Identification of Changing Ribosome Protein Compositions using Mass Spectrometry

Samir, Parimal; Browne, Christopher M.; Rahul, .; Sun, Ming; Shen, Biyi; Liu, Wen; Frank, Joachim; Link, Andrew J.

doi:10.1002/pmic.201800217

Cited by 38 publications

(44 citation statements)

References 56 publications

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“…A more plausible hypothesis is that free, extra-ribosomal RPs in axons are incorporated into pre-existing ribosomes in the axon through the replacement or addition of components. This model is consistent with recent proteomics and cryoelectron microscopy studies, which showed the presence of ribosomes lacking specific RP components in eukaryotic cells (Shi et al., 2017, Slavov et al., 2015, Samir et al., 2018). It seems possible that axonal RP synthesis plays an important role in ribosome maintenance, particularly for the surface ribosomal components that may be prone to damage (Figures 3 and S3).…”

Section: Discussionsupporting

confidence: 92%

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

et al. 2019

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SummaryRibosome assembly occurs mainly in the nucleolus, yet recent studies have revealed robust enrichment and translation of mRNAs encoding many ribosomal proteins (RPs) in axons, far away from neuronal cell bodies. Here, we report a physical and functional interaction between locally synthesized RPs and ribosomes in the axon. We show that axonal RP translation is regulated through a sequence motif, CUIC, that forms an RNA-loop structure in the region immediately upstream of the initiation codon. Using imaging and subcellular proteomics techniques, we show that RPs synthesized in axons join axonal ribosomes in a nucleolus-independent fashion. Inhibition of axonal CUIC-regulated RP translation decreases local translation activity and reduces axon branching in the developing brain, revealing the physiological relevance of axonal RP synthesis in vivo. These results suggest that axonal translation supplies cytoplasmic RPs to maintain/modify local ribosomal function far from the nucleolus in neurons.

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Section: Discussionsupporting

confidence: 92%

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

et al. 2019

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“…In addition, the allocation of individual RPs was compared between cells cultivated in rich or minimal medium ( Fig. 4 D ), since previous work has highlighted changes in ribosomal stoichiometry ( 28 – 30 ) in changing growth environments. However, the analysis shows a highly consistent increase in all quantified RP subunits, including mitochondrial RP subunits ( SI Appendix , Fig.…”

Section: The Decreased Proteome Allocation For Amino Acid Biosynthesimentioning

confidence: 99%

Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media

Björkeroth

Campbell

Malina

et al. 2020

Proc. Natl. Acad. Sci. U.S.A.

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Several recent studies have shown that the concept of proteome constraint, i.e., the need for the cell to balance allocation of its proteome between different cellular processes, is essential for ensuring proper cell function. However, there have been no attempts to elucidate how cells’ maximum capacity to grow depends on protein availability for different cellular processes. To experimentally address this, we cultivated Saccharomyces cerevisiae in bioreactors with or without amino acid supplementation and performed quantitative proteomics to analyze global changes in proteome allocation, during both anaerobic and aerobic growth on glucose. Analysis of the proteomic data implies that proteome mass is mainly reallocated from amino acid biosynthetic processes into translation, which enables an increased growth rate during supplementation. Similar findings were obtained from both aerobic and anaerobic cultivations. Our findings show that cells can increase their growth rate through increasing its proteome allocation toward the protein translational machinery.

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“…These paralogs have highly similar, if not identical, amino acid sequences and have similar patterns of transcriptional regulation (Gasch et al 2000). Some recent studies have suggested that these paralogs can impart functional specialization (e.g., Haarer et al 2007;Komili et al 2007;Samir et al 2018;Segev and Gerst 2018). Nevertheless, while studying potential instances of such specialization it is important to keep in mind that the RP knockout collection has acquired additional mutations and duplications, which might mask or produce phenotypes (Steffen et al 2012).…”

Section: The Expression Of Ribosomal Protein Paralogs Is Differentialmentioning

confidence: 99%

Does functional specialization of ribosomes really exist?

Ferretti

Karbstein

2019

RNA

109

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It has recently become clear that ribosomes are much more heterogeneous than previously thought, with diversity arising from rRNA sequence and modifications, ribosomal protein (RP) content and posttranslational modifications (PTMs), as well as bound nonribosomal proteins. In some cases, the existence of these diverse ribosome populations has been verified by biochemical or structural methods. Furthermore, knockout or knockdown of RPs can diversify ribosome populations, while also affecting the translation of some mRNAs (but not others) with biological consequences. However, the effects on translation arising from depletion of diverse proteins can be highly similar, suggesting that there may be a more general defect in ribosome function or stability, perhaps arising from reduced ribosome numbers. Consistently, overall reduced ribosome numbers can differentially affect subclasses of mRNAs, necessitating controls for specificity. Moreover, in order to study the functional consequences of ribosome diversity, perturbations including affinity tags and knockouts are introduced, which can also affect the outcome of the experiment. Here we review the available literature to carefully evaluate whether the published data support functional diversification, defined as diverse ribosome populations differentially affecting translation of distinct mRNA (classes). Based on these observations and the commonly observed cellular responses to perturbations in the system, we suggest a set of important controls to validate functional diversity, which should include gainof-function assays and the demonstration of inducibility under physiological conditions.

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Identification of Changing Ribosome Protein Compositions using Mass Spectrometry

Cited by 38 publications

References 56 publications

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

On-Site Ribosome Remodeling by Locally Synthesized Ribosomal Proteins in Axons

Proteome reallocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media

Does functional specialization of ribosomes really exist?

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