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Relevant bibliographies by topics / Large ribosomal subunit

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Academic literature on the topic 'Large ribosomal subunit'

Author: Grafiati

Published: 7 September 2022

Last updated: 18 September 2022

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Journal articles on the topic "Large ribosomal subunit"

1

Siibak, Triinu, Lauri Peil, Liqun Xiong, Alexander Mankin, Jaanus Remme, and Tanel Tenson. "Erythromycin- and Chloramphenicol-Induced Ribosomal Assembly Defects Are Secondary Effects of Protein Synthesis Inhibition." Antimicrobial Agents and Chemotherapy 53, no. 2 (November 24, 2008): 563–71. http://dx.doi.org/10.1128/aac.00870-08.

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ABSTRACT Several protein synthesis inhibitors are known to inhibit ribosome assembly. This may be a consequence of direct binding of the antibiotic to ribosome precursor particles, or it could result indirectly from loss of coordination in the production of ribosomal components due to the inhibition of protein synthesis. Here we demonstrate that erythromycin and chloramphenicol, inhibitors of the large ribosomal subunit, affect the assembly of both the large and small subunits. Expression of a small erythromycin resistance peptide acting in cis on mature ribosomes relieves the erythromycin-mediated assembly defect for both subunits. Erythromycin treatment of bacteria expressing a mixture of erythromycin-sensitive and -resistant ribosomes produced comparable effects on subunit assembly. These results argue in favor of the view that erythromycin and chloramphenicol affect the assembly of the large ribosomal subunit indirectly.

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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 (July 21, 2022): 39–49. http://dx.doi.org/10.32607/actanaturae.11541.

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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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Petrov, Anton S., Burak Gulen, Ashlyn M. Norris, Nicholas A. Kovacs, Chad R. Bernier, Kathryn A. Lanier, George E. Fox, et al. "History of the ribosome and the origin of translation." Proceedings of the National Academy of Sciences 112, no. 50 (November 30, 2015): 15396–401. http://dx.doi.org/10.1073/pnas.1509761112.

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We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.

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Aoyama, Ryo, Keiko Masuda, Masaru Shimojo, Takashi Kanamori, Takuya Ueda, and Yoshihiro Shimizu. "In vitro reconstitution of the Escherichia coli 70S ribosome with a full set of recombinant ribosomal proteins." Journal of Biochemistry 171, no. 2 (November 8, 2021): 227–37. http://dx.doi.org/10.1093/jb/mvab121.

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Abstract Many studies of the reconstitution of the Escherichia coli small ribosomal subunit from its individual molecular parts have been reported, but contrastingly, similar studies of the large ribosomal subunit have not been well performed to date. Here, we describe protocols for preparing the 33 ribosomal proteins of the E. coli 50S subunit and demonstrate successful reconstitution of a functionally active 50S particle that can perform protein synthesis in vitro. We also successfully reconstituted both ribosomal subunits (30S and 50S) and 70S ribosomes using a full set of recombinant ribosomal proteins by integrating our developed method with the previously developed fully recombinant-based integrated synthesis, assembly and translation. The approach described here makes a major contribution to the field of ribosome engineering and could be fundamental to the future studies of ribosome assembly processes.

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Moy, Terence I., and Pamela A. Silver. "Requirements for the nuclear export of the small ribosomal subunit." Journal of Cell Science 115, no. 14 (July 15, 2002): 2985–95. http://dx.doi.org/10.1242/jcs.115.14.2985.

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Eukaryotic ribosome biogenesis requires multiple steps of nuclear transport because ribosomes are assembled in the nucleus while protein synthesis occurs in the cytoplasm. Using an in situ RNA localization assay in the yeast Saccharomyces cerevisiae, we determined that efficient nuclear export of the small ribosomal subunit requires Yrb2, a factor involved in Crm1-mediated export. Furthermore, in cells lacking YRB2, the stability and abundance of the small ribosomal subunit is decreased in comparison with the large ribosomal subunit. To identify additional factors affecting small subunit export, we performed a large-scale screen of temperature-sensitive mutants. We isolated new alleles of several nucleoporins and Ran-GTPase regulators. Together with further analysis of existing mutants,we show that nucleoporins previously shown to be defective in ribosomal assembly are also defective in export of the small ribosomal subunit.

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Jiang, Mengxi, Kaustuv Datta, Angela Walker, John Strahler, Pia Bagamasbad, Philip C. Andrews, and Janine R. Maddock. "The Escherichia coli GTPase CgtAE Is Involved in Late Steps of Large Ribosome Assembly." Journal of Bacteriology 188, no. 19 (October 1, 2006): 6757–70. http://dx.doi.org/10.1128/jb.00444-06.

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ABSTRACT The bacterial ribosome is an extremely complicated macromolecular complex the in vivo biogenesis of which is poorly understood. Although several bona fide assembly factors have been identified, their precise functions and temporal relationships are not clearly defined. Here we describe the involvement of an Escherichia coli GTPase, CgtAE, in late steps of large ribosomal subunit biogenesis. CgtAE belongs to the Obg/CgtA GTPase subfamily, whose highly conserved members are predominantly involved in ribosome function. Mutations in CgtAE cause both polysome and rRNA processing defects; small- and large-subunit precursor rRNAs accumulate in a cgtAE mutant. In this study we apply a new semiquantitative proteomic approach to show that CgtAE is required for optimal incorporation of certain late-assembly ribosomal proteins into the large ribosomal subunit. Moreover, we demonstrate the interaction with the 50S ribosomal subunits of specific nonribosomal proteins (including heretofore uncharacterized proteins) and define possible temporal relationships between these proteins and CgtAE. We also show that purified CgtAE associates with purified ribosomal particles in the GTP-bound form. Finally, CgtAE cofractionates with the mature 50S but not with intermediate particles accumulated in other large ribosome assembly mutants.

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Ling, Clarence, and Dmitri N. Ermolenko. "Initiation factor 2 stabilizes the ribosome in a semirotated conformation." Proceedings of the National Academy of Sciences 112, no. 52 (December 14, 2015): 15874–79. http://dx.doi.org/10.1073/pnas.1520337112.

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Intersubunit rotation and movement of the L1 stalk, a mobile domain of the large ribosomal subunit, have been shown to accompany the elongation cycle of translation. The initiation phase of protein synthesis is crucial for translational control of gene expression; however, in contrast to elongation, little is known about the conformational rearrangements of the ribosome during initiation. Bacterial initiation factors (IFs) 1, 2, and 3 mediate the binding of initiator tRNA and mRNA to the small ribosomal subunit to form the initiation complex, which subsequently associates with the large subunit by a poorly understood mechanism. Here, we use single-molecule FRET to monitor intersubunit rotation and the inward/outward movement of the L1 stalk of the large ribosomal subunit during the subunit-joining step of translation initiation. We show that, on subunit association, the ribosome adopts a distinct conformation in which the ribosomal subunits are in a semirotated orientation and the L1 stalk is positioned in a half-closed state. The formation of the semirotated intermediate requires the presence of an aminoacylated initiator, fMet-tRNAfMet, and IF2 in the GTP-bound state. GTP hydrolysis by IF2 induces opening of the L1 stalk and the transition to the nonrotated conformation of the ribosome. Our results suggest that positioning subunits in a semirotated orientation facilitates subunit association and support a model in which L1 stalk movement is coupled to intersubunit rotation and/or IF2 binding.

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8

Stern, Seth, and Prakash Purohit. "An oligonucleotide analog approach to the decoding region of 16S rRNA." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 899–905. http://dx.doi.org/10.1139/o95-097.

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Despite the passage of about 30 years since the discovery of the translational activities of ribosomes and the outlining of the roles of the large and small subunits, the actual molecular basis for the mRNA decoding activities of the small subunit has remained essentially obscure. In this paper, we describe a new approach using oligonucleotide analogs of 16S ribosomal RNA, in which the small ribosomal subunit is effectively deconstructed into a smaller more experimentally tractable form. Specifically, we review the results of experiments using an oligonucleotide analog of the decoding region of 16S ribosomal RNA, suggesting that the decoding region is the functional core of the small subunit, that it contacts both mRNA codons and tRNA anticodons, and that it mediates and probably enhances codon–anticodon base pairing, that is, decoding.Key words: translation, ribosome, 30S, 16S, RNA, decoding, antibiotic.

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Levy, Michael, Reuven Falkovich, Shirley S. Daube, and Roy H. Bar-Ziv. "Autonomous synthesis and assembly of a ribosomal subunit on a chip." Science Advances 6, no. 16 (April 2020): eaaz6020. http://dx.doi.org/10.1126/sciadv.aaz6020.

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Ribosome biogenesis is an efficient and complex assembly process that has not been reconstructed outside a living cell so far, yet is the most critical step for establishing a self-replicating artificial cell. We recreated the biogenesis of Escherichia coli’s small ribosomal subunit by synthesizing and capturing all its ribosomal proteins and RNA on a chip. Surface confinement provided favorable conditions for autonomous stepwise assembly of new subunits, spatially segregated from original intact ribosomes. Our real-time fluorescence measurements revealed hierarchal assembly, cooperative interactions, unstable intermediates, and specific binding to large ribosomal subunits. Using only synthetic genes, our methodology is a crucial step toward creation of a self-replicating artificial cell and a general strategy for the mechanistic investigation of diverse multicomponent macromolecular machines.

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Bhattacharya, Arpita, Kerri B. McIntosh, Ian M. Willis, and Jonathan R. Warner. "Why Dom34 Stimulates Growth of Cells with Defects of 40S Ribosomal Subunit Biosynthesis." Molecular and Cellular Biology 30, no. 23 (September 27, 2010): 5562–71. http://dx.doi.org/10.1128/mcb.00618-10.

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ABSTRACT A set of genome-wide screens for proteins whose absence exacerbates growth defects due to pseudo-haploinsufficiency of ribosomal proteins in Saccharomyces cerevisiae identified Dom34 as being particularly important for cell growth when there is a deficit of 40S ribosomal subunits. In contrast, strains with a deficit of 60S ribosomal proteins were largely insensitive to the loss of Dom34. The slow growth of cells lacking Dom34 and haploinsufficient for a protein of the 40S subunit is caused by a severe shortage of 40S subunits available for translation initiation due to a combination of three effects: (i) the natural deficiency of 40S subunits due to defective synthesis, (ii) the sequestration of 40S subunits due to the large accumulation of free 60S subunits, and (iii) the accumulation of ribosomes “stuck” in a distinct 80S form, insensitive to the Mg2+ concentration, and at least temporarily unavailable for further translation. Our data suggest that these stuck ribosomes have neither mRNA nor tRNA. We postulate, based on our results and on previously published work, that the stuck ribosomes arise because of the lack of Dom34, which normally resolves a ribosome stalled due to insufficient tRNAs, to structural problems with its mRNA, or to a defect in the ribosome itself.

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Dissertations / Theses on the topic "Large ribosomal subunit"

1

Oristian, Daniel S. "Skeletal phenotype of mice lacking HIP/RPL29, a component of the large ribosomal subunit." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 70 p, 2007. http://proquest.umi.com/pqdweb?did=1397900441&sid=6&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Ho, Hei Ngam Jennifer. "Functional characterization of yeast NMD3 in the biogenesis and transport of the large (60S) ribosomal subunit /." Full text (PDF) from UMI/Dissertation Abstracts International, 2000. http://wwwlib.umi.com/cr/utexas/fullcit?p3004287.

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3

Ohmayer, Uli [Verfasser], and Herbert [Akademischer Betreuer] Tschochner. "Studies on the assembly process of large subunit ribosomal proteins in S.cerevisiae / Uli Ohmayer. Betreuer: Herbert Tschochner." Regensburg : Universitätsbibliothek Regensburg, 2014. http://d-nb.info/1077095961/34.

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4

Hurtado, Ana Isabel. "Large-subunit ribosomal RNA gene of Helicobacter and Campylobacter species : its role in genotypic identification and typing." Thesis, Queen Mary, University of London, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265831.

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5

Saini, Jagmohan [Verfasser]. "Structural and dynamic insights into oxazolidinone binding, selectivity and resistance to the large ribosomal subunit / Jagmohan Saini." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2018. http://d-nb.info/1154307018/34.

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6

Khreiss, Ali. "Dbp6, une ARN hélicase requise pour les étapes précoces de la synthèse de la grande sous-unité du ribosome eucaryotes." Thesis, Toulouse 3, 2022. http://www.theses.fr/2022TOU30061.

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L'activité de traduction des ribosomes est portée directement par les ARN ribosomiques (ARNr) qui composent ses deux sous-unités. La grande sous-unité (60S) est formée par les ARNr 25S, 5.8S et 5S et la petite sous-unité (40S) est formée par l'ARNr 18S. Un des principaux buts de la biogenèse des ribosomes est de convertir les ARNr en molécules correctement repliées et donc actives. La production des sous-unités ribosomiques est le résultat d'étapes successives de maturation de particules précurseurs, les pré-60S et les pré-40S, précurseurs de la grande (60S) et la petite (40S) sous-unité ribosomique, respectivement. Des protéines ribosomiques, des facteurs d'assemblage (FA) et des petites particules ribonucléoprotéique (snoRNPs) sont impliquées dans ces étapes successives. Ces facteurs jouent des rôles importants dans l'organisation spatiale et le maintien de l'intégrité structurelle des ARNr. Les ARN hélicases forment le plus grand groupe des FA et peuvent moduler les interactions ARN-ARN et ARN-protéine. Elles forment des candidates potentielles du repliement tridimensionnelle des ARNr. Cependant, les mécanismes par lesquels ces enzymes participent à la production des ribosomes restent vagues. Dans cette étude, on se focalise sur la fonction de l'ARN hélicase à boîte DEAD Dbp6 dans la structuration précoce de l'ARNr de la grande sous-unité ribosomique (60S). Dbp6 est essentielle pour la production de la grande sous-unité ribosomique. En son absence la production de la première particule pré-60S est inhibée. Néanmoins, l'importance des activités enzymatiques de Dbp6 pour la production de la première particule pré-60S n'ont pas été évalué et ses substrats ARN n'ont pas été déterminé. Dans notre étude, nous avons démontré que Dbp6 montre les activités biochimiques attendues, tels que l'hydrolyse d'ATP et la liaison à l'ARN. Dbp6 n'a pas montré une activité de dissociation de brins d'ARN (hélicase) dans les conditions testées dans le laboratoire. Nous avons pu identifier et étudier une activité d'association de brins (annealing) qui est contrôlée par l'ATP. En étudiant des mutants de Dbp6 qui ciblent les motifs conservés du cœur hélicase, nous avons établi que l'hydrolyse ATP est importante mais pas essentielle pour la survie cellulaire. Cependant, l'activité d'annealing semble jouer un rôle clé dans la fonction moléculaire de l'enzyme. Nous avons ensuite identifié les substrats in vivo de Dbp6 par l'expérience de pontage aux UV et analyse de l'ADNc (CRAC). Cela a montré que Dbp6 interagie principalement avec des snoARN qui se lient dans la région 5' de l'ARNr 25S et parmi lesquels certains sont des snoARN orphelins qui ne guident pas de modifications chimiques de nucléotides. Ces résultats soutiennent la notion que Dbp6 pourrait participer à l'organisation spatiale de cette région de l'ARNr de la grande sous-unité par l'intermédiaire des snoARN chaperons
The translation activity of ribosomes is directly held by the ribosomal RNAs (rRNAs) composing its two subunits. The large ribosomal subunit (60S) is formed of the 25S, 5.8S and 5S rRNAs and the small ribosomal subunit (40S) of the 18S rRNA. One of the main goals of ribosome biogenesis is to turn the rRNAs into correctly folded and active molecules. The production of the ribosomal subunits is the result of successive processing and maturation steps of precursor particles, the pre-60S and the pre-40S particles, precursors of the large (60S) and small (40S) ribosomal subunits, respectively. Ribosomal proteins (RPs), assembly factors (AFs) and small ribonucleoprotein particles (snoRNPs) are implicated in these successive steps. These factors play important roles in the spatial organization and in maintaining the structural integrity of the rRNAs. RNA helicases form the largest group of AFs and can modulate RNA-RNA and RNA-protein interactions. They form potential candidates for the tridimensional folding of the rRNAs. However, the mechanisms by which these enzymes participate in ribosomal particles production remain vague. In this study, we focus on the DEAD-box RNA helicase Dbp6's function in the early structuring of rRNAs of the large ribosomal subunit (60S). Dbp6 is essential for the production of the large ribosomal subunits. In its absence the production of the first pre-60S particle is impaired. Nevertheless, Dbp6 enzymatic activities' importance for the first pre-60S particle production has not been assessed nor have its RNA substrates been determined. In our study, we demonstrated that Dbp6 displays expected biochemical activities, such as ATP hydrolysis and RNA binding. Dbp6 did not show any RNA strands dissociation activity (helicase activity) in the conditions tested in the laboratory. We were able to identify and study a strand association activity (annealing activity) that is controlled by ATP. By studying Dbp6's mutants targeting the conserved helicase core motifs, we established that ATP hydrolysis is important but not essential for cell survival. However, the annealing activity seems to play a key role in the molecular function of the enzyme. We then identified Dbp6 in vivo substrates by in vivo cross-linking and analysis of cDNA experiment (CRAC). This showed that Dbp6 mostly interacts with snoRNAs that bind the 5' region of the 25S rRNA of which several are orphan snoRNA that do not guide the chemical modification of nucleotides. These findings support the notion that Dbp6 might participate in the spatial organization of this region of the large subunit rRNA by the intermediate of chaperoning snoRNAs

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Aime, Mary Catherine. "Generic concepts in the Crepidotaceae as inferred from nuclear large subunit ribosomal DNA sequences, morphology, and basidiospore dormancy patterns." Thesis, Virginia Tech, 1998. http://hdl.handle.net/10919/32285.

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The Crepidotaceae (Imai) Singer (Basidiomycetes: Agaricales) represents a proposed family of saprophytic fungi containing five agaricoid (Crepidotus, Tubaria, Melanomphalia, Simocybe, Pleurotellus) and four cyphelloid (Episphaeria, Phaeosolenia, Pellidiscus, Chromocyphella) genera. Several contemporary classification systems exist that delegate some or all of these genera to other agaric families. Phylogenetic relationships for the most prevalent genera in the Crepidotaceae were investigated using nuclear large subunit ribosomal DNA (LSU rDNA) sequences. Parsimony analysis of the molecular data supports the Singer classification of Crepidotus, Melanomphalia, and Simocybe as a single monophyletic unit within the Agaricales. The affinities of the genus Tubaria remain uncertain. Crepidotus (Fr.) Staude is the largest and most phenotypically variable genus in the Crepidotaceae. Sequencing of the LSU rDNA region for a cross-section of morphologically diverse species suggests that Crepidotus is not a monophyletic genus. Analysis of morphological characters for 23 Crepidotus taxa shows that characters traditionally applied for infrageneric classification of Crepidotus are homoplasic in origin, but that less commonly emphasized characters such as spore shape and ultrastructure of spore wall ornamentation may be indicative of monophyletic clades for this complex. A unique pattern of basidiospore dormancy and germination, unknown in any other species of agaric, is reported for 11 species of Crepidotus. Similar patterns were also encountered in species of Simocybe and Melanomphalia. In these species an endogenous period of spore dormancy of four to six months is followed by an activation period where the factors necessary for subsequent germination appear to involve a minimal nutritional component, water, and exposure to light.
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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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Gamalinda, Michael. "Ribosomal Proteins Orchestrate the Biogenesis of Eukaryotic Large Ribosomal Subunits in a Sequential Fashion." Research Showcase @ CMU, 2014. http://repository.cmu.edu/dissertations/441.

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Ribosome biogenesis in eukaryotes involves the transcription, folding, and processing of ribosomal RNA (rRNA), as well as the concomitant assembly of ribosomal proteins. Several hundred trans-acting assembly factors also play a role in the complex process of ribosome biogenesis. Investigations of the construction of ribosomes have focused primarily on the roles of these assembly factors. Little is understood about how ribosomal proteins (r-proteins) function in ribosomal subunit biogenesis in vivo, in either prokaryotes or eukaryotes. I began by focusing on a subset of r-proteins surrounding the polypeptide exit tunnel of the large ribosomal subunit in yeast. R-proteins in this neighborhood, namely L17, L26, L35, and L37, are of importance because they fail to assemble with preribosomes when early pre-rRNA processing steps are blocked. I showed that these rproteins are important for the next pre-rRNA processing, cleavage of the ITS2 spacer sequence in 27SB pre-rRNA. Interestingly, I showed that this biogenesis defect is not due to changes in structure of ITS2. Instead, these r-proteins are required for stable recruitment of key assembly factors that function in this event. I then carried out a global survey of the majority of r-proteins in the 60S subunit. I found that co-transcriptional binding of r-proteins influences post-transcriptional stabilization of 60S subunit structural neighborhoods. This led to a model wherein structural domains of eukaryotic large ribosomal subunits are constructed in a hierarchical fashion. Assembly begins at the convex solvent side, followed by the polypeptide exit tunnel, the intersubunit side, and finally the central protuberance. This hierarchy serves as an initial framework to further understand 60S assembly in vivo. I also showed that pre-ribosomes become more stable as assembly proceeds and that the final steps in 60S maturation occur around regions important for ribosome function. My results also support the hypothesis that the formation of the 3’ end of 27S pre-rRNA is important for early steps of 60S assembly occurring near the 5’ end of pre-rRNA. I also studied the functions of conserved and eukaryote-specific extensions of rproteins that are intrinsically disordered. This revealed distinct roles of extensions in 60S subunit biogenesis and supported a model for the sequential binding of globular and then extended domains of r-proteins during ribosome assembly. My surprising finding for a eukaryote-specific r-protein tail highlights the importance of understanding why several yeast r-proteins have evolved extra sequences that are conserved in higher eukaryotes. Together, these investigations revealed important principles governing ribosome assembly. Furthermore, striking similarities and differences between assembly of bacterial and eukaryotic large ribosomal subunits also emerged, providing insights into how these RNA–protein particles evolved.

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Kaminishi, Tatsuya, Andreas Schedlbauer, Attilio Fabbretti, Letizia Brandi, Lizarralde Borja Ochoa, Cheng-Guang He, Pohl Milon, Sean R. Connell, Claudio O. Gualerzi, and Paola Fucini. "Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A." Oxford University Press, 2015. http://hdl.handle.net/10757/608247.

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Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its primary mode of action involves sterically restricting access of the incoming aminoacyl-tRNA to the PTC.
Bizkaia:Talent and the European Union's Seventh Framework Program (Marie Curie Actions; COFUND; to S.C., A.S., T.K.); Marie Curie Actions Career Integration Grant (PCIG14-GA-2013-632072 to P.F.); Ministerio de Economía Y Competitividad (CTQ2014-55907-R to P.F., S.C.); FIRB Futuro in Ricerca from the Italian Ministero dell'Istruzione, dell'Universitá e della Ricerca (RBFR130VS5_001 to A.F.); Peruvian Programa Nacional de Innovación para la Competitividad y Productividad (382-PNICP-PIBA-2014 (to P.M. and A.F.)). Funding for open access charge: Institutional funding.
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Books on the topic "Large ribosomal subunit"

1

Humpert, Andrea J. Systematics of the genus Ramaria inferred from nuclear large subunit and mitochondrial small subunit ribosomal DNA sequences. 1999.

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Grubisha, Lisa C. Systematics of the genus Rhizopogon inferred from nuclear ribosomal DNA large subunit and internal transcribed spacer sequences. 1998.

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Amberg, Sean M. Nucleotide sequence of two chloroplast genes from a Chlorella-like green alga: The large subunit of Ribulose-1,5-bisphosphate carboxylase/oxygenase and ribosomal protein S14. 1989.

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Book chapters on the topic "Large ribosomal subunit"

1

Ludwig, W. "Structure and Phylogenetic Information of Large Subunit Ribosomal RNA." In Studies in Classification, Data Analysis, and Knowledge Organization, 289–97. Berlin, Heidelberg: Springer Berlin Heidelberg, 1992. http://dx.doi.org/10.1007/978-3-642-46757-8_30.

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Ban, Nenad, Poul Nissen, Peter B. Moore, and Thomas A. Steitz. "Crystal Structure of the Large Ribosomal Subunit at 5-Angstrom Resolution." In The Ribosome, 11–20. Washington, DC, USA: ASM Press, 2014. http://dx.doi.org/10.1128/9781555818142.ch2.

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Barbet-Massin, Emeline, Eli van der Sluis, Joanna Musial, Roland Beckmann, and Bernd Reif. "Reconstitution of Isotopically Labeled Ribosomal Protein L29 in the 50S Large Ribosomal Subunit for Solution-State and Solid-State NMR." In Protein Complex Assembly, 87–100. New York, NY: Springer New York, 2018. http://dx.doi.org/10.1007/978-1-4939-7759-8_6.

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Chen, R., and D. Fink. "Computing the Structure of Large Complexes: Modeling the 16S Ribosoma RNA." In Biological NMR Spectroscopy. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195094688.003.0025.

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Ribosomes are the sites of messenger RNA (mRNA) translation to protein, and thus are crucial to the normal functioning of all cells. These ribonucleoprotein particles are composed of a small (30S) subunit and a large (50S) subunit. The 30S subunit, in turn, is composed of a strand of RNA (16S rRNA) and 21 proteins ranging in molecular weight from 9 kD to 61 kD. Studies have demonstrated that ribosomal RNA is necessary for normal ribosome function and protein production (Dahlberg, 1989; Noller, 1991). In particular, 16S rRNA is essential for normal assembly and function of the 30S subunit, which is responsible for translation initiation (Hardestyand Kramer, 1985). Elucidating the structure of 16S rRNA could greatly aid our understanding of the molecular mechanisms for protein translation, and such basic structural information could ultimately have wide-ranging importance in fields such as pharmacology and drug design. Because of the difficulties associated with X-ray analysis of large complexes such as the ribosome (Eisenstein et al., 1991), high-resolution structural data for the 16S rRNA remain sparse. However, neutron diffraction studies have determined the relative positions of the 30S proteins (Capel et al., 1988), which, along with the reported 16S rRNA-protein interactions (Noller, 1991, Noller et al., unpublished; Brimacombe, 1991), enable low-resolution structural models—showing how the RNA associates with the protein components—to be built. Several studies have sought to take advantage of these structural data for the 308 subunit. Stern et al. have used interactive model building to produce a three-dimensional 16S rRNA structure (Stern et al., 1988). This method can produce viable models, but is hindered somewhat by subjectivity intrinsic to the process and by the nonexhaustive nature of its conformation search. Hubbard and Hearst have used distance geometry techniques to model the RNA structure, but did not incorporate neutron diffraction data on the protein positions (Hubbard and Hearst, 1991). Malhotra and Harvey have used an energy minimization technique to produce a set of possible conformations for 16S rRNA; their study, however, depends on electron microscopic studies on the molecule to provide initial information on surface topology (Malhotra, 1994).

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Nissen, Poul, Joseph A. Ippolito, Nenad Ban, Peter B. Moore, and Thomas A. Steitz. "RNA tertiary interactions in the large ribosomal subunit: The A-minor motif." In Structural Insights into Gene Expression and Protein Synthesis, 512–16. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0061.

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Hansen, Jeffrey L., Joseph A. Ippolito, Nenad Ban, Poul Nissen, Peter B. Moore, and Thomas A. Steitz. "The Structures of Four Macrolide Antibiotics Bound to the Large Ribosomal Subunit." In Structural Insights into Gene Expression and Protein Synthesis, 525–36. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0063.

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Ban, Nenad, Betty Freeborn, Poul Nissen, Pawel Penczek, Robert A. Grassucci, Robert Sweet, Joachim Frank, Peter B. Moore, and Thomas A. Steitz. "A 9 Å Resolution X-Ray Crystallographic Map of the Large Ribosomal Subunit." In Structural Insights into Gene Expression and Protein Synthesis, 467–77. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0057.

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Ban, Nenad, Poul Nissen, Jeffrey Hansen, Peter B. Moore, and Thomas A. Steitz. "The Complete Atomic Structure of the Large Ribosomal Subunit at 2.4 Å Resolution." In Structural Insights into Gene Expression and Protein Synthesis, 485–500. WORLD SCIENTIFIC, 2020. http://dx.doi.org/10.1142/9789811215865_0059.

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Ban, Nenad, Betty Freeborn, Poul Nissen, Pawel Penczek, Robert A. Grassucci, Robert Sweet, Joachim Frank, Peter B. Moore, and Thomas A. Steitz. "A 9 Å Resolution X-Ray Crystallographic Map of the Large Ribosomal Subunit." In Series in Structural Biology, 245–55. World Scientific, 2018. http://dx.doi.org/10.1142/9789813234864_0023.

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Ballesta, Juan P. G., and Miguel Remacha. "The Large Ribosomal Subunit Stalk as a Regulatory Element of the Eukaryotic Translational Machinery." In Progress in Nucleic Acid Research and Molecular Biology, 157–93. Elsevier, 1996. http://dx.doi.org/10.1016/s0079-6603(08)60193-2.

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Reports on the topic "Large ribosomal subunit"

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Ostersetzer-Biran, Oren, and Jeffrey Mower. Novel strategies to induce male sterility and restore fertility in Brassicaceae crops. United States Department of Agriculture, January 2016. http://dx.doi.org/10.32747/2016.7604267.bard.

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Abstract Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for rRNAs, tRNAs and some mitochondrial proteins. Although all mitochondria have probably evolved from a common alpha-proteobacterial ancestor, notable genomic reorganizations have occurred in the mtDNAs of different eukaryotic lineages. Plant mtDNAs are notably larger and more variable in size (ranging from 70~11,000 kbp in size) than the mrDNAs in higher animals (16~19 kbp). Another unique feature of plant mitochondria includes the presence of both circular and linear DNA fragments, which undergo intra- and intermolecular recombination. DNA-seq data indicate that such recombination events result with diverged mitochondrial genome configurations, even within a single plant species. One common plant phenotype that emerges as a consequence of altered mtDNA configuration is cytoplasmic male sterility CMS (i.e. reduced production of functional pollen). The maternally-inherited male sterility phenotype is highly valuable agriculturally. CMS forces the production of F1 hybrids, particularly in predominantly self-pollinating crops, resulting in enhanced crop growth and productivity through heterosis (i.e. hybrid vigor or outbreeding enhancement). CMS lines have been implemented in some cereal and vegetables, but most crops still lack a CMS system. This work focuses on the analysis of the molecular basis of CMS. We also aim to induce nuclear or organellar induced male-sterility in plants, and to develop a novel approach for fertility restoration. Our work focuses on Brassicaceae, a large family of flowering plants that includes Arabidopsis thaliana, a key model organism in plant sciences, as well as many crops of major economic importance (e.g., broccoli, cauliflower, cabbage, and various seeds for oil production). In spite of the genomic rearrangements in the mtDNAs of plants, the number of genes and the coding sequences are conserved among different mtDNAs in angiosperms (i.e. ~60 genes encoding different tRNAs, rRNAs, ribosomal proteins and subunits of the respiratory system). Yet, in addition to the known genes, plant mtDNAs also harbor numerous ORFs, most of which are not conserved among species and are currently of unknown function. Remarkably, and relevant to our study, CMS in plants is primarily associated with the expression of novel chimericORFs, which likely derive from recombination events within the mtDNAs. Whereas the CMS loci are localized to the mtDNAs, the factors that restore fertility (Rfs) are identified as nuclear-encoded RNA-binding proteins. Interestingly, nearly all of the Rf’s are identified as pentatricopeptide repeat (PPR) proteins, a large family of modular RNA-binding proteins that mediate several aspects of gene expression primarily in plant organelles. In this project we proposed to develop a system to test the ability of mtORFs in plants, which are closely related to known CMS factors. We will induce male fertility in various species of Brassicaceae, and test whether a down-relation in the expression of the recombinantCMS-genes restores fertility, using synthetically designed PPR proteins.

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