1
|
Runda ME, de Kok NAW, Schmidt S. Rieske Oxygenases and Other Ferredoxin-Dependent Enzymes: Electron Transfer Principles and Catalytic Capabilities. Chembiochem 2023; 24:e202300078. [PMID: 36964978 DOI: 10.1002/cbic.202300078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/24/2023] [Accepted: 03/24/2023] [Indexed: 03/27/2023]
Abstract
Enzymes that depend on sophisticated electron transfer via ferredoxins (Fds) exhibit outstanding catalytic capabilities, but despite decades of research, many of them are still not well understood or exploited for synthetic applications. This review aims to provide a general overview of the most important Fd-dependent enzymes and the electron transfer processes involved. While several examples are discussed, we focus in particular on the family of Rieske non-heme iron-dependent oxygenases (ROs). In addition to illustrating their electron transfer principles and catalytic potential, the current state of knowledge on structure-function relationships and the mode of interaction between the redox partner proteins is reviewed. Moreover, we highlight several key catalyzed transformations, but also take a deeper dive into their engineerability for biocatalytic applications. The overall findings from these case studies highlight the catalytic capabilities of these biocatalysts and could stimulate future interest in developing additional Fd-dependent enzyme classes for synthetic applications.
Collapse
Affiliation(s)
- Michael E Runda
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Niels A W de Kok
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sandy Schmidt
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| |
Collapse
|
2
|
Hecko S, Schiefer A, Badenhorst CPS, Fink MJ, Mihovilovic MD, Bornscheuer UT, Rudroff F. Enlightening the Path to Protein Engineering: Chemoselective Turn-On Probes for High-Throughput Screening of Enzymatic Activity. Chem Rev 2023; 123:2832-2901. [PMID: 36853077 PMCID: PMC10037340 DOI: 10.1021/acs.chemrev.2c00304] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Many successful stories in enzyme engineering are based on the creation of randomized diversity in large mutant libraries, containing millions to billions of enzyme variants. Methods that enabled their evaluation with high throughput are dominated by spectroscopic techniques due to their high speed and sensitivity. A large proportion of studies relies on fluorogenic substrates that mimic the chemical properties of the target or coupled enzymatic assays with an optical read-out that assesses the desired catalytic efficiency indirectly. The most reliable hits, however, are achieved by screening for conversions of the starting material to the desired product. For this purpose, functional group assays offer a general approach to achieve a fast, optical read-out. They use the chemoselectivity, differences in electronic and steric properties of various functional groups, to reduce the number of false-positive results and the analytical noise stemming from enzymatic background activities. This review summarizes the developments and use of functional group probes for chemoselective derivatizations, with a clear focus on screening for enzymatic activity in protein engineering.
Collapse
Affiliation(s)
- Sebastian Hecko
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Astrid Schiefer
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Christoffel P S Badenhorst
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Michael J Fink
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford St, Cambridge, Massachusetts 02138, United States
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| | - Uwe T Bornscheuer
- Institute of Biochemistry, Dept. of Biotechnology & Enzyme Catalysis, University of Greifswald, Felix-Hausdorff-Str. 4, 17489 Greifswald, Germany
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, OC-163, TU Wien, Getreidemarkt 9, 1060 Vienna, Austria
| |
Collapse
|
3
|
Osifalujo EA, Preston‐Herrera C, Betts PC, Satterwhite LR, Froese JT. Improving Toluene Dioxygenase Activity for Ester‐Functionalized Substrates through Enzyme Engineering. ChemistrySelect 2022. [DOI: 10.1002/slct.202200753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Cristina Preston‐Herrera
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
- Cristina Preston-Herrera Department of Chemistry and Chemical Biology Cornell University 122 Baker Laboratory Ithaca NY USA 14853
| | - Phillip C. Betts
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| | - Louis R. Satterwhite
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| | - Jordan T. Froese
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| |
Collapse
|
4
|
Preston-Herrera C, Jackson AS, Bachmann BO, Froese JT. Development and application of a high throughput assay system for the detection of Rieske dioxygenase activity. Org Biomol Chem 2021; 19:775-784. [PMID: 33439179 DOI: 10.1039/d0ob02412k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Herein we report the development of a new periodate-based reactive assay system for the fluorescent detection of the cis-diol metabolites produced by Rieske dioxygenases. This sensitive and diastereoselective assay system successfully evaluates the substrate scope of Rieske dioxygenases and determines the relative activity of a rationally designed Rieske dioxygenase variant library. The high throughput capacity of the assay system enables rapid and efficient substrate scope investigations and screening of large dioxygenase variant libraries.
Collapse
Affiliation(s)
| | - Aaron S Jackson
- Department of Chemistry, Ball State University, 2000 W Riverside Ave, Muncie, IN 47306, USA.
| | - Brian O Bachmann
- Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, TN 37235, USA
| | - Jordan T Froese
- Department of Chemistry, Ball State University, 2000 W Riverside Ave, Muncie, IN 47306, USA.
| |
Collapse
|
5
|
Abstract
On the occasion of Professor Frances H. Arnold's recent acceptance of the 2018 Nobel Prize in Chemistry, we honor her numerous contributions to the fields of directed evolution and biocatalysis. Arnold pioneered the development of directed evolution methods for engineering enzymes as biocatalysts. Her highly interdisciplinary research has provided a ground not only for understanding the mechanisms of enzyme evolution but also for developing commercially viable enzyme biocatalysts and biocatalytic processes. In this Account, we highlight some of her notable contributions in the past three decades in the development of foundational directed evolution methods and their applications in the design and engineering of enzymes with desired functions for biocatalysis. Her work has created a paradigm shift in the broad catalysis field.
Collapse
Affiliation(s)
- Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - S. B. Jennifer Kan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Huimin Zhao
- Departments of Chemical and Biomolecular Engineering, Chemistry, and Biochemistry, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
6
|
Halder JM, Nestl BM, Hauer B. Semirational Engineering of the Naphthalene Dioxygenase fromPseudomonassp. NCIB 9816-4 towards Selective Asymmetric Dihydroxylation. ChemCatChem 2017. [DOI: 10.1002/cctc.201701262] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Julia M. Halder
- Institute of Biochemistry and Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bettina M. Nestl
- Institute of Biochemistry and Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| | - Bernhard Hauer
- Institute of Biochemistry and Technical Biochemistry; Universitaet Stuttgart; Allmandring 31 70569 Stuttgart Germany
| |
Collapse
|
7
|
Wong TS, Wu N, Roccatano D, Zacharias M, Schwaneberg U. Sensitive Assay for Laboratory Evolution of Hydroxylases toward Aromatic and Heterocyclic Compounds. ACTA ACUST UNITED AC 2016; 10:246-52. [PMID: 15809320 DOI: 10.1177/1087057104273336] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Powerful directed evolution methods have been developed for tailoring proteins to our needs in industrial applications. Here, the authors report a medium-throughput assay system designed for screening mutant libraries of oxygenases capable of inserting a hydroxyl group into a C-H bond of aromatic or O-heterocyclic compounds and for exploring the substrate profile of oxygenases. The assay system is based on 4-aminoantipyrine (4-AAP), a colorimetric phenol detection reagent. By using 2 detection wavelengths (509 nm and 600 nm), the authors achieved a linear response from 50 to 800 μM phenol and standard deviations below 11% in 96-well plate assays. The monooxygenase P450 BM-3 and its F87A mutant were used as a model system for medium-throughput assay development, identification of novel substrates (e.g., phenoxytoluene, phenylallyether, and coumarone), and discovery of P450 BM-3 F87A mutants with 8-fold improvement in 3-phenoxytoluene hydroxylation activity. This activity increase was achieved by screening a saturation mutagenesis library of amino acid position Y51 using the 4-AAP protocol in the 96-well format.
Collapse
Affiliation(s)
- T S Wong
- International University Bremen (IUB), Campus Ring 8, 28759 Bremen, Germany
| | | | | | | | | |
Collapse
|
8
|
Lee JK, Ang EL, Zhao H. Probing the substrate specificity of aminopyrrolnitrin oxygenase (PrnD) by mutational analysis. J Bacteriol 2006; 188:6179-83. [PMID: 16923884 PMCID: PMC1595372 DOI: 10.1128/jb.00259-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular modeling and mutational analysis (site-directed mutagenesis and saturation mutagenesis) were used to probe the molecular determinants of the substrate specificity of aminopyrrolnitrin oxygenase (PrnD) from Pseudomonas fluorescens Pf-5. There are 17 putative substrate-contacting residues, and mutations at two of the positions, positions 312 and 277, could modulate the enzyme substrate specificity separately or in combination. Interestingly, several of the mutants obtained exhibited higher catalytic efficiency (approximately two- to sevenfold higher) with the physiological substrate aminopyrrolnitrin than the wild-type enzyme exhibited.
Collapse
Affiliation(s)
- Jung-Kul Lee
- Department of Chemical and Biomolecular Engineering, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | | | | |
Collapse
|
9
|
Abstract
Image-based screening (IBS) has proven itself with whole-well assays in which throughput and assay miniaturization are priorities. Recent interest, however, has centered upon the use of automated imaging technology to conduct assays at subcellular resolution. These in vitro assays have the potential to increase lead quality at early stages in drug discovery. Subcellular IBS is not yet mature and, although some assays provide reliable data at reasonable throughput, many others have yet to demonstrate robust application. Developments in image acquisition, analysis and informatics technologies are ongoing and are expected to broaden the usefulness of subcellular IBS.
Collapse
Affiliation(s)
- Peter Ramm
- Invicta Research Inc., 290 Riverview Boulevard, St Catharines, ON L2T 3N4, Canada.
| |
Collapse
|
10
|
Sondossi M, Barriault D, Sylvestre M. Metabolism of 2,2'- and 3,3'-dihydroxybiphenyl by the biphenyl catabolic pathway of Comamonas testosteroni B-356. Appl Environ Microbiol 2004; 70:174-81. [PMID: 14711640 PMCID: PMC321272 DOI: 10.1128/aem.70.1.174-181.2004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The purpose of this investigation was to examine the capacity of the biphenyl catabolic enzymes of Comamonas testosteroni B-356 to metabolize dihydroxybiphenyls symmetrically substituted on both rings. Data show that 3,3'-dihydroxybiphenyl is by far the preferred substrate for strain B-356. However, the dihydrodiol metabolite is very unstable and readily tautomerizes to a dead-end metabolite or is dehydroxylated by elimination of water. The tautomerization route is the most prominent. Thus, a very small fraction of the substrate is converted to other hydroxylated and acidic metabolites. Although 2,2'-dihydroxybiphenyl is a poor substrate for strain B-356 biphenyl dioxygenase, metabolites were produced by the biphenyl catabolic enzymes, leading to production of 2-hydroxybenzoic acid. Data show that the major route of metabolism involves, as a first step, a direct dehydroxylation of one of the ortho-substituted carbons to yield 2,3,2'-trihydroxybiphenyl. However, other metabolites resulting from hydroxylation of carbons 5 and 6 of 2,2'-dihydroxybiphenyl were also produced, leading to dead-end metabolites.
Collapse
Affiliation(s)
- M Sondossi
- Department of Microbiology, Weber State University, Ogden, Utah 84408, USA
| | | | | |
Collapse
|
11
|
Barriault D, Plante MM, Sylvestre M. Family shuffling of a targeted bphA region to engineer biphenyl dioxygenase. J Bacteriol 2002; 184:3794-800. [PMID: 12081948 PMCID: PMC135170 DOI: 10.1128/jb.184.14.3794-3800.2002] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this work we used a new strategy designed to reduce the size of the library that needs to be explored in family shuffling to evolve new biphenyl dioxygenases (BPDOs). Instead of shuffling the whole gene, we have targeted a fragment of bphA that is critical for enzyme specificity. We also describe a new protocol to screen for more potent BPDOs that is based on the detection of catechol metabolites from chlorobiphenyls. Several BphA variants with extended potency to degrade polychlorinated biphenyls (PCBs) were obtained by shuffling critical segments of bphA genes from Burkholderia sp. strain LB400, Comamonas testosteroni B-356, and Rhodococcus globerulus P6. Unlike all parents, these variants exhibited high activity toward 2,2'-, 3,3'-, and 4,4'-dichlorobiphenyls and were able to oxygenate the very persistent 2,6-dichlorobiphenyl. The data showed that the replacement of a short segment (335TFNNIRI341) of LB400 BphA by the corresponding segment (333GINTIRT339) of B-356 BphA or P6 BphA contributes to relax the enzyme toward PCB substrates.
Collapse
Affiliation(s)
- Diane Barriault
- Institut National de la Recherche Scientifique INRS-Institut Armand-Frappier, Université du Québec, Pointe-Claire, Canada
| | | | | |
Collapse
|
12
|
Abstract
Oxygenase enzymes have seen limited practical applications because of their complexity, poor stabilities, and often low catalytic rates. However, their ability to perform difficult chemistry with high selectivity and specificity has kept oxygenases at the forefront of engineering efforts. Growing understanding of structure-function relationships and improved protein engineering methods are paving the way for applications of oxygenases in chemical synthesis and bioremediation.
Collapse
Affiliation(s)
- Patrick C Cirino
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | | |
Collapse
|
13
|
Abstract
In vitro recombination of homologous genes (family shuffling) has been proposed as an effective search strategy for laboratory evolution of genes and proteins. Few data are available, however, on the composition of shuffled gene libraries, from which one could assess the efficiency of recombination and optimize protocols. Here, probe hybridization is used in a macroarray format to analyze chimeric DNA libraries created by DNA shuffling. Characterization of hundreds of shuffled genes encoding dioxygenases has elucidated important biases in the shuffling reaction. As expected, crossovers are favored in regions of high sequence identity. A sequence-based model of homologous recombination that captures this observed bias was formulated using the experimental results. The chimeric genes were found to show biases in the incorporation of sequences from certain parents, even before selection. Statistically different patterns of parental incorporation in genes expressing functional proteins can help to identify key sequence-function relationships.
Collapse
Affiliation(s)
- John M Joern
- Division of Chemistry and Chemical Engineering 210-41, California Institute of Technology, Pasadena, CA 91125, USA
| | | | | |
Collapse
|
14
|
Sakamoto T, Joern JM, Arisawa A, Arnold FH. Laboratory evolution of toluene dioxygenase to accept 4-picoline as a substrate. Appl Environ Microbiol 2001; 67:3882-7. [PMID: 11525981 PMCID: PMC93105 DOI: 10.1128/aem.67.9.3882-3887.2001] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We are using directed evolution to extend the range of dioxygenase-catalyzed biotransformations to include substrates that are either poorly accepted or not accepted at all by the naturally occurring enzymes. Here we report on the oxidation of a heterocyclic substrate, 4-picoline, by toluene dioxygenase (TDO) and improvement of the enzyme's activity by laboratory evolution. The biotransformation of 4-picoline proceeds at only approximately 4.5% of the rate of the natural reaction on toluene. Random mutagenesis, saturation mutagenesis, and screening directly for product formation using a modified Gibbs assay generated mutant TDO 3-B38, in which the wild-type stop codon was replaced with a codon encoding threonine. Escherichia coli-expressed TDO 3-B38 exhibited 5.6 times higher activity toward 4-picoline and approximately 20% more activity towards toluene than wild-type TDO. The product of the biotransformation of 4-picoline is 3-hydroxy-4-picoline; no cis-diols of 4-picoline were observed.
Collapse
Affiliation(s)
- T Sakamoto
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | | | | | | |
Collapse
|