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Bordeleau E, Stogios PJ, Evdokimova E, Koteva K, Savchenko A, Wright GD. Mechanistic plasticity in ApmA enables aminoglycoside promiscuity for resistance. Nat Chem Biol 2024; 20:234-242. [PMID: 37973888 DOI: 10.1038/s41589-023-01483-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 10/12/2023] [Indexed: 11/19/2023]
Abstract
The efficacy of aminoglycoside antibiotics is waning due to the acquisition of diverse resistance mechanisms by bacteria. Among the most prevalent are aminoglycoside acetyltransferases (AACs) that inactivate the antibiotics through acetyl coenzyme A-mediated modification. Most AACs are members of the GCN5 superfamily of acyltransferases which lack conserved active site residues that participate in catalysis. ApmA is the first reported AAC belonging to the left-handed β-helix superfamily. These enzymes are characterized by an essential active site histidine that acts as an active site base. Here we show that ApmA confers broad-spectrum aminoglycoside resistance with a molecular mechanism that diverges from other detoxifying left-handed β-helix superfamily enzymes and canonical GCN5 AACs. We find that the active site histidine plays different functions depending on the acetyl-accepting aminoglycoside substrate. This flexibility in the mechanism of a single enzyme underscores the plasticity of antibiotic resistance elements to co-opt protein catalysts in the evolution of drug detoxification.
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Affiliation(s)
- Emily Bordeleau
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Kalinka Koteva
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada
- Center for Structural Genomics of Infectious Diseases (CSGID) University of Calgary, Calgary, Alberta, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Gerard D Wright
- David Braley Centre for Antibiotics Discovery, M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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Alekseeva MG, Rudakova NN, Ratkin AV, Mavletova DA, Danilenko VN. Resistome in Streptomyces rimosus - A Reservoir of Aminoglycoside Antibiotics Resistance Genes. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:723-730. [PMID: 37748869 DOI: 10.1134/s0006297923060019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/20/2023] [Accepted: 04/20/2023] [Indexed: 09/27/2023]
Abstract
Investigation of aminoglycoside acetyltransferases in actinobacteria of the genus Streptomyces is an integral part of the study of soil bacteria as the main reservoir and possible source of drug resistance genes. Previously, we have identified and biochemically characterized three aminoglycoside phosphotransferases, which cause resistance to kanamycin, neomycin, paromomycin, streptomycin, and hygromycin B in the strain Streptomyces rimosus ATCC 10970 (producing oxytetracycline), which is resistant to most natural aminoglycoside antibiotics. In the presented work, it was shown that the resistance of this strain to other AGs is associated with the presence of the enzyme aminoglycoside acetyltransferase, belonging to the AAC(2') subfamily. Induction of the expression of the gene, designated by us as aac(2')-If, in Escherichia coli cells determines resistance to a wide range of natural aminoglycoside antibiotics (neomycin, gentamicin, tobramycin, sisomycin, and paromomycin) and increases minimum inhibitory concentrations of these antibiotics.
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Affiliation(s)
- Maria G Alekseeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Natalya N Rudakova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Anatoly V Ratkin
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Dilara A Mavletova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Valeriy N Danilenko
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, 119991, Russia
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Khairullina ZZ, Makarov GI, Tereshchenkov AG, Buev VS, Lukianov DA, Polshakov VI, Tashlitsky VN, Osterman IA, Sumbatyan NV. Conjugates of Desmycosin with Fragments of Antimicrobial Peptide Oncocin: Synthesis, Antibacterial Activity, Interaction with Ribosome. BIOCHEMISTRY. BIOKHIMIIA 2022; 87:871-889. [PMID: 36180983 DOI: 10.1134/s0006297922090024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/18/2022] [Indexed: 06/16/2023]
Abstract
Design and synthesis of conjugates consisting of the macrolide antibiotic desmycosin and fragments of the antibacterial peptide oncocin were performed in attempt to develop new antimicrobial compounds. New compounds were shown to bind to the E. coli 70S ribosomes, to inhibit bacterial protein synthesis in vitro, as well as to suppress bacterial growth. The conjugates of N-terminal hexa- and tripeptide fragments of oncocin and 3,2',4''-triacetyldesmycosin were found to be active against some strains of macrolide-resistant bacteria. By simulating molecular dynamics of the complexes of these compounds with the wild-type bacterial ribosomes and with ribosomes, containing A2059G 23S RNA mutation, the specific structural features of their interactions were revealed.
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Affiliation(s)
| | | | - Andrey G Tereshchenkov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Vitaly S Buev
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, 119992, Russia
| | - Dmitrii A Lukianov
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Vladimir I Polshakov
- Faculty of Fundamental Medicine, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Vadim N Tashlitsky
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Ilya A Osterman
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, 143025, Russia
| | - Natalia V Sumbatyan
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
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Wang S, Wei L, Gao Y, Rong Y, Zha Z, Lv Y, Feng Z. Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics. J Appl Microbiol 2022; 133:898-907. [PMID: 35543338 DOI: 10.1111/jam.15615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 03/30/2022] [Indexed: 11/30/2022]
Abstract
AIMS The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut. METHODS AND RESULTS A library of human fecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labeled aac(6')-Iao and rmtI respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin. CONCLUSIONS Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition. SIGNIFICANCE AND IMPACT OF STUDY Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.
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Affiliation(s)
- Shaochen Wang
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Lin Wei
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yuejiao Gao
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Yufeng Rong
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhengqi Zha
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Yunbin Lv
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Zhiyang Feng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing, China
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Ma X, Jiang K, Zhou C, Xue Y, Ma Y. Identification and characterization of a novel GNAT superfamily N α -acetyltransferase from Salinicoccus halodurans H3B36. Microb Biotechnol 2022; 15:1652-1665. [PMID: 34985185 PMCID: PMC9049628 DOI: 10.1111/1751-7915.13998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 11/28/2022] Open
Abstract
Nα -acetyl-α-lysine was found as a new type of compatible solutes that acted as an organic cytoprotectant in the strain of Salinicoccus halodurans H3B36. A novel lysine Nα -acetyltransferase gene (shkat), encoding an enzyme that catalysed the acetylation of lysine exclusively at α position, was identified from this moderate halophilic strain and expressed in Escherichia coli. Sequence analysis indicated ShKAT contained a highly conserved pyrophosphate-binding loop (Arg-Gly-Asn-Gly-Asn-Gly), which was a signature of the GNAT superfamily. ShKAT exclusively recognized free amino acids as substrate, including lysine and other basic amino acids. The enzyme showed a wide range of optimal pH value and was tolerant to high-alkali and high-salinity conditions. As a new member of the GNAT superfamily, the ShKAT was the first enzyme recognized free lysine as substrate. We believe this work gives an expanded perspective of the GNAT superfamily, and reveals great potential of the shkat gene to be applied in genetic engineering for resisting extreme conditions.
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Affiliation(s)
- Xiaochen Ma
- Institute of Microbiology, CAS, Beijing, 100101, China
| | - Kai Jiang
- College of Life Science and Technology, Inner Mongolia Normal University, Hohhot, Inner Mongolia, 010022, China
| | - Cheng Zhou
- Institute of Microbiology, CAS, Beijing, 100101, China
| | - Yanfen Xue
- Institute of Microbiology, CAS, Beijing, 100101, China
| | - Yanhe Ma
- Institute of Microbiology, CAS, Beijing, 100101, China
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Zhang C, Sun L, Wang D, Li Y, Zhang L, Wang L, Peng J. Advances in antimicrobial resistance testing. Adv Clin Chem 2022; 111:1-68. [DOI: 10.1016/bs.acc.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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