Arabidopsis protein arginine methyltransferase 3 is required for ribosome biogenesis by affecting precursor ribosomal RNA processing

Abstract

Ribosome biogenesis is a fundamental and tightly regulated cellular process, including synthesis, processing, and assembly of rRNAs with ribosomal proteins. Protein arginine methyltransferases (PRMTs) have been implicated in many important biological processes, such as ribosome biogenesis. Two alternative precursor rRNA (prerRNA) processing pathways coexist in yeast and mammals; however, how PRMT affects ribosome biogenesis remains largely unknown. Here we show that Arabidopsis PRMT3 (AtPRMT3) is required for ribosome biogenesis by affecting pre-rRNA processing. Disruption of AtPRMT3 results in pleiotropic developmental defects, imbalanced polyribosome profiles, and aberrant pre-rRNA processing. We further identify an alternative pre-rRNA processing pathway in Arabidopsis and demonstrate that AtPRMT3 is required for the balance of these two pathways to promote normal growth and development. Our work uncovers a previously unidentified function of PRMT in posttranscriptional regulation of rRNA, revealing an extra layer of complexity in the regulation of ribosome biogenesis.arginine methylation | protein arginine methyltransferase | AtPRMT3 | ribosome biogenesis | rRNA processing T he fundamental, complicated, and highly cooperative process of ribosome biogenesis involves ribosomal DNA (rDNA) transcription, precursor rRNA (pre-rRNA) processing, and assembly with ribosomal proteins and related assembly factors (1, 2). As a multistep, error prone, and energy-consuming process, ribosome biogenesis is also highly regulated (3, 4). In eukaryotic cells, mutations in ribosomal proteins or ribosome assembly factors usually lead to aberrant pre-rRNA processing (5-7) and activation of the polyadenylation-mediated RNA quality control system (4, 8, 9), resulting in various genetic diseases in humans (10, 11).Work in budding yeast, Saccharomyces cerevisiae, has deciphered the mechanisms of ribosome biogenesis (1, 2, 12). After transcription by RNA polymerase I and site-specific modification by small nucleolar ribonucleoproteins, the nascent 35S rRNA, the common precursor of 18S, 5.8S, and 25S rRNAs, is quickly assembled with many assembly factors and ribosomal proteins into small subunit processome/90S preribosomal particles (13-15). Then it mainly undergoes the "U3-dependent cleavage occurs first" pathway, which first removes the 5′ external transcribed sequence (5′ ETS) of 35S rRNA, to generate the 32S rRNA (16, 17). Next, after cleavage at the A2 site of intergenic transcribed sequence 1 (ITS1) between 18S rRNA and 5.8S rRNA, the 90S preribosomal particle splits into two independent complexes of pre-40S and pre-60S ribosomal particles. Finally, ribosomal subunits are further matured and assembled into 80S ribosomes for translation in the cytoplasm (12). However, in contrast to budding yeast, pre-rRNA processing in Xenopus laevis oocytes, mouse cells, and human cells preferentially cleave in ITS1 before the complete removal of the 5′ ETS (18-21), which may represent a common pathway in metazoans.In plants, a pre-rRNA processi...

atBRX1-1 and atBRX1-2 are involved in an alternative rRNA processing pathway in Arabidopsis thaliana

“…Although this intermediate has been observed previously (Zakrzewska-Placzek et al 2010;Missbach et al 2013;Weis et al 2014), the processing steps/cleavage sites by which it is generated have remained unclear until now. Furthermore, p3, p42, p43, and p5 recognize the recently described 32S pre-rRNA (Hang et al 2014) that comigrates with 33S(P ′ ) under these conditions (Fig. 4B,D).…”

“…An alternative pre-rRNA processing route starting comparable to Pathway 1 was proposed in parallel by Hang and coworkers who described the 32S pre-rRNA (Hang et al 2014). …”

“…It was suggested, that cleavage at site A 3 is the first processing event following P-site cleavage in the 5 ′ ETS, which contains a specific insertion in Arabidopsis upstream of the P-site (Sáez-Vasquez et al 2004;Zakrzewska-Placzek et al 2010;Missbach et al 2013;Weis et al 2014), implying a processing pathway analogous to the major pathway in mammalian cells (Henras et al 2014). However, an alternative processing route has also been suggested (Hang et al 2014;Weis et al 2014).…”

Arabidopsis small nucleolar RNA monitors the efficient pre-rRNA processing during ribosome biogenesis

“…This pathway starts with an early cleavage of ITS1 at the A3 site, followed by complete elimination of the 5′-ETS (7,8). Recently a minor pathway, known as "5′ ETS-first pathway," also has been reported to coexist in plants and has been shown to resemble the strict processing pathway in yeast (9,10). Each of the processes of rRNA transcription, processing, and modification has been shown to require snoRNAs (11).…”

Update: Post-translational protein modifications in plant metabolism

“…Lys methylation can be reversed by the action of multiple Lys demethylases, but Arg demethylases have yet to be identified (Biggar and Li, 2015). Ribosomal proteins are enriched among methylated proteins, and methylation appears important for ribosome biogenesis (ribosomal RNA maturation) and perhaps function, as also demonstrated by an Arabidopsis mutant for a cytosolic Arg methyltransferase (PRMT3; Hang et al, 2014).…”