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Chen Y, Boggess EE, Ocasio ER, Warner A, Kerns L, Drapal V, Gossling C, Ross W, Gourse RL, Shao Z, Dickerson J, Mansell TJ, Jarboe LR. Reverse engineering of fatty acid-tolerant Escherichia coli identifies design strategies for robust microbial cell factories. Metab Eng 2020; 61:120-130. [PMID: 32474056 DOI: 10.1016/j.ymben.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 02/05/2020] [Accepted: 05/02/2020] [Indexed: 10/24/2022]
Abstract
Adaptive laboratory evolution is often used to improve the performance of microbial cell factories. Reverse engineering of evolved strains enables learning and subsequent incorporation of novel design strategies via the design-build-test-learn cycle. Here, we reverse engineer a strain of Escherichia coli previously evolved for increased tolerance of octanoic acid (C8), an attractive biorenewable chemical, resulting in increased C8 production, increased butanol tolerance, and altered membrane properties. Here, evolution was determined to have occurred first through the restoration of WaaG activity, involved in the production of lipopolysaccharides, then an amino acid change in RpoC, a subunit of RNA polymerase, and finally mutation of the BasS-BasR two component system. All three mutations were required in order to reproduce the increased growth rate in the presence of 20 mM C8 and increased cell surface hydrophobicity; the WaaG and RpoC mutations both contributed to increased C8 titers, with the RpoC mutation appearing to be the major driver of this effect. Each of these mutations contributed to changes in the cell membrane. Increased membrane integrity and rigidity and decreased abundance of extracellular polymeric substances can be attributed to the restoration of WaaG. The increase in average lipid tail length can be attributed to the RpoCH419P mutation, which also confers tolerance to other industrially-relevant inhibitors, such as furfural, vanillin and n-butanol. The RpoCH419P mutation may impact binding or function of the stringent response alarmone ppGpp to RpoC site 1. Each of these mutations provides novel strategies for engineering microbial robustness, particularly at the level of the microbial cell membrane.
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Affiliation(s)
- Yingxi Chen
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Erin E Boggess
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA; Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Efrain Rodriguez Ocasio
- NSF Center for Biorenewable Chemicals (CBiRC) Research Experience for Undergraduates, Ames, IA, 50011, USA; Industrial Biotechnology Program, University of Puerto Rico Mayagüez, 00681, Puerto Rico
| | - Aric Warner
- Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Lucas Kerns
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Victoria Drapal
- NSF Center for Biorenewable Chemicals (CBiRC) Research Experience for Undergraduates, Ames, IA, 50011, USA; Department of Biological Systems Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68508, USA
| | - Chloe Gossling
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Wilma Ross
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Richard L Gourse
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Zengyi Shao
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Julie Dickerson
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA; Bioinformatics & Computational Biology Graduate Program, Iowa State University, Ames, IA, 50011, USA
| | - Thomas J Mansell
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA.
| | - Laura R Jarboe
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA; Interdepartmental Microbiology Graduate Program, Iowa State University, Ames, IA, 50011, USA.
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Megarity CF. Engineering enzyme catalysis: an inverse approach. Biosci Rep 2019; 39:BSR20181107. [PMID: 30700569 PMCID: PMC6900428 DOI: 10.1042/bsr20181107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 01/22/2019] [Accepted: 01/24/2019] [Indexed: 11/17/2022] Open
Abstract
Enzymes' inherent chirality confers their exquisite enantiomeric specificity and makes their use as green alternatives to chiral metal complexes or chiral organocatalysts invaluable to the fine chemical industry. The most prevalent way to alter enzyme activity in terms of regioselectivity and stereoselectivity for both industry and fundamental research is to engineer the enzyme. In a recent article by Keinänen et al., published in Bioscience Reports 2018, 'Controlling the regioselectivity and stereoselectivity of FAD-dependent polyamine oxidases with the use of amine-attached guide molecules as conformational modulators', an inverse approach was presented that focuses on the manipulation of the enzyme substrate rather than the enzyme. This approach not only uncovered dormant enantioselectivity in related enzymes but allowed for its control by the use of guide molecules simply added to the reaction solution or covalently linked to an achiral scaffold molecule.
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Affiliation(s)
- Clare F Megarity
- Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QR, U.K.
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Kim E, Leverage WT, Liu Y, Panzella L, Alfieri ML, Napolitano A, Bentley WE, Payne GF. Paraquat-Melanin Redox-Cycling: Evidence from Electrochemical Reverse Engineering. ACS Chem Neurosci 2016; 7:1057-67. [PMID: 27246915 DOI: 10.1021/acschemneuro.6b00007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Parkinson's disease is a neurodegenerative disorder associated with oxidative stress and the death of melanin-containing neurons of the substantia nigra. Epidemiological evidence links exposure to the pesticide paraquat (PQ) to Parkinson's disease, and this link has been explained by a redox cycling mechanism that induces oxidative stress. Here, we used a novel electrochemistry-based reverse engineering methodology to test the hypothesis that PQ can undergo reductive redox cycling with melanin. In this method, (i) an insoluble natural melanin (from Sepia melanin) and a synthetic model melanin (having a cysteinyldopamine-melanin core and dopamine-melanin shell) were entrapped in a nonconducting hydrogel film adjacent to an electrode, (ii) the film-coated electrode was immersed in solutions containing PQ (putative redox cycling reductant) and a redox cycling oxidant (ferrocene dimethanol), (iii) sequences of input potentials (i.e., voltages) were imposed to the underlying electrode to systematically engage reductive and oxidative redox cycling, and (iv) output response currents were analyzed for signatures of redox cycling. The response characteristics of the PQ-melanin systems to various input potential sequences support the hypothesis that PQ can directly donate electrons to melanin. This observation of PQ-melanin redox interactions demonstrates an association between two components that have been individually linked to oxidative stress and Parkinson's disease. Potentially, melanin's redox activity could be an important component in understanding the etiology of neurological disorders such as Parkinson's disease.
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Affiliation(s)
- Eunkyoung Kim
- Institute
for Bioscience and Biotechnology Research, University of Maryland 5115 Plant Sciences Building College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - W. Taylor Leverage
- Institute
for Bioscience and Biotechnology Research, University of Maryland 5115 Plant Sciences Building College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - Yi Liu
- Institute
for Bioscience and Biotechnology Research, University of Maryland 5115 Plant Sciences Building College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - Lucia Panzella
- Department
of Chemical Sciences, University of Naples Federico II Via Cintia
4, I-80126 Naples, Italy
| | - Maria Laura Alfieri
- Department
of Chemical Sciences, University of Naples Federico II Via Cintia
4, I-80126 Naples, Italy
| | - Alessandra Napolitano
- Department
of Chemical Sciences, University of Naples Federico II Via Cintia
4, I-80126 Naples, Italy
| | - William E. Bentley
- Institute
for Bioscience and Biotechnology Research, University of Maryland 5115 Plant Sciences Building College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
| | - Gregory F. Payne
- Institute
for Bioscience and Biotechnology Research, University of Maryland 5115 Plant Sciences Building College Park, Maryland 20742, United States
- Fischell
Department of Bioengineering University of Maryland, College Park, Maryland 20742, United States
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