Origin of subclass B3 metallo-β-lactamases

What is it about?

Antibiotic resistance is a steadily increasing global problem and raising antibiotic resistance can fundamentally shake up the clinical care, with the potential to return us to the pre-antibiotic era. Carbapenem is a ‘last resort’ drug for treating infections of multidrug-resistant Gram-negative pathogenic bacteria. The effectiveness of carbapenem is continuously challenged by the emergence and spread of new resistance mechanisms. As a consequence, infections caused by resistant bacteria do not respond standard treatments, leading to prolonged illness and increased risk of death. With high mortality rates, carbapenem-resistant Gram-negative bacteria are rapidly emerging as a cause of opportunistic infections. This situation has caused a ‘global crisis’ of antibiotics. Carbapenem resistance in Gram-negative bacteria is mostly due to the production of carbapenemases (carbapenem-hydrolysing β-lactamases). Metallo-β-lactamases (MBLs) are one of the largest and most efficient groups of carbapenemases. Most MBLs are broad-spectrum enzymes that also hydrolyse cephalosporins. Together with the worldwide spread of MBL-encoding genes such as NDM-1 gene of multidrug-resistant Superbugs, these facts raise an alarming clinical problem. However, there is the enigma that the evolutionary origin of MBLs conferring critical antibiotic resistance threats is unknown. To solve this problem, this study reports the dual activity of PNGM-1 (the first subclass B3 MBL from the deep-sea sediments that predate the antibiotic era), pinpointing the ancient origin of subclass B3 MBLs. We demonstrate that PNGM-1 has the dual activity with the true β-lactamase (MBL) and tRNase Z activity, which means that PNGM-1 is thought to evolve from a tRNase Z.

Featured Image

Photo by Aaron Burden on Unsplash

Photo by Aaron Burden on Unsplash

Why is it important?

Our functional, phylogenetic and structural analyses of PNGM-1, and their comparison with those of all MBL types and structurally-representative MBL fold proteins of the MBL superfamily, reveal that the B3 metallo-β-lactamase activity of PNGM-1 is a promiscuous activity and subclass B3 metallo-β-lactamases are thought to evolve from PNGM-1. This article provides a foundation for the evolution of tRNase Z into subclass B3 metallo-β-lactamases through the dual activity of PNGM-1. Taken together, we suggest that subclass B3 MBLs arose through an evolutionary trajectory (tRNase Z → PNGM-1→ subclass B3 MBLs) and the ancient origin of subclass B3 MBLs is a tRNase Z. Fortunately, if a B1/B2 MBL with the dual activity like PNGM-1 could be identified in the future, we would understand the ancient origin of subclasses B1/B2 MBLs. In addition, this molecular evolutionary process (dimer interfacial deformation to prevent dimerization of an ancestral protein such as a tRNase Z, dimer) provides a new strategy to develop novel enzymes (e.g., class B MBLs, monomer). To date novel enzymes have rationally been designed by two main approaches: (i) grafting of a reactive catalytic motif into a protein scaffold; and (ii) amino acid substitutions to improve catalytic activity or to create new catalytic activities.

Perspectives