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Chi B, Li F, Wang X, Pan H, Yi X, Liu Y, Zhan J, Zhang X, Zhou H, Wang W. DMF mineralization and substrate specificity mechanism of Aminobacter ciceronei DMFA1. ENVIRONMENTAL RESEARCH 2024; 245:117980. [PMID: 38142731 DOI: 10.1016/j.envres.2023.117980] [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: 11/05/2023] [Revised: 12/04/2023] [Accepted: 12/16/2023] [Indexed: 12/26/2023]
Abstract
N,N-dimethylformamide (DMF) is widely used in various industries, but its direct release into water poses high risks to human beings. Although a lot of DMF-degrading bacteria has been isolated, limited studies focus on the degradation preference among DMF and its analogues. In this study, an efficient DMF mineralization bacterium designated Aminobacter ciceronei DMFA1 was isolated from marine sediment. When exposed to a 0.2% DMF (∼1900 mg/L), strain DMFA1 exhibited a degradation efficiency of 100% within 4 days. The observed growth using formamide as the sole carbon source implied the possible DMF degradation pathway of strain DMFA1. Meanwhile,the strain DMFA1 possesses a broad-spectrum substrate degradation, which could effectively degraded 0.2% N,N-dimethylacetamide (DMAC) and N-methylformamide (NMF). Genomic analysis further confirmed the supposed pathway through annotating the genes encoding N, N-dimethylformamidase (DMFase), formamidase, and formate dehydrogenase. The existence of sole DMFase indicating its substrate specificity controlled the preference of DMAc of strain DMFA1. By integrating multiple sequence alignment, homology modeling and molecular docking, the preference of the DMFase in strain DMFA1 towards DMAc are related to: 1) Mutations in key active site residues; 2) the absence of small subunit; and 3) no energy barrier for substrates entering the active site.
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Affiliation(s)
- Baihui Chi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Fei Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xukang Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Haixia Pan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xianliang Yi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Yang Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Jingjing Zhan
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Xuwang Zhang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China
| | - Hao Zhou
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Ocean Science and Technology, Panjin Campus, Dalian University of Technology, China.
| | - Wenyuan Wang
- State Key Laboratory of Coastal and Offshore Engineering, Dalian University of Technology, Dalian, 116024, China.
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Tassoulas LJ, Rankin JA, Elias MH, Wackett LP. Dinickel enzyme evolved to metabolize the pharmaceutical metformin and its implications for wastewater and human microbiomes. Proc Natl Acad Sci U S A 2024; 121:e2312652121. [PMID: 38408229 DOI: 10.1073/pnas.2312652121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/12/2024] [Indexed: 02/28/2024] Open
Abstract
Metformin is the first-line treatment for type II diabetes patients and a pervasive pollutant with more than 180 million kg ingested globally and entering wastewater. The drug's direct mode of action is currently unknown but is linked to effects on gut microbiomes and may involve specific gut microbial reactions to the drug. In wastewater treatment plants, metformin is known to be transformed by microbes to guanylurea, although genes encoding this metabolism had not been elucidated. In the present study, we revealed the function of two genes responsible for metformin decomposition (mfmA and mfmB) found in isolated bacteria from activated sludge. MfmA and MfmB form an active heterocomplex (MfmAB) and are members of the ureohydrolase protein superfamily with binuclear metal-dependent activity. MfmAB is nickel-dependent and catalyzes the hydrolysis of metformin to dimethylamine and guanylurea with a catalytic efficiency (kcat/KM) of 9.6 × 103 M-1s-1 and KM for metformin of 0.82 mM. MfmAB shows preferential activity for metformin, being able to discriminate other close substrates by several orders of magnitude. Crystal structures of MfmAB show coordination of binuclear nickel bound in the active site of the MfmA subunit but not MfmB subunits, indicating that MfmA is the active site for the MfmAB complex. Mutagenesis of residues conserved in the MfmA active site revealed those critical to metformin hydrolase activity and its small substrate binding pocket allowed for modeling of bound metformin. This study characterizes the products of the mfmAB genes identified in wastewater treatment plants on three continents, suggesting that metformin hydrolase is widespread globally in wastewater.
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Affiliation(s)
- Lambros J Tassoulas
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, Minneapolis, MN 55455
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108
| | - Joel A Rankin
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, Minneapolis, MN 55455
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108
| | - Mikael H Elias
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, Minneapolis, MN 55455
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108
| | - Lawrence P Wackett
- Department of Biochemistry, Biophysics, and Molecular Biology, University of Minnesota, Minneapolis, MN 55455
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108
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Schuldiner S. On the link between antibiotic resistance, diabetes, and wastewater. J Gen Physiol 2024; 156:e202313533. [PMID: 38294433 PMCID: PMC10829510 DOI: 10.1085/jgp.202313533] [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] [Indexed: 02/01/2024] Open
Abstract
The study by Lucero et al. (https://doi.org/10.1085/jgp.202313464) sheds light on the remarkable capabilities of bacterial transporters to adapt to new selective pressures. Their findings provide insight into the mechanism of a subtype of SMR transporters.
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Affiliation(s)
- Shimon Schuldiner
- Department of Biological Chemistry, Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel
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Short B. SMR transporters meet the challenge of metformin metabolites. J Gen Physiol 2024; 156:e202413549. [PMID: 38324209 PMCID: PMC10849910 DOI: 10.1085/jgp.202413549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024] Open
Abstract
JGP study (Lucero et al. http://www.doi.org/10.1085/jgp.202313464) shows that members of the SMRGdx subtype can export the degradation products of metformin, helping bacteria adapt to high environmental levels of the commonly prescribed diabetes medication.
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Affiliation(s)
- Ben Short
- Science Writer, Rockefeller University Press, New York, NY, USA
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Lucero RM, Demirer K, Yeh TJ, Stockbridge RB. Transport of metformin metabolites by guanidinium exporters of the small multidrug resistance family. J Gen Physiol 2024; 156:e202313464. [PMID: 38294434 PMCID: PMC10829512 DOI: 10.1085/jgp.202313464] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/01/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
Proteins from the small multidrug resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in the metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid-supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologs. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologs, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homolog, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homolog Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.
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Affiliation(s)
- Rachael M. Lucero
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Kemal Demirer
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Randy B. Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Program in Biophysics, University of Michigan, Ann Arbor, MI, USA
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Tassoulas LJ, Wackett LP. Insights into the action of the pharmaceutical metformin: Targeted inhibition of the gut microbial enzyme agmatinase. iScience 2024; 27:108900. [PMID: 38318350 PMCID: PMC10839685 DOI: 10.1016/j.isci.2024.108900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/06/2023] [Accepted: 01/09/2024] [Indexed: 02/07/2024] Open
Abstract
Metformin is the first-line treatment for type 2 diabetes, yet its mechanism of action is not fully understood. Recent studies suggest metformin's interactions with gut microbiota are responsible for exerting therapeutic effects. In this study, we report that metformin targets the gut microbial enzyme agmatinase, as a competitive inhibitor, which may impair gut agmatine catabolism. The metformin inhibition constant (Ki) of E. coli agmatinase is 1 mM and relevant in the gut where the drug concentration is 1-10 mM. Metformin analogs phenformin, buformin, and galegine are even more potent inhibitors of E. coli agmatinase (Ki = 0.6, 0.1, and 0.007 mM, respectively) suggesting a shared mechanism. Agmatine is a known effector of human host metabolism and has been reported to augment metformin's therapeutic effects for type 2 diabetes. This gut-derived inhibition mechanism gives new insights on metformin's action in the gut and may lead to significant discoveries in improving metformin therapy.
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Affiliation(s)
- Lambros J. Tassoulas
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
| | - Lawrence P. Wackett
- Department of Biochemistry, Biophysics & Molecular Biology, University of Minnesota, Minneapolis, MN 55455, USA
- BioTechnology Institute, University of Minnesota, St. Paul, MN 55108, USA
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Lucero RM, Demirer K, Yeh TJ, Stockbridge RB. Transport of metformin metabolites by guanidinium exporters of the Small Multidrug Resistance family. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.10.552832. [PMID: 37645731 PMCID: PMC10461911 DOI: 10.1101/2023.08.10.552832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Proteins from the Small Multidrug Resistance (SMR) family are frequently associated with horizontally transferred multidrug resistance gene arrays found in bacteria from wastewater and the human-adjacent biosphere. Recent studies suggest that a subset of SMR transporters might participate in metabolism of the common pharmaceutical metformin by bacterial consortia. Here, we show that both genomic and plasmid-associated transporters of the SMRGdx functional subtype export byproducts of microbial metformin metabolism, with particularly high export efficiency for guanylurea. We use solid supported membrane electrophysiology to evaluate the transport kinetics for guanylurea and native substrate guanidinium by four representative SMRGdx homologues. Using an internal reference to normalize independent electrophysiology experiments, we show that transport rates are comparable for genomic and plasmid-associated SMRGdx homologues, and using a proteoliposome-based transport assay, we show that 2 proton:1 substrate transport stoichiometry is maintained. Additional characterization of guanidinium and guanylurea export properties focuses on the structurally characterized homologue, Gdx-Clo, for which we examined the pH dependence and thermodynamics of substrate binding and solved an x-ray crystal structure with guanylurea bound. Together, these experiments contribute in two main ways. By providing the first detailed kinetic examination of the structurally characterized SMRGdx homologue Gdx-Clo, they provide a functional framework that will inform future mechanistic studies of this model transport protein. Second, this study casts light on a potential role for SMRGdx transporters in microbial handling of metformin and its microbial metabolic byproducts, providing insight into how native transport physiologies are co-opted to contend with new selective pressures.
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Affiliation(s)
| | - Kemal Demirer
- Department of Molecular, Cellular, and Developmental Biology
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Randy B Stockbridge
- Program in Chemical Biology
- Department of Molecular, Cellular, and Developmental Biology
- Program in Biophysics, University of Michigan, Ann Arbor, MI 48109, USA
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