Dual activity of PNGM-1 pinpoints the evolutionary origin of subclass B3 metallo- β -lactamases: a molecular and evolutionary study

Abstract

Resistance to β-lactams is one of the most serious problems associated with Gram-negative infections. β-Lactamases are able to hydrolyze β-lactams such as cephalosporins and/or carbapenems. Evolutionary origin of metallo-β-lactamases (MBLs), conferring critical antibiotic resistance threats, remains unknown. We discovered PNGM-1, the novel subclass B3 MBL, in deep-sea sediments that predate the antibiotic era. Here, our phylogenetic analysis suggests that PNGM-1 yields insights into the evolutionary origin of subclass B3 MBLs. We reveal the structural similarities between tRNase Zs and PNGM-1, and demonstrate that PNGM-1 has both MBL and tRNase Z activities, 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 MBLs and tRNase Zs. These comparisons revealed that the B3 MBL activity of PNGM-1 is a promiscuous activity and subclass B3 MBLs are thought to have evolved through PNGM-1 activity.

Freshwater viral metagenome reveals novel and functional phage-borne antibiotic resistance genes

“…The catalytic efficiencies (k cat /k m ) of HRV-1 for cefotaxime (4.1 × 10 3 M −1 S −1 ) and ceftazidime (3.3 × 10 3 M −1 S −1 ) were 2-and 26fold higher than those of GES-14 (1.8 × and 0.125 × 10 3 M −1 S −1 , respectively) belonging to class A ESBL [45]. In addition, the k cat /k m of HRVM-1 for imipenem (5.0 × 10 2 M −1 s −1 ) was similar to those of PNGM-1 (5.5 × 10 2 M −1 s −1 ) [46] from a deep-sea sediment metagenome and CAR-1 (9.6 × 10 2 M −1 s −1 ) [47] from Erwinia carotovora that belong to subclass B3 MBL. The kinetic data for HRV-1 and HRVM-1 were consistent with the determined MICs (Fig.…”

Broad spectrum antibiotic-degrading metallo-β-lactamases are phylogenetically diverse

“…Fewer B2-type MBLs are currently known; they are phylogenetically related to B1 MBLs but are characterized by a preference for “last line” carbapenem substrates (Sun et al, 2016 ). While B3-type MBLs share low sequence similarity to B1 and B2 enzymes (< 20% amino acid (aa) identity), they have a substrate range similar to that of B1 MBLs (Selleck et al, 2016 ; Lee et al, 2019 ). MBLs contain catalytic centres that can accommodate two closely spaced Zn 2+ ions bound in the α and β sites with similar yet distinct sequence motifs (B1: His116, His118, His196 and Asp120, Cys221, His263 (i.e., HHH/DCH) for the α and β sites, respectively; B2: NHH/DCH; B3: HHH/DHH).…”

RNA-hydrolyzing activity of metallo-β-lactamase IMP-1

“…These include several non-native MBL reactions that have never been catalyzed by MBL-superfamily enzymes [ 29 ]. PNGM-1, which was isolated from a functional metagenomic library from deep-sea sediments from Edison Seamount, was recently reported to exhibit both β-lactamase and endoribonuclease activities, even though the k cat values of its β-lactamase activity were 10 3 –10 4 -fold lower than those of usual clinically identified MBLs [ 30 ]. It seems plausible that a basic catalytic mechanism is conserved in the MBL-superfamily enzymes and that each enzyme is customized for a certain substrate by a particular arrangement of the residues surrounding the active site, the addition of extra loops or domains, and through a specific metal ion-binding mode.…”