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Cited by 15RNA and protein synthesis mechanismsAntibiotic Resistance in BacteriaAntimicrobial Resistance in Staphylococcus

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Antibiotic hyper-resistance in a class I aminoacyl-tRNA synthetase with altered active site signature motif

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Brkic, A., Leibundgut, M., Jablonska, J., Zanki, V., Car, Z., Petrovic Perokovic, V., Marsavelski, A., Ban, N., Gruic-Sovulj, I.·2023·Nature Communications
DOI 10.1038/s41467-023-41244-3PMC PMC10485003

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Abstract

Antibiotics target key biological processes that include protein synthesis. Bacteria respond by developing resistance, which increases rapidly due to antibiotics overuse. Mupirocin, a clinically used natural antibiotic, inhibits isoleucyl-tRNA synthetase (IleRS), an enzyme that links isoleucine to its tRNA Ile for protein synthesis. Two IleRSs, mupirocin-sensitive IleRS1 and resistant IleRS2, coexist in bacteria. The latter may also be found in resistant Staphylococcus aureus clinical isolates. Here, we describe the structural basis of mupirocin resistance and unravel a mechanism of hyper-resistance evolved by some IleRS2 proteins. We surprisingly find that an up to 10 3 -fold increase in resistance originates from alteration of the HIGH motif, a signature motif of the class I aminoacyl-tRNA synthetases to which IleRSs belong. The structural analysis demonstrates how an altered HIGH motif could be adopted in IleRS2 but not IleRS1, providing insight into an elegant mechanism for coevolution of the key catalytic motif and associated antibiotic resistance.

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Research works printed but not linked: 60

  1. Bhattacharjee, M. K. In Chemistry of Antibiotics and Related Drugs 129–151 (Springer, 2016). · DOI
  2. Pang, L., Weeks, S. D. & Van Aerschot, A. Aminoacyl-trna synthetases as valuable targets for antimicrobial drug discovery. Int. J. Mol. Sci. 22, 1–34 (2021).
  3. Peterson, E. & Kaur, P. Antibiotic resistance mechanisms in bacteria: relationships between resistance determinants of antibiotic producers, environmental bacteria, and clinical pathogens. Front. Microbiol. 9, 2928 (2018). · DOI
  4. Gomez, M. A. R. & Ibba, M. Aminoacyl-tRNA synthetases. RNA 26, 910 (2020). · DOI
  5. Tawfik, D. S. & Gruic-Sovulj, I. How evolution shapes enzyme selectivity – lessons from aminoacyl-tRNA synthetases and other amino acid utilizing enzymes. FEBS J. 287, 1284–1305 (2020). · DOI
  6. Ribas de Pouplana, L. & Schimmel, P. Two classes of tRNA synthetases suggested by sterically compatible dockings on tRNA acceptor stem. Cell 104, 191–193 (2001). · DOI
  7. Eriani, G., Delarue, M., Poch, O., Gangloff, J. & Moras, D. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature 347, 203–206 (1990). · DOI
  8. Gruic-Sovulj, I., Longo, L. M., Jabłońska, J. & Tawfik, D. S. The evolutionary history of the HUP domain. Crit. Rev. Biochem. Mol. Biol. https://doi.org/10.1080/10409238.2021.1957764 (2021). · DOI
  9. Nagel, G. M. & Doolittle, R. F. Evolution and relatedness in two aminoacyl-tRNA synthetase families. Proc. Natl Acad. Sci. USA 88, 8121–8125 (1991). · DOI
  10. Borgford, T. J., Gray, T. E., Brand, N. J. & Fersht, A. R. Site-directed mutagenesis reveals transition-state stabilization as a general catalytic mechanism for aminoacyl-tRNA synthetases. Biochemistry 26, 7246–7250 (1987). · DOI
  11. Perona, J. J., Rould, M. A. & Steitz, T. A. Structural basis for transfer RNA aminoacylation by Escherichia coli glutaminyl-tRNA synthetase. Biochemistry 32, 8758–8771 (1993). · DOI
  12. Leatherbarrow, R. J., Fersht, A. R. & Winter, G. Transition-state stabilization in the mechanism of tyrosyl-tRNA synthetase revealed by protein engineering. Proc. Natl Acad. Sci. USA 82, 7840–7844 (1985). · DOI
  13. Hughes, J. & Mellows, G. Inhibition of isoleucyl-transfer ribonucleic acid synthetase in Escherichia coli by pseudomonic acid. Biochem. J. 176, 305–318 (1978). · DOI
  14. Silvian, L. F., Wang, J. & Steitz, T. A. Insights into editing from an Ile-tRNA synthetase structure with tRNA(Ile) and mupirocin. Science 285, 1074–1077 (1999). · DOI
  15. Nakama, T., Nureki, O. & Yokoyama, S. Structural basis for the recognition of isoleucyl-adenylate and an antibiotic, mupirocin, by isoleucyl-tRNA synthetase. J. Biol. Chem. 276, 47387–47393 (2001). · DOI
  16. Sassanfar, M., Kranz, J. E., Gallant, P., Schimmel, P. & Shiba, K. A eubacterial Mycobacterium tuberculosis tRNA synthetase is eukaryote- like and resistant to a eubacterial-specific antisynthetase drug. Biochemistry 35, 9995–10003 (1996). · DOI
  17. Cvetesic, N. et al. Naturally occurring isoleucyl-tRNA synthetase without tRNA-dependent pre-transfer editing. J. Biol. Chem. 291, 8618–8631 (2016). · DOI
  18. Hughes, J. & Mellows, G. Interaction of pseudomonic acid A with Escherichia coli B isoleucyl-tRNA synthetase. Biochem. J. 191, 209–219 (1980). · DOI
  19. Pope, A. J. et al. Characterization of isoleucyl-tRNA synthetase from Staphylococcus aureus: II. Mechanism of inhibition by reaction intermediate and pseudomonic acid analogues studied using transient and steady-state kinetics. J. Biol. Chem. 273, 31691–31701 (1999). · DOI
  20. Yanagisawa, T. & Kawakami, M. How does Pseudomonas fluorescens avoid suicide from its antibiotic pseudomonic acid? Evidence for two evolutionarily distinct isoleucyl-tRNA synthetases conferring self-defense. J. Biol. Chem. 278, 25887–25894 (2003). · DOI
  21. Zanki, V., Bozic, B., Mocibob, M., Ban, N. & Gruic-Sovulj, I. A pair of isoleucyl-tRNA synthetases in Bacilli fulfill complementary roles to enhance fitness and provide antibiotic resistance. Protein Sci. 31, e4418 (2022). · DOI
  22. Hurdle, J. G., O’Neill, A. J., Ingham, E., Fishwick, C. & Chopra, I. Analysis of mupirocin resistance and fitness in Staphylococcus aureus by molecular genetic and structural modeling techniques. Antimicrob. Agents Chemother. 48, 4366–4376 (2004). · DOI
  23. Gupta, R. S., Patel, S., Saini, N. & Chen, S. Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus bacillus limiting it only to the members of the Subtilis and Cereus clades of species. Int. J. Syst. Evol. Microbiol. 70, 5753–5798 (2020). · DOI
  24. Jabłońska, J. & Tawfik, D. S. The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation. Nat. Ecol. Evol. 5, 442–448 (2021). · DOI
  25. Chung, S., Kim, S., Ryu, S. H., Hwang, K. Y. & Cho, Y. Structural basis for the antibiotic resistance of eukaryotic isoleucyl-trna synthetase. Mol. Cells 43, 350–359 (2020).
  26. Chen, B. et al. Inhibitory mechanism of reveromycin A at the tRNA binding site of a class I synthetase. Nat. Commun. 12, 1616 (2021).
  27. Kobayashi, T. et al. Structural snapshots of the KMSKS loop rearrangement for amino acid activation by bacterial tyrosyl-tRNA synthetase. J. Mol. Biol. 346, 105–117 (2005). · DOI
  28. Fersht, A. R. et al. Hydrogen bonding and biological specificity analysed by protein engineering. Nature 314, 235–238 (1985). · DOI
  29. Fersht, A. R. The hydrogen bond in molecular recognition. Trends Biochem. Sci. 12, 301–304 (1987). · DOI
  30. Koshland, D. E. Application of a theory of enzyme specificity to protein synthesis. Proc. Natl Acad. Sci. USA 44, 98–104 (1958). · DOI
  31. Arenz, S. & Wilson, D. N. Bacterial protein synthesis as a target for antibiotic inhibition. Cold Spring Harb. Perspect. Med. 6, a025361 (2016). · DOI
  32. Thomas, C. M., Hothersall, J., Willis, C. L. & Simpson, T. J. Resistance to and synthesis of the antibiotic mupirocin. Nat. Rev. Microbiol. 8, 281–289 (2010). · DOI
  33. Hurdle, J. G., O’Neill, A. J. & Chopra, I. Prospects for aminoacyl-tRNA synthetase inhibitors as new antimicrobial agents. Antimicrob. Agents Chemother. 49, 4821–4833 (2005). · DOI
  34. Marion, O., Gao, X., Marcus, S. & Hall, D. G. Synthesis and preliminary antibacterial evaluation of simplified thiomarinol analogs. Bioorg. Med. Chem. 17, 1006–1017 (2009). · DOI
  35. Racher, K. I., Kalmar, G. B. & Borgford, T. J. Expression and characterization of a recombinant yeast isoleucyl-tRNA synthetase. J. Biol. Chem. 266, 17158–17164 (1991). · DOI
  36. Palencia, A. et al. Structural dynamics of the aminoacylation and proofreading functional cycle of bacterial leucyl-tRNA synthetase. Nat. Struct. Mol. Biol. 19, 677–684 (2012). · DOI
  37. McCusker, K. P. & Fujimori, D. G. The chemistry of peptidyltransferase center-targeted antibiotics: enzymatic resistance and approaches to countering resistance. ACS Chem. Biol. 7, 64–72 (2012). · DOI
  38. Nagel, G. M. & Doolittle, R. F. Phylogenetic analysis of the aminoacyl-tRNA synthetases. J. Mol. Evol. 40, 487–498 (1995). · DOI
  39. Schmitt, E., Panvert, M., Blanquet, S. & Mechulam, Y. Transition state stabilization by the ‘high’ motif of class I aminoacyl-tRNA synthetases: the case of Escherichia coli methionyl-tRNA synthetase. Nucleic Acids Res. 23, 4793–4798 (1995). · DOI
  40. Dulic, M., Cvetesic, N., Perona, J. J. & Gruic-Sovulj, I. Partitioning of tRNA-dependent editing between pre- and post-transfer pathways in class I aminoacyl-tRNA synthetases. J. Biol. Chem. 285, 23799–23809 (2010). · DOI
  41. Wells, J. A., Vasser, M. & Powers, D. B. Cassette mutagenesis: an efficient method for generation of multiple mutations at defined sites. Gene 34, 315–323 (1985). · DOI
  42. Cvetesic, N. & Gruic-Sovulj, I. Synthetic and editing reactions of aminoacyl-tRNA synthetases using cognate and non-cognate amino acid substrates. Methods 113, 13–26 (2017). · DOI
  43. Kabsch, W. XDS. Acta Crystallogr. D Biol. Crystallogr. 66, 125–132 (2010). · DOI · Paper page
  44. Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. Sect. D Struct. Biol. 75, 861–877 (2019). · DOI · Paper page
  45. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. Sect. D Biol. Crystallogr. 66, 486–501 (2010). · DOI · Paper page
  46. Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012). · DOI · Paper page
  47. Katoh, K., Misawa, K., Kuma, K. I. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002). · DOI · Paper page
  48. Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009). · DOI
  49. Price, M. N., Dehal, P. S. & Arkin, A. P. Fasttree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol. Biol. Evol. 26, 1641–1650 (2009). · DOI · Paper page
  50. Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24, 1586–1591 (2007). · DOI · Paper page
  51. Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021). · DOI
  52. Maier, J. A. et al. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J. Chem. Theory Comput. 11, 3696–3713 (2015). · DOI
  53. Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W. & Klein, M. L. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926–935 (1983). · DOI
  54. Ryckaert, J. P., Ciccotti, G. & Berendsen, H. J. C. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327–341 (1977). · DOI
  55. Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., Dinola, A. & Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684–3690 (1984). · DOI
  56. Le Grand, S., Götz, A. W. & Walker, R. C. SPFP: speed without compromise - a mixed precision model for GPU accelerated molecular dynamics simulations. Comput. Phys. Commun. 184, 374–380 (2013). · DOI
  57. Roe, D. R. & Cheatham, T. E. PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J. Chem. Theory Comput. 9, 3084–3095 (2013). · DOI
  58. Kabsch, W. & Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen‐bonded and geometrical features. Biopolymers 22, 2577–2637 (1983). · DOI · Paper page
  59. Heacock, D., Forsyth, C. J., Shiba, K. & Musier-Forsyth, K. Synthesis and aminoacyl-tRNA synthetase inhibitory activity of prolyl adenylate analogs. Bioorg. Chem. 24, 273–289 (1996). · DOI
  60. Vondenhoff, G. H. M. et al. Extended targeting potential and improved synthesis of Microcin C analogs as antibacterials. Bioorg. Med. Chem. 19, 5462–5467 (2011). · DOI

Metadata

Authors
Brkic, A., Leibundgut, M., Jablonska, J., Zanki, V., Car, Z., Petrovic Perokovic, V., Marsavelski, A., Ban, N., & Gruic-Sovulj, I.
Affiliations
  • ETH Zurich (CH)
  • University of Zagreb (HR)
Corresponding author
Ban, N.
ORCID
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2023-09-07
Volume
14
Issue
1
Pages
5498-5498
ISSN
2041-1723 (ISSN-L)
DOI
10.1038/s41467-023-41244-3
PMC
PMC10485003
OpenAlex
W4386507605
Cited by
15
References
3
Citations by year
2026: 7 · 2025: 3 · 2024: 5
FWCI
1.34
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DORA PSI (Paul Scherrer Institute) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
  • ETH Zürich Research Collection
Funders
  • Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung
  • Hrvatska Zaklada za Znanost (IP-2016-06-6272, KK.01.1.1.02.0016)
  • European Regional Development Fund (KK.01.1, KK.01.1.1.02.0016)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Health Sciences › Medicine › Microbiology (medical) › Antibiotic Resistance in Bacteria
  • Health Sciences › Medicine › Infectious Diseases › Antimicrobial Resistance in Staphylococcus
Keywords
mupirocin resistance, isoleucyl-tRNA synthetase, class I aminoacyl-tRNA synthetase, antibiotic resistance mechanisms, Staphylococcus aureus, protein synthesis inhibition
MeSH terms
Amino Acyl-tRNA Synthetases, Anti-Bacterial Agents, Drug Resistance, Microbial, Isoleucine, Mupirocin, Catalytic Domain, Methicillin-Resistant Staphylococcus aureus

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