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Journal articles on the topic 'Ribosomal heterogeneity'

Author: Grafiati

Published: 7 September 2022

Last updated: 18 September 2022

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1

Shiao, Yih-Horng. "Promising Assays for Examining a Putative Role of Ribosomal Heterogeneity in COVID-19 Susceptibility and Severity." Life 12, no. 2 (January 28, 2022): 203. http://dx.doi.org/10.3390/life12020203.

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The heterogeneity of ribosomes, characterized by structural variations, arises from differences in types, numbers, and/or post-translational modifications of participating ribosomal proteins (RPs), ribosomal RNAs (rRNAs) sequence variants plus post-transcriptional modifications, and additional molecules essential for forming a translational machinery. The ribosomal heterogeneity within an individual organism or a single cell leads to preferential translations of selected messenger RNA (mRNA) transcripts over others, especially in response to environmental cues. The role of ribosomal heterogeneity in SARS-CoV-2 coronavirus infection, propagation, related symptoms, or vaccine responses is not known, and a technique to examine these has not yet been developed. Tools to detect ribosomal heterogeneity or to profile translating mRNAs independently cannot identify unique or specialized ribosome(s) along with corresponding mRNA substrate(s). Concurrent characterizations of RPs and/or rRNAs with mRNA substrate from a single ribosome would be critical to decipher the putative role of ribosomal heterogeneity in the COVID-19 disease, caused by the SARS-CoV-2, which hijacks the host ribosome to preferentially translate its RNA genome. Such a protocol should be able to provide a high-throughput screening of clinical samples in a large population that would reach a statistical power for determining the impact of a specialized ribosome to specific characteristics of the disease. These characteristics may include host susceptibility, viral infectivity and transmissibility, severity of symptoms, antiviral treatment responses, and vaccine immunogenicity including its side effect and efficacy. In this study, several state-of-the-art techniques, in particular, chemical probing of ribosomal components or rRNA structures, proximity ligation to generate rRNA-mRNA chimeras for sequencing, nanopore gating of individual ribosomes, nanopore RNA sequencing and/or structural analyses, single-ribosome mass spectrometry, and microfluidic droplets for separating ribosomes or indexing rRNAs/mRNAs, are discussed. The key elements for further improvement and proper integration of the above techniques to potentially arrive at a high-throughput protocol for examining individual ribosomes and their mRNA substrates in a clinical setting are also presented.

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2

Li, Wenzhu, Jing Zhang, Wenpeng Cheng, Yuze Li, Jinwen Feng, Jun Qin, and Xiangwei He. "Differential Paralog-Specific Expression of Multiple Small Subunit Proteins Cause Variations in Rpl42/eL42 Incorporation in Ribosome in Fission Yeast." Cells 11, no. 15 (August 2, 2022): 2381. http://dx.doi.org/10.3390/cells11152381.

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Ribosomes within a cell are commonly viewed as biochemically homogenous RNA–protein super-complexes performing identical functions of protein synthesis. However, recent evidence suggests that ribosomes may be a more dynamic macromolecular complex with specialized roles. Here, we present extensive genetic and molecular evidence in the fission yeast S. pombe that the paralogous genes for many ribosomal proteins (RPs) are functionally different, despite that they encode the same ribosomal component, often with only subtle differences in the sequences. Focusing on the rps8 paralog gene deletions rps801d and rps802d, we showed that the mutant cells differ in the level of Rpl42p in actively translating ribosomes and that their phenotypic differences reside in the Rpl42p level variation instead of the subtle protein sequence difference between Rps801p and Rps802p. Additional 40S ribosomal protein paralog pairs also exhibit similar phenotypic differences via differential Rpl42p levels in actively translating ribosomes. Together, our work identifies variations in the Rpl42p level as a potential form of ribosome heterogeneity in biochemical compositions and suggests a possible connection between large and small subunits during ribosome biogenesis that may cause such heterogeneity. Additionally, it illustrates the complexity of the underlying mechanisms for the genetic specificity of ribosome paralogs.

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3

Jovanovic, Bogdan, Lisa Schubert, Fabian Poetz, and Georg Stoecklin. "Tagging of RPS9 as a tool for ribosome purification and identification of ribosome-associated proteins." Archives of Biological Sciences, no. 00 (2020): 57. http://dx.doi.org/10.2298/abs20120557j.

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Ribosomes, the catalytic machinery required for protein synthesis, are comprised of 4 ribosomal RNAs and about 80 ribosomal proteins in mammals. Ribosomes further interact with numerous associated factors that regulate their biogenesis and function. As mutations of ribosomal proteins and ribosome associated proteins cause many diseases, it is important to develop tools by which ribosomes can be purified efficiently and with high specificity. Here, we designed a method to purify ribosomes from human cell lines by C-terminally tagging human RPS9, a protein of the small ribosomal subunit. The tag consists of a flag peptide and a streptavidin-binding peptide (SBP) separated by the tobacco etch virus (TEV) protease cleavage site. We demonstrate that RPS9-Flag-TEV-SBP (FTS) is efficiently incorporated into the ribosome without interfering with regular protein synthesis. Using HeLa-GFP-G3BP1 cells stably expressing RPS9-FTS or, as a negative control, mCherry-FTS, we show that complete ribosomes as well as numerous ribosome-associated proteins are efficiently and specifically purified following pull-down of RPS9-FTS using streptavidin beads. This tool will be helpful for the characterization of human ribosome heterogeneity, post-translational modifications of ribosomal proteins, and changes in ribosome-associated factors after exposing human cells to different stimuli and conditions.

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4

Ghulam, Mustafa Malik, Mathieu Catala, and Sherif Abou Elela. "Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress." Nucleic Acids Research 48, no. 4 (December 21, 2019): 1954–68. http://dx.doi.org/10.1093/nar/gkz1183.

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Abstract In Saccharomyces cerevisiae, most ribosomal proteins are synthesized from duplicated genes, increasing the potential for ribosome heterogeneity. However, the contribution of these duplicated genes to ribosome production and the mechanism determining their relative expression remain unclear. Here we demonstrate that in most cases, one of the two gene copies generate the bulk of the active ribosomes under normal growth conditions, while the other copy is favored only under stress. To understand the origin of these differences in paralog expression and their contribution to ribosome heterogeneity we used RNA polymerase II ChIP-Seq, RNA-seq, polyribosome association and peptide-based mass-spectrometry to compare their transcription potential, splicing, mRNA abundance, translation potential, protein abundance and incorporation into ribosomes. In normal conditions a post-transcriptional expression hierarchy of the duplicated ribosomal protein genes is the product of the efficient splicing, high stability and efficient translation of the major paralog mRNA. Exposure of the cell to stress modifies the expression ratio of the paralogs by repressing the expression of the major paralog and thus increasing the number of ribosomes carrying the minor paralog. Together the data indicate that duplicated ribosomal protein genes underlie a modular network permitting the modification of ribosome composition in response to changing growth conditions.

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5

Sulima and Dinman. "The Expanding Riboverse." Cells 8, no. 10 (October 5, 2019): 1205. http://dx.doi.org/10.3390/cells8101205.

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Subverting the conventional concept of “the” ribosome, a wealth of information gleaned from recent studies is revealing a much more diverse and dynamic ribosomal reality than has traditionally been thought possible. A diverse array of researchers is collectively illuminating a universe of heterogeneous and adaptable ribosomes harboring differences in composition and regulatory capacity: These differences enable specialization. The expanding universe of ribosomes not only comprises an incredible richness in ribosomal specialization between species, but also within the same tissues and even cells. In this review, we discuss ribosomal heterogeneity and speculate how the emerging understanding of the ribosomal repertoire is impacting the biological sciences today. Targeting pathogen-specific and pathological “diseased” ribosomes promises to provide new treatment options for patients, and potential applications for “designer ribosomes” are within reach. Our deepening understanding of and ability to manipulate the ribosome are establishing both the technological and theoretical foundations for major advances for the 21st century and beyond.

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6

Chaillou, Thomas. "Ribosome specialization and its potential role in the control of protein translation and skeletal muscle size." Journal of Applied Physiology 127, no. 2 (August 1, 2019): 599–607. http://dx.doi.org/10.1152/japplphysiol.00946.2018.

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The ribosome is typically viewed as a supramolecular complex with constitutive and invariant capacity in mediating translation of mRNA into protein. This view has been challenged by recent research revealing that ribosome composition could be heterogeneous, and this heterogeneity leads to functional ribosome specialization. This review presents the idea that ribosome heterogeneity results from changes in its various components, including variations in ribosomal protein (RP) composition, posttranslational modifications of RPs, changes in ribosomal-associated proteins, alternative forms of rRNA, and posttranscriptional modifications of rRNAs. Ribosome heterogeneity could be orchestrated at several levels and may depend on numerous factors, such as the subcellular location, cell type, tissue specificity, the development state, cell state, ribosome biogenesis, RP turnover, physiological stimuli, and circadian rhythm. Ribosome specialization represents a completely new concept for the regulation of gene expression. Specialized ribosomes could modulate several aspects of translational control, such as mRNA translation selectivity, translation initiation, translational fidelity, and translation elongation. Recent research indicates that the expression of Rpl3 is markedly increased, while that of Rpl3l is highly reduced during mouse skeletal muscle hypertrophy. Moreover, Rpl3l overexpression impairs the growth and myogenic fusion of myotubes. Although the function of Rpl3 and Rpl3l in the ribosome remains to be clarified, these findings suggest that ribosome specialization may be potentially involved in the control of protein translation and skeletal muscle size. Limited data concerning ribosome specialization are currently available in skeletal muscle. Future investigations have the potential to delineate the function of specialized ribosomes in skeletal muscle.

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7

Amirbeigiarab, Susan, Parnian Kiani, Ana Velazquez Sanchez, Christoph Krisp, Andriy Kazantsev, Lars Fester, Hartmut Schlüter, and Zoya Ignatova. "Invariable stoichiometry of ribosomal proteins in mouse brain tissues with aging." Proceedings of the National Academy of Sciences 116, no. 45 (October 21, 2019): 22567–72. http://dx.doi.org/10.1073/pnas.1912060116.

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Across phyla, the ribosomes—the central molecular machines for translation of genetic information—exhibit an overall preserved architecture and a conserved functional core. The natural heterogeneity of the ribosome periodically phases a debate on their functional specialization and the tissue-specific variations of the ribosomal protein (RP) pool. Using sensitive differential proteomics, we performed a thorough quantitative inventory of the protein composition of ribosomes from 3 different mouse brain tissues, i.e., hippocampus, cortex, and cerebellum, across various ages, i.e., juvenile, adult, and middle-aged mouse groups. In all 3 brain tissues, in both monosomal and polysomal ribosome fractions, we detected an invariant set of 72 of 79 core RPs, RACK1 and 2 of the 8 RP paralogs, the stoichiometry of which remained constant across different ages. The amount of a few RPs punctually varied in either one tissue or one age group, but these fluctuations were within the tight bounds of the measurement noise. Further comparison with the ribosomes from a high-metabolic-rate organ, e.g., the liver, revealed protein composition identical to that of the ribosomes from the 3 brain tissues. Together, our data show an invariant protein composition of ribosomes from 4 tissues across different ages of mice and support the idea that functional heterogeneity may arise from factors other than simply ribosomal protein stoichiometry.

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8

Bates, Christian, Simon J. Hubbard, and Mark P. Ashe. "Ribosomal flavours: an acquired taste for specific mRNAs?" Biochemical Society Transactions 46, no. 6 (November 12, 2018): 1529–39. http://dx.doi.org/10.1042/bst20180160.

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The regulation of translation is critical in almost every aspect of gene expression. Nonetheless, the ribosome is historically viewed as a passive player in this process. However, evidence is accumulating to suggest that variations in the ribosome can have an important influence on which mRNAs are translated. Scope for variation is provided via multiple avenues, including heterogeneity at the level of both ribosomal proteins and ribosomal RNAs and their covalent modifications. Together, these variations provide the potential for hundreds, if not thousands, of flavours of ribosome, each of which could have idiosyncratic preferences for the translation of certain messenger RNAs. Indeed, perturbations to this heterogeneity appear to affect specific subsets of transcripts and manifest as cell-type-specific diseases. This review provides a historical perspective of the ribosomal code hypothesis, before outlining the various sources of heterogeneity, their regulation and functional consequences for the cell.

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9

Mageeney, Catherine M., and Vassie C. Ware. "Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster." Molecular Biology of the Cell 30, no. 17 (August 2019): 2240–53. http://dx.doi.org/10.1091/mbc.e19-02-0086.

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The functional significance of ribosome heterogeneity in development and differentiation is relatively unexplored. We present the first in vivo evidence of ribosome heterogeneity playing a role in specific mRNA translation in a multicellular eukaryote. Eukaryotic-specific ribosomal protein paralogues eRpL22 and eRpL22-like are essential in development and required for sperm maturation and fertility in Drosophila. eRpL22 and eRpL22-like roles in spermatogenesis are not completely interchangeable. Flies depleted of eRpL22 and rescued by eRpL22-like overexpression have reduced fertility, confirming that eRpL22-like cannot substitute fully for eRpL22 function, and that paralogues have functionally distinct roles, not yet defined. We investigated the hypothesis that specific RNAs differentially associate with eRpL22 or eRpL22-like ribosomes, thereby establishing distinct ribosomal roles. RNA-seq identified 12,051 transcripts (mRNAs/noncoding RNAs) with 50% being enriched on specific polysome types. Analysis of ∼10% of the most abundant mRNAs suggests ribosome specialization for translating groups of mRNAs expressed at specific stages of spermatogenesis. Further, we show enrichment of “model” eRpL22-like polysome-associated testis mRNAs can occur outside the germline within S2 cells transfected with eRpL22-like, indicating that germline-specific factors are not required for selective translation. This study reveals specialized roles in translation for eRpL22 and eRpL22-like ribosomes in germline differentiation.

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10

Poitevin, Frédéric, Artem Kushner, Xinpei Li, and Khanh Dao Duc. "Structural Heterogeneities of the Ribosome: New Frontiers and Opportunities for Cryo-EM." Molecules 25, no. 18 (September 17, 2020): 4262. http://dx.doi.org/10.3390/molecules25184262.

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The extent of ribosomal heterogeneity has caught increasing interest over the past few years, as recent studies have highlighted the presence of structural variations of the ribosome. More precisely, the heterogeneity of the ribosome covers multiple scales, including the dynamical aspects of ribosomal motion at the single particle level, specialization at the cellular and subcellular scale, or evolutionary differences across species. Upon solving the ribosome atomic structure at medium to high resolution, cryogenic electron microscopy (cryo-EM) has enabled investigating all these forms of heterogeneity. In this review, we present some recent advances in quantifying ribosome heterogeneity, with a focus on the conformational and evolutionary variations of the ribosome and their functional implications. These efforts highlight the need for new computational methods and comparative tools, to comprehensively model the continuous conformational transition pathways of the ribosome, as well as its evolution. While developing these methods presents some important challenges, it also provides an opportunity to extend our interpretation and usage of cryo-EM data, which would more generally benefit the study of molecular dynamics and evolution of proteins and other complexes.

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11

Kavanagh, T. A., and J. N. Timmis. "Heterogeneity in cucumber ribosomal DNA." Theoretical and Applied Genetics 72, no. 3 (June 1986): 337–45. http://dx.doi.org/10.1007/bf00288570.

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12

Martinez-Seidel, Federico, Olga Beine-Golovchuk, Yin-Chen Hsieh, Kheloud El Eshraky, Michal Gorka, Bo-Eng Cheong, Erika V. Jimenez-Posada, et al. "Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis." International Journal of Molecular Sciences 22, no. 11 (June 7, 2021): 6160. http://dx.doi.org/10.3390/ijms22116160.

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Ribosome biogenesis is essential for plants to successfully acclimate to low temperature. Without dedicated steps supervising the 60S large subunits (LSUs) maturation in the cytosol, e.g., Rei-like (REIL) factors, plants fail to accumulate dry weight and fail to grow at suboptimal low temperatures. Around REIL, the final 60S cytosolic maturation steps include proofreading and assembly of functional ribosomal centers such as the polypeptide exit tunnel and the P-Stalk, respectively. In consequence, these ribosomal substructures and their assembly, especially during low temperatures, might be changed and provoke the need for dedicated quality controls. To test this, we blocked ribosome maturation during cold acclimation using two independent reil double mutant genotypes and tested changes in their ribosomal proteomes. Additionally, we normalized our mutant datasets using as a blank the cold responsiveness of a wild-type Arabidopsis genotype. This allowed us to neglect any reil-specific effects that may happen due to the presence or absence of the factor during LSU cytosolic maturation, thus allowing us to test for cold-induced changes that happen in the early nucleolar biogenesis. As a result, we report that cold acclimation triggers a reprogramming in the structural ribosomal proteome. The reprogramming alters the abundance of specific RP families and/or paralogs in non-translational LSU and translational polysome fractions, a phenomenon known as substoichiometry. Next, we tested whether the cold-substoichiometry was spatially confined to specific regions of the complex. In terms of RP proteoforms, we report that remodeling of ribosomes after a cold stimulus is significantly constrained to the polypeptide exit tunnel (PET), i.e., REIL factor binding and functional site. In terms of RP transcripts, cold acclimation induces changes in RP families or paralogs that are significantly constrained to the P-Stalk and the ribosomal head. The three modulated substructures represent possible targets of mechanisms that may constrain translation by controlled ribosome heterogeneity. We propose that non-random ribosome heterogeneity controlled by specialized biogenesis mechanisms may contribute to a preferential or ultimately even rigorous selection of transcripts needed for rapid proteome shifts and successful acclimation.

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13

Monaco, Piero, Virginie Marcel, Jean-Jacques Diaz, and Frédéric Catez. "2′-O-Methylation of Ribosomal RNA: Towards an Epitranscriptomic Control of Translation?" Biomolecules 8, no. 4 (October 3, 2018): 106. http://dx.doi.org/10.3390/biom8040106.

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Ribosomal RNA (rRNA) undergoes post-transcriptional modification of over 200 nucleotides, predominantly 2′-O-methylation (2′-O-Me). 2′-O-Methylation protects RNA from hydrolysis and modifies RNA strand flexibility but does not contribute to Watson-Crick base pairing. The contribution of 2′-O-Me to the translational capacity of ribosomes has been established. Yet, how 2′-O-Me participates in ribosome biogenesis and ribosome functioning remains unclear. The development of 2′-O-Me quantitative mapping methods has contributed to the demonstration that these modifications are not constitutive but rather provide heterogeneity to the ribosomal population. Moreover, recent advances in ribosome structure analysis and in vitro translation assays have proven, for the first time, that 2′-O-Me contributes to regulating protein synthesis. This review highlights the recent data exploring the impact of 2′-O-Me on ribosome structure and function, and the emerging idea that the rRNA epitranscriptome is involved in translational control.

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14

Zang, Hannah, Robert Shackelford, Alice Bewley, and Alexander E. Beeser. "Mutational Analyses of the Cysteine-Rich Domain of Yvh1, a Protein Required for Translational Competency in Yeast." Biology 11, no. 8 (August 22, 2022): 1246. http://dx.doi.org/10.3390/biology11081246.

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Ribosome assembly is a complex biological process facilitated by >200 trans-acting factors (TAFs) that function as scaffolds, place-holders or complex remodelers to promote efficient and directional ribosomal subunit assembly but are not themselves part of functional ribosomes. One such yeast TAF is encoded by Mrt4 which assembles onto pre-60S complexes in the nuclear compartment and remains bound to pre-60S complexes as they are exported into the cytoplasm. There, Mrt4 is displaced from pre-60S complexes facilitating the subsequent addition of the ribosomal stalk complex (P0/P1/P2). Ribosomal stalk proteins interact with translational GTPases (trGTPase) which facilitate and control protein synthesis on the ribosome. The rRNA-binding domain of Mrt4 is structurally similar to P0, with both proteins binding to the same interface of pre-60S subunits in a mutually exclusive manner; the addition of the ribosomal stalk therefore requires the displacement of Mrt4 from pre-60S subunits. Mrt4 removal requires the C-terminal cysteine-rich domain (CRD) of the dual-specificity phosphatase Yvh1. Unlike many other TAFs, yeast lacking Yvh1 are viable but retain Mrt4 on cytoplasmic pre-60S complexes precluding ribosomal stalk addition. Although Yvh1’s role in Mrt4 removal is well established, how Yvh1 accomplishes this is largely unknown. Here, we report an unbiased genetic screen to isolate Yvh1 variants that fail to displace Mrt4 from pre-60S ribosomes. Bioorthogonal non-canonical amino acid tagging (BONCAT) approaches demonstrate that these YVH1 loss-of-function variants also display defects in nascent protein production. The further characterization of one LOF variant, Yvh1F283L, establishes it as an expression-dependent, dominant-negative variant capable of interfering with endogenous Yvh1 function, and we describe how this Yvh1 variant can be used as a novel probe to better understand ribosome maturation and potentially ribosome heterogeneity in eukaryotes.

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Gonzalez, Iris Laudien, James E. Sylvester, and Roy D. Schmickel. "Human 28S ribosomal RNA sequence heterogeneity." Nucleic Acids Research 16, no. 21 (1988): 10213–24. http://dx.doi.org/10.1093/nar/16.21.10213.

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16

Heissenberger, Clemens, Lisa Liendl, Fabian Nagelreiter, Yulia Gonskikh, Guohuan Yang, Elena M. Stelzer, Teresa L. Krammer, et al. "Loss of the ribosomal RNA methyltransferase NSUN5 impairs global protein synthesis and normal growth." Nucleic Acids Research 47, no. 22 (November 13, 2019): 11807–25. http://dx.doi.org/10.1093/nar/gkz1043.

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Abstract Modifications of ribosomal RNA expand the nucleotide repertoire and thereby contribute to ribosome heterogeneity and translational regulation of gene expression. One particular m5C modification of 25S ribosomal RNA, which is introduced by Rcm1p, was previously shown to modulate stress responses and lifespan in yeast and other small organisms. Here, we report that NSUN5 is the functional orthologue of Rcm1p, introducing m5C3782 into human and m5C3438 into mouse 28S ribosomal RNA. Haploinsufficiency of the NSUN5 gene in fibroblasts from William Beuren syndrome patients causes partial loss of this modification. The N-terminal domain of NSUN5 is required for targeting to nucleoli, while two evolutionary highly conserved cysteines mediate catalysis. Phenotypic consequences of NSUN5 deficiency in mammalian cells include decreased proliferation and size, which can be attributed to a reduction in total protein synthesis by altered ribosomes. Strikingly, Nsun5 knockout in mice causes decreased body weight and lean mass without alterations in food intake, as well as a trend towards reduced protein synthesis in several tissues. Together, our findings emphasize the importance of single RNA modifications for ribosome function and normal cellular and organismal physiology.

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Chen, Yu-Xiang, Zhi-yu Xu, Xueliang Ge, Jia-Yao Hong, Suparna Sanyal, Zhi John Lu, and Babak Javid. "Selective translation by alternative bacterial ribosomes." Proceedings of the National Academy of Sciences 117, no. 32 (July 28, 2020): 19487–96. http://dx.doi.org/10.1073/pnas.2009607117.

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Alternative ribosome subunit proteins are prevalent in the genomes of diverse bacterial species, but their functional significance is controversial. Attempts to study microbial ribosomal heterogeneity have mostly relied on comparing wild-type strains with mutants in which subunits have been deleted, but this approach does not allow direct comparison of alternate ribosome isoforms isolated from identical cellular contexts. Here, by simultaneously purifying canonical and alternative RpsR ribosomes fromMycobacterium smegmatis, we show that alternative ribosomes have distinct translational features compared with their canonical counterparts. Both alternative and canonical ribosomes actively take part in protein synthesis, although they translate a subset of genes with differential efficiency as measured by ribosome profiling. We also show that alternative ribosomes have a relative defect in initiation complex formation. Furthermore, a strain ofM. smegmatisin which the alternative ribosome protein operon is deleted grows poorly in iron-depleted medium, uncovering a role for alternative ribosomes in iron homeostasis. Our work confirms the distinct and nonredundant contribution of alternative bacterial ribosomes for adaptation to hostile environments.

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Kim, Joon, Hag Dong Kim, and Hee Woong Yang. "HETEROGENEITY OF SENESCENT RIBOSOME COMPLEX AFFECTS THE TRANSLATIONAL EFFICIENCY OF SENESCENCE RELATED MRNAS." Innovation in Aging 3, Supplement_1 (November 2019): S100. http://dx.doi.org/10.1093/geroni/igz038.376.

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Abstract The ribosome, a protein factory, has a lateral stalk known as the ribosomal P complex made up of rpLP0, rpLP1, and rpLP2. It plays an important role in translation by recruiting translational factors. One of these proteins, rpLP2, was decreased in translating ribosome when cellular senescence was induced. Additionally, Y-box binding protein-1 (YB-1), a multifunctional protein that regulates the transcription and translation, was also reduced in polysomal fraction of senescent cells. We have discovered that rpLP2 depletion in heterogeneous ribosome causes the detachment of YB-1 in polysomes and link to cellular senescence. Here, we also have found that a decrement of CK2α or GRK2 on senescent cells induced an increment of unphosphorylated rpLP2, resulting in the release of YB-1 from a ribosome complex. The heterogeneous senescent ribosome has different translational efficiency for some senescence related genes such as AHR, RAB27B, FEZ1, and DDIT4. Our results revealed that the decrease of rpLP1/rpLP2 and YB-1 in translating senescent ribosomes is not specific to cell type or stress type. Furthermore, the same phenomenon was observed in aged mouse liver. Taken together, our results suggest that the senescent ribosome complex appears to have low levels of rpLP1/ rpLP2 and YB-1, resulting in the alteration of translational efficiency for senescence related genes. (Journals of Gerontology: Biological Sciences, 2019 in press)

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Giavalisco, Patrick, Daniel Wilson, Thomas Kreitler, Hans Lehrach, Joachim Klose, Johan Gobom, and Paola Fucini. "High heterogeneity within the ribosomal proteins of the Arabidopsis thaliana 80S ribosome." Plant Molecular Biology 57, no. 4 (March 2005): 577–91. http://dx.doi.org/10.1007/s11103-005-0699-3.

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Etter, A., V. Bernard, M. Kenzelmann, H. Tobler, and F. Muller. "Ribosomal heterogeneity from chromatin diminution in Ascaris lumbricoides." Science 265, no. 5174 (August 12, 1994): 954–56. http://dx.doi.org/10.1126/science.8052853.

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21

Ford, Dianne. "Ribosomal heterogeneity – A new inroad for pharmacological innovation." Biochemical Pharmacology 175 (May 2020): 113874. http://dx.doi.org/10.1016/j.bcp.2020.113874.

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22

Peterka, M., and G. Avguŝtin. "ribosomal RNA genes fromPrevotella bryantii: Organization and heterogeneity." Folia Microbiologica 46, no. 1 (February 2001): 67–70. http://dx.doi.org/10.1007/bf02825889.

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23

Fan, Wenjun, Eetu Eklund, Rachel M. Sherman, Hester Liu, Stephanie Pitts, Brittany Ford, N. V. Rajeshkumar, and Marikki Laiho. "Widespread genetic heterogeneity of human ribosomal RNA genes." RNA 28, no. 4 (February 2, 2022): 478–92. http://dx.doi.org/10.1261/rna.078925.121.

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Polymorphism drives survival under stress and provides adaptability. Genetic polymorphism of ribosomal RNA (rRNA) genes derives from internal repeat variation of this multicopy gene, and from interindividual variation. A considerable amount of rRNA sequence heterogeneity has been proposed but has been challenging to estimate given the scarcity of accurate reference sequences. We identified four rDNA copies on chromosome 21 (GRCh38) with 99% similarity to recently introduced reference sequence KY962518.1. We customized a GATK bioinformatics pipeline using the four rDNA loci, spanning a total 145 kb, for variant calling and used high-coverage whole-genome sequencing (WGS) data from the 1000 Genomes Project to analyze variants in 2504 individuals from 26 populations. We identified a total of 3791 variant positions. The variants positioned nonrandomly on the rRNA gene. Invariant regions included the promoter, early 5′ ETS, most of 18S, 5.8S, ITS1, and large areas of the intragenic spacer. A total of 470 variant positions were observed on 28S rRNA. The majority of the 28S rRNA variants were located on highly flexible human-expanded rRNA helical folds ES7L and ES27L, suggesting that these represent positions of diversity and are potentially under continuous evolution. Several variants were validated based on RNA-seq analyses. Population analyses showed remarkable ancestry-linked genetic variance and the presence of both high penetrance and frequent variants in the 5′ ETS, ITS2, and 28S regions segregating according to the continental populations. These findings provide a genetic view of rRNA gene array heterogeneity and raise the need to functionally assess how the 28S rRNA variants affect ribosome functions.

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Barna, Maria. "Specialized Ribosomes: A New Frontier in Gene Regulation, Organismal Biology, & Evolution." Blood 128, no. 22 (December 2, 2016): SCI—41—SCI—41. http://dx.doi.org/10.1182/blood.v128.22.sci-41.sci-41.

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Abstract The central dogma of molecular biology has for decades served as an explanation for the flow of genetic information within a biological system. In so far as the normal flow of biological information from mRNA to protein, the ribosome has been perceived to decode the genome with essentially machine-like precision; serving as an integral but largely passive participant in the synthesis of all effector proteins across all kingdoms of life. Importantly, a large class of human diseases collectively known as 'ribosomopathies' are characterized by mutations in ribosome components that lead to devastating human conditions including bone marrow failure for which the underlying molecular basis remains poorly understood. In this respect, our research has changed the view that ribosomes carry out largely rote-like functions by demonstrating that not all of the millions of ribosomes within each cell are the same and that ribosome heterogeneity provides a novel means for diversity of the proteins that can be produced in specific cells, tissues, and organisms. I will present our work centered on providing a roadmap for the characterization of ribosome composition at a single cell level and during cellular differentiation. We employed a highly quantitative mass spectrometry-based approach to precisely quantify the abundance of each ribosomal protein (RP) as well as a large cohort of auxiliary ribosome associating factors belonging to actively translating ribosomes within embryonic stem cells. This led to the identification of a subset of ribosomes that are heterogeneous for RP composition. To further address the functional role of ribosome heterogeneity in translational control of the mammalian genome, we employed CRISPR/Cas9 to endogenously tag and purify heterogeneous ribosome populations. We then developed an adapted ribosome profiling method to precisely quantify and characterize the nature of mRNAs translated by distinct heterogenous ribosomes genome-wide. This led to the identification of subpools of transcripts, critical for key cellular processes including cell signaling, metabolism, growth, proliferation and survival, which are selectively translated by specific types of ribosomes. Most remarkably, there are specific metabolic pathways where almost every single component is selectively translated by specialized ribosomes demarcated by a single RP. I will further present recent findings on the mechanisms by which ribosome-mediated control of gene expression is encoded by structured RNA regulons within 5'UTRs. Together, these studies reveal a critical link between ribosome heterogeneity and specialized translational control of the mammalian genome, which adds an important layer of control to the post-transcriptional circuitry of gene regulation and may be critically perturbed in human diseases. Disclosures No relevant conflicts of interest to declare.

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25

Lilleorg, Silva, Kaspar Reier, Arto Pulk, Aivar Liiv, Triin Tammsalu, Lauri Peil, Jamie H. D. Cate, and Jaanus Remme. "Bacterial ribosome heterogeneity: Changes in ribosomal protein composition during transition into stationary growth phase." Biochimie 156 (January 2019): 169–80. http://dx.doi.org/10.1016/j.biochi.2018.10.013.

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26

Song, Xin-Ming, Arne Forsgren, and Håkan Janson. "Fragmentation heterogeneity of 23S ribosomal RNA in Haemophilus species." Gene 230, no. 2 (April 1999): 287–93. http://dx.doi.org/10.1016/s0378-1119(99)00063-3.

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27

Hernández-Hermenegildo, Ricardo A., Lilia Bernal, Laura V. Jiménez-Pérez, Irma Bernal-Lugo, and Estela Sánchez de Jiménez. "Ribosomal Heterogeneity of Maize Tissues: Insights of Biological Relevance." Plant Molecular Biology Reporter 36, no. 3 (June 2018): 491–99. http://dx.doi.org/10.1007/s11105-018-1080-4.

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28

ARISUE, N., T. HASHIMOTO, and H. YOSHIKAWA. "Sequence heterogeneity of the small subunit ribosomal RNA genes among Blastocystis isolates." Parasitology 126, no. 1 (January 2003): 1–9. http://dx.doi.org/10.1017/s0031182002002640.

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Genes encoding small subunit ribosomal RNA (SSUrRNA) of 16 Blastocystis isolates from humans and other animals were amplified by the polymerase chain reaction, and the corresponding fragments were cloned and sequenced. Alignment of these sequences with the previously reported ones indicated the presence of 7 different sequence patterns in the highly variable regions of the small subunit ribosomal RNA. Phylogenetic reconstruction analysis using Proteromonas lacertae as the outgroup clearly demonstrated that the 7 groups with the different sequence patterns are separated to form independent clades, 5 of which consisted of the Blastocystis isolates from both humans (B. hominis) and other animals. The presence of 3 higher order clades was also clearly supported in the phylogenetic tree. However, a relationship among the 4 groups including these 3 higher order clades was not settled with statistical confidence. The remarkable heterogeneity of small subunit ribosomal RNAs among different Blastocystis isolates found in this study confirmed, with sequence-based evidence, that these organisms are genetically highly divergent in spite of their morphological identity. The highly variable small subunit ribosomal RNA regions among the distinct groups will provide useful information for the development of group-specific diagnostic primers.

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29

Delany, Mary E., and Alex B. Krupkin. "Molecular characterization of ribosomal gene variation within and among NORs segregating in specialized populations of chicken." Genome 42, no. 1 (February 1, 1999): 60–71. http://dx.doi.org/10.1139/g98-110.

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The molecular organization of the 18S, 5.8S, and 28S ribosomal RNA gene repeat units, located at the single nucleolus organizer region (NOR) locus in the chicken, was investigated in genetically distinct populations of research and commercial chickens. Substantial gene repeat variation within and among NORs was documented. Intact ribosomal gene repeat size ranged from 11 kb to over 50 kb. Unique combinations of ribosomal genes, of different size, were specific to particular populations. It was determined that the basis for the ribosomal gene repeat size variation was intergenic spacer (IGS) length heterogeneity. Interestingly, in different populations, the location of the variation that contributes to length heterogeneity was specific to particular IGS subregions. In addition to IGS variation, an inbred line of Red Jungle Fowl exhibited coding region variation. Ribosomal gene copy number variation was also studied, and line averages ranged from 279 to 368. Average rDNA array size (a function of copy number and gene repeat length) was calculated for each of the populations and found to vary over a range of two megabases, from 5 to 7 Mb.Key words: rDNA, NOR, IGS, genetic variation, chicken.

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30

Fushimi, Hirotoshi, Katsuko Komatsu, Tsuneo Namba, and Masaharu Isobe. "Genetic Heterogeneity of Ribosomal RNA Gene andmatK Gene inPanax notoginseng." Planta Medica 66, no. 7 (October 2000): 659–61. http://dx.doi.org/10.1055/s-2000-8636.

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31

Spalter, Rachael A., David Walsh, Rosalind A. Reeves, David J. Saul, Russell D. Gray, Peter L. Bergquist, Lincoln Mackenzie, and Patricia R. Bergquist. "Sequence heterogeneity of the ribosomal RNA intergenic region Alexandrium species." Biochemical Systematics and Ecology 25, no. 3 (April 1997): 231–39. http://dx.doi.org/10.1016/s0305-1978(96)00111-1.

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32

Kelly, Robert J., Robert D. Johnson, and Albert Siegel. "Heterogeneity and organization of the ribosomal RNA genes ofCucurbita maxima." Plant Molecular Biology 14, no. 6 (June 1990): 927–33. http://dx.doi.org/10.1007/bf00019390.

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33

van de Waterbeemd, Michiel, Kyle L. Fort, Dmitriy Boll, Maria Reinhardt-Szyba, Andrew Routh, Alexander Makarov, and Albert J. R. Heck. "High-fidelity mass analysis unveils heterogeneity in intact ribosomal particles." Nature Methods 14, no. 3 (January 23, 2017): 283–86. http://dx.doi.org/10.1038/nmeth.4147.

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34

Ochi, K. "Electrophoretic Heterogeneity of Ribosomal Protein AT-L30 among Actinomycete Genera." International Journal of Systematic Bacteriology 42, no. 1 (January 1, 1992): 144–50. http://dx.doi.org/10.1099/00207713-42-1-144.

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35

Carraway, M., S. Tzipori, and G. Widmer. "Identification of genetic heterogeneity in the Cryptosporidium parvum ribosomal repeat." Applied and environmental microbiology 62, no. 2 (1996): 712–16. http://dx.doi.org/10.1128/aem.62.2.712-716.1996.

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36

Simon, C. J., and N. F. Weeden. "Molecular Analysis and Cloning of Malus Ribosomal DNA." Journal of the American Society for Horticultural Science 117, no. 1 (January 1992): 164–68. http://dx.doi.org/10.21273/jashs.117.1.164.

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The ribosomal genes of the two crab apple (Malus) genotypes White Angel' and `Robusta 5' were characterized to determine the extent of between- and within-genotype heterogeneity. Initial investigations with a cloned sequence of soybean rDNA failed to detect some Malus intergenic spacer region fragments. An alternative probing method that used electrophoretically purified Malus rDNA was developed. Double-digests of total genomic DNA with combinations of 13 restriction endonucleases identified the positions of 35 restriction sites. Restriction site polymorphism was observed both between and within the crab apple genotypes. Ribosomal DNA from White Angel' was cloned in phage and plasmid vectors and mapped with 11 enzymes. The region of the spacer causing length heterogeneity was identified. These clones should be useful as genetic markers and for examining population dynamics and systematic of Malus and closely related taxa.

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37

Shireman, Jack, Eric Gauchat, Heather Eckart, Cheol Park, Anindita Basu, Sebastian Pott, and Atique Ahmed. "TMIC-32. PARALLEL SINGLE CELL NUCLEOSOME OCCUPANCY AND RNA SEQUENCING ON RECURRENT GBM." Neuro-Oncology 21, Supplement_6 (November 2019): vi254. http://dx.doi.org/10.1093/neuonc/noz175.1066.

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Abstract Nearly all patients diagnosed with Glioblastoma (GBM) will experience a fatal recurrence of the tumor. Thought to be in part driven by immense tumor heterogeneity it is important to explore the small subpopulations of tumor cells with in depth single cell sequencing pre and post therapy in order to understand recurrence. To this end, we created an experimental in vivo pipeline that allows us profile not only gene expression changes during therapy, but also epigenetic shifts due to methylation across the genome at the single cell level from a single tumor. Single Cell NomE-Seq libraries were created and correctly identified characteristic CTCF binding regions within DNase1 hypersensitivity regions when compared back to representative encode data sets. Primary tumors analyzed by single cell RNA sequencing showed enrichment for on average 5 significant principle components (St. Dev >2 verified by Elbow Plot). Comparatively, recurrent temozolomide (TMZ) exposed tumors averaged 10 significant principle components (St. Dev >2 verified by Elbow Plot) suggesting TMZ therapy causes tumors to diversify their gene expression profiles. For direct comparison samples were merged into a continuous data set and dimensional analysis with TSNE reduction (15 dimensions used) identified 6 unique clusters, with one cluster being over-represented by cells from recurrent, TMZ exposed mice. Gene Ontology analysis on expression values contained within in this cluster demonstrated significant enrichment for ribosome biogenesis/ribosomal structure, (p=2.87e-17) and mRNA catabolic processes (p=2.47e-30). Further, comparison to a similar data set gathered using cells in vitro culture conditions demonstrates superior intraturmoral heterogeneity from cells isolated freshly from the brains of mice as opposed to tissue culture, indicating the effectiveness of our model for assaying heterogeneity. Ultimately, these data illuminate possible new mechanisms for TMZ induced ribosomal modifications underlying intraturmoral heterogeneity in GBM and provide an expandable technique for further experimentation.

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38

Borkiewicz, Lidia, Mateusz Mołoń, Eliza Molestak, Przemysław Grela, Patrycja Horbowicz-Drożdżal, Leszek Wawiórka, and Marek Tchórzewski. "Functional Analysis of the Ribosomal uL6 Protein of Saccharomyces cerevisiae." Cells 8, no. 7 (July 13, 2019): 718. http://dx.doi.org/10.3390/cells8070718.

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The genome-wide duplication event observed in eukaryotes represents an interesting biological phenomenon, extending the biological capacity of the genome at the expense of the same genetic material. For example, most ribosomal proteins in Saccharomyces cerevisiae are encoded by a pair of paralogous genes. It is thought that gene duplication may contribute to heterogeneity of the translational machinery; however, the exact biological function of this event has not been clarified. In this study, we have investigated the functional impact of one of the duplicated ribosomal proteins, uL6, on the translational apparatus together with its consequences for aging of yeast cells. Our data show that uL6 is not required for cell survival, although lack of this protein decreases the rate of growth and inhibits budding. The uL6 protein is critical for the efficient assembly of the ribosome 60S subunit, and the two uL6 isoforms most likely serve the same function, playing an important role in the adaptation of translational machinery performance to the metabolic needs of the cell. The deletion of a single uL6 gene significantly extends the lifespan but only in cells with a high metabolic rate. We conclude that the maintenance of two copies of the uL6 gene enables the cell to cope with the high demands for effective ribosome synthesis.

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39

Fierro, J. F., F. Parra, L. M. Quiros, C. Hardisson, and J. A. Salas. "Heterogeneity of the ribosomal protein pattern in mycelium of Streptomyces species." FEMS Microbiology Letters 41, no. 3 (May 1987): 283–87. http://dx.doi.org/10.1111/j.1574-6968.1987.tb02212.x.

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40

Shippen-Lentz, Dorothy, Talat Afroze, and Anne Carmel Vezza. "Heterogeneity and expression of the Plasmodium falciparum 5.8S ribosomal RNA genes." Molecular and Biochemical Parasitology 38, no. 1 (January 1990): 113–20. http://dx.doi.org/10.1016/0166-6851(90)90211-4.

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41

La Volpe, Adriana, Antonio Simeone, Maurizio D'Esposito, Luigi Scotto, Vincenzo Fidanza, Antonietta de Falco, and Edoardo Boncinelli. "Molecular analysis of the heterogeneity region of the human ribosomal spacer." Journal of Molecular Biology 183, no. 2 (May 1985): 213–23. http://dx.doi.org/10.1016/0022-2836(85)90214-1.

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42

Ganley, Austen R. D., and Barry Scott. "Extraordinary Ribosomal Spacer Length Heterogeneity in a Neotyphodium Endophyte Hybrid: Implications for Concerted Evolution." Genetics 150, no. 4 (December 1, 1998): 1625–37. http://dx.doi.org/10.1093/genetics/150.4.1625.

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Abstract An extraordinary level of length heterogeneity was found in the ribosomal DNA (rDNA) of an asexual hybrid Neotyphodium grass endophyte, isolate Lp1. This hybrid Neotyphodium endophyte is an interspecific hybrid between two grass endophytes, Neotyphodium lolii, and a sexual form, Epichlöe typhina, and the length heterogeneity was not found in either of these progenitor species. The length heterogeneity in the hybrid is localized to the intergenic spacer (IGS) and is the result of copy-number variation of a tandemly repeated subrepeat class within the IGS, the 111-/119-bp subrepeats. Copy number variation of this subrepeat class appears to be a consequence of mitotic unequal crossing over that occurs between these subrepeats. This implies that unequal crossing over plays a role in the concerted evolution of the whole rDNA. Changes in the pattern of IGS length variants occurred in just two rounds of single-spore purification. Analysis of the IGS length heterogeneity revealed features that are unexpected in a simple model of unequal crossing over. Potential refinements of the molecular details of unequal crossing over are presented, and we also discuss evidence for a combination of homogenization mechanisms that drive the concerted evolution of the Lp1 rDNA.

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43

Ochi, K. "Heterogeneity of Ribosomal Proteins among Streptomyces Species and its Application to Identification." Microbiology 135, no. 10 (October 1, 1989): 2635–42. http://dx.doi.org/10.1099/00221287-135-10-2635.

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44

Cázares, Febe, Rebecca Manning-Cela, and Isaura Meza. "Heterogeneity of the ribosomal DNA episome in strains and species of Entamoeba." Molecular Microbiology 12, no. 4 (May 1994): 607–12. http://dx.doi.org/10.1111/j.1365-2958.1994.tb01047.x.

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45

Coenye, Tom, and Peter Vandamme. "Intragenomic heterogeneity between multiple 16S ribosomal RNA operons in sequenced bacterial genomes." FEMS Microbiology Letters 228, no. 1 (November 2003): 45–49. http://dx.doi.org/10.1016/s0378-1097(03)00717-1.

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46

Absi, M., J. P. La Vergne, A. Marzouki, F. Giraud, D. Rigal, A. M. Reboud, J. P. Reboud, and J. C. Monier. "Heterogeneity of ribosomal autoantibodies from human, murine and canine connective tissue diseases." Immunology Letters 23, no. 1 (November 1989): 35–41. http://dx.doi.org/10.1016/0165-2478(89)90152-1.

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47

Kupriyanova, N. S., D. V. Shibalev, A. S. Voronov, and A. P. Ryskov. "Enhanced heterogeneity of the LR2 segment in the human ribosomal intergenic spacer." Gene 425, no. 1-2 (December 2008): 44–47. http://dx.doi.org/10.1016/j.gene.2008.08.009.

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48

Sugihara, Yoshihiko, Hiroki Honda, Tomoharu Iida, Takuma Morinaga, Shingo Hino, Tetsuya Okajima, Tsukasa Matsuda, and Daita Nadano. "Proteomic Analysis of Rodent Ribosomes Revealed Heterogeneity Including Ribosomal Proteins L10-like, L22-like 1, and L39-like." Journal of Proteome Research 9, no. 3 (March 5, 2010): 1351–66. http://dx.doi.org/10.1021/pr9008964.

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49

McCallum, F. S., and B. E. H Maden. "Human 18 S ribosomal RNA sequence inferred from DNA sequence. Variations in 18 S sequences and secondary modification patterns between vertebrates." Biochemical Journal 232, no. 3 (December 15, 1985): 725–33. http://dx.doi.org/10.1042/bj2320725.

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We have determined the DNA sequences encoding 18 S ribosomal RNA in man and in the frog, Xenopus borealis. We have also corrected the Xenopus laevis 18 S sequence: an A residue follows G-684 in the sequence. These and other available data provide a number of representative examples of variation in primary structure and secondary modification of 18 S ribosomal RNA between different groups of vertebrates. First, Xenopus laevis and Xenopus borealis 18 S ribosomal genes differ from each other by only two base substitutions, and we have found no evidence of intraspecies heterogeneity within the 18 S ribosomal DNA of Xenopus (in contrast to the Xenopus transcribed spacers). Second, the human 18 S sequence differs from that of Xenopus by approx. 6.5%. About 4% of the differences are single base changes; the remainder comprise insertions in the human sequence and other changes affecting several nucleotides. Most of these more extensive changes are clustered in a relatively short region between nucleotides 190 and 280 in the human sequence. Third, the human 18 S sequence differs from non-primate mammalian sequences by only about 1%. Fourth, nearly all of the 47 methyl groups in mammalian 18 S ribosomal RNA can be located in the sequence. The methyl group distribution corresponds closely to that in Xenopus, but there are several extra methyl groups in mammalian 18 S ribosomal RNA. Finally, minor revisions are made to the estimated numbers of pseudouridines in human and Xenopus 18 S ribosomal RNA.

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C., Paulina Uribe, Benjamin A. Suarez-Isla, and Romilio T. Espejo. "RIBOSOMAL RNA HETEROGENEITY AND IDENTIFICATION OF TOXIC DINOFLAGELLATE CULTURES BY HETERODUPLEX MOBILITY ASSAY." Journal of Phycology 35, no. 4 (August 1999): 884–88. http://dx.doi.org/10.1046/j.1529-8817.1999.3540884.x.

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