1
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Banerjee D, Yunus IS, Wang X, Kim J, Srinivasan A, Menchavez R, Chen Y, Gin JW, Petzold CJ, Martin HG, Magnuson JK, Adams PD, Simmons BA, Mukhopadhyay A, Kim J, Lee TS. Genome-scale and pathway engineering for the sustainable aviation fuel precursor isoprenol production in Pseudomonas putida. Metab Eng 2024; 82:157-170. [PMID: 38369052 DOI: 10.1016/j.ymben.2024.02.004] [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: 07/28/2023] [Revised: 01/10/2024] [Accepted: 02/10/2024] [Indexed: 02/20/2024]
Abstract
Sustainable aviation fuel (SAF) will significantly impact global warming in the aviation sector, and important SAF targets are emerging. Isoprenol is a precursor for a promising SAF compound DMCO (1,4-dimethylcyclooctane) and has been produced in several engineered microorganisms. Recently, Pseudomonas putida has gained interest as a future host for isoprenol bioproduction as it can utilize carbon sources from inexpensive plant biomass. Here, we engineer metabolically versatile host P. putida for isoprenol production. We employ two computational modeling approaches (Bilevel optimization and Constrained Minimal Cut Sets) to predict gene knockout targets and optimize the "IPP-bypass" pathway in P. putida to maximize isoprenol production. Altogether, the highest isoprenol production titer from P. putida was achieved at 3.5 g/L under fed-batch conditions. This combination of computational modeling and strain engineering on P. putida for an advanced biofuels production has vital significance in enabling a bioproduction process that can use renewable carbon streams.
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ian S Yunus
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xi Wang
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jinho Kim
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aparajitha Srinivasan
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Russel Menchavez
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jennifer W Gin
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Hector Garcia Martin
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Paul D Adams
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Energy Processes & Materials Division, Pacific Northwest National Laboratory, Richland, WA, 99354, USA.
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis St., Emeryville, CA, 94608, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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2
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Froning M, Grütering C, Blank LM, Hayen H. Determination of double bond positions in methyl ketones by gas chromatography-mass spectrometry using dimethyl disulfide derivatives. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9457. [PMID: 36512472 DOI: 10.1002/rcm.9457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
RATIONALE Methyl ketones are of interest for the application as biofuels. The fatty acid metabolism of different microbes has been rearranged to achieve a sustainable production of methyl ketones. The biofuel properties and possible further chemical modifications of these methyl ketones are influenced by their chain length, as well as their degree of saturation and the corresponding double bond position. METHODS A method based on gas chromatography-electron ionization; mass spectrometry (GC-EI-MS) was used to determine the double bond position of methyl ketones. Derivatization using dimethyl disulfide (DMDS) and an iodine catalyst enabled the activation of the double bonds for selective fragmentation during electron ionization. The cleavage led to key fragments in the Orbitrap high-resolution mass spectrum and allowed the unequivocal localization of the double bond position of the respective monounsaturated methyl ketone. RESULTS The double bond position of several medium chain length methyl ketones originating from the gram-negative bacterium Pseudomonas taiwanensis (P. taiwanensis) VLB120 was determined. The DMDS derivatives of methyl ketones can yield isobaric fragment ions for different possible double bond positions, which can be distinguished only using high-resolution MS. The double bond position of all methyl ketones deriving from P. taiwanensis VLB120 was the same, counting from the end of the aliphatic chain, and was determined as ω-7. CONCLUSIONS The derivatization of medium chain length monounsaturated methyl ketones with DMDS allowed the determination of the corresponding double bond position via GC-EI-MS. High-resolution MS is needed to differentiate possible double bond positions that yield isobaric fragment ions.
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Affiliation(s)
- Matti Froning
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
| | - Carolin Grütering
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Lars M Blank
- Institute of Applied Microbiology, Aachen Biology and Biotechnology, RWTH Aachen University, Aachen, Germany
| | - Heiko Hayen
- Institute of Inorganic and Analytical Chemistry, University of Münster, Münster, Germany
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3
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Ziegler AL, Grütering C, Poduschnick L, Mitsos A, Blank LM. Co-feeding enhances the yield of methyl ketones. J Ind Microbiol Biotechnol 2023; 50:kuad029. [PMID: 37704397 PMCID: PMC10521942 DOI: 10.1093/jimb/kuad029] [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: 04/12/2023] [Accepted: 09/11/2023] [Indexed: 09/15/2023]
Abstract
The biotechnological production of methyl ketones is a sustainable alternative to fossil-derived chemical production. To date, the best host for microbial production of methyl ketones is a genetically engineered Pseudomonas taiwanensis VLB120 ∆6 pProd strain, achieving yields of 101 mgg-1 on glucose in batch cultivations. For competitiveness with the petrochemical production pathway, however, higher yields are necessary. Co-feeding can improve the yield by fitting the carbon-to-energy ratio to the organism and the target product. In this work, we developed co-feeding strategies for P. taiwanensis VLB120 ∆6 pProd by combined metabolic modeling and experimental work. In a first step, we conducted flux balance analysis with an expanded genome-scale metabolic model of iJN1463 and found ethanol as the most promising among five cosubstrates. Next, we performed cultivations with ethanol and found the highest reported yield in batch production of methyl ketones with P. taiwanensis VLB120 to date, namely, 154 mg g-1 methyl ketones. However, ethanol is toxic to the cell, which reflects in a lower substrate consumption and lower product concentrations when compared to production on glucose. Hence, we propose cofeeding ethanol with glucose and find that, indeed, higher concentrations than in ethanol-fed cultivation (0.84 g Laq-1 with glucose and ethanol as opposed to 0.48 g Laq-1 with only ethanol) were achieved, with a yield of 85 mg g-1. In a last step, comparing experimental with computational results suggested the potential for improving the methyl ketone yield by fed-batch cultivation, in which cell growth and methyl ketone production are separated into two phases employing optimal ethanol to glucose ratios. ONE-SENTENCE SUMMARY By combining computational and experimental work, we demonstrate that feeding ethanol in addition to glucose improves the yield of biotechnologically produced methyl ketones.
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Affiliation(s)
- Anita L Ziegler
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
| | - Carolin Grütering
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, 52074 Aachen, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Leon Poduschnick
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, 52074 Aachen, Germany
| | - Alexander Mitsos
- JARA-ENERGY, 52056 Aachen, Germany
- Process Systems Engineering (AVT.SVT), RWTH Aachen University, 52074 Aachen, Germany
- Institute of Energy and Climate Research: Energy Systems Engineering (IEK-10), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), RWTH Aachen University, 52074 Aachen, Germany
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4
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Park MR, Gauttam R, Fong B, Chen Y, Lim HG, Feist AM, Mukhopadhyay A, Petzold CJ, Simmons BA, Singer SW. Revealing oxidative pentose metabolism in new Pseudomonas putida isolates. Environ Microbiol 2023; 25:493-504. [PMID: 36465038 PMCID: PMC10107873 DOI: 10.1111/1462-2920.16296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
The Pseudomonas putida group in the Gammaproteobacteria has been intensively studied for bioremediation and plant growth promotion. Members of this group have recently emerged as promising hosts to convert intermediates derived from plant biomass to biofuels and biochemicals. However, most strains of P. putida cannot metabolize pentose sugars derived from hemicellulose. Here, we describe three isolates that provide a broader view of the pentose sugar catabolism in the P. putida group. One of these isolates clusters with the well-characterized P. alloputida KT2440 (Strain BP6); the second isolate clustered with plant growth-promoting strain P. putida W619 (Strain M2), while the third isolate represents a new species in the group (Strain BP8). Each of these isolates possessed homologous genes for oxidative xylose catabolism (xylDXA) and a potential xylonate transporter. Strain M2 grew on arabinose and had genes for oxidative arabinose catabolism (araDXA). A CRISPR interference (CRISPRi) system was developed for strain M2 and identified conditionally essential genes for xylose growth. A glucose dehydrogenase was found to be responsible for initial oxidation of xylose and arabinose in strain M2. These isolates have illuminated inherent diversity in pentose catabolism in the P. putida group and may provide alternative hosts for biomass conversion.
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Affiliation(s)
- Mee-Rye Park
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rahul Gauttam
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Bonnie Fong
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hyun Gyu Lim
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Adam M Feist
- Joint BioEnergy Institute, Emeryville, California, USA
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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5
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Valencia LE, Incha MR, Schmidt M, Pearson AN, Thompson MG, Roberts JB, Mehling M, Yin K, Sun N, Oka A, Shih PM, Blank LM, Gladden J, Keasling JD. Engineering Pseudomonas putida KT2440 for chain length tailored free fatty acid and oleochemical production. Commun Biol 2022; 5:1363. [PMID: 36509863 PMCID: PMC9744835 DOI: 10.1038/s42003-022-04336-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/02/2022] [Indexed: 12/15/2022] Open
Abstract
Despite advances in understanding the metabolism of Pseudomonas putida KT2440, a promising bacterial host for producing valuable chemicals from plant-derived feedstocks, a strain capable of producing free fatty acid-derived chemicals has not been developed. Guided by functional genomics, we engineered P. putida to produce medium- and long-chain free fatty acids (FFAs) to titers of up to 670 mg/L. Additionally, by taking advantage of the varying substrate preferences of paralogous native fatty acyl-CoA ligases, we employed a strategy to control FFA chain length that resulted in a P. putida strain specialized in producing medium-chain FFAs. Finally, we demonstrate the production of oleochemicals in these strains by synthesizing medium-chain fatty acid methyl esters, compounds useful as biodiesel blending agents, in various media including sorghum hydrolysate at titers greater than 300 mg/L. This work paves the road to produce high-value oleochemicals and biofuels from cheap feedstocks, such as plant biomass, using this host.
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Affiliation(s)
- Luis E. Valencia
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Matthew R. Incha
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Matthias Schmidt
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.1957.a0000 0001 0728 696XInstitute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Allison N. Pearson
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Mitchell G. Thompson
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Jacob B. Roberts
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Marina Mehling
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Kevin Yin
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA
| | - Ning Sun
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,Advanced Biofuels and Bioproducts Process Demonstration Unit, Emeryville, CA 94608 USA
| | - Asun Oka
- grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,Advanced Biofuels and Bioproducts Process Demonstration Unit, Emeryville, CA 94608 USA
| | - Patrick M. Shih
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720 USA ,grid.184769.50000 0001 2231 4551Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Lars M. Blank
- grid.1957.a0000 0001 0728 696XInstitute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - John Gladden
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.474523.30000000403888279Biomanufacturing and Biomaterials Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Jay D. Keasling
- grid.451372.60000 0004 0407 8980Joint BioEnergy Institute, Emeryville, CA 94608 USA ,grid.184769.50000 0001 2231 4551Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Bioengineering, University of California, Berkeley, CA 94720 USA ,grid.47840.3f0000 0001 2181 7878Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA 94720 USA ,grid.5170.30000 0001 2181 8870Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark ,Center for Synthetic Biochemistry, Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technologies, Shenzhen, China
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6
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Czajka JJ, Banerjee D, Eng T, Menasalvas J, Yan C, Munoz NM, Poirier BC, Kim YM, Baker SE, Tang YJ, Mukhopadhyay A. Tuning a high performing multiplexed-CRISPRi Pseudomonas putida strain to further enhance indigoidine production. Metab Eng Commun 2022; 15:e00206. [PMID: 36158112 PMCID: PMC9494242 DOI: 10.1016/j.mec.2022.e00206] [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: 05/03/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/30/2022] Open
Abstract
In this study, a 14-gene edited Pseudomonas putida KT2440 strain for heterologous indigoidine production was examined using three distinct omic datasets. Transcriptomic data indicated that CRISPR/dCpf1-interference (CRISPRi) mediated multiplex repression caused global gene expression changes, implying potential undesirable changes in metabolic flux. 13C-metabolic flux analysis (13C-MFA) revealed that the core P. putida flux network after CRISPRi repression was conserved, with moderate reduction of TCA cycle and pyruvate shunt activity along with glyoxylate shunt activation during glucose catabolism. Metabolomic results identified a change in intracellular TCA metabolites and extracellular metabolite secretion profiles (sugars and succinate overflow) in the engineered strains. These omic analyses guided further strain engineering, with a random mutagenesis screen first identifying an optimal ribosome binding site (RBS) for Cpf1 that enabled stronger product-substrate pairing (1.6-fold increase). Then, deletion strains were constructed with excision of the PHA operon (ΔphaAZC-IID) resulting in a 2.2-fold increase in indigoidine titer over the optimized Cpf1-RBS construct at the end of the growth phase (∼6 h). The maximum indigoidine titer (at 72 h) in the ΔphaAZC-IID strain had a 1.5-fold and 1.8-fold increase compared to the optimized Cpf1-RBS construct and the original strain, respectively. Overall, this study demonstrated that integration of omic data types is essential for understanding responses to complex metabolic engineering designs and directly quantified the effect of such modifications on central metabolism.
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Affiliation(s)
- Jeffrey J Czajka
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Javier Menasalvas
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Chunsheng Yan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathalie Munoz Munoz
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Brenton C Poirier
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Young-Mo Kim
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.,Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Scott E Baker
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, 63130, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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7
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Zhang G, Zhang C, Wang Z, Wang Q, Nielsen J, Dai Z. Dual β-oxidation pathway and transcription factor engineering for methyl ketones production in Saccharomyces cerevisiae. Metab Eng 2022; 73:225-234. [PMID: 35987431 DOI: 10.1016/j.ymben.2022.08.004] [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: 05/14/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 10/15/2022]
Abstract
Methyl ketones (MK) are highly valuable fatty acid derivatives with broad applications. Microbes based biosynthesis represents an alternative route for production of these usually fossil based chemicals. In this study, we reported metabolic engineering of Saccharomyces cerevisiae to produce MK, including 2-nonanone, 2-undecanone, 2-tridecanone and 2-pentadecanone. Besides enhancing inherent peroxisomal fatty acids β-oxidation cycle, a novel heterologous cytosolic fatty acids β-oxidation pathway was constructed, and this resulted in an increased production of MK by 2-fold. To increase carbon fluxes to methyl ketones, the supply of precursors was enhanced by engineering lipid metabolism, including improving the intracellular biosynthesis of acyl-CoAs, weakening the consumption of acyl-CoAs for lipids storage, and reinforcing activation of free fatty acids to acyl-CoAs. Hereby the titer of MK was improved by 7-fold, reaching 143.72 mg/L. Finally, transcription factor engineering was employed to increase the biosynthesis of methyl ketones and it was found that overexpression of ADR1 can mimic the oleate activated biogenesis and proliferation of peroxisomes, which resulted in a further increased production of MK by 28%. With these modifications and optimization, up to 845 mg/L total MK were produced from glucose in fed-batch fermentation, which is the highest titer of methyl ketones reported produced by fungi.
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Affiliation(s)
- Ge Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Chao Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Zheng Wang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Qinhong Wang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Department of Biology and Biological Engineering, Chalmers University of Technology, SE 412 96, Gothenburg, Sweden.
| | - Zongjie Dai
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; National Technology Innovation Center of Synthetic Biology, Tianjin, 300308, China.
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8
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Complete Genome Sequences of Five Isolated Pseudomonas Strains that Catabolize Pentose Sugars and Aromatic Compounds Obtained from Lignocellulosic Biomass. Microbiol Resour Announc 2022; 11:e0098721. [PMID: 35377177 PMCID: PMC9022564 DOI: 10.1128/mra.00987-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We report on complete genome sequences of five Pseudomonas soil isolates that are capable of metabolizing pentose sugars and aromatic monomers. These complete genome sequence data provide insight into possible alternative hosts for the production of biofuels and bio-based chemicals from lignocellulosic feedstock.
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9
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Mortimer JC, Gilliham M. SpaceHort: redesigning plants to support space exploration and on-earth sustainability. Curr Opin Biotechnol 2021; 73:246-252. [PMID: 34563931 DOI: 10.1016/j.copbio.2021.08.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/09/2021] [Accepted: 08/31/2021] [Indexed: 12/21/2022]
Abstract
Crewed missions to Mars are planned within the next twenty years. Production of food and materials in situ will eventually be necessary for mission success. This will require the development of crops which can thrive in environments we can sustain in Space. Here, we discuss the challenges we must solve to provide adequate nutrition to support long term Space habitation. Further, we propose that plants are an ideal biomanufacturing platform for producing pharmaceuticals and biomaterials on demand. Designing Space plants requires advances in our ability to engineer plant biology in a predictive manner. Parallel development of suitable tightly controlled growth environments, including extensive monitoring and sensing, will also be a key enabler. Collectively, such research promises to deliver solutions for progressing sustainable closed environment agriculture on Earth.
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Affiliation(s)
- Jenny C Mortimer
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA.
| | - Matthew Gilliham
- School of Agriculture, Food and Wine & Waite Research Institute, University of Adelaide, Glen Osmond, SA, Australia.
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11
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Hao Z, Yogiswara S, Wei T, Benites VT, Sinha A, Wang G, Baidoo EEK, Ronald PC, Scheller HV, Loqué D, Eudes A. Expression of a bacterial 3-dehydroshikimate dehydratase (QsuB) reduces lignin and improves biomass saccharification efficiency in switchgrass (Panicum virgatum L.). BMC PLANT BIOLOGY 2021; 21:56. [PMID: 33478381 PMCID: PMC7819203 DOI: 10.1186/s12870-021-02842-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/13/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Lignin deposited in plant cell walls negatively affects biomass conversion into advanced bioproducts. There is therefore a strong interest in developing bioenergy crops with reduced lignin content or altered lignin structures. Another desired trait for bioenergy crops is the ability to accumulate novel bioproducts, which would enhance the development of economically sustainable biorefineries. As previously demonstrated in the model plant Arabidopsis, expression of a 3-dehydroshikimate dehydratase in plants offers the potential for decreasing lignin content and overproducing a value-added metabolic coproduct (i.e., protocatechuate) suitable for biological upgrading. RESULTS The 3-dehydroshikimate dehydratase QsuB from Corynebacterium glutamicum was expressed in the bioenergy crop switchgrass (Panicum virgatum L.) using the stem-specific promoter of an O-methyltransferase gene (pShOMT) from sugarcane. The activity of pShOMT was validated in switchgrass after observation in-situ of beta-glucuronidase (GUS) activity in stem nodes of plants carrying a pShOMT::GUS fusion construct. Under controlled growth conditions, engineered switchgrass lines containing a pShOMT::QsuB construct showed reductions of lignin content, improvements of biomass saccharification efficiency, and accumulated higher amount of protocatechuate compared to control plants. Attempts to generate transgenic switchgrass lines carrying the QsuB gene under the control of the constitutive promoter pZmUbi-1 were unsuccessful, suggesting possible toxicity issues associated with ectopic QsuB expression during the plant regeneration process. CONCLUSION This study validates the transfer of the QsuB engineering approach from a model plant to switchgrass. We have demonstrated altered expression of two important traits: lignin content and accumulation of a co-product. We found that the choice of promoter to drive QsuB expression should be carefully considered when deploying this strategy to other bioenergy crops. Field-testing of engineered QsuB switchgrass are in progress to assess the performance of the introduced traits and agronomic performances of the transgenic plants.
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Affiliation(s)
- Zhangying Hao
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Sasha Yogiswara
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Tong Wei
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
- Present address: State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, 518000 China
| | - Veronica Teixeira Benites
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Anagh Sinha
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - George Wang
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Edward E. K. Baidoo
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Pamela C. Ronald
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant Pathology and the Genome Center, University of California, Davis, CA 95616 USA
| | - Henrik V. Scheller
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Plant and Microbial Biology, University of California-Berkeley, Berkeley, CA 94720 USA
| | - Dominique Loqué
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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12
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Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl JP, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun 2020; 11:5385. [PMID: 33097726 PMCID: PMC7584609 DOI: 10.1038/s41467-020-19171-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brenda Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970, Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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13
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Thompson MG, Incha MR, Pearson AN, Schmidt M, Sharpless WA, Eiben CB, Cruz-Morales P, Blake-Hedges JM, Liu Y, Adams CA, Haushalter RW, Krishna RN, Lichtner P, Blank LM, Mukhopadhyay A, Deutschbauer AM, Shih PM, Keasling JD. Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing. Appl Environ Microbiol 2020; 86:e01665-20. [PMID: 32826213 PMCID: PMC7580535 DOI: 10.1128/aem.01665-20] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 12/13/2022] Open
Abstract
With its ability to catabolize a wide variety of carbon sources and a growing engineering toolkit, Pseudomonas putida KT2440 is emerging as an important chassis organism for metabolic engineering. Despite advances in our understanding of the organism, many gaps remain in our knowledge of the genetic basis of its metabolic capabilities. The gaps are particularly noticeable in our understanding of both fatty acid and alcohol catabolism, where many paralogs putatively coding for similar enzymes coexist, making biochemical assignment via sequence homology difficult. To rapidly assign function to the enzymes responsible for these metabolisms, we leveraged random barcode transposon sequencing (RB-Tn-Seq). Global fitness analyses of transposon libraries grown on 13 fatty acids and 10 alcohols produced strong phenotypes for hundreds of genes. Fitness data from mutant pools grown on fatty acids of varying chain lengths indicated specific enzyme substrate preferences and enabled us to hypothesize that DUF1302/DUF1329 family proteins potentially function as esterases. From the data, we also postulate catabolic routes for the two biogasoline molecules isoprenol and isopentanol, which are catabolized via leucine metabolism after initial oxidation and activation with coenzyme A (CoA). Because fatty acids and alcohols may serve as both feedstocks and final products of metabolic-engineering efforts, the fitness data presented here will help guide future genomic modifications toward higher titers, rates, and yields.IMPORTANCE To engineer novel metabolic pathways into P. putida, a comprehensive understanding of the genetic basis of its versatile metabolism is essential. Here, we provide functional evidence for the putative roles of hundreds of genes involved in the fatty acid and alcohol metabolism of the bacterium. These data provide a framework facilitating precise genetic changes to prevent product degradation and to channel the flux of specific pathway intermediates as desired.
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Affiliation(s)
- Mitchell G Thompson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
| | - Matthew R Incha
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Allison N Pearson
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Matthias Schmidt
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - William A Sharpless
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Christopher B Eiben
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Centro de Biotecnología FEMSA, Instituto Tecnológico y de Estudios Superiores de Monterrey, Monterrey, México
| | - Jacquelyn M Blake-Hedges
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Catharine A Adams
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Haushalter
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rohith N Krishna
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick Lichtner
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Lars M Blank
- Institute of Applied Microbiology (iAMB), Aachen Biology and Biotechnology (ABBt), RWTH Aachen University, Aachen, Germany
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Adam M Deutschbauer
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Patrick M Shih
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant Biology, University of California, Davis, California, USA
- Environmental and Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Joint Program in Bioengineering, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Institute for Quantitative Biosciences, University of California, Berkeley, California, USA
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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14
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Nies SC, Alter TB, Nölting S, Thiery S, Phan ANT, Drummen N, Keasling JD, Blank LM, Ebert BE. High titer methyl ketone production with tailored Pseudomonas taiwanensis VLB120. Metab Eng 2020; 62:84-94. [PMID: 32810591 DOI: 10.1016/j.ymben.2020.08.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 07/13/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022]
Abstract
Methyl ketones present a group of highly reduced platform chemicals industrially produced from petroleum-derived hydrocarbons. They find applications in the fragrance, flavor, pharmacological, and agrochemical industries, and are further discussed as biodiesel blends. In recent years, intense research has been carried out to achieve sustainable production of these molecules by re-arranging the fatty acid metabolism of various microbes. One challenge in the development of a highly productive microbe is the high demand for reducing power. Here, we engineered Pseudomonas taiwanensis VLB120 for methyl ketone production as this microbe has been shown to sustain exceptionally high NAD(P)H regeneration rates. The implementation of published strategies resulted in 2.1 g Laq-1 methyl ketones in fed-batch fermentation. We further increased the production by eliminating competing reactions suggested by metabolic analyses. These efforts resulted in the production of 9.8 g Laq-1 methyl ketones (corresponding to 69.3 g Lorg-1 in the in situ extraction phase) at 53% of the maximum theoretical yield. This represents a 4-fold improvement in product titer compared to the initial production strain and the highest titer of recombinantly produced methyl ketones reported to date. Accordingly, this study underlines the high potential of P. taiwanensis VLB120 to produce methyl ketones and emphasizes model-driven metabolic engineering to rationalize and accelerate strain optimization efforts.
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Affiliation(s)
- Salome C Nies
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - Tobias B Alter
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - Sophia Nölting
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - Susanne Thiery
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - An N T Phan
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - Noud Drummen
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - Jay D Keasling
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark; Lawrence Berkeley National Laboratory, Biological Systems and Engineering Division, Berkeley, CA, 94720, USA; Virtual Institute of Microbial Stress and Survival, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Dept. of Bioengineering, University of California, Berkeley, CA, 94720, USA; Dept. of Chemical Engineering, University of California, Berkeley, CA, 94720, USA; Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Lars M Blank
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany
| | - Birgitta E Ebert
- iAMB-Institute of Applied Microbiology, ABBt-Aachen Biology and Biotechnology, RWTH Aachen University, DE, Germany; Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia.
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15
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Yan Q, Simmons TR, Cordell WT, Hernández Lozada NJ, Breckner CJ, Chen X, Jindra MA, Pfleger BF. Metabolic engineering of β-oxidation to leverage thioesterases for production of 2-heptanone, 2-nonanone and 2-undecanone. Metab Eng 2020; 61:335-343. [PMID: 32479802 DOI: 10.1016/j.ymben.2020.05.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 01/06/2023]
Abstract
Medium-chain length methyl ketones are potential blending fuels due to their cetane numbers and low melting temperatures. Biomanufacturing offers the potential to produce these molecules from renewable resources such as lignocellulosic biomass. In this work, we designed and tested metabolic pathways in Escherichia coli to specifically produce 2-heptanone, 2-nonanone and 2-undecanone. We achieved substantial production of each ketone by introducing chain-length specific acyl-ACP thioesterases, blocking the β-oxidation cycle at an advantageous reaction, and introducing active β-ketoacyl-CoA thioesterases. Using a bioprospecting approach, we identified fifteen homologs of E. coli β-ketoacyl-CoA thioesterase (FadM) and evaluated the in vivo activity of each against various chain length substrates. The FadM variant from Providencia sneebia produced the most 2-heptanone, 2-nonanone, and 2-undecanone, suggesting it has the highest activity on the corresponding β-ketoacyl-CoA substrates. We tested enzyme variants, including acyl-CoA oxidases, thiolases, and bi-functional 3-hydroxyacyl-CoA dehydratases to maximize conversion of fatty acids to β-keto acyl-CoAs for 2-heptanone, 2-nonanone, and 2-undecanone production. In order to address the issue of product loss during fermentation, we applied a 20% (v/v) dodecane layer in the bioreactor and built an external water cooling condenser connecting to the bioreactor heat-transferring condenser coupling to the condenser. Using these modifications, we were able to generate up to 4.4 g/L total medium-chain length methyl ketones.
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Affiliation(s)
- Qiang Yan
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Trevor R Simmons
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - William T Cordell
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Néstor J Hernández Lozada
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Christian J Breckner
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Xuanqi Chen
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Michael A Jindra
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Brian F Pfleger
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, 53706, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Wisconsin-Madison, Madison, WI, 53706, USA; Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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16
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Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120's Metabolism. Appl Environ Microbiol 2020; 86:AEM.03038-19. [PMID: 32245760 DOI: 10.1128/aem.03038-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/18/2020] [Indexed: 12/14/2022] Open
Abstract
Obligate aerobic organisms rely on a functional electron transport chain for energy conservation and NADH oxidation. Because of this essential requirement, the genes of this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance and energy shortage under fluctuating environmental conditions. We here investigated the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of corresponding genes on its physiology and metabolism. While a mutant lacking all three NADH dehydrogenases seemed to be nonviable, the single or double knockout mutant strains displayed no, or only a weak, phenotype. Only the mutant deficient in both type 2 dehydrogenases showed a clear phenotype with biphasic growth behavior and a strongly reduced growth rate in the second phase. In-depth analyses of the metabolism of the generated mutants, including quantitative physiological experiments, transcript analysis, proteomics, and enzyme activity assays revealed distinct responses to type 2 and type 1 dehydrogenase deletions. An overall high metabolic flexibility enables P. taiwanensis to cope with the introduced genetic perturbations and maintain stable phenotypes, likely by rerouting of metabolic fluxes. This metabolic adaptability has implications for biotechnological applications. While the phenotypic robustness is favorable in large-scale applications with inhomogeneous conditions, the possible versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic engineering efforts.IMPORTANCE While Pseudomonas has the capability for high metabolic activity and the provision of reduced redox cofactors important for biocatalytic applications, exploitation of this characteristic might be hindered by high, constitutive activity of and, consequently, competition with the NADH dehydrogenases of the respiratory chain. The in-depth analysis of NADH dehydrogenase mutants of Pseudomonas taiwanensis VLB120 presented here provides insight into the phenotypic and metabolic response of this strain to these redox metabolism perturbations. This high degree of metabolic flexibility needs to be taken into account for rational engineering of this promising biotechnological workhorse toward a host with a controlled and efficient supply of redox cofactors for product synthesis.
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17
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Lin CY, Eudes A. Strategies for the production of biochemicals in bioenergy crops. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:71. [PMID: 32318116 PMCID: PMC7158082 DOI: 10.1186/s13068-020-01707-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/02/2020] [Indexed: 05/12/2023]
Abstract
Industrial crops are grown to produce goods for manufacturing. Rather than food and feed, they supply raw materials for making biofuels, pharmaceuticals, and specialty chemicals, as well as feedstocks for fabricating fiber, biopolymer, and construction materials. Therefore, such crops offer the potential to reduce our dependency on petrochemicals that currently serve as building blocks for manufacturing the majority of our industrial and consumer products. In this review, we are providing examples of metabolites synthesized in plants that can be used as bio-based platform chemicals for partial replacement of their petroleum-derived counterparts. Plant metabolic engineering approaches aiming at increasing the content of these metabolites in biomass are presented. In particular, we emphasize on recent advances in the manipulation of the shikimate and isoprenoid biosynthetic pathways, both of which being the source of multiple valuable compounds. Implementing and optimizing engineered metabolic pathways for accumulation of coproducts in bioenergy crops may represent a valuable option for enhancing the commercial value of biomass and attaining sustainable lignocellulosic biorefineries.
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Affiliation(s)
- Chien-Yuan Lin
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Aymerick Eudes
- Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
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