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da Silva AS, Adriani PP, de Oliveira GS, Rocha ARL, Perpétuo EA, Dias MVB, Chambergo FS. Biochemical characterization of an esterase from Thermobifida fusca YX with acetyl xylan esterase activity. Mol Biol Rep 2024; 51:767. [PMID: 38878205 DOI: 10.1007/s11033-024-09601-7] [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: 02/25/2024] [Accepted: 05/01/2024] [Indexed: 06/29/2024]
Abstract
BACKGROUND Esterases (EC 3.1.1.X) are enzymes that catalyze the hydrolysis ester bonds. These enzymes have large potential for diverse applications in fine industries, particularly in pharmaceuticals, cosmetics, and bioethanol production. METHODS AND RESULTS In this study, a gene encoding an esterase from Thermobifida fusca YX (TfEst) was successfully cloned, and its product was overexpressed in Escherichia coli and purified using affinity chromatography. The TfEst kinetic assay revealed catalytic efficiencies of 0.58 s-1 mM-1, 1.09 s-1 mM-1, and 0.062 s-1 mM-1 against p-Nitrophenyl acetate, p-Nitrophenyl butyrate, and 1-naphthyl acetate substrates, respectively. Furthermore, TfEst also exhibited activity in a pH range from 6.0 to 10.0, with maximum activity at pH 8.0. The enzyme demonstrated a half-life of 20 min at 70 °C. Notably, TfEst displayed acetyl xylan esterase activity as evidenced by the acetylated xylan assay. The structural prediction of TfEst using AlphaFold indicated that has an α/β-hydrolase fold, which is consistent with other esterases. CONCLUSIONS The enzyme stability over a broad pH range and its activity at elevated temperatures make it an appealing candidate for industrial processes. Overall, TfEst emerges as a promising enzymatic tool with significant implications for the advancement of biotechnology and biofuels industries.
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Affiliation(s)
- Adriana S da Silva
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil
| | - Patricia P Adriani
- Departamento de Farmacologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Gabriel S de Oliveira
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Elen A Perpétuo
- Bio4Tec, Centro de Capacitação e Pesquisa em Meio Ambiente, CEPEMA-POLI-USP, Universidade de São Paulo, Cubatão, Brazil
- Institute of Marine Sciences (IMar), Federal University of Sao Paulo, Santos, Brazil
| | - Marcio V B Dias
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Felipe S Chambergo
- Escola de Artes, Ciências e HumanidadesErmelino Matarazzo, Universidade de São Paulo, 1000 Av. Arlindo Bettio, São Paulo, CEP: 3828-000, Brazil.
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Nguyen DL, Hwang J, Kim EJ, Lee JH, Han SJ. Production and Characterization of a Recombinant Cold-Active Acetyl Xylan Esterase from Psychrophilic Paenibacillus sp. R4 Strain. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822040123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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3
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Carbohydrate esterase family 16 contains fungal hemicellulose acetyl esterases (HAEs) with varying specificity. N Biotechnol 2022; 70:28-38. [DOI: 10.1016/j.nbt.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 11/18/2022]
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4
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Purohit A, Singh G, Yadav SK. Chimeric bi-functional enzyme possessing xylanase and deacetylase activity for hydrolysis of agro-biomass rich in acetylated xylan. Colloids Surf B Biointerfaces 2021; 204:111832. [PMID: 33984614 DOI: 10.1016/j.colsurfb.2021.111832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 05/04/2021] [Accepted: 05/07/2021] [Indexed: 10/21/2022]
Abstract
Here, a chimeric bifunctional enzyme was developed for two activities xylanase and deacetylase. Chimeric enzyme was designed by combining the relevant amino acid stretches from two different parent sequences, such as polysaccharide/xylan deacetylase (ref id: MT682066) and xylanase (ref id WP_110897546.1). Five different hypothetical chimeras were developed and one of the best predicted chimeric protein GA_2(syn_SKYAP01) was synthesized. The GA_2(syn_SKYAP01) possessed the specific activity of 14.905 ± 0.8 U/mg for deacetylase and 100.87 ± 14.2 U/mg for xylanase. Optimum level of both the activities together was achieved at pH 5 and 60 °C. The chimeric protein was also found to be stable at higher temperature of 71°C. Functionality of the developed chimeric protein for both the activities was confirmed by the hydrolysis of commercial xylan into xylooligosaccharides and the release of acetic acid from glucose pentacetate and 7-amino cephalosporin. The designed bifunctional enzyme was found to be highly efficient.
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Affiliation(s)
- Anjali Purohit
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India
| | - Gurjant Singh
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India
| | - Sudesh Kumar Yadav
- Center of Innovative and Applied Bioprocessing (CIAB), Sector-81 (Knowledge City), Mohali, 140306, PB, India.
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5
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Crystal structure and functional characterization of a cold-active acetyl xylan esterase (PbAcE) from psychrophilic soil microbe Paenibacillus sp. PLoS One 2018; 13:e0206260. [PMID: 30379876 PMCID: PMC6209228 DOI: 10.1371/journal.pone.0206260] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/09/2018] [Indexed: 12/27/2022] Open
Abstract
Cold-active acetyl xylan esterases allow for reduced bioreactor heating costs in bioenergy production. Here, we isolated and characterized a cold-active acetyl xylan esterase (PbAcE) from the psychrophilic soil microbe Paenibacillus sp. R4. The enzyme hydrolyzes glucose penta-acetate and xylan acetate, reversibly producing acetyl xylan from xylan, and it shows higher activity at 4°C than at 25°C. We solved the crystal structure of PbAcE at 2.1-Å resolution to investigate its active site and the reason for its low-temperature activity. Structural analysis showed that PbAcE forms a hexamer with a central substrate binding tunnel, and the inter-subunit interactions are relatively weak compared with those of its mesophilic and thermophilic homologs. PbAcE also has a shorter loop and different residue composition in the β4–α3 and β5–α4 regions near the substrate binding site. Flexible subunit movements and different active site loop conformations may enable the strong low-temperature activity and broad substrate specificity of PbAcE. In addition, PbAcE was found to have strong activity against antibiotic compound substrates, such as cefotaxime and 7-amino cephalosporanic acid (7-ACA). In conclusion, the PbAcE structure and our biochemical results provide the first example of a cold-active acetyl xylan esterase and a starting template for structure-based protein engineering.
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Sista Kameshwar AK, Qin W. Understanding the structural and functional properties of carbohydrate esterases with a special focus on hemicellulose deacetylating acetyl xylan esterases. Mycology 2018; 9:273-295. [PMID: 30533253 PMCID: PMC6282417 DOI: 10.1080/21501203.2018.1492979] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 06/21/2018] [Indexed: 11/29/2022] Open
Abstract
Acetyl and methyl esterifications are two major naturally found substitutions in the plant cell-wall polysaccharides. The non-cellulosic plant cell-wall polysaccharides such as pectin and hemicellulose are differentially esterified by the O-acetyl and methyl groups to cease the action of various hydrolytic enzymes secreted by different fungi and bacterial species. Thus, microorganisms have emerged with a special class of enzymes known as carbohydrate esterases (CE). The CE catalyse O-de, N-deacetylation of acetylated saccharide residues (esters or amides, where sugars play the role of alcohol/amine/acid). Carbohydrate active enzyme (CAZy) database has classified CE into 16 classes, of which hemicellulose deacetylating CE were grouped into eight classes (CE-1 to CE-7 and CE-16). Various plant biomass degrading fungi and bacteria secretes acetyl xylan esterases (AcXE); however, these enzymes exhibit varied substrate specificities. AcXE and xylanases-coupled pretreatment methods exhibit significant applications, such as enhancing animal feedstock, baking industry, production of food additives, paper and pulp, xylitol production and biorefinery-based industries, respectively. Thus, understanding the structural and functional properties of acetyl xylan esterase will significantly aid in developing the efficient AcXE with wide range of industrial applications.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, Thunder Bay, Ontario, Canada
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7
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Adesioye FA, Makhalanyane TP, Vikram S, Sewell BT, Schubert WD, Cowan DA. Structural Characterization and Directed Evolution of a Novel Acetyl Xylan Esterase Reveals Thermostability Determinants of the Carbohydrate Esterase 7 Family. Appl Environ Microbiol 2018; 84:e02695-17. [PMID: 29453256 PMCID: PMC5881061 DOI: 10.1128/aem.02695-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 01/26/2018] [Indexed: 02/04/2023] Open
Abstract
A hot desert hypolith metagenomic DNA sequence data set was screened in silico for genes annotated as acetyl xylan esterases (AcXEs). One of the genes identified encoded an ∼36-kDa protein (Axe1NaM1). The synthesized gene was cloned and expressed, and the resulting protein was purified. NaM1 was optimally active at pH 8.5 and 30°C and functionally stable at salt concentrations of up to 5 M. The specific activity and catalytic efficiency were 488.9 U mg-1 and 3.26 × 106 M-1 s-1, respectively. The crystal structure of wild-type NaM1 was solved at a resolution of 2.03 Å, and a comparison with the structures and models of more thermostable carbohydrate esterase 7 (CE7) family enzymes and variants of NaM1 from a directed evolution experiment suggests that reduced side-chain volume of protein core residues is relevant to the thermal stability of NaM1. Surprisingly, a single point mutation (N96S) not only resulted in a simultaneous improvement in thermal stability and catalytic efficiency but also increased the acyl moiety substrate range of NaM1.IMPORTANCE AcXEs belong to nine carbohydrate esterase families (CE1 to CE7, CE12, and CE16), of which CE7 enzymes possess a unique and narrow specificity for acetylated substrates. All structurally characterized members of this family are moderately to highly thermostable. The crystal structure of a novel, mesophilic CE7 AcXE (Axe1NaM1), from a soil metagenome, provides a basis for comparisons with thermostable CE7 enzymes. Using error-prone PCR and site-directed mutagenesis, we enhanced both the stability and activity of the mesophilic AcXE. With comparative structural analyses, we have also identified possible thermal stability determinants. These are valuable for understanding the thermal stability of enzymes within this family and as a guide for future protein engineering of CE7 and other α/β hydrolase enzymes.
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Affiliation(s)
- Fiyinfoluwa A Adesioye
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Thulani P Makhalanyane
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Bryan T Sewell
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Genetics, University of Pretoria, Pretoria, South Africa
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8
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Deacetylation of sialic acid by esterases potentiates pneumococcal neuraminidase activity for mucin utilization, colonization and virulence. PLoS Pathog 2017; 13:e1006263. [PMID: 28257499 PMCID: PMC5352144 DOI: 10.1371/journal.ppat.1006263] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 03/15/2017] [Accepted: 02/27/2017] [Indexed: 01/19/2023] Open
Abstract
Pneumococcal neuraminidase is a key enzyme for sequential deglycosylation of host glycans, and plays an important role in host survival, colonization, and pathogenesis of infections caused by Streptococcus pneumoniae. One of the factors that can affect the activity of neuraminidase is the amount and position of acetylation present in its substrate sialic acid. We hypothesised that pneumococcal esterases potentiate neuraminidase activity by removing acetylation from sialic acid, and that will have a major effect on pneumococcal survival on mucin, colonization, and virulence. These hypotheses were tested using isogenic mutants and recombinant esterases in microbiological, biochemical and in vivo assays. We found that pneumococcal esterase activity is encoded by at least four genes, SPD_0534 (EstA) was found to be responsible for the main esterase activity, and the pneumococcal esterases are specific for short acyl chains. Assay of esterase activity by using natural substrates showed that both the Axe and EstA esterases could use acetylated xylan and Bovine Sub-maxillary Mucin (BSM), a highly acetylated substrate, but only EstA was active against tributyrin (triglyceride). Incubation of BSM with either Axe or EstA led to the acetate release in a time and concentration dependent manner, and pre-treatment of BSM with either enzyme increased sialic acid release on subsequent exposure to neuraminidase A. qRT-PCR results showed that the expression level of estA and axe increased when exposed to BSM and in respiratory tissues. Mutation of estA alone or in combination with nanA (codes for neuraminidase A), or the replacement of its putative serine active site to alanine, reduced the pneumococcal ability to utilise BSM as a sole carbon source, sialic acid release, colonization, and virulence in a mouse model of pneumococcal pneumonia.
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9
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10
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Abstract
Colorimetric detection of reaction products is typically preferred for initial surveys of acetyl xylan esterase (AcXE) activity. This chapter will describe common colorimetric methods, and variations thereof, for measuring AcXE activities on commercial, synthesized, and natural substrates. Whereas assays using pNP-acetate, α-naphthyl acetate, and 4-methylumbelliferyl acetate (4MUA) are emphasized, common methods used to measure AcXE activity towards carbohydrate analogs (e.g., acetylated p-nitrophenyl β-D-xylopyranosides) and various acetylated xylans are also described. Strengths and limitations of the colorimetric assays are highlighted.
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Affiliation(s)
- Galina Mai-Gisondi
- Department of Bioproducts and Biosystems, Aalto University, 00076, Kemistintie 1, Espoo, Aalto, Finland
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
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11
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Zarafeta D, Moschidi D, Ladoukakis E, Gavrilov S, Chrysina ED, Chatziioannou A, Kublanov I, Skretas G, Kolisis FN. Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases. Sci Rep 2016; 6:38886. [PMID: 27991516 PMCID: PMC5171882 DOI: 10.1038/srep38886] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/14/2016] [Indexed: 11/09/2022] Open
Abstract
Biocatalysts exerting activity against ester bonds have a broad range of applications in modern biotechnology. Here, we have identified a new esterolytic enzyme by screening a metagenomic sample collected from a hot spring in Kamchatka, Russia. Biochemical characterization of the new esterase, termed EstDZ2, revealed that it is highly active against medium chain fatty acid esters at temperatures between 25 and 60 °C and at pH values 7-8. The new enzyme is moderately thermostable with a half-life of more than six hours at 60 °C, but exhibits exquisite stability against high concentrations of organic solvents. Phylogenetic analysis indicated that EstDZ2 is likely an Acetothermia enzyme that belongs to a new family of bacterial esterases, for which we propose the index XV. One distinctive feature of this new family, is the presence of a conserved GHSAG catalytic motif. Multiple sequence alignment, coupled with computational modelling of the three-dimensional structure of EstDZ2, revealed that the enzyme lacks the largest part of the "cap" domain, whose extended structure is characteristic for the closely related Family IV esterases. Thus, EstDZ2 appears to be distinct from known related esterolytic enzymes, both in terms of sequence characteristics, as well as in terms of three-dimensional structure.
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Affiliation(s)
- Dimitra Zarafeta
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Danai Moschidi
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Efthymios Ladoukakis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
| | - Sergey Gavrilov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Evangelia D. Chrysina
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Aristotelis Chatziioannou
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Ilya Kublanov
- Winogradsky Institute of Microbiology, Research Center for Biotechnology Russian Academy of Sciences, Moscow, Russian Federation
| | - Georgios Skretas
- Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Fragiskos N. Kolisis
- Laboratory of Biotechnology, School of Chemical Engineering, National Technical University of Athens, Athens, Greece
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12
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McKary MG, Abendroth J, Edwards TE, Johnson RJ. Structural Basis for the Strict Substrate Selectivity of the Mycobacterial Hydrolase LipW. Biochemistry 2016; 55:7099-7111. [PMID: 27936614 DOI: 10.1021/acs.biochem.6b01057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The complex life cycle of Mycobacterium tuberculosis requires diverse energy mobilization and utilization strategies facilitated by a battery of lipid metabolism enzymes. Among lipid metabolism enzymes, the Lip family of mycobacterial serine hydrolases is essential to lipid scavenging, metabolic cycles, and reactivation from dormancy. On the basis of the homologous rescue strategy for mycobacterial drug targets, we have characterized the three-dimensional structure of full length LipW from Mycobacterium marinum, the first structure of a catalytically active Lip family member. LipW contains a deep, expansive substrate-binding pocket with only a narrow, restrictive active site, suggesting tight substrate selectivity for short, unbranched esters. Structural alignment reinforced this strict substrate selectivity of LipW, as the binding pocket of LipW aligned most closely with the bacterial acyl esterase superfamily. Detailed kinetic analysis of two different LipW homologues confirmed this strict substrate selectivity, as each homologue selected for unbranched propionyl ester substrates, irrespective of the alcohol portion of the ester. Using comprehensive substitutional analysis across the binding pocket, the strict substrate selectivity of LipW for propionyl esters was assigned to a narrow funnel in the acyl-binding pocket capped by a key hydrophobic valine residue. The polar, negatively charged alcohol-binding pocket also contributed to substrate orientation and stabilization of rotameric states in the catalytic serine. Together, the structural, enzymatic, and substitutional analyses of LipW provide a connection between the structure and metabolic properties of a Lip family hydrolase that refines its biological function in active and dormant tuberculosis infection.
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Affiliation(s)
- Magy G McKary
- Department of Chemistry, Butler University , 4600 Sunset Avenue, Indianapolis, Indiana 46208, United States
| | - Jan Abendroth
- Beryllium Discovery Corporation, Seattle Structural Genomics Center for Infectious Disease (SSGCID) , 7869 Northeast Day Road West, Bainbridge Island, Washington 98110, United States
| | - Thomas E Edwards
- Beryllium Discovery Corporation, Seattle Structural Genomics Center for Infectious Disease (SSGCID) , 7869 Northeast Day Road West, Bainbridge Island, Washington 98110, United States
| | - R Jeremy Johnson
- Department of Chemistry, Butler University , 4600 Sunset Avenue, Indianapolis, Indiana 46208, United States
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13
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Mokoena N, Mathiba K, Tsekoa T, Steenkamp P, Rashamuse K. Application of termite hindgut metagenome derived carboxyl ester hydrolases in the modification of cephalosporin substrates. Biochem Biophys Rep 2015; 4:44-51. [PMID: 29124186 PMCID: PMC5668906 DOI: 10.1016/j.bbrep.2015.08.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 08/20/2015] [Accepted: 08/24/2015] [Indexed: 11/26/2022] Open
Abstract
In the pharmaceutical industry, de-acetylated cephalosporins are highly valuable starting materials for producing semi-synthetic β-lactam antibiotics. In this study a fosmid metagenome library from termite hindgut symbionts was screened for carboxyl ester hydrolases capable of de-acetylating cephalosporins. Recombinant Escherichia coli clones with esterolytic phenotypes on tributyrin agar plates were selected and further tested for de-acetylating activity against Cephalothin and 7-aminocephalosporanic acid (7-ACA). Two clones displaying de-acetylating activity were sequenced and the corresponding two carboxyl ester hydrolase encoding genes (axeA and axeB) belonging to the carbohydrate esterase family 7 (CE7) were identified. The primary structure of both the axeA and axeB revealed the presence of G-X-S-X-G sequence motif and respective subunit molecular masses of 40 kDa. In addition to de-acetylating cephalosporin based molecules, the two enzymes were also shown to be true esterases based on their preferences for short chain length fatty acid esters. Esterases (AxeA and AxeB) contained classical G-X-S-x-G motif and showed deacetylating activities against cephalosporin substrates. AxeA and AxeB can be useful in the biocatalytic modification of cephalosporin molecules.
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Affiliation(s)
- Nobalanda Mokoena
- CSIR Biosciences, Biomanufacturing Technology Competence Area, Brummeria, Pretoria 0001, South Africa
| | - Kgama Mathiba
- CSIR Biosciences, Biomanufacturing Technology Competence Area, Brummeria, Pretoria 0001, South Africa
| | - Tsepo Tsekoa
- CSIR Biosciences, Biomanufacturing Technology Competence Area, Brummeria, Pretoria 0001, South Africa
| | - Paul Steenkamp
- CSIR Biosciences, Biomanufacturing Technology Competence Area, Brummeria, Pretoria 0001, South Africa.,Department of Biochemistry, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa
| | - Konanani Rashamuse
- CSIR Biosciences, Biomanufacturing Technology Competence Area, Brummeria, Pretoria 0001, South Africa
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14
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Engineering of a CPC acylase using a facile pH indicator assay. ACTA ACUST UNITED AC 2014; 41:1617-25. [DOI: 10.1007/s10295-014-1501-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/13/2014] [Indexed: 11/25/2022]
Abstract
Abstract
Cephalosporin C (CPC) acylase is important for the one-step production of 7-aminocephalosporanic acid (7-ACA), a key intermediate for cephalosporin antibiotics. However, its application is hampered by the low activity, substrate inhibition, and product inhibition. In this study, two rounds of combinatorial active-site saturation testing (CASTing) were carried out on the CPC acylase acyII from Pseudomonas SE83, and one mutant H57βA/H70βY with no substrate inhibition was obtained. For further engineering to reduce the product inhibition, a quick pH indicator assay was developed, allowing for real-time monitoring of the product inhibition in the presence of added 7-ACA. The utility of the assay was demonstrated by screening six libraries of site-directed saturation mutagenesis libraries of H57βA/H70βY. A new mutant H57βA/H70βY/I176βN was obtained, which showed a k cat 3.26-fold and a K IP 3.08-fold that of the wild type, respectively. Given the commercial value of the enzyme, both this pH indicator assay and the triple mutant should be useful for further engineering of the enzyme to increase the specific activity and to decrease the product inhibition.
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15
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Hedge MK, Gehring AM, Adkins CT, Weston LA, Lavis LD, Johnson RJ. The structural basis for the narrow substrate specificity of an acetyl esterase from Thermotoga maritima. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1824:1024-30. [DOI: 10.1016/j.bbapap.2012.05.009] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 05/09/2012] [Accepted: 05/22/2012] [Indexed: 10/28/2022]
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16
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Levisson M, Han GW, Deller MC, Xu Q, Biely P, Hendriks S, Ten Eyck LF, Flensburg C, Roversi P, Miller MD, McMullan D, von Delft F, Kreusch A, Deacon AM, van der Oost J, Lesley SA, Elsliger MA, Kengen SWM, Wilson IA. Functional and structural characterization of a thermostable acetyl esterase from Thermotoga maritima. Proteins 2012; 80:1545-59. [PMID: 22411095 DOI: 10.1002/prot.24041] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/10/2012] [Accepted: 01/18/2012] [Indexed: 11/06/2022]
Abstract
TM0077 from Thermotoga maritima is a member of the carbohydrate esterase family 7 and is active on a variety of acetylated compounds, including cephalosporin C. TM0077 esterase activity is confined to short-chain acyl esters (C2-C3), and is optimal around 100°C and pH 7.5. The positional specificity of TM0077 was investigated using 4-nitrophenyl-β-D-xylopyranoside monoacetates as substrates in a β-xylosidase-coupled assay. TM0077 hydrolyzes acetate at positions 2, 3, and 4 with equal efficiency. No activity was detected on xylan or acetylated xylan, which implies that TM0077 is an acetyl esterase and not an acetyl xylan esterase as currently annotated. Selenomethionine-substituted and native structures of TM0077 were determined at 2.1 and 2.5 Å resolution, respectively, revealing a classic α/β-hydrolase fold. TM0077 assembles into a doughnut-shaped hexamer with small tunnels on either side leading to an inner cavity, which contains the six catalytic centers. Structures of TM0077 with covalently bound phenylmethylsulfonyl fluoride and paraoxon were determined to 2.4 and 2.1 Å, respectively, and confirmed that both inhibitors bind covalently to the catalytic serine (Ser188). Upon binding of inhibitor, the catalytic serine adopts an altered conformation, as observed in other esterase and lipases, and supports a previously proposed catalytic mechanism in which Ser hydroxyl rotation prevents reversal of the reaction and allows access of a water molecule for completion of the reaction.
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Affiliation(s)
- Mark Levisson
- Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703 HB, Wageningen, The Netherlands
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Wang Y, Yu H, Zhang J, Luo H, Shen Z. Double knockout of β-lactamase and cephalosporin acetyl esterase genes from Escherichia coli reduces cephalosporin C decomposition. J Biosci Bioeng 2012; 113:737-41. [PMID: 22382016 DOI: 10.1016/j.jbiosc.2012.02.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Revised: 01/23/2012] [Accepted: 02/02/2012] [Indexed: 11/28/2022]
Abstract
The phenomenon of CPC decomposition occurs in Escherichia coli JM105/pMKC-sCPCacy during the one-step enzymatic conversion of cephalosporin C (CPC) into 7-aminocephalosporanic acid (7-ACA) by CPC acylase (sCPCAcy) for synthesis of cephalosporin antibiotics. E. coli JM105/pMKC-sCPCacy can constitutively produce sCPCacy as a fusion protein with maltose binding protein (MBP). Control experiments verified that the cell lysis solution from the host E. coli JM105 resulted in CPC decomposition by approximately 15%. Two miscellaneous enzymes, β-lactamase (AmpC) and cephalosporin acetyl esterase (Aes), are believed to play a major role in the degradation of CPC. Using the Red recombination system, the genes ampC, aes or both ampC and aes were knocked out from the chromosome of E. coli JM105 to generate the engineers: E. coli JM105(ΔampC), E. coli JM105(Δaes) and E. coli JM105(ΔampC, Δaes). The CPC decomposition was reduced to 12.2% in E. coli JM105(Δaes), 1.3% in E. coli JM105(ΔampC), and even undetectable in ampC-aes double knockout cells of E. coli JM105(ΔampC, Δaes). When catalyzed by crude MBP-sCPCAcy isolated from E. coli JM105(ΔampC, Δaes)/pMKC-sCPCacy (3377U·l(-1)), the CPC utilization efficiency increased to 98.4% from the original 88.7%. Similar results were obtained for the ampC-aes double knockout host derived from E. coli JM109(DE3) and the CPC utilization efficiency enhanced to 99.3% in the catalysis of crude sCPCAcy harvested from E. coli JM109(DE3, ΔampC, Δaes)/pET28-sCPCacy.
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Affiliation(s)
- Ying Wang
- Institute of Biochemical Engineering, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P R China
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Yu K, Hu S, Huang J, Mei LH. A high-throughput colorimetric assay to measure the activity of glutamate decarboxylase. Enzyme Microb Technol 2011; 49:272-6. [DOI: 10.1016/j.enzmictec.2011.06.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2010] [Revised: 05/03/2011] [Accepted: 06/06/2011] [Indexed: 11/25/2022]
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The crystal structure of the cephalosporin deacetylating enzyme acetyl xylan esterase bound to paraoxon explains the low sensitivity of this serine hydrolase to organophosphate inactivation. Biochem J 2011; 436:321-30. [DOI: 10.1042/bj20101859] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Organophosphorus insecticides and nerve agents irreversibly inhibit serine hydrolase superfamily enzymes. One enzyme of this superfamily, the industrially important (for β-lactam antibiotic synthesis) AXE/CAH (acetyl xylan esterase/cephalosporin acetyl hydrolase) from the biotechnologically valuable organism Bacillus pumilus, exhibits low sensitivity to the organophosphate paraoxon (diethyl-p-nitrophenyl phosphate, also called paraoxon-ethyl), reflected in a high Ki for it (~5 mM) and in a slow formation (t½~1 min) of the covalent adduct of the enzyme and for DEP (E-DEP, enzyme–diethyl phosphate, i.e. enzyme–paraoxon). The crystal structure of the E-DEP complex determined at 2.7 Å resolution (1 Å=0.1 nm) reveals strain in the active Ser181-bound organophosphate as a likely cause for the limited paraoxon sensitivity. The strain results from active-site-size limitation imposed by bulky conserved aromatic residues that may exclude as substrates esters having acyl groups larger than acetate. Interestingly, in the doughnut-like homohexamer of the enzyme, the six active sites are confined within a central chamber formed between two 60°-staggered trimers. The exclusive access to this chamber through a hole around the three-fold axis possibly limits the size of the xylan natural substrates. The enzyme provides a rigid scaffold for catalysis, as reflected in the lack of movement associated with paraoxon adduct formation, as revealed by comparing this adduct structure with that also determined in the present study at 1.9 Å resolution for the paraoxon-free enzyme.
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Wang L, Mavisakalyan V, Tillier ERM, Clark GW, Savchenko AV, Yakunin AF, Master ER. Mining bacterial genomes for novel arylesterase activity. Microb Biotechnol 2011; 3:677-90. [PMID: 21255363 PMCID: PMC3815341 DOI: 10.1111/j.1751-7915.2010.00185.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
One hundred and seventy-one genes encoding potential esterases from 11 bacterial genomes were cloned and overexpressed in Escherichia coli; 74 of the clones produced soluble proteins. All 74 soluble proteins were purified and screened for esterase activity; 36 proteins showed carboxyl esterase activity on short-chain esters, 17 demonstrated arylesterase activity, while 38 proteins did not exhibit any activity towards the test substrates. Esterases from Rhodopseudomonas palustris (RpEST-1, RpEST-2 and RpEST-3), Pseudomonas putida (PpEST-1, PpEST-2 and PpEST-3), Pseudomonas aeruginosa (PaEST-1) and Streptomyces avermitilis (SavEST-1) were selected for detailed biochemical characterization. All of the enzymes showed optimal activity at neutral or alkaline pH, and the half-life of each enzyme at 50°C ranged from < 5 min to over 5 h. PpEST-3, RpEST-1 and RpEST-2 demonstrated the highest specific activity with pNP-esters; these enzymes were also among the most stable at 50°C and in the presence of detergents, polar and non-polar organic solvents, and imidazolium ionic liquids. Accordingly, these enzymes are particularly interesting targets for subsequent application trials. Finally, biochemical and bioinformatic analyses were compared to reveal sequence features that could be correlated to enzymes with arylesterase activity, facilitating subsequent searches for new esterases in microbial genome sequences.
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Affiliation(s)
- Lijun Wang
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada
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Anh DH, Cheunrungsikul K, Wichitwechkarn J, Surareungchai W. A colorimetric assay for determination of methyl parathion using recombinant methyl parathion hydrolase. Biotechnol J 2011; 6:565-71. [PMID: 21381204 DOI: 10.1002/biot.201000348] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2010] [Revised: 12/22/2010] [Accepted: 01/24/2011] [Indexed: 11/10/2022]
Abstract
A simple, rapid and sensitive colorimetric dipstick assay for the detection of the organophosphorous insecticide methyl parathion (MPT) residue in vegetables was developed. The assay was based on the hydrolysis of MPT by a recombinant methyl parathion hydrolase (recMPH), the encoding gene of which was isolated from Burkholderia cepacia, a soil bacterium indigenous to Thailand. This reaction generates protons leading to a change in pH that correlates with the amount of MPH present. Hence, the pH indicator bromothymol blue was used to monitor the MPH hydrolysis as the associated color changes can be observed by the naked eye. The recMPH was immobilized on a PVDF membrane to establish a dipstick assay format. The assays could detect MPT residues in spiked vegetable samples at the concentration of 1 mg/L without using analytical instrumentation. The test is reusable and stable for up to 3 months in the absence of any preservatives.
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Affiliation(s)
- Dau Hung Anh
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
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Persson M, Palcic MM. A high-throughput pH indicator assay for screening glycosyltransferase saturation mutagenesis libraries. Anal Biochem 2008; 378:1-7. [DOI: 10.1016/j.ab.2008.03.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2007] [Revised: 03/04/2008] [Accepted: 03/04/2008] [Indexed: 10/22/2022]
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Characterization of a new rhamnogalacturonan acetyl esterase from Bacillus halodurans C-125 with a new putative carbohydrate binding domain. J Bacteriol 2007; 190:1375-82. [PMID: 18083818 DOI: 10.1128/jb.01104-07] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BH1115 is a gene from Bacillus halodurans strain C-125 that hypothetically encodes a rhamnogalacturonan acetyl esterase (RGAE) of the CE-12 family. As confirmation, this gene was cloned, and the product was expressed in Escherichia coli strain Rosetta (DE3) cells and purified. The enzyme obtained was monomeric, with a molecular mass of 45 kDa, and exhibited alkaliphilic properties. A study of the inhibition of the activity by some modulators confirmed that the catalytic triad for the esterase activity was Ser-His-Asp. This enzyme also presents broad substrate specificity and is active toward 7-aminocephalosporanic acid, cephalosporin C, p-nitrophenyl acetate, beta-naphthyl acetate, glucose pentaacetate, and acetylated xylan. Moreover, RGAE from B. halodurans achieves a synergistic effect with xylanase A toward acetylated xylan. As a member of the SGNH family, it does not adopt the common alpha/beta hydrolase fold. The homology between the folds of RGAE from Aspergillus aculeatus and the hypothetical YxiM precursor from Bacillus subtilis, which both belong to the SGNH family, illustrates the divergence of such proteins from a common ancestor. Furthermore, the enzyme possesses a putative substrate binding region at the N terminus of the protein which has never been described to date for any RGAE.
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