Dual activity of PNGM-1, a metallo-β-lactamase and tRNase Z, pinpoints the evolutionary origin of subclass B3 metallo-β-lactamases

Lee, J. H.; Takahashi, M.; Jeon, J. H.; Kang, L.-W.; Seki, M.; Park, K. S.; Hong, M.-K.; Park, Y. S.; Kim, T. Y.; Karim, A. M.; Lee, J.-H.; Nashimoto, M.; Lee, S. H.

doi:10.1101/575373

bioRxiv · 10.1101/575373

Dual activity of PNGM-1, a metallo-β-lactamase and tRNase Z, pinpoints the evolutionary origin of subclass B3 metallo-β-lactamases

Lee, J. H.·Takahashi, M.·Jeon, J. H.·Kang, L.-W.·Seki, M.·Park, K. S.·Hong, M.-K.·Park, Y. S.·Kim, T. Y.·Karim, A. M.·Lee, J.-H.·Nashimoto, M.·Lee, S. H.

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Abstract

Antibiotic resistance is a steadily increasing global problem which could lead to a fundamental upheaval in clinical care with the potential to return us to the pre-antibiotic era1-4. The production of {beta}-lactamases, a group of enzymes that confer antibiotic resistance in Gram-negative bacteria, is now one of the major barriers in treating Gram-negative infections5. {beta}-Lactamases are classified according to their catalytic mechanisms into serine {beta}-lactamases and metallo-{beta}-lactamases6,7. There are functional and structural similarities between serine {beta}-lactamases and penicillin-binding proteins, and so serine {beta}-lactamases are thought to have evolved from a penicillin-binding protein7,8. Given the functional and structural differences between serine {beta}-lactamases and metallo-{beta}-lactamases, metallo-{beta}-lactamases are thought to have evolved from a protein other than a penicillin-binding protein, but to date this ancestor remains unknown8-11. We discovered PNGM-1, the first subclass B3 metallo-{beta}-lactamase, in deep-sea sediments that predate the antibiotic era12. Here we discover the dual activity of PNGM-1, pinpointing the evolutionary origin of subclass B3 metallo-{beta}-lactamases. Phylogenetic analysis suggested that PNGM-1 could yield insights into the evolutionary origin of subclass B3 metallo-{beta}-lactamases. We reveal the structural similarities between tRNase Zs and PNGM-1, which prompted us to investigate their evolutionary relationship and the possibility of them possessing dual enzymatic activities. We demonstrate that PNGM-1 has dual activity with both true metallo-{beta}-lactamase and tRNase Z activity, suggesting that PNGM-1 is thought to have evolved from a tRNase Z. We also show kinetic and structural comparisons between PNGM-1 and other proteins including subclass B3 metallo-{beta}-lactamases and tRNase Zs. These comparisons revealed that the B3 metallo-{beta}-lactamase activity of PNGM-1 is a promiscuous activity and subclass B3 metallo-{beta}-lactamases are thought to have evolved through PNGM-1 activity. Our work provides a foundation for the evolution of tRNase Z into subclass B3 metallo-{beta}-lactamases through the dual activity of PNGM-1.

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Lee, J. H., Takahashi, M., Jeon, J. H., Kang, L.-W., Seki, M., Park, K. S., Hong, M.-K., Park, Y. S., Kim, T. Y., Karim, A. M., Lee, J.-H., Nashimoto, M., Lee, S. H.. 2019-03-13. Dual activity of PNGM-1, a metallo-β-lactamase and tRNase Z, pinpoints the evolutionary origin of subclass B3 metallo-β-lactamases. https://doi.org/10.1101/575373

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