1
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Küng C, Vanella R, Nash MA. Directed evolution of Rhodotorula gracilisd-amino acid oxidase using single-cell hydrogel encapsulation and ultrahigh-throughput screening. REACT CHEM ENG 2023; 8:1960-1968. [PMID: 37496730 PMCID: PMC10366730 DOI: 10.1039/d3re00002h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/15/2023] [Indexed: 07/28/2023]
Abstract
Engineering catalytic and biophysical properties of enzymes is an essential step en route to advanced biomedical and industrial applications. Here, we developed a high-throughput screening and directed evolution strategy relying on single-cell hydrogel encapsulation to enhance the performance of d-Amino acid oxidase from Rhodotorula gracilis (RgDAAOx), a candidate enzyme for cancer therapy. We used a cascade reaction between RgDAAOx variants surface displayed on yeast and horseradish peroxidase (HRP) in the bulk media to trigger enzyme-mediated crosslinking of phenol-bearing fluorescent alginate macromonomers, resulting in hydrogel formation around single yeast cells. The fluorescent hydrogel capsules served as an artificial phenotype and basis for pooled library screening by fluorescence activated cell sorting (FACS). We screened a RgDAAOx variant library containing ∼106 clones while lowering the d-Ala substrate concentration over three sorting rounds in order to isolate variants with low Km. After three rounds of FACS sorting and regrowth, we isolated and fully characterized four variants displayed on the yeast surface. We identified variants with a more than 5-fold lower Km than the parent sequence, with an apparent increase in substrate binding affinity. The mutations we identified were scattered across the RgDAAOx structure, demonstrating the difficulty in rationally predicting allosteric sites and highlighting the advantages of scalable library screening technologies for evolving catalytic enzymes.
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Affiliation(s)
- Christoph Küng
- Institute of Physical Chemistry, Department of Chemistry, University of Basel 4058 Basel Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich 4058 Basel Switzerland
| | - Rosario Vanella
- Institute of Physical Chemistry, Department of Chemistry, University of Basel 4058 Basel Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich 4058 Basel Switzerland
| | - Michael A Nash
- Institute of Physical Chemistry, Department of Chemistry, University of Basel 4058 Basel Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich 4058 Basel Switzerland
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2
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Morellon-Sterling R, Tavano O, Bolivar JM, Berenguer-Murcia Á, Vela-Gutiérrez G, Sabir JSM, Tacias-Pascacio VG, Fernandez-Lafuente R. A review on the immobilization of pepsin: A Lys-poor enzyme that is unstable at alkaline pH values. Int J Biol Macromol 2022; 210:682-702. [PMID: 35508226 DOI: 10.1016/j.ijbiomac.2022.04.224] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 11/05/2022]
Abstract
Pepsin is a protease used in many different applications, and in many instances, it is utilized in an immobilized form to prevent contamination of the reaction product. This enzyme has two peculiarities that make its immobilization complex. The first one is related to the poor presence of primary amino groups on its surface (just one Lys and the terminal amino group). The second one is its poor stability at alkaline pH values. Both features make the immobilization of this enzyme to be considered a complicated goal, as most of the immobilization protocols utilize primary amino groups for immobilization. This review presents some of the attempts to get immobilized pepsin biocatalyst and their applications. The high density of anionic groups (Asp and Glu) make the anion exchange of the enzyme simpler, but this makes many of the strategies utilized to immobilize the enzyme (e.g., amino-glutaraldehyde supports) more related to a mixed ion exchange/hydrophobic adsorption than to real covalent immobilization. Finally, we propose some possibilities that can permit not only the covalent immobilization of this enzyme, but also their stabilization via multipoint covalent attachment.
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Affiliation(s)
- Roberto Morellon-Sterling
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Student of Departamento de Biología Molecular, Universidad Autónoma de Madrid, Darwin 2, Campus UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Olga Tavano
- Faculty of Nutrition, Alfenas Federal Univ., 700 Gabriel Monteiro da Silva St, Alfenas, MG 37130-000, Brazil
| | - Juan M Bolivar
- Chemical and Materials Engineering Department, Faculty of Chemical Sciences, Complutense University of Madrid, Complutense Ave., Madrid 28040, Spain
| | - Ángel Berenguer-Murcia
- Departamento de Química Inorgánica e Instituto Universitario de Materiales, Universidad de Alicante, Alicante, Spain
| | - Gilber Vela-Gutiérrez
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico
| | - Jamal S M Sabir
- Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Veymar G Tacias-Pascacio
- Facultad de Ciencias de la Nutrición y Alimentos, Universidad de Ciencias y Artes de Chiapas, Lib. Norte Pte. 1150, 29039 Tuxtla Gutiérrez, Chiapas, Mexico; Tecnológico Nacional de México, Instituto Tecnológico de Tuxtla Gutiérrez, Carretera Panamericana Km. 1080, 29050 Tuxtla Gutiérrez, Chiapas, Mexico.
| | - Roberto Fernandez-Lafuente
- Departamento de Biocatálisis, ICP-CSIC, Marie Curie 2, Campus UAM-CSIC Cantoblanco, 28049 Madrid, Spain; Center of Excellence in Bionanoscience Research, External Scientific Advisory Academics, King Abdulaziz University, Jeddah 21589, Saudi Arabia.
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3
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Roda S, Fernandez-Lopez L, Cañadas R, Santiago G, Ferrer M, Guallar V. Computationally Driven Rational Design of Substrate Promiscuity on Serine Ester Hydrolases. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Laura Fernandez-Lopez
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Rubén Cañadas
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Gerard Santiago
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
- Nostrum Biodiscovery S.L., Barcelona 08028, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid 28049, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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4
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Dhoke GV, Ensari Y, Hacibaloglu DY, Gärtner A, Ruff AJ, Bocola M, Davari MD. Reversal of Regioselectivity in Zinc-Dependent Medium-Chain Alcohol Dehydrogenase from Rhodococcus erythropolis toward Octanone Derivatives. Chembiochem 2020; 21:2957-2965. [PMID: 32415803 PMCID: PMC7689849 DOI: 10.1002/cbic.202000247] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Indexed: 12/24/2022]
Abstract
The zinc-dependent medium-chain alcohol dehydrogenase from Rhodococcus erythropolis (ReADH) is one of the most versatile biocatalysts for the stereoselective reduction of ketones to chiral alcohols. Despite its known broad substrate scope, ReADH only accepts carbonyl substrates with either a methyl or an ethyl group adjacent to the carbonyl moiety; this limits its use in the synthesis of the chiral alcohols that serve as a building blocks for pharmaceuticals. Protein engineering to expand the substrate scope of ReADH toward bulky substitutions next to carbonyl group (ethyl 2-oxo-4-phenylbutyrate) opens up new routes in the synthesis of ethyl-2-hydroxy-4-phenylbutanoate, an important intermediate for anti-hypertension drugs like enalaprilat and lisinopril. We have performed computer-aided engineering of ReADH toward ethyl 2-oxo-4-phenylbutyrate and octanone derivatives. W296, which is located in the small binding pocket of ReADH, sterically restricts the access of ethyl 2-oxo-4-phenylbutyrate, octan-3-one or octan-4-one toward the catalytic zinc ion and thereby limits ReADH activity. Computational analysis was used to identify position W296 and site-saturation mutagenesis (SSM) yielded an improved variant W296A with a 3.6-fold improved activity toward ethyl 2-oxo-4-phenylbutyrate when compared to WT ReADH (ReADH W296A: 17.10 U/mg and ReADH WT: 4.7 U/mg). In addition, the regioselectivity of ReADH W296A is shifted toward octanone substrates. ReADH W296A has a more than 16-fold increased activity toward octan-4-one (ReADH W296A: 0.97 U/mg and ReADH WT: 0.06 U/mg) and a more than 30-fold decreased activity toward octan-2-one (ReADH W296A: 0.23 U/mg and ReADH WT: 7.69 U/mg). Computational and experimental results revealed the role of position W296 in controlling the substrate scope and regiopreference of ReADH for a variety of carbonyl substrates.
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Affiliation(s)
- Gaurao V Dhoke
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Yunus Ensari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.,Kafkas University, Faculty of Engineering and Architecture, Department of Bioengineering, full address?, Kars, Turkey
| | - Dinc Yasat Hacibaloglu
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Anna Gärtner
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Anna Joëlle Ruff
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Marco Bocola
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Mehdi D Davari
- Lehrstuhl für Biotechnologie, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
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Haque RU, Paradisi F, Allers T. Haloferax volcanii for biotechnology applications: challenges, current state and perspectives. Appl Microbiol Biotechnol 2019; 104:1371-1382. [PMID: 31863144 PMCID: PMC6985049 DOI: 10.1007/s00253-019-10314-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 12/05/2019] [Accepted: 12/10/2019] [Indexed: 01/08/2023]
Abstract
Haloferax volcanii is an obligate halophilic archaeon with its origin in the Dead Sea. Simple laboratory culture conditions and a wide range of genetic tools have made it a model organism for studying haloarchaeal cell biology. Halophilic enzymes of potential interest to biotechnology have opened up the application of this organism in biocatalysis, bioremediation, nanobiotechnology, bioplastics and the biofuel industry. Functionally active halophilic proteins can be easily expressed in a halophilic environment, and an extensive genetic toolkit with options for regulated protein overexpression has allowed the purification of biotechnologically important enzymes from different halophiles in H. volcanii. However, corrosion mediated damage caused to stainless-steel bioreactors by high salt concentrations and a tendency to form biofilms when cultured in high volume are some of the challenges of applying H. volcanii in biotechnology. The ability to employ expressed active proteins in immobilized cells within a porous biocompatible matrix offers new avenues for exploiting H. volcanii in biotechnology. This review critically evaluates the various application potentials, challenges and toolkits available for using this extreme halophilic organism in biotechnology.
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Affiliation(s)
- R U Haque
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.,School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.,Warwick Integrative Synthetic Biology Centre, School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK
| | - F Paradisi
- School of Chemistry, University Park, University of Nottingham, Nottingham, NG7 2RD, UK.,Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - T Allers
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK.
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Cassidy J, Paradisi F. Haloquadratum walsbyi Yields a Versatile, NAD +/NADP + Dual Affinity, Thermostable, Alcohol Dehydrogenase (HwADH). Mol Biotechnol 2018; 60:420-426. [PMID: 29654471 DOI: 10.1007/s12033-018-0083-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This study presents the first example of an alcohol dehydrogenase (ADH) from the halophilic archaeum Haloquadratum walsbyi (HwADH). A hexahistidine-tagged recombinant HwADH was heterologously overexpressed in Haloferax volcanii. HwADH was purified in one step and was found to be thermophilic with optimal activity at 65 °C. HwADH was active in the presence of 10% (v/v) organic solvent. The enzyme displayed dual cofactor specificity and a broad substrate scope, and maximum activity was detected with benzyl alcohol and 2-phenyl-1-propanol. HwADH accepted aromatic ketones, acetophenone and phenylacetone as substrates. The enzyme also accepted cyclohexanol and aromatic secondary alcohols, 1-phenylethanol and 4-phenyl-2-butanol. H. walsbyi may offer an excellent alternative to other archaeal sources to expand the toolbox of halophilic biocatalysts.
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Affiliation(s)
- Jennifer Cassidy
- School of Chemistry, University of Nottingham, University Park, NG7 2RD, UK
- Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Francesca Paradisi
- School of Chemistry, University of Nottingham, University Park, NG7 2RD, UK.
- Synthesis and Solid State Pharmaceutical Centre (SSPC), School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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7
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Carucci C, Bruen L, Gascón V, Paradisi F, Magner E. Significant Enhancement of Structural Stability of the Hyperhalophilic ADH from Haloferax volcanii via Entrapment on Metal Organic Framework Support. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:8274-8280. [PMID: 29920206 DOI: 10.1021/acs.langmuir.8b01037] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The use of an in situ immobilization procedure for the immobilization of hyperhalophilic alcohol dehydrogenase in a metal organic framework material is described. The easy and rapid in situ immobilization process enables retention of activity over a broad range of pH and temperature together with a decrease in the halophilicity of the enzyme. The catalytic activity of the immobilized enzyme was studied in nonaqueous solvent mixtures with the highest retention of activity in aqueous solutions of methanol and acetonitrile. The approach demonstrates that this immobilization method can be extended to hyperhalophilic enzymes with enhancements in activity and stability.
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Affiliation(s)
- Cristina Carucci
- Department of Chemical Sciences, Bernal Institute , University of Limerick , Limerick V94 T9PX , Ireland
| | - Larah Bruen
- Centre for Synthesis and Chemical Biology , University College Dublin , Dublin 4 Ireland
| | - Victoria Gascón
- Department of Chemical Sciences, Bernal Institute , University of Limerick , Limerick V94 T9PX , Ireland
| | - Francesca Paradisi
- Centre for Synthesis and Chemical Biology , University College Dublin , Dublin 4 Ireland
- School of Chemistry , University of Nottingham , University Park Campus, Nottingham NG7 2RD , United Kingdom
| | - Edmond Magner
- Department of Chemical Sciences, Bernal Institute , University of Limerick , Limerick V94 T9PX , Ireland
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8
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Melis R, Rosini E, Pirillo V, Pollegioni L, Molla G. In vitro evolution of an l-amino acid deaminase active on l-1-naphthylalanine. Catal Sci Technol 2018. [DOI: 10.1039/c8cy01380b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
l-Amino acid deaminase from Proteus myxofaciens (PmaLAAD) is a promising biocatalyst for enantioselective biocatalysis that can be exploited to produce optically pure d-amino acids or α-keto acids.
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Affiliation(s)
- Roberta Melis
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Elena Rosini
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Valentina Pirillo
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Loredano Pollegioni
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
| | - Gianluca Molla
- Dipartimento di Biotecnologie e Scienze della Vita
- Università degli Studi dell'Insubria
- 21100 Varese
- Italy
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