Ribosome Biogenesis in Plants: From Functional 45S Ribosomal DNA Organization to Ribosome Assembly Factors

Abstract

The transcription of 18S, 5.8S, and 18S rRNA genes (45S rDNA), cotranscriptional processing of pre-rRNA, and assembly of mature rRNA with ribosomal proteins are the linchpins of ribosome biogenesis. In yeast (Saccharomyces cerevisiae) and animal cells, hundreds of pre-rRNA processing factors have been identified and their involvement in ribosome assembly determined. These studies, together with structural analyses, have yielded comprehensive models of the pre-40S and pre-60S ribosome subunits as well as the largest cotranscriptionally assembled preribosome particle: the 90S/small subunit processome. Here, we present the current knowledge of the functional organization of 45S rDNA, pre-rRNA transcription, rRNA processing activities, and ribosome assembly factors in plants, focusing on data from Arabidopsis (Arabidopsis thaliana). Based on yeast and mammalian cell studies, we describe the ribonucleoprotein complexes and RNA-associated activities and discuss how they might specifically affect the production of 40S and 60S subunits. Finally, we review recent findings concerning pre-rRNA processing pathways and a novel mechanism involved in a ribosome stress response in plants.

Figure 1.

Graphic Representation of Ribosome Biogenesis in Eukaryotic Cells. Transcription of rDNA (45S, 47S, and 35S in Arabidopsis, mammals, and yeast, respectively) requires RNA Pol I activity and a subset of GTFs. Transcribed transcript contains the 18S, 5.8S, and 25S (in Arabidopsis and yeast)/28S (in mammals) rRNAs and is first cotranscriptionally processed into pre-rRNA precursor (35S in Arabidopsis and yeast or 45S in mammals). Processing of pre-rRNAs into mature 18S, 5.8S, and 25S/28S rRNA involves multiple endonucleolytic and exonucleolytic cleavages and the modification of numerous rRNA residues, mainly pseudouridylation and 2′-O-ribose methylation, by snoRNP complexes (see Figure 3). 18S rRNAs assemble with ribosomal proteins RPSs (S for small) to form 40S ribosome subunits, while 5.8S and 25S/28S assemble with ribosomal proteins RPLs (L for large) and 5S rRNA transcribed by RNA Pol III. Assembly and transport of ribosomal particles from the nucleolus to the cytoplasm requires hundreds of specific 40S and 60S RBFs (Figures 4 and 5; Supplemental Data Sets 3 and 4). The 40S and 60S ribosomal subunits join to form translationally competent ribosomes.

Figure 2.

45S rDNA Organization in Arabidopsis Accession Col-0. (A) The figure illustrates the localization of 45S rDNA tandem repeat units in the NORs immediately adjacent to telomeres (TEL) on chromosomes 2 and 4. 45S rDNA units are separated by IGSs, which each contain repeated SalI box elements, SP1 and SP2, and the GP. The 45S rDNA transcribed sequence contains structural rRNAs (18S, 5.8S, and 25S) separated by external (5′ETS and 3′ETS) and internal (ITS1 and ITS2) transcribed spacers. Within the 5′ETS is the A¹²³B motif and a 1.2-kb insertion, which contain D and C motifs. In the 3′ETS are polymorphic R1 to R5 elements that allow the 45S rDNA variants VAR1 through VAR5 to be discriminated. (B) The image illustrates the distribution of 45S rDNA variants in NOR2 (VAR1 and VAR3a) and NOR4 (VAR2a/b, VAR3b/c, and VAR4; Chandrasekhara et al., 2016) and the repression of NOR2 during plant development.

Figure 3.

35S Pre-rRNA Processing Pathways. The figure illustrates the 45S pre-rRNA and cleavage sites in the ETS and ITS sequences. In the current models, the 5′ETS of 45S pre-rRNAs is trimmed by XRN2 before being cleaved at the P site by a nucleolin-U3 snoRNP complex. The 3′ETS is cleaved by the RNase III endonuclease, RTL2. Structural rRNAs are methylated by C/D snoRNP (2-O-ribose methylation) or pseudouridylated by H/ACA snoRNP complexes. The resulting 35S(P) pre-rRNA follows either pathway 1, 5′ETS-first (minor), pathway 2, ITS1-first (major), or pathway 3, ITS2-first. Specific processing events in pathway 1, 2, or 3 are shown in the boxes. The characterized protein factors required for RNA modification (C/D and H/ACA snoRNP and TRL), endonucleolytic cleavages (nucleolin-U3 snoRNP, RTL2, and NOB1), or exonucleolytic cleavages (XRN2, AtRRP6L2, and AtRRP41) are indicated.

Figure 4.

Model for Processome Assembly and the Maturation of Pre-40S Particles in Arabidopsis. The picture illustrates UtpA (green), UtpB (blue), UtpC (yellow), U3 snoRNP (violet), Dbp4/Enp2/Brf2 (pink), and Mpp10/Imp3/Imp4 (brown) subcomplexes. Arabidopsis homologs (NuGWD1/Utp5, Nucleolin/Nrs1, Utp25, THAL1/Utp3, RH57/Rock1, RH10/Rrp3, and SW3/Dbp8) or specific (PCP1/2) factors that interact with processome factors or subunits are represented in dark blue. Arabidopsis homologs that interact with the processome and are required for pre-40S maturation and transport are represented in red. Known or predicted Arabidopsis homologs are labeled in white and those not yet identified in black. The anticipated assembly of pre-60S particles on nascent pre-RNA is shown. Assembly might initiate on full-length rRNA precursor or after cleavage at A₂/A₃ sites that release processome factor precursors and pre-40S particles. The figure was adapted and drawn from models of the assembly steps of the 90S/SSU-processome and pre-40S in yeast and mammalian cells (Soltanieh et al., 2014; Cerezo et al., 2019). Accession numbers for all the Arabidopsis factors are provided in Supplemental Data Set 2.

Figure 5.

Model for the Assembly and Maturation of Pre-60S Particles in Arabidopsis. The picture illustrates the so-called yeast 60S particle in the nucleolus (Ssf1 and Nsa), nucleoplasm (Arx1/Rsa4, Rix1/Rea1, and Arx1/Nmd3/Mex67), and cytoplasm (Lsg1). Arabidopsis homologs of yeast processome factors and subcomplexes (blue and violet), protein export (red), and GTPase (orange) activities are represented. Those not yet identified are shown in gray. Plant GTS1, orthologous to human WDR39, is represented in dark green. The figure was adapted and drawn from simplified models of the assembly steps of the 60S particles in yeast (Shchepachev and Tollervey, 2016; Kressler et al., 2017). Accession numbers for all the Arabidopsis factors are provided in Supplemental Data Set 4.