Academic literature on the topic 'Ribosomal heterogeneity'

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

L'ischémie cardiaque, définie comme la baisse de perfusion sanguine d'une partie du cœur, soumet les cellules à différents stress induits par la baisse de l'apport en oxygène et nutriments. S'ils perdurent, ces stress induisent la mort cellulaire et par la suite un infarctus du myocarde. Afin de rétablir l'homéostasie tissulaire et de revasculariser le tissu ischémique, les cellules activent différents mécanismes tels que l'angiogenèse et la lymphangiogenèse. Mon projet de thèse a porté sur l'étude de ces voies et leur régulation au niveau traductionnel dans des cardiomyocytes soumis à différents stress. L'analyse semi-globale du transcriptome et du traductome en condition hypoxique nous a montré que, dans les cardiomyocytes, les gènes (lymph)angiogéniques sont majoritairement régulés au niveau traductionnel. Parmi ces gènes, ceux possédant des structures IRES (Internal Ribosome Entry Site) sont recrutés de manière plus efficace dans les polysomes. Or, la régulation de la traduction via ces structures représente un mécanisme-clé dans la réponse à l'hypoxie. Nous avons identifié une protéine, la vasohibine 1, liée à l'ARN et présentant lors de l'hypoxie une fonction d'ITAF (IRES Trans-Acting Factor). Dans un deuxième volet de cette thèse, nous avons caractérisé le rôle d'un long ARN non codant, Neat1, dans la régulation de la traduction IRES dépendante en réponse à l'hypoxie. Neat1 est le composant principal d'un corps nucléaire, le paraspeckle, qui se forme en réponse au stress. Le paraspeckle est formé de Neat1 et de plusieurs protéines qui interagissent avec ce long ARNnc, dont certaines présentent aussi une fonction d'ITAF, suggérant un rôle du paraspeckle dans le contrôle de la traduction. Ainsi nous avons identifié par des expériences de déplétion que Neat1, plus particulièrement sa grande isoforme Neat1-2, possède un rôle d'ITAF qui régule tous les IRES des facteurs (lymph)angiogéniques. D'autres composants du paraspeckle, p54nrb et pSPC1, régulent différents sous-groupes d'ARNm à IRES. L'analyse de l'intéractome de p54nrb a permis d'identifier de nouveaux partenaires nucléaires et cytoplasmiques de cette protéine, spécifiques de l'hypoxie, dont la protéine ribosomique uS5 (RPS2) et la nucléoline, qui présentent elles aussi une fonction d'ITAF. Ces résultats suggèrent que le paraspeckle pourrait être une plateforme d'assemblage de l'IRESome, complexe responsable de la traduction IRES-dépendante, dont Neat1 est un acteur majeur. Le troisième volet de ma thèse porte sur l'identification de ribosomes spécialisés responsables de la traduction IRES-dépendante lors du stress. L'analyse de la composition des polysomes de cardiomyocytes humains soumis à un stress du RE nous a permis de découvrir plusieurs protéines ribosomiques mitochondriales associées aux polysomes. Pour certaines d'entre elles cette association augmente significativement (MRPS15, MRPS12) alors que pour d'autres elle diminue lors du stress (MRPS35, MRPL52), appuyant le concept de ribosomes spécialisés. Nous avons par la suite confirmé l'interaction de MRPS15 avec le ribosome en réalisant des expériences de PLA (proximity ligation assay) et d'immunoprécipitations. De plus MRPS15 comporte une fraction cytoplasmique qui augmente en réponse au stress. [...]
Cardiac ischemia, defined as a blood perfusion diminution in a part of the heart, subjects cells to various stresses caused by oxygen and nutrient supply diminution. If they persist, these stresses induce cell death and subsequently myocardial infarction. In order to restore tissue homeostasis as well as the vascularization of ischemic tissue, cells activate various mechanisms such as angiogenesis and lymphangiogenesis. My thesis project focused on the study of these pathways and their regulation at the translational level in cardiomyocytes subjected to different stresses. The semi-global analysis of the transcriptome and the translatome in hypoxic condition showed us that angiogenic and lymphangiogenic genes are not drastically regulated at the transcriptional level while the majority of them are induced at the translational level in murine cardiomyocytes. Among these genes, those having IRES (Internal Ribosome Entry Site) structures are recruited more efficiently into polysomes. Regulation of translation through the presence of these structures is a key mechanism in the response to hypoxia. We have identified a protein, vasohibin 1, bound to FGF1 IRES and presenting during hypoxia an ITAF (IRES Trans-Acting Factor) function. In a second part of this thesis work, we characterized the key role of a long non-coding RNA, Neat1, in the regulation of IRES-dependent translation in response to hypoxia. Neat1 is the main component of a nuclear body, the paraspeckle, which forms in response to stress. The paraspeckle is made up of Neat1 and several proteins, that interact with this long ncRNA, and are also known to exhibit ITAF function, hence the hypothesis of a role of the paraspeckle in the control of translation. Thus we have identified by depletion experiments, that Neat1, more particularly the long isoform of this ncRNA, Neat1-2, has a role of ITAF promoting the IRES-dependent translation of angiogenic and lymphangiogenic factors. Other components of the paraspeckle, p54nrb and pSPC1, regulate different subgroups of IRESs. The analysis of the interactome of p54nrb by mass spectrometry allowed to identify new nuclear and cytoplasmic partner specific of hypoxia, among them the ribosomal protein uS5 (RPS2) and nucleolin, which both present an ITAF function. These results suggest that the paraspeckle could be an assembly platform for IRESome, a complex responsible for IRES-dependent translation, and that Neat1 is a key regulator of this mechanism. The third part of my thesis concerns the identification of specialized ribosomes involved in IRES-dependent translation during stress. Analysis of the composition of polysomes of human cardiomyocytes under endoplasmic reticulum (ER) stress allowed us to discover several mitochondrial ribosomal proteins associated with the polysomes. Cellular stresses induced a switch in polysome composition, inducing an increase of the association with some mitochondrial ribosomal proteins (MRPS12 and MRPS15) while others were decreased (MRPS35 and MRPL52). The rest of the study focused on MRPS15. First, experiments with PLA (proximity ligation assay) and immunoprecipitations from cytosolic and polysomal fractions confirmed the interaction of this mitochondrial protein with the ribosome. In addition, a cytoplasmic fraction of MRPS15 increases in response to stress. [...]

Les protéines sont responsables de pratiquement toutes les fonctions performées au sein du corps cellulaire et de ses alentours. Le contrôle de l’expression génique détermine l’abondance, la localisation et le moment de la production de protéines dans la cellule. Il s’agit de l’un des processus centraux à la régulation de la physiologie et du fonctionnement cellulaire. La moindre perte de balance dans ce complexe système engendre des conséquences majeures sur l’intégrité cellulaire, menant au développement de plusieurs maladies parfois incurables. La traduction de l’ARN messager en produit protéique constitue la dernière étape de l’expression génique. Elle est régulée de plusieurs façons, intrinsèques et extrinsèques à la séquence. Il s’agit également du processus cellulaire le plus coûteux en termes d’énergie. Le profilage des ribosomes (Ribo-Seq) figure parmi les récentes et prometteuses technologies ayant permis une meilleure étude des mécanismes de régulation de la traduction. Ces résultats contiennent toutefois la présence de variabilité et de bruits de nature infondée. Ce travail présente la mise en place d’une stratégie permettant la dissociation de signaux d’origine biologique de ceux ayant une origine technique. Ceci est effectué au travers de la mise en place de profiles consensus de densité ribosomale extrait d’une analyse comparative de plusieurs expériences de Ribo-Seq chez la levure (Saccharomyces cerevisiae). Les signaux biologiques dérivés par les profils consensus correspondent avec les signatures de pauses ribosomales connues, telles que les scores de repliements de l’ARNm et la charge des acides aminés. Épatamment, notre stratégie a également permis l’identification de séquences différentiellement transcrites (DT). Ces dernières jouent un rôle sur la cinétique de la phase d’élongation de la traduction, elles comportent notamment une surreprésentation de codons associés aux modifications des ARNs de transfert (tRNAs). Elles se retrouvent d’ailleurs impliquées dans le maintien de l’homéostase cellulaire, ayant une présence marquée chez des gènes prenants part aux mécanismes de biosynthèse de la macromolécule ribosomale ainsi que chez les ARNms aux sublocalisations cellulaires précises, notamment chez les mitochondries et le réticulum endoplasmique (ER). En plus de démontrer les possibilités de découvertes offertes par la technique du Ribo-Seq, cette étude présente une évidence de la nature dynamique et hétérogène du processus de traduction chez la cellule eucaryote. Elle démontre également le rôle de l’information directement encodée dans la séquence dans l’optimisation générale de l’homéostasie cellulaire.
Proteins are responsible for virtually all functions performed within and in the surroundings of a cell. The control of gene expression, which determines the amount, localisation and timing of protein production in the cell, is the central processes in the regulation of cellular physiology and function. Any disturbance in this complex system can generate important consequences on cellular integrity, sometimes leading to incurable diseases. The translation of messenger RNA into a protein product is the last step of the gene expression mechanism. It can be regulated in manifold ways, both intrinsically and extrinsically to the transcript sequence. It is also the costliest cellular process in terms of energy. Ribosome profiling (Ribo-Seq) is one of the recent and promising technologies making it possible to better study the mechanisms of translation regulation. Its results have however been shown to display variability in reproducibility and to contain noise of uncharted sources. This work presents the implementation of a strategy for dissociating signals of biological origin from those of technical origin. This is performed by the computation of a consensus profile of ribosomal density derived from a comparative analysis of several Ribo-Seq experiments in yeast (Saccharomyces cerevisiae). The biological signals derived by the consensus profiles correspond with signatures of known ribosomal pauses, such as mRNA folding strength and amino acid charges. Amazingly, our strategy also enabled the identification of differentially transcribed (DT) sequences. The latter have shown an over-representation of codons associated with modifications of transfer RNAs (tRNAs). They are also involved in the control of cellular homeostasis, exhibiting a marked presence in genes involved in ribosome biosynthesis as well as in mRNAs with precise translation sub-localization, particularly in mitochondria and the endoplasmic reticulum (ER). In addition to demonstrating the possibilities of discovery offered by the Ribo-Seq technique, this study also presents evidence of the dynamic and heterogeneous nature of the translation process in the eukaryotic cell. It also showcases its diverse regulatory mechanisms and the role of information directly encoded in the sequence in the general optimization of cellular homeostasis.

Trypanosoma cruzi, the etiological agent of Chagas disease, presents considerable heterogeneity among populations of isolates within the sylvatic and domestic cycle. This study aims to evaluate the genetic diversity of 14 isolates collected from specimens of Triatoma vitticeps from Triunfo, Conceição de Macabu, and Santa Maria Madalena cities (Rio de Janeiro—Brazil). By using PCR based on the mini-exon gene, all isolates showed a profile characteristic of bands zymodeme III and with a lower intensity characteristic of TcII. To verify possible hybrids among the strains analyzed, the polymorphisms analysis of the MSH2 gene was performed. HhaI restriction enzyme digestion products resulted in characteristic TcII fragments only, demonstrating the absence of hybrids strains. In our attempt to characterize isolation in accordance with the reclassification of T. cruzi into six new groups called DTUs (“discrete typing unit”), we genotyped the mitochondrial cytochrome oxidase subunit two gene, ribosomal RNA gen (24Sα rDNA), and the spliced leader intergenic region (SL-IR). This procedure showed that TcII, TcIII, and TcIV are circulating in this area. This highlights the diversity of parasites infecting specimens of T. vitticeps, emphasizing the habit of wild type and complexity of the region epidemiological study that presents potential mixed populations.