RNA species can guide more than one modification, compensating for the presence of single hairpin H/ACA snoRNA in these organisms. Placing the predicted modifications on the rRNA secondary structure revealed hypermodification regions mostly in domains which are modified in other eukaryotes, in addition to trypanosome-specific modifications.

2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania

“…The high resolution cryo-EM map obtained in this study has also enabled the direct visualization of the unusual rRNA modification pattern in Leishmania . Some of these modification loci were recently predicted using bioinformatics tools (Eliaz et al, 2015), and our structure provides an experimental evidence for the existence of these modifications on the leishmanial ribosome. The L. donovani LSU atomic model presented here will serve as a reliable template for future structure-based drug design.…”

“…One particularly interesting peculiarity of kinetoplastids lies in their cytosolic ribosomes, which include an unusual segmentation of their large subunit (LSU) 26S rRNA (Hernández et al, 2014), extensive number of rRNA modification sites (Eliaz et al, 2015), and enlarged rRNA expansions (Gao et al, 2005; Hashem et al, 2013). Many studies have focused on these unique features in trypanosomatid ribosomes aiming at exploiting them as targets for the development of novel anti-parasitic drugs (Michaeli et al, 2012).…”

Stem-Loop RT-qPCR as an Efficient Tool for the Detection and Quantification of Small RNAs in Giardia lamblia

“…Some snoRNAs also serve as precursors for the biogenesis of mature miRNAs that participate in gene regulation [5,9,10,58]. This is the case for some snoRNAs of G. lamblia [6,7].…”

“…lamblia [4]. Small nucleolar RNA (snoRNA) has been identified as a source of microRNAs (miRNAs) in some protozoans and metazoans [5,6,7,8,9,10]. These miRNAs are small RNA molecules that regulate gene expression in lower and higher eukaryotes, but they have not been studied in detail in Giardia [11], although the origins and evolution of miRNAs and other regulatory small RNAs have been extensively characterized [12].…”

Euglena Transcript Processing

“…The majority of these modifications are 2′-O-methylations (Nm) (209) and pseudouridines (Ψ) (119) contradicting the usual trend of multicellular organismal rRNA being more heavily modified than that of simpler organisms. In addition to having conserved modifications at many positions also modified in other eukaryotes, E. gracilis also appears to contain a large number of species-specific and euglenozoanspecific modifications (Schnare and Gray 2011;Eliaz et al 2015). In eukaryotes, the two most prevalent modifications in rRNA are isomerization of uridine to Ψ and 2′-O-methylation (Li et al 2016;Sharma and Lafontaine 2015).…”