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Journal articles on the topic 'Ribosome binding sites'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

Márquez, V., D. N. Wilson, and K. H. Nierhaus. "Functions and interplay of the tRNA-binding sites of the ribosome." Biochemical Society Transactions 30, no. 2 (2002): 133–40. http://dx.doi.org/10.1042/bst0300133.

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The ribosome translates the genetic information of an mRNA molecule into a sequence of amino acids. The ribosome utilizes tRNAs to connect elements of the RNA and protein worlds during protein synthesis, i.e. an anticodon as a unit of genetic information with the corresponding amino acid as a building unit of proteins. Three tRNA-binding sites are located on the ribosome, termed the A, P and E sites. In recent years the tRNA-binding sites have been localized on the ribosome by three different techniques, small-angle neutron scattering, cryo-electron microscopy and X-ray analyses of 70 S crysta

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2

Prinz, Anke, Enno Hartmann, and Kai-Uwe Kalies. "Sec61p Is the Main Ribosome Receptor in the Endoplasmic Reticulum of Saccharomyces cerevisiae." Biological Chemistry 381, no. 9-10 (2000): 1025–28. http://dx.doi.org/10.1515/bc.2000.126.

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Abstract A characteristic feature of the co-translational protein translocation into the endoplasmic reticulum (ER) is the tight association of the translating ribosomes with the translocation sites in the membrane. Biochemical analyses identified the Sec61 complex as the main ribosome receptor in the ER of mammalian cells. Similar experiments using purified homologues from the yeast Saccharomyces cerevisiae, the Sec61p complex and the Ssh1p complex, respectively, demonstrated that they bind ribosomes with an affinity similar to that of the mammalian Sec61 complex. However, these studies did n

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3

Dorner, S., and A. Barta. "Probing Ribosome Structure by Europium-Induced RNA Cleavage." Biological Chemistry 380, no. 2 (1999): 243–51. http://dx.doi.org/10.1515/bc.1999.032.

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AbstractDivalent metal ions are absolutely required for the structure and catalytic activities of ribosomes. They are partly coordinated to highly structured RNA, which therefore possesses high-affinity metal ion binding pockets. As metalion induced RNA cleavages are useful for characterising metal ion binding sites and RNA structures, we analysed europium (Eu3+) induced specific cleavages in both 16S and 23S rRNA ofE. coli. The cleavage sites were identified by primer extension and compared to those previously identified for calcium, lead, magnesium, and manganese ions. Several Eu3+cleavage s

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Aseev, Leonid V., Ludmila S. Koledinskaya, and Irina V. Boni. "Extraribosomal Functions of Bacterial Ribosomal Proteins—An Update, 2023." International Journal of Molecular Sciences 25, no. 5 (2024): 2957. http://dx.doi.org/10.3390/ijms25052957.

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Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein–protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can fu

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Krüger, Tim, Hanswalter Zentgraf, and Ulrich Scheer. "Intranucleolar sites of ribosome biogenesis defined by the localization of early binding ribosomal proteins." Journal of Cell Biology 177, no. 4 (2007): 573–78. http://dx.doi.org/10.1083/jcb.200612048.

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Considerable efforts are being undertaken to elucidate the processes of ribosome biogenesis. Although various preribosomal RNP complexes have been isolated and molecularly characterized, the order of ribosomal protein (r-protein) addition to the emerging ribosome subunits is largely unknown. Furthermore, the correlation between the ribosome assembly pathway and the structural organization of the dedicated ribosome factory, the nucleolus, is not well established. We have analyzed the nucleolar localization of several early binding r-proteins in human cells, applying various methods, including l

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6

Schaletzky, Julia, and Tom A. Rapoport. "Ribosome Binding to and Dissociation from Translocation Sites of the Endoplasmic Reticulum Membrane." Molecular Biology of the Cell 17, no. 9 (2006): 3860–69. http://dx.doi.org/10.1091/mbc.e06-05-0439.

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We have addressed how ribosome-nascent chain complexes (RNCs), associated with the signal recognition particle (SRP), can be targeted to Sec61 translocation channels of the endoplasmic reticulum (ER) membrane when all binding sites are occupied by nontranslating ribosomes. These competing ribosomes are known to be bound with high affinity to tetramers of the Sec61 complex. We found that the membrane binding of RNC–SRP complexes does not require or cause the dissociation of prebound nontranslating ribosomes, a process that is extremely slow. SRP and its receptor target RNCs to a free population

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7

Auerbach, Tamar, Inbal Mermershtain, Chen Davidovich, et al. "The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics." Proceedings of the National Academy of Sciences 107, no. 5 (2010): 1983–88. http://dx.doi.org/10.1073/pnas.0914100107.

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Crystallographic analysis revealed that the 17-member polyketide antibiotic lankacidin produced by Streptomyces rochei binds at the peptidyl transferase center of the eubacterial large ribosomal subunit. Biochemical and functional studies verified this finding and showed interference with peptide bond formation. Chemical probing indicated that the macrolide lankamycin, a second antibiotic produced by the same species, binds at a neighboring site, at the ribosome exit tunnel. These two antibiotics can bind to the ribosome simultaneously and display synergy in inhibiting bacterial growth. The bi

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8

Wittmann-Liebold, Brigitte, Monika Ühlein, Henning Urlaub, Eva-Christina Müller, Albrecht Otto, and Oliver Bischof. "Structural and functional implications in the eubacterial ribosome as revealed by protein–rRNA and antibiotic contact sites." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1187–97. http://dx.doi.org/10.1139/o95-128.

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Contact sites between protein and rRNA in 30S and 50S ribosomal subunits of Escherichia coli and Bacillus stearothermophilus were investigated at the molecular level using UV and 2–iminothiolane as cross-linkers. Thirteen ribosomal proteins (S3, S4, S7, S14, S17, L2, L4, L6, L14, L27, L28, L29, andL36) from these organisms were cross-linked in direct contact with the RNAs, and the peptide stretches as well as amino acids involved were identified. Further, the binding sites of puromycin and spiramycin were established at die peptide level in several proteins that were found to constitute me ant

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9

Kalies, K. U., D. Görlich, and T. A. Rapoport. "Binding of ribosomes to the rough endoplasmic reticulum mediated by the Sec61p-complex." Journal of Cell Biology 126, no. 4 (1994): 925–34. http://dx.doi.org/10.1083/jcb.126.4.925.

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The cotranslational translocation of proteins across the ER membrane involves the tight binding of translating ribosomes to the membrane, presumably to ribosome receptors. The identity of the latter has been controversial. One putative receptor candidate is Sec61 alpha, a multi-spanning membrane protein that is associated with two additional membrane proteins (Sec61 beta and gamma) to form the Sec61p-complex. Other receptors of 34 and 180 kD have also been proposed on the basis of their ability to bind at low salt concentration ribosomes lacking nascent chains. We now show that the Sec61p-comp

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10

Lytle, J. Robin, Lily Wu, and Hugh D. Robertson. "The Ribosome Binding Site of Hepatitis C Virus mRNA." Journal of Virology 75, no. 16 (2001): 7629–36. http://dx.doi.org/10.1128/jvi.75.16.7629-7636.2001.

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ABSTRACT Hepatitis C virus (HCV) infects an estimated 170 million people worldwide, the majority of whom develop a chronic infection which can lead to severe liver disease, and for which no generally effective treatment yet exists. A promising target for treatment is the internal ribosome entry site (IRES) of HCV, a highly conserved domain within a highly variable RNA. Never before have the ribosome binding sites of any IRES domains, cellular or viral, been directly characterized. Here, we reveal that the HCV IRES sequences most closely associated with 80S ribosomes during protein synthesis in

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11

Raden, David, Weiqun Song та Reid Gilmore. "Role of the Cytoplasmic Segments of Sec61α in the Ribosome-Binding and Translocation-Promoting Activities of the Sec61 Complex". Journal of Cell Biology 150, № 1 (2000): 53–64. http://dx.doi.org/10.1083/jcb.150.1.53.

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The Sec61 complex performs a dual function in protein translocation across the RER, serving as both the high affinity ribosome receptor and the translocation channel. To define regions of the Sec61 complex that are involved in ribosome binding and translocation promotion, ribosome-stripped microsomes were subjected to limited digestions using proteases with different cleavage specificities. Protein immunoblot analysis using antibodies specific for the NH2 and COOH terminus of Sec61α was used to map the location of proteolysis cleavage sites. We observed a striking correlation between the loss

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Espah Borujeni, Amin, Anirudh S. Channarasappa, and Howard M. Salis. "Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites." Nucleic Acids Research 42, no. 4 (2013): 2646–59. http://dx.doi.org/10.1093/nar/gkt1139.

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Abstract The ribosome’s interactions with mRNA govern its translation rate and the effects of post-transcriptional regulation. Long, structured 5′ untranslated regions (5′ UTRs) are commonly found in bacterial mRNAs, though the physical mechanisms that determine how the ribosome binds these upstream regions remain poorly defined. Here, we systematically investigate the ribosome’s interactions with structured standby sites, upstream of Shine–Dalgarno sequences, and show that these interactions can modulate translation initiation rates by over 100-fold. We find that an mRNA’s translation initiat

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13

Ehrenbolger, Kai, Nathan Jespersen, Himanshu Sharma, et al. "Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome." PLOS Biology 18, no. 10 (2020): e3000958. http://dx.doi.org/10.1371/journal.pbio.3000958.

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Assembling and powering ribosomes are energy-intensive processes requiring fine-tuned cellular control mechanisms. In organisms operating under strict nutrient limitations, such as pathogenic microsporidia, conservation of energy via ribosomal hibernation and recycling is critical. The mechanisms by which hibernation is achieved in microsporidia, however, remain poorly understood. Here, we present the cryo–electron microscopy structure of the ribosome from Paranosema locustae spores, bound by the conserved eukaryotic hibernation and recycling factor Lso2. The microsporidian Lso2 homolog adopts

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14

Caban, Kelvin, Scott A. Kinzy, and Paul R. Copeland. "The L7Ae RNA Binding Motif Is a Multifunctional Domain Required for the Ribosome-Dependent Sec Incorporation Activity of Sec Insertion Sequence Binding Protein 2." Molecular and Cellular Biology 27, no. 18 (2007): 6350–60. http://dx.doi.org/10.1128/mcb.00632-07.

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ABSTRACT The decoding of specific UGA codons as selenocysteine is specified by the Sec insertion sequence (SECIS) element. Additionally, Sec-tRNA[Ser]Sec and the dedicated Sec-specific elongation factor eEFSec are required but not sufficient for nonsense suppression. SECIS binding protein 2 (SBP2) is also essential for Sec incorporation, but its precise role is unknown. In addition to binding the SECIS element, SBP2 binds stably and quantitatively to ribosomes. To determine the function of the SBP2-ribosome interaction, conserved amino acids throughout the SBP2 L7Ae RNA binding motif were muta

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15

Zhang, Ling, Ying-Hui Wang, Xing Zhang, Laura Lancaster, Jie Zhou, and Harry F. Noller. "The structural basis for inhibition of ribosomal translocation by viomycin." Proceedings of the National Academy of Sciences 117, no. 19 (2020): 10271–77. http://dx.doi.org/10.1073/pnas.2002888117.

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Viomycin, an antibiotic that has been used to fight tuberculosis infections, is believed to block the translocation step of protein synthesis by inhibiting ribosomal subunit dissociation and trapping the ribosome in an intermediate state of intersubunit rotation. The mechanism by which viomycin stabilizes this state remains unexplained. To address this, we have determined cryo-EM and X-ray crystal structures of Escherichia coli 70S ribosome complexes trapped in a rotated state by viomycin. The 3.8-Å resolution cryo-EM structure reveals a ribosome trapped in the hybrid state with 8.6° intersubu

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16

Yan, Kang, Eric Hunt, John Berge, Earl May, Robert A. Copeland, and Richard R. Gontarek. "Fluorescence Polarization Method To Characterize Macrolide-Ribosome Interactions." Antimicrobial Agents and Chemotherapy 49, no. 8 (2005): 3367–72. http://dx.doi.org/10.1128/aac.49.8.3367-3372.2005.

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ABSTRACT A fluorescence polarization assay is described that measures the binding of fluorescently labeled erythromycin to 70S ribosomes from Escherichia coli and the displacement of the erythromycin from these ribosomes. The assay has been validated with several macrolide derivatives and other known antibiotics. We demonstrate that this assay is suitable for determining the dissociation constants of novel compounds that have binding sites overlapping those of macrolides. This homogeneous binding assay provides a valuable tool for defining structure-activity relationships among compounds durin

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17

Dantley, Kathi A., H. Kathleen Dannelly, and Vickers Burdett. "Binding Interaction between Tet(M) and the Ribosome: Requirements for Binding." Journal of Bacteriology 180, no. 16 (1998): 4089–92. http://dx.doi.org/10.1128/jb.180.16.4089-4092.1998.

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ABSTRACT Tet(M) protein interacts with the protein biosynthesis machinery to render this process resistant to tetracycline by a mechanism which involves release of the antibiotic from the ribosome in a reaction dependent on GTP hydrolysis. To clarify this resistance mechanism further, the interaction of Tet(M) with the ribosome has been examined by using a gel filtration assay with radioactively labelled Tet(M) protein. The presence of GTP and 5′-guanylyl imido diphosphate, but not GDP, promoted Tet(M)-ribosome complex formation. Furthermore, thiostrepton, which inhibits the activities of elon

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18

Smethurst, Daniel G. J., Nikolay Kovalev, Erica R. McKenzie, Dimitri G. Pestov, and Natalia Shcherbik. "Iron-mediated degradation of ribosomes under oxidative stress is attenuated by manganese." Journal of Biological Chemistry 295, no. 50 (2020): 17200–17214. http://dx.doi.org/10.1074/jbc.ra120.015025.

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Protein biosynthesis is fundamental to cellular life and requires the efficient functioning of the translational machinery. At the center of this machinery is the ribosome, a ribonucleoprotein complex that depends heavily on Mg2+ for structure. Recent work has indicated that other metal cations can substitute for Mg2+, raising questions about the role different metals may play in the maintenance of the ribosome under oxidative stress conditions. Here, we assess ribosomal integrity following oxidative stress both in vitro and in cells to elucidate details of the interactions between Fe2+ and th

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Planta, Rudi J., Paula M. Gonçalves, and Willem H. Mager. "Global regulators of ribosome biosynthesis in yeast." Biochemistry and Cell Biology 73, no. 11-12 (1995): 825–34. http://dx.doi.org/10.1139/o95-090.

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Three abundant ubiquitous DNA-binding protein factors appear to play a major role in the control of ribosome biosynthesis in yeast. Two of these factors mediate the regulation of transcription of ribosomal protein genes (rp-genes) in yeasts. Most yeast rp-genes are under transcriptional control of Rap1p (repressor–activator protein), while a small subset of rp-genes is activated through Abf1p (ARS binding factor). The third protein, designated Reb1p (rRNA enhancer binding protein), which binds strongly to two sites located upstream of the enhancer and the promoter of the rRNA operon, respectiv

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20

Ehrenberg, Måns, Nese Bilgin, Vildan Dincbas, Reza Karimi, Diarmaid Hughes, and Farhad Abdulkarim. "tRNA–ribosome interactions." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1049–54. http://dx.doi.org/10.1139/o95-112.

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Direct measurements of the rates of dissociation of dipeptidyl-tRNA from the ribosome show that hyperaccurate SmP and SmD ribosomes have unstable A-site binding of peptidyl-tRNA, while P-site binding is extremely stable in relation to the wild type. Error-prone Ram ribosomes, on the other hand, have stable A-site and unstable P-site binding of peptidyl-tRNA. At least for these mutant ribosomes, we conclude that stabilization of peptidyl-tRNA in one site destabilizes binding in the other. Elongation factor Tu (EF-Tu) undergoes a dramatic structural transition from its GDP-bound form to its acti

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Johnson, Alex G., Rosslyn Grosely, Alexey N. Petrov, and Joseph D. Puglisi. "Dynamics of IRES-mediated translation." Philosophical Transactions of the Royal Society B: Biological Sciences 372, no. 1716 (2017): 20160177. http://dx.doi.org/10.1098/rstb.2016.0177.

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Viral internal ribosome entry sites (IRESs) are unique RNA elements, which use stable and dynamic RNA structures to recruit ribosomes and drive protein synthesis. IRESs overcome the high complexity of the canonical eukaryotic translation initiation pathway, often functioning with a limited set of eukaryotic initiation factors. The simplest types of IRESs are typified by the cricket paralysis virus intergenic region (CrPV IGR) and hepatitis C virus (HCV) IRESs, both of which independently form high-affinity complexes with the small (40S) ribosomal subunit and bypass the molecular processes of c

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Prokhorova, Irina, Roger B. Altman, Muminjon Djumagulov, et al. "Aminoglycoside interactions and impacts on the eukaryotic ribosome." Proceedings of the National Academy of Sciences 114, no. 51 (2017): E10899—E10908. http://dx.doi.org/10.1073/pnas.1715501114.

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Aminoglycosides are chemically diverse, broad-spectrum antibiotics that target functional centers within the bacterial ribosome to impact all four principle stages (initiation, elongation, termination, and recycling) of the translation mechanism. The propensity of aminoglycosides to induce miscoding errors that suppress the termination of protein synthesis supports their potential as therapeutic interventions in human diseases associated with premature termination codons (PTCs). However, the sites of interaction of aminoglycosides with the eukaryotic ribosome and their modes of action in eukar

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23

Au, Hilda H., Gabriel Cornilescu, Kathryn D. Mouzakis, et al. "Global shape mimicry of tRNA within a viral internal ribosome entry site mediates translational reading frame selection." Proceedings of the National Academy of Sciences 112, no. 47 (2015): E6446—E6455. http://dx.doi.org/10.1073/pnas.1512088112.

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The dicistrovirus intergenic region internal ribosome entry site (IRES) adopts a triple-pseudoknotted RNA structure and occupies the core ribosomal E, P, and A sites to directly recruit the ribosome and initiate translation at a non-AUG codon. A subset of dicistrovirus IRESs directs translation in the 0 and +1 frames to produce the viral structural proteins and a +1 overlapping open reading frame called ORFx, respectively. Here we show that specific mutations of two unpaired adenosines located at the core of the three-helical junction of the honey bee dicistrovirusIsraeli acute paralysis virus

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Wu, Yun, Meng-Ting Ni, Ying-Hui Wang, et al. "Structural basis of translation inhibition by a valine tRNA-derived fragment." Life Science Alliance 7, no. 6 (2024): e202302488. http://dx.doi.org/10.26508/lsa.202302488.

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Translational regulation by non-coding RNAs is a mechanism commonly used by cells to fine-tune gene expression. A fragment derived from an archaeal valine tRNA (Val-tRF) has been previously identified to bind the small subunit of the ribosome and inhibit translation inHaloferax volcanii. Here, we present three cryo-electron microscopy structures of Val-tRF bound to the small subunit ofSulfolobus acidocaldariusribosomes at resolutions between 4.02 and 4.53 Å. Within these complexes, Val-tRF was observed to bind to conserved RNA-interacting sites, including the ribosomal decoding center. The bin

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Tate, Warren P., Elizabeth S. Poole, Julie A. Horsfield, et al. "Translational termination efficiency in both bacteria and mammals is regulated by the base following the stop codon." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1095–103. http://dx.doi.org/10.1139/o95-118.

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The translational stop signal and polypeptide release factor (RF) complexed with Escherichia coli ribosomes have been shown to be in close physical contact by site-directed photochemical cross-linking experiments. The RF has a protease-sensitive site in a highly conserved exposed loop that is proposed to interact with the peptidyltransferase center of the ribosome. Loss of peptidyl–tRNA hydrolysis activity and enhanced codon–ribosome binding by the cleaved RF is consistent with a model whereby the RF spans the decoding and peptidyltransferase centers of the ribosome with domains of the RF link

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Barrick, Doug, Keith Villanueba, John Childs, et al. "Quantitative analysis of ribosome binding sites in E.coli." Nucleic Acids Research 22, no. 7 (1994): 1287–95. http://dx.doi.org/10.1093/nar/22.7.1287.

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Huang, Chih-Ting, Yei-Chen Lai, Szu-Yun Chen, Meng-Ru Ho, Yun-Wei Chiang, and Shang-Te Danny Hsu. "Structural polymorphism and substrate promiscuity of a ribosome-associated molecular chaperone." Magnetic Resonance 2, no. 1 (2021): 375–86. http://dx.doi.org/10.5194/mr-2-375-2021.

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Abstract. Trigger factor (TF) is a highly conserved multi-domain molecular chaperone that exerts its chaperone activity at the ribosomal tunnel exit from which newly synthesized nascent chains emerge. TF also displays promiscuous substrate binding for a large number of cytosolic proteins independent of ribosome binding. We asked how TF recognizes a variety of substrates while existing in a monomer–dimer equilibrium. Paramagnetic nuclear magnetic resonance (NMR) and electron spin resonance (ESR) spectroscopy were used to show that dimeric TF displays a high degree of structural polymorphism in

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Buyan, Andrey, Ivan Kulakovskiy, and Sergey Dmitriev. "Abstract P-22: Enhanced Crosslinking and Immunoprecipitation (Eclip) Data Reveal Interactions of RNA Binding Proteins with the Human Ribosome." International Journal of Biomedicine 11, Suppl_1 (2021): S21. http://dx.doi.org/10.21103/ijbm.11.suppl_1.p22.

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Background: The ribosome is a protein-synthesizing molecular machine composed of four ribosomal RNAs (rRNAs) and dozens of ribosomal proteins. In mammals, the ribosome has a complicated structure with an additional outer layer of rRNA, including large tentacle-like extensions. A number of RNA binding proteins (RBPs) interact with this layer to assist ribosome biogenesis, nuclear export and decay, or to modulate translation. Plenty of methods have been developed in the last decade in order to study such protein-RNA interactions, including RNA pulldown and crosslinking-immunoprecipitation (CLIP)

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Krawczyk, Szymon J., Marta Leśniczak-Staszak, Ewelina Gowin, and Witold Szaflarski. "Mechanistic Insights into Clinically Relevant Ribosome-Targeting Antibiotics." Biomolecules 14, no. 10 (2024): 1263. http://dx.doi.org/10.3390/biom14101263.

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Antibiotics targeting the bacterial ribosome are essential to combating bacterial infections. These antibiotics bind to various sites on the ribosome, inhibiting different stages of protein synthesis. This review provides a comprehensive overview of the mechanisms of action of clinically relevant antibiotics that target the bacterial ribosome, including macrolides, lincosamides, oxazolidinones, aminoglycosides, tetracyclines, and chloramphenicol. The structural and functional details of antibiotic interactions with ribosomal RNA, including specific binding sites, interactions with rRNA nucleot

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NEKHAI, Sergei A., Vladimir E. BELETZKIJ, and Dmitri M. GRAIFER. "Influence of systematic error on the shape of the Scatchard plot of tRNAPhe binding to eukaryotic ribosomes." Biochemical Journal 325, no. 2 (1997): 401–4. http://dx.doi.org/10.1042/bj3250401.

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Scatchard plots of tRNAPhe binding to poly(U)-programmed human 80 S ribosomes can be curved, either concave upwards or concave downwards, depending on the experimental conditions. The influence of a systematic error on the shape of the Scatchard plots has been analysed in a model experiment where the binding proceeds at two independent sites. The Scatchard plot for this binding model has a concave-upwards shape. When the concentration of the ribosomes is kept constant, a small systematic error in tRNA concentration changes this Scatchard plot markedly to a concave-downwards plot as though a co

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Lisevich, Irina, Dmitrii Lukianov, Daniel Wilson, Petr Sergiev, Olga Dontsova, and Ilya Osterman. "Abstract OR-4: New Antibiotic Binding Site on the 30S Ribosomal Subunit." International Journal of Biomedicine 11, Suppl_1 (2021): S8—S9. http://dx.doi.org/10.21103/ijbm.11.suppl_1.or4.

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Background: Antibiotic resistance becomes one of the main problems of modern medicine; therefore, the development of new antibacterial compounds is absolutely necessary. The ribosome is the target for a lot of different antibiotics; there are several main binding sites on the ribosome – decoding center, peptidyl-transferase center, and ribosome exit tunnel. Modification or mutation of nucleotides in these sites could make cells resistant to structurally different antibiotics. Methods: pDualrep2 reporter system was used for detection of the protein synthesis inhibitors in cultural broths of new

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Weiner, Iddo, Noam Shahar, Pini Marco, Iftach Yacoby, and Tamir Tuller. "Solving the Riddle of the Evolution of Shine-Dalgarno Based Translation in Chloroplasts." Molecular Biology and Evolution 36, no. 12 (2019): 2854–60. http://dx.doi.org/10.1093/molbev/msz210.

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Abstract Chloroplasts originated from an ancient cyanobacterium and still harbor a bacterial-like genome. However, the centrality of Shine–Dalgarno ribosome binding, which predominantly regulates proteobacterial translation initiation, is significantly decreased in chloroplasts. As plastid ribosomal RNA anti-Shine–Dalgarno elements are similar to their bacterial counterparts, these sites alone cannot explain this decline. By computational simulation we show that upstream point mutations modulate the local structure of ribosomal RNA in chloroplasts, creating significantly tighter structures aro

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Unoson, Cecilia, and E. Gerhart H. Wagner. "Dealing with stable structures at ribosome binding sites: Bacterial translation and ribosome standby." RNA Biology 4, no. 3 (2007): 113–17. http://dx.doi.org/10.4161/rna.4.3.5350.

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Kimura, Takatsugu, Kuniaki Takagi, Yuya Hirata, Yoichi Hase, Akira Muto, and Hyouta Himeno. "Ribosome-Small-Subunit-Dependent GTPase Interacts with tRNA-Binding Sites on the Ribosome." Journal of Molecular Biology 381, no. 2 (2008): 467–77. http://dx.doi.org/10.1016/j.jmb.2008.06.023.

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Gnanasundram, Sivakumar Vadivel, Isabelle C. Kos-Braun, and Martin Koš. "At least two molecules of the RNA helicase Has1 are simultaneously present in pre-ribosomes during ribosome biogenesis." Nucleic Acids Research 47, no. 20 (2019): 10852–64. http://dx.doi.org/10.1093/nar/gkz767.

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Abstract The RNA helicase Has1 is involved in the biogenesis of both small and large ribosomal subunits. How it performs these separate roles is not fully understood. Here we provide evidence that at least two molecules of Has1 are temporarily present at the same time in 90S pre-ribosomes. We identified multiple Has1 binding sites in the 18S, 5.8S and 25S rRNAs. We show that while the Has1 catalytic activity is not required for binding to 5.8S/25S region in pre-rRNA, it is essential for binding to 18S sites. After the cleavage of pre-rRNA at the A2 site, Has1 remains associated not only with p

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Pickering, Becky M., Sally A. Mitchell, Keith A. Spriggs, Mark Stoneley, and Anne E. Willis. "Bag-1 Internal Ribosome Entry Segment Activity Is Promoted by Structural Changes Mediated by Poly(rC) Binding Protein 1 and Recruitment of Polypyrimidine Tract Binding Protein 1." Molecular and Cellular Biology 24, no. 12 (2004): 5595–605. http://dx.doi.org/10.1128/mcb.24.12.5595-5605.2004.

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ABSTRACT We have shown previously that an internal ribosome entry segment (IRES) directs the synthesis of the p36 isoform of Bag-1 and that polypyrimidine tract binding protein 1 (PTB-1) and poly(rC) binding protein 1 (PCBP1) stimulate IRES-mediated translation initiation in vitro and in vivo. Here, a secondary structural model of the Bag-1 IRES has been derived by using chemical and enzymatic probing data as constraints on the RNA folding algorithm Mfold. The ribosome entry window has been identified within this structural model and is located in a region in which many residues are involved i

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Parker, Melissa D., Elise S. Brunk, Adam J. Getzler, and Katrin Karbstein. "The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage." PLOS Biology 22, no. 4 (2024): e3001767. http://dx.doi.org/10.1371/journal.pbio.3001767.

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The 18S rRNA sequence is highly conserved, particularly at its 3′-end, which is formed by the endonuclease Nob1. How Nob1 identifies its target sequence is not known, and in vitro experiments have shown Nob1 to be error-prone. Moreover, the sequence around the 3′-end is degenerate with similar sites nearby. Here, we used yeast genetics, biochemistry, and next-generation sequencing to investigate a role for the ATPase Rio1 in monitoring the accuracy of the 18S rRNA 3′-end. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-medi

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Buddeweg, Anne, Kundan Sharma, Henning Urlaub, and Ruth A. Schmitz. "sRNA41affects ribosome binding sites within polycistronic mRNAs inMethanosarcina mazeiGö1." Molecular Microbiology 107, no. 5 (2018): 595–609. http://dx.doi.org/10.1111/mmi.13900.

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David-Eden, Hilda, Alexander S. Mankin, and Yael Mandel-Gutfreund. "Structural signatures of antibiotic binding sites on the ribosome." Nucleic Acids Research 38, no. 18 (2010): 5982–94. http://dx.doi.org/10.1093/nar/gkq411.

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May, E. E., M. A. Vouk, and D. L. Bitzer. "Classification of Escherichia coli K-12 ribosome binding sites." IEEE Engineering in Medicine and Biology Magazine 25, no. 1 (2006): 90–97. http://dx.doi.org/10.1109/memb.2006.1578668.

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Jomaa, Ahmad, Nikhil Jain, Joseph H. Davis, James R. Williamson, Robert A. Britton, and Joaquin Ortega. "Functional domains of the 50S subunit mature late in the assembly process." Nucleic Acids Research 42, no. 5 (2013): 3419–35. http://dx.doi.org/10.1093/nar/gkt1295.

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Abstract Despite the identification of many factors that facilitate ribosome assembly, the molecular mechanisms by which they drive ribosome biogenesis are poorly understood. Here, we analyze the late stages of assembly of the 50S subunit using Bacillus subtilis cells depleted of RbgA, a highly conserved GTPase. We found that RbgA-depleted cells accumulate late assembly intermediates bearing sub-stoichiometric quantities of ribosomal proteins L16, L27, L28, L33a, L35 and L36. Using a novel pulse labeling/quantitative mass spectrometry technique, we show that this particle is physiologically re

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Arenz, Stefan, Manuel F. Juette, Michael Graf, et al. "Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome." Proceedings of the National Academy of Sciences 113, no. 27 (2016): 7527–32. http://dx.doi.org/10.1073/pnas.1604790113.

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The ribosome is one of the major targets for therapeutic antibiotics; however, the rise in multidrug resistance is a growing threat to the utility of our current arsenal. The orthosomycin antibiotics evernimicin (EVN) and avilamycin (AVI) target the ribosome and do not display cross-resistance with any other classes of antibiotics, suggesting that they bind to a unique site on the ribosome and may therefore represent an avenue for development of new antimicrobial agents. Here we present cryo-EM structures of EVN and AVI in complex with the Escherichia coli ribosome at 3.6- to 3.9-Å resolution.

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Dorner, S., N. Polacek, U. Schulmeister, C. Panuschka, and A. Barta. "Molecular aspects of the ribosomal peptidyl transferase." Biochemical Society Transactions 30, no. 6 (2002): 1131–37. http://dx.doi.org/10.1042/bst0301131.

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The proteins in a living cell are synthesized on a large bipartite ribonucleoprotein complex termed the ribosome. The peptidyl transferase, which polymerizes amino acids to yield peptides, is localized on the large subunit. Biochemical investigations over the past 35 years have led to the hypothesis that rRNA has a major role in all ribosomal functions. The recent high resolution X-ray structures of the ribosomal subunits clearly demonstrated that peptidyl transfer is an RNA-mediated process. As all ribosomal activities are dependent on bivalent metal ions, as is the case for most ribozymes, w

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

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The nucleolus is the site of ribosome biosynthesis, but is now known to have other functions as well. In the present study we have investigated how the distribution of signal recognition particle (SRP) RNA within the nucleolus relates to the known sites of ribosomal RNA synthesis, processing, and nascent ribosome assembly (i.e., the fibrillar centers, the dense fibrillar component (DFC), and the granular component). Very little SRP RNA was detected in fibrillar centers or the DFC of the nucleolus, as defined by the RNA polymerase I–specific upstream binding factor and the protein fibrillarin,

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Rozanska, Agata, Ricarda Richter-Dennerlein, Joanna Rorbach, et al. "The human RNA-binding protein RBFA promotes the maturation of the mitochondrial ribosome." Biochemical Journal 474, no. 13 (2017): 2145–58. http://dx.doi.org/10.1042/bcj20170256.

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Accurate assembly and maturation of human mitochondrial ribosomes is essential for synthesis of the 13 polypeptides encoded by the mitochondrial genome. This process requires the correct integration of 80 proteins, 1 mt (mitochondrial)-tRNA and 2 mt-rRNA species, the latter being post-transcriptionally modified at many sites. Here, we report that human ribosome-binding factor A (RBFA) is a mitochondrial RNA-binding protein that exerts crucial roles in mitoribosome biogenesis. Unlike its bacterial orthologue, RBFA associates mainly with helices 44 and 45 of the 12S rRNA in the mitoribosomal sma

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Nürenberg-Goloub, Elina, Holger Heinemann, Milan Gerovac, and Robert Tampé. "Ribosome recycling is coordinated by processive events in two asymmetric ATP sites of ABCE1." Life Science Alliance 1, no. 3 (2018): e201800095. http://dx.doi.org/10.26508/lsa.201800095.

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Ribosome recycling orchestrated by ABCE1 is a fundamental process in protein translation and mRNA surveillance, connecting termination with initiation. Beyond the plenitude of well-studied translational GTPases, ABCE1 is the only essential factor energized by ATP, delivering the energy for ribosome splitting via two nucleotide-binding sites by a yet unknown mechanism. Here, we define how allosterically coupled ATP binding and hydrolysis events in ABCE1 empower ribosome recycling. ATP occlusion in the low-turnover control site II promotes formation of the pre-splitting complex and facilitates A

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Cooper, Helena B., Kurt L. Krause, and Paul P. Gardner. "Finding priority bacterial ribosomes for future structural and antimicrobial research based upon global RNA and protein sequence analysis." PeerJ 11 (March 22, 2023): e14969. http://dx.doi.org/10.7717/peerj.14969.

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Ribosome-targeting antibiotics comprise over half of antibiotics used in medicine, but our fundamental knowledge of their binding sites is derived primarily from ribosome structures of non-pathogenic species. These include Thermus thermophilus, Deinococcus radiodurans and the archaean Haloarcula marismortui, as well as the commensal and sometimes pathogenic organism, Escherichia coli. Advancements in electron cryomicroscopy have allowed for the determination of more ribosome structures from pathogenic bacteria, with each study highlighting species-specific differences that had not been observe

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Lee, Lauren, and Justen B. Whittall. "WDR75: An essential protein for ribosome assembly undergoing purifying selection." PLOS ONE 20, no. 2 (2025): e0318395. https://doi.org/10.1371/journal.pone.0318395.

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Ribosomes, vital for life, consist of a large subunit and a small subunit (SSU), the latter is crucial for translation initiation and mRNA binding. The SSU processome, a 71-protein multimer in humans, is an intermediate in ribosome formation. One of its constituents, WDR75 plays a pivotal role by binding to an evolutionary conserved motif in the external transcribed spacer region of the rRNA to help form the SSU. Herein, we explore mammalian WDR75 molecular evolution, 3D structure, and phylogeny in light of its essential role in the SSU processome. We predict to find the footprint of purifying

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Fernandez, Samantha G., Lucas Ferguson та Nicholas T. Ingolia. "Ribosome rescue factor PELOTA modulates translation start site choice for C/EBPα protein isoforms". Life Science Alliance 7, № 7 (2024): e202302501. http://dx.doi.org/10.26508/lsa.202302501.

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Translation initiation at alternative start sites can dynamically control the synthesis of two or more functionally distinct protein isoforms from a single mRNA. Alternate isoforms of the developmental transcription factor CCAAT/enhancer-binding protein α (C/EBPα) produced from different start sites exert opposing effects during myeloid cell development. This choice between alternative start sites depends on sequence features of theCEBPAtranscript, including a regulatory uORF, but the molecular basis is not fully understood. Here, we identify the factors that affect C/EBPα isoform choice using

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Wower, Jacek, Iwona K. Wower, Stanislav V. Kirillov, Kirill V. Rosen, Robert A. Zimmermann, and Stephen S. Hixson. "Peptidyl transferase and beyond." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1041–47. http://dx.doi.org/10.1139/o95-111.

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The peptidyl transferase center of the Escherichia coli ribosome encompasses a number of 50S-subunit proteins as well as several specific segments of the 23S rRNA. Although our knowledge of the role that both ribosomal proteins and 23S rRNA play in peptide bond formation has steadily increased, the location, organization, and molecular structure of the peptidyl transferase center remain poorly defined. Over the past 10 years, we have developed a variety of photoaffinity reagents and strategies for investigating the topography of tRNA binding sites on the ribosome. In particular, we have used t

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