1
|
Branson Y, Schnell B, Zurr C, Bayer T, Badenhorst CPS, Wei R, Bornscheuer UT. An Extremely Sensitive Ultra-High Throughput Growth Selection Assay for the Identification of Amidase Activity. Appl Microbiol Biotechnol 2024; 108:392. [PMID: 38910173 PMCID: PMC11194204 DOI: 10.1007/s00253-024-13233-z] [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: 04/12/2024] [Revised: 06/05/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
In the last decades, biocatalysis has offered new perspectives for the synthesis of (chiral) amines, which are essential building blocks for pharmaceuticals, fine and bulk chemicals. In this regard, amidases have been employed due to their broad substrate scope and their independence from expensive cofactors. To expand the repertoire of amidases, tools for their rapid identification and characterization are greatly demanded. In this work an ultra-high throughput growth selection assay based on the production of the folate precursor p-aminobenzoic acid (PABA) is introduced to identify amidase activity. PABA-derived amides structurally mimic the broad class of commonly used chromogenic substrates derived from p-nitroaniline. This suggests that the assay should be broadly applicable for the identification of amidases. Unlike conventional growth selection assays that rely on substrates as nitrogen or carbon source, our approach requires PABA in sub-nanomolar concentrations, making it exceptionally sensitive and ideal for engineering campaigns that aim at enhancing amidase activities from minimally active starting points, for example. The presented assay offers flexibility in the adjustment of sensitivity to suit project-specific needs using different expression systems and fine-tuning with the antimetabolite sulfathiazole. Application of this PABA-based assay facilitates the screening of millions of enzyme variants on a single agar plate within two days, without the need for laborious sample preparation or expensive instruments, with transformation efficiency being the only limiting factor. KEY POINTS: • Ultra-high throughput assay (tens of millions on one agar plate) for amidase screening • High sensitivity by coupling selection to folate instead of carbon or nitrogen source • Highly adjustable in terms of sensitivity and expression of the engineering target.
Collapse
Affiliation(s)
- Yannick Branson
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Bjarne Schnell
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Celine Zurr
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Thomas Bayer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Christoffel P S Badenhorst
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Ren Wei
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany
| | - Uwe T Bornscheuer
- Department of Biotechnology & Enzyme Catalysis, Institute of Biochemistry, University of Greifswald, 17487, Greifswald, Germany.
| |
Collapse
|
2
|
Yang Y, Zhang ZW, Liu RX, Ju HY, Bian XK, Zhang WZ, Zhang CB, Yang T, Guo B, Xiao CL, Bai H, Lu WY. Research progress in bioremediation of petroleum pollution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:46877-46893. [PMID: 34254241 DOI: 10.1007/s11356-021-15310-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/01/2021] [Indexed: 06/13/2023]
Abstract
With the enhancement of environmental protection awareness, research on the bioremediation of petroleum hydrocarbon environmental pollution has intensified. Bioremediation has received more attention due to its high efficiency, environmentally friendly by-products, and low cost compared with the commonly used physical and chemical restoration methods. In recent years, bacterium engineered by systems biology strategies have achieved biodegrading of many types of petroleum pollutants. Those successful cases show that systems biology has great potential in strengthening petroleum pollutant degradation bacterium and accelerating bioremediation. Systems biology represented by metabolic engineering, enzyme engineering, omics technology, etc., developed rapidly in the twentieth century. Optimizing the metabolic network of petroleum hydrocarbon degrading bacterium could achieve more concise and precise bioremediation by metabolic engineering strategies; biocatalysts with more stable and excellent catalytic activity could accelerate the process of biodegradation by enzyme engineering; omics technology not only could provide more optional components for constructions of engineered bacterium, but also could obtain the structure and composition of the microbial community in polluted environments. Comprehensive microbial community information lays a certain theoretical foundation for the construction of artificial mixed microbial communities for bioremediation of petroleum pollution. This article reviews the application of systems biology in the enforce of petroleum hydrocarbon degradation bacteria and the construction of a hybrid-microbial degradation system. Then the challenges encountered in the process and the application prospects of bioremediation are discussed. Finally, we provide certain guidance for the bioremediation of petroleum hydrocarbon-polluted environment.
Collapse
Affiliation(s)
- Yong Yang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Zhan-Wei Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Rui-Xia Liu
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Hai-Yan Ju
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Xue-Ke Bian
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Wan-Ze Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Chuan-Bo Zhang
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China
| | - Ting Yang
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Bing Guo
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - Chen-Lei Xiao
- CNOOC EnerTech-Safety & Environmental Protection Co., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China
| | - He Bai
- China Offshore Environmental Service Ltd., Tianwei Industrial Park, No. 75 Taihua Rd, TEDA, Tianjin, 300457, China.
- Tianjin Huakan Environmental Protection Technology Co. Ltd., No. 67 Guangrui West Rd, Hedong District, Tianjin, 300170, China.
| | - Wen-Yu Lu
- School of Chemical Engineering and Technology, Tianjin University, No.135, Ya Guan Rd, Jinnan District, Tianjin, 300350, China.
| |
Collapse
|
3
|
Tang Q, Pavlidis IV, Badenhorst CPS, Bornscheuer UT. From Natural Methylation to Versatile Alkylations Using Halide Methyltransferases. Chembiochem 2021; 22:2584-2590. [PMID: 33890381 PMCID: PMC8453949 DOI: 10.1002/cbic.202100153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/22/2021] [Indexed: 11/06/2022]
Abstract
Halide methyltransferases (HMTs) enable the enzymatic synthesis of S-adenosyl-l-methionine (SAM) from S-adenosyl-l-homocysteine (SAH) and methyl iodide. Characterisation of a range of naturally occurring HMTs and subsequent protein engineering led to HMT variants capable of synthesising ethyl, propyl, and allyl analogues of SAM. Notably, HMTs do not depend on chemical synthesis of methionine analogues, as required by methionine adenosyltransferases (MATs). However, at the moment MATs have a much broader substrate scope than the HMTs. Herein we provide an overview of the discovery and engineering of promiscuous HMTs and how these strategies will pave the way towards a toolbox of HMT variants for versatile chemo- and regioselective biocatalytic alkylations.
Collapse
Affiliation(s)
- Qingyun Tang
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
| | - Ioannis V. Pavlidis
- Dept. of ChemistryUniversity of CreteVoutes University Campus70013HeraklionGreece
| | | | - Uwe T. Bornscheuer
- Institute of BiochemistryUniversity of GreifswaldFelix-Hausdorff-Str. 417489GreifswaldGermany
| |
Collapse
|
4
|
Aslan‐Üzel AS, Beier A, Kovář D, Cziegler C, Padhi SK, Schuiten ED, Dörr M, Böttcher D, Hollmann F, Rudroff F, Mihovilovic MD, Buryška T, Damborský J, Prokop Z, Badenhorst CPS, Bornscheuer UT. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 2020; 12:2032-2039. [PMID: 32362951 PMCID: PMC7188320 DOI: 10.1002/cctc.201901891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well-established GC-MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide-producing enzymes.
Collapse
Affiliation(s)
- Aşkın S. Aslan‐Üzel
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Andy Beier
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - David Kovář
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Clemens Cziegler
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | - Santosh K. Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life SciencesUniversity of HyderabadGachibowli500046India
| | - Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Mark Dörr
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Dominique Böttcher
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyDelft2629 HZ (TheNetherlands
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | | | - Tomáš Buryška
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Zbyněk Prokop
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| |
Collapse
|
5
|
Sun Z, Rokita SE. Toward a Halophenol Dehalogenase from Iodotyrosine Deiodinase via Computational Design. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Zuodong Sun
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| | - Steven E. Rokita
- Department of Chemistry, Johns Hopkins University, 3400 N. Charles St., Baltimore, Maryland 21218, United States
| |
Collapse
|
7
|
Dörr M, Fibinger MP, Last D, Schmidt S, Santos-Aberturas J, Böttcher D, Hummel A, Vickers C, Voss M, Bornscheuer UT. Fully automatized high-throughput enzyme library screening using a robotic platform. Biotechnol Bioeng 2016; 113:1421-32. [DOI: 10.1002/bit.25925] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Revised: 12/15/2015] [Accepted: 12/28/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Mark Dörr
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Michael P.C. Fibinger
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Daniel Last
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Sandy Schmidt
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Javier Santos-Aberturas
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Dominique Böttcher
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Anke Hummel
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Clare Vickers
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Moritz Voss
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology and Enzyme Catalysis; Institute of Biochemistry; Greifswald University; Felix-Hausdorff-Str. 4 Greifswald 17489 Germany
| |
Collapse
|