1
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Sychantha D, Chen X, Koteva K, Prehna G, Wright GD. Targeting bacterial nickel transport with aspergillomarasmine A suppresses virulence-associated Ni-dependent enzymes. Nat Commun 2024; 15:4036. [PMID: 38740750 DOI: 10.1038/s41467-024-48232-1] [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: 06/02/2023] [Accepted: 04/23/2024] [Indexed: 05/16/2024] Open
Abstract
Microbial Ni2+ homeostasis underpins the virulence of several clinical pathogens. Ni2+ is an essential cofactor in urease and [NiFe]-hydrogenases involved in colonization and persistence. Many microbes produce metallophores to sequester metals necessary for their metabolism and starve competing neighboring organisms. The fungal metallophore aspergillomarasmine A (AMA) shows narrow specificity for Zn2+, Ni2+, and Co2+. Here, we show that this specificity allows AMA to block the uptake of Ni2+ and attenuate bacterial Ni-dependent enzymes, offering a potential strategy for reducing virulence. Bacterial exposure to AMA perturbs H2 metabolism, ureolysis, struvite crystallization, and biofilm formation and shows efficacy in a Galleria mellonella animal infection model. The inhibition of Ni-dependent enzymes was aided by Zn2+, which complexes with AMA and competes with the native nickelophore for the uptake of Ni2+. Biochemical analyses demonstrated high-affinity binding of AMA-metal complexes to NikA, the periplasmic substrate-binding protein of the Ni2+ uptake system. Structural examination of NikA in complex with Ni-AMA revealed that the coordination geometry of Ni-AMA mimics the native ligand, Ni-(L-His)2, providing a structural basis for binding AMA-metal complexes. Structure-activity relationship studies of AMA identified regions of the molecule that improve NikA affinity and offer potential routes for further developing this compound as an anti-virulence agent.
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Affiliation(s)
- David Sychantha
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
| | - Xuefei Chen
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Kalinka Koteva
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Gerd Prehna
- Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada
| | - Gerard D Wright
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.
- M.G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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2
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Funck D, Sinn M, Forlani G, Hartig JS. Guanidine production by plant homoarginine-6-hydroxylases. eLife 2024; 12:RP91458. [PMID: 38619227 PMCID: PMC11018352 DOI: 10.7554/elife.91458] [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] [Indexed: 04/16/2024] Open
Abstract
Metabolism and biological functions of the nitrogen-rich compound guanidine have long been neglected. The discovery of four classes of guanidine-sensing riboswitches and two pathways for guanidine degradation in bacteria hint at widespread sources of unconjugated guanidine in nature. So far, only three enzymes from a narrow range of bacteria and fungi have been shown to produce guanidine, with the ethylene-forming enzyme (EFE) as the most prominent example. Here, we show that a related class of Fe2+- and 2-oxoglutarate-dependent dioxygenases (2-ODD-C23) highly conserved among plants and algae catalyze the hydroxylation of homoarginine at the C6-position. Spontaneous decay of 6-hydroxyhomoarginine yields guanidine and 2-aminoadipate-6-semialdehyde. The latter can be reduced to pipecolate by pyrroline-5-carboxylate reductase but more likely is oxidized to aminoadipate by aldehyde dehydrogenase ALDH7B in vivo. Arabidopsis has three 2-ODD-C23 isoforms, among which Din11 is unusual because it also accepted arginine as substrate, which was not the case for the other 2-ODD-C23 isoforms from Arabidopsis or other plants. In contrast to EFE, none of the three Arabidopsis enzymes produced ethylene. Guanidine contents were typically between 10 and 20 nmol*(g fresh weight)-1 in Arabidopsis but increased to 100 or 300 nmol*(g fresh weight)-1 after homoarginine feeding or treatment with Din11-inducing methyljasmonate, respectively. In 2-ODD-C23 triple mutants, the guanidine content was strongly reduced, whereas it increased in overexpression plants. We discuss the implications of the finding of widespread guanidine-producing enzymes in photosynthetic eukaryotes as a so far underestimated branch of the bio-geochemical nitrogen cycle and propose possible functions of natural guanidine production.
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Affiliation(s)
- Dietmar Funck
- Department of Chemistry, University of KonstanzKonstanzGermany
| | - Malte Sinn
- Department of Chemistry, University of KonstanzKonstanzGermany
| | - Giuseppe Forlani
- Department of Life Science and Biotechnology, University of FerraraFerraraItaly
| | - Jörg S Hartig
- Department of Chemistry, University of KonstanzKonstanzGermany
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3
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Dong L, Li S, Huang J, Li WJ, Ali M. Co-occurrence, toxicity, and biotransformation pathways of metformin and its intermediate product guanylurea: Current state and future prospects for enhanced biodegradation strategy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:171108. [PMID: 38395159 DOI: 10.1016/j.scitotenv.2024.171108] [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: 11/18/2023] [Revised: 01/29/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
Abstract
Accumulation of metformin and its biotransformation product "guanylurea" are posing an increasing concern due to their low biodegradability under natural attenuated conditions. Therefore, in this study, we reviewed the unavoidable function of metformin in human body and the route of its release in different water ecosystems. In addition, metformin and its biotransformation product guanylurea in aquatic environments caused certain toxic effects on aquatic organisms which include neurotoxicity, endocrine disruption, production of ROS, and acetylcholinesterase disturbance in aquatic organisms. Moreover, microorganisms are the first to expose and deal with the release of these contaminants, therefore, the mechanisms of biodegradation pathways of metformin and guanylurea under aerobic and anaerobic environments were studied. It has been reported that certain microbes, such as Aminobacter sp. and Pseudomonas putida can carry potential enzymatic pathways to degrade the dead-end product "guanylurea", and hence guanylurea is no longer the dead-end product of metformin. However, these microbes can easily be affected by certain geochemical cycles, therefore, we proposed certain strategies that can be helpful in the enhanced biodegradation of metformin and its biotransformation product guanylurea. A better understanding of the biodegradation potential is imperative to improve the use of these approaches for the sustainable and cost-effective remediation of the emerging contaminants of concern, metformin and guanylurea in the near future.
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Affiliation(s)
- Lei Dong
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Shuai Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China; School of Life Science, Jiaying University, Meizhou, China
| | - Jie Huang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China
| | - Wen-Jun Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China; State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.
| | - Mukhtiar Ali
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Life Sciences, Sun Yat-sen University, Guangzhou, China; Advanced Water Technology Laboratory, National University of Singapore (Suzhou) Research Institute, Suzhou, Jiangsu 215123, China..
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4
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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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5
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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: 3] [Impact Index Per Article: 3.0] [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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6
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Gaikwad SR, Punekar NS, Pathan EK. Characterization of a novel 4-guanidinobutyrase from Candida parapsilosis. FEMS Yeast Res 2024; 24:foae003. [PMID: 38242845 PMCID: PMC10833137 DOI: 10.1093/femsyr/foae003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 12/07/2023] [Accepted: 01/17/2024] [Indexed: 01/21/2024] Open
Abstract
Enzymes of the ureohydrolase superfamily are specific in recognizing their substrates. While looking to broaden the substrate specificity of 4-guanidinobutyrase (GBase), we isolated a yeast, typed as Candida parapsilosis (NCIM 3689), that efficiently utilized both 4-guanidinobutyrate (GB) and 3-guanidinopropionate (GP) as a sole source of nitrogen. A putative GBase sequence was identified from its genome upon pBLAST query using the GBase sequence from Aspergillus niger (AnGBase). The C. parapsilosis GBase (CpGBase) ORF was PCR amplified, cloned, and sequenced. Further, the functional CpGBase protein expressed in Saccharomyces cerevisiae functioned as GBase and 3-guanidinopropionase (GPase). S. cerevisiae cannot grow on GB or GP. However, the transformants expressing CpGBase acquired the ability to utilize and grow on both GB and GP. The expressed CpGBase protein was enriched and analyzed for substrate saturation and product inhibition by γ-aminobutyric acid and β-alanine. In contrast to the well-characterized AnGBase, CpGBase from C. parapsilosis is a novel ureohydrolase and showed hyperbolic saturation for GB and GP with comparable efficiency (Vmax/KM values of 3.4 and 2.0, respectively). With the paucity of structural information and limited active site data available on ureohydrolases, CpGBase offers an excellent paradigm to explore this class of enzymes.
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Affiliation(s)
- Santoshkumar R Gaikwad
- Molecular Enzymology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
| | - Narayan S Punekar
- Molecular Enzymology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad 580011, Karnataka, India
| | - Ejaj K Pathan
- Molecular Enzymology Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, Maharashtra, India
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Lavale, Pune 412115, Maharashtra, India
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7
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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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8
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Focht CM, Hiller DA, Grunseich SG, Strobel SA. Translation regulation by a guanidine-II riboswitch is highly tunable in sensitivity, dynamic range, and apparent cooperativity. RNA (NEW YORK, N.Y.) 2023; 29:1126-1139. [PMID: 37130702 PMCID: PMC10351892 DOI: 10.1261/rna.079560.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/05/2023] [Indexed: 05/04/2023]
Abstract
Riboswitches function as important translational regulators in bacteria. Comprehensive mutational analysis of transcriptional riboswitches has been used to probe the energetic intricacies of interplay between the aptamer and expression platform, but translational riboswitches have been inaccessible to massively parallel techniques. The guanidine-II (gdm-II) riboswitch is an exclusively translational class. We have integrated RelE cleavage with next-generation sequencing to quantify ligand-dependent changes in translation initiation for all single and double mutations of the Pseudomonas aeruginosa gdm-II riboswitch, a total of more than 23,000 variants. This extensive mutational analysis is consistent with the prominent features of the bioinformatic consensus. These data indicate, unexpectedly, that direct sequestration of the Shine-Dalgarno sequence is dispensable for riboswitch function. Additionally, this comprehensive data set reveals important positions not identified in previous computational and crystallographic studies. Mutations in the variable linker region stabilize alternate conformations. The double mutant data reveal the functional importance of the previously modeled P0b helix formed by the 5' and 3' tails that serves as the basis for translational control. Additional mutations to GU wobble base pairs in both P1 and P2 reveal how the apparent cooperativity of the system involves an intricate network of communication between the two binding sites. This comprehensive examination of a translational riboswitch's expression platform illuminates how the riboswitch is precisely tuned and tunable with regard to ligand sensitivity, the amplitude of expression between ON and OFF states, and the cooperativity of ligand binding.
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Affiliation(s)
- Caroline M Focht
- Institute of Biochemical Design and Discovery, Yale University, West Haven, Connecticut 06516, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - David A Hiller
- Institute of Biochemical Design and Discovery, Yale University, West Haven, Connecticut 06516, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
| | - Sabrina G Grunseich
- Institute of Biochemical Design and Discovery, Yale University, West Haven, Connecticut 06516, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
| | - Scott A Strobel
- Institute of Biochemical Design and Discovery, Yale University, West Haven, Connecticut 06516, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06510, USA
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, USA
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9
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Lin S, Li S, Ouyang T, Chen G. Site-2 Protease Slr1821 Regulates Carbon/Nitrogen Homeostasis during Ammonium Stress Acclimation in Cyanobacterium Synechocystis sp. PCC 6803. Int J Mol Sci 2023; 24:ijms24076606. [PMID: 37047577 PMCID: PMC10094980 DOI: 10.3390/ijms24076606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 03/25/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
Excess ammonium imposes toxicity and stress response in cyanobacteria. How cyanobacteria acclimate to NH4+ stress is so far poorly understood. Here, Synechocystis sp. PCC6803 S2P homolog Slr1821 was identified as the essential regulator through physiological characterization and transcriptomic analysis of its knockout mutant. The proper expression of 60% and 67% of the NH4+ activated and repressed genes, respectively, were actually Slr1821-dependent since they were abolished or reversed in ∆slr1821. Synechocystis 6803 suppressed nitrogen uptake and assimilation, ammonium integration and mobilization of other nitrogen sources upon NH4+ stress. Opposite regulation on genes for assimilation of nitrogen and carbon, such as repression of nitrogen regulatory protein PII, PII interactive protein PirC and activation of carbon acquisition regulator RcbR, demonstrated that Synechocystis 6803 coordinated regulation to maintain carbon/nitrogen homeostasis under increasing nitrogen, while functional Slr1821 was indispensable for most of this coordinated regulation. Additionally, slr1821 knockout disrupted the proper response of regulators and transporters in the ammonium-specific stimulon, and resulted in defective photosynthesis as well as compromised translational and transcriptional machinery. These results provide new insight into the coordinated regulation of nutritional fluctuation and the functional characterization of S2Ps. They also provide new targets for bioengineering cyanobacteria in bioremediation and improving ammonium tolerance in crop plants.
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Affiliation(s)
- Shiqi Lin
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
| | - Shiliang Li
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
| | - Tong Ouyang
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
| | - Gu Chen
- School of Food Sciences and Engineering, South China University of Technology, 381 Wushan Road, Guangzhou 510641, China
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10
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Hausinger RP. Five decades of metalloenzymology. Enzymes 2023; 54:71-105. [PMID: 37945178 DOI: 10.1016/bs.enz.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
Metalloenzymes have been detailed in The Enzymes since its inception over half a century ago. Here, I review selected metal-containing enzyme highlights from early chapters in this series and I describe advances made since those contributions. Three topics are emphasized: nickel-containing enzymes, Fe(II)/2-oxoglutarate-dependent oxygenases, and enzymes containing non-canonical iron-sulfur clusters.
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Affiliation(s)
- Robert P Hausinger
- Departments of Microbiology & Molecular Genetics and Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.
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11
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Hauth F, Funck D, Hartig JS. A standalone editing protein deacylates mischarged canavanyl-tRNAArg to prevent canavanine incorporation into proteins. Nucleic Acids Res 2023; 51:2001-2010. [PMID: 36626933 PMCID: PMC10018355 DOI: 10.1093/nar/gkac1197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/16/2022] [Accepted: 12/06/2022] [Indexed: 01/12/2023] Open
Abstract
Error-free translation of the genetic code into proteins is vitally important for all organisms. Therefore, it is crucial that the correct amino acids are loaded onto their corresponding tRNAs. This process is highly challenging when aminoacyl-tRNA-synthetases encounter structural analogues to the native substrate like the arginine antimetabolite canavanine. To circumvent deleterious incorporation due to tRNA mischarging, editing mechanisms have evolved. However, only for half of the tRNA synthetases, editing activity is known and only few specific standalone editing proteins have been described. Understanding the diverse mechanisms resulting in error-free protein synthesis is of great importance. Here, we report the discovery of a protein that is upregulated upon canavanine stimulation in bacteria that live associated with canavanine-producing plants. We demonstrate that it acts as standalone editing protein specifically deacylating canavanylated tRNAArg. We therefore propose canavanyl-tRNAArgdeacylase (CtdA) as systematic name. Knockout strains show severe growth defects in canavanine-containing media and incorporate high amounts of canavanine into the proteome. CtdA is frequently found under control of guanidine riboswitches, revealing a functional connection of canavanine and guanidine metabolisms. Our results are the first to show editing activity towards mischarged tRNAArg and add to the puzzle of how faithful translation is ensured in nature.
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Dietmar Funck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S Hartig
- To whom correspondence should be addressed. Tel: +49 7531 88 4575;
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12
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Li T, Xu ZJ, Zhou NY. Aerobic Degradation of the Antidiabetic Drug Metformin by Aminobacter sp. Strain NyZ550. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:1510-1519. [PMID: 36624085 DOI: 10.1021/acs.est.2c07669] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Metformin is becoming one of the most common emerging contaminants in surface and wastewater. Its biodegradation generally leads to the accumulation of guanylurea in the environment, but the microorganisms and mechanisms involved in this process remain elusive. Here, Aminobacter sp. strain NyZ550 was isolated and characterized for its ability to grow on metformin as a sole source of carbon, nitrogen, and energy under oxic conditions. This isolate also assimilated a variety of nitrogenous compounds, including dimethylamine. Hydrolysis of metformin by strain NyZ550 was accompanied by a stoichiometric accumulation of guanylurea as a dead-end product. Based on ion chromatography, gas chromatography-mass spectrometry, and comparative transcriptomic analyses, dimethylamine was identified as an additional hydrolytic product supporting the growth of the strain. Notably, a microbial mixture consisting of strain NyZ550 and an engineered Pseudomonas putida PaW340 expressing a guanylurea hydrolase was constructed for complete elimination of metformin and its persistent product guanylurea. Overall, our results not only provide new insights into the metformin biodegradation pathway, leading to the commonly observed accumulation of guanylurea in the environment, but also open doors for the complete degradation of the new pollutant metformin.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Zhi-Jing Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
| | - Ning-Yi Zhou
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240 Shanghai, China
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13
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Lenkeit F, Eckert I, Sinn M, Hauth F, Hartig JS, Weinberg Z. A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity. RNA Biol 2023; 20:10-19. [PMID: 36548032 PMCID: PMC9788692 DOI: 10.1080/15476286.2022.2160562] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Riboswitches are regulatory RNAs that specifically bind a small molecule or ion. Like metabolite-binding proteins, riboswitches can evolve new ligand specificities, and some examples of this phenomenon have been validated. As part of work based on comparative genomics to discover novel riboswitches, we encountered a candidate riboswitch with striking similarities to the recently identified guanidine-IV riboswitch. This candidate riboswitch, the Gd4v motif, is predicted in four distinct bacterial phyla, thus almost as widespread as the guanidine-IV riboswitch. Bioinformatic and experimental analysis suggest that the Gd4v motif is a riboswitch that binds a ligand other than guanidine. It is found associated with gene classes that differ from genes regulated by confirmed guanidine riboswitches. In inline-probing assays, we showed that free guanidine binds only weakly to one of the tested sequences of the variant. Further tested compounds did not show binding, attenuation of transcription termination, or activation of a genetic reporter construct. We characterized an N-acetyltransferase frequently associated with the Gd4v motif and compared its substrate preference to an N-acetyltransferase that occurs under control of guanidine-IV riboswitches. The substrates of this Gd4v-motif-associated enzyme did not show activity for Gd4v RNA binding or transcription termination. Hence, the ligand of the candidate riboswitch motif remains unidentified. The variant RNA motif is predominantly found in gut metagenome sequences, hinting at a ligand that is highly relevant in this environment. This finding is a first step to determining the identity of this unknown ligand, and understanding how guanidine-IV-riboswitch-like structures can evolve to bind different ligands.
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Affiliation(s)
- Felina Lenkeit
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Iris Eckert
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany
| | - Malte Sinn
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Franziskus Hauth
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457Konstanz, Germany,CONTACT Jörg S. Hartig
| | - Zasha Weinberg
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany,Zasha Weinberg Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107Leipzig, Germany
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14
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Sinn M, Stanoppi M, Hauth F, Fleming JR, Funck D, Mayans O, Hartig JS. Guanidino acid hydrolysis by the human enzyme annotated as agmatinase. Sci Rep 2022; 12:22088. [PMID: 36543883 PMCID: PMC9772407 DOI: 10.1038/s41598-022-26655-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Guanidino acids such as taurocyamine, guanidinobutyrate, guanidinopropionate, and guanidinoacetate have been detected in humans. However, except for guanidionacetate, which is a precursor of creatine, their metabolism and potential functions remain poorly understood. Agmatine has received considerable attention as a potential neurotransmitter and the human enzyme so far annotated as agmatinase (AGMAT) has been proposed as an important modulator of agmatine levels. However, conclusive evidence for the assigned enzymatic activity is lacking. Here we show that AGMAT hydrolyzed a range of linear guanidino acids but was virtually inactive with agmatine. Structural modelling and direct biochemical assays indicated that two naturally occurring variants differ in their substrate preferences. A negatively charged group in the substrate at the end opposing the guanidine moiety was essential for efficient catalysis, explaining why agmatine was not hydrolyzed. We suggest to rename AGMAT as guanidino acid hydrolase (GDAH). Additionally, we demonstrate that the GDAH substrates taurocyamine, guanidinobutyrate and guanidinopropionate were produced by human glycine amidinotransferase (GATM). The presented findings show for the first time an enzymatic activity for GDAH/AGMAT. Since agmatine has frequently been proposed as an endogenous neurotransmitter, the current findings clarify important aspects of the metabolism of agmatine and guanidino acid derivatives in humans.
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Affiliation(s)
- Malte Sinn
- grid.9811.10000 0001 0658 7699Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Marco Stanoppi
- grid.9811.10000 0001 0658 7699Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Franziskus Hauth
- grid.9811.10000 0001 0658 7699Department of Chemistry, University of Konstanz, Konstanz, Germany ,grid.9811.10000 0001 0658 7699Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
| | - Jennifer R. Fleming
- grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Dietmar Funck
- grid.9811.10000 0001 0658 7699Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Olga Mayans
- grid.9811.10000 0001 0658 7699Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany ,grid.9811.10000 0001 0658 7699Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jörg S. Hartig
- grid.9811.10000 0001 0658 7699Department of Chemistry, University of Konstanz, Konstanz, Germany ,grid.9811.10000 0001 0658 7699Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Konstanz, Germany
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15
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Chaignaud P, Gruffaz C, Borreca A, Fouteau S, Kuhn L, Masbou J, Rouy Z, Hammann P, Imfeld G, Roche D, Vuilleumier S. A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source. Microorganisms 2022; 10:2302. [PMID: 36422372 PMCID: PMC9699525 DOI: 10.3390/microorganisms10112302] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 08/31/2023] Open
Abstract
Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source. Strain MD1 degrades metformin into dimethylamine used for growth, and guanylurea as a side-product. Sequence analysis of its fully assembled genome showed its affiliation to Aminobacter niigataensis. Differential proteomics and transcriptomics, as well as mini-transposon mutagenesis of the strain, point to genes and proteins essential for growth with metformin and potentially associated with hydrolytic C-N cleavage of metformin or with cellular transport of metformin and guanylurea. The obtained results suggest the recent evolution of the growth-supporting capacity of strain MD1 to degrade metformin. Our results identify candidate proteins of the enzymatic system for metformin transformation in strain MD1 and will inform future research on the fate of metformin and its degradation products in the environment and in humans.
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Affiliation(s)
- Pauline Chaignaud
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Christelle Gruffaz
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
| | - Adrien Borreca
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
- Institut Terre et Environnement de Strasbourg, UMR 7063 CNRS, ENGEES, Université de Strasbourg, 67000 Strasbourg, France
| | - Stéphanie Fouteau
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université d’Evry, Université Paris-Saclay, CEDEX, 91057 Evry, France
| | - Lauriane Kuhn
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FR 1589 CNRS, CEDEX, 67084 Strasbourg, France
| | - Jérémy Masbou
- Institut Terre et Environnement de Strasbourg, UMR 7063 CNRS, ENGEES, Université de Strasbourg, 67000 Strasbourg, France
| | - Zoé Rouy
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université d’Evry, Université Paris-Saclay, CEDEX, 91057 Evry, France
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg-Esplanade, Institut de Biologie Moléculaire et Cellulaire, FR 1589 CNRS, CEDEX, 67084 Strasbourg, France
| | - Gwenaël Imfeld
- Institut Terre et Environnement de Strasbourg, UMR 7063 CNRS, ENGEES, Université de Strasbourg, 67000 Strasbourg, France
| | - David Roche
- Génomique Métabolique, Genoscope, Institut de Biologie François Jacob, Commissariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université d’Evry, Université Paris-Saclay, CEDEX, 91057 Evry, France
| | - Stéphane Vuilleumier
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156 CNRS, Université de Strasbourg, 67000 Strasbourg, France
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16
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Burata OE, Yeh TJ, Macdonald CB, Stockbridge RB. Still rocking in the structural era: A molecular overview of the small multidrug resistance (SMR) transporter family. J Biol Chem 2022; 298:102482. [PMID: 36100040 PMCID: PMC9574504 DOI: 10.1016/j.jbc.2022.102482] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/24/2022] [Accepted: 09/07/2022] [Indexed: 11/20/2022] Open
Abstract
The small multidrug resistance (SMR) family is composed of widespread microbial membrane proteins that fulfill different transport functions. Four functional SMR subtypes have been identified, which variously transport the small, charged metabolite guanidinium, bulky hydrophobic drugs and antiseptics, polyamines, and glycolipids across the membrane bilayer. The transporters possess a minimalist architecture, with ∼100-residue subunits that require assembly into homodimers or heterodimers for transport. In part because of their simple construction, the SMRs are a tractable system for biochemical and biophysical analysis. Studies of SMR transporters over the last 25 years have yielded deep insights for diverse fields, including membrane protein topology and evolution, mechanisms of membrane transport, and bacterial multidrug resistance. Here, we review recent advances in understanding the structures and functions of SMR transporters. New molecular structures of SMRs representing two of the four functional subtypes reveal the conserved structural features that have permitted the emergence of disparate substrate transport functions in the SMR family and illuminate structural similarities with a distantly related membrane transporter family, SLC35/DMT.
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Affiliation(s)
- Olive E Burata
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Trevor Justin Yeh
- Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Randy B Stockbridge
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan, USA; Program in Biophysics, University of Michigan, Ann Arbor, Michigan, USA; Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA.
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17
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Hauth F, Buck H, Stanoppi M, Hartig JS. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chem Biol 2022; 3:1240-1250. [PMID: 36320885 PMCID: PMC9533460 DOI: 10.1039/d2cb00128d] [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: 05/24/2022] [Accepted: 08/18/2022] [Indexed: 12/02/2022] Open
Abstract
Canavanine, the δ-oxa-analogue of arginine, is produced as one of the main nitrogen storage compounds in legume seeds and has repellent properties. Its toxicity originates from incorporation into proteins as well as arginase-mediated hydrolysis to canaline that forms stable oximes with carbonyls. So far no pathway or enzyme has been identified acting specifically on canavanine. Here we report the characterization of a novel PLP-dependent enzyme, canavanine-γ-lyase, that catalyzes the elimination of hydroxyguanidine from canavanine to subsequently yield homoserine. Homoserine-dehydrogenase, aspartate–semialdehyde–dehydrogenase and ammonium–aspartate–lyase activities are also induced for facilitating canavanine utilization. We demonstrate that this novel pathway is found in certain Pseudomonas species and the Rhizobiales symbionts of legumes. The findings broaden the diverse reactions that the versatile class of PLP-dependent enzymes is able to catalyze. Since canavanine utilization is found prominently in root-associated bacteria, it could have important implications for the establishment and maintenance of the legume rhizosphere. A novel degradation pathway enables rhizosphere-associated bacteria to utilize canavanine.![]()
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Affiliation(s)
- Franziskus Hauth
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Hiltrun Buck
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Marco Stanoppi
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
| | - Jörg S. Hartig
- Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
- Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany
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