ANTIBIOTICS TARGETING RIBOSOMES: Resistance, Selectivity, Synergism, and Cellular Regulation

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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 binding site of lankacidin and lankamycin partially overlap with the binding site of another pair of synergistic antibiotics, the streptogramins. Thus, at least two pairs of structurally dissimilar compounds have been selected in the course of evolution to act synergistically by targeting neighboring sites in the ribosome. These results underscore the importance of the corresponding ribosomal sites for development of clinically relevant synergistic antibiotics and demonstrate the utility of structural analysis for providing new directions for drug discovery.lankamycin | ribosomes | synergism | resistance | rRNA

Section: Discussionmentioning

confidence: 99%

The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics

Auerbach

Mermershtain

Davidovich

et al. 2010

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“…The ribosome biogenesis mutants apum23 and rpl4 displayed varied sensitivity to translational inhibitors, as a result of putative aberrant ribosome structure and function (24,42). Therefore, we evaluated the ribosomal function in atprmt3 using antibiotics with known targets in the ribosome (44,45). The atprmt3 mutants exhibited marked resistance to several aminoglycoside antibiotics, including kanamycin, gentamicin, streptomycin, and spectinomycin (Fig.…”

Section: Disruption Of Atprmt3 Confers Pleiotropic Developmental Defectsmentioning

confidence: 99%

Arabidopsis protein arginine methyltransferase 3 is required for ribosome biogenesis by affecting precursor ribosomal RNA processing

Hang

Liu

Ahmad

et al. 2014

Ribosome biogenesis is a fundamental and tightly regulated cellular process, including synthesis, processing, and assembly of rRNAs with ribosomal proteins. Protein arginine methyltransferases (PRMTs) have been implicated in many important biological processes, such as ribosome biogenesis. Two alternative precursor rRNA (prerRNA) processing pathways coexist in yeast and mammals; however, how PRMT affects ribosome biogenesis remains largely unknown. Here we show that Arabidopsis PRMT3 (AtPRMT3) is required for ribosome biogenesis by affecting pre-rRNA processing. Disruption of AtPRMT3 results in pleiotropic developmental defects, imbalanced polyribosome profiles, and aberrant pre-rRNA processing. We further identify an alternative pre-rRNA processing pathway in Arabidopsis and demonstrate that AtPRMT3 is required for the balance of these two pathways to promote normal growth and development. Our work uncovers a previously unidentified function of PRMT in posttranscriptional regulation of rRNA, revealing an extra layer of complexity in the regulation of ribosome biogenesis.arginine methylation | protein arginine methyltransferase | AtPRMT3 | ribosome biogenesis | rRNA processing T he fundamental, complicated, and highly cooperative process of ribosome biogenesis involves ribosomal DNA (rDNA) transcription, precursor rRNA (pre-rRNA) processing, and assembly with ribosomal proteins and related assembly factors (1, 2). As a multistep, error prone, and energy-consuming process, ribosome biogenesis is also highly regulated (3, 4). In eukaryotic cells, mutations in ribosomal proteins or ribosome assembly factors usually lead to aberrant pre-rRNA processing (5-7) and activation of the polyadenylation-mediated RNA quality control system (4, 8, 9), resulting in various genetic diseases in humans (10, 11).Work in budding yeast, Saccharomyces cerevisiae, has deciphered the mechanisms of ribosome biogenesis (1, 2, 12). After transcription by RNA polymerase I and site-specific modification by small nucleolar ribonucleoproteins, the nascent 35S rRNA, the common precursor of 18S, 5.8S, and 25S rRNAs, is quickly assembled with many assembly factors and ribosomal proteins into small subunit processome/90S preribosomal particles (13-15). Then it mainly undergoes the "U3-dependent cleavage occurs first" pathway, which first removes the 5′ external transcribed sequence (5′ ETS) of 35S rRNA, to generate the 32S rRNA (16, 17). Next, after cleavage at the A2 site of intergenic transcribed sequence 1 (ITS1) between 18S rRNA and 5.8S rRNA, the 90S preribosomal particle splits into two independent complexes of pre-40S and pre-60S ribosomal particles. Finally, ribosomal subunits are further matured and assembled into 80S ribosomes for translation in the cytoplasm (12). However, in contrast to budding yeast, pre-rRNA processing in Xenopus laevis oocytes, mouse cells, and human cells preferentially cleave in ITS1 before the complete removal of the 5′ ETS (18-21), which may represent a common pathway in metazoans.In plants, a pre-rRNA processi...

“…Nevertheless, species specificity in clinically relevant properties, particularly the modes of acquiring antibiotic resistance, have been identified (8). Given the knowledge that small structural differences between bacterial species can affect drug binding (9), for the progress of structure-based drug design, it is imperative to have a high-resolution crystal structure of the ribosome and its subunits from the pathogenic bacterial species. As a first step toward this goal, we determined the structure of large ribosomal subunit of the pathogen S. aureus (SA50S).…”

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confidence: 99%

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

Eyal

Matzov

Krupkin

et al. 2015

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121

151

The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.