Статті в журналах: "Specialized ribosome"

1

Guo, Huili. "Specialized ribosomes and the control of translation." Biochemical Society Transactions 46, no. 4 (July 9, 2018): 855–69. http://dx.doi.org/10.1042/bst20160426.

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The control of translation is increasingly recognized as a major factor in determining protein levels in the cell. The ribosome — the cellular machine that mediates protein synthesis — is typically seen as a key, but invariant, player in this process. This is because translational control is thought to be mediated by other auxiliary factors while ribosome recruitment is seen as the end-point of regulation. However, recent developments have made it clear that heterogeneous ribosome types can exist in different tissues, and more importantly, that these ribosomes can preferentially translate different subsets of mRNAs. In so doing, heterogeneous ribosomes could be key regulatory players in differentiation and development. Here, we examine current evidence for the existence of different ribosome types and how they might arise. In particular, we will take a close look at the mechanisms through which these ribosomes might mediate selective mRNA translation. We also summarize recently developed techniques/approaches that will aid in our understanding of the functions of such specialized ribosomes.

2

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.

3

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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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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Dalla Venezia, Nicole, Anne Vincent, Virginie Marcel, Frédéric Catez, and Jean-Jacques Diaz. "Emerging Role of Eukaryote Ribosomes in Translational Control." International Journal of Molecular Sciences 20, no. 5 (March 11, 2019): 1226. http://dx.doi.org/10.3390/ijms20051226.

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Translation is one of the final steps that regulate gene expression. The ribosome is the effector of translation through to its role in mRNA decoding and protein synthesis. Many mechanisms have been extensively described accounting for translational regulation. However it emerged only recently that ribosomes themselves could contribute to this regulation. Indeed, though it is well-known that the translational efficiency of the cell is linked to ribosome abundance, studies recently demonstrated that the composition of the ribosome could alter translation of specific mRNAs. Evidences suggest that according to the status, environment, development, or pathological conditions, cells produce different populations of ribosomes which differ in their ribosomal protein and/or RNA composition. Those observations gave rise to the concept of “specialized ribosomes”, which proposes that a unique ribosome composition determines the translational activity of this ribosome. The current review will present how technological advances have participated in the emergence of this concept, and to which extent the literature sustains this concept today.

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Baudin-Baillieu, Agnès, and Olivier Namy. "Saccharomyces cerevisiae, a Powerful Model for Studying rRNA Modifications and Their Effects on Translation Fidelity." International Journal of Molecular Sciences 22, no. 14 (July 10, 2021): 7419. http://dx.doi.org/10.3390/ijms22147419.

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Ribosomal RNA is a major component of the ribosome. This RNA plays a crucial role in ribosome functioning by ensuring the formation of the peptide bond between amino acids and the accurate decoding of the genetic code. The rRNA carries many chemical modifications that participate in its maturation, the formation of the ribosome and its functioning. In this review, we present the different modifications and how they are deposited on the rRNA. We also describe the most recent results showing that the modified positions are not 100% modified, which creates a heterogeneous population of ribosomes. This gave rise to the concept of specialized ribosomes that we discuss. The knowledge accumulated in the yeast Saccharomyces cerevisiae is very helpful to better understand the role of rRNA modifications in humans, especially in ribosomopathies.

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Leclerc, Daniel, and Léa Brakier-Gingras. "Study of the function of Escherichia coli ribosomal RNA through site-directed mutagenesis." Biochemistry and Cell Biology 68, no. 1 (January 1, 1990): 169–79. http://dx.doi.org/10.1139/o90-023.

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Various approaches have been developed to study how mutations in Escherichia coli ribosomal RNA affect the function of the ribosome. Most of them are in vivo approaches, where mutations are introduced in a specialized plasmid harboring the ribosomal RNA genes. The mutated plasmids are then expressed in an appropriate host, where they can confer resistance to antibiotics whose target is the ribosome. Conditions can be used where the host ribosomal RNA genes or the host ribosomes are selectively inactivated, and the effect of the mutations on ribosome assembly and function can be studied. Another approach, which has been developed mainly with 16S ribosomal RNA, can be used entirely in vitro. In this approach, a plasmid has been constructed which contains the 16S ribosomal RNA gene under control of a T7 promoter. Mutations can be introduced in the 16S ribosomal RNA sequence and the mutated 16S ribosomal RNAs are produced by in vitro transcription. It is then possible to investigate how the mutations affect the assembly of the 16S ribosomal RNA into 30S subunits and the activity of the reconstituted 30S subunits in cell-free protein synthesis assays. Although these approaches are recent, they have already provided a large body of interesting information, relating specific RNA sequences to interactions with ribosomal proteins, to ribosome function, and to its response to antibiotics.Key words: ribosomal RNA, ribosome, site-directed mutagenesis, antibiotic resistance.

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Kampen, Kim R., Sergey O. Sulima, Stijn Vereecke, and Kim De Keersmaecker. "Hallmarks of ribosomopathies." Nucleic Acids Research 48, no. 3 (July 27, 2019): 1013–28. http://dx.doi.org/10.1093/nar/gkz637.

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Abstract Ribosomopathies are diseases caused by defects in ribosomal constituents or in factors with a role in ribosome assembly. Intriguingly, congenital ribosomopathies display a paradoxical transition from early symptoms due to cellular hypo-proliferation to an elevated cancer risk later in life. Another association between ribosome defects and cancer came into view after the recent discovery of somatic mutations in ribosomal proteins and rDNA copy number changes in a variety of tumor types, giving rise to somatic ribosomopathies. Despite these clear connections between ribosome defects and cancer, the molecular mechanisms by which defects in this essential cellular machinery are oncogenic only start to emerge. In this review, the impact of ribosomal defects on the cellular function and their mechanisms of promoting oncogenesis are described. In particular, we discuss the emerging hallmarks of ribosomopathies such as the appearance of ‘onco-ribosomes’ that are specialized in translating oncoproteins, dysregulation of translation-independent extra-ribosomal functions of ribosomal proteins, rewired cellular protein and energy metabolism, and extensive oxidative stress leading to DNA damage. We end by integrating these findings in a model that can provide an explanation how ribosomopathies could lead to the transition from hypo- to hyper-proliferation in bone marrow failure syndromes with elevated cancer risk.

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Wang, Xiangxiang, Zhiyong Yue, Feifei Xu, Sufang Wang, Xin Hu, Junbiao Dai, and Guanghou Zhao. "Coevolution of ribosomal RNA expansion segment 7L and assembly factor Noc2p specializes the ribosome biogenesis pathway between Saccharomyces cerevisiae and Candida albicans." Nucleic Acids Research 49, no. 8 (April 6, 2021): 4655–67. http://dx.doi.org/10.1093/nar/gkab218.

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Abstract Ribosomes of different species share an evolutionarily conserved core, exhibiting flexible shells formed partially by the addition of species-specific ribosomal RNAs (rRNAs) with largely unexplored functions. In this study, we showed that by swapping the Saccharomyces cerevisiae 25S rRNA genes with non-S. cerevisiae homologs, species-specific rRNA variations caused moderate to severe pre-rRNA processing defects. Specifically, rRNA substitution by the Candida albicans caused severe growth defects and deficient pre-rRNA processing. We observed that such defects could be attributed primarily to variations in expansion segment 7L (ES7L) and could be restored by an assembly factor Noc2p mutant (Noc2p-K384R). We showed that swapping ES7L attenuated the incorporation of Noc2p and other proteins (Erb1p, Rrp1p, Rpl6p and Rpl7p) into pre-ribosomes, and this effect could be compensated for by Noc2p-K384R. Furthermore, replacement of Noc2p with ortholog from C. albicans could also enhance the incorporation of Noc2p and the above proteins into pre-ribosomes and consequently restore normal growth. Taken together, our findings help to elucidate the roles played by the species-specific rRNA variations in ribosomal biogenesis and further provide evidence that coevolution of rRNA expansion segments and cognate assembly factors specialized the ribosome biogenesis pathway, providing further insights into the function and evolution of ribosome.

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Skorski, Patricia, Prune Leroy, Olivier Fayet, Marc Dreyfus, and Sylvie Hermann-Le Denmat. "The Highly Efficient Translation Initiation Region from the Escherichia coli rpsA Gene Lacks a Shine-Dalgarno Element." Journal of Bacteriology 188, no. 17 (September 1, 2006): 6277–85. http://dx.doi.org/10.1128/jb.00591-06.

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ABSTRACT The translational initiation region (TIR) of the Escherichia coli rpsA gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position −91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD. Here, we have tested this hypothesis with the “specialized ribosome” approach. Depending upon the constructs used, translation initiation was decreased three- to sevenfold upon changing the conserved GGA to CCU. However, although chemical probing showed that the mutated trinucleotides were accessible, no restoration was observed when the ribosome anti-SD was symmetrically changed from CCUCC to GGAGG. When the same change was introduced in the SD from a conventional TIR as a control, activity was stimulated. This result suggests that the GGA trinucleotides do not form a discontinuous SD. Others hypotheses that may account for their role are discussed. Curiously, we also find that, when expressed at moderate level (30 to 40% of total ribosomes), specialized ribosomes are only twofold disadvantaged over normal ribosomes for the translation of bulk cellular mRNAs. These findings suggest that, under these conditions, the SD-anti-SD interaction plays a significant but not essential role for the synthesis of bulk cellular proteins.

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Hillman, Gabrielle A., and Michael F. Henry. "The yeast protein Mam33 functions in the assembly of the mitochondrial ribosome." Journal of Biological Chemistry 294, no. 25 (May 3, 2019): 9813–29. http://dx.doi.org/10.1074/jbc.ra119.008476.

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Mitochondrial ribosomes are functionally specialized for the synthesis of several essential inner membrane proteins of the respiratory chain. Although remarkable progress has been made toward understanding the structure of mitoribosomes, the pathways and factors that facilitate their biogenesis remain largely unknown. The long unstructured domains of unassembled ribosomal proteins are highly prone to misfolding and often require dedicated chaperones to prevent aggregation. To date, chaperones that ensure safe delivery to the assembling ribosome have not been identified in the mitochondrion. In this study, a respiratory synthetic lethality screen revealed a role for an evolutionarily conserved mitochondrial matrix protein called Mam33 in Saccharomyces cerevisiae mitoribosome biogenesis. We found that the absence of Mam33 results in misassembled, aggregated ribosomes and a respiratory lethal phenotype in combination with other ribosome-assembly mutants. Using sucrose gradient sedimentation, native affinity purifications, in vitro binding assays, and SILAC-based quantitative proteomics, we found that Mam33 does not associate with the mature mitoribosome, but directly binds a subset of unassembled large subunit proteins. Based on these data, we propose that Mam33 binds specific mitoribosomal proteins to ensure proper assembly.

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Sarnow, P., R. C. Cevallos, and E. Jan. "Takeover of host ribosomes by divergent IRES elements." Biochemical Society Transactions 33, no. 6 (October 26, 2005): 1479–82. http://dx.doi.org/10.1042/bst0331479.

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The ribosome is the macromolecular machinery in the host cell for which all viruses have to compete. Early in infection, the viral mRNAs have to compete with the host for both the ribosomes and for the limited pool of eukaryotic initiation factors that are needed to facilitate the recruitment of ribosomes to both viral and cellular mRNAs. To circumvent this competition, certain viruses have evolved to recruit ribosomes to IRESs (internal ribosome entry sites), highly specialized RNA elements that are located at the 5′-end of the viral genomes. Here, we discuss how divergent IRES elements can recruit ribosomes and start protein synthesis with only a minimal set of eukaryotic translation initiation factors, and how this mode of translation initiation aids viral gene amplification during early onset of innate immune responses.

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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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Xue, Shifeng, and Maria Barna. "Cis-regulatory RNA elements that regulate specialized ribosome activity." RNA Biology 12, no. 10 (September 22, 2015): 1083–87. http://dx.doi.org/10.1080/15476286.2015.1085149.

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Shaikh, Arshad Ali, Louis-Felix Nothias, Santosh K. Srivastava, Pieter C. Dorrestein, and Kapil Tahlan. "Specialized Metabolites from Ribosome Engineered Strains of Streptomyces clavuligerus." Metabolites 11, no. 4 (April 13, 2021): 239. http://dx.doi.org/10.3390/metabo11040239.

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Bacterial specialized metabolites are of immense importance because of their medicinal, industrial, and agricultural applications. Streptomyces clavuligerus is a known producer of such compounds; however, much of its metabolic potential remains unknown, as many associated biosynthetic gene clusters are silent or expressed at low levels. The overexpression of ribosome recycling factor (frr) and ribosome engineering (induced rpsL mutations) in other Streptomyces spp. has been reported to increase the production of known specialized metabolites. Therefore, we used an overexpression strategy in combination with untargeted metabolomics, molecular networking, and in silico analysis to annotate 28 metabolites in the current study, which have not been reported previously in S. clavuligerus. Many of the newly described metabolites are commonly found in plants, further alluding to the ability of S. clavuligerus to produce such compounds under specific conditions. In addition, the manipulation of frr and rpsL led to different metabolite production profiles in most cases. Known and putative gene clusters associated with the production of the observed compounds are also discussed. This work suggests that the combination of traditional strain engineering and recently developed metabolomics technologies together can provide rapid and cost-effective strategies to further speed up the discovery of novel natural products.

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Cassaignau, Anaïs M. E., Lisa D. Cabrita, and John Christodoulou. "How Does the Ribosome Fold the Proteome?" Annual Review of Biochemistry 89, no. 1 (June 20, 2020): 389–415. http://dx.doi.org/10.1146/annurev-biochem-062917-012226.

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Folding of polypeptides begins during their synthesis on ribosomes. This process has evolved as a means for the cell to maintain proteostasis, by mitigating the risk of protein misfolding and aggregation. The capacity to now depict this cellular feat at increasingly higher resolution is providing insight into the mechanistic determinants that promote successful folding. Emerging from these studies is the intimate interplay between protein translation and folding, and within this the ribosome particle is the key player. Its unique structural properties provide a specialized scaffold against which nascent polypeptides can begin to form structure in a highly coordinated, co-translational manner. Here, we examine how, as a macromolecular machine, the ribosome modulates the intrinsic dynamic properties of emerging nascent polypeptide chains and guides them toward their biologically active structures.

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Prossliner, Thomas, Kristoffer Skovbo Winther, Michael Askvad Sørensen, and Kenn Gerdes. "Ribosome Hibernation." Annual Review of Genetics 52, no. 1 (November 23, 2018): 321–48. http://dx.doi.org/10.1146/annurev-genet-120215-035130.

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Protein synthesis consumes a large fraction of available resources in the cell. When bacteria encounter unfavorable conditions and cease to grow, specialized mechanisms are in place to ensure the overall reduction of costly protein synthesis while maintaining a basal level of translation. A number of ribosome-associated factors are involved in this regulation; some confer an inactive, hibernating state of the ribosome in the form of 70S monomers (RaiA; this and the following are based on Escherichia coli nomenclature) or 100S dimers (RMF and HPF homologs), and others inhibit translation at different stages in the translation cycle (RsfS, YqjD and paralogs, SRA, and EttA). Stationary phase cells therefore exhibit a complex array of different ribosome subpopulations that adjusts the translational capacity of the cell to the encountered conditions and ensures efficient reactivation of translation when conditions improve. Here, we review the current state of research regarding stationary phase-specific translation factors, in particular ribosome hibernation factors and other forms of translational regulation in response to stress conditions.

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Politz, Joan C., Laura B. Lewandowski, and Thoru Pederson. "Signal recognition particle RNA localization within the nucleolus differs from the classical sites of ribosome synthesis." Journal of Cell Biology 159, no. 3 (November 11, 2002): 411–18. http://dx.doi.org/10.1083/jcb.200208037.

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The nucleolus is the site of ribosome biosynthesis, but is now known to have other functions as well. In the present study we have investigated how the distribution of signal recognition particle (SRP) RNA within the nucleolus relates to the known sites of ribosomal RNA synthesis, processing, and nascent ribosome assembly (i.e., the fibrillar centers, the dense fibrillar component (DFC), and the granular component). Very little SRP RNA was detected in fibrillar centers or the DFC of the nucleolus, as defined by the RNA polymerase I–specific upstream binding factor and the protein fibrillarin, respectively. Some SRP RNA was present in the granular component, as marked by the protein B23, indicating a possible interaction with ribosomal subunits at a later stage of maturation. However, a substantial portion of SRP RNA was also detected in regions of the nucleolus where neither B23, UBF, or fibrillarin were concentrated. Dual probe in situ hybridization experiments confirmed that a significant fraction of nucleolar SRP RNA was not spatially coincident with 28S ribosomal RNA. These results demonstrate that SRP RNA concentrates in an intranucleolar location other than the classical stations of ribosome biosynthesis, suggesting that there may be nucleolar regions that are specialized for other functions.

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El Mortaji, Lamya, Sylvie Aubert, Eloïse Galtier, Christine Schmitt, Karine Anger, Yulia Redko, Yves Quentin, and Hilde De Reuse. "The Sole DEAD-Box RNA Helicase of the Gastric PathogenHelicobacter pyloriIs Essential for Colonization." mBio 9, no. 2 (March 27, 2018): e02071-17. http://dx.doi.org/10.1128/mbio.02071-17.

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ABSTRACTPresent in every kingdom of life, generally in multiple copies, DEAD-box RNA helicases are specialized enzymes that unwind RNA secondary structures. They play major roles in mRNA decay, ribosome biogenesis, and adaptation to cold temperatures. Most bacteria have multiple DEAD-box helicases that present both specialized and partially redundant functions. By using phylogenomics, we revealed that theHelicobactergenus, including the major gastric pathogenH. pylori, is among the exceptions, as it encodes a sole DEAD-box RNA helicase. InH. pylori, this helicase, designated RhpA, forms a minimal RNA degradosome together with the essential RNase, RNase J, a major player in the control of RNA decay. Here, we usedH. pylorias a model organism with a sole DEAD-box helicase and investigated the role of this helicase inH. pyloriphysiology, ribosome assembly, and duringin vivocolonization. Our data showed that RhpA is dispensable for growth at 37°C but crucial at 33°C, suggesting an essential role of the helicase in cold adaptation. Moreover, we found that a ΔrhpAmutant was impaired in motility and deficient in colonization of the mouse model. RhpA is involved in the maturation of 16S rRNA at 37°C and is associated with translating ribosomes. At 33°C, RhpA is, in addition, recruited to individual ribosomal subunits. Finally, via its role in the RNA degradosome, RhpA directs the regulation of the expression of its partner, RNase J. RhpA is thus a multifunctional enzyme that, inH. pylori, plays a central role in gene regulation and in the control of virulence.IMPORTANCEWe present the results of our study on the role of RhpA, the sole DEAD-box RNA helicase encoded by the major gastric pathogenHelicobacter pylori. We observed that all theHelicobacterspecies possess such a sole helicase, in contrast to most free-living bacteria. RhpA is not essential for growth ofH. pyloriunder normal conditions. However, deletion ofrhpAleads to a motility defect and to total inhibition of the ability ofH. pylorito colonize a mouse model. We also demonstrated that this helicase encompasses most of the functions of its specialized orthologs described so far. We found that RhpA is a key element of the bacterial adaptation to colder temperatures and plays a minor role in ribosome biogenesis. Finally, RhpA regulates transcription of thernjgene encoding RNase J, its essential partner in the minimalH. pyloriRNA degradosome, and thus plays a crucial role in the control of RNA decay.

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Caesar, Stefanie, Markus Greiner, and Gabriel Schlenstedt. "Kap120 Functions as a Nuclear Import Receptor for Ribosome Assembly Factor Rpf1 in Yeast." Molecular and Cellular Biology 26, no. 8 (April 15, 2006): 3170–80. http://dx.doi.org/10.1128/mcb.26.8.3170-3180.2006.

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ABSTRACT The nucleocytoplasmic exchange of macromolecules is mediated by receptors specialized in passage through the nuclear pore complex. The majority of these receptors belong to the importin β protein family, which has 14 members in Saccharomyces cerevisiae. Nine importins carry various cargos from the cytoplasm into the nucleus, whereas four exportins mediate nuclear export. Kap120 is the only receptor whose transport cargo has not been found previously. Here, we characterize Kap120 as an importin for the ribosome maturation factor Rpf1, which was identified in a two-hybrid screen. Kap120 binds directly to Rpf1 in vitro and is released by Ran-GTP. At least three parallel import pathways exist for Rpf1, since nuclear import is defective in strains with the importins Kap120, Kap114, and Nmd5 deleted. Both kap120 and rpf1 mutants accumulate large ribosomal subunits in the nucleus. The nuclear accumulation of 60S ribosomal subunits in kap120 mutants is abolished upon RPF1 overexpression, indicating that Kap120 does not function in the actual ribosomal export step but rather in import of ribosome maturation factors.

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SYDORSKYY, Yaroslav, David J. DILWORTH, Brendan HALLORAN, Eugene C. YI, Taras MAKHNEVYCH, Richard W. WOZNIAK, and John D. AITCHISON. "Nop53p is a novel nucleolar 60S ribosomal subunit biogenesis protein." Biochemical Journal 388, no. 3 (June 7, 2005): 819–26. http://dx.doi.org/10.1042/bj20041297.

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Ribosome biogenesis in Saccharomyces cerevisiae occurs primarily in a specialized nuclear compartment termed the nucleolus within which the rRNA genes are transcribed by RNA polymerase I into a large 35 S rRNA precursor. The ensuing association/dissociation and catalytic activity of numerous trans-acting protein factors, RNAs and ribosomal proteins ultimately leads to the maturation of the precursor rRNAs into 25, 5.8 and 18 S rRNAs and the formation of mature cytoplasmic 40 and 60 S ribosomal subunits. Although many components involved in ribosome biogenesis have been identified, our understanding of this essential cellular process remains limited. In the present study we demonstrate a crucial role for the previously uncharacterized nucleolar protein Nop53p (Ypl146p) in ribosome biogenesis. Specifically, Nop53p appears to be most important for biogenesis of the 60 S subunit. It physically interacts with rRNA processing factors, notably Cbf5p and Nop2p, and co-fractionates specifically with pre-60 S particles on sucrose gradients. Deletion or mutations within NOP53 cause significant growth defects and display significant 60 S subunit deficiencies, an imbalance in the 40 S:60 S ratio, as revealed by polysome profiling, and defects in progression beyond the 27 S stage of 25 S rRNA maturation during 60 S biogenesis.

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Kodiha, Mohamed, Hicham Mahboubi, Dusica Maysinger, and Ursula Stochaj. "Gold Nanoparticles Impinge on Nucleoli and the Stress Response in MCF7 Breast Cancer Cells." Nanobiomedicine 3 (January 1, 2016): 3. http://dx.doi.org/10.5772/62337.

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Cancer cells can take up gold nanoparticles of different morphologies. These particles interact with the plasma membrane and often travel to intracellular organelles. Among organelles, the nucleus is especially susceptible to the damage that is inflicted by gold nanoparticles. Located inside the nucleus, nucleoli are specialized compartments that transcribe ribosomal RNA genes, produce ribosomes and function as cellular stress sensors. Nucleoli are particularly prone to gold nanoparticle-induced injury. As such, small spherical gold nanoparticles and gold nanoflowers interfere with the transcription of ribosomal DNA. However, the underlying mechanisms are not fully understood. In this study, we examined the effects of gold nanoparticles on nucleolar proteins that are critical to ribosome biogenesis and other cellular functions. We show that B23/nucleophosmin, a nucleolar protein that is tightly linked to cancer, is significantly affected by gold nanoparticles. Furthermore, gold nanoparticles impinge on the cellular stress response, as they reduce the abundance of the molecular chaperone hsp70 and O-GlcNAc modified proteins in the nucleus and nucleoli. Together, our studies set the stage for the development of nanomedicines that target the nucleolus to eradicate proliferating cancer cells.

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Wood, Thomas K., and Steven W. Peretti. "Construction of a specialized-ribosome vector or cloned-gene expression inE. coli." Biotechnology and Bioengineering 38, no. 8 (October 20, 1991): 891–906. http://dx.doi.org/10.1002/bit.260380811.

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24

Praszkier, J., and A. J. Pittard. "Pseudoknot-Dependent Translational Coupling in repBA Genes of the IncB Plasmid pMU720 Involves Reinitiation." Journal of Bacteriology 184, no. 20 (October 15, 2002): 5772–80. http://dx.doi.org/10.1128/jb.184.20.5772-5780.2002.

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ABSTRACT Replication of the IncB miniplasmid pMU720 requires synthesis of the replication initiator protein, RepA, whose translation is coupled to that of a leader peptide, RepB. The unusual feature of this system is that translational coupling in repBA has to be activated by the formation of a pseudoknot immediately upstream of the repA Shine-Dalgarno sequence. A small antisense RNA, RNAI, controls replication of pMU720 by interacting with repBA mRNA to inhibit expression of repA both directly, by preventing formation of the pseudoknot, and indirectly, by inhibiting translation of repB. The mechanism of translational coupling in repBA was investigated using the specialized ribosome system, which directs a subpopulation of ribosomes that carry an altered anti-Shine-Dalgarno sequence to translate mRNA molecules whose Shine-Dalgarno sequences have been altered to be complementary to the mutant anti-Shine-Dalgarno sequence. Our data indicate that translation of repA involves reinitiation by the ribosome that has terminated translation of repB. The role of the pseudoknot in this process and its effect on the control of copy number in pMU720 are discussed.

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Inada, Toshifumi. "Quality controls induced by aberrant translation." Nucleic Acids Research 48, no. 3 (January 17, 2020): 1084–96. http://dx.doi.org/10.1093/nar/gkz1201.

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Abstract During protein synthesis, translating ribosomes encounter many challenges imposed by various types of defective mRNAs that can lead to reduced cellular fitness and, in some cases, even threaten cell viability. Aberrant translation leads to activation of one of several quality control pathways depending on the nature of the problem. These pathways promote the degradation of the problematic mRNA as well as the incomplete translation product, the nascent polypeptide chain. Many of these quality control systems feature critical roles for specialized regulatory factors that work in concert with conventional factors. This review focuses on the mechanisms used by these quality control pathways to recognize aberrant ribosome stalling and discusses the conservation of these systems.

26

Hui, A., and H. A. de Boer. "Specialized ribosome system: preferential translation of a single mRNA species by a subpopulation of mutated ribosomes in Escherichia coli." Proceedings of the National Academy of Sciences 84, no. 14 (July 1, 1987): 4762–66. http://dx.doi.org/10.1073/pnas.84.14.4762.

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27

Nguyen, Fabian, Agata L. Starosta, Stefan Arenz, Daniel Sohmen, Alexandra Dönhöfer, and Daniel N. Wilson. "Tetracycline antibiotics and resistance mechanisms." Biological Chemistry 395, no. 5 (May 1, 2014): 559–75. http://dx.doi.org/10.1515/hsz-2013-0292.

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AbstractThe ribosome and protein synthesis are major targets within the cell for inhibition by antibiotics, such as the tetracyclines. The tetracycline family of antibiotics represent a large and diverse group of compounds, ranging from the naturally produced chlortetracycline, introduced into medical usage in the 1940s, to second and third generation semi-synthetic derivatives of tetracycline, such as doxycycline, minocycline and more recently the glycylcycline tigecycline. Here we describe the mode of interaction of tetracyclines with the ribosome and mechanism of action of this class of antibiotics to inhibit translation. Additionally, we provide an overview of the diverse mechanisms by which bacteria obtain resistance to tetracyclines, ranging from efflux, drug modification, target mutation and the employment of specialized ribosome protection proteins.

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Hui, A. S., D. H. Eaton, and H. A. de Boer. "Mutagenesis at the mRNA decoding site in the 16S ribosomal RNA using the specialized ribosome system in Escherichia coli." EMBO Journal 7, no. 13 (December 1988): 4383–88. http://dx.doi.org/10.1002/j.1460-2075.1988.tb03337.x.

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29

Huang, Yi-Shuian, and Wen-Hsin Lu. "Decoding hidden messages in neurons: insights from epitranscriptome-controlled and specialized ribosome-controlled translation." Current Opinion in Neurobiology 48 (February 2018): 64–70. http://dx.doi.org/10.1016/j.conb.2017.10.018.

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30

Huang, Wendi, Yunchao Ling, Sirui Zhang, Qiguang Xia, Ruifang Cao, Xiaojuan Fan, Zhaoyuan Fang, Zefeng Wang, and Guoqing Zhang. "TransCirc: an interactive database for translatable circular RNAs based on multi-omics evidence." Nucleic Acids Research 49, no. D1 (October 19, 2020): D236—D242. http://dx.doi.org/10.1093/nar/gkaa823.

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Abstract TransCirc (https://www.biosino.org/transcirc/) is a specialized database that provide comprehensive evidences supporting the translation potential of circular RNAs (circRNAs). This database was generated by integrating various direct and indirect evidences to predict coding potential of each human circRNA and the putative translation products. Seven types of evidences for circRNA translation were included: (i) ribosome/polysome binding evidences supporting the occupancy of ribosomes onto circRNAs; (ii) experimentally mapped translation initiation sites on circRNAs; (iii) internal ribosome entry site on circRNAs; (iv) published N-6-methyladenosine modification data in circRNA that promote translation initiation; (v) lengths of the circRNA specific open reading frames; (vi) sequence composition scores from a machine learning prediction of all potential open reading frames; (vii) mass spectrometry data that directly support the circRNA encoded peptides across back-splice junctions. TransCirc provides a user-friendly searching/browsing interface and independent lines of evidences to predicte how likely a circRNA can be translated. In addition, several flexible tools have been developed to aid retrieval and analysis of the data. TransCirc can serve as an important resource for investigating the translation capacity of circRNAs and the potential circRNA-encoded peptides, and can be expanded to include new evidences or additional species in the future.

31

Leipold, Robert J., and Prasad Dhurjati. "Construction and characterization of a specialized ribosome system for the overproduction of proteins in Escherichia coli." Biotechnology Progress 9, no. 4 (July 1993): 345–54. http://dx.doi.org/10.1021/bp00022a001.

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32

Wu, X. Q., P. Iyengar, and U. L. RajBhandary. "Ribosome-initiator tRNA complex as an intermediate in translation initiation in Escherichia coli revealed by use of mutant initiator tRNAs and specialized ribosomes." EMBO Journal 15, no. 17 (September 1996): 4734–39. http://dx.doi.org/10.1002/j.1460-2075.1996.tb00850.x.

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33

Pichon, Xavier, Amandine Bastide, Adham Safieddine, Racha Chouaib, Aubin Samacoits, Eugenia Basyuk, Marion Peter, Florian Mueller, and Edouard Bertrand. "Visualization of single endogenous polysomes reveals the dynamics of translation in live human cells." Journal of Cell Biology 214, no. 6 (September 5, 2016): 769–81. http://dx.doi.org/10.1083/jcb.201605024.

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Translation is an essential step in gene expression. In this study, we used an improved SunTag system to label nascent proteins and image translation of single messenger ribonucleoproteins (mRNPs) in human cells. Using a dedicated reporter RNA, we observe that translation of single mRNPs stochastically turns on and off while they diffuse through the cytoplasm. We further measure a ribosome density of 1.3 per kilobase and an elongation rate of 13–18 amino acids per second. Tagging the endogenous POLR2A gene revealed similar elongation rates and ribosomal densities and that nearly all messenger RNAs (mRNAs) are engaged in translation. Remarkably, tagging of the heavy chain of dynein 1 (DYNC1H1) shows this mRNA accumulates in foci containing three to seven RNA molecules. These foci are translation sites and thus represent specialized translation factories. We also observe that DYNC1H1 polysomes are actively transported by motors, which may deliver the mature protein at appropriate cellular locations. The SunTag should be broadly applicable to study translational regulation in live single cells.

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Lee, A. S. Y., R. Burdeinick-Kerr, and S. P. J. Whelan. "A ribosome-specialized translation initiation pathway is required for cap-dependent translation of vesicular stomatitis virus mRNAs." Proceedings of the National Academy of Sciences 110, no. 1 (November 19, 2012): 324–29. http://dx.doi.org/10.1073/pnas.1216454109.

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35

Iborra, F. J., D. A. Jackson, and P. R. Cook. "The path of RNA through nuclear pores: apparent entry from the sides into specialized pores." Journal of Cell Science 113, no. 2 (January 15, 2000): 291–302. http://dx.doi.org/10.1242/jcs.113.2.291.

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The path that RNA takes through nuclear pores was mapped using two high-resolution techniques. Unexpectedly, no RNA in HL60 cells was detected by immunogold labelling in the central axis of the pore complex on its way to the transporter at the nuclear membrane; instead, it was distributed around the sides, apparently entering just before the membrane. In rat liver nuclei, poly(A)(+) RNA, hnRNPs A1 and C, mrnp 41, ASF, and a phosphorylated subset of SR proteins were also distributed like mRNA, as were various transport factors and their cargoes (NTF2, Ran, RCC1, karyopherin (beta), Rch1, transportin (alpha), m(2,2,7)-trimethylG). Many pores were associated with particular transport factors/cargoes to the exclusion of others; some were associated with poly(A)(+) RNA or phosphorylated SR proteins (but not NTF2), others with NTF2 (but not poly(A)(+) RNA or the SR proteins). Electron spectroscopic imaging confirmed these results. Some pores contained phosphorus-rich RNA apparently entering from the sides; others lacked any phosphorus, and were surrounded by a ribosome-free zone in the cytoplasm. The results also suggest that pores have different functional zones where SR proteins are dephosphorylated, and where hnRNP C is removed from messages.

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Martínez-Salas, Encarnación, Almudena Pacheco, Paula Serrano, and Noemi Fernandez. "New insights into internal ribosome entry site elements relevant for viral gene expression." Journal of General Virology 89, no. 3 (March 1, 2008): 611–26. http://dx.doi.org/10.1099/vir.0.83426-0.

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A distinctive feature of positive-strand RNA viruses is the presence of high-order structural elements at the untranslated regions (UTR) of the genome that are essential for viral RNA replication. The RNA of all members of the family Picornaviridae initiate translation internally, via an internal ribosome entry site (IRES) element present in the 5′ UTR. IRES elements consist of cis-acting RNA structures that usually require specific RNA-binding proteins for translational machinery recruitment. This specialized mechanism of translation initiation is shared with other viral RNAs, e.g. from hepatitis C virus and pestivirus, and represents an alternative to the cap-dependent mechanism. In cells infected with many picornaviruses, proteolysis or changes in phosphorylation of key host factors induces shut off of cellular protein synthesis. This event occurs simultaneously with the synthesis of viral gene products since IRES activity is resistant to the modifications of the host factors. Viral gene expression and RNA replication in positive-strand viruses is further stimulated by viral RNA circularization, involving direct RNA–RNA contacts between the 5′ and 3′ ends as well as RNA-binding protein bridges. In this review, we discuss novel insights into the mechanisms that control picornavirus gene expression and compare them to those operating in other positive-strand RNA viruses.

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Lombardi, Silvia, Maria Francesca Testa, Mirko Pinotti, and Alessio Branchini. "Molecular Insights into Determinants of Translational Readthrough and Implications for Nonsense Suppression Approaches." International Journal of Molecular Sciences 21, no. 24 (December 11, 2020): 9449. http://dx.doi.org/10.3390/ijms21249449.

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The fidelity of protein synthesis, a process shaped by several mechanisms involving specialized ribosome regions and external factors, ensures the precise reading of sense and stop codons. However, premature termination codons (PTCs) arising from mutations may, at low frequency, be misrecognized and result in PTC suppression, named ribosome readthrough, with production of full-length proteins through the insertion of a subset of amino acids. Since some drugs have been identified as readthrough inducers, this fidelity drawback has been explored as a therapeutic approach in several models of human diseases caused by nonsense mutations. Here, we focus on the mechanisms driving translation in normal and aberrant conditions, the potential fates of mRNA in the presence of a PTC, as well as on the results obtained in the research of efficient readthrough-inducing compounds. In particular, we describe the molecular determinants shaping the outcome of readthrough, namely the nucleotide and protein context, with the latter being pivotal to produce functional full-length proteins. Through the interpretation of experimental and mechanistic findings, mainly obtained in lysosomal and coagulation disorders, we also propose a scenario of potential readthrough-favorable features to achieve relevant rescue profiles, representing the main issue for the potential translatability of readthrough as a therapeutic strategy.

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Mokas, Sophie, John R. Mills, Cristina Garreau, Marie-Josée Fournier, Francis Robert, Prabhat Arya, Randal J. Kaufman, Jerry Pelletier, and Rachid Mazroui. "Uncoupling Stress Granule Assembly and Translation Initiation Inhibition." Molecular Biology of the Cell 20, no. 11 (June 2009): 2673–83. http://dx.doi.org/10.1091/mbc.e08-10-1061.

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Cytoplasmic stress granules (SGs) are specialized regulatory sites of mRNA translation that form under different stress conditions known to inhibit translation initiation. The formation of SG occurs via two pathways; the eukaryotic initiation factor (eIF) 2α phosphorylation-dependent pathway mediated by stress and the eIF2α phosphorylation-independent pathway mediated by inactivation of the translation initiation factors eIF4A and eIF4G. In this study, we investigated the effects of targeting different translation initiation factors and steps in SG formation in HeLa cells. By depleting eIF2α, we demonstrate that reduced levels of the eIF2.GTP.Met-tRNAiMet ternary translation initiation complexes is sufficient to induce SGs. Likewise, reduced levels of eIF4B, eIF4H, or polyA-binding protein, also trigger SG formation. In contrast, depletion of the cap-binding protein eIF4E or preventing its assembly into eIF4F results in modest SG formation. Intriguingly, interfering with the last step of translation initiation by blocking the recruitment of 60S ribosome either with 2-(4-methyl-2,6-dinitroanilino)-N-methylpropionamideis or through depletion of the large ribosomal subunits protein L28 does not induce SG assembly. Our study identifies translation initiation steps and factors involved in SG formation as well as those that can be targeted without induction of SGs.

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Vertel, B. M., A. Velasco, S. LaFrance, L. Walters, and K. Kaczman-Daniel. "Precursors of chondroitin sulfate proteoglycan are segregated within a subcompartment of the chondrocyte endoplasmic reticulum." Journal of Cell Biology 109, no. 4 (October 1, 1989): 1827–36. http://dx.doi.org/10.1083/jcb.109.4.1827.

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Immunocytochemical methods were used at the levels of light and electron microscopy to examine the intracellular compartments of chondrocytes involved in extracellular matrix biosynthesis. The results of our studies provide morphological evidence for the compartmentalization of secretory proteins in the ER. Precursors of the large chondroitin sulfate proteoglycan (CSPG), the major proteoglycan species produced by chondrocytes, were present in the Golgi complex. In addition, CSPG precursors were localized in specialized regions of the ER. Link protein, a separate gene product which functions to stabilize extracellular aggregates of CSPG monomers with hyaluronic acid, was segregated similarly. In contrast, type II procollagen, another major secretory molecule produced by chondrocytes, was found homogeneously distributed throughout the ER. The CSPG precursor-containing ER compartment exhibits a variable tubulo-vesicular morphology but is invariably recognized as an electronlucent, smooth membrane-bounded region continuous with typical ribosome-studded elements of the rough ER. The observation that this ER structure does not stain with antibodies against resident ER proteins also suggests that the compartment is a specialized region distinct from the main part of the ER. These results support recent studies that consider the ER as a compartmentalized organelle and are discussed in light of the possible implications for proteoglycan biosynthesis and processing.

40

Thao, MyLo L., Nancy A. Moran, Patrick Abbot, Eric B. Brennan, Daniel H. Burckhardt, and Paul Baumann. "Cospeciation of Psyllids and Their Primary Prokaryotic Endosymbionts." Applied and Environmental Microbiology 66, no. 7 (July 1, 2000): 2898–905. http://dx.doi.org/10.1128/aem.66.7.2898-2905.2000.

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ABSTRACT Psyllids are plant sap-feeding insects that harbor prokaryotic endosymbionts in specialized cells within the body cavity. Four-kilobase DNA fragments containing 16S and 23S ribosomal DNA (rDNA) were amplified from the primary (P) endosymbiont of 32 species of psyllids representing three psyllid families and eight subfamilies. In addition, 0.54-kb fragments of the psyllid nuclear genewingless were also amplified from 26 species. Phylogenetic trees derived from 16S-23S rDNA and from the host winglessgene are very similar, and tests of compatibility of the data sets show no significant conflict between host and endosymbiont phylogenies. This result is consistent with a single infection of a shared psyllid ancestor and subsequent cospeciation of the host and the endosymbiont. In addition, the phylogenies based on DNA sequences generally agreed with psyllid taxonomy based on morphology. The 3′ end of the 16S rDNA of the P endosymbionts differs from that of other members of the domainBacteria in the lack of a sequence complementary to the mRNA ribosome binding site. The rate of sequence change in the 16S-23S rDNA of the psyllid P endosymbiont was considerably higher than that of other bacteria, including other fast-evolving insect endosymbionts. The lineage consisting of the P endosymbionts of psyllids was given the designation Candidatus Carsonella (gen. nov.) with a single species, Candidatus Carsonella ruddii (sp. nov.).

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Willis, Ian M., and Robyn D. Moir. "Signaling to and from the RNA Polymerase III Transcription and Processing Machinery." Annual Review of Biochemistry 87, no. 1 (June 20, 2018): 75–100. http://dx.doi.org/10.1146/annurev-biochem-062917-012624.

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RNA polymerase (Pol) III has a specialized role in transcribing the most abundant RNAs in eukaryotic cells, transfer RNAs (tRNAs), along with other ubiquitous small noncoding RNAs, many of which have functions related to the ribosome and protein synthesis. The high energetic cost of producing these RNAs and their central role in protein synthesis underlie the robust regulation of Pol III transcription in response to nutrients and stress by growth regulatory pathways. Downstream of Pol III, signaling impacts posttranscriptional processes affecting tRNA function in translation and tRNA cleavage into smaller fragments that are increasingly attributed with novel cellular activities. In this review, we consider how nutrients and stress control Pol III transcription via its factors and its negative regulator, Maf1. We highlight recent work showing that the composition of the tRNA population and the function of individual tRNAs is dynamically controlled and that unrestrained Pol III transcription can reprogram central metabolic pathways.

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Hendricks, L. C., M. McCaffery, G. E. Palade, and M. G. Farquhar. "Disruption of endoplasmic reticulum to Golgi transport leads to the accumulation of large aggregates containing beta-COP in pancreatic acinar cells." Molecular Biology of the Cell 4, no. 4 (April 1993): 413–24. http://dx.doi.org/10.1091/mbc.4.4.413.

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When transport between the rough endoplasmic reticulum (ER) and Golgi complex is blocked by Brefeldin A (BFA) treatment or ATP depletion, the Golgi apparatus and associated transport vesicles undergo a dramatic reorganization. Because recent studies suggest that coat proteins such as beta-COP play an important role in the maintenance of the Golgi complex, we have used immunocytochemistry to determine the distribution of beta-COP in pancreatic acinar cells (PAC) in which ER to Golgi transport was blocked by BFA treatment or ATP depletion. In controls, beta-COP was associated with Golgi cisternae and transport vesicles as expected. Upon BFA treatment, PAC Golgi cisternae are dismantled and replaced by clusters of remnant vesicles surrounded by typical ER transitional elements that are generally assumed to represent the exit site of vesicular carriers for ER to Golgi transport. In BFA-treated PAC, beta-COP was concentrated in large (0.5-1.0 micron) aggregates closely associated with remnant Golgi membranes. In addition to typical ER transitional elements, we detected a new type of transitional element that consists of specialized regions of rough ER (RER) with ribosome-free ends that touched or extended into the beta-COP containing aggregates. In ATP-depleted PAC, beta-COP was not detected on Golgi membranes but was concentrated in similar large aggregates found on the cis side of the Golgi stacks. The data indicate that upon arrest of ER to Golgi transport by either BFA treatment or energy depletion, beta-COP dissociates from PAC Golgi membranes and accumulates as large aggregates closely associated with specialized ER elements. The latter may correspond to either the site of entry or exit for vesicles recycling between the Golgi and the RER.

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Segev, Nadav, and Jeffrey E. Gerst. "Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins." Journal of Cell Biology 217, no. 1 (November 8, 2017): 117–26. http://dx.doi.org/10.1083/jcb.201706059.

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Genome duplication in eukaryotes created paralog pairs of ribosomal proteins (RPs) that show high sequence similarity/identity. However, individual paralogs can confer vastly different effects upon cellular processes, e.g., specific yeast paralogs regulate actin organization, bud site selection, and mRNA localization, although how specificity is conferred is unknown. Changes in the RP composition of ribosomes might allow for specialized translation of different subsets of mRNAs, yet it is unclear whether specialized ribosomes exist and if paralog specificity controls translation. Using translatome analyses, we show that the translation of mitochondrial proteins is highly down-regulated in yeast lacking RP paralogs required for normal mitochondrial function (e.g., RPL1b). Although RPL1a and RPL1b encode identical proteins, Rpl1b-containing ribosomes confer more efficient translation of respiration-related proteins. Thus, ribosomes varying in RP composition may confer specialized functions, and RP paralog specificity defines a novel means of translational control.

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Forester, Craig M., Zhen Shi, Maria Barna, and Davide Ruggero. "A Tailor-Made Protein Synthesis Program Drives Erythroid Development and Disease." Blood 126, no. 23 (December 3, 2015): 3581. http://dx.doi.org/10.1182/blood.v126.23.3581.3581.

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Abstract Erythropoiesis constitutes the largest demand on the hematopoietic system due to its extraordinary production on a daily basis. The erythroid proteome requires an integration of multiple external cues to coordinate programs of differentiation as well as maintenance of erythroid precursors. The biomedical relevance of this critical process is underscored by recent findings showing impaired ribosome function in an entire class of clinical disorders with severe impairments in erythroid differentiation, known as ribosomopathies, which remain poorly understood. One of the main signaling pathways controlling post-transcriptional gene expression during erythropoiesis is the mTOR pathway. mTOR activation downstream of SCF/Epo in erythroid progenitors controls the activity of the major cap-binding protein eIF4E. However, the functional role of eIF4E during erythropoiesis and protein synthesis control in this cell type remains unexplored. Here we show that eIF4E activity, through mTOR-dependent phosphorylation of its inhibitory protein 4EBP1, unexpectedly undergoes a dynamic switch between early erythroid precursor populations and during terminal erythrocyte maturation, where eIF4E becomes progressively silenced. Employing a unique eIF4E transgenic mouse model, we strikingly show that overexpression of eIF4E in the bone marrow compartment results in an early accumulation of erythrocyte precursors and a block in erythrocyte differentiation. Surprisingly, this new role of eIF4E in erythropoiesis is independent from control of global protein synthesis but instead may promote a specialized program of translation control that is customized for erythroid cell function. Employing state of the art unbiased proteomics, our work is uncovering distinct networks of proteins, whose expression levels are controlled by eIF4E dosage during specific phases of erythrocyte maturation. Together, our research highlights a novel molecular program linking exquisite regulation of eIF4E activity to specialized translational control underlying erythroid development, providing unprecedented insight into the etiology of erythroid dysfunction in ribosomopathies. Disclosures No relevant conflicts of interest to declare.

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Segev, Nadav, and Jeffrey E. Gerst. "Correction: Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins." Journal of Cell Biology 217, no. 3 (January 31, 2018): 1155. http://dx.doi.org/10.1083/jcb.20170605901292018c.

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46

Wang, Rejean L., Luning Sun, and Thomas W. O'Brien⁎. "Specialized ribosomes in mammalian mitochondria." Mitochondrion 11, no. 4 (July 2011): 673. http://dx.doi.org/10.1016/j.mito.2011.03.109.

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47

Leipold, Robert J., and Prasad Dhurjati. "Specialized ribosomes in Escherichia coli." Biotechnology Progress 9, no. 5 (September 1993): 443–49. http://dx.doi.org/10.1021/bp00023a001.

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48

Haag, Eric S., and Jonathan D. Dinman. "Still Searching for Specialized Ribosomes." Developmental Cell 48, no. 6 (March 2019): 744–46. http://dx.doi.org/10.1016/j.devcel.2019.03.005.

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49

Peterson, Bret N., Jonathan L. Portman, Ying Feng, Jeffrey Wang, and Daniel A. Portnoy. "Secondary structure of the mRNA encoding listeriolysin O is essential to establish the replicative niche ofL. monocytogenes." Proceedings of the National Academy of Sciences 117, no. 38 (September 2, 2020): 23774–81. http://dx.doi.org/10.1073/pnas.2004129117.

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Intracellular pathogens are responsible for an enormous amount of worldwide morbidity and mortality, and each has evolved specialized strategies to establish and maintain their replicative niche.Listeria monocytogenesis a facultative intracellular pathogen that secretes a pore-forming cytolysin called listeriolysin O (LLO), which disrupts the phagosomal membrane and, thereby, allows the bacteria access to their replicative niche in the cytosol. Nonsynonymous and synonymous mutations in a PEST-like domain near the LLO N terminus cause enhanced LLO translation during intracellular growth, leading to host cell death and loss of virulence. Here, we explore the mechanism of translational control and show that there is extensive codon restriction within the PEST-encoding region of the LLO messenger RNA (mRNA) (hly). This region has considerable complementarity with the 5′ UTR and is predicted to form an extensive secondary structure that overlaps the ribosome binding site. Analysis of both 5′ UTR and synonymous mutations in the PEST-like domain that are predicted to disrupt the secondary structure resulted in up to a 10,000-fold drop in virulence during mouse infection, while compensatory double mutants restored virulence to WT levels. We showed by dynamic protein radiolabeling that LLO synthesis was growth phase-dependent. These data provide a mechanism to explain how the bacteria regulate translation of LLO to promote translation during starvation in a phagosome while repressing it during growth in the cytosol. These studies also provide a molecular explanation for codon bias at the 5′ end of this essential determinant of pathogenesis.

50

Cleuren, Audrey C. A., Martijn A. van der Ent, Hui Jiang, Kristina L. Hunker, Andrew Yee, David R. Siemieniak, Grietje Molema, William C. Aird, Santhi K. Ganesh, and David Ginsburg. "The in vivo endothelial cell translatome is highly heterogeneous across vascular beds." Proceedings of the National Academy of Sciences 116, no. 47 (November 11, 2019): 23618–24. http://dx.doi.org/10.1073/pnas.1912409116.

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Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression after EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single-cell suspensions for fluorescence-activated cell sorting or single-cell RNA sequencing analysis. Comparison of our EC-TRAP with published single-cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole-tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole-tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.

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