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Browning DF, Hobman JL, Busby SJW. Laboratory strains of Escherichia coli K-12: things are seldom what they seem. Microb Genom 2023; 9:mgen000922. [PMID: 36745549 PMCID: PMC9997739 DOI: 10.1099/mgen.0.000922] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli K-12 was originally isolated 100 years ago and since then it has become an invaluable model organism and a cornerstone of molecular biology research. However, despite its pedigree, since its initial isolation E. coli K-12 has been repeatedly cultured, passaged and mutagenized, resulting in an organism that carries many genetic changes. To understand more about this important model organism, we have sequenced the genomes of two ancestral K-12 strains, WG1 and EMG2, considered to be the progenitors of many key laboratory strains. Our analysis confirms that these strains still carry genetic elements such as bacteriophage lambda (λ) and the F plasmid, but also indicates that they have undergone extensive laboratory-based evolution. Thus, scrutinizing the genomes of ancestral E. coli K-12 strains leads us to examine whether E. coli K-12 is a sufficiently robust model organism for 21st century microbiology.
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Affiliation(s)
- Douglas F Browning
- School of Biosciences, College of Health and Life Sciences, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - Jon L Hobman
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Loughborough LE12 5RD, UK
| | - Stephen J W Busby
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
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2
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Furutate S, Abe H, Tsuge T. Thermal properties of poly(3-hydroxy-2-methylbutyrate-co-3-hydroxybutyrate) copolymers with narrow comonomer-unit compositional distributions. Polym J 2021. [DOI: 10.1038/s41428-021-00545-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Scheel RA, Ho T, Kageyama Y, Masisak J, McKenney S, Lundgren BR, Nomura CT. Optimizing a Fed-Batch High-Density Fermentation Process for Medium Chain-Length Poly(3-Hydroxyalkanoates) in Escherichia coli. Front Bioeng Biotechnol 2021; 9:618259. [PMID: 33718339 PMCID: PMC7953831 DOI: 10.3389/fbioe.2021.618259] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/08/2021] [Indexed: 11/15/2022] Open
Abstract
Production of medium chain-length poly(3-hydroxyalkanoates) [PHA] polymers with tightly defined compositions is an important area of research to expand the application and improve the properties of these promising biobased and biodegradable materials. PHA polymers with homopolymeric or defined compositions exhibit attractive material properties such as increased flexibility and elasticity relative to poly(3-hydroxybutyrate) [PHB]; however, these polymers are difficult to biosynthesize in native PHA-producing organisms, and there is a paucity of research toward developing high-density cultivation methods while retaining compositional control. In this study, we developed and optimized a fed-batch fermentation process in a stirred tank reactor, beginning with the biosynthesis of poly(3-hydroxydecanoate) [PHD] from decanoic acid by β-oxidation deficient recombinant Escherichia coli LSBJ using glucose as a co-substrate solely for growth. Bacteria were cultured in two stages, a biomass accumulation stage (37°C, pH 7.0) with glucose as the primary carbon source and a PHA biosynthesis stage (30°C, pH 8.0) with co-feeding of glucose and a fatty acid. Through iterative optimizations of semi-defined media composition and glucose feed rate, 6.0 g of decanoic acid was converted to PHD with an 87.5% molar yield (4.54 g L-1). Stepwise increases in the amount of decanoic acid fed during the fermentation correlated with an increase in PHD, resulting in a final decanoic acid feed of 25 g converted to PHD at a yield of 89.4% (20.1 g L-1, 0.42 g L-1 h-1), at which point foaming became uncontrollable. Hexanoic acid, octanoic acid, 10-undecenoic acid, and 10-bromodecanoic acid were all individually supplemented at 20 g each and successfully polymerized with yields ranging from 66.8 to 99.0% (9.24 to 18.2 g L-1). Using this bioreactor strategy, co-fatty acid feeds of octanoic acid/decanoic acid and octanoic acid/10-azidodecanoic acid (8:2 mol ratio each) resulted in the production of their respective copolymers at nearly the same ratio and at high yield, demonstrating that these methods can be used to control PHA copolymer composition.
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Affiliation(s)
- Ryan A. Scheel
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Truong Ho
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Yuki Kageyama
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
- Division of Applied Chemistry, Department of Engineering, Hokkaido University, Sapporo, Japan
| | - Jessica Masisak
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Seamus McKenney
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Benjamin R. Lundgren
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
| | - Christopher T. Nomura
- Department of Chemistry, State University of New York College of Environmental Science and Forestry, Syracuse, NY, United States
- Department of Biological Sciences, College of Science, University of Idaho, Moscow, ID, United States
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Hernández Lozada NJ, Simmons TR, Xu K, Jindra MA, Pfleger BF. Production of 1-octanol in Escherichia coli by a high flux thioesterase route. Metab Eng 2020; 61:352-359. [PMID: 32707169 DOI: 10.1016/j.ymben.2020.07.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 07/07/2020] [Indexed: 10/23/2022]
Abstract
1-octanol is a valuable molecule in the chemical industry, where it is used as a plasticizer, as a precursor in the production of linear low-density polyethylene (LLDPE), and as a growth inhibitor of tobacco plant suckers. Due to the low availability of eight-carbon acyl chains in natural lipid feedstocks and the selectivity challenges in petrochemical routes to medium-chain fatty alcohols,1-octanol sells for the highest price among the fatty alcohol products. As an alternative, metabolic engineers have pursued sustainable 1-octanol production via engineered microbes. Here, we report demonstration of gram per liter titers in the model bacterium Escherichia coli via the development of a pathway composed of a thioesterase, an acyl-CoA synthetase, and an acyl-CoA reductase. In addition, the impact of deleting fermentative pathways was explored E. coli K12 MG1655 strain for production of octanoic acid, a key octanol precursor. In order to overcome metabolic flux barriers, bioprospecting experiments were performed to identify acyl-CoA synthetases with high activity towards octanoic acid and acyl-CoA reductases with high activity to produce 1-octanol from octanoyl-CoA. Titration of expression of key pathway enzymes was performed and a strain with the full pathway integrated on the chromosome was created. The final strain produced 1-octanol at 1.3 g/L titer and a >90% C8 specificity from glycerol. In addition to the metabolic engineering efforts, this work addressed some of the technical challenges that arise when quantifying 1-octanol produced from cultures grown under fully aerobic conditions where evaporation and stripping are prevalent.
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Affiliation(s)
- Néstor J Hernández Lozada
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Trevor R Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Ke Xu
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Michael A Jindra
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI, 53706, USA.
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Mehrer CR, Rand JM, Incha MR, Cook TB, Demir B, Motagamwala AH, Kim D, Dumesic JA, Pfleger BF. Growth-coupled bioconversion of levulinic acid to butanone. Metab Eng 2019; 55:92-101. [PMID: 31226347 PMCID: PMC6859897 DOI: 10.1016/j.ymben.2019.06.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 06/04/2019] [Accepted: 06/14/2019] [Indexed: 11/28/2022]
Abstract
Common strategies for conversion of lignocellulosic biomass to chemical products center on deconstructing biomass polymers into fermentable sugars. Here, we demonstrate an alternative strategy, a growth-coupled, high-yield bioconversion, by feeding cells a non-sugar substrate, by-passing central metabolism, and linking a key metabolic step to generation of acetyl-CoA that is required for biomass and energy generation. Specifically, we converted levulinic acid (LA), an established degradation product of lignocellulosic biomass, to butanone (a.k.a. methyl-ethyl ketone - MEK), a widely used industrial solvent. Our strategy combines a catabolic pathway from Pseudomonas putida that enables conversion of LA to 3-ketovaleryl-CoA, a CoA transferase that generates 3-ketovalerate and acetyl-CoA, and a decarboxylase that generates 2-butanone. By removing the ability of E. coli to consume LA and supplying excess acetate as a carbon source, we built a strain of E. coli that could convert LA to butanone at high yields, but at the cost of significant acetate consumption. Using flux balance analysis as a guide, we built a strain of E. coli that linked acetate assimilation to production of butanone. This strain was capable of complete bioconversion of LA to butanone with a reduced acetate requirement and increased specific productivity. To demonstrate the bioconversion on real world feedstocks, we produced LA from furfuryl alcohol, a compound readily obtained from biomass. These LA feedstocks were found to contain inhibitors that prevented cell growth and bioconversion of LA to butanone. We used a combination of column chromatography and activated carbon to remove the toxic compounds from the feedstock, resulting in LA that could be completely converted to butanone. This work motivates continued collaboration between chemical and biological catalysis researchers to explore alternative conversion pathways and the technical hurdles that prevent their rapid deployment.
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Affiliation(s)
- Christopher R Mehrer
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Jacqueline M Rand
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Matthew R Incha
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Taylor B Cook
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - Benginur Demir
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Ali Hussain Motagamwala
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Daniel Kim
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States
| | - James A Dumesic
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States; DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, United States.
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6
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Increased synthesis of poly(3-hydroxydodecanoate) by random mutagenesis of polyhydroxyalkanoate synthase. Appl Microbiol Biotechnol 2018; 102:7927-7934. [PMID: 30032431 DOI: 10.1007/s00253-018-9230-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/05/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
Abstract
Poly(3-hydroxydodecanoate) [P(3HDD)], a medium-chain-length polyhydroxyalkanoate (PHA), is expected to be used as a novel type of bioplastic characterized by a soft and transparent nature. In this study, to achieve a high yield of P(3HDD), PHA synthase was modified through random mutagenesis of a region of the PHA synthase 1 gene from Pseudomonas putida KT2440 (phaC1Pp). Screening of the mutant library using a β-oxidation-deficient Escherichia coli LSBJ was performed. As a result, four mutants, designated w10, w14, w309, and w311, were selected from 10,000 mutants. The w311 mutant had two amino acid replacements (E358G and N398S), and showed the highest production of P(3HDD) with increased polymer molecular weights when compared to the native enzyme. Saturation mutagenesis at the N398 position, which was found to be highly conserved among Pseudomonas PhaCs, revealed that amino acids with hydrophobic and smaller residues either retained or increased P(3HDD) production. This study demonstrates the benefit of using the PHA synthase mutants to enhance the production of P(3HDD).
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Mehrer CR, Incha MR, Politz MC, Pfleger BF. Anaerobic production of medium-chain fatty alcohols via a β-reduction pathway. Metab Eng 2018; 48:63-71. [PMID: 29807110 DOI: 10.1016/j.ymben.2018.05.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/11/2018] [Accepted: 05/23/2018] [Indexed: 11/17/2022]
Abstract
In this report, we identify the relevant factors to increase production of medium chain n-alcohols through an expanded view of the reverse β-oxidation pathway. We began by creating a base strain capable of producing medium chain n-alcohols from glucose using a redox-balanced and growth-coupled metabolic engineering strategy. By dividing the heterologous enzymes in the pathway into different modules, we were able to identify and evaluate homologs of each enzyme within the pathway and identify several capable of enhancing medium chain alcohol titers and/or selectivity. In general, the identity of the trans-2-enoyl-CoA reductase (TER) and the direct overexpression of the thiolase (FadA) and β-hydroxy-acyl-CoA reductase (FadB) improved alcohol titer and the identity of the FadBA complex influenced the dominant chain length. Next, we linked the anaerobically induced VHb promoter from Vitreoscilla hemoglobin to each gene to remove the need for chemical inducers and ensure robust expression. The highest performing strain with the autoinduced reverse β-oxidation pathway produced n-alcohols at titers of 1.8 g/L with an apparent molar yield of 0.2 on glucose consumed in rich medium (52% of theoretical yield).
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Affiliation(s)
- Christopher R Mehrer
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Matthew R Incha
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Mark C Politz
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 3629 Engineering Hall, 1415 Engineering Drive, Madison, WI 53706, United States; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI 53706, United States.
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