1
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Lee Y, Kim K, Choi M, Seo SW. Natural transformation of Vibrio natriegens with large genetic cluster enables alginate assimilation for isopentenol production. BIORESOURCE TECHNOLOGY 2024; 406:130988. [PMID: 38885723 DOI: 10.1016/j.biortech.2024.130988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/14/2024] [Accepted: 06/14/2024] [Indexed: 06/20/2024]
Abstract
Alginate is a major component of brown macroalgae, and its efficient utilization is critical for developing sustainable technologies. Vibrio natriegens is a fast-growing marine bacterium that has gained massive attention due to its potential as an alternative industrial chassis. However, V. natriegens cannot naturally metabolize alginate, limiting its usage in marine biomass conversion. In this study, V. natriegens was engineered to utilize marine biomass, kelp, as a carbon source. A total of 33.8 kb of the genetic cluster for alginate assimilation from Vibrio sp. dhg was integrated into V. natriegens by natural transformation. Engineered V. natriegens was further modified to produce 1.8 mg/L of isopentenol from 16 g/L of crude kelp powder. This study not only presents the very first case in which V. natriegens can be naturally transformed with large DNA fragments but also highlights the potential of this strain for converting marine biomass into valuable products.
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Affiliation(s)
- Yungyu Lee
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Keonwoo Kim
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Mincheol Choi
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea
| | - Sang Woo Seo
- School of Chemical and Biological Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Interdisciplinary Program in Bioengineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Bio-MAX Institute, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea; Institute of Bio Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Korea.
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2
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Nascimento JL, Junior ASL, Alves TV. The Interplay between the Temperature and Pressure on the Reaction Pathways of the Prenol Oxidation by Hydroxyl Radicals. Chemphyschem 2024; 25:e202400341. [PMID: 38878294 DOI: 10.1002/cphc.202400341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/03/2024] [Indexed: 07/16/2024]
Abstract
Despite prenol emerging as a next-generation biofuel, some questions about its mechanism still need to be adequately proposed to rationalize its consumption and evaluate its efficiency in spark-ignition (SI) engines. Here, we present new insights into the reaction mechanism of prenol (3-methyl-2-buten-1-ol) with OH radicals as a function of temperature and pressure. We have determined that the different temperature and pressure conditions control the preferred products. At combustion temperatures and low pressures, OH-addition adducts are suppressed, increasing the formation of α and δ allylic radicals responsible for the auto-ignition.
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Affiliation(s)
- Joel Leitão Nascimento
- Departamento de Físico-Química, Instituto de Química, Universidade Federal da Bahia - Salvador, Bahia, 40170-115, Brazil
| | - Adalberto S L Junior
- Departamento de Físico-Química, Instituto de Química, Universidade Federal da Bahia - Salvador, Bahia, 40170-115, Brazil
| | - Tiago Vinicius Alves
- Departamento de Físico-Química, Instituto de Química, Universidade Federal da Bahia - Salvador, Bahia, 40170-115, Brazil
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3
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Zhou J, Xu S, Li H, Xi H, Cheng W, Yang C. A Ribulose-5-phosphate Shunt from the Calvin-Benson Cycle to Methylerythritol Phosphate Pathway for Enhancing Photosynthetic Terpenoid Production. ACS Synth Biol 2024; 13:876-887. [PMID: 38362836 DOI: 10.1021/acssynbio.3c00675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Cyanobacteria are attractive hosts for photosynthetic terpenoid production, using CO2 as the sole carbon source. Although the methylerythritol phosphate (MEP) pathway is superior to the mevalonate pathway for cyanobacterial terpenoid synthesis, the first reaction of the MEP pathway, which is catalyzed by 1-deoxy-d-xylulose-5-phosphate (DXP) synthase, involves complex regulation and carbon loss. Here, we constructed a direct route linking ribulose-5-phosphate (Ru5P) in the Calvin-Benson (CB) cycle with DXP in the MEP pathway in a cyanobacterium to increase the terpenoid yield from CO2 and bypass the DXS-targeted regulations. By employing the adaptive laboratory evolution, we identified new RibB variants including RibB 90-92del with a high activity of synthesizing DXP from Ru5P. These RibB variants were introduced into Synechococcus elongatus, resulting in the significantly increased photosynthetic production of isopentenol. The 13C tracer experiments demonstrated a direct carbon flow from Ru5P in the CB cycle to the MEP pathway; thus, this direct route was denoted as the Ru5P shunt. The strain harboring the Ru5P shunt produced 105.2 mg L-1 of isopentenol with an average rate of 17.5 mg L-1 d-1 under continuous light conditions, which is higher than those ever reported for five-carbon alcohol production by photoautotrophic microorganisms. Utilization of the Ru5P shunt in cyanobacterial cells also improved the pinene production, which demonstrates that this shunt can be used to enhance the photosynthetic production of diverse terpenoids.
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Affiliation(s)
- Jie Zhou
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suxian Xu
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huachao Xi
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenbo Cheng
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chen Yang
- CAS-Key Laboratory of Synthetic Biology, Key Laboratory of Plant Carbon Capture, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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4
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Kim J, Lee TS. Enhancing isoprenol production by systematically tuning metabolic pathways using CRISPR interference in E. coli. Front Bioeng Biotechnol 2023; 11:1296132. [PMID: 38026852 PMCID: PMC10659101 DOI: 10.3389/fbioe.2023.1296132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Regulation of metabolic gene expression is crucial for maximizing bioproduction titers. Recent engineering tools including CRISPR/Cas9, CRISPR interference (CRISPRi), and CRISPR activation (CRISPRa) have enabled effective knock-out, knock-down, and overexpression of endogenous pathway genes, respectively, for advanced strain engineering. CRISPRi in particular has emerged as a powerful tool for gene repression through the use of a deactivated Cas9 (dCas9) protein and target guide RNA (gRNA). By constructing gRNA arrays, CRISPRi has the capacity for multiplexed gene downregulation across multiple orthogonal pathways for enhanced bioproduction titers. In this study, we harnessed CRISPRi to downregulate 32 essential and non-essential genes in E. coli strains heterologously expressing either the original mevalonate pathway or isopentenyl diphosphate (IPP) bypass pathway for isoprenol biosynthesis. Isoprenol remains a candidate bioproduct both as a drop-in blend additive and as a precursor for the high-performance sustainable aviation fuel, 1,4-dimethylcyclooctane (DMCO). Of the 32 gRNAs targeting genes associated with isoprenol biosynthesis, a subset was found to vastly improve product titers. Construction of a multiplexed gRNA library based on single guide RNA (sgRNA) performance enabled simultaneous gene repression, yielding a 3 to 4.5-fold increase in isoprenol titer (1.82 ± 0.19 g/L) on M9-MOPS minimal medium. We then scaled the best performing CRISPRi strain to 2-L fed-batch cultivation and demonstrated translatable titer improvements, ultimately obtaining 12.4 ± 1.3 g/L isoprenol. Our strategy further establishes CRISPRi as a powerful tool for tuning metabolic flux in production hosts and that titer improvements are readily scalable with potential for applications in industrial bioproduction.
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Affiliation(s)
- Jinho Kim
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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5
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Cortada-Garcia J, Daly R, Arnold SA, Burgess K. Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Sci Rep 2023; 13:12990. [PMID: 37563133 PMCID: PMC10415327 DOI: 10.1038/s41598-023-39661-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowing a more unbiased approach, but data interpretation using multivariate analysis is usually not straightforward and requires time and effort. Here we show, for the first time, the application of metabolic pathway enrichment analysis using untargeted and targeted metabolomics data to identify genetic targets for bioprocess improvement in a more streamlined way. The analysis of an Escherichia coli succinate production bioprocess with this methodology revealed three significantly modulated pathways during the product formation phase: the pentose phosphate pathway, pantothenate and CoA biosynthesis and ascorbate and aldarate metabolism. From these, the two former pathways are consistent with previous efforts to improve succinate production in Escherichia coli. Furthermore, to the best of our knowledge, ascorbate and aldarate metabolism is a newly identified target that has so far never been explored for improving succinate production in this microorganism. This methodology therefore represents a powerful tool for the streamlined identification of strain engineering targets that can accelerate bioprocess optimisation.
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Affiliation(s)
- Joan Cortada-Garcia
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, UK
| | - S Alison Arnold
- Ingenza Ltd., Roslin Innovation Centre, Roslin, EH25 9RG, UK
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK.
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6
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Lei M, Qiu Z, Guan L, Xiang Z, Zhao GR. Metabolic Engineering for Efficient Production of Z,Z-Farnesol in E. coli. Microorganisms 2023; 11:1583. [PMID: 37375090 DOI: 10.3390/microorganisms11061583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Z,Z-farnesol (Z,Z-FOH), the all-cis isomer of farnesol, holds enormous potential for application in cosmetics, daily chemicals, and pharmaceuticals. In this study, we aimed to metabolically engineer Escherichia coli to produce Z,Z-FOH. First, we tested five Z,Z-farnesyl diphosphate (Z,Z-FPP) synthases that catalyze neryl diphosphate to form Z,Z-FPP in E. coli. Furthermore, we screened thirteen phosphatases that could facilitate the dephosphorylation of Z,Z-FPP to produce Z,Z-FOH. Finally, through site-directed mutagenesis of cis-prenyltransferase, the optimal mutant strain was able to produce 572.13 mg/L Z,Z-FOH by batch fermentation in a shake flask. This achievement represents the highest reported titer of Z,Z-FOH in microbes to date. Notably, this is the first report on the de novo biosynthesis of Z,Z-FOH in E. coli. This work represents a promising step toward developing synthetic E. coli cell factories for the de novo biosynthesis of Z,Z-FOH and other cis-configuration terpenoids.
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Affiliation(s)
- Mengyang Lei
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Zetian Qiu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Leilei Guan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Zheng Xiang
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Guang-Rong Zhao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
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7
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Carruthers DN, Kim J, Mendez-Perez D, Monroe E, Myllenbeck N, Liu Y, Davis RW, Sundstrom E, Lee TS. Microbial production of high octane and high sensitivity olefinic ester biofuels. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:60. [PMID: 37016410 PMCID: PMC10071710 DOI: 10.1186/s13068-023-02301-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/08/2023] [Indexed: 04/06/2023]
Abstract
BACKGROUND Advanced spark ignition engines require high performance fuels with improved resistance to autoignition. Biologically derived olefinic alcohols have arisen as promising blendstock candidates due to favorable octane numbers and synergistic blending characteristics. However, production and downstream separation of these alcohols are limited by their intrinsic toxicity and high aqueous solubility, respectively. Bioproduction of carboxylate esters of alcohols can improve partitioning and reduce toxicity, but in practice has been limited to saturated esters with characteristically low octane sensitivity. If olefinic esters retain the synergistic blending characteristics of their alcohol counterparts, they could improve the bioblendstock combustion performance while also retaining the production advantages of the ester moiety. RESULTS Optimization of Escherichia coli isoprenoid pathways has led to high titers of isoprenol and prenol, which are not only excellent standalone biofuel and blend candidates, but also novel targets for esterification. Here, a selection of olefinic esters enhanced blendstock performance according to their degree of unsaturation and branching. E. coli strains harboring optimized mevalonate pathways, thioester pathways, and heterologous alcohol acyltransferases (ATF1, ATF2, and SAAT) were engineered for the bioproduction of four novel olefinic esters. Although prenyl and isoprenyl lactate titers were limited to 1.48 ± 0.41 mg/L and 5.57 ± 1.36 mg/L, strains engineered for prenyl and isoprenyl acetate attained titers of 176.3 ± 16.0 mg/L and 3.08 ± 0.27 g/L, respectively. Furthermore, prenyl acetate (20% bRON = 125.8) and isoprenyl acetate (20% bRON = 108.4) exhibited blend properties comparable to ethanol and significantly better than any saturated ester. By further scaling cultures to a 2-L bioreactor under fed-batch conditions, 15.0 ± 0.9 g/L isoprenyl acetate was achieved on minimal medium. Metabolic engineering of acetate pathway flux further improved titer to attain an unprecedented 28.0 ± 1.0 g/L isoprenyl acetate, accounting for 75.7% theoretical yield from glucose. CONCLUSION Our study demonstrated novel bioproduction of four isoprenoid oxygenates for fuel blending. Our optimized E. coli production strain generated an unprecedented titer of isoprenyl acetate and when paired with its favorable blend properties, may enable rapid scale-up of olefinic alcohol esters for use as a fuel blend additive or as a precursor for longer-chain biofuels and biochemicals.
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Affiliation(s)
- David N Carruthers
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Jinho Kim
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Daniel Mendez-Perez
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Eric Monroe
- Sandia National Laboratories, Livermore, CA, 94551, USA
| | | | - Yuzhong Liu
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA
| | - Ryan W Davis
- Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Eric Sundstrom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | - Taek Soon Lee
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA, 94608, USA.
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8
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Yan W, Cao Z, Ding M, Yuan Y. Design and construction of microbial cell factories based on systems biology. Synth Syst Biotechnol 2023; 8:176-185. [PMID: 36874510 PMCID: PMC9979088 DOI: 10.1016/j.synbio.2022.11.001] [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: 09/05/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
Environmental sustainability is an increasingly important issue in industry. As an environmentally friendly and sustainable way, constructing microbial cell factories to produce all kinds of valuable products has attracted more and more attention. In the process of constructing microbial cell factories, systems biology plays a crucial role. This review summarizes the recent applications of systems biology in the design and construction of microbial cell factories from four perspectives, including functional genes/enzymes discovery, bottleneck pathways identification, strains tolerance improvement and design and construction of synthetic microbial consortia. Systems biology tools can be employed to identify functional genes/enzymes involved in the biosynthetic pathways of products. These discovered genes are introduced into appropriate chassis strains to build engineering microorganisms capable of producing products. Subsequently, systems biology tools are used to identify bottleneck pathways, improve strains tolerance and guide design and construction of synthetic microbial consortia, resulting in increasing the yield of engineered strains and constructing microbial cell factories successfully.
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Affiliation(s)
- Wenlong Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
| | - Zhibei Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
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9
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Ng P, Khoo LW, Thong A, Chew W. Optimization of extraction conditions for LC-ToF-MS analysis of mevalonate pathway metabolites in engineered E. coli strain via statistical experimental designs. Talanta 2023; 254:124182. [PMID: 36527912 DOI: 10.1016/j.talanta.2022.124182] [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: 08/12/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Isoprenoids give rise to many functional products used today such as flavours, fragrances and even pharmaceutical compounds. Mevalonate pathway metabolites are the key intermediates that affect the production yield of isoprenoids. With increasing demand and benefit of isoprenoids, the present study adopts Analytical Quality-by-Design (AQbD) approach to establish an efficacious extraction protocol prior to the determination of mevalonate pathway metabolites in an engineered Escherichia coli model. The statistical experimental design approach, described in this work, has successfully validated an optimised sample preparation method i.e., using acetonitrile: 50 mM ammonium formate (pH 9.5) (7:3) (ACN73) at -20 °C for 10 min without solvent evaporation to retain the targeted mevalonate metabolites in engineered E. coli strain. The study also demonstrates the use of liquid chromatography paired with a Time-of-Flight Mass Spectrometer (LC-ToF-MS) for the quantitative analysis of the mevalonate pathway metabolites in E. coli. The analytical method was validated in accordance with guidelines in Metabolomics Standards Initiative and ICH Q2 (R1) with analyte spike recoveries at 80% and above. In short, the present study overcomes the one-variable-at-a-time (OVAT) limitations in analytical development, minimises metabolite losses and gives better cost and time efficiencies by eliminating the solvent evaporation and swapping process. This work highlights the importance of analytical methods development in microbial metabolomics studies.
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Affiliation(s)
- Pnelope Ng
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, 138669, Singapore
| | - Leng Wei Khoo
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, 138669, Singapore
| | - Aaron Thong
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, 138669, Singapore
| | - Wee Chew
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A*STAR), Singapore, 138669, Singapore.
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10
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Wang X, Baidoo EEK, Kakumanu R, Xie S, Mukhopadhyay A, Lee TS. Engineering isoprenoids production in metabolically versatile microbial host Pseudomonas putida. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:137. [PMID: 36510293 PMCID: PMC9743605 DOI: 10.1186/s13068-022-02235-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/04/2022] [Indexed: 06/17/2023]
Abstract
With the increasing need for microbial bioproduction to replace petrochemicals, it is critical to develop a new industrial microbial workhorse that improves the conversion of lignocellulosic carbon to biofuels and bioproducts in an economically feasible manner. Pseudomonas putida KT2440 is a promising microbial host due to its capability to grow on a broad range of carbon sources and its high tolerance to xenobiotics. In this study, we engineered P. putida KT2440 to produce isoprenoids, a vast category of compounds that provide routes to many petrochemical replacements. A heterologous mevalonate (MVA) pathway was engineered to produce potential biofuels isoprenol (C5) and epi-isozizaene (C15) for the first time in P. putida. We compared the difference between three different isoprenoid pathways in P. putida on isoprenol production and achieved 104 mg/L of isoprenol production in a batch flask experiment through optimization of the strain. As P. putida can natively consume isoprenol, we investigated how to prevent this self-consumption. We discovered that supplementing L-glutamate in the medium can effectively prevent isoprenol consumption in P. putida and metabolomics analysis showed an insufficient energy availability and an imbalanced redox status during isoprenol degradation. We also showed that the engineered P. putida strain can produce isoprenol using aromatic substrates such as p-coumarate as the sole carbon source, and this result demonstrates that P. putida is a valuable microbial chassis for isoprenoids to achieve sustainable biofuel production from lignocellulosic biomass.
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Affiliation(s)
- Xi Wang
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ramu Kakumanu
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Silvia Xie
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Molecular & Cell Biology, University of California, Berkeley, CA, 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute (JBEI), 5885 Hollis St., Emeryville, CA, 94608, USA.
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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11
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Nascimento JL, Junior ASL, Alves TV. Prenol as a Next-Generation Biofuel or Additive: A Comprehension of the Hydrogen Abstraction Reactions by a H Atom. J Phys Chem A 2022; 126:4791-4800. [PMID: 35839446 DOI: 10.1021/acs.jpca.2c03305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Thermal rate coefficients for the hydrogen abstraction reactions of prenol (3-methyl-2-butenol) by a hydrogen atom were calculated with the multipath canonical variational theory with small-curvature tunneling (MP-CVT/SCT). The conformational search was performed with a dual-level approach, and the multistructural torsional anharmonicity effects were corrected through the rovibrational partition function calculated with the multistructural method based on a coupled torsional potential (MS-T(C)). This methodology allows us to estimate the thermal rate constants in the temperature range of 200-2500 K and fit them into two analytical expressions. Differences between the number of conformations on the torsional potential energy surfaces for prenol and the transition state decrease the thermal rate constants for the H-abstraction at the α carbon. An opposite behavior was detected for the abstractions on the δ site. The product branching ratios were calculated using single-structure and multipath approaches. The product distributions from the former are shown to be inadequate for studying the mechanism under combustion conditions. The values estimated from MP-CVT/SCT rate coefficients indicated that the radicals from (Rα) and (Rδ)/(Rδ') are formed in considerable amounts. These species are fundamental in comprehending the inhibition and promotion of the autoignition phenomena.
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Affiliation(s)
- Joel Leitão Nascimento
- Departamento de Físico-Química, Instituto de Química, Universidade Federal da Bahia Rua Barão de Jeremoabo, 147, Salvador, Bahia 40170-115, Brazil
| | - Adalberto S Lima Junior
- Departamento de Físico-Química, Instituto de Química, Universidade Federal da Bahia Rua Barão de Jeremoabo, 147, Salvador, Bahia 40170-115, Brazil
| | - Tiago Vinicius Alves
- Departamento de Físico-Química, Instituto de Química, Universidade Federal da Bahia Rua Barão de Jeremoabo, 147, Salvador, Bahia 40170-115, Brazil
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12
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Li G, Zhang Z, Wu M, Chen X, Yin M, Jiang Y, Huang X, Jiang C, Han L. The discovery of germacradienol synthase: Construction of genetically-engineered strain, glycosylated modification, bioactive evaluation of germacradienol. Bioorg Chem 2022; 124:105819. [DOI: 10.1016/j.bioorg.2022.105819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/28/2022]
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13
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Yunus IS, Lee TS. Applications of targeted proteomics in metabolic engineering: advances and opportunities. Curr Opin Biotechnol 2022; 75:102709. [DOI: 10.1016/j.copbio.2022.102709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/15/2022] [Accepted: 02/23/2022] [Indexed: 12/22/2022]
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14
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Hans S, Kumar N, Gohil N, Khambhati K, Bhattacharjee G, Deb SS, Maurya R, Kumar V, Reshamwala SMS, Singh V. Rebooting life: engineering non-natural nucleic acids, proteins and metabolites in microorganisms. Microb Cell Fact 2022; 21:100. [PMID: 35643549 PMCID: PMC9148472 DOI: 10.1186/s12934-022-01828-y] [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] [Received: 01/05/2022] [Accepted: 05/15/2022] [Indexed: 12/01/2022] Open
Abstract
The surging demand of value-added products has steered the transition of laboratory microbes to microbial cell factories (MCFs) for facilitating production of large quantities of important native and non-native biomolecules. This shift has been possible through rewiring and optimizing different biosynthetic pathways in microbes by exercising frameworks of metabolic engineering and synthetic biology principles. Advances in genome and metabolic engineering have provided a fillip to create novel biomolecules and produce non-natural molecules with multitude of applications. To this end, numerous MCFs have been developed and employed for production of non-natural nucleic acids, proteins and different metabolites to meet various therapeutic, biotechnological and industrial applications. The present review describes recent advances in production of non-natural amino acids, nucleic acids, biofuel candidates and platform chemicals.
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15
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Kothandaraman J, Cosimbescu L, Swita MS. Solvent-Induced Selectivity of Isoprene From Bio-Derived Prenol. Front Chem 2022; 10:879129. [PMID: 35655703 PMCID: PMC9152107 DOI: 10.3389/fchem.2022.879129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022] Open
Abstract
In this work we demonstrate the selective catalytic conversion of prenol, which is an allylic alcohol that can be prepared from renewable resources to isoprene. The catalyst is an inexpensive molybdenum complex (Molyvan L) designed and used as an additive for lubricants. Isoprene is generated under relatively mild reaction parameters at 130–150°C, for 2 h, under vapor pressure conditions that do not exceed 50 psi. Two cases were studied: one in which Molyvan L was dissolved in a base oil at 1% concentration (weight/weight) and then mixed with a solvent and prenol and the other in which neat Molyvan L was introduced in the reaction and the base oil was replaced with the solvent and prenol. We investigated the selectivity of the reaction using the following solvents in both cases: dodecane, dodecanol, isododecane, octane, blendstock for oxygenate blending (BOB3), a fuel surrogate, a polyalphaolefin (PAO4), and methoxy polyethylene glycol (methoxy PEG350). Although conversion of prenol was above 94% in all experiments, isoprene was formed with various degrees of efficiency alongside a prenol isomeric alcohol, diprenyl ether and mixed ether via intramolecular and intermolecular dehydration reactions. Dodecane appeared to have the highest level of selectivity initially in base oil so we studied the effect of various dodecane-like solvents on isoprene yield and product profile. Surprisingly, octane (similar to dodecane) and isododecane (branched alkane) generated insignificant amounts of byproducts, essentially providing the highly desired isoprene with a very high selectivity. Branching of the solvent does not appear to have an effect on selectivity. Another advantage of this catalyst is the low loadings required to effect the transformation; that is, 0.25% (weight/volume) in the cases using neat Molyvan L and 0.5% (weight/volume) in the cases using Molyvan L dissolved in the base oil. Provided that prenol can be produced in large scale from bioresources, this work would enable the sustainable production of isoprene, in good yield, and with very high selectivity.
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16
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Liu H, Arbing MA, Bowie JU. Expanding the use of ethanol as a feedstock for cell-free synthetic biochemistry by implementing acetyl-CoA and ATP generating pathways. Sci Rep 2022; 12:7700. [PMID: 35546163 PMCID: PMC9095697 DOI: 10.1038/s41598-022-11653-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Accepted: 04/20/2022] [Indexed: 12/01/2022] Open
Abstract
Ethanol is a widely available carbon compound that can be increasingly produced with a net negative carbon balance. Carbon-negative ethanol might therefore provide a feedstock for building a wider range of sustainable chemicals. Here we show how ethanol can be converted with a cell free system into acetyl-CoA, a central precursor for myriad biochemicals, and how we can use the energy stored in ethanol to generate ATP, another key molecule important for powering biochemical pathways. The ATP generator produces acetone as a value-added side product. Our ATP generator reached titers of 27 ± 6 mM ATP and 59 ± 15 mM acetone with maximum ATP synthesis rate of 2.8 ± 0.6 mM/h and acetone of 7.8 ± 0.8 mM/h. We illustrated how the ATP generating module can power cell-free biochemical pathways by converting mevalonate into isoprenol at a titer of 12.5 ± 0.8 mM and a maximum productivity of 1.0 ± 0.05 mM/h. These proof-of-principle demonstrations may ultimately find their way to the manufacture of diverse chemicals from ethanol and other simple carbon compounds.
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Affiliation(s)
- Hongjiang Liu
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles, Boyer Hall, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA
| | - Mark A Arbing
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles, Boyer Hall, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA
| | - James U Bowie
- Department of Chemistry and Biochemistry, Molecular Biology Institute, UCLA-DOE Institute of Genomics and Proteomics, University of California Los Angeles, Boyer Hall, 611 Charles E. Young Dr. E, Los Angeles, CA, 90095-1570, USA.
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17
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Rinaldi MA, Ferraz CA, Scrutton NS. Alternative metabolic pathways and strategies to high-titre terpenoid production in Escherichia coli. Nat Prod Rep 2022; 39:90-118. [PMID: 34231643 PMCID: PMC8791446 DOI: 10.1039/d1np00025j] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are a diverse group of chemicals used in a wide range of industries. Microbial terpenoid production has the potential to displace traditional manufacturing of these compounds with renewable processes, but further titre improvements are needed to reach cost competitiveness. This review discusses strategies to increase terpenoid titres in Escherichia coli with a focus on alternative metabolic pathways. Alternative pathways can lead to improved titres by providing higher orthogonality to native metabolism that redirects carbon flux, by avoiding toxic intermediates, by bypassing highly-regulated or bottleneck steps, or by being shorter and thus more efficient and easier to manipulate. The canonical 2-C-methyl-D-erythritol 4-phosphate (MEP) and mevalonate (MVA) pathways are engineered to increase titres, sometimes using homologs from different species to address bottlenecks. Further, alternative terpenoid pathways, including additional entry points into the MEP and MVA pathways, archaeal MVA pathways, and new artificial pathways provide new tools to increase titres. Prenyl diphosphate synthases elongate terpenoid chains, and alternative homologs create orthogonal pathways and increase product diversity. Alternative sources of terpenoid synthases and modifying enzymes can also be better suited for E. coli expression. Mining the growing number of bacterial genomes for new bacterial terpenoid synthases and modifying enzymes identifies enzymes that outperform eukaryotic ones and expand microbial terpenoid production diversity. Terpenoid removal from cells is also crucial in production, and so terpenoid recovery and approaches to handle end-product toxicity increase titres. Combined, these strategies are contributing to current efforts to increase microbial terpenoid production towards commercial feasibility.
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Affiliation(s)
- Mauro A Rinaldi
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Clara A Ferraz
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology, Department of Chemistry, School of Natural Sciences, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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18
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Satta A, Lu Z, Plan MR, Esquirol L, Ebert BE. Microbial Production, Extraction, and Quantitative Analysis of Isoprenoids. Methods Mol Biol 2022; 2469:239-259. [PMID: 35508844 DOI: 10.1007/978-1-0716-2185-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Isoprenoids, also known as terpenes or terpenoids, are compounds made of one or more isoprene (C5H8) moieties and constitute the largest class of natural products. They play diverse roles in biology and have broad industrial uses as flavors, fragrances, biofuels, polymers, agricultural chemicals, and medicines. Most isoprenoids are secondary plant metabolites and only produced in very low amounts. To make these valuable compounds economically accessible, significant efforts in the culture and engineering of microbial cells for isoprenoid biosynthesis have been made in the last decades. The protocols presented here describe lab-scale cultivation of microbes, either naturally producing or engineered, for isoprenoid production, the extraction of products and their quantification by high-performance liquid chromatography. Examples of isoprenoids covered in this chapter include (C10) mono-, (C15) sesqui-, (C20) di-, (C30) tri-, and (C40) tetraterpenoids. We focus on yeast and cyanobacteria as production systems, but the protocols can be adapted for other organisms.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Manuel R Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.
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19
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Mohamed SY, Monge-Palacios M, Giri BR, Khaled F, Liu D, Farooq A, Sarathy SM. The Effect of Hydrogen Bonding on the Reactivity of OH Radicals with Prenol and Isoprenol: A Shock Tube and Multi-Structural Torsional Variational Transition State Theory Study. Phys Chem Chem Phys 2022; 24:12601-12620. [DOI: 10.1039/d2cp00737a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence of two functional groups (OH and double bond) in C5 methyl-substituted enols (i.e., isopentenols), such as 3-methyl-2-buten-1-ol (prenol) and 3-methyl-3-buten-1-ol (isoprenol), makes them excellent biofuel candidates as fuel...
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20
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Carruthers DN, Lee TS. Diversifying Isoprenoid Platforms via Atypical Carbon Substrates and Non-model Microorganisms. Front Microbiol 2021; 12:791089. [PMID: 34925299 PMCID: PMC8677530 DOI: 10.3389/fmicb.2021.791089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/10/2021] [Indexed: 01/07/2023] Open
Abstract
Isoprenoid compounds are biologically ubiquitous, and their characteristic modularity has afforded products ranging from pharmaceuticals to biofuels. Isoprenoid production has been largely successful in Escherichia coli and Saccharomyces cerevisiae with metabolic engineering of the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways coupled with the expression of heterologous terpene synthases. Yet conventional microbial chassis pose several major obstacles to successful commercialization including the affordability of sugar substrates at scale, precursor flux limitations, and intermediate feedback-inhibition. Now, recent studies have challenged typical isoprenoid paradigms by expanding the boundaries of terpene biosynthesis and using non-model organisms including those capable of metabolizing atypical C1 substrates. Conversely, investigations of non-model organisms have historically informed optimization in conventional microbes by tuning heterologous gene expression. Here, we review advances in isoprenoid biosynthesis with specific focus on the synergy between model and non-model organisms that may elevate the commercial viability of isoprenoid platforms by addressing the dichotomy between high titer production and inexpensive substrates.
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Affiliation(s)
- David N Carruthers
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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21
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Bahls MO, Platz L, Morgado G, Schmidt GW, Panke S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metab Eng 2021; 69:98-111. [PMID: 34767976 DOI: 10.1016/j.ymben.2021.10.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/21/2021] [Accepted: 10/31/2021] [Indexed: 12/18/2022]
Abstract
The biosynthesis of short-chain alcohols is a carbon-neutral alternative to petroleum-derived production, but strain screening operations are encumbered by laborious analytics. Here, we built, characterized and applied whole cell biosensors by directed evolution of the transcription factor AlkS for screening microbial strain libraries producing industrially relevant alcohols. A selected AlkS variant was applied for in situ product detection in two screening applications concerning key steps in alcohol production. Further, the biosensor strains enabled the implementation of an automated, robotic platform-based workflow with data clustering, which readily allowed the identification of significantly improved strain variants for isopentanol production.
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Affiliation(s)
- Maximilian O Bahls
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Lukas Platz
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gaspar Morgado
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Gregor W Schmidt
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland
| | - Sven Panke
- Department of Biosystems Science and Engineering, ETH Zurich, Switzerland.
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22
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Keasling J, Garcia Martin H, Lee TS, Mukhopadhyay A, Singer SW, Sundstrom E. Microbial production of advanced biofuels. Nat Rev Microbiol 2021; 19:701-715. [PMID: 34172951 DOI: 10.1038/s41579-021-00577-w] [Citation(s) in RCA: 80] [Impact Index Per Article: 26.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Concerns over climate change have necessitated a rethinking of our transportation infrastructure. One possible alternative to carbon-polluting fossil fuels is biofuels produced by engineered microorganisms that use a renewable carbon source. Two biofuels, ethanol and biodiesel, have made inroads in displacing petroleum-based fuels, but their uptake has been limited by the amounts that can be used in conventional engines and by their cost. Advanced biofuels that mimic petroleum-based fuels are not limited by the amounts that can be used in existing transportation infrastructure but have had limited uptake due to costs. In this Review, we discuss engineering metabolic pathways to produce advanced biofuels, challenges with substrate and product toxicity with regard to host microorganisms and methods to engineer tolerance, and the use of functional genomics and machine learning approaches to produce advanced biofuels and prospects for reducing their costs.
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Affiliation(s)
- Jay Keasling
- Joint BioEnergy Institute, Emeryville, CA, USA. .,Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, USA. .,Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA. .,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. .,Center for Biosustainability, Danish Technical University, Lyngby, Denmark. .,Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, China.
| | - Hector Garcia Martin
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,DOE Agile BioFoundry, Emeryville, CA, USA.,BCAM,Basque Center for Applied Mathematics, Bilbao, Spain.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Steven W Singer
- Joint BioEnergy Institute, Emeryville, CA, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eric Sundstrom
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, USA
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23
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Luo ZW, Ahn JH, Chae TU, Choi SY, Park SY, Choi Y, Kim J, Prabowo CPS, Lee JA, Yang D, Han T, Xu H, Lee SY. Metabolic Engineering of
Escherichia
coli. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Hoffman SM, Alvarez M, Alfassi G, Rein DM, Garcia-Echauri S, Cohen Y, Avalos JL. Cellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeasts. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:157. [PMID: 34274018 PMCID: PMC8285809 DOI: 10.1186/s13068-021-02008-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 07/05/2021] [Indexed: 05/16/2023]
Abstract
BACKGROUND Future expansion of corn-derived ethanol raises concerns of sustainability and competition with the food industry. Therefore, cellulosic biofuels derived from agricultural waste and dedicated energy crops are necessary. To date, slow and incomplete saccharification as well as high enzyme costs have hindered the economic viability of cellulosic biofuels, and while approaches like simultaneous saccharification and fermentation (SSF) and the use of thermotolerant microorganisms can enhance production, further improvements are needed. Cellulosic emulsions have been shown to enhance saccharification by increasing enzyme contact with cellulose fibers. In this study, we use these emulsions to develop an emulsified SSF (eSSF) process for rapid and efficient cellulosic biofuel production and make a direct three-way comparison of ethanol production between S. cerevisiae, O. polymorpha, and K. marxianus in glucose and cellulosic media at different temperatures. RESULTS In this work, we show that cellulosic emulsions hydrolyze rapidly at temperatures tolerable to yeast, reaching up to 40-fold higher conversion in the first hour compared to microcrystalline cellulose (MCC). To evaluate suitable conditions for the eSSF process, we explored the upper temperature limits for the thermotolerant yeasts Kluyveromyces marxianus and Ogataea polymorpha, as well as Saccharomyces cerevisiae, and observed robust fermentation at up to 46, 50, and 42 °C for each yeast, respectively. We show that the eSSF process reaches high ethanol titers in short processing times, and produces close to theoretical yields at temperatures as low as 30 °C. Finally, we demonstrate the transferability of the eSSF technology to other products by producing the advanced biofuel isobutanol in a light-controlled eSSF using optogenetic regulators, resulting in up to fourfold higher titers relative to MCC SSF. CONCLUSIONS The eSSF process addresses the main challenges of cellulosic biofuel production by increasing saccharification rate at temperatures tolerable to yeast. The rapid hydrolysis of these emulsions at low temperatures permits fermentation using non-thermotolerant yeasts, short processing times, low enzyme loads, and makes it possible to extend the process to chemicals other than ethanol, such as isobutanol. This transferability establishes the eSSF process as a platform for the sustainable production of biofuels and chemicals as a whole.
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Affiliation(s)
- Shannon M Hoffman
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA
| | - Maria Alvarez
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA
- Department of Chemical Engineering, University of Vigo, 36310, Vigo, Spain
| | - Gilad Alfassi
- Department of Biotechnology Engineering, ORT Braude College, Karmiel, Israel
| | - Dmitry M Rein
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - Sergio Garcia-Echauri
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA
| | - Yachin Cohen
- Department of Chemical Engineering, Technion-Israel Institute of Technology, Haifa, Israel
| | - José L Avalos
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ, 08544, USA.
- The Andlinger Center for Energy and the Environment, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA.
- Princeton Environmental Institute, Princeton University, Princeton, NJ, 08544, USA.
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25
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Lei D, Qiu Z, Wu J, Qiao B, Qiao J, Zhao GR. Combining Metabolic and Monoterpene Synthase Engineering for de Novo Production of Monoterpene Alcohols in Escherichia coli. ACS Synth Biol 2021; 10:1531-1544. [PMID: 34100588 DOI: 10.1021/acssynbio.1c00081] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The monoterpene alcohols acyclic nerol and bicyclic borneol are widely applied in the food, cosmetic, and pharmaceutical industries. The emerging synthetic biology enables microbial production to be a promising alternative for supplying monoterpene alcohols in an efficient and sustainable approach. In this study, we combined metabolic and plant monoterpene synthase engineering to improve the de novo production of nerol and borneol in prene-overproducing Escherichia coli. We engineered the growth-orthogonal neryl diphosphate (NPP) as the universal precursor of monoterpene alcohol biosynthesis and coexpressed nerol synthase (GmNES) from Glycine max to generate nerol or coexpressed the truncated bornyl diphosphate synthase (LdtBPPS) from Lippia dulcis for borneol production. Further, through site-directed mutation of LdtBPPS based on the structural simulation, we screened multiple variants that markedly elevated the production of acyclic nerol or bicyclic borneol, of which the LdtBPPSS488T mutant outperformed the wild-type LdtBPPS on borneol synthesis and the LdtBPPSF612A variant was superior to GmNES on nerol production. Subsequently, we overexpressed the endogenous Nudix hydrolase NudJ to facilitate the dephosphorylation of precursors and boosted the production of nerol and borneol from glucose. Finally, after the optimization of the fermentation process, the engineered strain ENO2 produced 966.55 mg/L nerol, and strain ENB57 generated 87.20 mg/L borneol in a shake flask, achieving the highest reported titers of nerol and borneol in microbes to date. This work shows a combinatorial engineering strategy for microbial production of natural terpene alcohols.
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Affiliation(s)
- Dengwei Lei
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Zetian Qiu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Jihua Wu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Bin Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Jianjun Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Tangxing Road 133, Nanshan District, Shenzhen 518071, China
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Runguphan W, Sae-Tang K, Tanapongpipat S. Recent advances in the microbial production of isopentanol (3-Methyl-1-butanol). World J Microbiol Biotechnol 2021; 37:107. [PMID: 34043086 DOI: 10.1007/s11274-021-03074-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/17/2021] [Indexed: 10/21/2022]
Abstract
As the effects of climate change become increasingly severe, metabolic engineers and synthetic biologists are looking towards greener sources for transportation fuels. The design and optimization of microorganisms to produce gasoline, diesel, and jet fuel compounds from renewable feedstocks can significantly reduce dependence on fossil fuels and thereby produce fewer emissions. Over the past two decades, a tremendous amount of research has contributed to the development of microbial strains to produce advanced fuel compounds, including branched-chain higher alcohols (BCHAs) such as isopentanol (3-methyl-1-butanol; 3M1B) and isobutanol (2-methyl-1-propanol). In this review, we provide an overview of recent advances in the development of microbial strains for the production of isopentanol in both conventional and non-conventional hosts. We also highlight metabolic engineering strategies that may be employed to enhance product titers, reduce end-product toxicity, and broaden the substrate range to non-sugar carbon sources. Finally, we offer glimpses into some promising future directions in the development of isopentanol producing microbial strains.
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Affiliation(s)
- Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, 12120, Pathumthani, Thailand.
| | - Kittapong Sae-Tang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, 12120, Pathumthani, Thailand
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, 12120, Pathumthani, Thailand
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27
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Escherichia coli as a platform microbial host for systems metabolic engineering. Essays Biochem 2021; 65:225-246. [PMID: 33956149 DOI: 10.1042/ebc20200172] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/19/2022]
Abstract
Bio-based production of industrially important chemicals and materials from non-edible and renewable biomass has become increasingly important to resolve the urgent worldwide issues including climate change. Also, bio-based production, instead of chemical synthesis, of food ingredients and natural products has gained ever increasing interest for health benefits. Systems metabolic engineering allows more efficient development of microbial cell factories capable of sustainable, green, and human-friendly production of diverse chemicals and materials. Escherichia coli is unarguably the most widely employed host strain for the bio-based production of chemicals and materials. In the present paper, we review the tools and strategies employed for systems metabolic engineering of E. coli. Next, representative examples and strategies for the production of chemicals including biofuels, bulk and specialty chemicals, and natural products are discussed, followed by discussion on materials including polyhydroxyalkanoates (PHAs), proteins, and nanomaterials. Lastly, future perspectives and challenges remaining for systems metabolic engineering of E. coli are discussed.
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Shukla V, Phulara SC. Impact of culture condition modulation on the high-yield, high-specificity and cost-effective production of terpenoids from microbial sources: A review. Appl Environ Microbiol 2021; 87:AEM.02369-20. [PMID: 33257314 PMCID: PMC7851692 DOI: 10.1128/aem.02369-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent years have seen a remarkable increase in the non-natural production of terpenoids from microbial route. This is due to the advancements in synthetic biology tools and techniques, which have overcome the challenges associated with the non-native production of terpenoids from microbial hosts. Although, microbes in their native form have ability to grow in wide range of physicochemical parameters such as, pH, temperature, agitation, aeration etc; however, after genetic modifications, culture conditions need to be optimized in order to achieve improved titers of desired terpenoids from engineered microbes. The physicochemical parameters together with medium supplements, such as, inducer, carbon and nitrogen source, and cofactor supply not only play an important role in high-yield production of target terpenoids from engineered host, but also reduce the accumulation of undesired metabolites in fermentation medium, thus facilitate product recovery. Further, for the economic production of terpenoids, the biomass derived sugars can be utilized together with the optimized culture conditions. In the present mini-review, we have highlighted the impact of culture conditions modulation on the high-yield and high-specificity production of terpenoids from engineered microbes. Lastly, utilization of economic feedstock has also been discussed for the cost-effective and sustainable production of terpenoids.
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Affiliation(s)
- Vibha Shukla
- Food, Drug and Chemical Toxicology Group, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow-226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur-522502, Andhra Pradesh, India
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Kim J, Baidoo EEK, Amer B, Mukhopadhyay A, Adams PD, Simmons BA, Lee TS. Engineering Saccharomyces cerevisiae for isoprenol production. Metab Eng 2021; 64:154-166. [PMID: 33581331 DOI: 10.1016/j.ymben.2021.02.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/29/2020] [Accepted: 02/04/2021] [Indexed: 12/27/2022]
Abstract
Isoprenol (3-methyl-3-butene-1-ol) is a valuable drop-in biofuel and an important precursor of several commodity chemicals. Synthetic microbial systems using the heterologous mevalonate pathway have recently been developed for the production of isoprenol in Escherichia coli, and a significant yield and titer improvement has been achieved through a decade of research. Saccharomyces cerevisiae has been widely used in the biotechnology industry for isoprenoid production, but there has been no good example of isoprenol production reported in this host. In this study, we engineered the budding yeast S. cerevisiae for improved biosynthesis of isoprenol. The strain engineered with the mevalonate pathway achieved isoprenol production at the titer of 36.02 ± 0.92 mg/L in the flask. The IPP (isopentenyl diphosphate)-bypass pathway, which has shown more efficient isoprenol production by avoiding the accumulation of the toxic intermediate in E. coli, was also constructed in S. cerevisiae and improved the isoprenol titer by 2-fold. We further engineered the strains by deleting a promiscuous endogenous kinase that could divert the pathway flux away from the isoprenol production and improved the titer to 130.52 ± 8.01 mg/L. Finally, we identified a pathway bottleneck using metabolomics analysis and overexpressed a promiscuous alkaline phosphatase to relieve this bottleneck. The combined efforts resulted in the titer improvement to 383.1 ± 31.62 mg/L in the flask. This is the highest isoprenol titer up to date in S. cerevisiae and this work provides the key strategies to engineer yeast as an industrial platform for isoprenol production.
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Affiliation(s)
- Jinho Kim
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Edward E K Baidoo
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Bashar Amer
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Paul D Adams
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Bioengineering, University of California, Berkeley, CA 94720, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Taek Soon Lee
- Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, CA 94608, USA; Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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Li Z, Li A, Hoyt JR, Dai W, Leng H, Li Y, Li W, Liu S, Jin L, Sun K, Feng J. Activity of bacteria isolated from bats against Pseudogymnoascus destructans in China. Microb Biotechnol 2021; 15:469-481. [PMID: 33559264 PMCID: PMC8867990 DOI: 10.1111/1751-7915.13765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/20/2021] [Indexed: 11/28/2022] Open
Abstract
White‐nose syndrome, a disease that is caused by the psychrophilic fungus Pseudogymnoascus destructans, has threatened several North America bat species with extinction. Recent studies have shown that East Asian bats are infected with P. destructans but show greatly reduced infections. While several factors have been found to contribute to these reduced infections, the role of specific microbes in limiting P. destructans growth remains unexplored. We isolated three bacterial strains with the ability to inhibit P. destructans, namely, Pseudomonas yamanorum GZD14026, Pseudomonas brenneri XRD11711 and Pseudomonas fragi GZD14479, from bats in China. Pseudomonas yamanorum, with the highest inhibition score, was selected to extract antifungal active substance. Combining mass spectrometry (MS) and nuclear magnetic resonance (NMR) spectroscopy analyses, we identified the active compound inhibiting P. destructans as phenazine‐1‐carboxylic acid (PCA), and the minimal inhibitory concentration (MIC) was 50.12 μg ml−1. Whole genome sequencing also revealed the existence of PCA biosynthesis gene clusters. Gas chromatography‐mass spectrometry (GC‐MS) analysis identified volatile organic compounds. The results indicated that 10 ppm octanoic acid, 100 ppm 3‐tert‐butyl‐4‐hydroxyanisole (isoprenol) and 100 ppm 3‐methyl‐3‐buten‐1‐ol (BHA) inhibited the growth of P. destructans. These results support that bacteria may play a role in limiting the growth of P. destructans on bats.
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Affiliation(s)
- Zhongle Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130018, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, 24060, USA
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Yanfei Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Wei Li
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Sen Liu
- Institute of Resources and Environment, Henan Polytechnic University, Jiaozuo, 454000, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Jiang Feng
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130018, China.,Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
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31
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Navale GR, Dharne MS, Shinde SS. Metabolic engineering and synthetic biology for isoprenoid production in Escherichia coli and Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2021; 105:457-475. [PMID: 33394155 DOI: 10.1007/s00253-020-11040-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/23/2020] [Accepted: 12/01/2020] [Indexed: 12/29/2022]
Abstract
Isoprenoids, often called terpenoids, are the most abundant and highly diverse family of natural organic compounds. In plants, they play a distinct role in the form of photosynthetic pigments, hormones, electron carrier, structural components of membrane, and defence. Many isoprenoids have useful applications in the pharmaceutical, nutraceutical, and chemical industries. They are synthesized by various isoprenoid synthase enzymes by several consecutive steps. Recent advancement in metabolic engineering and synthetic biology has enabled the production of these isoprenoids in the heterologous host systems like Escherichia coli and Saccharomyces cerevisiae. Both heterologous systems have been engineered for large-scale production of value-added isoprenoids. This review article will provide the detailed description of various approaches used for engineering of methyl-D-erythritol-4-phosphate (MEP) and mevalonate (MVA) pathway for synthesizing isoprene units (C5) and ultimate production of diverse isoprenoids. The review particularly highlighted the efforts taken for the production of C5-C20 isoprenoids by metabolic engineering techniques in E. coli and S. cerevisiae over a decade. The challenges and strategies are also discussed in detail for scale-up and engineering of isoprenoids in the heterologous host systems.Key points• Isoprenoids are beneficial and valuable natural products.• E. coli and S. cerevisiae are the promising host for isoprenoid biosynthesis.• Emerging techniques in synthetic biology enabled the improved production.• Need to expand the catalogue and scale-up of un-engineered isoprenoids. Metabolic engineering and synthetic biology for isoprenoid production in Escherichia coli and Saccharomyces cerevisiae.
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Affiliation(s)
- Govinda R Navale
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 001, India
| | - Mahesh S Dharne
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 001, India.
| | - Sandip S Shinde
- NCIM Resource Centre, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India. .,Department Industrial and Chemical Engineering, Institute of Chemical Technology Mumbai Marathwada Campus, Jalna, 431213, India.
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32
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Heterologous biosynthesis as a platform for producing new generation natural products. Curr Opin Biotechnol 2020; 66:123-130. [DOI: 10.1016/j.copbio.2020.06.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 06/27/2020] [Accepted: 06/30/2020] [Indexed: 12/18/2022]
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33
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Muldoon JA, Harvey BG. Bio-Based Cycloalkanes: The Missing Link to High-Performance Sustainable Jet Fuels. CHEMSUSCHEM 2020; 13:5777-5807. [PMID: 32810345 DOI: 10.1002/cssc.202001641] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/14/2020] [Indexed: 05/12/2023]
Abstract
The development of sustainable energy solutions that reduce global carbon emissions, while maintaining high living standards, is one of the grand challenges of the current century. Transportation fuels are critical to economic development, globalization, and the advancement of society. Although ground vehicles and small aircraft are beginning a slow transition toward electric propulsion with energy sourced from solar radiation or wind, the extreme power requirements of jet aircraft require a more concentrated source of energy that is conveniently provided by liquid hydrocarbon fuels. This Review describes recent efforts to develop efficient routes for the conversion of crude biomass sources (e. g., lignocellulose) to cycloalkanes. These cycloalkanes impart advantageous properties to jet fuels, including increased density, higher volumetric heat of combustion, and enhanced operability. The combination of bio-based cycloalkanes and synthetic paraffinic kerosenes allows for the preparation of 100 % bio-based fuels that can outperform conventional petroleum-based fuels. In this Review methods are described that convert biomass-derived small molecules, including furfural, furfuryl alcohol, 5-hydroxymethylfurfural, cyclic ketones, phenolics, acyclic ketones, cyclic alcohols, furans, esters, and alkenes to high-density cycloalkanes. In addition to describing the chemical transformations and catalysts that have been developed to efficiently produce various cycloalkanes, this Review includes summaries of key fuel properties, which highlight the ability to generate fuels with customized performance metrics. This work is intended to inspire other researchers to study the conversion of sustainable feedstocks to full-performance aviation fuels. An acceleration of this research is critical to reducing the carbon footprint of commercial and military aviation on a timescale that will help blunt the impacts of global warming.
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Affiliation(s)
- Jake A Muldoon
- US NAVY, NAWCWD, Research Department, Chemistry Branch, China Lake, California, 93555, USA
| | - Benjamin G Harvey
- US NAVY, NAWCWD, Research Department, Chemistry Branch, China Lake, California, 93555, USA
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34
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Lawson CE, Martí JM, Radivojevic T, Jonnalagadda SVR, Gentz R, Hillson NJ, Peisert S, Kim J, Simmons BA, Petzold CJ, Singer SW, Mukhopadhyay A, Tanjore D, Dunn JG, Garcia Martin H. Machine learning for metabolic engineering: A review. Metab Eng 2020; 63:34-60. [PMID: 33221420 DOI: 10.1016/j.ymben.2020.10.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/22/2020] [Accepted: 10/31/2020] [Indexed: 12/14/2022]
Abstract
Machine learning provides researchers a unique opportunity to make metabolic engineering more predictable. In this review, we offer an introduction to this discipline in terms that are relatable to metabolic engineers, as well as providing in-depth illustrative examples leveraging omics data and improving production. We also include practical advice for the practitioner in terms of data management, algorithm libraries, computational resources, and important non-technical issues. A variety of applications ranging from pathway construction and optimization, to genetic editing optimization, cell factory testing, and production scale-up are discussed. Moreover, the promising relationship between machine learning and mechanistic models is thoroughly reviewed. Finally, the future perspectives and most promising directions for this combination of disciplines are examined.
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Affiliation(s)
- Christopher E Lawson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Jose Manuel Martí
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Tijana Radivojevic
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sai Vamshi R Jonnalagadda
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Reinhard Gentz
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nathan J Hillson
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Sean Peisert
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; University of California Davis, Davis, CA, 95616, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Pacific Northwest National Laboratory, Richland, 99354, WA, USA
| | - Blake A Simmons
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA
| | - Steven W Singer
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA
| | - Aindrila Mukhopadhyay
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA
| | - Deepti Tanjore
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Advanced Biofuels and Bioproducts Process Development Unit, Emeryville, CA, 94608, USA
| | | | - Hector Garcia Martin
- Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA; Joint BioEnergy Institute, Emeryville, CA, 94608, USA; DOE Agile BioFoundry, Emeryville, CA, 94608, USA; Basque Center for Applied Mathematics, 48009, Bilbao, Spain; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, USA.
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35
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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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36
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Phulara SC, Pandey S, Jha A, Chauhan PS, Gupta P, Shukla V. Hemiterpene compound, 3,3-dimethylallyl alcohol promotes longevity and neuroprotection in Caenorhabditis elegans. GeroScience 2020; 43:791-807. [PMID: 32725551 PMCID: PMC8110639 DOI: 10.1007/s11357-020-00241-w] [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: 12/22/2019] [Accepted: 07/22/2020] [Indexed: 10/23/2022] Open
Abstract
Terpenes and their derivatives have been used conventionally as potential dietary supplements to boost the nutritional value of endless food products. Several plant-based complex terpenoid and their derivatives have been reported for a wide range of medicinal and nutritional properties. However, their simple counterparts, whose production is relatively easy, sustainable, and economic from food-grade microbial sources, have not been studied yet for any such biological activities. The present study aimed to investigate the longevity-promoting property and neuromodulatory effects of 3,3-dimethylallyl alcohol (Prenol), one of the simplest forms of terpenoid and a constituent of fruit aroma, in the animal model Caenorhabditis elegans. Prenol supplementation (0.25 mM) augmented the lifespan of wild-type nematodes by 22.8% over the non-treated worms. Moreover, a suspended amyloid-β induced paralysis and reduced α-synuclein aggregation were observed in Prenol-treated worms. The lifespan extending properties of Prenol were correlated with ameliorated physiological parameters and increased stress (heat and oxidative) tolerance in C. elegans. In silico and gene-specific mutant studies showed that pro-longevity transcription factors DAF-16, HSF-1, and SKN-1 were involved in the improved lifespan and health-span of Prenol-treated worms. Transgenic green fluorescent protein-reporter gene expression analysis and relative mRNA quantification (using real-time PCR) demonstrated an increase in the expression of DAF-16, HSF-1, and SKN-1 transcription factors and their downstream target genes in Prenol-treated worms. Together, the findings suggest that small molecules, like Prenol, could be explored as a potential alternate to develop therapeutics against aging and age-related ailments.
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Affiliation(s)
- Suresh Chandra Phulara
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Vaddeswaram, Guntur, Andhra Pradesh, 522502, India
| | - Swapnil Pandey
- Microbial Technology Division, CSIR-National Botanical Research Institute, 436, Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Anubhuti Jha
- Department of Biotechnology, National Institute of Technology Raipur, G.E. Road, Raipur, Chhattisgarh, 492010, India
| | - Puneet Singh Chauhan
- Microbial Technology Division, CSIR-National Botanical Research Institute, 436, Rana Pratap Marg, Lucknow, 226001, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pratima Gupta
- Department of Biotechnology, National Institute of Technology Raipur, G.E. Road, Raipur, Chhattisgarh, 492010, India.
| | - Virendra Shukla
- Department of Biochemistry and Molecular Biology, IMRIC, Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem, 9112102, Jerusalem, Israel.
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Liang L, Liu R, Freed EF, Eckert CA. Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2-C6 Bioalcohol Production. Front Bioeng Biotechnol 2020; 8:710. [PMID: 32719784 PMCID: PMC7347752 DOI: 10.3389/fbioe.2020.00710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022] Open
Abstract
Biofuel production from renewable and sustainable resources is playing an increasingly important role within the fuel industry. Among biofuels, bioethanol has been most widely used as an additive for gasoline. Higher alcohols can be blended at a higher volume compared to ethanol and generate lower greenhouse gas (GHG) emissions without a need to change current fuel infrastructures. Thus, these fuels have the potential to replace fossil fuels in support of more environmentally friendly processes. This review summarizes the efforts to enhance bioalcohol production in engineered Escherichia coli over the last 5 years and analyzes the current challenges for increasing productivities for industrial applications.
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Affiliation(s)
- Liya Liang
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
- National Renewable Energy Laboratory, Golden, CO, United States
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de Bruijn WJC, Levisson M, Beekwilder J, van Berkel WJH, Vincken JP. Plant Aromatic Prenyltransferases: Tools for Microbial Cell Factories. Trends Biotechnol 2020; 38:917-934. [PMID: 32299631 DOI: 10.1016/j.tibtech.2020.02.006] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 01/09/2023]
Abstract
In plants, prenylation of aromatic compounds, such as (iso)flavonoids and stilbenoids, by membrane-bound prenyltransferases (PTs), is an essential step in the biosynthesis of many bioactive compounds. Prenylated aromatic compounds have various health-beneficial properties that are interesting for industrial applications, but their exploitation is limited due to their low abundance in nature. Harnessing plant aromatic PTs for prenylation in microbial cell factories may be a sustainable and economically viable alternative. Limitations in prenylated aromatic compound production have been identified, including availability of prenyl donor substrate. In this review, we summarize the current knowledge about plant aromatic PTs and discuss promising strategies towards the optimized production of prenylated aromatic compounds by microbial cell factories.
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Affiliation(s)
- Wouter J C de Bruijn
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands
| | - Mark Levisson
- Laboratory of Plant Physiology, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, Netherlands
| | - Jules Beekwilder
- Wageningen Plant Research, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, Netherlands
| | - Willem J H van Berkel
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands
| | - Jean-Paul Vincken
- Laboratory of Food Chemistry, Wageningen University & Research, Bornse Weilanden 9, 6708 WG, Wageningen, Netherlands.
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Eiben CB, Tian T, Thompson MG, Mendez-Perez D, Kaplan N, Goyal G, Chiniquy J, Hillson NJ, Lee TS, Keasling JD. Adenosine Triphosphate and Carbon Efficient Route to Second Generation Biofuel Isopentanol. ACS Synth Biol 2020; 9:468-474. [PMID: 32149502 DOI: 10.1021/acssynbio.9b00402] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Climate change necessitates the development of CO2 neutral or negative routes to chemicals currently produced from fossil carbon. In this paper we demonstrate a pathway from the renewable resource glucose to next generation biofuel isopentanol by pairing the isovaleryl-CoA biosynthesis pathway from Myxococcus xanthus and a butyryl-CoA reductase from Clostridium acetobutylicum. The best plasmid and Escherichia coli strain combination makes 80.50 ± 8.08 (SD) mg/L of isopentanol after 36 h under microaerobic conditions with an oleyl alcohol overlay. In addition, the system also shows a strong preference for isopentanol production over prenol in microaerobic conditions. Finally, the pathway requires zero adenosine triphosphate and can be paired theoretically with nonoxidative glycolysis, the combination being redox balanced from glucose thus avoiding unnecessary carbon loss as CO2. These pathway properties make the isovaleryl-CoA pathway an attractive isopentanol production route for further optimization.
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Affiliation(s)
- Christopher B. Eiben
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94270, United States
- Department of Bioengineering, University of California, San Francisco, California 94143, United States
| | - Tian Tian
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Mitchell G. Thompson
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California 94270, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel Mendez-Perez
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nurgul Kaplan
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Garima Goyal
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Chiniquy
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Agile BioFoundry, Emeryville, California 94608, United States
| | - Taek Soon Lee
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D. Keasling
- Department of Bioengineering, University of California, Berkeley, Berkeley, California 94270, United States
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, Berkeley, California 94270, United States
- Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, California 94270, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Ren J, Lee J, Na D. Recent advances in genetic engineering tools based on synthetic biology. J Microbiol 2020; 58:1-10. [PMID: 31898252 DOI: 10.1007/s12275-020-9334-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/19/2019] [Accepted: 11/05/2019] [Indexed: 12/26/2022]
Abstract
Genome-scale engineering is a crucial methodology to rationally regulate microbiological system operations, leading to expected biological behaviors or enhanced bioproduct yields. Over the past decade, innovative genome modification technologies have been developed for effectively regulating and manipulating genes at the genome level. Here, we discuss the current genome-scale engineering technologies used for microbial engineering. Recently developed strategies, such as clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9, multiplex automated genome engineering (MAGE), promoter engineering, CRISPR-based regulations, and synthetic small regulatory RNA (sRNA)-based knockdown, are considered as powerful tools for genome-scale engineering in microbiological systems. MAGE, which modifies specific nucleotides of the genome sequence, is utilized as a genome-editing tool. Contrastingly, synthetic sRNA, CRISPRi, and CRISPRa are mainly used to regulate gene expression without modifying the genome sequence. This review introduces the recent genome-scale editing and regulating technologies and their applications in metabolic engineering.
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Affiliation(s)
- Jun Ren
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jingyu Lee
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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41
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Microbiological Advances in Bioactives from High Altitude. MICROBIOLOGICAL ADVANCEMENTS FOR HIGHER ALTITUDE AGRO-ECOSYSTEMS & SUSTAINABILITY 2020. [DOI: 10.1007/978-981-15-1902-4_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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42
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Kang A, Mendez-Perez D, Goh EB, Baidoo EE, Benites VT, Beller HR, Keasling JD, Adams PD, Mukhopadhyay A, Lee TS. Optimization of the IPP-bypass mevalonate pathway and fed-batch fermentation for the production of isoprenol in Escherichia coli. Metab Eng 2019; 56:85-96. [DOI: 10.1016/j.ymben.2019.09.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/23/2019] [Accepted: 09/06/2019] [Indexed: 12/24/2022]
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Rosenkoetter KE, Kennedy CR, Chirik PJ, Harvey BG. [4+4]-Cycloaddition of Isoprene for the Production of High-Performance Bio-Based Jet Fuel. GREEN CHEMISTRY : AN INTERNATIONAL JOURNAL AND GREEN CHEMISTRY RESOURCE : GC 2019; 21:5616-5623. [PMID: 33790688 PMCID: PMC8009188 DOI: 10.1039/c9gc02404b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Isoprene was efficiently converted to 1,6-dimethyl-1,5-cyclooctadiene (DMCOD) by selective [4+4]-cycloaddition with a catalyst formed by in situ reduction of [(MePI)FeCl(μ-Cl)]2 (MePI = [2-(2,6-(CH3)2-C6H3-N=C(CH3))-C4H5N]). DMCOD was isolated in 92% yield, at the preparative scale, with a catalyst loading of 0.025 mol%, and a TON of 3680. Catalytic hydrogenation of DMCOD yielded 1,4-dimethylcyclooctane (DMCO). The cyclic structure and ring strain of DMCO afforded gravimetric and volumetric net heats of combustion 2.4 and 9.2% higher, respectively, than conventional jet fuel. In addition, the presence of methyl branches at two sites resulted in a -20 °C kinematic viscosity of 4.17 mm2 s-1, 48 % lower than the maximum allowed value for conventional jet fuel. The ability to derive isoprene and related alcohols readily from abundant biomass sources, coupled with the highly efficient [Fe]-catalyzed [4+4]-cycloaddition described herein, suggests that this process holds great promise for the economical production of high-performance, bio-based jet fuel blendstocks.
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Affiliation(s)
- Kyle E Rosenkoetter
- US NAVY, NAWCWD, Research Department, Chemistry Division, China Lake, California 93555
| | - C Rose Kennedy
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Paul J Chirik
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Benjamin G Harvey
- US NAVY, NAWCWD, Research Department, Chemistry Division, China Lake, California 93555
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44
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Eiben CB, de Rond T, Bloszies C, Gin J, Chiniquy J, Baidoo EEK, Petzold CJ, Hillson NJ, Fiehn O, Keasling JD. Mevalonate Pathway Promiscuity Enables Noncanonical Terpene Production. ACS Synth Biol 2019; 8:2238-2247. [PMID: 31576747 DOI: 10.1021/acssynbio.9b00230] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Lepidoptera (butterflies and moths) make the six-carbon compounds homoisopentenyl pyrophosphate (HIPP) and homodimethylallyl pyrophosphate (HDMAPP) that are incorporated into 16, 17, and 18 carbon farnesyl pyrophosphate (FPP) analogues. In this work we heterologously expressed the lepidopteran modified mevalonate pathway, a propionyl-CoA ligase, and terpene cyclases in E. coli to produce several novel terpenes containing 16 carbons. Changing the terpene cyclase generated different novel terpene product profiles. To further validate the new compounds we confirmed 13C propionate was incorporated, and that the masses and fragmentation patterns were consistent with novel 16 carbon terpenes by GC-QTOF. On the basis of the available farnesyl pyrophosphate analogues lepidoptera produce, this approach should greatly expand the reachable biochemical space with applications in areas where terpenes have traditionally found uses.
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Affiliation(s)
- Christopher B. Eiben
- Department of Bioengineering, University of California, San Francisco, California 94143, United States
| | - Tristan de Rond
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California 92093, United States
| | - Clayton Bloszies
- National Institute of Health West Coast Metabolomics Center, University of California Davis, Davis, California 95616, United States
| | - Jennifer Gin
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Jennifer Chiniquy
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Edward E. K. Baidoo
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Christopher J. Petzold
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Nathan J. Hillson
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Department of Energy Agile BioFoundry, Emeryville, California 94608, United States
| | - Oliver Fiehn
- National Institute of Health West Coast Metabolomics Center, University of California Davis, Davis, California 95616, United States
| | - Jay D. Keasling
- Department of Energy Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94270, United States
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
- Center for Synthetic Biochemistry, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
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45
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Petersen A, Crocoll C, Halkier BA. De novo production of benzyl glucosinolate in Escherichia coli. Metab Eng 2019; 54:24-34. [DOI: 10.1016/j.ymben.2019.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/11/2019] [Accepted: 02/24/2019] [Indexed: 12/30/2022]
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The isoprenoid alcohol pathway, a synthetic route for isoprenoid biosynthesis. Proc Natl Acad Sci U S A 2019; 116:12810-12815. [PMID: 31186357 DOI: 10.1073/pnas.1821004116] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The more than 50,000 isoprenoids found in nature are all derived from the 5-carbon diphosphates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Natively, IPP and DMAPP are generated by the mevalonate (MVA) and 2-C-methyl-d-erythritol-4-phosphate (MEP) pathways, which have been engineered to produce compounds with numerous applications. However, as these pathways are inherently constrained by carbon, energy inefficiencies, and their roles in native metabolism, engineering for isoprenoid biosynthesis at high flux, titer, and yield remains a challenge. To overcome these limitations, here we develop an alternative synthetic pathway termed the isoprenoid alcohol (IPA) pathway that centers around the synthesis and subsequent phosphorylation of IPAs. We first established a lower IPA pathway for the conversion of IPAs to isoprenoid pyrophosphate intermediates that enabled the production of greater than 2 g/L geraniol from prenol as well as limonene, farnesol, diaponeurosporene, and lycopene. We then designed upper IPA pathways for the generation of (iso)prenol from central carbon metabolites with the development of a route to prenol enabling its synthesis at more than 2 g/L. Using prenol as the linking intermediate further facilitated an integrated IPA pathway that resulted in the production of nearly 0.6 g/L total monoterpenoids from glycerol as the sole carbon source. The IPA pathway provides an alternative route to isoprenoids that is more energy efficient than native pathways and can serve as a platform for targeting a repertoire of isoprenoid compounds with application as high-value pharmaceuticals, commodity chemicals, and fuels.
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O’Kane PT, Dudley QM, McMillan AK, Jewett MC, Mrksich M. High-throughput mapping of CoA metabolites by SAMDI-MS to optimize the cell-free biosynthesis of HMG-CoA. SCIENCE ADVANCES 2019; 5:eaaw9180. [PMID: 31183410 PMCID: PMC6551189 DOI: 10.1126/sciadv.aaw9180] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/02/2019] [Indexed: 05/30/2023]
Abstract
Metabolic engineering uses enzymes to produce small molecules with industrial, pharmaceutical, and energy applications. However, efforts to optimize enzymatic pathways for commercial production are limited by the throughput of assays for quantifying metabolic intermediates and end products. We developed a multiplexed method for profiling CoA-dependent pathways that uses a cysteine-terminated peptide to covalently capture CoA-bound metabolites. Captured metabolites are then rapidly separated from the complex mixture by immobilization onto arrays of self-assembled monolayers and directly quantified by SAMDI mass spectrometry. We demonstrate the throughput of the assay by characterizing the cell-free synthesis of HMG-CoA, a key intermediate in the biosynthesis of isoprenoids, collecting over 10,000 individual spectra to map more than 800 unique reaction conditions. We anticipate that our rapid and robust analytical method will accelerate efforts to engineer metabolic pathways.
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Affiliation(s)
- Patrick T. O’Kane
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Quentin M. Dudley
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
| | - Aislinn K. McMillan
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
| | - Michael C. Jewett
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
| | - Milan Mrksich
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Department of Chemistry, Northwestern University, Evanston, IL, USA
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, USA
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48
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Morris DM, Quintana RL, Harvey BG. High-Performance Jet Fuels Derived from Bio-Based Alkenes by Iron-Catalyzed [2+2] Cycloaddition. CHEMSUSCHEM 2019; 12:1646-1652. [PMID: 30908903 DOI: 10.1002/cssc.201802588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/18/2019] [Accepted: 01/23/2019] [Indexed: 06/09/2023]
Abstract
A series of high-performance cycloparaffinic fuels have been generated by [2+2] cycloaddition of the bio-derived alkenes 1-hexene, isoprene, and 1-pentene, catalyzed by a low-valent iron pyridine(diimine) complex [(Me PDI)Fe(N2 )2 (μ-N2 )] [Me PDI=N,N'-(2,6-pyridinediyldiethylidyne)bis(2,6-dimethylbenzenamine)]. Reactions with 1-pentene and 1-hexene resulted in 85 % selectivity to 1,2-cyclobutanes, and 12 % selectivity to acyclic alkenes generated by β-hydride elimination. Self-dimerization of isoprene was sluggish and generated heavier oligomer products, but cross-dimerization of isoprene with 1-hexene afforded primarily a 1,3-cyclobutane product, along with isomers of acyclic C11 mixed dimers. Hydrocarbon mixtures were hydrogenated and fractionally distilled to yield finished fuel mixtures in overall yields of 83-93 % at the multigram scale. The fuels exhibited densities ranging between 0.767 and 0.783 g mL-1 , and net heats of combustion (NHOC) of up to 120.6 kBtu gal-1 (43.8 MJ kg-1 ). These values are higher than conventional synthetic paraffinic kerosenes owing to the higher density and ring strain afforded by the cyclobutane rings. The fuel mixtures also exhibited extremely low viscosities ranging from 2.38 to 4.78 mm2 s-1 at -20 °C, due in part to the presence of the acyclic dimers. The excellent fuel properties of the product mixtures, selectivity for dimer products, high yields, and the ability to use simple bio-derived alkenes as substrates, make the [Fe]-catalyzed [2+2] cycloaddition of unactivated alkenes a compelling route to the synthesis of sustainable high-performance fuels.
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Affiliation(s)
- David M Morris
- Chemistry Division, US NAVY, NAWCWD, Research Department, China Lake, California, 93555, USA
| | - Roxanne L Quintana
- Chemistry Division, US NAVY, NAWCWD, Research Department, China Lake, California, 93555, USA
| | - Benjamin G Harvey
- Chemistry Division, US NAVY, NAWCWD, Research Department, China Lake, California, 93555, USA
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Phulara SC, Chaturvedi P, Chaurasia D, Diwan B, Gupta P. Modulation of culture medium confers high-specificity production of isopentenol in Bacillus subtilis. J Biosci Bioeng 2019; 127:458-464. [DOI: 10.1016/j.jbiosc.2018.10.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 09/27/2018] [Accepted: 10/03/2018] [Indexed: 11/25/2022]
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50
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Flores A, Wang X, Nielsen DR. Recent trends in integrated bioprocesses: aiding and expanding microbial biofuel/biochemical production. Curr Opin Biotechnol 2019; 57:82-87. [PMID: 30877994 DOI: 10.1016/j.copbio.2019.02.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 01/16/2019] [Accepted: 02/05/2019] [Indexed: 01/04/2023]
Abstract
Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ product separation are poised to help address this intrinsic problem, but suffer their own unique shortcomings. To improve and expand the utility of this versatile bioprocessing strategy, recent innovations have focused on developing more effective separation materials and novel process configurations, as well as adapting designs to accommodate semi-continuous modes of operation. As a result, integrated bioprocesses are finding new applications to aid the biosynthesis of an ever-growing list of bioproducts. Emerging applications, meanwhile, are exploring the further expansion of such designs to interface microbial and chemical catalysts, leading to new and versatile routes for the one-pot synthesis of an even greater diversity of renewable products.
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Affiliation(s)
- Andrew Flores
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, United States
| | - Xuan Wang
- School of Life Sciences, Arizona State University, United States
| | - David R Nielsen
- Chemical Engineering Program, School for Engineering of Matter, Transport, and Energy, Arizona State University, United States.
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