1
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Naseri G, Koffas MAG. Application of combinatorial optimization strategies in synthetic biology. Nat Commun 2020; 11:2446. [PMID: 32415065 PMCID: PMC7229011 DOI: 10.1038/s41467-020-16175-y] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 04/15/2020] [Indexed: 12/26/2022] Open
Abstract
In the first wave of synthetic biology, genetic elements, combined into simple circuits, are used to control individual cellular functions. In the second wave of synthetic biology, the simple circuits, combined into complex circuits, form systems-level functions. However, efforts to construct complex circuits are often impeded by our limited knowledge of the optimal combination of individual circuits. For example, a fundamental question in most metabolic engineering projects is the optimal level of enzymes for maximizing the output. To address this point, combinatorial optimization approaches have been established, allowing automatic optimization without prior knowledge of the best combination of expression levels of individual genes. This review focuses on current combinatorial optimization methods and emerging technologies facilitating their applications.
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Affiliation(s)
- Gita Naseri
- Institut für Chemie, Humboldt Universität zu Berlin, 12489, Berlin, Germany.
| | - Mattheos A G Koffas
- Center for Biotechnology, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, USA.
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
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2
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Wiltschi B, Cernava T, Dennig A, Galindo Casas M, Geier M, Gruber S, Haberbauer M, Heidinger P, Herrero Acero E, Kratzer R, Luley-Goedl C, Müller CA, Pitzer J, Ribitsch D, Sauer M, Schmölzer K, Schnitzhofer W, Sensen CW, Soh J, Steiner K, Winkler CK, Winkler M, Wriessnegger T. Enzymes revolutionize the bioproduction of value-added compounds: From enzyme discovery to special applications. Biotechnol Adv 2020; 40:107520. [DOI: 10.1016/j.biotechadv.2020.107520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 10/18/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
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3
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Kang SY, Heo KT, Hong YS. Optimization of Artificial Curcumin Biosynthesis in E. coli by Randomized 5'-UTR Sequences To Control the Multienzyme Pathway. ACS Synth Biol 2018; 7:2054-2062. [PMID: 30160937 DOI: 10.1021/acssynbio.8b00198] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One of the optimization strategies of an artificial biosynthetic metabolic flux with a multienzyme pathway is when the enzyme concentrations are present at the appropriate ratios rather than at their maximum expression. Thus, many recent research efforts have focused on the development of tools that fine-tune the enzyme expression, and these research efforts have facilitated the search for the optimum balance between pathway expression and cell viability. However, the rational approach has some limitations in finding the most optimized expression ratio in in vivo systems. In our study, we focused on fine-tuning the expression level of a six-enzyme reaction for the artificial biosynthesis of curcumin by screening a library of 5'-untranslational region (UTR) sequence mutants made by a multiplex automatic genome engineering (MAGE) tool. From the screening results, a variant (6M08rv) showed about a 38.2-fold improvement in the production of curcumin compared to the parent strain, in which the calculated expression levels of 4-coumarate:CoA ligase (4CL) and phenyldiketide-CoA synthase (DCS), two of the six enzymes, were much lower than those of the parent strain.
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Affiliation(s)
- Sun-Young Kang
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungbuk 28116, Korea
| | - Kyung Taek Heo
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungbuk 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34141, Korea
| | - Young-Soo Hong
- Anticancer Agents Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 30 Yeongudanji-ro, Ochang-eup, Cheongju-si, Chungbuk 28116, Korea
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon 34141, Korea
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4
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Garcia-Ruiz E, HamediRad M, Zhao H. Pathway Design, Engineering, and Optimization. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2018; 162:77-116. [PMID: 27629378 DOI: 10.1007/10_2016_12] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
The microbial metabolic versatility found in nature has inspired scientists to create microorganisms capable of producing value-added compounds. Many endeavors have been made to transfer and/or combine pathways, existing or even engineered enzymes with new function to tractable microorganisms to generate new metabolic routes for drug, biofuel, and specialty chemical production. However, the success of these pathways can be impeded by different complications from an inherent failure of the pathway to cell perturbations. Pursuing ways to overcome these shortcomings, a wide variety of strategies have been developed. This chapter will review the computational algorithms and experimental tools used to design efficient metabolic routes, and construct and optimize biochemical pathways to produce chemicals of high interest.
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Affiliation(s)
- Eva Garcia-Ruiz
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Mohammad HamediRad
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
- Departments of Chemistry, Biochemistry, and Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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5
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Abstract
When aiming to produce a target chemical at high yield, titer, and productivity, various combinations of genetic parts available to build the target pathway can generate a large number of strains for characterization. This engineering approach will become increasingly laborious and expensive when seeking to develop desirable strains for optimal production of a large space of biochemicals due to extensive screening. Our recent theoretical development of modular cell (MODCELL) design principles can offer a promising solution for rapid generation of optimal strains by coupling a modular cell with exchangeable production modules in a plug-and-play fashion. In this study, we experimentally validated some design properties of MODCELL by demonstrating the following: (i) a modular (chassis) cell is required to couple with a production module, a heterologous ethanol pathway, as a testbed, (ii) degree of coupling between the modular cell and production modules can be modulated to enhance growth and product synthesis, (iii) a modular cell can be used as a host to select an optimal pyruvate decarboxylase (PDC) of the ethanol production module and to help identify a hypothetical PDC protein, and (iv) adaptive laboratory evolution based on growth selection of the modular cell can enhance growth and product synthesis rates. We envision that the MODCELL design provides a powerful prototype for modular cell engineering to rapidly create optimal strains for synthesis of a large space of biochemicals.
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Affiliation(s)
- Brandon Wilbanks
- Department of Chemical and
Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Donovan S. Layton
- Department of Chemical and
Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Sergio Garcia
- Department of Chemical and
Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Cong T. Trinh
- Department of Chemical and
Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
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6
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Abstract
Biocontainment systems are crucial for preventing genetically modified organisms from escaping into natural ecosystems. Here, we describe the orthogonal ribosome biofirewall, which consists of an activation circuit and a degradation circuit. The activation circuit is a genetic AND gate based on activation of the encrypted pathway by the orthogonal ribosome in response to specific environmental signals. The degradation circuit is a genetic NOT gate with an output of I-SceI homing endonuclease, which conditionally degrades the orthogonal ribosome genes. We demonstrate that the activation circuit can be flexibly incorporated into genetic circuits and metabolic pathways for encryption. The plasmid-based encryption of the deoxychromoviridans pathway and the genome-based encryption of lacZ are tightly regulated and can decrease the expression to 7.3% and 7.8%, respectively. We validated the ability of the degradation circuit to decrease the expression levels of the target plasmids and the orthogonal rRNA (O-rRNA) plasmids to 0.8% in lab medium and 0.76% in nonsterile soil medium, respectively. Our orthogonal ribosome biofirewall is a versatile platform that can be useful in biosafety research and in the biotechnology industry.
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Affiliation(s)
- Bin Jia
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hao Qi
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Bing-Zhi Li
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Shuo Pan
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Duo Liu
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Hong Liu
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
| | - Yizhi Cai
- School
of Biological Sciences, University of Edinburgh, Daniel Rutherford Building G.24,
The King’s Buildings, Edinburgh EH9 3BF, United Kingdom
| | - Ying-Jin Yuan
- Key
Laboratory of Systems Bioengineering (Ministry of Education), School
of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, PR China
- SynBio
Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, PR China
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7
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Combinatorial pathway optimization for streamlined metabolic engineering. Curr Opin Biotechnol 2017; 47:142-151. [DOI: 10.1016/j.copbio.2017.06.014] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 06/19/2017] [Indexed: 11/20/2022]
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8
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Zhang MM, Wang Y, Ang EL, Zhao H. Engineering microbial hosts for production of bacterial natural products. Nat Prod Rep 2016; 33:963-87. [PMID: 27072804 PMCID: PMC4963277 DOI: 10.1039/c6np00017g] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Covering up to end 2015Microbial fermentation provides an attractive alternative to chemical synthesis for the production of structurally complex natural products. In most cases, however, production titers are low and need to be improved for compound characterization and/or commercial production. Owing to advances in functional genomics and genetic engineering technologies, microbial hosts can be engineered to overproduce a desired natural product, greatly accelerating the traditionally time-consuming strain improvement process. This review covers recent developments and challenges in the engineering of native and heterologous microbial hosts for the production of bacterial natural products, focusing on the genetic tools and strategies for strain improvement. Special emphasis is placed on bioactive secondary metabolites from actinomycetes. The considerations for the choice of host systems will also be discussed in this review.
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Affiliation(s)
- Mingzi M Zhang
- Metabolic Engineering Research Laboratory, Science and Engineering Institutes, Agency for Science, Technology and Research, Singapore
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9
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Jin P, Kang Z, Zhang J, Zhang L, Du G, Chen J. Combinatorial Evolution of Enzymes and Synthetic Pathways Using One-Step PCR. ACS Synth Biol 2016; 5:259-68. [PMID: 26751617 DOI: 10.1021/acssynbio.5b00240] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA engineering is the fundamental motive driving the rapid development of modern biotechnology. Here, we present a versatile evolution method termed "rapidly efficient combinatorial oligonucleotides for directed evolution" (RECODE) for rapidly introducing multiple combinatorial mutations to the target DNA by combined action of a thermostable high-fidelity DNA polymerase and a thermostable DNA Ligase in one reaction system. By applying this method, we rapidly constructed a variant library of the rpoS promoters (with activity of 8-460%), generated a novel heparinase from the highly specific leech hyaluronidase (with more than 30 mutant residues) and optimized the heme biosynthetic pathway by combinatorial evolution of regulatory elements and pathway enzymes (2500 ± 120 mg L(-1) with 20-fold increase). The simple RECODE method enabled researchers the unparalleled ability to efficiently create diverse mutant libraries for rapid evolution and optimization of enzymes and synthetic pathways.
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Affiliation(s)
- Peng Jin
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Zhen Kang
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
- The
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry
of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Junli Zhang
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Linpei Zhang
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Guocheng Du
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
- The
Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry
of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Jian Chen
- The
Key Laboratory of Industrial Biotechnology, Ministry of Education,
School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Synergetic
Innovation Center of Food Safety and Nutrition, Jiangnan University, Wuxi, Jiangsu 214122, China
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10
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Gourinchas G, Busto E, Killinger M, Richter N, Wiltschi B, Kroutil W. A synthetic biology approach for the transformation of l-α-amino acids to the corresponding enantiopure (R)- or (S)-α-hydroxy acids. Chem Commun (Camb) 2015; 51:2828-31. [PMID: 25574527 DOI: 10.1039/c4cc08286a] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Combinatorial assembly and variation of promoters on a single expression plasmid allowed the balance of the catalytic steps of a three enzyme (l-AAD, HIC, FDH) cascade in E. coli. The designer cell catalyst quantitatively transformed l-amino acids to the corresponding optically pure (R)- and (S)-α-hydroxy acids at up to 200 mM substrate concentration.
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Affiliation(s)
- Geoffrey Gourinchas
- Austrian Centre of Industrial Biotechnology (ACIB), Petersgasse 14, 8010 Graz, Austria.
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11
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Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng 2015; 31:13-21. [DOI: 10.1016/j.ymben.2015.06.006] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 12/17/2022]
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12
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Luo Y, Li BZ, Liu D, Zhang L, Chen Y, Jia B, Zeng BX, Zhao H, Yuan YJ. Engineered biosynthesis of natural products in heterologous hosts. Chem Soc Rev 2015; 44:5265-90. [PMID: 25960127 PMCID: PMC4510016 DOI: 10.1039/c5cs00025d] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. However, the native producers often suffer from low productivity and titers. Here we summarize the recent applications of heterologous biosynthesis for the production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. In addition, we will discuss the new tools and strategies at multi-scale levels including gene, pathway, genome and community levels for highly efficient heterologous biosynthesis of natural products.
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Affiliation(s)
- Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China.
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13
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Exploring the potential impact of an expanded genetic code on protein function. Proc Natl Acad Sci U S A 2015; 112:6961-6. [PMID: 26038548 DOI: 10.1073/pnas.1507741112] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With few exceptions, all living organisms encode the same 20 canonical amino acids; however, it remains an open question whether organisms with additional amino acids beyond the common 20 might have an evolutionary advantage. Here, we begin to test that notion by making a large library of mutant enzymes in which 10 structurally distinct noncanonical amino acids were substituted at single sites randomly throughout TEM-1 β-lactamase. A screen for growth on the β-lactam antibiotic cephalexin afforded a unique p-acrylamido-phenylalanine (AcrF) mutation at Val-216 that leads to an increase in catalytic efficiency by increasing kcat, but not significantly affecting KM. To understand the structural basis for this enhanced activity, we solved the X-ray crystal structures of the ligand-free mutant enzyme and of the deacylation-defective wild-type and mutant cephalexin acyl-enzyme intermediates. These structures show that the Val-216-AcrF mutation leads to conformational changes in key active site residues-both in the free enzyme and upon formation of the acyl-enzyme intermediate-that lower the free energy of activation of the substrate transacylation reaction. The functional changes induced by this mutation could not be reproduced by substitution of any of the 20 canonical amino acids for Val-216, indicating that an expanded genetic code may offer novel solutions to proteins as they evolve new activities.
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14
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Reddy TR, Kelsall EJ, Fevat LMS, Munson SE, Cowley SM. Differential requirements of singleplex and multiplex recombineering of large DNA constructs. PLoS One 2015; 10:e0125533. [PMID: 25954970 PMCID: PMC4425527 DOI: 10.1371/journal.pone.0125533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022] Open
Abstract
Recombineering is an in vivo genetic engineering technique involving homologous recombination mediated by phage recombination proteins. The use of recombineering methodology is not limited by size and sequence constraints and therefore has enabled the streamlined construction of bacterial strains and multi-component plasmids. Recombineering applications commonly utilize singleplex strategies and the parameters are extensively tested. However, singleplex recombineering is not suitable for the modification of several loci in genome recoding and strain engineering exercises, which requires a multiplex recombineering design. Defining the main parameters affecting multiplex efficiency especially the insertion of multiple large genes is necessary to enable efficient large-scale modification of the genome. Here, we have tested different recombineering operational parameters of the lambda phage Red recombination system and compared singleplex and multiplex recombineering of large gene sized DNA cassettes. We have found that optimal multiplex recombination required long homology lengths in excess of 120 bp. However, efficient multiplexing was possible with only 60 bp of homology. Multiplex recombination was more limited by lower amounts of DNA than singleplex recombineering and was greatly enhanced by use of phosphorothioate protection of DNA. Exploring the mechanism of multiplexing revealed that efficient recombination required co-selection of an antibiotic marker and the presence of all three Red proteins. Building on these results, we substantially increased multiplex efficiency using an ExoVII deletion strain. Our findings elucidate key differences between singleplex and multiplex recombineering and provide important clues for further improving multiplex recombination efficiency.
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Affiliation(s)
- Thimma R. Reddy
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - Emma J. Kelsall
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - Léna M. S. Fevat
- Center for Fisheries, Environment and Aquaculture Sciences, Lowestoft, NR33 0HT, United Kingdom
| | - Sarah E. Munson
- ES Cell Facility, Center for Core Biotechnology Services, Leicester, LE1 9HN, United Kingdom
| | - Shaun M. Cowley
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, United Kingdom
- * E-mail:
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15
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Eckdahl TT, Campbell AM, Heyer LJ, Poet JL, Blauch DN, Snyder NL, Atchley DT, Baker EJ, Brown M, Brunner EC, Callen SA, Campbell JS, Carr CJ, Carr DR, Chadinha SA, Chester GI, Chester J, Clarkson BR, Cochran KE, Doherty SE, Doyle C, Dwyer S, Edlin LM, Evans RA, Fluharty T, Frederick J, Galeota-Sprung J, Gammon BL, Grieshaber B, Gronniger J, Gutteridge K, Henningsen J, Isom B, Itell HL, Keffeler EC, Lantz AJ, Lim JN, McGuire EP, Moore AK, Morton J, Nakano M, Pearson SA, Perkins V, Parrish P, Pierson CE, Polpityaarachchige S, Quaney MJ, Slattery A, Smith KE, Spell J, Spencer M, Taye T, Trueblood K, Vrana CJ, Whitesides ET. Programmed evolution for optimization of orthogonal metabolic output in bacteria. PLoS One 2015; 10:e0118322. [PMID: 25714374 PMCID: PMC4340930 DOI: 10.1371/journal.pone.0118322] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Current use of microbes for metabolic engineering suffers from loss of metabolic output due to natural selection. Rather than combat the evolution of bacterial populations, we chose to embrace what makes biological engineering unique among engineering fields - evolving materials. We harnessed bacteria to compute solutions to the biological problem of metabolic pathway optimization. Our approach is called Programmed Evolution to capture two concepts. First, a population of cells is programmed with DNA code to enable it to compute solutions to a chosen optimization problem. As analog computers, bacteria process known and unknown inputs and direct the output of their biochemical hardware. Second, the system employs the evolution of bacteria toward an optimal metabolic solution by imposing fitness defined by metabolic output. The current study is a proof-of-concept for Programmed Evolution applied to the optimization of a metabolic pathway for the conversion of caffeine to theophylline in E. coli. Introduced genotype variations included strength of the promoter and ribosome binding site, plasmid copy number, and chaperone proteins. We constructed 24 strains using all combinations of the genetic variables. We used a theophylline riboswitch and a tetracycline resistance gene to link theophylline production to fitness. After subjecting the mixed population to selection, we measured a change in the distribution of genotypes in the population and an increased conversion of caffeine to theophylline among the most fit strains, demonstrating Programmed Evolution. Programmed Evolution inverts the standard paradigm in metabolic engineering by harnessing evolution instead of fighting it. Our modular system enables researchers to program bacteria and use evolution to determine the combination of genetic control elements that optimizes catabolic or anabolic output and to maintain it in a population of cells. Programmed Evolution could be used for applications in energy, pharmaceuticals, chemical commodities, biomining, and bioremediation.
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Affiliation(s)
- Todd T. Eckdahl
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
- * E-mail:
| | - A. Malcolm Campbell
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Laurie J. Heyer
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Jeffrey L. Poet
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - David N. Blauch
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America
| | - Nicole L. Snyder
- Department of Chemistry, Davidson College, Davidson, North Carolina, United States of America
| | - Dustin T. Atchley
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erich J. Baker
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Micah Brown
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Elizabeth C. Brunner
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sean A. Callen
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jesse S. Campbell
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Caleb J. Carr
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - David R. Carr
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Spencer A. Chadinha
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Grace I. Chester
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Josh Chester
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Ben R. Clarkson
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kelly E. Cochran
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Shannon E. Doherty
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Catherine Doyle
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sarah Dwyer
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Linnea M. Edlin
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Rebecca A. Evans
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Taylor Fluharty
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Janna Frederick
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jonah Galeota-Sprung
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Betsy L. Gammon
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Brandon Grieshaber
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jessica Gronniger
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Katelyn Gutteridge
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Joel Henningsen
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Bradley Isom
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Hannah L. Itell
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erica C. Keffeler
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Andrew J. Lantz
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Jonathan N. Lim
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Erin P. McGuire
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Alexander K. Moore
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Jerrad Morton
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Meredith Nakano
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Sara A. Pearson
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Virginia Perkins
- Department of Computer Science, Math and Physics, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Phoebe Parrish
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Claire E. Pierson
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Sachith Polpityaarachchige
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Michael J. Quaney
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Abagael Slattery
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kathryn E. Smith
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Jackson Spell
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Morgan Spencer
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
| | - Telavive Taye
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - Kamay Trueblood
- Department of Biology, Missouri Western State University, Saint Joseph, Missouri, United States of America
| | - Caroline J. Vrana
- Department of Biology, Davidson College, Davidson, North Carolina, United States of America
| | - E. Tucker Whitesides
- Department of Mathematics and Computer Science, Davidson College, Davidson, North Carolina, United States of America
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