Ribosome heterogeneity and specialisation in musculoskeletal physiology and pathology

Figures

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  Figure 1. The essentials of eukaryotic ribosome biogenesis. Ribosome biogenesis is a multi-step process that spans three cellular compartments—nucleolus, nucleoplasm, and cytoplasm. The main steps are: (i) rDNA transcription generating 47S pre-rRNA and 5S rRNAs; (ii) 47S pre-rRNA processing, 18S, 5.8S, and 28S maturation; (iii) post-transcriptional modifications (PTMs) of rRNAs by snoRNAs; (iv) import of ribosomal proteins (RPs) and ribosome biogenesis factors into the nucleus, assembly of pre-ribosomal subunits, quality check, nucleolar export; (v) ribosome maturation and quality control. SnoRNAs are small nucleolar RNAs, whose main function is to guide site-directionality of the rRNA PTMs and, in some cases, also aid specific 47S pre-rRNA processing steps—eg, U3 snoRNA or RMRP (the ribonuclease mitochondrial RNA processing). Abbreviations: 2′-O-me, ribose 2′-O-methylation; C/D snoRNA, box C/D small nucleolar RNA; DKC1, pseudouridine synthase dyskerin; FBL, methyltransferase fibrillarin; H/ACA snoRNA, box H/ACA small nucleolar RNA; LSU, large ribosomal subunit; RP, ribosomal protein; rRNA, ribosomal RNA; SSU, small ribosomal subunit; ψ, pseudouridylation. Figure created using BioRender.

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  Figure 2. (A) Sources of ribosome heterogeneity. The ribosome is in the middle (40S in green, 60S in blue). Each section represents a different level of ribosome heterogeneity. Alternative coloring indicates variation (rRNA sequence variants, RP paralogues, isoforms). P represents phosphorylation, Ub symbolizes ubiquitination. (B) Proposed mechanisms of ribosome specialization. (I) Ribosomes interact with mRNAs 5′ untranslated regions (5′ UTRs) which contain specific secondary structures, IRES, upstream ORFs (uORFs), or modified nucleotides (eg, N6-methyladenosine) that regulate translation of given mRNA.58 (II) Ribosomes’ interactions with specific RAPs also affect translation. For example, several paralogues and isoforms of translation initiation factors exist in eukaryotes, and data suggest they have different affinities for subsets of mRNAs, thus affecting their translation.59 (III) Regulation of translational elongation might also play a role in translation regulation.60 (IV) Interactions between ribosomes and a group of ribosome-associated non-coding RNAs (rancRNAs) have been described and suggested to repress translation.61 Abbreviations: 2′-O-me, ribose 2′-O-methylation; RAP,…

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  Figure 3. Emerging technologies and methodologies in ribosome-centered research. Abbreviations: ARC-MS, active ribosome capture-MS; cryo-EM, cryo-electron microscopy; MS, mass spectrometry; PTM, post-transcriptional modification; RAPIDASH, RAP identification by affinity to sulfhydryl-charged resin; RAPPL, RNA affinity purification using poly-lysine; ribo–STAMP, ribosome surveying targets by APOBEC-mediated profiling; rRNA, ribosomal RNA; SEC, size-exclusion chromatography; sciRibo, single-cell resolution ribosome profiling; smFRET, single-molecule Förster resonance energy transfer; SMRT seq, single-molecule real-time sequencing. Figure created using BioRender.

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  Figure 4. Generalized summary of the key findings on ribosome heterogeneity and specialization in MSK (patho)biology. Abbreviations: 2′-O-me, ribose 2′-O-methylation; OA, osteoarthritis; RAP, ribosome-associated protein; RP, ribosomal protein; rRNA, ribosomal RNA; snoRNA, small nucleolar RNA; ψ, pseudouridylation. Figure created using BioRender.