Academic literature on the topic 'Ribosomal maturation'
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Journal articles on the topic "Ribosomal maturation"
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Moraleva, Anastasia A., Alexander S. Deryabin, Yury P. Rubtsov, Maria P. Rubtsova, and Olga A. Dontsova. "Eukaryotic Ribosome Biogenesis: The 60S Subunit." Acta Naturae 14, no. 2 (2022): 39–49. http://dx.doi.org/10.32607/actanaturae.11541.
Full textAbstract:
Ribosome biogenesis is consecutive coordinated maturation of ribosomal precursors in the nucleolus, nucleoplasm, and cytoplasm. The formation of mature ribosomal subunits involves hundreds of ribosomal biogenesis factors that ensure ribosomal RNA processing, tertiary structure, and interaction with ribosomal proteins. Although the main features and stages of ribosome biogenesis are conservative among different groups of eukaryotes, this process in human cells has become more complicated due to the larger size of the ribosomes and pre-ribosomes and intricate regulatory pathways affecting 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. A previous part of this review summarized recent data on the processing of the primary rRNA transcript and compared the maturation of the small 40S subunit in yeast and human cells. This part of the review focuses on the biogenesis of the large 60S subunit of eukaryotic ribosomes.
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Shayan, Ramtin, Dana Rinaldi, Natacha Larburu, et al. "Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy." Molecules 25, no. 5 (2020): 1125. http://dx.doi.org/10.3390/molecules25051125.
Full textAbstract:
Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the “resolution revolution” of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a “vibrating” or “wriggling” stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position.
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Yu, Ting, and Fuxing Zeng. "Chloramphenicol Interferes with 50S Ribosomal Subunit Maturation via Direct and Indirect Mechanisms." Biomolecules 14, no. 10 (2024): 1225. http://dx.doi.org/10.3390/biom14101225.
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Chloramphenicol (CAM), a well-known broad-spectrum antibiotic, inhibits peptide bond formation in bacterial ribosomes. It has been reported to affect ribosome assembly mainly through disrupting the balance of ribosomal proteins. The present study investigates the multifaceted effects of CAM on the maturation of the 50S ribosomal subunit in Escherichia coli (E. coli). Using label-free quantitative mass spectrometry (LFQ-MS), we observed that CAM treatment also leads to the upregulation of assembly factors. Further cryo-electron microscopy (cryo-EM) analysis of the ribosomal precursors characterized the CAM-treatment-accumulated pre-50S intermediates. Heterogeneous reconstruction identified 26 distinct pre-50S intermediates, which were categorized into nine main states based on their structural features. Our structural analysis highlighted that CAM severely impedes the formation of the central protuberance (CP), H89, and H58 during 50S ribosomal subunit maturation. The ELISA assay further demonstrated the direct binding of CAM to the ribosomal precursors, suggesting that the interference with 50S maturation occurs through a combination of direct and indirect mechanisms. These findings provide new insights into the mechanism of the action of CAM and provide a foundation for a better understanding of the assembly landscapes of the ribosome.
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Moraleva, Anastasia A., Alexander S. Deryabin, Yury P. Rubtsov, Maria P. Rubtsova, and Olga A. Dontsova. "Eukaryotic Ribosome Biogenesis: The 40S Subunit." Acta Naturae 14, no. 1 (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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Sleiman, Sophie, and Francois Dragon. "Recent Advances on the Structure and Function of RNA Acetyltransferase Kre33/NAT10." Cells 8, no. 9 (2019): 1035. http://dx.doi.org/10.3390/cells8091035.
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Ribosome biogenesis is one of the most energy demanding processes in the cell. In eukaryotes, the main steps of this process occur in the nucleolus and include pre-ribosomal RNA (pre-rRNA) processing, post-transcriptional modifications, and assembly of many non-ribosomal factors and ribosomal proteins in order to form mature and functional ribosomes. In yeast and humans, the nucleolar RNA acetyltransferase Kre33/NAT10 participates in different maturation events, such as acetylation and processing of 18S rRNA, and assembly of the 40S ribosomal subunit. Here, we review the structural and functional features of Kre33/NAT10 RNA acetyltransferase, and we underscore the importance of this enzyme in ribosome biogenesis, as well as in acetylation of non-ribosomal targets. We also report on the role of human NAT10 in Hutchinson–Gilford progeria syndrome.
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Bikmullin, Aydar G., Bulat Fatkhullin, Artem Stetsenko, et al. "Yet Another Similarity between Mitochondrial and Bacterial Ribosomal Small Subunit Biogenesis Obtained by Structural Characterization of RbfA from S. aureus." International Journal of Molecular Sciences 24, no. 3 (2023): 2118. http://dx.doi.org/10.3390/ijms24032118.
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Ribosome biogenesis is a complex and highly accurate conservative process of ribosomal subunit maturation followed by association. Subunit maturation comprises sequential stages of ribosomal RNA and proteins’ folding, modification and binding, with the involvement of numerous RNAses, helicases, GTPases, chaperones, RNA, protein-modifying enzymes, and assembly factors. One such assembly factor involved in bacterial 30S subunit maturation is ribosomal binding factor A (RbfA). In this study, we present the crystal (determined at 2.2 Å resolution) and NMR structures of RbfA as well as the 2.9 Å resolution cryo-EM reconstruction of the 30S–RbfA complex from Staphylococcus aureus (S. aureus). Additionally, we show that the manner of RbfA action on the small ribosomal subunit during its maturation is shared between bacteria and mitochondria. The obtained results clarify the function of RbfA in the 30S maturation process and its role in ribosome functioning in general. Furthermore, given that S. aureus is a serious human pathogen, this study provides an additional prospect to develop antimicrobials targeting bacterial pathogens.
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Martinez-Seidel, Federico, Olga Beine-Golovchuk, Yin-Chen Hsieh, et al. "Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis." International Journal of Molecular Sciences 22, no. 11 (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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Warren, Alan J. "Shwachman-Diamond Syndrome and the Quality Control of Ribosome Assembly." Blood 128, no. 22 (2016): SCI—42—SCI—42. http://dx.doi.org/10.1182/blood.v128.22.sci-42.sci-42.
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Abstract The synthesis of new ribosomes is a fundamental conserved process in all cells. Ribosomes are pre-assembled in the nucleus and subsequently exported to the cytoplasm where they acquire functionality through a series of final maturation steps that include formation of the catalytic center, recruitment of the last remaining ribosomal proteins and the removal of inhibitory assembly factors. Surprisingly, a number of key factors (SBDS, DNAJC21, RPL10 (uL16)) involved in late cytoplasmic maturation of the large (60S) ribosomal subunit are mutated in both inherited and sporadic forms of leukemia. In particular, biallelic mutations in the SBDS gene cause Shwachman-Diamond syndrome (SDS), a recessive bone marrow failure disorder with significant predisposition to acute myeloid leukemia. By using the latest advances in single-particle cryo-electron microscopy to elucidate the function of the SBDS protein, we have uncovered an elegant mechanism that couples final maturation of the 60S subunit to a quality control assessment of the structural integrity of the active sites of the ribosome. Further molecular dissection of this pathway may inform novel therapeutic strategies for SDS and leukemia more generally. References: 1. Weis F, Giudice E, Churcher M,et al. Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat Struct Mol Biol, (2015) Nov;22(11):914-9. 2. Wong CC, Traynor D, Basse N, et al. Defective ribosome assembly in Shwachman-Diamond syndrome. Plenary Paper, Blood. 2011 Oct 20;118(16):4305-12. 3. Finch AJ, Hilcenko C, Basse N, et al. Uncoupling of GTP hydrolysis from eIF6 release on the ribosome causes Shwachman-Diamond syndrome. Genes Dev (2011) 25: 917-929. 4. Menne TM, Goyenechea B, Sánchez-Puig N, et al. The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast. Nature Genetics (2007) 39: 486-95. Disclosures No relevant conflicts of interest to declare.
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Graifer, Dmitri, and Galina Karpova. "Eukaryotic protein uS19: a component of the decoding site of ribosomes and a player in human diseases." Biochemical Journal 478, no. 5 (2021): 997–1008. http://dx.doi.org/10.1042/bcj20200950.
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Proteins belonging to the universal ribosomal protein (rp) uS19 family are constituents of small ribosomal subunits, and their conserved globular parts are involved in the formation of the head of these subunits. The eukaryotic rp uS19 (previously known as S15) comprises a C-terminal extension that has no homology in the bacterial counterparts. This extension is directly implicated in the formation of the ribosomal decoding site and thereby affects translational fidelity in a manner that has no analogy in bacterial ribosomes. Another eukaryote-specific feature of rp uS19 is its essential participance in the 40S subunit maturation due to the interactions with the subunit assembly factors required for the nuclear exit of pre-40S particles. Beyond properties related to the translation machinery, eukaryotic rp uS19 has an extra-ribosomal function concerned with its direct involvement in the regulation of the activity of an important tumor suppressor p53 in the Mdm2/Mdmx-p53 pathway. Mutations in the RPS15 gene encoding rp uS19 are linked to diseases (Diamond Blackfan anemia, chronic lymphocytic leukemia and Parkinson's disease) caused either by defects in the ribosome biogenesis or disturbances in the functioning of ribosomes containing mutant rp uS19, likely due to the changed translational fidelity. Here, we review currently available data on the involvement of rp uS19 in the operation of the translational machinery and in the maturation of 40S subunits, on its extra-ribosomal function, and on relationships between mutations in the RPS15 gene and certain human diseases.
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Schedlbauer, Andreas, Idoia Iturrioz, Borja Ochoa-Lizarralde, et al. "A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit." Science Advances 7, no. 23 (2021): eabf7547. http://dx.doi.org/10.1126/sciadv.abf7547.
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While a structural description of the molecular mechanisms guiding ribosome assembly in eukaryotic systems is emerging, bacteria use an unrelated core set of assembly factors for which high-resolution structural information is still missing. To address this, we used single-particle cryo–electron microscopy to visualize the effects of bacterial ribosome assembly factors RimP, RbfA, RsmA, and RsgA on the conformational landscape of the 30S ribosomal subunit and obtained eight snapshots representing late steps in the folding of the decoding center. Analysis of these structures identifies a conserved secondary structure switch in the 16S ribosomal RNA central to decoding site maturation and suggests both a sequential order of action and molecular mechanisms for the assembly factors in coordinating and controlling this switch. Structural and mechanistic parallels between bacterial and eukaryotic systems indicate common folding features inherent to all ribosomes.
Dissertations / Theses on the topic "Ribosomal maturation"
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Nord, Stefan. "The importance of maturation factors in 30S ribosomal subunit assembly." Doctoral thesis, Umeå universitet, Institutionen för molekylärbiologi (Teknisk-naturvetenskaplig fakultet), 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-35890.
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The assembly of the ribosome is a complex process that needs to be highly efficient to support maximum growth. Although the individual subunits of the ribosome can be reconstituted in vitro, such a reaction is inefficient in comparison to the assembly rate in vivo. What differentiates the in vivo from the in vitro assembly is primarily the presence of ribosome assembly proteins. These are proteins that assist in the assembly of the ribosomal subunits but are not part of the mature ribosome. In bacteria, the ribosome assembly proteins include rRNA processing enzymes and rRNA/ribosomal protein (r-protein) modifying enzymes. One set of ribosome assembly proteins, the ribosome maturation factors, have been difficult to classify due to their differences in structure and their apparent lack of similarities with regard to function. As part of this thesis, the previously uncharacterized RimP (ribosome maturation) protein formerly known as P15A or YhbC, was studied. Deletion of the rimP gene affected the growth rate more severely at 44°C than at 37°C and 30°C. Polysome profile analysis revealed a decrease in the amount of translating ribosomes and a corresponding increase in the amount of free 50S and 30S ribosomal subunits. The disproportionate large increase in 50S relative to 30S subunits indicated a 30S assembly defect. RimP was shown to localize to the 30S ribosomal subunit, and an accumulation of 17S rRNA, a precursor to 16S rRNA, supports a role for RimP in 30S subunit maturation. The results from in vitro reconstitution experiments have given valuable insights in the assembly of the 30S subunit. By using a recently developed method, the role of ribosome maturation factors Era, RimM and RimP during in vitro reconstitutions of the 30S subunit was investigated. Era was found to increase the incorporation rate for most of the late binding r-proteins, while RimM and RimP had more specific effects. RimM increased the incorporation rate for r-proteins S19 and S9 and inhibited the incorporation of S13 and S12, whereas RimP increased the incorporation rate primarily for S12 and S5. A comparison of the ribosome maturation factors RimP and RbfA (ribosome binding factor A) revealed structural similarities between the N-terminal domain of RimP and the single domain of RbfA. RbfA is a 15 kDa protein that was found to high copy-suppress a dominant C23U 16S rRNA mutation giving rise to cold-sensitivity in E. coli. A number of chromosomal suppressor mutations that increased the growth rate of an rbfA null mutant were isolated. The five strongest suppressor mutations were localized to the rpsE gene, for r-protein S5 and resulted in amino acid substitutions in three positions: G87A, G87S, G91A, A127V and A127T. These alterations improved translation and the processing of 16S rRNA in the rbfA null mutant. Moreover, they also suppressed the slow growth of the C23U rRNA mutant at 30, 37 and 44°C.<br>Monteringen av ribosomen är en komplex process som måste vara effektiv för cellen skall kunna växa så fort som möjligt. Det är visat sedan tidigare att ribosomens två subenheter kan monteras ihop in vitro och sedan vara del av en ribosom som gungerar vid proteinsyntes, dock är den typen av rekonstrueringsreaktioner mycket ineffektiva i jämförelse med vad som krävs in vivo. Skillnaden mellan dessa två tillstånd är primärt in vivo-reaktionens närvaro av hjälpproteiner. Hjälpproteinerna assisterar monteringen av ribosomens subenheter men är själva inte en del av den färdiga ribosomen. Inom denna klass av proteiner återfinns proteiner som t.ex. processerar ribosomalt RNA och proteiner som modifierar ribosomalt RNA och ribosomala protein. En klass av hjälpproteiner, mognadsfaktorerna, har varit svåra att klassificera på grund av strukturella olikheter och en brist på funktionella likheter. En del i detta avhandlingsarbete var karaktäriseringen av den tidigare okända mognadsfaktorn RimP, tidigare kallad YhbC eller P15A. En deletion av rimP hade störst påverkan på tillväxthastigheten vid 44°C, men effekter kunde även ses vid 30°C och 37°C. En analys av den ribosomala statusen visade på en minskning av ribosomer aktiva i translation och en motsvarande ökning av fria 50S- och 30S-subenheter. Den oproportionerligt höga ökningen av fria 50S-subenheter, i relation till 30S-subenheter, indikerade att något var fel i monteringen av 30S-subenheten. RimP-proteinet återfanns lokaliserat till fria 30S-subenheter, och en ökning av omoget 16S ribosomalt RNA i en stam som saknar RimP stödjer dess roll i monteringen av 30S-subenheten. Rekonstrueringsexperiment In vitro har gett många värdefulla ledtrådar till hur 30S-subenheten monteras ihop. Genom att använda en nyligen utvecklad metod kunde vi undersöka hur mognadsfaktorerna Era, RimM och RimP påverkade monteringen av ribosomens 30S subenhet in vitro. Era ökade inkorporeringshastigheten av många av de ribosomala proteiner som inkorporeras sent i monteringen av 30S, medans RimM och RimP uppvisade mer specifika effekter. RimM ökade inkorporeringshastigheten för de ribosomala proteinerna S19 och S9, men dessutom inhiberade RimM inkorporeringen av de ribosomala proteinerna S13 och S12. RimP uppvisade den tydligaste effekten av de undersökta proteinerna genom att kraftigt öka 8 inkorporeringshastigheten för det ribosomala proteinet S12, och ökade även inkorporeringshastigheten för det ribosomala proteinet S5. En jämförelse av de två mognadsfaktorerna RbfA och RimP visade på strukturella likheter mellan RimP:s N-terminala domän och den enda domänen hos RbfA. RbfA är ett 15 kDa protein som upptäcktes som en hög-kopiesupressor av en dominant C23U-mutation i 16S ribosomalt RNA som leder till köld-känslighet hos E. coli. Ett antal kromosomala supressormutationer som ökade tillväxthastigheten för en mutant som saknar RbfA isolerades och de fem starkaste av dessa lokaliserades till rpsE genen som kodar för det ribosomala proteinet S5. Mutationerna gav upphov till aminosyra utbyten i tre positioner i S5: G87A, G87S, G91A, A127T och A127V. Förändringarna i S5 förbättrade translationen och processningen av 16S ribosomalt RNA i mutantensom saknar RbfA. Dessutom förbättrade mutationerna tillväxthastigheten hos C23U-mutanten vid 30, 37 och 44°C.
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Trinquier, Aude. "Coupling between transfer RNA maturation and ribosomal RNA processing in Bacillus subtilis." Thesis, Université de Paris (2019-....), 2019. http://www.theses.fr/2019UNIP7066.
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La synthèse des protéines cellulaires requiert à la fois des ribosomes fonctionnels et des ARN de transfert (ARNt) matures comme molécules adaptatrices. Les ribosomes sont de larges complexes ribonucléoprotéiques dont la biogenèse représente la plupart de la transcription cellulaire et consomme une majeure partie de l’énergie de la cellule. Par conséquent, la biogenèse des ribosomes fait l’objet d’une régulation importante afin d’ajuster le nombre de ribosomes aux besoins de la cellule et de dégrader efficacement les particules défectueuses qui pourraient interférer avec la traduction. Les ARNs ribosomiques (ARNr) et les ARNt sont tous deux transcrits sous formes de précurseurs et sont universellement maturés pour devenir fonctionnels pour la traduction. Ce travail de thèse a permis de mettre en évidence un couplage entre la maturation des ARNt et la biogenèse des ribosomes chez la bactérie modèle à Gram positif Bacillus subtilis. Ainsi, l’accumulation d’ARNt immatures lors d’une déplétion en enzymes de maturation, abolit spécifiquement la maturation en 3’ de l’ARNr 16S par l’endoribonucléase YqfG/YbeY, dernière étape dans la formation de la petite sous-unité ribosomique (30S). Nous avons mis en évidence que ce défaut de maturation résultait d’un défaut d’assemblage tardif du 30S coïncidant avec des changements d’expression de plusieurs facteurs d’assemblage du ribosome. Nous avons montré que cette modulation d’expression provenait d’effets transcriptionel et post-transcriptionel. De façon inédite, nos résultats indiquent que l’accumulation d’ARNt immatures est perçue par RelA (le facteur de la réponse stringente), déclenchant la production de (p)ppGpp. Nous avons observé que cette synthèse de (p)ppGpp et la baisse concomitante des niveaux de GTP cellulaire, inhibe la maturation de l’ARNr 16S en 3’, probablement via un blocage des GTPases impliquées dans l’assemblage des ribosomes. L’inhibition de la maturation de l’ARNr 16S côté 3’ est supposée conduire, par la suite, à une dégradation des particules partiellement assemblées par la RNase R. Ainsi, nos résultats supportent un modèle où RelA jouerait un rôle central ; en percevant une déficience de maturation des ARNt et en ajustant, en conséquence, la biogenèse des ribosomes via la production de (p)ppGpp. Ce mécanisme de couplage permettrait de maintenir un équilibre fonctionnel entre ARNt et ARNr, les deux composants majeurs de la machinerie de traduction<br>Cellular protein synthesis both requires functional ribosomes and mature transfer RNAs (tRNAs) as adapter molecules. The ribosomes are large essential ribonucleoprotein complexes whose biogenesis accounts for most of cellular transcription and consumes a major portion of the cell’s energy. Ribosome biogenesis is therefore tightly adjusted to the cellular needs and actively surveilled to rapidly degrade defective particles that could interfere with translation. Interestingly, tRNAs and ribosomal RNAs (rRNAs) are both transcribed from longer primary transcripts and universally require processing to become functional for translation. In this thesis, I have characterized a coupling mechanism between tRNA processing and ribosome biogenesis in the Gram-positive model organism Bacillus subtilis. Accumulation of immature tRNAs during tRNA maturase depletion, specifically abolishes 16S rRNA 3’ processing by the endonuclease YqfG/YbeY, the last step in small ribosomal subunit formation. We showed that this maturation deficiency resulted from a late small subunit (30S) assembly defect coinciding with changes in expression of several key 30S assembly cofactors, mediated by both transcriptional and post-transcriptional effects. Interestingly, our results indicate that accumulation of immature tRNAs is sensed by the stringent factor RelA and triggers (p)ppGpp production. We showed that (p)ppGpp synthesis and the accompanying decrease in GTP levels inhibits 16S rRNA 3’ processing, most likely by affecting GTPases involved in ribosome assembly. The inhibition of 16S rRNA 3’ processing is thought to further lead to degradation of partially assembled particles by RNase R. Thus, we propose a model where RelA senses temporary slow-downs in tRNA maturation and this leads to an appropriate readjustment of ribosome biogenesis. This coupling mechanism would maintain the physiological balance between tRNAs and rRNAs, the two major components of the translation machinery
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Akhtar, Y. "Studies on the maturation pathway of ribosomal precursor RNA : Analysis of Xenopus ribosomal RNA synthesised by transcription in vitro." Thesis, University of Liverpool, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.382054.
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Durovic, Peter Vincent. "Characterisation of a novel pathway for ribosomal RNA maturation in Sulfolobus acidocaldarius." Thesis, University of British Columbia, 1993. http://hdl.handle.net/2429/41498.
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Since the initial proposition that the archaebacteria form a primary kingdom as
distinct as that of the eubacteria or the eukaryotes, sequence data generated from the
ribosomal RNA genes have flooded the databases and periodicals. Phylogenetic trees based on
these sequences have been constructed to map the finest details of topology and branching
order within the archaebacteria. Yet, despite the plethora of sequence data, relatively little was
discovered regarding rRNAgene regulation, transcript processing and requirements for mature
ribosome function. The aim of this study is to analyze possible novel regulatory mechanisms
in the rRNA genes of the extremely thermoacidophilic archaebacterium Sulfolobus
acidoccddccrius.
The three ribosomal RNA genes were cloned and sequenced. The gene organization was
confirmed to differ from that of the halophilic archaebacteria and the eubacteria: the 5S gene
was not linked to the 16S and 23S operon, and the operon lacked recognizable tRNA
sequences. Southern hybridization unveiled, and sequence data confirmed a long-standing
confusion regarding species identity. The previously published Sulfolobus acidocaldarius 5S
sequence was shown to have been attributed to the wrong species.
Mapping experiments showed that both transcripts initiated downstream of a
previously defined archaebacteria! promoter sequence. While sequence data showed the 5S
transcript start site and end site to be coincidental with the mature 5S termini, the 16S-23S
transcript was shown to contain a 143 nucleotide transcribed leader sequence, a 138
nucleotide intergenic sequence, and a trailer sequence of at least 105 nucleotides. Inverted
repeat sequences within these transcribed non-coding regions allow for the formation of
numerous stem-loops conforming to a semi-conserved archaebacterial structure. While no
processing took place within the 5S transcript, extensive processing of the 16S-23S transcript
was observed. Of the 12 processing sites mapped, only 6 could be accounted for in the context
of precursor processing and maturation events known directly or inferred by analogy from the
halophilic archaebacteria and the eubacteria. Alignment of the remaining sites revealed a
non-trivial sequence and structural similarity. If the novel processing indeed took place in the postulated context, it would mark a
radical departure from the expected maturation mechanism thought to predate the speciation
of archaebacteria and eubacteria. To examine this possibility, in vitro transcripts from
judiciously selected DNA fragments were subjected to cell-free extract. Analysis of the resultant
cleavage products confirmed the presence not only of a novel processing activity mediated by a
ribonucleoprotein complex but also of a novel processing pathway. Based on the locations of
the novel processing sites within the primary 16S-23S transcript, a model for transcriptional
regulation independent of polycistronic linkage is presented.<br>Medicine, Faculty of<br>Medical Genetics, Department of<br>Graduate
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Intine, Robert V. A. "Structural features of the 5' ETS in Schizosaccharomyces pombe essential for ribosomal RNA maturation." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0006/NQ40374.pdf.
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Braun, Christina [Verfasser], and Jorge [Akademischer Betreuer] Perez-Fernandez. "Functional characterization of Pol5 in the maturation of both ribosomal subunits / Christina Braun ; Betreuer: Jorge Perez-Fernandez." Regensburg : Universitätsbibliothek Regensburg, 2020. http://d-nb.info/1220080578/34.
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Teubl, Fabian [Verfasser], and Joachim [Akademischer Betreuer] Griesenbeck. "Structural and Functional Studies on the Role of Noc3p for Large Ribosomal Subunit Maturation in Saccharomyces cerevisiae / Fabian Teubl ; Betreuer: Joachim Griesenbeck." Regensburg : Universitätsbibliothek Regensburg, 2020. http://d-nb.info/1223198138/34.
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TAVERNITI, VALERIO. "RNA MATURATION/DEGRADATION IN MYCOBACTERIA: IN VIVO AND IN VITRO CHARACTERIZATION OF RNASE J AND RNASE E." Doctoral thesis, Università degli Studi di Milano, 2011. http://hdl.handle.net/2434/151782.
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Escherichia coli and Bacillus subtilis have very different sets of ribonucleases, in particular the presence of RNase E and RNase J, respectively, that have been used to explain significant differences in RNA metabolism between these the two model organisms. However, these studies might have somewhat polarized our view of RNA metabolism, while recent works outline models of RNA degradation that are more similar than has been thought. In fact, the recent characterization of RNase Y as the scaffold for the degradosome assembly in B. subtilis lead to the consideration that RNA degradation in B. subtilis might begin through an endonucleolitycal cleavage, followed by exonucleolytical degradation.
In this work, we have identified a functional RNase J in Mycobacterium smegmatis and characterized its in vitro 5’-3’ exo- and endonucleolytic activities. Furthermore, we constructed two mutants in M. smegmatis rnj: a conditional and a knock out mutant, thus demonstrating that in M. smegmatis the gene is not essential, contrary to the RNase J1 function in B. subtilis.
In M. smegmatis RNase J co-exists with RNase E, a configuration that enabled us to study how these two key nucleases collaborate. A conditional mutant in the rne gene was constructed, demonstrating that this function is essential for M. smegmatis, as it is in E. coli. Moreover, a conditional mutant in Mycobacterium tuberculosis, confirmed its essentiality also in this organism.
We studied the respective roles of the M. smegmatis RNase J and RNAse E ribonucleases in the 5’ end maturation of the katG transcript, previously demonstrated to derive from an endoribonucleolytic processing. Here we find that RNase E is responsible of the specific cleavage of the 5’ katG end.
Further, we show that RNase E and RNase J are involved in the 5’ end processing of all three ribosomal RNAs. Thus the maturation pathways of rRNAs in M. smegmatis are quite different from those observed in both E. coli and B. subtilis. Studying organisms containing different combinations of key ribonucleases can thus significantly broaden our view of the strategies directing RNA metabolism used by various organisms.
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Dumont, Julien. "Contrôle des divisions asymétriques et de l'arrêt CSF dans l'ovocyte de souris : rôles de la GTPase Ran, de la Formine-2 et de p90rsk." Paris 6, 2006. http://www.theses.fr/2006PA066357.
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Bertrand, Alexis. "Caractérisation fonctionnelle de mutations somatiques compensatrices d'elF6 dans le contexte du syndrome de Shwachman- Diamond." Electronic Thesis or Diss., université Paris-Saclay, 2024. http://www.theses.fr/2024UPASL089.
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Le syndrome de Shwachman Diamond (SDS) est une ribosomopathie génétique rare entraînant une altération de la synthèse protéique associée à de nombreux symptômes, notamment une insuffisance médullaire et une neutropénie pouvant évoluer vers un syndrome de myélodysplasie ou une leucémie myéloïde aiguë. Les mutations bialléliques du gène SBDS sont responsables de plus de 90 % des cas de SDS et nous avons récemment identifié des mutations bialléliques EFL1 comme une nouvelle cause génétique de SDS. SBDS et EFL1 évincent le facteur elF6 de la sous-unité ribosomale pré60S, permettant à cette dernière d'interagir avec la sous-unité 40S pour former le ribosome mature 80S. L'acquisition naturelle d'événements génétiques somatiques au fil du temps participe au développement des maladies liées à l'âge et au développement des cancers. Cependant, dans les maladies mendéliennes, ces événements peuvent, dans de rares cas, contrer l'effet délétère de la mutation germinale et conférer un avantage sélectif aux cellules somatiquement modifiées, un phénomène appelé sauvetage génétique somatique (SGR). Nous avons récemment montré que plusieurs événements génétiques somatiques affectantl'expression ou la fonction d'elF6 sont fréquemment détectés dans les clones sanguins de patients atteints de SDS mais pas chez les individus sains, suggérant un mécanisme de SGR. Alors que la plupart de ces mutations somatiques induisent une déstabilisation de elF6 ou une haploinsuffisance d'EIF6, une mutation récurrente (N106S) n'affecte pas l'expression/stabilité d'elF6 mais réduit sa capacité à interagir avec la sous-unité 60S. Afin d'étudier plus en détail les conséquences fonctionnelles de l'haploinsuffisance de EIF6 et de la mutation N106S dans un contexte de SDS, j'ai introduit via CRISPR/Cas9 ces mutations dans des lignées fibroblastiques immortalisées de patients SDS et de contrôle. Ces modèles cellulaires originaux ont permis de déterminer l'impact de la mutation N106S sur la la localisation et la fonction d'elF6 mais aussi de préciser les effets de ces mutations sur plusieurs aspects du « fitness » cellulaire, notamment la biogenèse des ribosomes, le taux de traduction et la prolifération cellulaire. Dans l'ensemble, le développement de ce modèle a aidé à caractériser comment la mutation N106S et l'haploinsuffisance somatique de elF6 confèrent un avantage sélectif dans les cellules déficientes en SBDS ou EFL1<br>Shwachman Diamond syndrome (SDS) is a rare genetic ribosomopathy leading to impaired protein synthesis, which causes numerous symptoms including bone marrow failure and neutropenia that can evolve to myelodysplasia syndrome or acute myeloid leukaemia. Biallelic mutations in the SBDS gene are responsible of above 90% of the SDS cases and we recently identified biallelic EFL1 mutations as a novel cause of SDS. SBDS together with EFL1 remove the anti-association factor elF6 from the pre60S ribosomal subunit, allowing its interaction with the 40S subunit to form the mature ribosome 80S. Natural acquisition of somatic genetic events over time participâtes to age-related diseases and cancer development. However, in Mendelian diseases these events can, in rare case, counteract the deleterious effect of the germline mutation and provide a sélective advantage to the somatically modified cells, a phenomenon dubbed Somatic Genetic Rescue (SGR). We recently showed that several somatic genetic events affecting the expression or function of elF6 are frequently detected in blood clones from SDS patients but not in healthy individuals, suggesting a mechanism of SGR. While most of these somatic mutations induce elF6 destabilization or EIF6 haploinsufficiency, one récurrent mutation (N106S) did not affect the expression of elF6 but rather impact its ability to interact with the 60S subunit. In order to further investigate the functional conséquences of ElF6 haploinsufficiency and N106S mutation in a context of SDS, I introduced via CRISPR/Cas9 these mutations in immortalized fibroblastic cell line from SDS patients and control. These original cellular models hâve made it possible to détermine the impact of the N106S mutation on the localisation and function of elF6 and also to clarify the effects of these mutations on several aspects of cellular fitness, in particular ribosome biogenesis, translation rate and cell prolifération. Overall, the development of these cellular models has helped to characterise how the somatic N106S mutation and elF6 haploinsufficiency confer a sélective advantage in cells déficient in SBDS or EFL1
Book chapters on the topic "Ribosomal maturation"
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Marshak, T. L., V. Mares, A. A. Karavanov, V. V. Nosikov, and V. Ya Brodsky. "Cell Differentiation According to Maturation of Nucleolar Apparatus and Topography of Ribosomal Genes." In Nuclear Structure and Function. Springer US, 1990. http://dx.doi.org/10.1007/978-1-4613-0667-2_27.
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Alix, Jean-Hervée. "Relationship Between Methylation and Maturation of Ribosomal RNA in Prokaryotic and Eukaryotic Cells." In Biological Methylation and Drug Design. Humana Press, 1986. http://dx.doi.org/10.1007/978-1-4612-5012-8_15.
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Hadjiolov, Asen A. "Maturation of Preribosomes." In The Nucleolus and Ribosome Biogenesis. Springer Vienna, 1985. http://dx.doi.org/10.1007/978-3-7091-8742-5_4.
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Braun, Christina, Robert Knüppel, Jorge Perez-Fernandez, and Sébastien Ferreira-Cerca. "Non-radioactive In Vivo Labeling of RNA with 4-Thiouracil." In Ribosome Biogenesis. Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2501-9_12.
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AbstractRNA molecules and their expression dynamics play essential roles in the establishment of complex cellular phenotypes and/or in the rapid cellular adaption to environmental changes. Accordingly, analyzing RNA expression remains an important step to understand the molecular basis controlling the formation of cellular phenotypes, cellular homeostasis or disease progression. Steady-state RNA levels in the cells are controlled by the sum of highly dynamic molecular processes contributing to RNA expression and can be classified in transcription, maturation and degradation. The main goal of analyzing RNA dynamics is to disentangle the individual contribution of these molecular processes to the life cycle of a given RNA under different physiological conditions. In the recent years, the use of nonradioactive nucleotide/nucleoside analogs and improved chemistry, in combination with time-dependent and high-throughput analysis, have greatly expanded our understanding of RNA metabolism across various cell types, organisms, and growth conditions.In this chapter, we describe a step-by-step protocol allowing pulse labeling of RNA with the nonradioactive nucleotide analog, 4-thiouracil, in the eukaryotic model organism Saccharomyces cerevisiae and the model archaeon Haloferax volcanii.
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Groves, Maria A., and Adrian A. Nickson. "Affinity Maturation of Phage Display Antibody Populations Using Ribosome Display." In Ribosome Display and Related Technologies. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-379-0_10.
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Hufton, Simon E. "Affinity Maturation and Functional Dissection of a Humanised Anti-RAGE Monoclonal Antibody by Ribosome Display." In Ribosome Display and Related Technologies. Springer New York, 2011. http://dx.doi.org/10.1007/978-1-61779-379-0_23.
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Himeno, Hyouta, Takefusa Tarusawa, Shion Ito, and Simon Goto. "Defective Ribosome Maturation or Function MakesEscherichia ColiCells Salt-Resistant." In Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria. John Wiley & Sons, Inc., 2016. http://dx.doi.org/10.1002/9781119004813.ch65.
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blatt, J. Roth. "Protein translocation and maturation in the mammalian Er." In Secretory Pathway. Oxford University PressOxford, 1994. http://dx.doi.org/10.1093/oso/9780198599425.003.0040.
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Abstract Virtually all of the information that has provided our current understanding of how proteins are selected for insertion into the mammalian ER has been obtained from in vitro studies of protein import into canine pancreatic microsomes. A model describing our current understanding of the early events in the mammalian secretory process is shown in Figure 1. Co-translational targeting of a nascent secretory polypeptide to the ER membrane is initiated by the high affinity binding of signal recognition particle (SRP) to the amino-terminal signal sequence as the latter emerges from the large ribosomal subunit1. SRP is a cytosolic ribonucleoprotein complex1 that binds the signal sequence, the ribosome, and an ER-specific receptor protein - docking protein (DP, also called the SRP receptor) 23. Binding of SRP to a ribosome-associated nascent polypeptide induces a pause in polypeptide chain elongation and concurrently mediates a high affinity interaction with docking protein at the ER membrane1 Binding of SRP to docking protein promotes two further events: (i) the formation of a stable receptor-mediated interaction between the ribosome and the ER membrane, and (ii) the release of the nascent chain from SRP and its insertion into the ER membrane.
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Elliott, David, and Michael Ladomery. "The biogenesis and nucleocytoplasmic traffic of non-coding RNAs." In Molecular Biology of RNA. Oxford University Press, 2015. http://dx.doi.org/10.1093/hesc/9780199671397.003.00014.
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This chapter explores non-coding RNAs (ncRNAs) that are processed during their biogenesis. It covers the processing and maturation of ribosomal RNA (rRNA), small nuclear RNA (snRNA), transfer RNA (tRNA), mitochondrial transcripts, and telomerase. It also gives an overview of the important aspects of RNA processing, including the RNA processing machinery that involves the action of other RNA molecules. The chapter reviews the main features of the biogenesis of ribosomal RNA, which is a process that is facilitated by a family of small RNA molecules known as the small nucleolar RNAs (snoRNAs). It describes the organization of rRNA processing in an important multifunctional nuclear organelle, the nucleolus.
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Deutscher, Murray P. "Chapter 9 Maturation and Degradation of Ribosomal RNA in Bacteria." In Progress in Molecular Biology and Translational Science. Elsevier, 2009. http://dx.doi.org/10.1016/s0079-6603(08)00809-x.
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