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In-cell kinetic stability is an essential trait in metallo-β-lactamase evolution

Nature Chemical Biology volume 19, pages 1116–1126 (2023)Cite this article

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Abstract

Protein stability is an essential property for biological function. In contrast to the vast knowledge on protein stability in vitro, little is known about the factors governing in-cell stability. Here we show that the metallo-β-lactamase (MBL) New Delhi MBL-1 (NDM-1) is a kinetically unstable protein on metal restriction that has evolved by acquiring different biochemical traits that optimize its in-cell stability. The nonmetalated (apo) NDM-1 is degraded by the periplasmic protease Prc that recognizes its partially unstructured C-terminal domain. Zn(II) binding renders the protein refractory to degradation by quenching the flexibility of this region. Membrane anchoring makes apo-NDM-1 less accessible to Prc and protects it from DegP, a cellular protease degrading misfolded, nonmetalated NDM-1 precursors. NDM variants accumulate substitutions at the C terminus that quench its flexibility, enhancing their kinetic stability and bypassing proteolysis. These observations link MBL-mediated resistance with the essential periplasmic metabolism, highlighting the importance of the cellular protein homeostasis.

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Fig. 1: Metal depletion can trigger degradation or aggregation of apo MBLs within the periplasm.
Fig. 2: Proteases Prc and DegP mediate the degradation of NDM-1.
Fig. 3: In vitro analysis of Prc and DegP proteolytic activity on MBLs.
Fig. 4: Prc forms complexes with apo-rNDM-1, and NlpI competes with apo-rNDM-1 for binding to the protease.
Fig. 5: Substitution A233V in rNDM-6 quenches C terminus dynamics of the apo form, reducing degradation by Prc and DegP compared to NDM-1.
Fig. 6: Life cycle of membrane-bound and soluble MBLs in the bacterial periplasm.

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Data availability

The data supporting the findings of this study are available within the article and its Supplementary Information files. The following protein structures were downloaded from the Research Collaboratory for Structural Bioinformatics PDB: apo-rNDM-1 (PDB 3SPU and PDB 3SBL), Prc (PDB 5WQL), holo-rNDM-1 (PDB 5ZGX), apo-rNDM-1 (PDB 3SBL), holo-rBcII (PDB 3I13), apo-rBcII (PDB 3I0V) and Prc K477A (PDB: 5WQL). Source data are provided with this paper.

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Acknowledgements

This research was supported by grants from the National Institutes of Health (grant nos. R01AI100560 to R.A.B. and A.J.V., R01AI063517 to R.A.B. and R01AI072219 to R.A.B.) and Agencia I+d+i to A.J.V. (grant no. PICT 2020-0031) and L.J.G. (grant no. PICT 2020-1923). This study was supported in part by funds and/or facilities provided by the Cleveland Department of Veterans Affairs, award no. 1I01BX001974 to R.A.B. from the Biomedical Laboratory Research & Development Service of the VA Office of Research and Development and the Geriatric Research Education and Clinical Center VISN 10 to R.A.B. The NMR instrumentation was provided by PLABEM at IBR. G.B. and M.M.G. were recipients of fellowships from CONICET. A.J.V. and L.J.G. are staff members from CONICET. We are grateful to Marina Avecilla for excellent technical assistance. We thank L. Giono for designing and drawing Fig. 6 and the Graphical Abstract.

Author information

Authors and Affiliations

  1. Instituto de Biología Molecular y Celular de Rosario (IBR, CONICET-UNR), Rosario, Argentina

    Lisandro J. González, Guillermo Bahr, Mariano M. González & Alejandro J. Vila

  2. Área Biofísica, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina

    Lisandro J. González, Guillermo Bahr, Mariano M. González & Alejandro J. Vila

  3. Research Service, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA

    Robert A. Bonomo

  4. Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, OH, USA

    Robert A. Bonomo

  5. Medical Service and GRECC, Veterans Affairs Northeast Ohio Healthcare System, Cleveland, OH, USA

    Robert A. Bonomo

  6. CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, OH, USA

    Robert A. Bonomo & Alejandro J. Vila

  7. Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH, USA

    Robert A. Bonomo

  8. Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, USA

    Robert A. Bonomo

  9. Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, OH, USA

    Robert A. Bonomo

  10. Department of Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA

    Robert A. Bonomo

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  1. Lisandro J. González
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Contributions

L.J.G. and A.J.V. crafted the main hypothesis and designed research. L.J.G. performed the microbiological, molecular biology and biochemical experiments, and NMR experiments on interactions and NDM-6 dynamics. G.B. carried out the experiments involving proteins in liposomes and part of the proteolysis experiments and M.M.G. performed the NMR experiments on NDM-1 and BcII. L.J.G., G.B., R.A.B. and A.J.V. wrote the paper, and all authors discussed the results and commented on the manuscript.

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Correspondence to Alejandro J. Vila.

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Extended data

Extended Data Fig. 1 SEC and negative staining TEM demonstrate formation of complexes between Prc K477A and apo-rNDM-1.

a) SDS-PAGE analysis of SEC fractions corresponding to samples containing Prc K477A and either holo-rNDM-1 (top) or apo-rNDM-1 (bottom). b) Negative staining TEM of Prc K477A (top) or complexes of Prc K477A and apo NDM-1 (bottom). Samples for TEM analysis were obtained from SEC of the corresponding mixtures (shown in Fig. 4a), at the elution volume (VE in mL) indicated. Panels a, b show one of two independent experiments.

Source data

Extended Data Fig. 2 NlpI blocks association of apo-rNDM-1 to Prc K477A, possibly by occupying the same binding site on the protease.

a) SDS-PAGE analysis of SEC fractions from the left panel, corresponding to samples containing NlpI and apo-rNDM-1, with (bottom) or without (top) Prc K477A (two independent repetitions). b) Structural alignment of the Prc:NlpI complex (PDB 5WQL) and the proposed complex of Prc and apo-rNDM-1 (from Fig. 4b). NlpI and apo-rNDM-1 are shown as yellow and green ribbons, respectively, while Prc is shown in a magenta surface representation.

Supplementary information

Supplementary Information

Supplementary Figs. 1–21; Tables 1–4; full, uncut gel images for Figs. 2, 8, 9 and 10; full, uncut gel images for Figs. 11, 12, 14, 15 and 17 and references.

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Source Data Fig. 1

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Source Data Fig. 5

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Source Data Extended Data Fig. 1

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González, L.J., Bahr, G., González, M.M. et al. In-cell kinetic stability is an essential trait in metallo-β-lactamase evolution. Nat Chem Biol 19, 1116–1126 (2023). https://doi.org/10.1038/s41589-023-01319-0

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