1
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Viola RE, Parungao GG, Blumenthal RM. A growth-based assay using fluorescent protein emission to screen for S-adenosylmethionine synthetase inhibitors. Drug Dev Res 2024; 85:e22122. [PMID: 37819020 DOI: 10.1002/ddr.22122] [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: 06/14/2023] [Revised: 09/07/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
The use of cell growth-based assays to identify inhibitory compounds is straightforward and inexpensive, but is also inherently insensitive and somewhat nonspecific. To overcome these limitations and develop a sensitive, specific cell-based assay, two different approaches were combined. To address the sensitivity limitation, different fluorescent proteins have been introduced into a bacterial expression system to serve as growth reporters. To overcome the lack of specificity, these protein reporters have been incorporated into a plasmid in which they are paired with different orthologs of an essential target enzyme, in this case l-methionine S-adenosyltransferase (MAT, AdoMet synthetase). Screening compounds that serve as specific inhibitors will reduce the growth of only a subset of strains, because these strains are identical, except for which target ortholog they carry. Screening several such strains in parallel not only reveals potential inhibitors but the strains also serve as specificity controls for one another. The present study makes use of an existing Escherichia coli strain that carries a deletion of metK, the gene for MAT. Transformation with these plasmids leads to a complemented strain that no longer requires externally supplied S-adenosylmethionine for growth, but its growth is now dependent on the activity of the introduced MAT ortholog. The resulting fluorescent strains provide a platform to screen chemical compound libraries and identify species-selective inhibitors of AdoMet synthetases. A pilot study of several chemical libraries using this platform identified new lead compounds that are ortholog-selective inhibitors of this enzyme family, some of which target the protozoal human pathogen Cryptosporidium parvum.
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Affiliation(s)
- Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| | - Gwenn G Parungao
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, Ohio, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, University of Toledo Health Sciences Campus, Toledo, Ohio, USA
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2
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Singh R, Thakur L, Kumar A, Singh S, Kumar S, Kumar M, Kumar Y, Kumar N. Comparison of freeze-thaw and sonication cycle-based methods for extracting AMR-associated metabolites from Staphylococcus aureus. Front Microbiol 2023; 14:1152162. [PMID: 37180233 PMCID: PMC10174324 DOI: 10.3389/fmicb.2023.1152162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/10/2023] [Indexed: 05/16/2023] Open
Abstract
Emerging antimicrobial resistance (AMR) among Gram-positive pathogens, specifically in Staphylococcus aureus (S. aureus), is becoming a leading public health concern demanding effective therapeutics. Metabolite modulation can improve the efficacy of existing antibiotics and facilitate the development of effective therapeutics. However, it remained unexplored for drug-resistant S. aureus (gentamicin and methicillin-resistant), primarily due to the dearth of optimal metabolite extraction protocols including a protocol for AMR-associated metabolites. Therefore, in this investigation, we have compared the performance of the two most widely used methods, i.e., freeze-thaw cycle (FTC) and sonication cycle (SC), alone and in combination (FTC + SC), and identified the optimal method for this purpose. A total of 116, 119, and 99 metabolites were identified using the FTC, SC, and FTC + SC methods, respectively, leading to the identification of 163 metabolites cumulatively. Out of 163, 69 metabolites were found to be associated with AMR in published literature consisting of the highest number of metabolites identified by FTC (57) followed by SC (54) and FTC + SC (40). Thus, the performances of FTC and SC methods were comparable with no additional benefits of combining both. Moreover, each method showed biasness toward specific metabolite(s) or class of metabolites, suggesting that the choice of metabolite extraction method shall be decided based on the metabolites of interest in the investigation.
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Affiliation(s)
- Rita Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
- Jawaharlal Nehru University, Delhi, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
- Jawaharlal Nehru University, Delhi, India
| | - Ashok Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Sevaram Singh
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
- Jawaharlal Nehru University, Delhi, India
| | - Shailesh Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Manoj Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
| | - Yashwant Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
- *Correspondence: Yashwant Kumar,
| | - Niraj Kumar
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, India
- Niraj Kumar,
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3
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Gade M, Tan LL, Damry AM, Sandhu M, Brock JS, Delaney A, Villar-Briones A, Jackson CJ, Laurino P. Substrate Dynamics Contribute to Enzymatic Specificity in Human and Bacterial Methionine Adenosyltransferases. JACS AU 2021; 1:2349-2360. [PMID: 34977903 PMCID: PMC8715544 DOI: 10.1021/jacsau.1c00464] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Indexed: 05/14/2023]
Abstract
Protein conformational changes can facilitate the binding of noncognate substrates and underlying promiscuous activities. However, the contribution of substrate conformational dynamics to this process is comparatively poorly understood. Here, we analyze human (hMAT2A) and Escherichia coli (eMAT) methionine adenosyltransferases that have identical active sites but different substrate specificity. In the promiscuous hMAT2A, noncognate substrates bind in a stable conformation to allow catalysis. In contrast, noncognate substrates sample stable productive binding modes less frequently in eMAT owing to altered mobility in the enzyme active site. Different cellular concentrations of substrates likely drove the evolutionary divergence of substrate specificity in these orthologues. The observation of catalytic promiscuity in hMAT2A led to the detection of a new human metabolite, methyl thioguanosine, that is produced at elevated levels in a cancer cell line. This work establishes that identical active sites can result in different substrate specificity owing to the effects of substrate and enzyme dynamics.
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Affiliation(s)
- Madhuri Gade
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Li Lynn Tan
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Adam M. Damry
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Mahakaran Sandhu
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Joseph S. Brock
- Research
School of Biology, Australian National University, Canberra 2601, Australia
| | - Andie Delaney
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
| | - Alejandro Villar-Briones
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
| | - Colin J. Jackson
- Research
School of Chemistry, Australian National
University, Canberra, 2601, Australia
- Australian
Research Council Centre of Excellence for Innovations in Peptide and
Protein Science, Research School of Chemistry, Australian National University, Canberra 2601, ACT, Australia
- Australian
Research Council Centre of Excellence in Synthetic Biology, Research
School of Chemistry, Australian National
University, Canberra 2601, ACT, Australia
| | - Paola Laurino
- Protein
Engineering and Evolution Unit, Okinawa
Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna 904-0495, Okinawa, Japan
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4
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Miousse IR, Ewing LE, Skinner CM, Pathak R, Garg S, Kutanzi KR, Melnyk S, Hauer-Jensen M, Koturbash I. Methionine dietary supplementation potentiates ionizing radiation-induced gastrointestinal syndrome. Am J Physiol Gastrointest Liver Physiol 2020; 318:G439-G450. [PMID: 31961718 PMCID: PMC7099489 DOI: 10.1152/ajpgi.00351.2019] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Methionine is an essential amino acid needed for a variety of processes in living organisms. Ionizing radiation depletes tissue methionine concentrations and leads to the loss of DNA methylation and decreased synthesis of glutathione. In this study, we aimed to investigate the effects of methionine dietary supplementation in CBA/CaJ mice after exposure to doses ranging from 3 to 8.5 Gy of 137Cs of total body irradiation. We report that mice fed a methionine-supplemented diet (MSD; 19.5 vs. 6.5 mg/kg in a methionine-adequate diet, MAD) developed acute radiation toxicity at doses as low as 3 Gy. Partial body irradiation performed with hindlimb shielding resulted in a 50% mortality rate in MSD-fed mice exposed to 8.5 Gy, suggesting prevalence of radiation-induced gastrointestinal syndrome in the development of acute radiation toxicity. Analysis of the intestinal microbiome demonstrated shifts in the gut ecology, observed along with the development of leaky gut syndrome and bacterial translocation into the liver. Normal gut physiology impairment was facilitated by alterations in the one-carbon metabolism pathway and was exhibited as decreases in circulating citrulline levels mirrored by decreased intestinal mucosal surface area and the number of surviving crypts. In conclusion, we demonstrate that a relevant excess of methionine dietary intake exacerbates the detrimental effects of exposure to ionizing radiation in the small intestine.NEW & NOTEWORTHY Methionine supplementation, instead of an anticipated health-promoting effect, sensitizes mice to gastrointestinal radiation syndrome. Mechanistically, excess of methionine negatively affects intestinal ecology, leading to a cascade of physiological, biochemical, and molecular alterations that impair normal gut response to a clinically relevant genotoxic stressor. These findings speak toward increasing the role of registered dietitians during cancer therapy and the necessity of a solid scientific background behind the sales of dietary supplements and claims regarding their benefits.
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Affiliation(s)
- Isabelle R. Miousse
- 1Department of Environmental and Occupation Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas,2Department of Biochemistry, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Laura E. Ewing
- 1Department of Environmental and Occupation Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas,3Department of Pharmacology and Toxicology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Charles M. Skinner
- 1Department of Environmental and Occupation Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas,4Center for Dietary Supplements Research, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Rupak Pathak
- 5Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Sarita Garg
- 5Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Kristy R. Kutanzi
- 1Department of Environmental and Occupation Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Stepan Melnyk
- 6Arkansas Children’s Research Institute, Little Rock, Arknsas
| | - Martin Hauer-Jensen
- 5Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Igor Koturbash
- 1Department of Environmental and Occupation Health, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas,4Center for Dietary Supplements Research, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, Arkansas
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5
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Cornelissen NV, Michailidou F, Muttach F, Rau K, Rentmeister A. Nucleoside-modified AdoMet analogues for differential methyltransferase targeting. Chem Commun (Camb) 2020; 56:2115-2118. [PMID: 31970375 PMCID: PMC7030947 DOI: 10.1039/c9cc07807j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methyltransferases (MTases) modify a wide range of biomolecules using S-adenosyl-l-methionine (AdoMet) as the cosubstrate. Synthetic AdoMet analogues are powerful tools to site-specifically introduce a variety of functional groups and exhibit potential to be converted only by distinct MTases. Extending the size of the substituent at the sulfur/selenium atom provides selectivity among MTases but is insufficient to discriminate between promiscuous MTases. We present a panel of AdoMet analogues differing in the nucleoside moiety (NM-AdoMets). These NM-AdoMets were efficiently produced by a previously uncharacterized methionine adenosyltransferase (MAT) from methionine and ATP analogues, such as ITP and N6-propargyl-ATP. The N6-modification changed the relative activity of three representative MTases up to 13-fold resulting in discrimination of substrates for the methyl transfer and could also be combined with transfer of allyl and propargyl groups.
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Affiliation(s)
- Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Fabian Muttach
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Kristina Rau
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
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6
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Zhang Y, Pan Y, Liu W, Zhou YJ, Wang K, Wang L, Sohail M, Ye M, Zou H, Zhao ZK. In vivo protein allylation to capture protein methylation candidates. Chem Commun (Camb) 2017; 52:6689-92. [PMID: 27115613 DOI: 10.1039/c6cc02386j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An approach combining in vivo protein allylation, chemical tagging and affinity enrichment was devised to capture protein methylation candidates in yeast S. cerevisiae. The study identified 167 hits, covering many proteins with known methylation events on different types of amino acid residues.
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Affiliation(s)
- Yixin Zhang
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Yanbo Pan
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Wujun Liu
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Keyun Wang
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Lei Wang
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Muhammad Sohail
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Mingliang Ye
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Hanfa Zou
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China.
| | - Zongbao K Zhao
- Division of Biotechnology, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China. and State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, CAS, 116023 Dalian, China
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7
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Parungao GG, Zhao M, Wang Q, Zano SP, Viola RE, Blumenthal RM. Complementation of a metK-deficient E. coli strain with heterologous AdoMet synthetase genes. MICROBIOLOGY-SGM 2017; 163:1812-1821. [PMID: 29111970 DOI: 10.1099/mic.0.000565] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
S-adenosyl-l-methionine (AdoMet) is an essential metabolite, playing a wide variety of metabolic roles. The enzyme that produces AdoMet from l-methionine and ATP (methionine adenosyltransferase, MAT) is thus an attractive target for anti-cancer and antimicrobial agents. It would be very useful to have a system that allows rapid identification of species-specific inhibitors of this essential enzyme. A previously generated E. coli strain, lacking MAT (∆metK) but containing a heterologous AdoMet transporter, was successfully complemented with heterologous metK genes from several bacterial pathogens, as well as with MAT genes from a fungal pathogen and Homo sapiens. The nine tested genes, which vary in both sequence and kinetic properties, all complemented strain MOB1490 well in rich medium. When these strains were grown in glucose minimal medium, growth delays or defects were observed with some specific metK genes, defects that were dramatically reduced if l-methionine was added to the medium.
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Affiliation(s)
- Gwenn G Parungao
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Mojun Zhao
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA.,Present address: Department of Pathology, Valley Pathologists Inc., Miami Valley Hospital, Dayton, OH 45409, USA
| | - Qinzhe Wang
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Stephen P Zano
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Ronald E Viola
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology and Program in Bioinformatics, University of Toledo Health Sciences Campus, Toledo, OH 43614, USA
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