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Готові списки джерел за темами / Large ribosomal subunit / Статті в журналах

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Статті в журналах з теми "Large ribosomal subunit"

Автор: Grafiati

Опубліковано: 7 вересня 2022

Оновлено: 19 липня 2025

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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 (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-med

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2

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.

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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

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3

Petrov, Anton S., Burak Gulen, Ashlyn M. Norris, et al. "History of the ribosome and the origin of translation." Proceedings of the National Academy of Sciences 112, no. 50 (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 f

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4

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 (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 ribos

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5

Moy, Terence I., and Pamela A. Silver. "Requirements for the nuclear export of the small ribosomal subunit." Journal of Cell Science 115, no. 14 (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 expor

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6

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 (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 subuni

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7

Jiang, Mengxi, Kaustuv Datta, Angela Walker, et al. "The Escherichia coli GTPase CgtAE Is Involved in Late Steps of Large Ribosome Assembly." Journal of Bacteriology 188, no. 19 (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; s

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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 (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 o

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9

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 (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 inter

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10

Gadal, Olivier, Daniela Strauß, Jacques Kessl, Bernard Trumpower, David Tollervey, and Ed Hurt. "Nuclear Export of 60S Ribosomal Subunits Depends on Xpo1p and Requires a Nuclear Export Sequence-Containing Factor, Nmd3p, That Associates with the Large Subunit Protein Rpl10p." Molecular and Cellular Biology 21, no. 10 (2001): 3405–15. http://dx.doi.org/10.1128/mcb.21.10.3405-3415.2001.

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ABSTRACT Nuclear export of ribosomes requires a subset of nucleoporins and the Ran system, but specific transport factors have not been identified. Using a large subunit reporter (Rpl25p-eGFP), we have isolated several temperature-sensitive ribosomal export (rix) mutants. One of these corresponds to the ribosomal protein Rpl10p, which interacts directly with Nmd3p, a conserved and essential protein associated with 60S subunits. We find that thermosensitive nmd3 mutants are impaired in large subunit export. Strikingly, Nmd3p shuttles between the nucleus and cytoplasm and is exported by the nucl

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11

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 (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 o

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12

Gregory, Brian, Nusrat Rahman, Ananth Bommakanti, et al. "The small and large ribosomal subunits depend on each other for stability and accumulation." Life Science Alliance 2, no. 2 (2019): e201800150. http://dx.doi.org/10.26508/lsa.201800150.

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The 1:1 balance between the numbers of large and small ribosomal subunits can be disturbed by mutations that inhibit the assembly of only one of the subunits. Here, we have investigated if the cell can counteract an imbalance of the number of the two subunits. We show that abrogating 60S assembly blocks 40S subunit accumulation. In contrast, cessation of the 40S pathways does not prevent 60S accumulation, but does, however, lead to fragmentation of the 25S rRNA in 60S subunits and formation of a 55S ribosomal particle derived from the 60S. We also present evidence suggesting that these events

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13

Fan, Haitian, Joseph Hahm, Stephen Diggs, J. Jefferson P. Perry, and Gregor Blaha. "Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli." Journal of Biological Chemistry 290, no. 34 (2015): 20856–64. http://dx.doi.org/10.1074/jbc.m115.659136.

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The translational GTPase BipA regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. Under these conditions, BipA associates with the small ribosomal subunit. BipA also has a second function to promote the efficiency of late steps in biogenesis of large ribosomal subunits at low temperatures, presumably while bound to the ribosome. During starvation, the cellular concentration of stress alarmone guanosine-3′, 5′-bis pyrophosphate (pp

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14

Pöll, Gisela, Michael Pilsl, Joachim Griesenbeck, Herbert Tschochner, and Philipp Milkereit. "Analysis of subunit folding contribution of three yeast large ribosomal subunit proteins required for stabilisation and processing of intermediate nuclear rRNA precursors." PLOS ONE 16, no. 11 (2021): e0252497. http://dx.doi.org/10.1371/journal.pone.0252497.

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In yeast and human cells many of the ribosomal proteins (r-proteins) are required for the stabilisation and productive processing of rRNA precursors. Functional coupling of r-protein assembly with the stabilisation and maturation of subunit precursors potentially promotes the production of ribosomes with defined composition. To further decipher mechanisms of such an intrinsic quality control pathway we analysed here the contribution of three yeast large ribosomal subunit r-proteins rpL2 (uL2), rpL25 (uL23) and rpL34 (eL34) for intermediate nuclear subunit folding steps. Structure models obtain

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15

Bachand, François, Daniel H. Lackner, Jürg Bähler, and Pamela A. Silver. "Autoregulation of Ribosome Biosynthesis by a Translational Response in Fission Yeast." Molecular and Cellular Biology 26, no. 5 (2006): 1731–42. http://dx.doi.org/10.1128/mcb.26.5.1731-1742.2006.

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ABSTRACT Maintaining the appropriate balance between the small and large ribosomal subunits is critical for translation and cell growth. We previously identified the 40S ribosomal protein S2 (rpS2) as a substrate of the protein arginine methyltransferase 3 (RMT3) and reported a misregulation of the 40S/60S ratio in rmt3 deletion mutants of Schizosaccharomyces pombe. For this study, using DNA microarrays, we have investigated the genome-wide biological response of rmt3-null cells to this ribosomal subunit imbalance. Whereas little change was observed at the transcriptional level, a number of ge

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16

Schuwirth, Barbara S., Maria A. Borovinskaya, Cathy W. Hau, et al. "Structures of the Bacterial Ribosome at 3.5 Å Resolution." Science 310, no. 5749 (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 t

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17

Oeffinger, Marlene. "Joining the interface: a site for Nmd3 association on 60S ribosome subunits." Journal of Cell Biology 189, no. 7 (2010): 1071–73. http://dx.doi.org/10.1083/jcb.201006033.

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The adaptor protein Nmd3 is required for Crm1-dependent export of large ribosomal subunits from the nucleus. In this issue, Sengupta et al. (2010. J. Cell Biol. doi:10.1083/jcb.201001124) identify a binding site for yeast Nmd3 on 60S ribosomal subunits using cryoelectron microscopy and suggest a conformational model for its release in the cytoplasm. The study provides the first detailed structural description of a ribosome biogenesis factor in complex with the large subunit.

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18

Schaefer, Laura, William C. Uicker, Catherine Wicker-Planquart, Anne-Emmanuelle Foucher, Jean-Michel Jault, and Robert A. Britton. "Multiple GTPases Participate in the Assembly of the Large Ribosomal Subunit in Bacillus subtilis." Journal of Bacteriology 188, no. 23 (2006): 8252–58. http://dx.doi.org/10.1128/jb.01213-06.

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ABSTRACT GTPases have been demonstrated to be necessary for the proper assembly of the ribosome in bacteria and eukaryotes. Here, we show that the essential GTPases YphC and YsxC are required for large ribosomal subunit biogenesis in Bacillus subtilis. Sucrose density gradient centrifugation of large ribosomal subunits isolated from YphC-depleted cells and YsxC-depleted cells indicates that they are similar to the 45S intermediate previously identified in RbgA-depleted cells. The sedimentation of the large-subunit intermediate isolated from YphC-depleted cells was identical to the intermediate

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19

Konikkat, Salini, and John L. Woolford,. "Principles of 60S ribosomal subunit assembly emerging from recent studies in yeast." Biochemical Journal 474, no. 2 (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

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20

Jiang, M., S. M. Sullivan, A. K. Walker, J. R. Strahler, P. C. Andrews, and J. R. Maddock. "Identification of Novel Escherichia coli Ribosome-Associated Proteins Using Isobaric Tags and Multidimensional Protein Identification Techniques." Journal of Bacteriology 189, no. 9 (2007): 3434–44. http://dx.doi.org/10.1128/jb.00090-07.

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ABSTRACT Biogenesis of the large ribosomal subunit requires the coordinate assembly of two rRNAs and 33 ribosomal proteins. In vivo, additional ribosome assembly factors, such as helicases, GTPases, pseudouridine synthetases, and methyltransferases, are also critical for ribosome assembly. To identify novel ribosome-associated proteins, we used a proteomic approach (isotope tagging for relative and absolute quantitation) that allows for semiquantitation of proteins from complex protein mixtures. Ribosomal subunits were separated by sucrose density centrifugation, and the relevant fractions wer

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21

Videira, A., M. L. Teles Grilo, S. Werner, and H. Bertrand. "Mitochondrial gene expression in a nuclear mutant of Neurospora deficient in large subunits of mitochondrial ribosomes." Genome 30, no. 5 (1988): 802–7. http://dx.doi.org/10.1139/g88-129.

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A new cytochrome a and b deficient nuclear mutant of Neurospora crassa, cyt-U-28, is defective in the assembly of large subunits of mitochondrial ribosomes. Nonetheless, this mutant overproduces apparently normal small subunits of mitochondrial ribosomes, even though it should be deficient for the S5 ribosomal protein required for assembly of the particles beyond the CAP30S stage. The mitochondria of cyt-U-28 indeed synthesize only small amounts of most mitochondrial polypeptides, including cytochrome oxidase subunits I, II, and III, contain very low amounts of the normal seven-polypeptide cyt

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22

Mandiyan, Valsan, and G. Ramananda Rao. "Separation of cytoplasmic ribosomal proteins of Microsporum canis." Canadian Journal of Microbiology 33, no. 4 (1987): 339–43. http://dx.doi.org/10.1139/m87-058.

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The cytoplasmic ribosomal proteins of Microsporum canis were characterised in basic–acidic and basic–SDS two-dimensional polyacrylamide gel electrophoresis systems. The small subunit contained 28 proteins and the large subunit 38 proteins. The molecular weights of these proteins were in the range of 32 500 to 7600 and 48 000 to 11 000 in the small and large subunits, respectively. The 80S ribosomes showed 65 and 66 protein spots in basic–acidic and basic–SDS gel systems, respectively.

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23

Maggi, Leonard B., Michael Kuchenruether, David Y. A. Dadey, et al. "Nucleophosmin Serves as a Rate-Limiting Nuclear Export Chaperone for the Mammalian Ribosome." Molecular and Cellular Biology 28, no. 23 (2008): 7050–65. http://dx.doi.org/10.1128/mcb.01548-07.

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ABSTRACT Nucleophosmin (NPM) (B23) is an essential protein in mouse development and cell growth; however, it has been assigned numerous roles in very diverse cellular processes. Here, we present a unified mechanism for NPM's role in cell growth; NPM directs the nuclear export of both 40S and 60S ribosomal subunits. NPM interacts with rRNA and large and small ribosomal subunit proteins and also colocalizes with large and small ribosomal subunit proteins in the nucleolus, nucleus, and cytoplasm. The transduction of NPM shuttling-defective mutants or the loss of Npm1 inhibited the nuclear export

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24

SZYMAŃSKI, Maciej, Mirosawa Z. BARCISZEWSKA, Volker A. ERDMANN, and Jan BARCISZEWSKI. "5 S rRNA: structure and interactions." Biochemical Journal 371, no. 3 (2003): 641–51. http://dx.doi.org/10.1042/bj20020872.

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5S rRNA is an integral component of the large ribosomal subunit in all known organisms. Despite many years of intensive study, the function of 5S rRNA in the ribosome remains unknown. Advances in the analysis of ribosome structure that have revealed the crystal structures of large ribosomal subunits and of the complete ribosome from various organisms put the results of studies on 5S rRNA in a new perspective. This paper summarizes recently published data on the structure and function of 5S rRNA and its interactions in complexes with proteins, within and outside the ribosome.

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25

Lavdovskaia, Elena, Kärt Denks, Franziska Nadler, et al. "Dual function of GTPBP6 in biogenesis and recycling of human mitochondrial ribosomes." Nucleic Acids Research 48, no. 22 (2020): 12929–42. http://dx.doi.org/10.1093/nar/gkaa1132.

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Abstract Translation and ribosome biogenesis in mitochondria require auxiliary factors that ensure rapid and accurate synthesis of mitochondrial proteins. Defects in translation are associated with oxidative phosphorylation deficiency and cause severe human diseases, but the exact roles of mitochondrial translation-associated factors are not known. Here we identify the functions of GTPBP6, a homolog of the bacterial ribosome-recycling factor HflX, in human mitochondria. Similarly to HflX, GTPBP6 facilitates the dissociation of ribosomes in vitro and in vivo. In contrast to HflX, GTPBP6 is also

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26

Saurer, Martin, David J. F. Ramrath, Moritz Niemann, et al. "Mitoribosomal small subunit biogenesis in trypanosomes involves an extensive assembly machinery." Science 365, no. 6458 (2019): 1144–49. http://dx.doi.org/10.1126/science.aaw5570.

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Mitochondrial ribosomes (mitoribosomes) are large ribonucleoprotein complexes that synthesize proteins encoded by the mitochondrial genome. An extensive cellular machinery responsible for ribosome assembly has been described only for eukaryotic cytosolic ribosomes. Here we report that the assembly of the small mitoribosomal subunit in Trypanosoma brucei involves a large number of factors and proceeds through the formation of assembly intermediates, which we analyzed by using cryo–electron microscopy. One of them is a 4-megadalton complex, referred to as the small subunit assemblosome, in which

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27

Datta, Kaustuv, Jennifer L. Fuentes, and Janine R. Maddock. "The Yeast GTPase Mtg2p Is Required for Mitochondrial Translation and Partially Suppresses an rRNA Methyltransferase Mutant,mrm2." Molecular Biology of the Cell 16, no. 2 (2005): 954–63. http://dx.doi.org/10.1091/mbc.e04-07-0622.

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The assembly of ribosomes involves the coordinated processing and modification of rRNAs with the temporal association of ribosomal proteins. This process is regulated by assembly factors such as helicases, modifying enzymes, and GTPases. In contrast to the assembly of cytoplasmic ribosomes, there is a paucity of information concerning the role of assembly proteins in the biogenesis of mitochondrial ribosomes. In this study, we demonstrate that the Saccharomyces cerevisiae GTPase Mtg2p (Yhr168wp) is essential for mitochondrial ribosome function. Cells lacking MTG2 lose their mitochondrial DNA,

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28

Ho, Jennifer Hei-Ngam, George Kallstrom, and Arlen W. Johnson. "Nmd3p Is a Crm1p-Dependent Adapter Protein for Nuclear Export of the Large Ribosomal Subunit." Journal of Cell Biology 151, no. 5 (2000): 1057–66. http://dx.doi.org/10.1083/jcb.151.5.1057.

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In eukaryotic cells, nuclear export of nascent ribosomal subunits through the nuclear pore complex depends on the small GTPase Ran. However, neither the nuclear export signals (NESs) for the ribosomal subunits nor the receptor proteins, which recognize the NESs and mediate export of the subunits, have been identified. We showed previously that Nmd3p is an essential protein from yeast that is required for a late step in biogenesis of the large (60S) ribosomal subunit. Here, we show that Nmd3p shuttles and that deletion of the NES from Nmd3p leads to nuclear accumulation of the mutant protein, i

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29

Pollutri, Daniela, and Marianna Penzo. "Ribosomal Protein L10: From Function to Dysfunction." Cells 9, no. 11 (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

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30

Möller-Hergt, Braulio Vargas, Andreas Carlström, Katharina Stephan, Axel Imhof, and Martin Ott. "The ribosome receptors Mrx15 and Mba1 jointly organize cotranslational insertion and protein biogenesis in mitochondria." Molecular Biology of the Cell 29, no. 20 (2018): 2386–96. http://dx.doi.org/10.1091/mbc.e18-04-0227.

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Mitochondrial gene expression in Saccharomyces cerevisiae is responsible for the production of highly hydrophobic subunits of the oxidative phosphorylation system. Membrane insertion occurs cotranslationally on membrane-bound mitochondrial ribosomes. Here, by employing a systematic mass spectrometry–based approach, we discovered the previously uncharacterized membrane protein Mrx15 that interacts via a soluble C-terminal domain with the large ribosomal subunit. Mrx15 contacts mitochondrial translation products during their synthesis and plays, together with the ribosome receptor Mba1, an overl

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31

Eisinger, D. P., F. A. Dick, and B. L. Trumpower. "Qsr1p, a 60S ribosomal subunit protein, is required for joining of 40S and 60S subunits." Molecular and Cellular Biology 17, no. 9 (1997): 5136–45. http://dx.doi.org/10.1128/mcb.17.9.5136.

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QSR1 is a recently discovered, essential Saccharomyces cerevisiae gene, which encodes a 60S ribosomal subunit protein. Thirty-one unique temperature-sensitive alleles of QSR1 were generated by regional codon randomization within a conserved 20-amino-acid sequence of the QSR1-encoded protein. The temperature-sensitive mutants arrest as viable, large, unbudded cells 24 to 48 h after a shift to 37 degrees C. Polysome and ribosomal subunit analysis by velocity gradient centrifugation of lysates from temperature-sensitive qsr1 mutants and from cells in which Qsr1p was depleted by down regulation of

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Liu, Zheng, Cristina Gutierrez-Vargas, Jia Wei, et al. "Structure and assembly model for the Trypanosoma cruzi 60S ribosomal subunit." Proceedings of the National Academy of Sciences 113, no. 43 (2016): 12174–79. http://dx.doi.org/10.1073/pnas.1614594113.

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Ribosomes of trypanosomatids, a family of protozoan parasites causing debilitating human diseases, possess multiply fragmented rRNAs that together are analogous to 28S rRNA, unusually large rRNA expansion segments, and r-protein variations compared with other eukaryotic ribosomes. To investigate the architecture of the trypanosomatid ribosomes, we determined the 2.5-Å structure of the Trypanosoma cruzi ribosome large subunit by single-particle cryo-EM. Examination of this structure and comparative analysis of the yeast ribosomal assembly pathway allowed us to develop a stepwise assembly model

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Boublik, M., and J. S. Wall. "Structure of rRNA in the ribosome." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (1992): 462–63. http://dx.doi.org/10.1017/s042482010012271x.

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Ribosomes are complex subcellular organelles playing a central role in protein biosynthesis. They are composed of more than fifty different proteins and three or four ribonucleic acids (rRNA) unevenly distributed (with no symmetry) between the large and small ribosomal subunit. It has been well established that ribosomal proteins and rRNAs are both involved in formation of the internal architecture of the ribosome as well as its function in protein synthesis. Understanding the fundamental relationship between structure and function requires establishment of the 3-D structure of the ribosome an

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34

Verma, J., and N. Agrawal. "Molecular characterization of Indian species of the genus Cornudiscoides Kulkarni, 1969 (Monogenoidea: Dactylogyridae)." Journal of Applied and Natural Science 13, no. 1 (2021): 1–7. http://dx.doi.org/10.31018/jans.v13i1.2434.

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Molecular characterization and phylogenetic study based on partial sequences of 28S and 18S ribosomal DNA (rDNA) of sixteen Indian species of the genus Cornudiscoides (Monogenoidea: Dactylogyridae) were conducted to decode the genetic relationship between them and with other members of the family Dactylogyridae. Blastn searches disclosed the significant similarity among the species of the Cornudiscoides for large ribosomal subunits as well as for small ribosomal subunit showing genetic relatedness. The phylogenetic tree using neighbour-joining (NJ) and minimum evolution (ME) methods for 28S ri

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Marshall, R. Andrew, Magdalena Dorywalska, and Joseph D. Puglisi. "Irreversible chemical steps control intersubunit dynamics during translation." Proceedings of the National Academy of Sciences 105, no. 40 (2008): 15364–69. http://dx.doi.org/10.1073/pnas.0805299105.

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The ribosome, a two-subunit macromolecular machine, deciphers the genetic code and catalyzes peptide bond formation. Dynamic rotational movement between ribosomal subunits is likely required for efficient and accurate protein synthesis, but direct observation of intersubunit dynamics has been obscured by the repetitive, multistep nature of translation. Here, we report a collection of single-molecule fluorescence resonance energy transfer assays that reveal a ribosomal intersubunit conformational cycle in real time during initiation and the first round of elongation. After subunit joining and d

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Umaer, Khan, Martin Ciganda, and Noreen Williams. "Ribosome Biogenesis in African Trypanosomes Requires Conserved and Trypanosome-Specific Factors." Eukaryotic Cell 13, no. 6 (2014): 727–37. http://dx.doi.org/10.1128/ec.00307-13.

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ABSTRACTLarge ribosomal subunit protein L5 is responsible for the stability and trafficking of 5S rRNA to the site of eukaryotic ribosomal assembly. InTrypanosoma brucei, in addition to L5, trypanosome-specific proteins P34 and P37 also participate in this process. These two essential proteins form a novel preribosomal particle through interactions with both the ribosomal protein L5 and 5S rRNA. We have generated a procyclic L5 RNA interference cell line and found that L5 itself is a protein essential for trypanosome growth, despite the presence of other 5S rRNA binding proteins. Loss of L5 de

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Fatkhullin, Bulat, Alexander Golubev, Natalia Garaeva, Shamil Validov, Azat Gabdulkhakov, and Marat Yusupov. "Y98 Mutation Leads to the Loss of RsfS Anti-Association Activity in Staphylococcus aureus." International Journal of Molecular Sciences 23, no. 18 (2022): 10931. http://dx.doi.org/10.3390/ijms231810931.

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Ribosomal silencing factor S (RsfS) is a conserved protein that plays a role in the mechanisms of ribosome shutdown and cell survival during starvation. Recent studies demonstrated the involvement of RsfS in the biogenesis of the large ribosomal subunit. RsfS binds to the uL14 ribosomal protein on the large ribosomal subunit and prevents its association with the small subunit. Here, we estimated the contribution of RsfS amino acid side chains at the interface between RsfS and uL14 to RsfS anti-association function in Staphylococcus aureus through in vitro experiments: centrifugation in sucrose

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Sengupta, Jayati, Cyril Bussiere, Jesper Pallesen, Matthew West, Arlen W. Johnson, and Joachim Frank. "Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit." Journal of Cell Biology 189, no. 7 (2010): 1079–86. http://dx.doi.org/10.1083/jcb.201001124.

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The nucleocytoplasmic shuttling protein Nmd3 is an adaptor for export of the 60S ribosomal subunit from the nucleus. Nmd3 binds to nascent 60S subunits in the nucleus and recruits the export receptor Crm1 to facilitate passage through the nuclear pore complex. In this study, we present a cryoelectron microscopy (cryo-EM) reconstruction of the 60S subunit in complex with Nmd3 from Saccharomyces cerevisiae. The density corresponding to Nmd3 is directly visible in the cryo-EM map and is attached to the regions around helices 38, 69, and 95 of the 25S ribosomal RNA (rRNA), the helix 95 region bein

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Horne, Z., and J. Hesketh. "Immunological localization of ribosomes in striated rat muscle. Evidence for myofibrillar association and ontological changes in the subsarcolemmal:myofibrillar distribution." Biochemical Journal 268, no. 1 (1990): 231–36. http://dx.doi.org/10.1042/bj2680231.

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Ribosome distribution in skeletal-muscle fibres was investigated immunohistochemically by using polyclonal antibodies raised against large-ribosomal-subunit proteins isolated from rat liver. Immunoblot analysis showed the antibodies to recognize five major proteins of the large subunit; these were identified as L4, L6, L7, L15 and L17 by two-dimensional electrophoresis. Immunohistochemistry of frozen rat skeletal-muscle sections showed staining of both the subsarcolemmal and intermyofibrillar cytoplasm. A distinct banding pattern was observed, and when peroxidase and phase-contrast images of t

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40

Fuchs, Gabriele, Alexey N. Petrov, Caleb D. Marceau, et al. "Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site." Proceedings of the National Academy of Sciences 112, no. 2 (2014): 319–25. http://dx.doi.org/10.1073/pnas.1421328111.

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Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data su

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Gupta, Ankit, Priyanka Shah, Afreen Haider, et al. "Reduced ribosomes of the apicoplast and mitochondrion of Plasmodium spp. and predicted interactions with antibiotics." Open Biology 4, no. 5 (2014): 140045. http://dx.doi.org/10.1098/rsob.140045.

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Apicomplexan protists such as Plasmodium and Toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. Although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. We carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite organellar or nuclear genomes, accompanied by a survey of ribosome assembly factors for the apicoplast

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Garaeva, Natalia, Aydar Bikmullin, Evelina Klochkova, Shamil Validov, Marat Yusupov, and Konstantin Usachev. "Abstract P-31: Assembly of the Complex of the 30S Ribosomal Subunit and the Ribosome Maturation Factor P from Staphylococcus aureus for Structural Studies by Cryo-Electron Microscopy." International Journal of Biomedicine 11, Suppl_1 (2021): S25. http://dx.doi.org/10.21103/ijbm.11.suppl_1.p31.

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Background: Staphylococcus aureus (S. aureus) is one of the main human pathogens causing numerous nosocomial soft tissue infections and is among the best-known causes of bacterial infections. The bacterial 70S ribosome consists of two subunits, designated the 30S (small) and 50S (large) subunits. The small subunit (30S) consists of 16S ribosomal RNA (rRNA), from which the assembly of 30S begins, and 21 ribosomal proteins (r-proteins). The ribosome maturation factor P (RimP protein) binds to the free 30S subunit. Strains lacking RimP accumulate immature 16S rRNA, and fewer polysomes and an incr

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43

Nikolaeva, Daria D., Mikhail S. Gelfand, and Sofya K. Garushyants. "Simplification of Ribosomes in Bacteria with Tiny Genomes." Molecular Biology and Evolution 38, no. 1 (2020): 58–66. http://dx.doi.org/10.1093/molbev/msaa184.

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Abstract The ribosome is an essential cellular machine performing protein biosynthesis. Its structure and composition are highly conserved in all species. However, some bacteria have been reported to have an incomplete set of ribosomal proteins. We have analyzed ribosomal protein composition in 214 small bacterial genomes (&lt;1 Mb) and found that although the ribosome composition is fairly stable, some ribosomal proteins may be absent, especially in bacteria with dramatically reduced genomes. The protein composition of the large subunit is less conserved than that of the small subunit. We

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Farrar, Jason E., Michelle Nater, Emi Caywood, et al. "Abnormalities of the large ribosomal subunit protein, Rpl35a, in Diamond-Blackfan anemia." Blood 112, no. 5 (2008): 1582–92. http://dx.doi.org/10.1182/blood-2008-02-140012.

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Abstract Diamond-Blackfan anemia (DBA) is an inherited bone marrow failure syndrome characterized by anemia, congenital abnormalities, and cancer predisposition. Small ribosomal subunit genes RPS19, RPS24, and RPS17 are mutated in approximately one-third of patients. We used a candidate gene strategy combining high-resolution genomic mapping and gene expression microarray in the analysis of 2 DBA patients with chromosome 3q deletions to identify RPL35A as a potential DBA gene. Sequence analysis of a cohort of DBA probands confirmed involvement RPL35A in DBA. shRNA inhibition shows that Rpl35a

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45

Li, Wenzhu, Jing Zhang, Wenpeng Cheng, et al. "Differential Paralog-Specific Expression of Multiple Small Subunit Proteins Cause Variations in Rpl42/eL42 Incorporation in Ribosome in Fission Yeast." Cells 11, no. 15 (2022): 2381. http://dx.doi.org/10.3390/cells11152381.

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Ribosomes within a cell are commonly viewed as biochemically homogenous RNA–protein super-complexes performing identical functions of protein synthesis. However, recent evidence suggests that ribosomes may be a more dynamic macromolecular complex with specialized roles. Here, we present extensive genetic and molecular evidence in the fission yeast S. pombe that the paralogous genes for many ribosomal proteins (RPs) are functionally different, despite that they encode the same ribosomal component, often with only subtle differences in the sequences. Focusing on the rps8 paralog gene deletions r

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Dey, Sandip, Chiranjit Biswas, and Jayati Sengupta. "The universally conserved GTPase HflX is an RNA helicase that restores heat-damaged Escherichia coli ribosomes." Journal of Cell Biology 217, no. 7 (2018): 2519–29. http://dx.doi.org/10.1083/jcb.201711131.

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The ribosome-associated GTPase HflX acts as an antiassociation factor upon binding to the 50S ribosomal subunit during heat stress in Escherichia coli. Although HflX is recognized as a guanosine triphosphatase, several studies have shown that the N-terminal domain 1 of HflX is capable of hydrolyzing adenosine triphosphate (ATP), but the functional role of its adenosine triphosphatase (ATPase) activity remains unknown. We demonstrate that E. coli HflX possesses ATP-dependent RNA helicase activity and is capable of unwinding large subunit ribosomal RNA. A cryo–electron microscopy structure of th

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Lin, Bin, Desiree A. Thayer, and Janine R. Maddock. "The Caulobacter crescentus CgtAC Protein Cosediments with the Free 50S Ribosomal Subunit." Journal of Bacteriology 186, no. 2 (2004): 481–89. http://dx.doi.org/10.1128/jb.186.2.481-489.2004.

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ABSTRACT The Obg family of GTPases is widely conserved and predicted to play an as-yet-unknown role in translation. Recent reports provide circumstantial evidence that both eukaryotic and prokaryotic Obg proteins are associated with the large ribosomal subunit. Here we provide direct evidence that the Caulobacter crescentus CgtAC protein is associated with the free large (50S) ribosomal subunit but not with 70S monosomes or with translating ribosomes. In contrast to the Bacillus subtilis and Escherichia coli proteins, CgtAC does not fractionate in a large complex by gel filtration, indicating

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Agmon, Ilana. "Hypothesis: Spontaneous Advent of the Prebiotic Translation System via the Accumulation of L-Shaped RNA Elements." International Journal of Molecular Sciences 19, no. 12 (2018): 4021. http://dx.doi.org/10.3390/ijms19124021.

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The feasibility of self-assembly of a translation system from prebiotic random RNA chains is a question that is central to the ability to conceive life emerging by natural processes. The spontaneous materialization of a translation system would have required the autonomous formation of proto-transfer RNA (tRNA) and proto-ribosome molecules that are indispensable for translating an RNA chain into a polypeptide. Currently, the vestiges of a non-coded proto-ribosome, which could have only catalyzed the formation of a peptide bond between random amino acids, is consensually localized in the region

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Fabret, Celine, and Olivier Namy. "Translational accuracy of a tethered ribosome." Nucleic Acids Research 49, no. 9 (2021): 5308–18. http://dx.doi.org/10.1093/nar/gkab259.

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Abstract Ribosomes are evolutionary conserved ribonucleoprotein complexes that function as two separate subunits in all kingdoms. During translation initiation, the two subunits assemble to form the mature ribosome, which is responsible for translating the messenger RNA. When the ribosome reaches a stop codon, release factors promote translation termination and peptide release, and recycling factors then dissociate the two subunits, ready for use in a new round of translation. A tethered ribosome, called Ribo-T, in which the two subunits are covalently linked to form a single entity, was recen

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Fisher, Ross, Adrianna Henson, Paola Quarello, et al. "Insights Into Diagnosis and Etiology of Diamond Blackfan Anemia by Analysis of Pre-rRNA Processing." Blood 120, no. 21 (2012): 3476. http://dx.doi.org/10.1182/blood.v120.21.3476.3476.

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Abstract Abstract 3476 Most cases of Diamond Blackfan anemia are caused by haploinsufficiency for genes encoding proteins of the large or small ribosomal subunit. All of the ribosomal proteins affected in DBA are essential components of the ribosome required for the assembly of their respective subunits, including processing of the primary pre-rRNA transcript to mature 18S, 5.8S, and 28S rRNAs. Pre-rRNA processing signatures associated with ribosomal protein haploinsufficiency demonstrate a role for individual proteins in subunit assembly and can differ depending on which protein is affected.

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