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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.
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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.
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Galmés MÀ, Nödling AR, He K, Luk LYP, Świderek K, Moliner V. Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases. Chem Sci 2022; 13:4779-4787. [PMID: 35655887 PMCID: PMC9067594 DOI: 10.1039/d2sc00778a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/14/2022] [Indexed: 11/29/2022] Open
Abstract
While there has been emerging interest in designing new enzymes to solve practical challenges, computer-based options to redesign catalytically active proteins are rather limited. Here, a rational QM/MM molecular dynamics strategy based on combining the best electrostatic properties of enzymes with activity in a common reaction is presented. The computational protocol has been applied to the re-design of the protein scaffold of an existing promiscuous esterase from Bacillus subtilis Bs2 to enhance its secondary amidase activity. After the alignment of Bs2 with a non-homologous amidase Candida antarctica lipase B (CALB) within rotation quaternions, a relevant spatial aspartate residue of the latter was transferred to the former as a means to favor the electrostatics of transition state formation, where a clear separation of charges takes place. Deep computational insights, however, revealed a significant conformational change caused by the amino acid replacement, provoking a shift in the pK a of the inserted aspartate and counteracting the anticipated catalytic effect. This prediction was experimentally confirmed with a 1.3-fold increase in activity. The good agreement between theoretical and experimental results, as well as the linear correlation between the electrostatic properties and the activation energy barriers, suggest that the presented computational-based investigation can transform in an enzyme engineering approach.
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Affiliation(s)
- Miquel À Galmés
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
| | - Alexander R Nödling
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Kaining He
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Louis Y P Luk
- School of Chemistry, Cardiff University Main Building, Park Pl Cardiff CF10 3AT UK +44 (0)29 2251 0161
| | - Katarzyna Świderek
- Department of Physical and Analytical Chemistry, Universitat Jaume I 12071 Castellón Spain +34 964728070
| | - Vicent Moliner
- BioComp Group, Institute of Advanced Materials (INAM), Universitat Jaume I 12071 Castellón Spain +34 964728084
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Galmés MÀ, Nödling AR, Luk L, Świderek K, Moliner V. Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes. ACS Catal 2021; 11:8635-8644. [PMID: 35875595 PMCID: PMC9299431 DOI: 10.1021/acscatal.1c02150] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
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Convergent evolution has resulted in nonhomologous enzymes that
contain similar active sites that catalyze the same primary and secondary
reactions. Comparing how these enzymes achieve their reaction promiscuity
can yield valuable insights to develop functions from the optimization
of latent activities. In this work, we have focused on the promiscuous
amidase activity in the esterase from Bacillus subtilis (Bs2) and compared with the same activity in the promiscuous lipase
B from Candida antarctica (CALB). The
study, combining multiscale quantum mechanics/molecular mechanics
(QM/MM) simulations, deep machine learning approaches, and experimental
characterization of Bs2 kinetics, confirms the amidase activity of
Bs2 and CALB. The computational results indicate that both enzymes
offer a slightly different reaction environment reflected by electrostatic
effects within the active site, thus resulting in a different reaction
mechanism during the acylation step. A convolutional neural network
(CNN) has been used to understand the conserved amino acids among
the evolved protein family and suggest that Bs2 provides a more robust
protein scaffold to perform future mutagenesis studies. Results derived
from this work will help reveal the origin of enzyme promiscuity,
which will find applications in enzyme (re)design, particularly in
creating a highly active amidase.
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Affiliation(s)
- Miquel À. Galmés
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Alexander R. Nödling
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Louis Luk
- Cardiff Catalysis Institute, School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Katarzyna Świderek
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
| | - Vicent Moliner
- Institute of Advanced Materials (INAM), Universitat Jaume I, 12071 Castellón, Spain
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Abstract
Hydrolytic enantioselective cleavage of different racemic non-steroidal anti-inflammatory drugs (NSAIDs) ester derivatives has been studied. An engineered esterase form Bacillus subtilis (BS2m) significantly outperformed homologous enzymes from Halomonas elongata (HeE) and Bacillus coagulants (BCE) in the enantioselective hydrolysis of naproxen esters. Structural analysis of the three active sites highlighted key differences which explained the substrate preference. Immobilization of a chimeric BS2m-T4 lysozyme fusion (BS2mT4L1) was improved by resin screening achieving twice the recovered activity (22.1 ± 5 U/g) with respect to what had been previously reported, and was utilized in a packed bed reactor. Continuous hydrolysis of α-methyl benzene acetic acid butyl ester as a model substrate was easily achieved, albeit at low concentration (1 mM). However, the high degree of insolubility of the naproxen butyl ester resulted in a slurry which could not be efficiently bioconverted, despite the addition of co-solvents and lower substrate concentration (1 mM). Addition of Triton® X-100 to the substrate mix yielded 24% molar conversion and 80% e.e. at a 5 mM scale with 5 min residence time and sufficient retention of catalytic efficiency after 6 h of use.
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Genetically Fused T4L Acts as a Shield in Covalent Enzyme Immobilisation Enhancing the Rescued Activity. Catalysts 2018. [DOI: 10.3390/catal8010040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Enzyme immobilisation is a common strategy to increase enzymes resistance and reusability in a variety of excellent ‘green’ applications. However, the interaction with the solid support often leads to diminished specific activity, especially when non-specific covalent binding to the carrier takes place which affects the delicate architecture of the enzyme. Here we developed a broadly applicable strategy where the T4-lysozyme (T4L) is genetically fused at the N-terminus of different enzymes and used as inert protein spacer which directly attaches to the carrier preventing shape distortion of the catalyst. Halomonas elongata aminotransferase (HEWT), Bacillus subtilis engineered esterase (BS2m), and horse liver alcohol dehydrogenase (HLADH) were used as model enzymes to elucidate the benefits of the spacer. While HEWT and HLADH activity and expression were diminished by the fused T4L, both enzymes retained almost quantitative activity after immobilisation. In the case of BS2m, the protective effect of the T4L effectively was important and led to up to 10-fold improvement in the rescued activity.
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Mechanism-Guided Discovery of an Esterase Scaffold with Promiscuous Amidase Activity. Catalysts 2016. [DOI: 10.3390/catal6060090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Gu J, Tong H, Ye L, Yu H. The role of aromatic residue W20 in the activity and enantioselectivity control of esterase BioH toward aryl substrate. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2015.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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López-Iglesias M, Gotor-Fernández V. Recent Advances in Biocatalytic Promiscuity: Hydrolase-Catalyzed Reactions for Nonconventional Transformations. CHEM REC 2015; 15:743-59. [PMID: 26147872 DOI: 10.1002/tcr.201500008] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Indexed: 01/03/2023]
Abstract
Enzymes have emerged in recent decades as ideal catalysts for synthetic transformations under mild reaction conditions. Their capacity to accelerate a myriad of biotransformations with high levels of selectivity and broad substrate specificity including excellent atom economy has led to a current full recognition. The six classes of enzymes (oxidoreductases, transferases, hydrolases, lyases, isomerases and ligases) possess outstanding abilities to perform specific modifications in target molecules. Nevertheless, in the last fifteen years, novel examples have appeared related to nonconventional processes catalyzed by various classes of biocatalysts. Amongst these, hydrolases have received special attention since they display remarkable activities in initially unexpected reactions such as carbon-carbon and carbon-heteroatom bond-formation reactions, oxidative processes and novel hydrolytic transformations. In this review, the main findings in this area will be disclosed, highlighting the catalytic properties of hydrolases not only to catalyze single processes but also multicomponent and tandem nonconventional reactions.
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Affiliation(s)
- María López-Iglesias
- Organic and Inorganic Chemistry Department, Biotechnology Institute of Asturias, Universidad de Oviedo, Avenida Julián Clavería s/n, Oviedo, 33006, Spain
| | - Vicente Gotor-Fernández
- Organic and Inorganic Chemistry Department, Biotechnology Institute of Asturias, Universidad de Oviedo, Avenida Julián Clavería s/n, Oviedo, 33006, Spain
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Hendil-Forssell P, Martinelle M, Syrén PO. Exploring water as building bricks in enzyme engineering. Chem Commun (Camb) 2015; 51:17221-4. [DOI: 10.1039/c5cc07162c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A de novo designed water pattern is used to achieve a 34-fold accelerated promiscuous enzyme catalysis by efficient transition state stabilization.
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Affiliation(s)
- Peter Hendil-Forssell
- KTH Royal Institute of Technology
- Division of Industrial Biotechnology
- AlbaNova University Centre
- 106 91 Stockholm
- Sweden
| | - Mats Martinelle
- KTH Royal Institute of Technology
- Division of Industrial Biotechnology
- AlbaNova University Centre
- 106 91 Stockholm
- Sweden
| | - Per-Olof Syrén
- KTH Royal Institute of Technology
- Division of Proteomics & Nanobiotechnology
- Science for Life Laboratory
- 171 21 Stockholm
- Sweden
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