The Arabidopsis 2′-O-Ribose-Methylation and Pseudouridylation Landscape of rRNA in Comparison to Human and Yeast

Abstract

Eukaryotic ribosome assembly starts in the nucleolus, where the ribosomal DNA (rDNA) is transcribed into the 35S pre-ribosomal RNA (pre-rRNA). More than two-hundred ribosome biogenesis factors (RBFs) and more than two-hundred small nucleolar RNAs (snoRNA) catalyze the processing, folding and modification of the rRNA in Arabidopsis thaliana. The initial pre-ribosomal 90S complex is formed already during transcription by association of ribosomal proteins (RPs) and RBFs. In addition, small nucleolar ribonucleoprotein particles (snoRNPs) composed of snoRNAs and RBFs catalyze the two major rRNA modification types, 2′-O-ribose-methylation and pseudouridylation. Besides these two modifications, rRNAs can also undergo base methylations and acetylation. However, the latter two modifications have not yet been systematically explored in plants. The snoRNAs of these snoRNPs serve as targeting factors to direct modifications to specific rRNA regions by antisense elements. Today, hundreds of different sites of modifications in the rRNA have been described for eukaryotic ribosomes in general. While our understanding of the general process of ribosome biogenesis has advanced rapidly, the diversities appearing during plant ribosome biogenesis is beginning to emerge. Today, more than two-hundred RBFs were identified by bioinformatics or biochemical approaches, including several plant specific factors. Similarly, more than two hundred snoRNA were predicted based on RNA sequencing experiments. Here, we discuss the predicted and verified rRNA modification sites and the corresponding identified snoRNAs on the example of the model plant Arabidopsis thaliana. Our summary uncovers the plant modification sites in comparison to the human and yeast modification sites.

The plant epitranscriptome: revisiting pseudouridine and 2′‐O‐methyl RNA modifications

“…In a recent study, 187 Ψ sites were discovered in Arabidopsis rRNA by genome-wide mapping ª 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 20, 1241-1256 (Sun et al, 2019). When comparing previously predicted Ψ sites in rRNA (Brown et al, 2003;Chen and Wu, 2009) with genomewide sequencing, the authors found evidence for 21 (of 32), 14 (of 25), and 1 (of 1) Ψ sites in large subunit (LSU) rRNA, small subunit (LSU), and 5.8S rRNA respectively (Sun et al, 2019).…”

“…Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd., 20, 1241-1256 (Sun et al, 2019). When comparing previously predicted Ψ sites in rRNA (Brown et al, 2003;Chen and Wu, 2009) with genomewide sequencing, the authors found evidence for 21 (of 32), 14 (of 25), and 1 (of 1) Ψ sites in large subunit (LSU) rRNA, small subunit (LSU), and 5.8S rRNA respectively (Sun et al, 2019). A detailed comparison of all Ψ sites in Arabidopsis, human and yeast rRNA was described by Streit and Schleiff (Streit and Schleiff, 2021).…”

“…Arabidopsis snRNAs also carry Ψs. In a recent study, 13 Ψ sites were detected in Arabidopsis snRNA by genome-wide mapping (Sun et al, 2019). It is currently unknown whether these sites are guided by snoRNAs or PUS enzymes and their biological significance remains to be explored.…”

“…Arabidopsis mRNAs also carry Ψs internally (Sun et al, 2019). In a recent study, ~451 Ψ sites were detected in Arabidopsis mRNA by genome-wide mapping (Sun et al, 2019).…”

“…Arabidopsis mRNAs also carry Ψs internally (Sun et al, 2019). In a recent study, ~451 Ψ sites were detected in Arabidopsis mRNA by genome-wide mapping (Sun et al, 2019). In contrast to m 6 A and m 5 C, Ψs are enriched in position 1 of triplet codons carrying uridine and underrepresented in the 3 0 UTR.…”