Dual functional roles of a novel bifunctional β-lactamase/esterase from Lactococcus garvieae

Le, Ly; Yoo, Woo-Kyoung; Wang, Ying; Jeon, Sangeun; Kim, Kyeong Kyu; Kim, Han-Woo; Kim, T Doohun

doi:10.1016/j.ijbiomac.2022.02.081

Cited by 9 publications

(4 citation statements)

References 46 publications

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“…Unlike other carboxylesterases that have the catalytic serine in the GxSxG motif, carboxylesterase group VIII has the same SxxK motif as beta-lactamases. Many studies have evaluated beta-lactams as substrates for carboxylesterases VIII, and most of them show activity against nitrocefin and cephalosporins of varying spectrum [ 53 – 55 ]. However, it is still not completely elucidated in which region of the molecule these enzymes act.…”

Section: Discussionmentioning

confidence: 99%

Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

de Souza,

Vieira,

dos Santos

et al. 2024

BMC Genomics

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Background Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher’s exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.

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Section: Discussionmentioning

confidence: 99%

Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

de Souza,

Vieira,

dos Santos

et al. 2024

BMC Genomics

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“…In silico analysis of the genomic DNA of L . garvieae has enabled the identification of several putative esterases/lipases [ 48 ]. Among the esterases, Lg EstI was characterized using biochemical and structural analyses.…”

Section: Discussionmentioning

confidence: 99%

Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae

Yoo

Wang

et al. 2023

PLoS ONE

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Esterase, a member of the serine hydrolase family, catalyzes the cleavage and formation of ester bonds with high regio- and stereospecificity, making them attractive biocatalysts for the synthesis of optically pure molecules. In this study, we performed an in-depth biochemical and structural characterization of a novel microbial acetylesterase, LgEstI, from the bacterial fish pathogen Lactococcus garvieae. The dimeric LgEstI displayed substrate preference for the short acyl chain of p-nitrophenyl esters and exhibited increased activity with F207A mutation. Comparative analysis with other esterases indicated that LgEstI has a narrow and shallow active site that may exhibit substrate specificity to short acyl chains. Unlike other esterases, LgEstI contains bulky residues such as Trp89, Phe194, and Trp217, which block the acyl chain channel. Furthermore, immobilized LgEstI retained approximately 90% of its initial activity, indicating its potential in industrial applications. This study expands our understanding of LgEstI and proposes novel ideas for improving its catalytic efficiency and substrate specificity for various applications.

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“…Unlike other carboxylesterases that have the catalytic serine in the GxSxG motif, carboxylesterase group VIII has the same SxxK motif as beta-lactamases. Many studies have evaluated beta-lactams as substrates for carboxylesterases VIII, and most of them show activity against nitroce n and cephalosporins of varying spectrum (44)(45)(46). However, it is still not completely elucidated in which region of the molecule these enzymes act.…”

Section: Discussionmentioning

confidence: 99%

Potential Involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

Souza,

Vieira,

Santos

et al. 2023

Preprint

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Background Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. Results In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter sp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. Motif analysis revealed that, in general, catalytic residues are less conserved in homologous groups than in beta-lactamases. Comparison of the frequency of presence of protein groups in genomes of resistant strains in relation to sensitive ones, indicated that some groups of homologous proteins of classes B and C are more frequent in genomes of resistant than sensitive strains, particularly in those resistant to carbapenems. Conclusions The beta-lactamase-like domain is present in various proteins from the PBP-like and MBL superfamilies, widely distributed in gram-negative bacteria of the ESKAPEE group. Despite hypothetical proteins with this domain not demonstrating beta-lactamase characteristics, they are closely related to homologous families that exhibit enzymatic promiscuity against beta-lactam antibiotics beyond their traditional functions. The association of these homologous enzymes with canonical beta-lactamases and the selective pressure from the extensive use of beta-lactam antibiotics may favor the eventual optimization of these functions.

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Dual functional roles of a novel bifunctional β-lactamase/esterase from Lactococcus garvieae

Cited by 9 publications

References 46 publications

Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

Potential involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

Crystal structure and biochemical analysis of acetylesterase (LgEstI) from Lactococcus garvieae

Potential Involvement of beta-lactamase homologous proteins in resistance to beta-lactam antibiotics in gram-negative bacteria of the ESKAPEE group

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