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Yang J, Zhang J, Zhu Z, Du G. The challenges and prospects of Escherichia coli as an organic acid production host under acid stress. Appl Microbiol Biotechnol 2021; 105:8091-107. [PMID: 34617140 DOI: 10.1007/s00253-021-11577-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/07/2021] [Accepted: 09/08/2021] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Organic acids have a wide range of applications and have attracted the attention of many industries, and their large-scale applications have led fermentation production to low-cost development. Among them, the microbial fermentation method, especially using Escherichia coli as the production host, has the advantages of fast growth and low energy consumption, and has gradually shown better advantages and prospects in organic acid fermentation production. IMPORTANCE However, when the opportunity comes, the acidified environment caused by the acid products accumulated during the fermentation process also challenges E. coli. The acid sensitivity of E. coli is a core problem that needs to be solved urgently. The addition of neutralizers in traditional operations led to the emergence of osmotic stress inadvertently, the addition of strong acid substances to recover products in the salt state not only increases production costs, but the discharged sewage is also harmful to the environment. ELABORATION This article summarizes the current status of the application of E. coli in the production of organic acids, and based on the impact of acid stress on the physiological state of cells and the impact of industrial production profits, put forward some new conjectures that can make up for the deficiencies in existing research and application. IMPLICATION At this point, the diversified transformation of E. coli has become a chassis microbe that is more suitable for industrial fermentation, enhancing industrial application value. KEY POINTS • E. coli is a potential host for high value-added organic acids production. • Classify the damage mechanism and coping strategies of E. coli when stimulated by acid molecules. • Multi-dimensional expansion tools are needed to create acid-resistant E. coli chassis.
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Yu L, Zhang S, Xu Y, Mi X, Xing T, Li J, Zhang L, Gao F, Jiang Y. Acid resistance of E. coli O157:H7 and O26:H11 exposure to lactic acid revealed by transcriptomic analysis. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2020.110352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kutscha R, Pflügl S. Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches. Int J Mol Sci 2020; 21:ijms21228777. [PMID: 33233586 PMCID: PMC7699770 DOI: 10.3390/ijms21228777] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/20/2023] Open
Abstract
Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.
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Song JW, Seo JH, Oh DK, Bornscheuer UT, Park JB. Design and engineering of whole-cell biocatalytic cascades for the valorization of fatty acids. Catal Sci Technol 2020. [DOI: 10.1039/c9cy01802f] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This review presents the key factors to construct a productive whole-cell biocatalytic cascade exemplified for the biotransformation of renewable fatty acids.
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Affiliation(s)
- Ji-Won Song
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
| | - Joo-Hyun Seo
- Department of Bio and Fermentation Convergence Technology
- Kookmin University
- Seoul 02707
- Republic of Korea
| | - Doek-Kun Oh
- Department of Bioscience and Biotechnology
- Konkuk University
- Seoul 143-701
- Republic of Korea
| | - Uwe T. Bornscheuer
- Institute of Biochemistry
- Department of Biotechnology & Enzyme Catalysis
- Greifswald University
- 17487 Greifswald
- Germany
| | - Jin-Byung Park
- Department of Food Science and Engineering
- Ewha Womans University
- Seoul 03760
- Republic of Korea
- Institute of Molecular Microbiology and Biosystems Engineering
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Santoscoy MC, Jarboe LR. Streamlined assessment of membrane permeability and its application to membrane engineering of Escherichia coli for octanoic acid tolerance. ACTA ACUST UNITED AC 2019; 46:843-53. [DOI: 10.1007/s10295-019-02158-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Accepted: 02/17/2019] [Indexed: 10/27/2022]
Abstract
Abstract
The economic viability of bio-production processes is often limited by damage to the microbial cell membrane and thus there is a demand for strategies to increase the robustness of the cell membrane. Damage to the microbial membrane is also a common mode of action by antibiotics. Membrane-impermeable DNA-binding dyes are often used to assess membrane integrity in conjunction with flow cytometry. We demonstrate that in situ assessment of the membrane permeability of E. coli to SYTOX Green is consistent with flow cytometry, with the benefit of lower experimental intensity, lower cost, and no need for a priori selection of sampling times. This method is demonstrated by the characterization of four membrane engineering strategies (deletion of aas, deletion of cfa, increased expression of cfa, and deletion of bhsA) for their effect on octanoic acid tolerance, with the finding that deletion of bhsA increased tolerance and substantially decreased membrane leakage.
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Shin J, Yu J, Park M, Kim C, Kim H, Park Y, Ban C, Seydametova E, Song YH, Shin CS, Chung KH, Woo JM, Chung H, Park JB, Kweon DH. Endocytosing Escherichia coli as a Whole-Cell Biocatalyst of Fatty Acids. ACS Synth Biol 2019; 8:1055-1066. [PMID: 31018087 DOI: 10.1021/acssynbio.8b00519] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Whole cell biocatalysts can be used to convert fatty acids into various value-added products. However, fatty acid transport across cellular membranes into the cytosol of microbial cells limits substrate availability and impairs membrane integrity, which in turn decreases cell viability and bioconversion activity. Because these problems are associated with the mechanism of fatty acid transport through membranes, a whole-cell biocatalyst that can form caveolae-like structures was generated to promote substrate endocytosis. Caveolin-1 ( CAV1) expression in Escherichia coli increased both the fatty acid transport rate and intracellular fatty acid concentrations via endocytosis of the supplemented substrate. Furthermore, fatty-acid endocytosis alleviated substrate cytotoxicity in E. coli. These traits attributed to bacterial endocytosis resulted in dramatically elevated biotransformation efficiencies in fed-batch and cell-recycle reaction systems when caveolae-forming E. coli was used for the bioconversion of ricinoleic acid (12-hydroxyoctadec-9-enoic acid) to ( Z)-11-(heptanoyloxy) undec-9-enoic acid. We propose that CAV1-mediated endocytosing E. coli represents a versatile tool for the biotransformation of hydrophobic substrates.
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Affiliation(s)
- Jonghyeok Shin
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jiwon Yu
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Myungseo Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Chakhee Kim
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hooyeon Kim
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yunjeong Park
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Choongjin Ban
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Emine Seydametova
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | | | | | - Kyung-Hwun Chung
- Electron Microscope Facility, Dental Research Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Min Woo
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Hyunwoo Chung
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Jin-Byung Park
- Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Dae-Hyuk Kweon
- Department of Integrative Biotechnology, College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Biomedical Institute for Convergence, Sungkyunkwan University, Suwon 16419, Republic of Korea
- Center for Biologics, Sungkyunkwan University, Suwon 16419, Republic of Korea
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Blevins MS, Klein DR, Brodbelt JS. Localization of Cyclopropane Modifications in Bacterial Lipids via 213 nm Ultraviolet Photodissociation Mass Spectrometry. Anal Chem 2019; 91:6820-6828. [PMID: 31026154 DOI: 10.1021/acs.analchem.9b01038] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Subtle structural features in bacterial lipids such as unsaturation elements can have vast biological implications. Cyclopropane rings have been correlated with tolerance to a number of adverse conditions in bacterial phospholipids. They have also been shown to play a major role in Mycobacterium tuberculosis ( M. tuberculosis or Mtb) pathogenesis as they occur in mycolic acids (MAs) in the mycobacterial cell. Traditional collisional activation methods allow elucidation of basic structural features of lipids but fail to reveal the presence and position of cyclopropane rings. Here, we employ 213 nm ultraviolet photodissociation mass spectrometry (UVPD-MS) for structural characterization of cyclopropane rings in bacterial phospholipids and MAs. Upon UVPD, dual cross-ring C-C cleavages on both sides of the cyclopropane ring are observed for cyclopropyl lipids, resulting in diagnostic pairs of fragment ions spaced 14 Da apart, thus enabling cyclopropane localization. These diagnostic pairs of ions corresponding to dual cross-ring cleavage are observed in both negative and positive ion modes and afford localization of multiple cyclopropane rings within a single lipid. This method was integrated with liquid chromatography (LC) for LC/UVPD-MS analysis of cyclopropyl glycerophospholipids in Escherichia coli ( E. coli) and for analysis of MAs in Mycobacterium bovis ( M. bovis) and M. tuberculosis lipid extracts.
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Affiliation(s)
- Molly S Blevins
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Dustin R Klein
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jennifer S Brodbelt
- Department of Chemistry , University of Texas at Austin , Austin , Texas 78712 , United States
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Valle-González ER, Jackman JA, Yoon BK, Park S, Sut TN, Cho NJ. Characterizing How Acidic pH Conditions Affect the Membrane-Disruptive Activities of Lauric Acid and Glycerol Monolaurate. Langmuir 2018; 34:13745-13753. [PMID: 30343569 DOI: 10.1021/acs.langmuir.8b02536] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Fatty acids and monoglycerides are single-chain lipid amphiphiles that interact with phospholipid membranes as part of various biological activities. For example, they can exhibit membrane-disruptive behavior against microbial pathogens on the human skin surface. Supported lipid bilayers (SLBs) provide a useful experimental platform to characterize these membrane-disruptive behaviors, although related studies have been limited to neutral pH conditions. Herein, we investigated how lauric acid (LA) and glycerol monolaurate (GML) interact with SLBs and cause membrane morphological changes under acidic pH conditions that are representative of the human skin surface. Although LA induces tubule formation under neutral pH conditions, we discovered that LA causes membrane phase separation under acidic pH conditions. By contrast, GML induced membrane budding in both pH environments, although there was more extensive membrane remodeling under acidic pH conditions. We discuss these findings in the context of how solution pH affects the ionization states and micellar aggregation properties of LA and GML as well as its effect on the bending stiffness of lipid bilayers. Collectively, the findings demonstrate that solution pH plays an important role in modulating the interaction of fatty acids and monoglycerides with phospholipid membranes, and hence influences the scope and potency of their membrane-disruptive activities.
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Affiliation(s)
- Elba R Valle-González
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
- Centre for Biomimetic Sensor Science , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
- Centre for Biomimetic Sensor Science , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
| | - Bo Kyeong Yoon
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
- Centre for Biomimetic Sensor Science , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
| | - Soohyun Park
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
- Centre for Biomimetic Sensor Science , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
| | - Tun Naw Sut
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
- Centre for Biomimetic Sensor Science , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering , Nanyang Technological University , 50 Nanyang Avenue , 639798 , Singapore
- Centre for Biomimetic Sensor Science , Nanyang Technological University , 50 Nanyang Drive , 637553 , Singapore
- School of Chemical and Biomedical Engineering , Nanyang Technological University , 62 Nanyang Drive , 637459 , Singapore
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Ahn JH, Lee JA, Bang J, Lee SY. Membrane engineering via trans-unsaturated fatty acids production improves succinic acid production in Mannheimia succiniciproducens. J Ind Microbiol Biotechnol 2018; 45:555-66. [PMID: 29380151 DOI: 10.1007/s10295-018-2016-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 01/23/2018] [Indexed: 12/11/2022]
Abstract
Engineering of microorganisms to produce desired bio-products with high titer, yield, and productivity is often limited by product toxicity. This is also true for succinic acid (SA), a four carbon dicarboxylic acid of industrial importance. Acid products often cause product toxicity to cells through several different factors, membrane damage being one of the primary factors. In this study, cis-trans isomerase from Pseudomonas aeruginosa was expressed in Mannheimia succiniciproducens to produce trans-unsaturated fatty acid (TUFA) and to reinforce the cell membrane of M. succiniciproducens. The engineered strain showed significant decrease in membrane fluidity as production of TUFA enabled tight packing of fatty acids, which made cells to possess more rigid cell membrane. As a result, the membrane-engineered M. succiniciproducens strain showed higher tolerance toward SA and increased production of SA compared with the control strain without membrane engineering. The membrane engineering approach employed in this study will be useful for increasing tolerance to, and consequently enhancing production of acid products.
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Wilbanks B, Trinh CT. Comprehensive characterization of toxicity of fermentative metabolites on microbial growth. Biotechnol Biofuels 2017; 10:262. [PMID: 29213315 PMCID: PMC5707818 DOI: 10.1186/s13068-017-0952-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 11/02/2017] [Indexed: 05/08/2023]
Abstract
BACKGROUND Volatile carboxylic acids, alcohols, and esters are natural fermentative products, typically derived from anaerobic digestion. These metabolites have important functional roles to regulate cellular metabolisms and broad use as food supplements, flavors and fragrances, solvents, and fuels. Comprehensive characterization of toxic effects of these metabolites on microbial growth under similar conditions is very limited. RESULTS We characterized a comprehensive list of thirty-two short-chain carboxylic acids, alcohols, and esters on microbial growth of Escherichia coli MG1655 under anaerobic conditions. We analyzed toxic effects of these metabolites on E. coli health, quantified by growth rate and cell mass, as a function of metabolite types, concentrations, and physiochemical properties including carbon number, chemical functional group, chain branching feature, energy density, total surface area, and hydrophobicity. Strain characterization revealed that these metabolites exert distinct toxic effects on E. coli health. We found that higher concentrations and/or carbon numbers of metabolites cause more severe growth inhibition. For the same carbon numbers and metabolite concentrations, we discovered that branched chain metabolites are less toxic than the linear chain ones. Remarkably, shorter alkyl esters (e.g., ethyl butyrate) appear less toxic than longer alkyl esters (e.g., butyl acetate). Regardless of metabolites, hydrophobicity of a metabolite, governed by its physiochemical properties, strongly correlates with the metabolite's toxic effect on E. coli health. CONCLUSIONS Short-chain alcohols, acids, and esters exhibit distinctive toxic effects on E. coli health. Hydrophobicity is a quantitative predictor to evaluate the toxic effect of a metabolite. This study sheds light on degrees of toxicity of fermentative metabolites on microbial health and further helps in the selection of desirable metabolites and hosts for industrial fermentation to overproduce them.
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Affiliation(s)
- Brandon Wilbanks
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Drive, Knoxville, TN 37996 USA
| | - Cong T. Trinh
- Department of Chemical and Biomolecular Engineering, University of Tennessee, 1512 Middle Drive, Knoxville, TN 37996 USA
- Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, USA
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Tan Z, Khakbaz P, Chen Y, Lombardo J, Yoon JM, Shanks JV, Klauda JB, Jarboe LR. Engineering Escherichia coli membrane phospholipid head distribution improves tolerance and production of biorenewables. Metab Eng 2017; 44:1-12. [DOI: 10.1016/j.ymben.2017.08.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 08/26/2017] [Accepted: 08/29/2017] [Indexed: 12/27/2022]
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Yoon BK, Jackman JA, Kim MC, Sut TN, Cho NJ. Correlating Membrane Morphological Responses with Micellar Aggregation Behavior of Capric Acid and Monocaprin. Langmuir 2017; 33:2750-2759. [PMID: 28263610 DOI: 10.1021/acs.langmuir.6b03944] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The interaction of single-chain lipid amphiphiles with phospholipid membranes is relevant to many scientific fields, including molecular evolution, medicine, and biofuels. Two widely studied compounds within this class are the medium-chain saturated fatty acid, capric acid, and its monoglyceride derivative, monocaprin. To date, most studies about these compounds have involved in vitro evaluation of their biological activities, while mechanistic details of how capric acid and monocaprin interact with phospholipid bilayers remain elusive. Herein, we investigated the effect of these two compounds on the morphological and fluidic properties of prefabricated, supported lipid bilayers (SLBs). The critical micelle concentration (CMC) of each compound was determined by fluorescence spectroscopy measurements. At or above its CMC, capric acid induced the formation of elongated tubules protruding from the SLB, as determined by quartz crystal microbalance-dissipation and fluorescence microscopy experiments. By contrast, monocaprin induced the formation of elongated tubules or membrane buds below and above its CMC, respectively. Fluorescence recovery after photobleaching (FRAP) experiments indicated that capric acid increased bilayer fluidity only above its CMC, whereas monocaprin increased bilayer fluidity both above and below its CMC. We discuss these findings in the context of the two compounds' structural properties, including net charge, molecular length and hydrogen-bonding capacity. Collectively, the findings demonstrate that capric acid and monocaprin differentially affect the morphological and fluidic properties of SLBs, and that the aggregation state of the compounds plays a critical role in modulating their interactions with phospholipid membranes.
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Affiliation(s)
- Bo Kyeong Yoon
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University , 50 Nanyang Drive, 637553, Singapore
| | - Joshua A Jackman
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University , 50 Nanyang Drive, 637553, Singapore
| | - Min Chul Kim
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University , 50 Nanyang Drive, 637553, Singapore
| | - Tun Naw Sut
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University , 50 Nanyang Drive, 637553, Singapore
| | - Nam-Joon Cho
- School of Materials Science and Engineering, Nanyang Technological University , 50 Nanyang Avenue, 639798, Singapore
- Centre for Biomimetic Sensor Science, Nanyang Technological University , 50 Nanyang Drive, 637553, Singapore
- School of Chemical and Biomedical Engineering, Nanyang Technological University , 62 Nanyang Drive, 637459, Singapore
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Rau MH, Calero P, Lennen RM, Long KS, Nielsen AT. Genome-wide Escherichia coli stress response and improved tolerance towards industrially relevant chemicals. Microb Cell Fact 2016; 15:176. [PMID: 27737709 PMCID: PMC5064937 DOI: 10.1186/s12934-016-0577-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 10/03/2016] [Indexed: 01/17/2023] Open
Abstract
Background Economically viable biobased production of bulk chemicals and biofuels typically requires high product titers. During microbial bioconversion this often leads to product toxicity, and tolerance is therefore a critical element in the engineering of production strains. Results Here, a systems biology approach was employed to understand the chemical stress response of Escherichia coli, including a genome-wide screen for mutants with increased fitness during chemical stress. Twelve chemicals with significant production potential were selected, consisting of organic solvent-like chemicals (butanol, hydroxy-γ-butyrolactone, 1,4-butanediol, furfural), organic acids (acetate, itaconic acid, levulinic acid, succinic acid), amino acids (serine, threonine) and membrane-intercalating chemicals (decanoic acid, geraniol). The transcriptional response towards these chemicals revealed large overlaps of transcription changes within and between chemical groups, with functions such as energy metabolism, stress response, membrane modification, transporters and iron metabolism being affected. Regulon enrichment analysis identified key regulators likely mediating the transcriptional response, including CRP, RpoS, OmpR, ArcA, Fur and GadX. These regulators, the genes within their regulons and the above mentioned cellular functions therefore constitute potential targets for increasing E. coli chemical tolerance. Fitness determination of genome-wide transposon mutants (Tn-seq) subjected to the same chemical stress identified 294 enriched and 336 depleted mutants and experimental validation revealed up to 60 % increase in mutant growth rates. Mutants enriched in several conditions contained, among others, insertions in genes of the Mar-Sox-Rob regulon as well as transcription and translation related gene functions. Conclusions The combination of the transcriptional response and mutant screening provides general targets that can increase tolerance towards not only single, but multiple chemicals. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0577-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martin Holm Rau
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Patricia Calero
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Rebecca M Lennen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Katherine S Long
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Alex T Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.
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Woo JM, Kim JW, Song JW, Blank LM, Park JB. Activation of the Glutamic Acid-Dependent Acid Resistance System in Escherichia coli BL21(DE3) Leads to Increase of the Fatty Acid Biotransformation Activity. PLoS One 2016; 11:e0163265. [PMID: 27681369 PMCID: PMC5040553 DOI: 10.1371/journal.pone.0163265] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 09/05/2016] [Indexed: 01/29/2023] Open
Abstract
The biosynthesis of carboxylic acids including fatty acids from biomass is central in envisaged biorefinery concepts. The productivities are often, however, low due to product toxicity that hamper whole-cell biocatalyst performance. Here, we have investigated factors that influence the tolerance of Escherichia coli to medium chain carboxylic acid (i.e., n-heptanoic acid)-induced stress. The metabolic and genomic responses of E. coli BL21(DE3) and MG1655 grown in the presence of n-heptanoic acid indicated that the GadA/B-based glutamic acid-dependent acid resistance (GDAR) system might be critical for cellular tolerance. The GDAR system, which is responsible for scavenging intracellular protons by catalyzing decarboxylation of glutamic acid, was inactive in E. coli BL21(DE3). Activation of the GDAR system in this strain by overexpressing the rcsB and dsrA genes, of which the gene products are involved in the activation of GadE and RpoS, respectively, resulted in acid tolerance not only to HCl but also to n-heptanoic acid. Furthermore, activation of the GDAR system allowed the recombinant E. coli BL21(DE3) expressing the alcohol dehydrogenase of Micrococcus luteus and the Baeyer-Villiger monooxygenase of Pseudomonas putida to reach 60% greater product concentration in the biotransformation of ricinoleic acid (i.e., 12-hydroxyoctadec-9-enoic acid (1)) into n-heptanoic acid (5) and 11-hydroxyundec-9-enoic acid (4). This study may contribute to engineering E. coli-based biocatalysts for the production of carboxylic acids from renewable biomass.
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Affiliation(s)
- Ji-Min Woo
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Kim
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Ji-Won Song
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
| | - Lars M. Blank
- Institute of Applied Microbiology - iAMB, Aachen Biology and Biotechnology - ABBt, RWTH Aachen University, Aachen, Germany
| | - Jin-Byung Park
- Department of Food Science & Engineering, Ewha Womans University, Seoul, 120-750, Republic of Korea
- * E-mail:
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15
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Sandoval NR, Papoutsakis ET. Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes. Curr Opin Microbiol 2016; 33:56-66. [PMID: 27376665 DOI: 10.1016/j.mib.2016.06.005] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 06/09/2016] [Accepted: 06/16/2016] [Indexed: 10/21/2022]
Abstract
Metabolite toxicity in microbes, particularly at the membrane, remains a bottleneck in the production of fuels and chemicals. Under chemical stress, native adaptation mechanisms combat hyper-fluidization by modifying the phospholipids in the membrane. Recent work in fluxomics reveals the mechanism of how membrane damage negatively affects energy metabolism while lipidomic and transcriptomic analyses show that strains evolved to be tolerant maintain membrane fluidity under stress through a variety of mechanisms such as incorporation of cyclopropanated fatty acids, trans-unsaturated fatty acids, and upregulation of cell wall biosynthesis genes. Engineered strains with modifications made in the biosynthesis of fatty acids, peptidoglycan, and lipopolysaccharide have shown increased tolerance to exogenous stress as well as increased production of desired metabolites of industrial importance. We review recent advances in elucidation of mechanisms or toxicity and tolerance as well as efforts to engineer the bacterial membrane and cell wall.
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Affiliation(s)
- Nicholas R Sandoval
- Department of Chemical and Biomolecular Engineering, Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, Molecular Biotechnology Laboratory, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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16
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Tan Z, Yoon JM, Nielsen DR, Shanks JV, Jarboe LR. Membrane engineering via trans unsaturated fatty acids production improves Escherichia coli robustness and production of biorenewables. Metab Eng 2016; 35:105-13. [DOI: 10.1016/j.ymben.2016.02.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Revised: 02/01/2016] [Accepted: 02/04/2016] [Indexed: 11/23/2022]
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17
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Sherkhanov S, Korman TP, Clarke SG, Bowie JU. Production of FAME biodiesel in E. coli by direct methylation with an insect enzyme. Sci Rep 2016; 6:24239. [PMID: 27053100 DOI: 10.1038/srep24239] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/23/2016] [Indexed: 12/13/2022] Open
Abstract
Most biodiesel currently in use consists of fatty acid methyl esters (FAMEs) produced by transesterification of plant oils with methanol. To reduce competition with food supplies, it would be desirable to directly produce biodiesel in microorganisms. To date, the most effective pathway for the production of biodiesel in bacteria yields fatty acid ethyl esters (FAEEs) at up to ~1.5 g/L. A much simpler route to biodiesel produces FAMEs by direct S-adenosyl-L-methionine (SAM) dependent methylation of free fatty acids, but FAME production by this route has been limited to only ~16 mg/L. Here we employ an alternative, broad spectrum methyltransferase, Drosophila melanogaster Juvenile Hormone Acid O-Methyltransferase (DmJHAMT). By introducing DmJHAMT in E. coli engineered to produce medium chain fatty acids and overproduce SAM, we obtain medium chain FAMEs at titers of 0.56 g/L, a 35-fold increase over titers previously achieved. Although considerable improvements will be needed for viable bacterial production of FAMEs and FAEEs for biofuels, it may be easier to optimize and transport the FAME production pathway to other microorganisms because it involves fewer enzymes.
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18
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Affiliation(s)
| | - Hal S. Alper
- McKetta Department of Chemical Engineering and
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712;
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19
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Royce LA, Yoon JM, Chen Y, Rickenbach E, Shanks JV, Jarboe LR. Evolution for exogenous octanoic acid tolerance improves carboxylic acid production and membrane integrity. Metab Eng 2015; 29:180-188. [DOI: 10.1016/j.ymben.2015.03.014] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Revised: 03/07/2015] [Accepted: 03/23/2015] [Indexed: 11/17/2022]
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20
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Rodríguez-Moyá M, Gonzalez R. Proteomic analysis of the response of Escherichia coli to short-chain fatty acids. J Proteomics. 2015;122:86-99. [PMID: 25845584 DOI: 10.1016/j.jprot.2015.03.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 03/13/2015] [Accepted: 03/29/2015] [Indexed: 01/03/2023]
Abstract
UNLABELLED Given their simple and easy-to-manipulate chemical structures, short-chain fatty acids (SCFAs) are valuable feedstocks for many industrial applications. While the microbial production of SCFAs by engineered Escherichia coli has been demonstrated recently, productivity and yields are limited by their antimicrobial properties. In this work, we performed a comparative proteomic analysis of E. coli under octanoic acid stress (15 mM) and identified the underlying mechanisms of SCFA toxicity. Out of a total of 33 spots differentially expressed at a p-value ≤ 0.05, nine differentially expressed proteins involved in transport and structural roles (OmpF, HPr, and FliC), oxidative stress (SodA, SodB, and TrxA), protein synthesis (PPiB and RpsA) and metabolic functions (HPr, PflB) were selected for further investigation. Our studies suggest that membrane damage and oxidative stress are the main routes of inhibition by SCFAs in E. coli. The outer membrane porin OmpF had the greatest impact on SCFA tolerance. Intracellular pH analysis on ompF mutants grown under octanoic acid stress indicated that this porin facilitates transport of SCFAs into the cell. The same response was observed under hexanoic acid stress, further supporting the role of OmpF in response to the presence of SCFAs. Furthermore, analysis of membrane protein expression revealed that other outer membrane porins are also involved in the response of E. coli to SCFAs. BIOLOGICAL SIGNIFICANCE This work covers the first known proteomic analysis to assess the inhibitory effect of SCFAs in E. coli. SCFAs are molecules of great interest in the industry, but their microbial production is limited by their antimicrobial properties. This work allowed identification of differentially expressed proteins in response to SCFA stress and demonstrated the relevance of short- and medium-chain FA transport across the cell membrane via outer membrane porins, providing valuable insights on the toxicity mechanism of SCFAs in E. coli. These results could also benefit future engineering efforts by guiding the design and construction of industrial strains that produce SCFAs with increased tolerance and productivity.
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21
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Liu P, Zhu X, Tan Z, Zhang X, Ma Y. Construction of Escherichia Coli Cell Factories for Production of Organic Acids and Alcohols. Adv Biochem Eng Biotechnol 2015; 155:107-40. [PMID: 25577396 DOI: 10.1007/10_2014_294] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Production of bulk chemicals from renewable biomass has been proved to be sustainable and environmentally friendly. Escherichia coli is the most commonly used host strain for constructing cell factories for production of bulk chemicals since it has clear physiological and genetic characteristics, grows fast in minimal salts medium, uses a wide range of substrates, and can be genetically modified easily. With the development of metabolic engineering, systems biology, and synthetic biology, a technology platform has been established to construct E. coli cell factories for bulk chemicals production. In this chapter, we will introduce this technology platform, as well as E. coli cell factories successfully constructed for production of organic acids and alcohols.
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Affiliation(s)
- Pingping Liu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China
| | - Zaigao Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Tianjin, China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, 32 West 7th Ave, Tianjin Airport Economic Area, Tianjin, 300308, China.
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
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22
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Przybylski D, Rohwerder T, Dilßner C, Maskow T, Harms H, Müller RH. Exploiting mixtures of H2, CO2, and O2 for improved production of methacrylate precursor 2-hydroxyisobutyric acid by engineered Cupriavidus necator strains. Appl Microbiol Biotechnol 2014; 99:2131-45. [DOI: 10.1007/s00253-014-6266-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 11/23/2014] [Accepted: 11/24/2014] [Indexed: 12/23/2022]
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