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.
Highlights
Ribosome biogenesis is an essential biochemical process in all existing organisms
Considering the importance of ribosomal RNA (rRNA) modifications for proper processing and maturation of rRNA and for the function of ribosomes, we discuss in the following the current knowledge on the rRNA modifications and small nucleolar RNAs (snoRNA) in Arabidopsis and compare these with the human and yeast modifications sites
The predicted 2 -ribose-O-me site at position Gm155, which hypothetically is targeted by snoR4a/4b, could not be confirmed by radiographic labeling of modified nucleotides in wheat-embryo (Lau et al, 1974), suggesting that this snoRNA is probably not involved in the modification but rather in rRNA processing in the internal transcribed spacer 2 (ITS2) region (Brown et al, 2001)
Summary
Ribosome biogenesis is an essential biochemical process in all existing organisms. The formation of functional ribosomes involves a huge number of different RNAs and proteins, which have to act in a defined order. Considering the importance of rRNA modifications for proper processing and maturation of rRNA and for the function of ribosomes, we discuss in the following the current knowledge on the rRNA modifications and snoRNAs in Arabidopsis and compare these with the human and yeast modifications sites. The known snoRNPs containing an H/ACA box snoRNA consist of the proteins dyskerin/NAP57 (pseudouridine synthase; Cbf5p in yeast), NHP2 (Nhp2p), NOP10 (Nop10p), and GAR1 (Gar1p) (Rodor et al, 2011; Figure 2A) Another minor class of snoRNAs unifies the mitochondrial RNA processing (MRP)-RNAs, a snoRNA family which lacks conserved boxes, but harbors rRNA processing activity (Bertrand and Fournier, 2013). A complementary analysis using RiboMethSeq for detection of 2 -O-ribose-me modifications yielded novel modification sites as well (Azevedo-Favory et al, 2020)
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