1
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Van Gelder K, Lindner SN, Hanson AD, Zhou J. Strangers in a foreign land: 'Yeastizing' plant enzymes. Microb Biotechnol 2024; 17:e14525. [PMID: 39222378 PMCID: PMC11368087 DOI: 10.1111/1751-7915.14525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 07/02/2024] [Indexed: 09/04/2024] Open
Abstract
Expressing plant metabolic pathways in microbial platforms is an efficient, cost-effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour-intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost-effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data-driven machine learning framework designed to extract 'yeastizing' rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design-build-test cycle.
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Affiliation(s)
- Kristen Van Gelder
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Steffen N. Lindner
- Department of Systems and Synthetic MetabolismMax Planck Institute of Molecular Plant PhysiologyPotsdamGermany
- Department of BiochemistryCharité Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt‐UniversitätBerlinGermany
| | - Andrew D. Hanson
- Horticultural Sciences DepartmentUniversity of FloridaGainesvilleFloridaUSA
| | - Juannan Zhou
- Department of BiologyUniversity of FloridaGainesvilleFloridaUSA
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2
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Ononugbo CM, Shimura Y, Yamano-Adachi N, Omasa T, Koga Y. Rational design approach to improve the solubility of the β-sandwich domain 1 of a thermophilic protein. J Biosci Bioeng 2024:S1389-1723(24)00188-9. [PMID: 39074993 DOI: 10.1016/j.jbiosc.2024.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/28/2024] [Accepted: 06/20/2024] [Indexed: 07/31/2024]
Abstract
The β-sandwich domain 1 (SD1) of islandisin is a stable thermophilic protein with surface loops that can be redesigned for specific target binding, architecturally comparable to the variable domain of immunoglobulin (IgG). SD1's propensity to aggregate due to incorrect folding and subsequent accumulation in Escherichia coli inclusion bodies limits its use in biotechnological applications. We rationally designed SD1 for improved variants that were expressed in soluble forms in E. coli while maintaining the intrinsic thermal stability of the protein (melting temperature (Tm) = 73). We used FoldX's ΔΔG predictions to find beneficial mutations and aggregation-prone regions (APRs) using Tango. The S26K substitution within protein core residues did not affect protein stability. Among the soluble mutants studied, the S26K/Q91P combination significantly improved the expression and solubility of SD1. We also examined the effects of the surface residue, pH, and concentration on the solubility of SD1. We showed that the surface polarity of proteins had little or no effect on solubility, whereas surface charges played a substantial role. The storage stability of several SD1 variants was impaired at pH values near their isoelectric point, and pH levels resulting in highly charged groups. We observed that mutations that create an uneven distribution of charged groups on the SD1 surface could enhance protein solubility by eliminating favorable protein-protein surface charge interactions. Our findings suggest that SD1 is mutationally tolerant to new functionalities, thus providing a novel perspective for the application of rational design to improve the solubility of targeted proteins.
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Affiliation(s)
- Chukwuebuka M Ononugbo
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yusaku Shimura
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Noriko Yamano-Adachi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Omasa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yuichi Koga
- Department of Applied Chemistry, Faculty of Engineering, Okayama University of Science, 1-1 Ridaicho, Kitaku, Okayama 700-0005, Japan.
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3
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Ndochinwa OG, Wang QY, Amadi OC, Nwagu TN, Nnamchi CI, Okeke ES, Moneke AN. Current status and emerging frontiers in enzyme engineering: An industrial perspective. Heliyon 2024; 10:e32673. [PMID: 38912509 PMCID: PMC11193041 DOI: 10.1016/j.heliyon.2024.e32673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/25/2024] Open
Abstract
Protein engineering mechanisms can be an efficient approach to enhance the biochemical properties of various biocatalysts. Immobilization of biocatalysts and the introduction of new-to-nature chemical reactivities are also possible through the same mechanism. Discovering new protocols that enhance the catalytic active protein that possesses novelty in terms of being stable, active, and, stereoselectivity with functions could be identified as essential areas in terms of concurrent bioorganic chemistry (synergistic relationship between organic chemistry and biochemistry in the context of enzyme engineering). However, with our current level of knowledge about protein folding and its correlation with protein conformation and activities, it is almost impossible to design proteins with specific biological and physical properties. Hence, contemporary protein engineering typically involves reprogramming existing enzymes by mutagenesis to generate new phenotypes with desired properties. These processes ensure that limitations of naturally occurring enzymes are not encountered. For example, researchers have engineered cellulases and hemicellulases to withstand harsh conditions encountered during biomass pretreatment, such as high temperatures and acidic environments. By enhancing the activity and robustness of these enzymes, biofuel production becomes more economically viable and environmentally sustainable. Recent trends in enzyme engineering have enabled the development of tailored biocatalysts for pharmaceutical applications. For instance, researchers have engineered enzymes such as cytochrome P450s and amine oxidases to catalyze challenging reactions involved in drug synthesis. In addition to conventional methods, there has been an increasing application of machine learning techniques to identify patterns in data. These patterns are then used to predict protein structures, enhance enzyme solubility, stability, and function, forecast substrate specificity, and assist in rational protein design. In this review, we discussed recent trends in enzyme engineering to optimize the biochemical properties of various biocatalysts. Using examples relevant to biotechnology in engineering enzymes, we try to expatiate the significance of enzyme engineering with how these methods could be applied to optimize the biochemical properties of a naturally occurring enzyme.
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Affiliation(s)
- Obinna Giles Ndochinwa
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Qing-Yan Wang
- State Key Laboratory of Biomass Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Academy of Sciences, Nanning, Guangxi, China
| | - Oyetugo Chioma Amadi
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | - Tochukwu Nwamaka Nwagu
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
| | | | - Emmanuel Sunday Okeke
- Department of Biochemistry, Faculty of Biological Sciences & Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Enugu State, 410001, Nigeria
- Institute of Environmental Health and Ecological Security, School of the Environment and Safety, Jiangsu University, 301 Xuefu Rd., 212013, Zhenjiang, Jiangsu, China
| | - Anene Nwabu Moneke
- Department of Microbiology, Faculty of Biological Science, University of Nigeria, Nsukka, Nigeria
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4
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Orsi E, Schada von Borzyskowski L, Noack S, Nikel PI, Lindner SN. Automated in vivo enzyme engineering accelerates biocatalyst optimization. Nat Commun 2024; 15:3447. [PMID: 38658554 PMCID: PMC11043082 DOI: 10.1038/s41467-024-46574-4] [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: 12/21/2023] [Accepted: 03/04/2024] [Indexed: 04/26/2024] Open
Abstract
Achieving cost-competitive bio-based processes requires development of stable and selective biocatalysts. Their realization through in vitro enzyme characterization and engineering is mostly low throughput and labor-intensive. Therefore, strategies for increasing throughput while diminishing manual labor are gaining momentum, such as in vivo screening and evolution campaigns. Computational tools like machine learning further support enzyme engineering efforts by widening the explorable design space. Here, we propose an integrated solution to enzyme engineering challenges whereby ML-guided, automated workflows (including library generation, implementation of hypermutation systems, adapted laboratory evolution, and in vivo growth-coupled selection) could be realized to accelerate pipelines towards superior biocatalysts.
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Affiliation(s)
- Enrico Orsi
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | | | - Stephan Noack
- Institute of Bio- and Geosciences, IBG-1: Biotechnology, Forschungszentrum Jülich, 52425, Jülich, Germany
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Steffen N Lindner
- Max Planck Institute of Molecular Plant Physiology, 14476, Potsdam-Golm, Germany.
- Department of Biochemistry, Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität, 10117, Berlin, Germany.
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5
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Jansen S, Mayer C. A Robust Growth-Based Selection Platform to Evolve an Enzyme via Dependency on Noncanonical Tyrosine Analogues. JACS AU 2024; 4:1583-1590. [PMID: 38665651 PMCID: PMC11040555 DOI: 10.1021/jacsau.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 04/28/2024]
Abstract
Growth-based selections evaluate the fitness of individual organisms at a population level. In enzyme engineering, such growth selections allow for the rapid and straightforward identification of highly efficient biocatalysts from extensive libraries. However, selection-based improvement of (synthetically useful) biocatalysts is challenging, as they require highly dependable strategies that artificially link their activities to host survival. Here, we showcase a robust and scalable growth-based selection platform centered around the complementation of noncanonical amino acid-dependent bacteria. Specifically, we demonstrate how serial passaging of populations featuring millions of carbamoylase variants autonomously selects biocatalysts with up to 90,000-fold higher initial rates. Notably, selection of replicate populations enriched diverse biocatalysts, which feature distinct amino acid motifs that drastically boost carbamoylase activity. As beneficial substitutions also originated from unintended copying errors during library preparation or cell division, we anticipate that our growth-based selection platform will be applicable to the continuous, autonomous evolution of diverse biocatalysts in the future.
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Affiliation(s)
- Suzanne
C. Jansen
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
| | - Clemens Mayer
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747
AG Groningen, The
Netherlands
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6
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Reed KB, d'Oelsnitz S, Brooks SM, Wells J, Zhao M, Trivedi A, Eshraghi S, Alper HS. Fluorescence-Based Screens for Engineering Enzymes Linked to Halogenated Tryptophan. ACS Synth Biol 2024; 13:1373-1381. [PMID: 38533851 DOI: 10.1021/acssynbio.3c00616] [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] [Indexed: 03/28/2024]
Abstract
Directed evolution is often limited by the throughput of accurate screening methods. Here we demonstrate the feasibility of utilizing a singular transcription factor (TF)-system that can be refactored in two ways (both as an activator and repressor). Specifically, we showcase the use of previously evolved 5-halo- or 6-halo-tryptophan-specific TF biosensors suitable for the detection of a halogenated tryptophan molecule in vivo. We subsequently validate the biosensor's utility for two halogenase-specific halo-tryptophan accumulation screens. First, we isolated 5-tryptophan-halogenase, XsHal, from a mixed pool of halogenases with 100% efficiency. Thereafter, we generated a targeted library of the catalytic residue of 6-tryptophan halogenase, Th-Hal, and isolated functioning halogenases with 100% efficiency. Lastly, we refactor the TF circuit to respond to the depletion of halogenated tryptophan and prototype a high-throughput biosensor-directed evolution scheme to screen for downstream enzyme variants capable of promiscuously converting halogenated tryptophan. Altogether, this work takes a significant step toward the rapid and higher throughput screening of halogenases and halo-tryptophan converting enzymes to further reinforce efforts to enable high-level bioproduction of halogenated chemicals.
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Affiliation(s)
- Kevin B Reed
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Simon d'Oelsnitz
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
| | | | - Jordan Wells
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Minye Zhao
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Adit Trivedi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Selina Eshraghi
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E. Dean Keeton Street Stop C0400, Austin, Texas 78712, United States
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, Texas 78712, United States
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7
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Hasan WANBW, Nezhad NG, Yaacob MA, Salleh AB, Rahman RNZRA, Leow TC. Shifting the pH profiles of Staphylococcus epidermidis lipase (SEL) and Staphylococcus hyicus lipase (SHL) through generating chimeric lipases by DNA shuffling strategy. World J Microbiol Biotechnol 2024; 40:106. [PMID: 38386107 DOI: 10.1007/s11274-024-03927-x] [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: 11/11/2023] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Enzymes are often required to function in a particular reaction condition by the industrial procedure. In order to identify critical residues affecting the optimum pH of Staphylococcal lipases, chimeric lipases from homologous lipases were generated via a DNA shuffling strategy. Chimeric 1 included mutations of G166S, K212E, T243A, H271Y. Chimeric 2 consisted of substitutions of K212E, T243A, H271Y. Chimeric 3 contained substitutions of K212E, R359L. From the screening results, the pH profiles for chimeric 1 and 2 lipases were shifted from pH 7 to 6. While the pH of chimeric 3 was shifted to 8. It seems the mutation of K212E in chimeric 1 and 2 decreased the pH to 6 by changing the electrostatic potential surface. Furthermore, chimeric 3 showed 10 ˚C improvement in the optimum temperature due to the rigidification of the catalytic loop through the hydrophobic interaction network. Moreover, the substrate specificity of chimeric 1 and 2 was increased towards the longer carbon length chains due to the mutation of T243A adjacent to the lid region through increasing the flexibility of the lid. Current study illustrated that directed evolution successfully modified lipase properties including optimum pH, temperature and substrate specificity through mutations, especially near catalytic and lid regions.
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Affiliation(s)
- Wan Atiqah Najiah Binti Wan Hasan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Mohd Adilin Yaacob
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abdul Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, 43400 UPM, Selangor, Malaysia.
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8
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Joho Y, Vongsouthi V, Gomez C, Larsen JS, Ardevol A, Jackson CJ. Improving plastic degrading enzymes via directed evolution. Protein Eng Des Sel 2024; 37:gzae009. [PMID: 38713696 PMCID: PMC11091475 DOI: 10.1093/protein/gzae009] [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: 12/15/2023] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/09/2024] Open
Abstract
Plastic degrading enzymes have immense potential for use in industrial applications. Protein engineering efforts over the last decade have resulted in considerable enhancement of many properties of these enzymes. Directed evolution, a protein engineering approach that mimics the natural process of evolution in a laboratory, has been particularly useful in overcoming some of the challenges of structure-based protein engineering. For example, directed evolution has been used to improve the catalytic activity and thermostability of polyethylene terephthalate (PET)-degrading enzymes, although its use for the improvement of other desirable properties, such as solvent tolerance, has been less studied. In this review, we aim to identify some of the knowledge gaps and current challenges, and highlight recent studies related to the directed evolution of plastic-degrading enzymes.
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Affiliation(s)
- Yvonne Joho
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, Victoria 3168, Australia
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Vanessa Vongsouthi
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Chloe Gomez
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Joachim S Larsen
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Synthetic Biology, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
| | - Albert Ardevol
- Manufacturing, Commonwealth Scientific and Industrial Research Organisation, Research Way, Clayton, Victoria 3168, Australia
- CSIRO Advanced Engineering Biology Future Science Platform, GPO Box 1700, Canberra, ACT 2601, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Synthetic Biology, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Sullivans Creek Rd, Canberra, ACT 2601, Australia
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9
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Stock M, Gorochowski TE. Open-endedness in synthetic biology: A route to continual innovation for biological design. SCIENCE ADVANCES 2024; 10:eadi3621. [PMID: 38241375 DOI: 10.1126/sciadv.adi3621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Design in synthetic biology is typically goal oriented, aiming to repurpose or optimize existing biological functions, augmenting biology with new-to-nature capabilities, or creating life-like systems from scratch. While the field has seen many advances, bottlenecks in the complexity of the systems built are emerging and designs that function in the lab often fail when used in real-world contexts. Here, we propose an open-ended approach to biological design, with the novelty of designed biology being at least as important as how well it fulfils its goal. Rather than solely focusing on optimization toward a single best design, designing with novelty in mind may allow us to move beyond the diminishing returns we see in performance for most engineered biology. Research from the artificial life community has demonstrated that embracing novelty can automatically generate innovative and unexpected solutions to challenging problems beyond local optima. Synthetic biology offers the ideal playground to explore more creative approaches to biological design.
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Affiliation(s)
- Michiel Stock
- KERMIT & Biobix, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Thomas E Gorochowski
- School of Biological Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
- BrisEngBio, School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
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10
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Shelake RM, Pramanik D, Kim JY. CRISPR base editor-based targeted random mutagenesis (BE-TRM) toolbox for directed evolution. BMB Rep 2024; 57:30-39. [PMID: 38053292 PMCID: PMC10828429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 07/26/2023] [Accepted: 08/16/2023] [Indexed: 12/07/2023] Open
Abstract
Directed evolution (DE) of desired locus by targeted random mutagenesis (TRM) tools is a powerful approach for generating genetic variations with novel or improved functions, particularly in complex genomes. TRM-based DE involves developing a mutant library of targeted DNA sequences and screening the variants for the desired properties. However, DE methods have for a long time been confined to bacteria and yeasts. Lately, CRISPR/Cas and DNA deaminase-based tools that circumvent enduring barriers such as longer life cycle, small library sizes, and low mutation rates have been developed to facilitate DE in native genetic environments of multicellular organisms. Notably, deaminase-based base editing-TRM (BE-TRM) tools have greatly expanded the scope and efficiency of DE schemes by enabling base substitutions and randomization of targeted DNA sequences. BE-TRM tools provide a robust platform for the continuous molecular evolution of desired proteins, metabolic pathway engineering, creation of a mutant library of desired locus to evolve novel functions, and other applications, such as predicting mutants conferring antibiotic resistance. This review provides timely updates on the recent advances in BE-TRM tools for DE, their applications in biology, and future directions for further improvements. [BMB Reports 2024; 57(1): 30-39].
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Dibyajyoti Pramanik
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Korea
- Division of Life Science, Gyeongsang National University, Jinju 52828, Korea
- R&D Center, Nulla Bio Inc., Jinju 52828, Korea
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11
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Mao Y, Huang C, Zhou X, Han R, Deng Y, Zhou S. Genetically Encoded Biosensor Engineering for Application in Directed Evolution. J Microbiol Biotechnol 2023; 33:1257-1267. [PMID: 37449325 PMCID: PMC10619561 DOI: 10.4014/jmb.2304.04031] [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: 04/20/2023] [Revised: 06/03/2023] [Accepted: 06/06/2023] [Indexed: 07/18/2023]
Abstract
Although rational genetic engineering is nowadays the favored method for microbial strain improvement, building up mutant libraries based on directed evolution for improvement is still in many cases the better option. In this regard, the demand for precise and efficient screening methods for mutants with high performance has stimulated the development of biosensor-based high-throughput screening strategies. Genetically encoded biosensors provide powerful tools to couple the desired phenotype to a detectable signal, such as fluorescence and growth rate. Herein, we review recent advances in engineering several classes of biosensors and their applications in directed evolution. Furthermore, we compare and discuss the screening advantages and limitations of two-component biosensors, transcription-factor-based biosensors, and RNA-based biosensors. Engineering these biosensors has focused mainly on modifying the expression level or structure of the biosensor components to optimize the dynamic range, specificity, and detection range. Finally, the applications of biosensors in the evolution of proteins, metabolic pathways, and genome-scale metabolic networks are described. This review provides potential guidance in the design of biosensors and their applications in improving the bioproduction of microbial cell factories through directed evolution.
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Affiliation(s)
- Yin Mao
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Chao Huang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Xuan Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Runhua Han
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yu Deng
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
| | - Shenghu Zhou
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, P.R. China
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12
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Chen JP, Gong JS, Su C, Li H, Xu ZH, Shi JS. Improving the soluble expression of difficult-to-express proteins in prokaryotic expression system via protein engineering and synthetic biology strategies. Metab Eng 2023; 78:99-114. [PMID: 37244368 DOI: 10.1016/j.ymben.2023.05.007] [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: 04/09/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023]
Abstract
Solubility and folding stability are key concerns for difficult-to-express proteins (DEPs) restricted by amino acid sequences and superarchitecture, resolved by the precise distribution of amino acids and molecular interactions as well as the assistance of the expression system. Therefore, an increasing number of tools are available to achieve efficient expression of DEPs, including directed evolution, solubilization partners, chaperones, and affluent expression hosts, among others. Furthermore, genome editing tools, such as transposons and CRISPR Cas9/dCas9, have been developed and expanded to construct engineered expression hosts capable of efficient expression ability of soluble proteins. Accounting for the accumulated knowledge of the pivotal factors in the solubility and folding stability of proteins, this review focuses on advanced technologies and tools of protein engineering, protein quality control systems, and the redesign of expression platforms in prokaryotic expression systems, as well as advances of the cell-free expression technologies for membrane proteins production.
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Affiliation(s)
- Jin-Ping Chen
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Gong
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China.
| | - Chang Su
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Heng Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China
| | - Zheng-Hong Xu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, School of Biotechnology, Jiangnan University, Wuxi, 214122, PR China; Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
| | - Jin-Song Shi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, PR China; Yixing Institute of Food and Biotechnology Co., Ltd, Yixing, 214200, PR China
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13
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Recent developments in the engineering of Rubisco activase for enhanced crop yield. Biochem Soc Trans 2023; 51:627-637. [PMID: 36929563 DOI: 10.1042/bst20221281] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023]
Abstract
Rubisco activase (RCA) catalyzes the release of inhibitory sugar phosphates from ribulose-1,6-biphosphate carboxylase/oxygenase (Rubisco) and can play an important role in biochemical limitations of photosynthesis under dynamic light and elevated temperatures. There is interest in increasing RCA activity to improve crop productivity, but a lack of understanding about the regulation of photosynthesis complicates engineering strategies. In this review, we discuss work relevant to improving RCA with a focus on advances in understanding the structural cause of RCA instability under heat stress and the regulatory interactions between RCA and components of photosynthesis. This reveals substantial variation in RCA thermostability that can be influenced by single amino acid substitutions, and that engineered variants can perform better in vitro and in vivo under heat stress. In addition, there are indications RCA activity is controlled by transcriptional, post-transcriptional, post-translational, and spatial regulation, which may be important for balancing between carbon fixation and light capture. Finally, we provide an overview of findings from recent field experiments and consider the requirements for commercial validation as part of efforts to increase crop yields in the face of global climate change.
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14
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Bierbaumer S, Nattermann M, Schulz L, Zschoche R, Erb TJ, Winkler CK, Tinzl M, Glueck SM. Enzymatic Conversion of CO 2: From Natural to Artificial Utilization. Chem Rev 2023; 123:5702-5754. [PMID: 36692850 PMCID: PMC10176493 DOI: 10.1021/acs.chemrev.2c00581] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Enzymatic carbon dioxide fixation is one of the most important metabolic reactions as it allows the capture of inorganic carbon from the atmosphere and its conversion into organic biomass. However, due to the often unfavorable thermodynamics and the difficulties associated with the utilization of CO2, a gaseous substrate that is found in comparatively low concentrations in the atmosphere, such reactions remain challenging for biotechnological applications. Nature has tackled these problems by evolution of dedicated CO2-fixing enzymes, i.e., carboxylases, and embedding them in complex metabolic pathways. Biotechnology employs such carboxylating and decarboxylating enzymes for the carboxylation of aromatic and aliphatic substrates either by embedding them into more complex reaction cascades or by shifting the reaction equilibrium via reaction engineering. This review aims to provide an overview of natural CO2-fixing enzymes and their mechanistic similarities. We also discuss biocatalytic applications of carboxylases and decarboxylases for the synthesis of valuable products and provide a separate summary of strategies to improve the efficiency of such processes. We briefly summarize natural CO2 fixation pathways, provide a roadmap for the design and implementation of artificial carbon fixation pathways, and highlight examples of biocatalytic cascades involving carboxylases. Additionally, we suggest that biochemical utilization of reduced CO2 derivates, such as formate or methanol, represents a suitable alternative to direct use of CO2 and provide several examples. Our discussion closes with a techno-economic perspective on enzymatic CO2 fixation and its potential to reduce CO2 emissions.
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Affiliation(s)
- Sarah Bierbaumer
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Maren Nattermann
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Luca Schulz
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | | | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Christoph K Winkler
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
| | - Matthias Tinzl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch Straße 10, 35043 Marburg, Germany
| | - Silvia M Glueck
- Institute of Chemistry, University of Graz, NAWI Graz, Heinrichstraße 28, 8010 Graz, Austria
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Woolley M, Chen Z. A PCR-free rapid protocol for one-pot construction of highly diverse genetic libraries. PLoS One 2022; 17:e0276338. [PMID: 36315516 PMCID: PMC9621413 DOI: 10.1371/journal.pone.0276338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 10/04/2022] [Indexed: 11/05/2022] Open
Abstract
In vitro protein display methods can access extensive libraries (e.g., 1012-1014) and play an increasingly important role in protein engineering. However, the preparation of large libraries remains a laborious and time-consuming process. Here we report an efficient one-pot ligation & elongation (L&E) method for sizeable synthetic library preparation free of PCR amplification or any purification steps. As a proof of concept, we constructed an ankyrin repeat protein templated synthetic library with 1011 variants in 150 μL volume. The entire process from the oligos to DNA template ready for transcription is linearly scalable and took merely 90 minutes. We believe this L&E method can significantly simplify the preparation of synthetic libraries and accelerate in vitro protein display experiments.
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Affiliation(s)
- Michael Woolley
- Microbial Pathogenesis and Immunology Department, Texas A&M Health Science Center, Bryan, Texas, United States of America
| | - Zhilei Chen
- Microbial Pathogenesis and Immunology Department, Texas A&M Health Science Center, Bryan, Texas, United States of America
- * E-mail:
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16
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High-throughput approaches to functional characterization of genetic variation in yeast. Curr Opin Genet Dev 2022; 76:101979. [PMID: 36075138 DOI: 10.1016/j.gde.2022.101979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022]
Abstract
Expansion of sequencing efforts to include thousands of genomes is providing a fundamental resource for determining the genetic diversity that exists in a population. Now, high-throughput approaches are necessary to begin to understand the role these genotypic changes play in affecting phenotypic variation. Saccharomyces cerevisiae maintains its position as an excellent model system to determine the function of unknown variants with its exceptional genetic diversity, phenotypic diversity, and reliable genetic manipulation tools. Here, we review strategies and techniques developed in yeast that scale classic approaches of assessing variant function. These approaches improve our ability to better map quantitative trait loci at a higher resolution, even for rare variants, and are already providing greater insight into the role that different types of mutations play in phenotypic variation and evolution not just in yeast but across taxa.
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