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Lu M, Sha Y, Kumar V, Xu Z, Zhai R, Jin M. Transcription factor-based biosensor: A molecular-guided approach for advanced biofuel synthesis. Biotechnol Adv 2024; 72:108339. [PMID: 38508427 DOI: 10.1016/j.biotechadv.2024.108339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/07/2024] [Accepted: 02/18/2024] [Indexed: 03/22/2024]
Abstract
As a sustainable and renewable alternative to petroleum fuels, advanced biofuels shoulder the responsibility of energy saving, emission reduction and environmental protection. Traditional engineering of cell factories for production of advanced biofuels lacks efficient high-throughput screening tools and regulating systems, impeding the improvement of cellular productivity and yield. Transcription factor-based biosensors have been widely applied to monitor and regulate microbial cell factory products due to the advantages of fast detection and in-situ screening. This review updates the design and application of transcription factor-based biosensors tailored for advanced biofuels and related intermediates. The construction and genetic parts selection principle of biosensors are discussed. Strategies to enhance the performance of biosensor, including regulating promoter strength and RBS strength, optimizing plasmid copy number, implementing genetic amplifier, and modulating the structure of transcription factor, have also been summarized. We further review the application of biosensors in high-throughput screening of new metabolic engineering targets, evolution engineering, confirmation of protein function, and dynamic regulation of metabolic flux for higher production of advanced biofuels. At last, we discuss the current limitations and future trends of transcription factor-based biosensors.
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Affiliation(s)
- Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yuanyuan Sha
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, United Kingdom
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China.
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Gu S, Zhu F, Zhang L, Wen J. Mid-Long Chain Dicarboxylic Acid Production via Systems Metabolic Engineering: Progress and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5555-5573. [PMID: 38442481 DOI: 10.1021/acs.jafc.4c00002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Mid-to-long-chain dicarboxylic acids (DCAi, i ≥ 6) are organic compounds in which two carboxylic acid functional groups are present at the terminal position of the carbon chain. These acids find important applications as structural components and intermediates across various industrial sectors, including organic compound synthesis, food production, pharmaceutical development, and agricultural manufacturing. However, conventional petroleum-based DCA production methods cause environmental pollution, making sustainable development challenging. Hence, the demand for eco-friendly processes and renewable raw materials for DCA production is rising. Owing to advances in systems metabolic engineering, new tools from systems biology, synthetic biology, and evolutionary engineering can now be used for the sustainable production of energy-dense biofuels. Here, we explore systems metabolic engineering strategies for DCA synthesis in various chassis via the conversion of different raw materials into mid-to-long-chain DCAs. Subsequently, we discuss the future challenges in this field and propose synthetic biology approaches for the efficient production and successful commercialization of these acids.
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Affiliation(s)
- Shanna Gu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Fuzhou Zhu
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
| | - Lin Zhang
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian 116045, China
| | - Jianping Wen
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
- Frontiers Science Center for Synthetic Biology (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072,China
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3
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Dou Y, Zhou X, Liu X, Hou J. Exoproteome analysis of Pseudomonas aeruginosa response to high alkane stress. Arch Microbiol 2024; 206:51. [PMID: 38175208 DOI: 10.1007/s00203-023-03749-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 11/15/2023] [Accepted: 11/15/2023] [Indexed: 01/05/2024]
Abstract
Microbial biodegradation serves as an effective approach to treat oil pollution. However, the application of such methods for the degrading long-chain alkanes still encounters significant challenges. Comparative proteomics has extensively studied the intracellular proteins of bacteria that degrade short- and medium-chain alkanes, but the role and mechanism of extracellular proteins in many microorganism remain unclear. To enhance our understanding of the roles of extracellular proteins in the adaptation to long-chain alkanes, a label-free LC-MS/MS strategy was applied for the relative quantification of extracellular proteins of Pseudomonas aeruginosa SJTD-1-M (ProteomeXchange identifier PXD014638). 444 alkane-sentitive proteins were acquired and their cell localization analysis was performed using the Pseudomonas Genome Database. Among them, 111 proteins were found to be located in extracellular or Outer Membrane Vesicles (OMVs). The alkane-induced abundance of 11 extracellular or OMV target proteins was confirmed by parallel reaction monitoring (PRM). Furthermore, we observed that the expression levels of three proteins (Pra, PA2815, and FliC) were associated with the carbon chain length of the added alkane in the culture medium. The roles of these proteins in cell mobility, alkane emulsification, assimilation, and degradation were further discussed. OMVs were found to contain a number of enzymes involved in alkane metabolism, fatty acid beta-oxidation, and the TCA cycle, suggesting their potential as sites for facilitated alkane degradation. In this sense, this exoproteome analysis contributes to a better understanding of the role of extracellular proteins in the hydrocarbon treatment process.
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Affiliation(s)
- Yue Dou
- School of Pharmacy, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
| | - Xuefeng Zhou
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
| | - Xipeng Liu
- School of Life Science and Biotechnology, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China
| | - Jingli Hou
- Instrumental Analysis Center of Shanghai Jiao Tong University, 800 Dong-Chuan Road, Shanghai, 200240, China.
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Bertelmann C, Mock M, Schmid A, Bühler B. Efficiency aspects of regioselective testosterone hydroxylation with highly active CYP450-based whole-cell biocatalysts. Microb Biotechnol 2024; 17:e14378. [PMID: 38018939 PMCID: PMC10832557 DOI: 10.1111/1751-7915.14378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023] Open
Abstract
Steroid hydroxylations belong to the industrially most relevant reactions catalysed by cytochrome P450 monooxygenases (CYP450s) due to the pharmacological relevance of hydroxylated derivatives. The implementation of respective bioprocesses at an industrial scale still suffers from several limitations commonly found in CYP450 catalysis, that is low turnover rates, enzyme instability, inhibition and toxicity related to the substrate(s) and/or product(s). Recently, we achieved a new level of steroid hydroxylation rates by introducing highly active testosterone-hydroxylating CYP450 BM3 variants together with the hydrophobic outer membrane protein AlkL into Escherichia coli-based whole-cell biocatalysts. However, the activity tended to decrease, which possibly impedes overall productivities and final product titres. In this study, a considerable instability was confirmed and subject to a systematic investigation regarding possible causes. In-depth evaluation of whole-cell biocatalyst kinetics and stability revealed a limitation in substrate availability due to poor testosterone solubility as well as inhibition by the main product 15β-hydroxytestosterone. Instability of CYP450 BM3 variants was disclosed as another critical factor, which is of general significance for CYP450-based biocatalysis. Presented results reveal biocatalyst, reaction and process engineering strategies auguring well for industrial implementation of the developed steroid hydroxylation platform.
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Affiliation(s)
| | - Magdalena Mock
- Department of Solar MaterialsLeipzigGermany
- Present address:
Department of Mechanical Engineering and Material SciencesGeorg Agricola University of Applied SciencesBochumGermany
| | | | - Bruno Bühler
- Department of Solar MaterialsLeipzigGermany
- Department of Microbial BiotechnologyHelmholtz Centre for Environmental Research GmbH–UFZLeipzigGermany
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A Novel FadL Homolog, AltL, Mediates Transport of Long-Chain Alkanes and Fatty Acids in Acinetobacter venetianus RAG-1. Appl Environ Microbiol 2022; 88:e0129422. [PMID: 36169310 PMCID: PMC9599521 DOI: 10.1128/aem.01294-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Due to the barrier effect of lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria, transporters are required for hydrophobic alkane uptake. However, there are few reports on long-chain alkane transporters. In this study, a potential long-chain alkane transporter (AltL) was screened in Acinetobacter venetianus RAG-1 by comparative transcriptome analysis. Growth and degradation experiments showed that altL deletion led to the loss of n-octacosane utilization capacity of RAG-1. To identify the function of AltL, we measured the existence and accumulation of alkanes in cells through the constructed alkane detection system and isotope transport experiment, which proved its long-chain alkane transport function. Growth experiments using different chain-length n-alkanes and fatty acids as substrates showed that AltL was responsible for the transport of (very) long-chain n-alkanes (C20 to C38) and fatty acids (C18A to C28A) and was also involved in the uptake of medium-chain n-alkanes (C16 to C18). Subsequently, we analyzed the distribution of AltL in bacteria, and found that AltL homologs are widespread in Gamma-, Beta-, and Deltaproteobacteria. An AltL homolog in Pseudomonas aeruginosa was also identified to participate in long-chain alkane transport by a gene deletion and growth assay. We also found that overexpression of altL in Pseudomonas aeruginosa enhanced the degradation of C16 to C32 n-alkanes. In addition, structure analysis showed that AltL has longer extracellular loops than other FadL family members, which may be involved in the binding of alkanes. These results showed that AltL is a novel transporter and that it is mainly responsible for the transport of long-chain n-alkanes and (very) long-chain fatty acids and has broad application potential. IMPORTANCE Petroleum pollution has caused great harm to the natural environment, and alkanes are the main components of petroleum. Many Gram-negative bacteria can use alkanes as carbon and energy sources, which is an important strategy for oil pollution remediation. Alkane uptake is the first step for its utilization. Hence, the characterization of transport proteins is of great significance for the recovery of oil pollution and other potential applications in industrial engineering bacteria. At present, some short- and medium-chain alkane transporters have been identified, but stronger hydrophobic long-chain alkane transporters have received little attention. In this study, the broad-spectrum transporter AltL, identified in RAG-1, makes up for the lack of research on the transport of long-chain alkanes and (very) long-chain fatty acids. Meanwhile, the structural features of longer extracellular loops might be related to its unique transport function on more hydrophobic and larger substrates, indicating it is a novel type alkane transporter.
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Microbial cell surface engineering for high-level synthesis of bio-products. Biotechnol Adv 2022; 55:107912. [PMID: 35041862 DOI: 10.1016/j.biotechadv.2022.107912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 02/08/2023]
Abstract
Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.
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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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8
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Kell DB. The Transporter-Mediated Cellular Uptake and Efflux of Pharmaceutical Drugs and Biotechnology Products: How and Why Phospholipid Bilayer Transport Is Negligible in Real Biomembranes. Molecules 2021; 26:5629. [PMID: 34577099 PMCID: PMC8470029 DOI: 10.3390/molecules26185629] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 09/03/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the years, my colleagues and I have come to realise that the likelihood of pharmaceutical drugs being able to diffuse through whatever unhindered phospholipid bilayer may exist in intact biological membranes in vivo is vanishingly low. This is because (i) most real biomembranes are mostly protein, not lipid, (ii) unlike purely lipid bilayers that can form transient aqueous channels, the high concentrations of proteins serve to stop such activity, (iii) natural evolution long ago selected against transport methods that just let any undesirable products enter a cell, (iv) transporters have now been identified for all kinds of molecules (even water) that were once thought not to require them, (v) many experiments show a massive variation in the uptake of drugs between different cells, tissues, and organisms, that cannot be explained if lipid bilayer transport is significant or if efflux were the only differentiator, and (vi) many experiments that manipulate the expression level of individual transporters as an independent variable demonstrate their role in drug and nutrient uptake (including in cytotoxicity or adverse drug reactions). This makes such transporters valuable both as a means of targeting drugs (not least anti-infectives) to selected cells or tissues and also as drug targets. The same considerations apply to the exploitation of substrate uptake and product efflux transporters in biotechnology. We are also beginning to recognise that transporters are more promiscuous, and antiporter activity is much more widespread, than had been realised, and that such processes are adaptive (i.e., were selected by natural evolution). The purpose of the present review is to summarise the above, and to rehearse and update readers on recent developments. These developments lead us to retain and indeed to strengthen our contention that for transmembrane pharmaceutical drug transport "phospholipid bilayer transport is negligible".
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Affiliation(s)
- Douglas B. Kell
- Department of Biochemistry and Systems Biology, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown St, Liverpool L69 7ZB, UK;
- Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Building 220, Kemitorvet, 2800 Kgs Lyngby, Denmark
- Mellizyme Biotechnology Ltd., IC1, Liverpool Science Park, Mount Pleasant, Liverpool L3 5TF, UK
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Park HA, Choi KY. α, ω-Oxyfunctionalization of C12 alkanes via whole-cell biocatalysis of CYP153A from Marinobacter aquaeolei and a new CYP from Nocardia farcinica IFM10152. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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10
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Yoo HW, Kim J, Patil MD, Park BG, Joo SY, Yun H, Kim BG. Production of 12-hydroxy dodecanoic acid methyl ester using a signal peptide sequence-optimized transporter AlkL and a novel monooxygenase. BIORESOURCE TECHNOLOGY 2019; 291:121812. [PMID: 31376668 DOI: 10.1016/j.biortech.2019.121812] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 07/11/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
In this study, a signal peptide of AlkL was replaced with other signal peptides to improve the soluble expression and thereby facilitate the transport of dodecanoic acid methyl ester (DAME) substrate into the E. coli. Consequently, AlkL with signal peptide FadL (AlkLf) showed higher transport activity toward DAME. Furthermore, the promoter optimization for the efficient heterologous expression of the transporter AlkLf and alkane monooxygenase (AlkBGT) system was conducted and resulted in increased ω-oxygenation activity of AlkBGT system. Moreover, bioinformatic studies led to the identification of novel monooxygenase from Pseudomonas pelagia (Pel), which exhibited 20% higher activity towards DAME as substrate compared to AlkB. Finally, the construction of a chimeric transporter and the expression of newly identified monooxygenase enabled the production of 44.8 ± 7.5 mM of 12-hydroxy dodecanoic acid methyl ester (HADME) and 31.8 ± 1.7 mM of dodecanedioic acid monomethyl ester (DDAME) in a two-phase reaction system.
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Affiliation(s)
- Hee-Wang Yoo
- Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea
| | - Joonwon Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Beom Gi Park
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Sung-Yeon Joo
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, Seoul, Republic of Korea
| | - Byung-Gee Kim
- Interdisciplinary Program of Bioengineering, Seoul National University, Seoul 08826, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826, Republic of Korea; School of Chemical and Biological Engineering, Seoul National University, Seoul, Republic of Korea; Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea.
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He Q, Bennett GN, San KY, Wu H. Biosynthesis of Medium-Chain ω-Hydroxy Fatty Acids by AlkBGT of Pseudomonas putida GPo1 With Native FadL in Engineered Escherichia coli. Front Bioeng Biotechnol 2019; 7:273. [PMID: 31681749 PMCID: PMC6812396 DOI: 10.3389/fbioe.2019.00273] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/01/2019] [Indexed: 12/19/2022] Open
Abstract
Hydroxy fatty acids (HFAs) are valuable compounds that are widely used in medical, cosmetic and food fields. Production of ω-HFAs via bioconversion by engineered Escherichia coli has received a lot of attention because this process is environmentally friendly. In this study, a whole-cell bio-catalysis strategy was established to synthesize medium-chain ω-HFAs based on the AlkBGT hydroxylation system from Pseudomonas putida GPo1. The effects of blocking the β-oxidation of fatty acids (FAs) and enhancing the transportation of FAs on ω-HFAs bio-production were also investigated. When fadE and fadD were deleted, the consumption of decanoic acid decreased, and the yield of ω-hydroxydecanoic acid was enhanced remarkably. Additionally, the co-expression of the FA transporter protein, FadL, played an important role in increasing the conversion rate of ω-hydroxydecanoic acid. As a result, the concentration and yield of ω-hydroxydecanoic acid in NH03(pBGT-fadL) increased to 309 mg/L and 0.86 mol/mol, respectively. This whole-cell bio-catalysis system was further applied to the biosynthesis of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid using octanoic acid and dodecanoic acid as substrates, respectively. The concentrations of ω-hydroxyoctanoic acid and ω-hydroxydodecanoic acid reached 275.48 and 249.03 mg/L, with yields of 0.63 and 0.56 mol/mol, respectively. This study demonstrated that the overexpression of AlkBGT coupled with native FadL is an efficient strategy to synthesize medium-chain ω-HFAs from medium-chain FAs in fadE and fadD mutant E. coli strains.
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Affiliation(s)
- Qiaofei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - George N. Bennett
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Ka-Yiu San
- Department of Bioengineering, Rice University, Houston, TX, United States
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, TX, United States
| | - Hui Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
- Shanghai Collaborative Innovation Center for Biomanufacturing Technology, Shanghai, China
- Key Laboratory of Bio-based Material Engineering of China National Light Industry Council, Shanghai, China
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12
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White BE, Fenner CJ, Smit MS, Harrison STL. Effect of cell permeability and dehydrogenase expression on octane activation by CYP153A6-based whole cell Escherichia coli catalysts. Microb Cell Fact 2017; 16:156. [PMID: 28931395 PMCID: PMC5607502 DOI: 10.1186/s12934-017-0763-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 09/07/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND The regeneration of cofactors and the supply of alkane substrate are key considerations for the biocatalytic activation of hydrocarbons by cytochrome P450s. This study focused on the biotransformation of n-octane to 1-octanol using resting Escherichia coli cells expressing the CYP153A6 operon, which includes the electron transport proteins ferredoxin and ferredoxin reductase. Glycerol dehydrogenase was co-expressed with the CYP153A6 operon to investigate the effects of boosting cofactor regeneration. In order to overcome the alkane supply bottleneck, various chemical and physical approaches to membrane permeabilisation were tested in strains with or without additional dehydrogenase expression. RESULTS Dehydrogenase co-expression in whole cells did not improve product formation and reduced the stability of the system at high cell densities. Chemical permeabilisation resulted in initial hydroxylation rates that were up to two times higher than the whole cell system, but severely impacted biocatalyst stability. Mechanical cell breakage led to improved enzyme stability, but additional dehydrogenase expression was necessary to improve product formation. The best-performing system (in terms of final titres) consisted of mechanically ruptured cells expressing additional dehydrogenase. This system had an initial activity of 1.67 ± 0.12 U/gDCW (32% improvement on whole cells) and attained a product concentration of 34.8 ± 1.6 mM after 24 h (22% improvement on whole cells). Furthermore, the system was able to maintain activity when biotransformation was extended to 72 h, resulting in a final product titre of 60.9 ± 1.1 mM. CONCLUSIONS This study suggests that CYP153A6 in whole cells is limited by coupling efficiencies rather than cofactor supply. However, the most significant limitation in the current system is hydrocarbon transport, with substrate import being the main determinant of hydroxylation rates, and product export playing a key role in system stability.
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Affiliation(s)
- Bronwyn E White
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa.,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Caryn J Fenner
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa.,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Martha S Smit
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa.,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa
| | - Susan T L Harrison
- Centre for Bioprocess Engineering Research (CeBER), Department of Chemical Engineering, University of Cape Town, Private Bag X3, Rondebosch, Cape Town, 7701, South Africa. .,South African DST-NRF Centre of Excellence in Catalysis, c*change, University of Cape Town, Private Bag, Rondebosch, Cape Town, 7701, South Africa.
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13
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Zhou X, Xing X, Hou J, Liu J. Quantitative proteomics analysis of proteins involved in alkane uptake comparing the profiling of Pseudomonas aeruginosa SJTD-1 in response to n-octadecane and n-hexadecane. PLoS One 2017; 12:e0179842. [PMID: 28662172 PMCID: PMC5491041 DOI: 10.1371/journal.pone.0179842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 06/05/2017] [Indexed: 12/22/2022] Open
Abstract
While many data are available on genes encoding proteins for degradation of hydrocarbons in bacteria, the impact of alkane on transporter protein expression is unclear. Pseudomonas aeruginosa SJTD-1 is a strain that can consume medium- and long-chain n-alkanes. In order to study the proteins involved in n-octadecane uptake, we use iTRAQ and label free comparative proteomics analysis to identify the proteins of alkane uptake in response to n-octadecane (C18) comparing with n-hexadecane (C16) in P. aeruginosa SJTD-1. A total of 1102 and 1249 proteins were identified by iTRAQ-based and label free quantitative methodologies, respectively. By application of 1.5 (iTRAQ) or 2-fold (label free) for upregulated and 0.65 (iTRAQ) or 0.5-fold (label free) for downregulated cutoff values, 91 and 99 proteins were found to be differentially expressed comparing SJTD-1 cultivated on C18 with C16 respectively. There are six proteins with the common differential expression by iTRAQ and label free-based methods. Results of bioinformational analysis suggested the involvement of bacterial chemotaxis in responds to C18. Additionally, quantitative reverse transcriptase PCR (qRT-PCR) results confirmed C18-induced change in levels of FleQ, FliC, NirS, FadL and FadD proteins and the role of the proteins in n-octadecane uptake was further discussed in P. aeruginosa. In conclusion, results of the present study provided information about possible target-related proteins of bacterial chemotaxis, swimming performance, alkane transport to stimulus of n-ctadecane rather than n-hexadecane in P. aeruginosa SJTD-1.
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Affiliation(s)
- Xuefeng Zhou
- School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xuejiao Xing
- School of Pharmacy, Shanghai Jiao Tong University, Shanghai, China
| | - Jingli Hou
- Instrumental Analysis Center of Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
| | - Jianhua Liu
- School of Life Science & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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14
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Accessing the structural and thermodynamic properties of ultra-thin layers of C32 adsorbed on a SiO 2 surface. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.01.065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Tan Z, Black W, Yoon JM, Shanks JV, Jarboe LR. Improving Escherichia coli membrane integrity and fatty acid production by expression tuning of FadL and OmpF. Microb Cell Fact 2017; 16:38. [PMID: 28245829 PMCID: PMC5331629 DOI: 10.1186/s12934-017-0650-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 02/22/2017] [Indexed: 11/26/2022] Open
Abstract
Background Construction of microbial biocatalysts for the production of biorenewables at economically viable yields and titers is frequently hampered by product toxicity. Membrane damage is often deemed as the principal mechanism of this toxicity, particularly in regards to decreased membrane integrity. Previous studies have attempted to engineer the membrane with the goal of increasing membrane integrity. However, most of these works focused on engineering of phospholipids and efforts to identify membrane proteins that can be targeted to improve fatty acid production have been unsuccessful. Results Here we show that deletion of outer membrane protein ompF significantly increased membrane integrity, fatty acid tolerance and fatty acid production, possibly due to prevention of re-entry of short chain fatty acids. In contrast, deletion of fadL resulted in significantly decreased membrane integrity and fatty acid production. Consistently, increased expression of fadL remarkably increased membrane integrity and fatty acid tolerance while also increasing the final fatty acid titer. This 34% increase in the final fatty acid titer was possibly due to increased membrane lipid biosynthesis. Tuning of fadL expression showed that there is a positive relationship between fadL abundance and fatty acid production. Combinatorial deletion of ompF and increased expression of fadL were found to have an additive role in increasing membrane integrity, and was associated with a 53% increase the fatty acid titer, to 2.3 g/L. Conclusions These results emphasize the importance of membrane proteins for maintaining membrane integrity and production of biorenewables, such as fatty acids, which expands the targets for membrane engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12934-017-0650-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zaigao Tan
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - William Black
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.,Department of Chemical Engineering and Materials Sciences, University of California, 916 Engineering Tower Irvine, Irvine, CA, 92697-2575, USA
| | - Jong Moon Yoon
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Jacqueline V Shanks
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Laura R Jarboe
- 4134 Biorenewables Research Laboratory, Department of Chemical and Biological Engineering, Iowa State University, Ames, IA, 50011, USA.
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