A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome – Nature
Maksimov, M. O., Pan, S. J. & James Link, A. Lasso peptides: structure, function, biosynthesis, and engineering. Nat. Prod. Rep. 29, 996–1006 (2012).
Google Scholar
Tietz, J. I. et al. A new genome-mining tool redefines the lasso peptide biosynthetic landscape. Nat. Chem. Biol. 13, 470–478 (2017).
Google Scholar
Barrett, S. E. & Mitchell, D. A. Advances in lasso peptide discovery, biosynthesis, and function. Trends Genet. 40, 950–968 (2024).
Google Scholar
Gavrish, E. et al. Lassomycin, a ribosomally synthesized cyclic peptide, kills Mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. Chem. Biol. 21, 509–518 (2014).
Google Scholar
Mukhopadhyay, J., Sineva, E., Knight, J., Levy, R. M. & Ebright, R. H. Antibacterial peptide microcin J25 inhibits transcription by binding within and obstructing the RNA polymerase secondary channel. Mol. Cell. 14, 739–751 (2004).
Google Scholar
Wilson, D. N. The A–Z of bacterial translation inhibitors. Crit. Rev. Biochem. Mol. Biol. 44, 393–433 (2009).
Google Scholar
Lin, J., Zhou, D., Steitz, T. A., Polikanov, Y. S. & Gagnon, M. G. Ribosome-targeting antibiotics: modes of action, mechanisms of resistance, and implications for drug design. Annu. Rev. Biochem. 87, 451–478 (2018).
Google Scholar
Antimicrobial Resistance, C. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399, 629–655 (2022).
Google Scholar
Jesudason, T. WHO publishes updated list of bacterial priority pathogens. Lancet Microbe 5, 100940 (2024).
Google Scholar
Liu, Y., Ding, S. Y., Shen, J. Z. & Zhu, K. Nonribosomal antibacterial peptides that target multidrug-resistant bacteria. Nat. Prod. Rep. 36, 573–592 (2019).
Google Scholar
Sieber, S. A. & Marahiel, M. A. Molecular mechanisms underlying nonribosomal peptide synthesis: Approaches to new antibiotics. Chem. Rev. 105, 715–738 (2005).
Google Scholar
Ongpipattanakul, C. et al. Mechanism of action of ribosomally synthesized and post-translationally modified peptides. Chem. Rev. 122, 14722–14814 (2022).
Google Scholar
Arnison, P. G. et al. Ribosomally synthesized and post-translationally modified peptide natural products: overview and recommendations for a universal nomenclature. Nat. Prod. Rep. 30, 108–160 (2013).
Google Scholar
Pfeiffer, I. P., Schroder, M. P. & Mordhorst, S. Opportunities and challenges of RiPP-based therapeutics. Nat. Prod. Rep. 41, 990–1019 (2024).
Google Scholar
Kuznedelov, K. et al. The antibacterial threaded-lasso peptide capistruin inhibits bacterial RNA polymerase. J. Mol. Biol. 412, 842–848 (2011).
Google Scholar
Weisblum, B. Erythromycin resistance by ribosome modification. Antimicrob. Agents Chemother. 39, 577–585 (1995).
Google Scholar
Smith, L. K. & Mankin, A. S. Transcriptional and translational control of the mlr operon, which confers resistance to seven classes of protein synthesis inhibitors. Antimicrob. Agents Chemother. 52, 1703–1712 (2008).
Google Scholar
Garneau-Tsodikova, S. & Labby, K. J. Mechanisms of resistance to aminoglycoside antibiotics: overview and perspectives. Medchemcomm 7, 11–27 (2016).
Google Scholar
Cook, M. A. et al. Lessons from assembling a microbial natural product and pre-fractionated extract library in an academic laboratory. J. Ind. Microbiol. Biotechnol. 50, kuad042 (2023).
Google Scholar
Nation, R. L. & Li, J. Colistin in the 21st century. Curr. Opin. Infect. Dis. 22, 535–543 (2009).
Google Scholar
Hancock, R. E. & Rozek, A. Role of membranes in the activities of antimicrobial cationic peptides. FEMS Microbiol. Lett. 206, 143–149 (2002).
Google Scholar
Quan, S., Skovgaard, O., McLaughlin, R. E., Buurman, E. T. & Squires, C. L. Markerless Escherichia coli rrn deletion strains for genetic determination of ribosomal binding sites. G3 5, 2555–2557 (2015).
Google Scholar
Orelle, C. et al. Tools for characterizing bacterial protein synthesis inhibitors. Antimicrob. Agents Chemother. 57, 5994–6004 (2013).
Google Scholar
Polikanov, Y. S., Aleksashin, N. A., Beckert, B. & Wilson, D. N. The mechanisms of action of ribosome-targeting peptide antibiotics. Front. Mol. Biosci. 5, 48 (2018).
Google Scholar
Pantel, L. et al. Odilorhabdins, antibacterial agents that cause miscoding by binding at a new ribosomal site. Mol. Cell 70, 83–94.e87 (2018).
Google Scholar
Peske, F., Savelsbergh, A., Katunin, V. I., Rodnina, M. V. & Wintermeyer, W. Conformational changes of the small ribosomal subunit during elongation factor G-dependent tRNA–mRNA translocation. J. Mol. Biol. 343, 1183–1194 (2004).
Google Scholar
Noller, H. F., Lancaster, L., Zhou, J. & Mohan, S. The ribosome moves: RNA mechanics and translocation. Nat. Struct. Mol. Biol. 24, 1021–1027 (2017).
Google Scholar
Rundlet, E. J. et al. Structural basis of early translocation events on the ribosome. Nature 595, 741–745 (2021).
Google Scholar
Orelle, C. et al. Identifying the targets of aminoacyl-tRNA synthetase inhibitors by primer extension inhibition. Nucleic Acids Res. 41, e144 (2013).
Google Scholar
Olivier, N. B. et al. Negamycin induces translational stalling and miscoding by binding to the small subunit head domain of the Escherichia coli ribosome. Proc. Natl Acad. Sci. USA 111, 16274–16279 (2014).
Google Scholar
Brenner, S. & Beckwith, J. Ochre mutants, a new class of suppressible nonsense mutants. J. Mol. Biol. 13, 629–637 (1965).
Google Scholar
Kohanski, M. A., Dwyer, D. J., Wierzbowski, J., Cottarel, G. & Collins, J. J. Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death. Cell 135, 679–690 (2008).
Google Scholar
Cao, L., Do, T. & Link, A. J. Mechanisms of action of ribosomally synthesized and posttranslationally modified peptides (RiPPs). J. Ind. Microbiol. Biotechnol. 48, kuab005 (2021).
Google Scholar
Carson, D. V., Juarez, R. J., Do, T., Yang, Z. J. & Link, A. J. Antimicrobial lasso peptide cloacaenodin utilizes a unique TonB-dependent transporter to access susceptible bacteria. ACS Chem. Biol. 19, 981–991 (2024).
Google Scholar
Do, T., Thokkadam, A., Leach, R. & Link, A. J. Phenotype-guided comparative genomics identifies the complete transport pathway of the antimicrobial lasso peptide ubonodin in burkholderia. ACS Chem. Biol. 17, 2332–2343 (2022).
Google Scholar
Miller, S., Goy, K., She, R., Spellberg, B. & Luna, B. Antimicrobial susceptibility testing performed in RPMI 1640 reveals azithromycin efficacy against carbapenem-resistant Acinetobacter baumannii and predicts in vivo outcomes in Galleria mellonella. Antimicrob. Agents Chemother. 67, e01320–e01322 (2023).
Google Scholar
Luna, B. et al. A nutrient-limited screen unmasks rifabutin hyperactivity for extensively drug-resistant Acinetobacter baumannii. Nat. Microbiol. 5, 1134–1143 (2020).
Google Scholar
Farha, M. A., French, S., Stokes, J. M. & Brown, E. D. Bicarbonate alters bacterial susceptibility to antibiotics by targeting the proton motive force. ACS Infect. Dis. 4, 382–390 (2018).
Google Scholar
Andersen, F. D. et al. Triculamin: an unusual lasso peptide with potent antimycobacterial activity. J. Nat. Prod. 85, 1514–1521 (2022).
Google Scholar
Ersoy, S. C. et al. Correcting a fundamental flaw in the paradigm for antimicrobial susceptibility testing. EBioMedicine 20, 173–181 (2017).
Google Scholar
Polikanov, Y. S. et al. Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA. Mol. Cell 56, 541–550 (2014).
Google Scholar
Chen, Z., Erickson, D. L. & Meng, J. Benchmarking hybrid assembly approaches for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing. BMC Genomics 21, 631 (2020).
Google Scholar
Blin, K. et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29–w35 (2021).
Google Scholar
Blin, K. et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res. 51, W46–w50 (2023).
Google Scholar
Tamura, K., Stecher, G. & Kumar, S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol. Biol. Evol. 38, 3022–3027 (2021).
Google Scholar
Gilchrist, C. L. M. & Chooi, Y.-H. clinker & clustermap.js: automatic generation of gene cluster comparison figures. Bioinformatics 37, 2473–2475 (2021).
Google Scholar
Waterhouse, A. M., Procter, J. B., Martin, D. M., Clamp, M. & Barton, G. J. Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189–1191 (2009).
Google Scholar
Bai, C. et al. Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces. Proc. Natl Acad. Sci. USA 112, 12181–12186 (2015).
Google Scholar
Hong, H. J., Hutchings, M. I., Hill, L. M. & Buttner, M. J. The role of the novel Fem protein VanK in vancomycin resistance in Streptomyces coelicolor. J. Biol. Chem. 280, 13055–13061 (2005).
Google Scholar
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
Google Scholar
Xu, M. et al. GPAHex-A synthetic biology platform for type IV–V glycopeptide antibiotic production and discovery. Nat. Commun. 11, 5232 (2020).
Google Scholar
Cox, G. et al. A common platform for antibiotic dereplication and adjuvant discovery. Cell Chem. Biol. 24, 98–109 (2017).
Google Scholar
Deatherage, D. E. & Barrick, J. E. Identification of mutations in laboratory-evolved microbes from next-generation sequencing data using breseq. Methods Mol. Biol. 1151, 165–188 (2014).
Google Scholar
Speers, A. E. & Cravatt, B. F. Profiling enzyme activities in vivo using click chemistry methods. Chem. Biol. 11, 535–546 (2004).
Google Scholar
Shimizu, Y. et al. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19, 751–755 (2001).
Google Scholar
Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006).
Google Scholar
Polikanov, Y. S., Blaha, G. M. & Steitz, T. A. How hibernation factors RMF, HPF, and YfiA turn off protein synthesis. Science 336, 915–918 (2012).
Google Scholar
Polikanov, Y. S., Steitz, T. A. & Innis, C. A. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat. Struct. Mol. Biol. 21, 787–793 (2014).
Google Scholar
Polikanov, Y. S., Melnikov, S. V., Soll, D. & Steitz, T. A. Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly. Nat. Struct. Mol. Biol. 22, 342–344 (2015).
Google Scholar
Syroegin, E. A., Aleksandrova, E. V. & Polikanov, Y. S. Insights into the ribosome function from the structures of non-arrested ribosome–nascent chain complexes. Nat. Chem. 15, 143–153 (2023).
Google Scholar
Aleksandrova, E. V. et al. Structural basis of Cfr-mediated antimicrobial resistance and mechanisms to evade it. Nat. Chem. Biol. 20, 867–876 (2024).
Google Scholar
Svetlov, M. S. et al. Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance. Nat. Chem. Biol. 17, 412–420 (2021).
Google Scholar
Chen, C. W. et al. Structural insights into the mechanism of overcoming Erm-mediated resistance by macrolides acting together with hygromycin-A. Nat. Commun. 14, 4196 (2023).
Google Scholar
Mitcheltree, M. J. et al. A synthetic antibiotic class overcoming bacterial multidrug resistance. Nature 599, 507–512 (2021).
Google Scholar
Kabsch, W. Xds. Acta Crystallogr. D 66, 125–132 (2010).
Google Scholar
McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007).
Google Scholar
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D 66, 213–221 (2010).
Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).
Google Scholar
Noeske, J. et al. High-resolution structure of the Escherichia coli ribosome. Nat. Struct. Mol. Biol. 22, 336–341 (2015).
Google Scholar
