Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?

AbstractBacterial ribosome rescue pathways that remove ribosomes stalled on mRNAs during translation have been proposed as novel antibiotic targets because they are essential in bacteria and are not conserved in humans. We previously reported the discovery of a family of acylaminooxadiazoles that selectively inhibit trans-translation, the main ribosome rescue pathway in bacteria. Here, we report optimization of the pharmacokinetic and antibiotic properties of the acylaminooxadiazoles, producing MBX-4132, which clears multiple-drug resistant Neisseria gonorrhoeae infection in mice after a single oral dose. Single particle cryogenic-EM studies of non-stop ribosomes show that acylaminooxadiazoles bind to a unique site near the peptidyl-transfer center and significantly alter the conformation of ribosomal protein bL27, suggesting a novel mechanism for specific inhibition of trans-translation by these molecules. These results show that trans-translation is a viable therapeutic target and reveal a new conformation within the bacterial ribosome that may be critical for ribosome rescue pathways.

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Genes on the circular code alphabet

Biosystems ◽

10.1016/j.biosystems.2021.104431 ◽

2021 ◽

pp. 104431

Author(s):

Christian J. Michel

Keyword(s):

Circular Code

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Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics

Nature Communications ◽

10.1038/s41467-021-24674-9 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Bertrand Beckert ◽

Elodie C. Leroy ◽

Shanmugapriya Sothiselvam ◽

Lars V. Bock ◽

Maxim S. Svetlov ◽

...

Keyword(s):

Antibiotic Resistance Genes ◽

Structural Basis ◽

Sequence Motifs ◽

Specific Sequence ◽

Bacterial Ribosome ◽

Translational Arrest ◽

Exit Tunnel ◽

Mechanistic Basis ◽

Dynamics Simulations ◽

Context Specific

AbstractMacrolides and ketolides comprise a family of clinically important antibiotics that inhibit protein synthesis by binding within the exit tunnel of the bacterial ribosome. While these antibiotics are known to interrupt translation at specific sequence motifs, with ketolides predominantly stalling at Arg/Lys-X-Arg/Lys motifs and macrolides displaying a broader specificity, a structural basis for their context-specific action has been lacking. Here, we present structures of ribosomes arrested during the synthesis of an Arg-Leu-Arg sequence by the macrolide erythromycin (ERY) and the ketolide telithromycin (TEL). Together with deep mutagenesis and molecular dynamics simulations, the structures reveal how ERY and TEL interplay with the Arg-Leu-Arg motif to induce translational arrest and illuminate the basis for the less stringent sequence-specific action of ERY over TEL. Because programmed stalling at the Arg/Lys-X-Arg/Lys motifs is used to activate expression of antibiotic resistance genes, our study also provides important insights for future development of improved macrolide antibiotics.

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The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly

Nucleic Acids Research ◽

10.1093/nar/gkw1231 ◽

2016 ◽

Vol 45 (3) ◽

pp. 1027-1040 ◽

Cited By ~ 12

Author(s):

Aida Razi ◽

Robert A. Britton ◽

Joaquin Ortega

Keyword(s):

Electron Microscopy ◽

Ribosome Assembly ◽

Cryo Electron Microscopy ◽

Bacterial Ribosome ◽

The Impact

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Structure-based design of agents targeting the bacterial ribosome

Bioorganic & Medicinal Chemistry Letters ◽

10.1016/s0960-894x(03)00495-5 ◽

2003 ◽

Vol 13 (15) ◽

pp. 2455-2458 ◽

Cited By ~ 24

Author(s):

Justin Bower ◽

Martin Drysdale ◽

Richard Hebdon ◽

Allan Jordan ◽

Georg Lentzen ◽

...

Keyword(s):

Bacterial Ribosome

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Proteomic profiling of the mitochondrial ribosome identifies Atp25 as a composite mitochondrial precursor protein

Molecular Biology of the Cell ◽

10.1091/mbc.e16-07-0513 ◽

2016 ◽

Vol 27 (20) ◽

pp. 3031-3039 ◽

Cited By ~ 15

Author(s):

Michael W. Woellhaf ◽

Frederik Sommer ◽

Michael Schroda ◽

Johannes M. Herrmann

Keyword(s):

Precursor Protein ◽

Ribosomal Biogenesis ◽

Proteomic Profiling ◽

Mitochondrial Translation ◽

Bacterial Ribosome ◽

Mitochondrial Ribosome ◽

Translation Apparatus ◽

The Matrix ◽

Processing Peptidase ◽

And Function

Whereas the structure and function of cytosolic ribosomes are well characterized, we only have a limited understanding of the mitochondrial translation apparatus. Using SILAC-based proteomic profiling, we identified 13 proteins that cofractionated with the mitochondrial ribosome, most of which play a role in translation or ribosomal biogenesis. One of these proteins is a homologue of the bacterial ribosome-silencing factor (Rsf). This protein is generated from the composite precursor protein Atp25 upon internal cleavage by the matrix processing peptidase MPP, and in this respect, it differs from all other characterized mitochondrial proteins of baker’s yeast. We observed that cytosolic expression of Rsf, but not of noncleaved Atp25 protein, is toxic. Our results suggest that eukaryotic cells face the challenge of avoiding negative interference from the biogenesis of their two distinct translation machineries.

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