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Crofts TS, Wang B, Spivak A, Gianoulis TA, Forsberg KJ, Gibson MK, Johnsky LA, Broomall SM, Rosenzweig CN, Skowronski EW, Gibbons HS, Sommer MOA, Dantas G. Shared strategies for β-lactam catabolism in the soil microbiome. Nat Chem Biol 2018; 14:556-564. [PMID: 29713061 PMCID: PMC5964007 DOI: 10.1038/s41589-018-0052-1] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 03/08/2018] [Indexed: 11/10/2022]
Abstract
The soil microbiome can produce, resist, or degrade antibiotics and even catabolize them. While resistance genes are widely distributed in the soil, there is a dearth of knowledge concerning antibiotic catabolism. Here we describe a pathway for penicillin catabolism in four isolates. Genomic and transcriptomic sequencing revealed β-lactamase, amidase, and phenylacetic acid catabolon upregulation. Knocking out part of the phenylacetic acid catabolon or an apparent penicillin utilization operon (put) resulted in loss of penicillin catabolism in one isolate. A hydrolase from the put operon was found to degrade in vitro benzylpenicilloic acid, the β-lactamase penicillin product. To test the generality of this strategy, an Escherichia coli strain was engineered to co-express a β-lactamase and a penicillin amidase or the put operon, enabling it to grow using penicillin or benzylpenicilloic acid, respectively. Elucidation of additional pathways may allow bioremediation of antibiotic-contaminated soils and discovery of antibiotic-remodeling enzymes with industrial utility.
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Affiliation(s)
- Terence S Crofts
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
| | - Bin Wang
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
| | - Aaron Spivak
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
| | - Tara A Gianoulis
- Wyss Institute for Biologically Inspired Engineering, Harvard, Cambridge, MA, USA
| | - Kevin J Forsberg
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Molly K Gibson
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA
| | - Lauren A Johnsky
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, USA
| | - Stacey M Broomall
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, USA
| | - C Nicole Rosenzweig
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, USA
| | - Evan W Skowronski
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, USA
- TMG Biosciences, LLC, Austin, TX, USA
| | - Henry S Gibbons
- US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Aberdeen, MD, USA
| | - Morten O A Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Gautam Dantas
- Department of Pathology and Immunology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA.
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA.
- Department of Molecular Microbiology, Washington University in St Louis School of Medicine, Saint Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, Saint Louis, MO, USA.
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2
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Guncheva M, Ivanov I, Galunsky B, Stambolieva N, Kaneti J. Kinetic studies and molecular modelling attribute a crucial role in the specificity and stereoselectivity of penicillin acylase to the pair ArgA145-ArgB263. ACTA ACUST UNITED AC 2004; 271:2272-9. [PMID: 15153118 DOI: 10.1111/j.1432-1033.2004.04170.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kinetic experiments with a substrate series of phenylacetyl-arylamides reveal that at least one polar group in the amine moiety is required for the proper orientation of the substrate in the large nucleophile-binding subsite of penicillin acylase of Escherichia coli. Quantum mechanical molecular modelling of enzyme-substrate interactions in the enzyme active site shows that in the case of substrates lacking local symmetry, the productive binding implies two nonsymmetrical arrangements with respect to the two positively charged guanidinium residues of ArgA145 and ArgB263. This indicates a crucial role of the specified arginine pair in the substrate- and stereoselectivity of penicillin acylase.
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Affiliation(s)
- Maya Guncheva
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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Ninkovic M, Riester D, Wirsching F, Dietrich R, Schwienhorst A. Fluorogenic Assay for Penicillin G Acylase Activity. Anal Biochem 2001; 292:228-33. [PMID: 11355855 DOI: 10.1006/abio.2001.5078] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A simple, highly sensitive, and rapid assay for high-throughput screening of penicillin G acylase-producing bacteria is presented. The method is based on the specific release of fluorescent 7-amino-4-methyl-coumarin through cleavage of phenylacetyl-4-methyl-coumaryl-7-amide by penicillin G acylase. The present method is suitable for screening pure enzymes as well as various penicillin G acylases like those from Escherichia coli, Proteus rettgeri, and Kluyvera citrophila in cell extracts. In addition, the new substrate was used for rapid assay of amidase activity in nondenaturing polyacrylamide gels.
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Affiliation(s)
- M Ninkovic
- Abteilung fuer Molekulare Genetik und Praeparative Molekularbiologie, Institut fuer Mikrobiologie und Genetik, Grisebachstrasse 8, Goettingen, 37077, Germany
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4
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Alkema WB, Floris R, Janssen DB. The use of chromogenic reference substrates for the kinetic analysis of penicillin acylases. Anal Biochem 1999; 275:47-53. [PMID: 10542108 DOI: 10.1006/abio.1999.4300] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Determination of kinetic parameters of penicillin acylases for phenylacetylated compounds is complicated due to the low K(m) values for these substrates, the lack of a spectroscopic signal, and the strong product inhibition by phenylacetic acid. To overcome these difficulties, a spectrophotometric method was developed, with which kinetic parameters could be determined by measuring the effects on the hydrolysis of the chromogenic reference substrate 2-nitro-5-[(phenylacetyl)amino]benzoic acid (NIPAB). To that end, spectrophotometric progress curves with NIPAB in the absence and presence of the phenylacetylated substrates and their products were measured and analyzed by numerical fitting to the appropriate equations for competing substrates with product inhibition. This analysis yielded kinetic constants for phenylacetylated substrates such as penicillin G, which are in close agreement with those obtained in independent initial velocity experiments. Using NIPAB analogs with lower k(cat)/K(m) values, kinetic parameters for the hydrolysis of cephalexin and penicillin V were determined. This method was suitable for determining the kinetic constants of penicillin acylases in periplasmic extracts from Escherichia coli, Alcaligenes faecalis, and Kluyvera citrophila. The use of chromogenic reference substrates thus appears to be a rapid and reliable method for determining kinetic constants with various substrates and enzymes.
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Affiliation(s)
- W B Alkema
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, Groningen, 9747 AG, The Netherlands
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Bouvrette P, Ziomek E. Use of delta-(alpha-aminoadipoyl) chromogenic amides in screening for aminoadipoyl amidohydrolases. Anal Biochem 1992; 200:315-20. [PMID: 1632495 DOI: 10.1016/0003-2697(92)90472-j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The synthesis of delta-(alpha-aminoadipoyl) aromatic amides and their use in screening for enzymes able to cleave delta-(alpha-aminoadipoyl) residues off the synthetic amides and cephalosporin C are described. A number of commercially available proteases and peptidases were not active with delta-(alpha-aminoadipoyl) chromogenic amides. Also, most tested microbial strains known to produce acylases did not hydrolyze these compounds. Only one microbial strain, Xanthomonas maltophila, had an appreciable activity toward the racemic form of chromogenic substrates. Activity measured in crude extracts from Xanthomonas cells indicated that this bacterium produces predominantly L-specific aminoadipoyl amidohydrolase and gamma-glutamyl hydrolase. A low level of cephalosporin C and glutaryl-cephalosporin acylase activities was also found.
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Affiliation(s)
- P Bouvrette
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
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6
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Zhang QJ, Xu WX, Shi L. 2-Nitro-5-(6-bromohexanoylamino)benzoic acid test paper method for detecting microorganisms capable of producing cephalosporin acylases. Anal Biochem 1991; 196:201-6. [PMID: 1776668 DOI: 10.1016/0003-2697(91)90453-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A novel method for detecting microorganisms capable of producing cephalosporin C (CPC) acylase and/or 7-(4-carboxybutanamido)cephalosporanic acid (GL-7-ACA) acylase has been developed. The method is based on the degradation of 2-nitro-5-(6-bromohexanoylamino)benzoic acid (NBHAB), a chromogenic substrate, into yellow 2-nitro-5-aminobenzoic acid by the action of the CPC acylase or the GL-7-ACA acylase. This method is very sensitive and quite specific, and has been successfully applied to screen the acylases from a variety of bacteria. A large number of colonies isolated on a plate surface from more than 67 samples and several known bacteria were tested by the NBHAB paper. Five NBHAB-positive strains and isolates were obtained. They were further examined by the reaction of their bacterial cells upon CPC and GL-7-ACA, respectively, and by thin-layer chromatography in order to distinguish the CPC acylase from the GL-7-ACA acylase.
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Affiliation(s)
- Q J Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing
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Martín J, Prieto I, Barbero JL, Pérez-Gil J, Mancheño JM, Arche R. Thermodynamic profiles of penicillin G hydrolysis catalyzed by wild-type and Met----Ala168 mutant penicillin acylases from Kluyvera citrophila. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1037:133-9. [PMID: 2306469 DOI: 10.1016/0167-4838(90)90158-c] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The Met-168 residue in penicillin acylase from Kluyvera citrophila was changed to Ala by oligonucleotide site-directed mutagenesis. The Ala-168 mutant exhibited different substrate specificity than wild-type and enhanced thermal stability. The thermodynamic profiles for penicillin G hydrolysis catalyzed by both enzymes were obtained from the temperature dependence of the steady-state kinetic parameters Km and kcat. The high values of enthalpy and entropy of activation determined for the binding of substrate suggest that an induced-fit-like mechanism takes place. The Met----Ala168 mutation unstabilizes the first transition-state (E..S not equal to) and the enzyme-substrate complex (ES) causing a decrease in association equilibrium and specificity constants in the enzyme. However, no change is observed in the acyl-enzyme formation. It is concluded that residue 168 is involved in the enzyme conformational rearrangements caused by the interaction of the acid moiety of the substrate at the active site.
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Affiliation(s)
- J Martín
- Departamento de Bioquímica y Biología Molecular I, Facultad de Química, Universidad Complutense, Madrid, Spain
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Boccù E, Carenza M, Lora S, Palma G, Veronese FM. Radiation-induced polymerization for the immobilization of penicillin acylase. Appl Biochem Biotechnol 1987; 15:1-10. [PMID: 3310873 DOI: 10.1007/bf02798502] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The immobilization of Escherichia coli penicillin acylase (EC 3.5.1.11) was investigated by radiation-induced polymerization of 2-hydroxyethyl methacrylate at low temperature. A leak-proof composite that does not swell in water was obtained by adding the cross-linking agent trimethylolpropane trimethacrylate to the monomer-aqueous enzyme mixture. Penicillin acylase, which was immobilized with greater than 70% yield, possessed a higher Km value toward the substrate 6-nitro-3-phenylacetamidobenzoic acid than the free enzyme form (Km = 1.7 X 10(-5) and 1 X 10(-5) M, respectively). The structural stability of immobilized penicillin acylase, as assessed by heat, guanidinium chloride, and pH denaturation profiles, was very similar to that of the free-enzyme form, thus suggesting that penicillin acylase was entrapped in its native state into aqueous free spaces of the polymer matrix.
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Affiliation(s)
- E Boccù
- Dipartimento di Scienze Farmaceutiche, Università di Padova, Italy
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9
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Zhang QJ, Zhang LF, Han HX, Zhang YY. A method for screening penicillin G acylase-producing bacteria by means of 2-nitro-5-phenylacetaminobenzoic acid test paper. Anal Biochem 1986; 156:413-6. [PMID: 3532862 DOI: 10.1016/0003-2697(86)90274-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A simple, rapid assay for screening penicillin G acylase-producing bacteria is presented. The method is based on the formation of yellow 2-nitro-5-aminobenzoic acid by penicillin G acylase acting on 2-nitro-5-phenylacetaminobenzoic acid (NIPAB). NIPAB test paper is briefly applied to bacterial colonies on the agar surface, which are subsequently scored individually on the paper by color; bright yellow indicates the presence of penicillin G acylase, natural color its absence. The present method is suitable not only for screening penicillin G acylase-production by a variety of bacteria but also for detection from a large number of transformant colonies of clones containing a gene encoding for the enzyme.
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10
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García J, Buesa J. An improved method to clone penicillin acylase genes: Cloning and expression in Escherichia coli of penicillin G acylase from Kluyvera citrophila. J Biotechnol 1986. [DOI: 10.1016/0168-1656(86)90001-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Barbero JL, Buesa JM, González de Buitrago G, Méndez E, Péz-Aranda A, García JL. Complete nucleotide sequence of the penicillin acylase gene from Kluyvera citrophila. Gene X 1986; 49:69-80. [PMID: 3032748 DOI: 10.1016/0378-1119(86)90386-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The penicillin acylase (PAC) from Kluyvera citrophila ATCC21285 has been purified to homogeneity and found to be composed of two non-identical subunits of 23 and 62 kDa, in contrast with the previous findings [Shimizu et al., Agr. Biol. Chem. 39 (1975) 1655-1661]. The nucleotide (nt) sequence of the K. citrophila pac gene contained in the 3-kb PvuI-HindIII fragment of pKAP1 [García and Buesa, J. Biotechnol. 3 (1986) 187-195] has been determined, showing that it encodes a protein of 844 amino acid (aa) residues. The aa analysis of the N-terminal and C-terminal sequences of the purified subunits showed that they were derived from a common precursor protein of 93.5 kDa, from which a signal peptide of 26 aa, responsible for the periplasmic translocation of the protein, and an internal connecting polypeptide of 54 aa, have been removed in the maturation of the PAC. The comparison of the nt sequences of the pac genes from K. citrophila and Escherichia coli ATCC11105 [Schumacher et al., Nucl. Acids Res. 14 (1986) 5713-5727] revealed 80% homology, suggesting a common ancestral pac gene origin. The results reported here should allow investigation of the unusual mechanism of maturation of this prokaryotic protein, as well as manipulation, using DNA recombinant techniques, of the catalytic properties of this industrially important enzyme.
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13
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McCullough JE. Gene Cloning in Bacilli Related to Enhanced Penicillin Acylase Production. ACTA ACUST UNITED AC 1983. [DOI: 10.1038/nbt1283-879] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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14
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Meevootisom V, Somsuk P, Prachaktam R, Flegel TW. Simple screening method for isolation of penicillin acylase-producing bacteria. Appl Environ Microbiol 1983; 46:1227-9. [PMID: 6316854 PMCID: PMC239545 DOI: 10.1128/aem.46.5.1227-1229.1983] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
A new screening method for bacteria capable of producing penicillin acylase is described. The method is based on the use of Serratia marcescens sensitive to 6-aminopenicillanic acid but comparatively resistant to benzylpenicillin. It is simple, quite specific, and requires no special equipment. It can also be used to screen for phenoxymethylpenicillin acylase activity. We also suggest an acidimetric method for rapid detection of cloned genes in genetic engineering studies of penicillin acylase.
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Konecny J, Schneider A, Sieber M. Kinetics and mechanism of acyl transfer by penicillin acylases. Biotechnol Bioeng 1983; 25:451-67. [DOI: 10.1002/bit.260250212] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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