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Invariable Stoichiometry of Ribosomal Proteins in Mouse Brain Tissues with Aging

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Invariable Stoichiometry of Ribosomal Proteins in Mouse Brain Tissues with Aging Correction BIOCHEMISTRY Correction for “Invariable stoichiometry of ribosomal proteins in first published October 21, 2019; 10.1073/pnas.1912060116 (Proc. mouse brain tissues with aging,” by Susan Amirbeigiarab, Parnian Natl. Acad. Sci. U.S.A. 116,22567–22572). Kiani, Ana Velazquez Sanchez, Christoph Krisp, Andriy Kazantsev, The authors note that Fig. 2 appeared incorrectly. The cor- Lars Fester, Hartmut Schlüter, and Zoya Ignatova, which was rected figure and its legend appear below. CORRECTION Fig. 2. Changes in expression of single RPs across tissue and age are not significant. (A and B) Comparison of the RP levels in tissues of the same age (A)or across ages within the same tissues (B). Gray, proteins of 60S; green or blue, proteins of 40S. Despite fluctuating expression, none of the proteins show significant changes in their amounts (FDR < 0.1) in the respective sample or population. Cer, cerebellum; HC, hippocampus; Cor, cortex; Liv, liver; W, week; M, month. Published under the PNAS license. First published November 18, 2019. www.pnas.org/cgi/doi/10.1073/pnas.1919014116 www.pnas.org PNAS | December 3, 2019 | vol. 116 | no. 49 | 24907 Downloaded by guest on September 27, 2021 Invariable stoichiometry of ribosomal proteins in mouse brain tissues with aging Susan Amirbeigiaraba, Parnian Kianib,1, Ana Velazquez Sancheza,1, Christoph Krispb, Andriy Kazantseva, Lars Festerc, Hartmut Schlüterb, and Zoya Ignatovaa,2 aBiochemistry and Molecular Biology, Department of Chemistry, University of Hamburg, 20146 Hamburg, Germany; bCenter for Diagnostics, Clinical Chemistry and Laboratory Medicine, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany; and cCenter for Experimental Medicine, Institute of Neuroanatomy, University Medical Center Hamburg Eppendorf, 20251 Hamburg, Germany Edited by Joseph D. Puglisi, Stanford University School of Medicine, Stanford, CA, and approved September 30, 2019 (received for review July 13, 2019) Across phyla, the ribosomes—the central molecular machines for tissues they decrease or remain constant (9–11). In addition, in- translation of genetic information—exhibit an overall preserved dividual RPs are exchanged at different rates with the cytoplasmic architecture and a conserved functional core. The natural hetero- pool of their free counterparts (12, 13). Collectively, these varia- geneity of the ribosome periodically phases a debate on their tions could potentially give a rise to ribosomes with different RP functional specialization and the tissue-specific variations of the pools across tissues. Do ribosomes differ in their protein compo- ribosomal protein (RP) pool. Using sensitive differential proteomics, sition across tissues, and does this composition change over the we performed a thorough quantitative inventory of the protein lifetime of the cell? composition of ribosomes from 3 different mouse brain tissues, In yeast, RP genes are generally duplicated, and incorporation i.e., hippocampus, cortex, and cerebellum, across various ages, of RP paralogs results in compositional heterogeneity of the ri- i.e., juvenile, adult, and middle-aged mouse groups. In all 3 brain bosomes (14). Genomes of humans and mammals encode mul- tissues, in both monosomal and polysomal ribosome fractions, we tiple copies of the 4 rRNAs (15, 16), and unlike yeast, most of detected an invariant set of 72 of 79 core RPs, RACK1 and 2 of the 8 the 79 RPs are typically encoded by a single gene. Of the 8 total RP paralogs, the stoichiometry of which remained constant across human paralogs (4, 17), few exhibit tissue-specific patterns of different ages. The amount of a few RPs punctually varied in either transcription; e.g., uL3-like is expressed in striated muscle (18) one tissue or one age group, but these fluctuations were within BIOCHEMISTRY anduL16-likeandeL39-likeintestis (19), supporting the hypoth- the tight bounds of the measurement noise. Further comparison with the ribosomes from a high-metabolic-rate organ, e.g., the esis of tissue-specific variations in ribosomal composition. However, liver, revealed protein composition identical to that of the ribo- the depletion or even complete deletion of some paralogs does not somes from the 3 brain tissues. Together, our data show an in- cause phenotypic effects, challenging the role of the paralogs as a variant protein composition of ribosomes from 4 tissues across unique component of the ribosomes in those tissues (20, 21). different ages of mice and support the idea that functional het- Compositional heterogeneity of ribosomes could have message- erogeneity may arise from factors other than simply ribosomal specific effects; i.e., subpools of ribosomes might be specialized in protein stoichiometry. translation of specific mRNAs, a hypothesis referred to as “spe- cialized ribosomes.” Ribosomes deficient in a single RP, such as ribosome | translation | mass spectrometry | neuronal tissues | aging Significance he molecular composition of ribosomes—a large complex Tcomposed of ribosomal RNA (rRNA) and ribosomal pro- Ribosomes—the universal biosynthesis machinery central to all teins (RPs)—varies from bacteria to eukaryotes and among or- cellular life—are composed of 4 ribosomal RNA (rRNA) and up to ganelles; however, the overall architecture is preserved and the 80 ribosomal proteins (RPs), yet detecting fluctuations in their RP functional unit of decoding and peptide bond formation are both composition with possible functional consequences remains a conserved (1). Along the phylogenetic tree, the ribosomes have challenge. Using quantitative proteomics we show an invariant evolved by idiosyncratic expansion of the RPs and rRNAs RP composition of ribosomes across 3 murine brain and liver without perturbing the conserved functional core (2). tissues. The RP pool does not change with age and remains Mammalian cells typically contain ∼106 cytoplasmic ribosomes, constant in tissues of juvenile, adult, and middle-aged mice and the question arises as to whether various types of cells main- groups. In a broader context, the high robustness in the overall tain homogenous pools of ribosomes with the exact same stoichi- protein architecture of the ribosomes across tissues and ages ometry of the individual RPs. Expression of functionally related implies that ribosomal heterogeneity, if any, may result from genes consisting of functional modules, e.g., RPs constituting the other processes, including postsynthesis modifications of rRNA ribosome, is conserved at great evolutionary distances by main- and RPs. taining coregulation while the regulatory mechanisms controlling Author contributions: S.A. and Z.I. designed research; S.A., P.K., and C.K. performed re- single genes can diverge (3). Across human tissues, the messenger search; L.F. contributed new reagents/analytic tools; S.A., P.K., A.V.S., C.K., A.K., H.S., and RNA (mRNA) levels of RPs span several orders of magnitude (4), Z.I. analyzed data; and S.A., A.V.S., and Z.I. wrote the paper. and the RP mRNA levels poorly correlate with the protein levels The authors declare no competing interest. (5), implying additional regulation at the level of translation of the This article is a PNAS Direct Submission. RP transcripts. In addition to their canonical role in translation, Published under the PNAS license. many RPs exhibit extraribosomal function (reviewed in ref. 6), Data deposition: The mass spectrometry proteomics data have been deposited in the which also suggests disproportional quantities of RPs. The half-life ProteomeXchange Consortium via the PRIDE partner repository, https://www.ebi.ac.uk/ of single RPs substantially differs for each individual RP (7), but pride/archive/ (dataset identifier PXD014138). also shows variation among tissues (8). On average, the protein 1P.K. and A.V.S. contributed equally to this work. lifetime is 3 times shorter in liver than in brain (8). Various tissues 2To whom correspondence may be addressed. Email: [email protected]. also exhibit different transcript dynamics over age. In brain tissues This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. of Caenorhabditis elegans or the short-lived fish Nothobranchius 1073/pnas.1912060116/-/DCSupplemental. fuzeri, the RP mRNA levels increase with age, while in other www.pnas.org/cgi/doi/10.1073/pnas.1912060116 PNAS Latest Articles | 1of6 eL38 or uS2 (22, 23), posttranslational modifications (24, 25), or of an outbred or wild-derived mouse that captures population detachment of ribosome-associated factors (26) provide examples variations (32, 33). Measurements of RP composition of mouse for tissue- and message-specific expression, prompting the debate embryonic stem cells and yeast suggest differential stoichiometry on whether a specialized ribosome pool may shape tissue devel- between monoribosomes (80S) and ribosomes engaged in poly- opment (27). This argument is challenged by recent observations somes (34); hence we separated the 80S monoribosomes from the in C. elegans that tissue diversification is efficiently maintained polysomes (SI Appendix,Fig.S1) and separately quantified their during embryonic development by maternal ribosomes and syn- RPs by tandem mass spectrometry (Fig. 1A). In total, 1,163 pro- thesis of a new distinct pool of ribosomes is not required (28). teins met the requirements for quantitative comparison between The argument for heterogeneous ribosomal pools conferring samples at a false discovery rate (FDR) of < 0.01. The numbers of message-specific expression is used
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