Ribosomal Crystallography: Peptide Bond Formation, Chaperone Assistance, and Antibiotics Inactivation

Yonath, Ada

doi:10.1007/978-1-4020-5900-1_11

Cited by 23 publications

(25 citation statements)

References 156 publications

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“…X-ray and cryo-electron microscopy (cryo-EM) analyses have provided a wealth of information regarding the structure of the ribosome peptidyl transferase center and interactions of the ribosome with mRNA, tRNAs, and translation factors (Yonath and Bashan 2004;Nilsson and Nissen 2005;Noller 2005;Ogle and Ramakrishnan 2005;Yonath 2005;Mitra and Frank 2006;Beringer and Rodnina 2007). Although it became clear that a primary role in ribosomal function belongs to rRNA (Beringer and Rodnina 2007), ribosomal proteins are nevertheless essential (Brodersen and Nissen 2005;Wilson and Nierhaus 2005;Dresios et al 2006).…”

Section: Introductionmentioning

confidence: 99%

Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5

Galkin

Bentley

Gupta

et al. 2007

RNA

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Ribosomal protein (rp) S5 belongs to a family of ribosomal proteins that includes bacterial rpS7. rpS5 forms part of the exit (E) site on the 40S ribosomal subunit and is essential for yeast viability. Human rpS5 is 67% identical and 79% similar to Saccharomyces cerevisiae rpS5 but lacks a negatively charged (pI ;3.27) 21 amino acid long N-terminal extension that is present in fungi. Here we report that replacement of yeast rpS5 with its human homolog yielded a viable yeast strain with a 20%-25% decrease in growth rate. This replacement also resulted in a moderate increase in the heavy polyribosomal components in the mutant strain, suggesting either translation elongation or termination defects, and in a reduction in the polyribosomal association of the elongation factors eEF3 and eEF1A. In addition, the mutant strain was characterized by moderate increases in +1 and À1 programmed frameshifting and hyperaccurate recognition of the UAA stop codon. The activities of the cricket paralysis virus (CrPV) IRES and two mammalian cellular IRESs (CAT-1 and SNAT-2) were also increased in the mutant strain. Consistently, the rpS5 replacement led to enhanced direct interaction between the CrPV IRES and the mutant yeast ribosomes. Taken together, these data indicate that rpS5 plays an important role in maintaining the accuracy of translation in eukaryotes and suggest that the negatively charged N-terminal extension of yeast rpS5 might affect the ribosomal recruitment of specific mRNAs.

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Section: Introductionmentioning

confidence: 99%

Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5

Galkin

Bentley

Gupta

et al. 2007

RNA

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“…For both naturally occurring and synthetic antibiotics, protein synthesis is a major target of antibiotic action. Bacterial protein synthesis inhibitors include the macrolides (e.g., erythromycin, clarithromycin, and azithromycin), clindamycin, chloramphenicol, the aminoglycosides (e.g., streptomycin, gentamicin, and amikacin), and the tetracyclines (2,18,49). The newest class of antibacterials, the synthetic oxazolidinones (exemplified by linezolid, the only novel and approved ribosomal inhibitor), also inhibit protein synthesis (21,45).…”

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confidence: 99%

Discovery and Analysis of 4 H -Pyridopyrimidines, a Class of Selective Bacterial Protein Synthesis Inhibitors

Ribble

Hill

Ochsner

et al. 2010

Antimicrob Agents Chemother

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Bacterial protein synthesis is the target for numerous natural and synthetic antibacterial agents. We have developed a poly(U) mRNA-directed aminoacylation/translation protein synthesis system composed of phenyltRNA synthetases, ribosomes, and ribosomal factors from Escherichia coli. This system, utilizing purified components, has been used for high-throughput screening of a small-molecule chemical library. We have identified a series of compounds that inhibit protein synthesis with 50% inhibitory concentrations (IC 50 s) ranging from 3 to 14 M. This series of compounds all contained the same central scaffold composed of tetrahydropyrido[4,3-d]pyrimidin-4-ol (e.g., 4H-pyridopyrimidine). All analogs contained an ortho pyridine ring attached to the central scaffold in the 2 position and either a five-or a six-member ring tethered to the 6-methylene nitrogen atom of the central scaffold. These compounds inhibited the growth of E. coli, Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis, with MICs ranging from 0.25 to 32 g/ml. Macromolecular synthesis (MMS) assays with E. coli and S. aureus confirmed that antibacterial activity resulted from specific inhibition of protein synthesis. Assays were developed for the steps performed by each component of the system in order to ascertain the target of the compounds, and the ribosome was found to be the site of inhibition.

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“…High-resolution crystal structures showed that macrolides and their derivatives bind to a specific pocket of the nascent protein exit tunnel (2,3,7,16,20,21,25,29), the universal feature of the large ribosomal subunit through which nascent proteins emerge. The same pocket is exploited by all members of the macrolide family, and effective inhibitory action is achieved when the drug consumes a significant portion of the tunnel cross-section (1,31,32). Typically, resistance to macrolides is acquired through either efflux or target-based alteration (methylation or mutation of nucleotides involved in drug binding [for reviews, see references 11 and 28]).…”

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23S rRNA 2058A→G Alteration Mediates Ketolide Resistance in Combination with Deletion in L22

Berisio

Corti

Pfister

et al. 2006

Antimicrob Agents Chemother

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Resistance to macrolides and ketolides occurs mainly via alterations in RNA moieties of the drug-binding site. Using an A2058G mutant of Mycobacterium smegmatis, additional telithromycin resistance was acquired via deletion of 15 residues from protein L22. Molecular modeling, based on the crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with telithromycin, shows that the telithromycin carbamate group is located in the proximity of the tip of the L22 hairpin-loop, allowing for weak interactions between them. These weak interactions may become more important once the loss of A2058 interactions destabilizes drug binding, presumably resulting in a shift of the drug toward the other side of the tunnel, namely, to the vicinity of L22. Hence, the deletion of 15 residues from L22 may further destabilize telithromycin binding and confer telithromycin resistance. Such deletions may also lead to notable differences in the tunnel outline, as well as to an increase of its diameter to a size, allowing the progression of the nascent chain.Ribosomes provide a target for several antibiotic families, among which is the macrolide-ketolide group. High-resolution crystal structures showed that macrolides and their derivatives bind to a specific pocket of the nascent protein exit tunnel (2,3,7,16,20,21,25,29), the universal feature of the large ribosomal subunit through which nascent proteins emerge. The same pocket is exploited by all members of the macrolide family, and effective inhibitory action is achieved when the drug consumes a significant portion of the tunnel cross-section (1, 31, 32). Typically, resistance to macrolides is acquired through either efflux or target-based alteration (methylation or mutation of nucleotides involved in drug binding [for reviews, see references 11 and 28]).Ketolides are an advanced generation of the macrolide antibiotics, which, in part, provide activity against macrolideresistant pathogens. They are semisynthetic derivatives of erythromycin, the first macrolide in use. Like erythromycin, ketolides are composed of a 14-membered macrolactone ring (Fig. 1). However, their macrolactone ring lacks a cladinose sugar and possesses a keto group at position 3, a cyclic carbamate, and an extended arm. Ketolides and macrolides share a similar, albeit not identical inhibitory mechanism. Owing to their more elaborated chemistry, in addition to their binding to the macrolide pocket, the ketolides extend further into the tunnel and interact with rather remote sites (2,20,29). Among ketolides, telithromycin carries an aryl-alkyl extension bound to its cyclic carbamate (Fig. 1). The crystal structure of the large ribosomal subunit from Deinococcus radiodurans (called D50S) in complex with telithromycin indicates that telithromycin interacts with 23S RNA domain II nucleotides (2, 29). This finding is consistent with a number of previous biochemical and mutagenesis studies showing that, in addition to nucleotides in domain V, domain II nucleotide A752 (Escherichia coli numbe...

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Ribosomal Crystallography: Peptide Bond Formation, Chaperone Assistance, and Antibiotics Inactivation

Cited by 23 publications

References 156 publications

Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5

Roles of the negatively charged N-terminal extension of Saccharomyces cerevisiae ribosomal protein S5 revealed by characterization of a yeast strain containing human ribosomal protein S5

Discovery and Analysis of 4 H -Pyridopyrimidines, a Class of Selective Bacterial Protein Synthesis Inhibitors

23S rRNA 2058A→G Alteration Mediates Ketolide Resistance in Combination with Deletion in L22

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