Artículos de revistas: "Ribosomal RNAs"

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Lejars, Maxence, Asaki Kobayashi y Eliane Hajnsdorf. "RNase III, Ribosome Biogenesis and Beyond". Microorganisms 9, n.º 12 (17 de diciembre de 2021): 2608. http://dx.doi.org/10.3390/microorganisms9122608.

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The ribosome is the universal catalyst for protein synthesis. Despite extensive studies, the diversity of structures and functions of this ribonucleoprotein is yet to be fully understood. Deciphering the biogenesis of the ribosome in a step-by-step manner revealed that this complexity is achieved through a plethora of effectors involved in the maturation and assembly of ribosomal RNAs and proteins. Conserved from bacteria to eukaryotes, double-stranded specific RNase III enzymes play a large role in the regulation of gene expression and the processing of ribosomal RNAs. In this review, we describe the canonical role of RNase III in the biogenesis of the ribosome comparing conserved and unique features from bacteria to eukaryotes. Furthermore, we report additional roles in ribosome biogenesis re-enforcing the importance of RNase III.

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Moritz, M., A. G. Paulovich, Y. F. Tsay y J. L. Woolford. "Depletion of yeast ribosomal proteins L16 or rp59 disrupts ribosome assembly." Journal of Cell Biology 111, n.º 6 (1 de diciembre de 1990): 2261–74. http://dx.doi.org/10.1083/jcb.111.6.2261.

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Two strains of Saccharomyces cerevisiae were constructed that are conditional for synthesis of the 60S ribosomal subunit protein, L16, or the 40S ribosomal subunit protein, rp59. These strains were used to determine the effects of depriving cells of either of these ribosomal proteins on ribosome assembly and on the synthesis and stability of other ribosomal proteins and ribosomal RNAs. Termination of synthesis of either protein leads to diminished accumulation of the subunit into which it normally assembles. Depletion of L16 or rp59 has no effect on synthesis of most other ribosomal proteins or ribosomal RNAs. However, most ribosomal proteins and ribosomal RNAs that are components of the same subunit as L16 or rp59 are rapidly degraded upon depletion of L16 or rp59, presumably resulting from abortive assembly of the subunit. Depletion of L16 has no effect on the stability of most components of the 40S subunit. Conversely, termination of synthesis of rp59 has no effect on the stability of most 60S subunit components. The implications of these findings for control of ribosome assembly and the order of assembly of ribosomal proteins into the ribosome are discussed.

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Jovanovic, Bogdan, Lisa Schubert, Fabian Poetz y Georg Stoecklin. "Tagging of RPS9 as a tool for ribosome purification and identification of ribosome-associated proteins". Archives of Biological Sciences, n.º 00 (2020): 57. http://dx.doi.org/10.2298/abs20120557j.

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

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Pollutri, Daniela y Marianna Penzo. "Ribosomal Protein L10: From Function to Dysfunction". Cells 9, n.º 11 (19 de noviembre de 2020): 2503. http://dx.doi.org/10.3390/cells9112503.

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Eukaryotic cytoplasmic ribosomes are highly structured macromolecular complexes made up of four different ribosomal RNAs (rRNAs) and 80 ribosomal proteins (RPs), which play a central role in the decoding of genetic code for the synthesis of new proteins. Over the past 25 years, studies on yeast and human models have made it possible to identify RPL10 (ribosomal protein L10 gene), which is a constituent of the large subunit of the ribosome, as an important player in the final stages of ribosome biogenesis and in ribosome function. Here, we reviewed the literature to give an overview of the role of RPL10 in physiologic and pathologic processes, including inherited disease and cancer.

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Moraleva, Anastasia A., Alexander S. Deryabin, Yury P. Rubtsov, Maria P. Rubtsova y Olga A. Dontsova. "Eukaryotic Ribosome Biogenesis: The 40S Subunit". Acta Naturae 14, n.º 1 (10 de mayo de 2022): 14–30. http://dx.doi.org/10.32607/actanaturae.11540.

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The formation of eukaryotic ribosomes is a sequential process of ribosomal precursors maturation in the nucleolus, nucleoplasm, and cytoplasm. Hundreds of ribosomal biogenesis factors ensure the accurate processing and formation of the ribosomal RNAs tertiary structure, and they interact with ribosomal proteins. Most of what we know about the ribosome assembly has been derived from yeast cell studies, and the mechanisms of ribosome biogenesis in eukaryotes are considered quite conservative. Although the main stages of ribosome biogenesis are similar across different groups of eukaryotes, this process in humans is much more complicated owing to the larger size of the ribosomes and pre-ribosomes and the emergence of regulatory pathways that affect their assembly and function. Many of the factors involved in the biogenesis of human ribosomes have been identified using genome-wide screening based on RNA interference. This review addresses the key aspects of yeast and human ribosome biogenesis, using the 40S subunit as an example. The mechanisms underlying these differences are still not well understood, because, unlike yeast, there are no effective methods for characterizing pre-ribosomal complexes in humans. Understanding the mechanisms of human ribosome assembly would have an incidence on a growing number of genetic diseases (ribosomopathies) caused by mutations in the genes encoding ribosomal proteins and ribosome biogenesis factors. In addition, there is evidence that ribosome assembly is regulated by oncogenic signaling pathways, and that defects in the ribosome biogenesis are linked to the activation of tumor suppressors.

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Shatskikh, Aleksei S., Elena A. Fefelova y Mikhail S. Klenov. "Functions of RNAi Pathways in Ribosomal RNA Regulation". Non-Coding RNA 10, n.º 2 (29 de marzo de 2024): 19. http://dx.doi.org/10.3390/ncrna10020019.

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Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.

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Konikkat, Salini y John L. Woolford,. "Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast". Biochemical Journal 474, n.º 2 (6 de enero de 2017): 195–214. http://dx.doi.org/10.1042/bcj20160516.

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Ribosome biogenesis requires the intertwined processes of folding, modification, and processing of ribosomal RNA, together with binding of ribosomal proteins. In eukaryotic cells, ribosome assembly begins in the nucleolus, continues in the nucleoplasm, and is not completed until after nascent particles are exported to the cytoplasm. The efficiency and fidelity of ribosome biogenesis are facilitated by >200 assembly factors and ∼76 different small nucleolar RNAs. The pathway is driven forward by numerous remodeling events to rearrange the ribonucleoprotein architecture of pre-ribosomes. Here, we describe principles of ribosome assembly that have emerged from recent studies of biogenesis of the large ribosomal subunit in the yeast Saccharomyces cerevisiae. We describe tools that have empowered investigations of ribosome biogenesis, and then summarize recent discoveries about each of the consecutive steps of subunit assembly.

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Roychowdhury, Amlan, Clément Joret, Gabrielle Bourgeois, Valérie Heurgué-Hamard, Denis L. J. Lafontaine y Marc Graille. "The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis". Nucleic Acids Research 47, n.º 14 (12 de junio de 2019): 7548–63. http://dx.doi.org/10.1093/nar/gkz529.

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Abstract Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.

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9

Collins, Jason C., Homa Ghalei, Joanne R. Doherty, Haina Huang, Rebecca N. Culver y Katrin Karbstein. "Ribosome biogenesis factor Ltv1 chaperones the assembly of the small subunit head". Journal of Cell Biology 217, n.º 12 (22 de octubre de 2018): 4141–54. http://dx.doi.org/10.1083/jcb.201804163.

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The correct assembly of ribosomes from ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) is critical, as indicated by the diseases caused by RP haploinsufficiency and loss of RP stoichiometry in cancer cells. Nevertheless, how assembly of each RP is ensured remains poorly understood. We use yeast genetics, biochemistry, and structure probing to show that the assembly factor Ltv1 facilitates the incorporation of Rps3, Rps10, and Asc1/RACK1 into the small ribosomal subunit head. Ribosomes from Ltv1-deficient yeast have substoichiometric amounts of Rps10 and Asc1 and show defects in translational fidelity and ribosome-mediated RNA quality control. These defects provide a growth advantage under some conditions but sensitize the cells to oxidative stress. Intriguingly, relative to glioma cell lines, breast cancer cells have reduced levels of LTV1 and produce ribosomes lacking RPS3, RPS10, and RACK1. These data describe a mechanism to ensure RP assembly and demonstrate how cancer cells circumvent this mechanism to generate diverse ribosome populations that can promote survival under stress.

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10

Leclerc, Daniel y Léa Brakier-Gingras. "Study of the function of Escherichia coli ribosomal RNA through site-directed mutagenesis". Biochemistry and Cell Biology 68, n.º 1 (1 de enero de 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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11

Cottilli, Patrick, Borja Belda-Palazón, Charith Raj Adkar-Purushothama, Jean-Pierre Perreault, Enrico Schleiff, Ismael Rodrigo, Alejandro Ferrando y Purificación Lisón. "Citrus exocortis viroid causes ribosomal stress in tomato plants". Nucleic Acids Research 47, n.º 16 (8 de agosto de 2019): 8649–61. http://dx.doi.org/10.1093/nar/gkz679.

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Abstract Viroids are naked RNAs that do not code for any known protein and yet are able to infect plants causing severe diseases. Because of their RNA nature, many studies have focused on the involvement of viroids in RNA-mediated gene silencing as being their pathogenesis mechanism. Here, the alterations caused by the Citrus exocortis viroid (CEVd) on the tomato translation machinery were studied as a new aspect of viroid pathogenesis. The presence of viroids in the ribosomal fractions of infected tomato plants was detected. More precisely, CEVd and its derived viroid small RNAs were found to co-sediment with tomato ribosomes in vivo, and to provoke changes in the global polysome profiles, particularly in the 40S ribosomal subunit accumulation. Additionally, the viroid caused alterations in ribosome biogenesis in the infected tomato plants, affecting the 18S rRNA maturation process. A higher expression level of the ribosomal stress mediator NAC082 was also detected in the CEVd-infected tomato leaves. Both the alterations in the rRNA processing and the induction of NAC082 correlate with the degree of viroid symptomatology. Taken together, these results suggest that CEVd is responsible for defective ribosome biogenesis in tomato, thereby interfering with the translation machinery and, therefore, causing ribosomal stress.

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Nazar, Ross N. "The Ribosome: A biochemist's mechano set". Canadian Journal of Biochemistry and Cell Biology 63, n.º 5 (1 de mayo de 1985): 313–18. http://dx.doi.org/10.1139/o85-046.

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A ribosome, the cellular site for protein synthesis, is a very complex organelle composed of a myriad of macromolecular substructures. As models for this complex structure, we have been examining the structures and interactions of eukaryotic 5S and 5.8S rRNAs using adaptations of rapid RNA gel sequencing techniques. Estimates for their higher order structures have been proposed or evaluated, sites of interaction with other ribosomal components have been delineated, and the topography of these RNAs within the intact ribosome or 60S subunit have been examined. The results indicate that a universal structure for the ribosomal RNAs may only be present within the ribosome, that these molecules are probably present, at least in part, within the ribosomal interface, and that the bases for interactions with other ribosomal components are strongly dependent on their higher order structure. The experimental approaches which underlie these studies are considered in this review and the significance of the results with respect to the function and evolution of the ribosome are briefly discussed.

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Ramagopal, S. "Unequal accumulation of 26S and 17S RNAs in ribosomes during spore germination in Dictyostelium discoideum". Canadian Journal of Microbiology 35, n.º 9 (1 de septiembre de 1989): 850–53. http://dx.doi.org/10.1139/m89-142.

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Ribosome synthesis was studied in spores at the swelling stage and compared with freshly emerged and logarithmically growing vegetative amoebae. During the swelling stage of spore germination, ribosome synthesis was abnormal. Newly made ribosomes accumulated unequal amounts of 26S and 17S rRNAs. The stoichiometric ratio 26S:17S was 0.5 in swelling spores, compared with 0.9 in amoebae. The relative level of pre-rRNA persisting in the nucleus was apparently 2- to 3-fold higher in swelling spores than in amoebae. All of the known ribosomal proteins, except for a few, were made during the swelling stage and were associated with the newly made ribosomes in expected amounts. Analysis of the 2′-O-methyl ribose content in the newly made rRNAs suggests that methylation was defective in swelling spores. Compared with growing amoebae, the methyl content was 30 and 64% less in 26S and 17S RNAs from the swelling stage, respectively. It is suggested that undermethylation could be partly responsible for the differential accumulation of newly made 26S and 17S RNAs during the early stages of spore germination in Dictyostelium discoideum.Key words: cellular slime mold, rRNA synthesis, ribosomal proteins, methylation, cell differentiation.

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Bonilauri, Bernardo, Fabiola Barbieri Holetz y Bruno Dallagiovanna. "Long Non-Coding RNAs Associated with Ribosomes in Human Adipose-Derived Stem Cells: From RNAs to Microproteins". Biomolecules 11, n.º 11 (11 de noviembre de 2021): 1673. http://dx.doi.org/10.3390/biom11111673.

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Ribosome profiling reveals the translational dynamics of mRNAs by capturing a ribosomal footprint snapshot. Growing evidence shows that several long non-coding RNAs (lncRNAs) contain small open reading frames (smORFs) that are translated into functional peptides. The difficulty in identifying bona-fide translated smORFs is a constant challenge in experimental and bioinformatics fields due to their unconventional characteristics. This motivated us to isolate human adipose-derived stem cells (hASC) from adipose tissue and perform a ribosome profiling followed by bioinformatics analysis of transcriptome, translatome, and ribosome-protected fragments of lncRNAs. Here, we demonstrated that 222 lncRNAs were associated with the translational machinery in hASC, including the already demonstrated lncRNAs coding microproteins. The ribosomal occupancy of some transcripts was consistent with the translation of smORFs. In conclusion, we were able to identify a subset of 15 lncRNAs containing 35 smORFs that likely encode functional microproteins, including four previously demonstrated smORF-derived microproteins, suggesting a possible dual role of these lncRNAs in hASC self-renewal.

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Mageeney, Catherine M. y Vassie C. Ware. "Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster". Molecular Biology of the Cell 30, n.º 17 (agosto de 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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Root-Bernstein, Robert y Meredith Root-Bernstein. "The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules". International Journal of Molecular Sciences 20, n.º 1 (2 de enero de 2019): 140. http://dx.doi.org/10.3390/ijms20010140.

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We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.

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Shiao, Yih-Horng. "Promising Assays for Examining a Putative Role of Ribosomal Heterogeneity in COVID-19 Susceptibility and Severity". Life 12, n.º 2 (28 de enero de 2022): 203. http://dx.doi.org/10.3390/life12020203.

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

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Kurata, Tatsuaki, Shinobu Nakanishi, Masayuki Hashimoto, Masato Taoka, Toshiaki Isobe y Jun-ichi Kato. "Subunit Composition of Ribosome in the yqgF Mutant Is Deficient in pre-16S rRNA Processing of Escherichia coli". Journal of Molecular Microbiology and Biotechnology 28, n.º 4 (2018): 179–82. http://dx.doi.org/10.1159/000494494.

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Escherichia coli 16S, 23S, and 5S ribosomal RNAs (rRNAs) are transcribed as a single primary transcript, which is subsequently processed into mature rRNAs by several RNases. Three RNases (RNase III, RNase E, and RNase G) were reported to function in processing the 5′-leader of precursor 16S rRNA (pre-16S rRNA). Previously, we showed that a novel essential YqgF is involved in that processing. Here we investigated the ribosome subunits of the yqgFts mutant by LC-MS/MS. The mutant ribosome had decreased copy numbers of ribosome protein S1, suggesting that the yqgF gene enables incorporation of ribosomal protein S1 into ribosome by processing of the 5′-end of pre-16S rRNA. The ribosome protein S1 is essential for translation in E. coli; therefore, our results suggest that YqgF converts the inactive form of newly synthesized ribosome into the active form at the final step of ribosome assembly.

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Bates, Christian, Simon J. Hubbard y Mark P. Ashe. "Ribosomal flavours: an acquired taste for specific mRNAs?" Biochemical Society Transactions 46, n.º 6 (12 de noviembre de 2018): 1529–39. http://dx.doi.org/10.1042/bst20180160.

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

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Ojha, Sandeep, Sulochan Malla y Shawn M. Lyons. "snoRNPs: Functions in Ribosome Biogenesis". Biomolecules 10, n.º 5 (18 de mayo de 2020): 783. http://dx.doi.org/10.3390/biom10050783.

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Ribosomes are perhaps the most critical macromolecular machine as they are tasked with carrying out protein synthesis in cells. They are incredibly complex structures composed of protein components and heavily chemically modified RNAs. The task of assembling mature ribosomes from their component parts consumes a massive amount of energy and requires greater than 200 assembly factors. Among the most critical of these are small nucleolar ribonucleoproteins (snoRNPs). These are small RNAs complexed with diverse sets of proteins. As suggested by their name, they localize to the nucleolus, the site of ribosome biogenesis. There, they facilitate multiple roles in ribosomes biogenesis, such as pseudouridylation and 2′-O-methylation of ribosomal (r)RNA, guiding pre-rRNA processing, and acting as molecular chaperones. Here, we reviewed their activity in promoting the assembly of ribosomes in eukaryotes with regards to chemical modification and pre-rRNA processing.

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Baßler, Jochen y Ed Hurt. "Eukaryotic Ribosome Assembly". Annual Review of Biochemistry 88, n.º 1 (20 de junio de 2019): 281–306. http://dx.doi.org/10.1146/annurev-biochem-013118-110817.

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Ribosomes, which synthesize the proteins of a cell, comprise ribosomal RNA and ribosomal proteins, which coassemble hierarchically during a process termed ribosome biogenesis. Historically, biochemical and molecular biology approaches have revealed how preribosomal particles form and mature in consecutive steps, starting in the nucleolus and terminating after nuclear export into the cytoplasm. However, only recently, due to the revolution in cryo–electron microscopy, could pseudoatomic structures of different preribosomal particles be obtained. Together with in vitro maturation assays, these findings shed light on how nascent ribosomes progress stepwise along a dynamic biogenesis pathway. Preribosomes assemble gradually, chaperoned by a myriad of assembly factors and small nucleolar RNAs, before they reach maturity and enter translation. This information will lead to a better understanding of how ribosome synthesis is linked to other cellular pathways in humans and how it can cause diseases, including cancer, if disturbed.

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Szaflarski, Witold, Marta Leśniczak-Staszak, Mateusz Sowiński, Sandeep Ojha, Anaïs Aulas, Dhwani Dave, Sulochan Malla, Paul Anderson, Pavel Ivanov y Shawn M. Lyons. "Early rRNA processing is a stress-dependent regulatory event whose inhibition maintains nucleolar integrity". Nucleic Acids Research 50, n.º 2 (20 de diciembre de 2021): 1033–51. http://dx.doi.org/10.1093/nar/gkab1231.

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Abstract The production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here, we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but is independently regulated. Failure to coordinately control ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils how the rapid translational shut-off in response to stress coordinates with rRNA synthesis production to maintain nucleolar integrity.

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Delihas, Nicolas. "Unusual 5 S ribosomal RNAs". FEBS Letters 221, n.º 2 (14 de septiembre de 1987): 189–93. http://dx.doi.org/10.1016/0014-5793(87)80923-7.

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Brierley, I. "Ribosomal frameshifting on viral RNAs". Journal of General Virology 76, n.º 8 (1 de agosto de 1995): 1885–92. http://dx.doi.org/10.1099/0022-1317-76-8-1885.

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25

Perrone-Capano, Carla, Carla Perrone-Capano, Marianna Crispino, Enrico Menichini, Barry B. Kaplan y Antonio Giuditta. "Ribosomal RNAs Synthesized by Isolated Squid Nerves and Ganglia Differ from Native Ribosomal RNAs". Journal of Neurochemistry 72, n.º 3 (7 de julio de 2008): 910–18. http://dx.doi.org/10.1046/j.1471-4159.1999.0720910.x.

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26

Chabronova, Alzbeta, Guus van den Akker, Bas A. C. Housmans, Marjolein M. J. Caron, Andy Cremers, Don A. M. Surtel, Mandy J. Peffers et al. "Depletion of SNORA33 Abolishes ψ of 28S-U4966 and Affects the Ribosome Translational Apparatus". International Journal of Molecular Sciences 24, n.º 16 (8 de agosto de 2023): 12578. http://dx.doi.org/10.3390/ijms241612578.

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Eukaryotic ribosomes are complex molecular nanomachines translating genetic information from mRNAs into proteins. There is natural heterogeneity in ribosome composition. The pseudouridylation (ψ) of ribosomal RNAs (rRNAs) is one of the key sources of ribosome heterogeneity. Nevertheless, the functional consequences of ψ-based ribosome heterogeneity and its relevance for human disease are yet to be understood. Using HydraPsiSeq and a chronic disease model of non-osteoarthritic primary human articular chondrocytes exposed to osteoarthritic synovial fluid, we demonstrated that the disease microenvironment is capable of instigating site-specific changes in rRNA ψ profiles. To investigate one of the identified differential rRNA ψ sites (28S-ψ4966), we generated SNORA22 and SNORA33 KO SW1353 cell pools using LentiCRISPRv2/Cas9 and evaluated the ribosome translational capacity by 35S-Met/Cys incorporation, assessed the mode of translation initiation and ribosomal fidelity using dual luciferase reporters, and assessed cellular and ribosomal proteomes by LC-MS/MS. We uncovered that the depletion of SNORA33, but not SNORA22, reduced 28S-ψ4966 levels. The resulting loss of 28S-ψ4966 affected ribosomal protein composition and function and led to specific changes in the cellular proteome. Overall, our pioneering findings demonstrate that cells dynamically respond to disease-relevant changes in their environment by altering their rRNA pseudouridylation profiles, with consequences for ribosome function and the cellular proteome relevant to human disease.

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27

Ochkasova, Anastasia, Grigory Arbuzov, Alexey Malygin y Dmitri Graifer. "Two “Edges” in Our Knowledge on the Functions of Ribosomal Proteins: The Revealed Contributions of Their Regions to Translation Mechanisms and the Issues of Their Extracellular Transport by Exosomes". International Journal of Molecular Sciences 24, n.º 14 (14 de julio de 2023): 11458. http://dx.doi.org/10.3390/ijms241411458.

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Ribosomal proteins (RPs), the constituents of the ribosome, belong to the most abundant proteins in the cell. A highly coordinated network of interactions implicating RPs and ribosomal RNAs (rRNAs) forms the functionally competent structure of the ribosome, enabling it to perform translation, the synthesis of polypeptide chain on the messenger RNA (mRNA) template. Several RPs contact ribosomal ligands, namely, those with transfer RNAs (tRNAs), mRNA or translation factors in the course of translation, and the contribution of a number of these particular contacts to the translation process has recently been established. Many ribosomal proteins also have various extra-ribosomal functions unrelated to translation. The least-understood and -discussed functions of RPs are those related to their participation in the intercellular communication via extracellular vesicles including exosomes, etc., which often carry RPs as passengers. Recently reported data show that such a kind of communication can reprogram a receptor cell and change its phenotype, which is associated with cancer progression and metastasis. Here, we review the state-of-art ideas on the implications of specific amino acid residues of RPs in the particular stages of the translation process in higher eukaryotes and currently available data on the transport of RPs by extracellular vesicles and its biological effects.

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28

Reza, Abu Musa Md Talimur y Yu-Guo Yuan. "microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins". Cells 10, n.º 1 (8 de enero de 2021): 110. http://dx.doi.org/10.3390/cells10010110.

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Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3′ untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5′ untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.

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29

Reza, Abu Musa Md Talimur y Yu-Guo Yuan. "microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins". Cells 10, n.º 1 (8 de enero de 2021): 110. http://dx.doi.org/10.3390/cells10010110.

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Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3′ untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5′ untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.

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30

Xu, Yuan y Ting F. Zhu. "Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs". Science 378, n.º 6618 (28 de octubre de 2022): 405–12. http://dx.doi.org/10.1126/science.abm0646.

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To synthesize a chirally inverted ribosome with the goal of building mirror-image biology systems requires the preparation of kilobase-long mirror-image ribosomal RNAs that make up the structural and catalytic core and about two-thirds of the molecular mass of the mirror-image ribosome. Here, we chemically synthesized a 100-kilodalton mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of the full-length mirror-image 5 S , 16 S , and 23 S ribosomal RNAs from enzymatically assembled long mirror-image genes. We further exploited the versatile mirror-image T7 transcription system for practical applications such as biostable mirror-image riboswitch sensor, long-term storage of unprotected kilobase-long l -RNA in water, and l -ribozyme–catalyzed l -RNA polymerization to serve as a model system for basic RNA research.

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31

Wang, Shuzhen, Zhiliang Li, Shiming Li, Rong Di, Chi-Tang Ho y Guliang Yang. "Ribosome-inactivating proteins (RIPs) and their important health promoting property". RSC Advances 6, n.º 52 (2016): 46794–805. http://dx.doi.org/10.1039/c6ra02946a.

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Ribosome-inactivating proteins (RIPs), widely present in plants, certain fungi and bacteria, can inhibit protein synthesis by removing one or more specific adenine residues from the large subunit of ribosomal RNAs (rRNAs).

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32

Noller, Harry F., John Paul Donohue y Robin R. Gutell. "The universally conserved nucleotides of the small subunit ribosomal RNAs". RNA 28, n.º 5 (3 de febrero de 2022): 623–44. http://dx.doi.org/10.1261/rna.079019.121.

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The ribosomal RNAs, along with their substrates the transfer RNAs, contain the most highly conserved nucleotides in all of biology. We have assembled a database containing structure-based alignments of sequences of the small-subunit rRNAs from organisms that span the entire phylogenetic spectrum, to identify the nucleotides that are universally conserved. In its simplest (bacterial and archaeal) forms, the small-subunit rRNA has ∼1500 nt, of which we identify 140 that are absolutely invariant among the 1961 species in our alignment. We examine the positions and detailed structural and functional interactions of these universal nucleotides in the context of a half century of biochemical and genetic studies and high-resolution structures of ribosome functional complexes. The vast majority of these nucleotides are exposed on the subunit interface surface of the small subunit, where the functional processes of the ribosome take place. However, only 40 of them have been directly implicated in specific ribosomal functions, such as contacting the tRNAs, mRNA, or translation factors. The roles of many other invariant nucleotides may serve to constrain the positions and orientations of those nucleotides that are directly involved in function. Yet others can be rationalized by participation in unusual noncanonical tertiary structures that may uniquely allow correct folding of the rRNA to form a functional ribosome. However, there remain at least 50 nt whose universal conservation is not obvious, serving as a metric for the incompleteness of our understanding of ribosome structure and function.

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33

Campos, Rafael K., H. R. Sagara Wijeratne, Premal Shah, Mariano A. Garcia-Blanco y Shelton S. Bradrick. "Ribosomal stalk proteins RPLP1 and RPLP2 promote biogenesis of flaviviral and cellular multi-pass transmembrane proteins". Nucleic Acids Research 48, n.º 17 (5 de septiembre de 2020): 9872–85. http://dx.doi.org/10.1093/nar/gkaa717.

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Abstract The ribosomal stalk proteins, RPLP1 and RPLP2 (RPLP1/2), which form the ancient ribosomal stalk, were discovered decades ago but their functions remain mysterious. We had previously shown that RPLP1/2 are exquisitely required for replication of dengue virus (DENV) and other mosquito-borne flaviviruses. Here, we show that RPLP1/2 function to relieve ribosome pausing within the DENV envelope coding sequence, leading to enhanced protein stability. We evaluated viral and cellular translation in RPLP1/2-depleted cells using ribosome profiling and found that ribosomes pause in the sequence coding for the N-terminus of the envelope protein, immediately downstream of sequences encoding two adjacent transmembrane domains (TMDs). We also find that RPLP1/2 depletion impacts a ribosome density for a small subset of cellular mRNAs. Importantly, the polarity of ribosomes on mRNAs encoding multiple TMDs was disproportionately affected by RPLP1/2 knockdown, implying a role for RPLP1/2 in multi-pass transmembrane protein biogenesis. These analyses of viral and host RNAs converge to implicate RPLP1/2 as functionally important for ribosomes to elongate through ORFs encoding multiple TMDs. We suggest that the effect of RPLP1/2 at TMD associated pauses is mediated by improving the efficiency of co-translational folding and subsequent protein stability.

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34

Zhu, Chengming, Qi Yan, Chenchun Weng, Xinhao Hou, Hui Mao, Dun Liu, Xuezhu Feng y Shouhong Guang. "Erroneous ribosomal RNAs promote the generation of antisense ribosomal siRNA". Proceedings of the National Academy of Sciences 115, n.º 40 (17 de septiembre de 2018): 10082–87. http://dx.doi.org/10.1073/pnas.1800974115.

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Ribosome biogenesis is a multistep process, during which mistakes can occur at any step of pre-rRNA processing, modification, and ribosome assembly. Misprocessed rRNAs are usually detected and degraded by surveillance machineries. Recently, we identified a class of antisense ribosomal siRNAs (risiRNAs) that down-regulate pre-rRNAs through the nuclear RNAi pathway. To further understand the biological roles of risiRNAs, we conducted both forward and reverse genetic screens to search for more suppressor of siRNA (susi) mutants. We isolated a number of genes that are broadly conserved from yeast to humans and are involved in pre-rRNA modification and processing. Among them, SUSI-2(ceRRP8) is homologous to human RRP8 and engages in m1A methylation of the 26S rRNA. C27F2.4(ceBUD23) is an m7G-methyltransferase of the 18S rRNA. E02H1.1(ceDIMT1L) is a predicted m6(2)Am6(2)A-methyltransferase of the 18S rRNA. Mutation of these genes led to a deficiency in modification of rRNAs and elicited accumulation of risiRNAs, which further triggered the cytoplasmic-to-nuclear and cytoplasmic-to-nucleolar translocations of the Argonaute protein NRDE-3. The rRNA processing deficiency also resulted in accumulation of risiRNAs. We also isolated SUSI-3(RIOK-1), which is similar to human RIOK1, that cleaves the 20S rRNA to 18S. We further utilized RNAi and CRISPR-Cas9 technologies to perform candidate-based reverse genetic screens and identified additional pre-rRNA processing factors that suppressed risiRNA production. Therefore, we concluded that erroneous rRNAs can trigger risiRNA generation and subsequently, turn on the nuclear RNAi-mediated gene silencing pathway to inhibit pre-rRNA expression, which may provide a quality control mechanism to maintain homeostasis of rRNAs.

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35

Burma, D. P., A. K. Srivastava, S. Srivastava, D. Dash, D. S. Tewari y B. Nag. "Do ribosomal RNAs act merely as scaffold for ribosomal proteins?" Journal of Biosciences 8, n.º 3-4 (agosto de 1985): 757–66. http://dx.doi.org/10.1007/bf02702774.

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36

Tishchenko, S. V., E. Yu Nikonova, N. A. Nevskaya, O. S. Nikonov, M. B. Garber y S. V. Nikonov. "Interactions of ribosomal protein L1 with ribosomal and messenger RNAs". Molecular Biology 40, n.º 4 (julio de 2006): 579–86. http://dx.doi.org/10.1134/s0026893306040108.

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37

Giovannoni, Stephen y Craig Cary. "Probing Marine Systems with Ribosomal RNAs". Oceanography 6, n.º 3 (1993): 95–104. http://dx.doi.org/10.5670/oceanog.1993.04.

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38

Parker, Michael S., Floyd R. Sallee, Edwards A. Park y Steven L. Parker. "Homoiterons and expansion in ribosomal RNAs". FEBS Open Bio 5, n.º 1 (1 de enero de 2015): 864–76. http://dx.doi.org/10.1016/j.fob.2015.10.005.

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39

Oostergetel, G. T., J. S. Wall, J. F. Hainfeld y M. Boublik. "Conformation of Free Ribosomal RNAs by STEM and Wet Film Technique as a Phylogenetic Probe". Proceedings, annual meeting, Electron Microscopy Society of America 43 (agosto de 1985): 498–99. http://dx.doi.org/10.1017/s0424820100119314.

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The similarity of ribosomes involvement in protein synthesis in evolutionarily distant species makes this cellular organelle an attractive phylogenetic probe. The evolutionary changes in ribosomes are reflected not only in the morphology of the ribosome but also in the composition and structure of its components - proteins and RNAs.We have investigated the extent of structural similarity of free rRNAs from baby hamster kidney (BHK) cells and Escherichia coli as examples of RNAs from a eukaryote and a prokaryote, respectively. Using dedicated STEM and “wet film” technique (Wall et al. these Proceedings) for specimen deposition we have improved considerably the resolution of RNA conformation in comparison to the glow discharge technique. A gallery of individual unstained freeze-dried 28S RNA molecules Isolated from the large (60S) ribosomal subunits from BHK cells, obtained by deposition from distilled water, is presented in Fig. 1a.

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40

Pulk, Arto y Jamie H. D. Cate. "Control of Ribosomal Subunit Rotation by Elongation Factor G". Science 340, n.º 6140 (27 de junio de 2013): 1235970. http://dx.doi.org/10.1126/science.1235970.

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Protein synthesis by the ribosome requires the translocation of transfer RNAs and messenger RNA by one codon after each peptide bond is formed, a reaction that requires ribosomal subunit rotation and is catalyzed by the guanosine triphosphatase (GTPase) elongation factor G (EF-G). We determined 3 angstrom resolution x-ray crystal structures of EF-G complexed with a nonhydrolyzable guanosine 5′-triphosphate (GTP) analog and bound to the Escherichia coli ribosome in different states of ribosomal subunit rotation. The structures reveal that EF-G binding to the ribosome stabilizes switch regions in the GTPase active site, resulting in a compact EF-G conformation that favors an intermediate state of ribosomal subunit rotation. These structures suggest that EF-G controls the translocation reaction by cycles of conformational rigidity and relaxation before and after GTP hydrolysis.

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41

Gebetsberger, Jennifer, Marek Zywicki, Andrea Künzi y Norbert Polacek. "tRNA-Derived Fragments Target the Ribosome and Function as Regulatory Non-Coding RNA inHaloferax volcanii". Archaea 2012 (2012): 1–11. http://dx.doi.org/10.1155/2012/260909.

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Nonprotein coding RNA (ncRNA) molecules have been recognized recently as major contributors to regulatory networks in controlling gene expression in a highly efficient manner. These RNAs either originate from their individual transcription units or are processing products from longer precursor RNAs. For example, tRNA-derived fragments (tRFs) have been identified in all domains of life and represent a growing, yet functionally poorly understood, class of ncRNA candidates. Here we present evidence that tRFs from the halophilic archaeonHaloferax volcaniidirectly bind to ribosomes. In the presented genomic screen of the ribosome-associated RNome, a 26-residue-long fragment originating from the 5′ part of valine tRNA was by far the most abundant tRF. The Val-tRF is processed in a stress-dependent manner and was found to primarily target the small ribosomal subunitin vitroandin vivo. As a consequence of ribosome binding, Val-tRF reduces protein synthesis by interfering with peptidyl transferase activity. Therefore this tRF functions as ribosome-bound small ncRNA capable of regulating gene expression inH. volcaniiunder environmental stress conditions probably by fine tuning the rate of protein production.

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42

Denovan-Wright, Eileen M. y Robert W. Lee. "Evidence that the fragmented ribosomal RNAs ofChlamydomonasmitochondria are associated with ribosomes". FEBS Letters 370, n.º 3 (21 de agosto de 1995): 222–26. http://dx.doi.org/10.1016/0014-5793(95)00837-y.

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43

Wang, Xiangxiang, Zhiyong Yue, Feifei Xu, Sufang Wang, Xin Hu, Junbiao Dai y 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, n.º 8 (6 de abril de 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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44

Schuwirth, Barbara S., Maria A. Borovinskaya, Cathy W. Hau, Wen Zhang, Antón Vila-Sanjurjo, James M. Holton y Jamie H. Doudna Cate. "Structures of the Bacterial Ribosome at 3.5 Å Resolution". Science 310, n.º 5749 (3 de noviembre de 2005): 827–34. http://dx.doi.org/10.1126/science.1117230.

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We describe two structures of the intact bacterial ribosome from Escherichia coli determined to a resolution of 3.5 angstroms by x-ray crystallography. These structures provide a detailed view of the interface between the small and large ribosomal subunits and the conformation of the peptidyl transferase center in the context of the intact ribosome. Differences between the two ribosomes reveal a high degree of flexibility between the head and the rest of the small subunit. Swiveling of the head of the small subunit observed in the present structures, coupled to the ratchet-like motion of the two subunits observed previously, suggests a mechanism for the final movements of messenger RNA (mRNA) and transfer RNAs (tRNAs) during translocation.

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45

Rabany, Ofri y Daphna Nachmani. "Small Nucleolar (Sno)RNA: Therapy Lays in Translation". Non-Coding RNA 9, n.º 3 (8 de junio de 2023): 35. http://dx.doi.org/10.3390/ncrna9030035.

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The ribosome is one of the largest complexes in the cell. Adding to its complexity are more than 200 RNA modification sites present on ribosomal RNAs (rRNAs) in a single human ribosome. These modifications occur in functionally important regions of the rRNA molecule, and they are vital for ribosome function and proper gene expression. Until recent technological advancements, the study of rRNA modifications and their profiles has been extremely laborious, leaving many questions unanswered. Small nucleolar RNAs (snoRNAs) are non-coding RNAs that facilitate and dictate the specificity of rRNA modification deposition, making them an attractive target for ribosome modulation. Here, we propose that through the mapping of rRNA modification profiles, we can identify cell-specific modifications with high therapeutic potential. We also describe the challenges of achieving the targeting specificity needed to implement snoRNAs as therapeutic targets in cancers.

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46

Rahul, Pachal y Dr Medda A. Satyaraj. "Ribosome Associated Protein Quality Control: Mechanism and Function". International Journal for Research in Applied Sciences and Biotechnology 9, n.º 1 (11 de febrero de 2022): 118–26. http://dx.doi.org/10.31033/ijrasb.9.1.14.

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Due to numerous reasons, including faulty m RNA, insufficient availability of charged t RNA, genetic errors, ribosomes are failed to synthesize protein sometimes. All organisms develop their machinery to recognize stalled ribosomes. Stalled ribosomes, results in the production of a truncated polypeptide which can affect cells. So, they must be eliminated, by mechanisms known as Ribosome-associated protein quality control (RQC). E3 ubiquitin ligase Ltn1 in RQC promotes clearance of 60S subunit and targets aberrant nascent polypeptides for proteasomal degradation. In eukaryotes, RQC facilitates the ribosomal rescue, where staled m RNAs release and allow to degrade and ribosomal subunits are to be recycled for further use. Ribosome-associated protein quality control in yeast is accomplished by Hel2-dependent ubiquitination of uS10 and RQC-trigger (RQT) complex. RQC in a mammal is done by ZNF598-dependent ubiquitination of collided ribosomes, which also activates signal integrator 3, a component of the ASCC complex. Human RQT (h RQT) is made up of ASCC3, ASCC2, TRIP4, which are orthologs of RNA helicase Slh1, ubiquitin-binding protein Cue3, and ykR023W protein respectively. Ubiquitin-binding activity and ATPase activity of ASCC2 and ASCC3 respectively, are important for RQC. So, it is obvious that the h RQT complex recognizes the ubiquitinated defective ribosome and induces subunit dissociation for RQC. Biogenesis of new polypeptide, folding, correct localization are the fundamental processes to maintain proteostasis, which involve various factors directly attached with ribosomes and chaperones. Ribosome-associated protein biogenesis factors mediate the cellular proteostasis network to form integrity.

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47

Cao, J. y A. P. Geballe. "Inhibition of nascent-peptide release at translation termination." Molecular and Cellular Biology 16, n.º 12 (diciembre de 1996): 7109–14. http://dx.doi.org/10.1128/mcb.16.12.7109.

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The transcript leader of the human cytomegalovirus (CMV) gpUL4 (gp48) gene contains a 22-codon upstream open reading frame (uORF2) that represses translation of the downstream cistron. Previous work demonstrated that ribosomes stall at the termination codon of uORF2 and, remarkably, that the coding information of uORF2 is required for both the translational repression and ribosomal stalling. We now provide evidence that the peptide product of uORF2 is synthesized and is retained in the ribosome in the form of a peptidyl-tRNA. Translation of the gp48 transcript leader in cell extracts produces the 2.4-kDa uORF2 peptide and a second product migrating with an apparent molecular mass of 20 kDa that represents the uORF2 peptide covalently linked to tRNA(Pro), the tRNA predicted to decode the carboxy-terminal codon of uORF2. The uORF2 peptidyl-tRNA is only detected after translation of RNAs containing uORF2 sequences that also inhibit downstream translation and cause ribosomal stalling. These data support a model in which the nascent uORF2 peptide blocks translation termination prior to hydrolysis of the peptidyl-tRNA bond. This blockade results in ribosomal stalling on the transcript leader which in turn impedes the access of ribosomes to the downstream cistron. This system illustrates that translation termination may be a critical step controlling expression of some eukaryotic genes.

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48

Marintchev, Assen y Gerhard Wagner. "Translation initiation: structures, mechanisms and evolution". Quarterly Reviews of Biophysics 37, n.º 3-4 (noviembre de 2004): 197–284. http://dx.doi.org/10.1017/s0033583505004026.

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Translation, the process of mRNA-encoded protein synthesis, requires a complex apparatus, composed of the ribosome, tRNAs and additional protein factors, including aminoacyl tRNA synthetases. The ribosome provides the platform for proper assembly of mRNA, tRNAs and protein factors and carries the peptidyl-transferase activity. It consists of small and large subunits. The ribosomes are ribonucleoprotein particles with a ribosomal RNA core, to which multiple ribosomal proteins are bound. The sequence and structure of ribosomal RNAs, tRNAs, some of the ribosomal proteins and some of the additional protein factors are conserved in all kingdoms, underlying the common origin of the translation apparatus. Translation can be subdivided into several steps: initiation, elongation, termination and recycling. Of these, initiation is the most complex and the most divergent among the different kingdoms of life. A great amount of new structural, biochemical and genetic information on translation initiation has been accumulated in recent years, which led to the realization that initiation also shows a great degree of conservation throughout evolution. In this review, we summarize the available structural and functional data on translation initiation in the context of evolution, drawing parallels between eubacteria, archaea, and eukaryotes. We will start with an overview of the ribosome structure and of translation in general, placing emphasis on factors and processes with relevance to initiation. The major steps in initiation and the factors involved will be described, followed by discussion of the structure and function of the individual initiation factors throughout evolution. We will conclude with a summary of the available information on the kinetic and thermodynamic aspects of translation initiation.

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49

Lykke-Andersen, Jens y Eric J. Bennett. "Protecting the proteome: Eukaryotic cotranslational quality control pathways". Journal of Cell Biology 204, n.º 4 (17 de febrero de 2014): 467–76. http://dx.doi.org/10.1083/jcb.201311103.

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The correct decoding of messenger RNAs (mRNAs) into proteins is an essential cellular task. The translational process is monitored by several quality control (QC) mechanisms that recognize defective translation complexes in which ribosomes are stalled on substrate mRNAs. Stalled translation complexes occur when defects in the mRNA template, the translation machinery, or the nascent polypeptide arrest the ribosome during translation elongation or termination. These QC events promote the disassembly of the stalled translation complex and the recycling and/or degradation of the individual mRNA, ribosomal, and/or nascent polypeptide components, thereby clearing the cell of improper translation products and defective components of the translation machinery.

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50

Tollervey, D. "Small Nucleolar RNAs Guide Ribosomal RNA Methylation". Science 273, n.º 5278 (23 de agosto de 1996): 1056–57. http://dx.doi.org/10.1126/science.273.5278.1056.

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Artículos de revistas sobre el tema "Ribosomal RNAs"

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