1
|
Huang Y, Ye Z, Wan X, Yao G, Duan J, Liu J, Yao M, Sun X, Deng Z, Shen K, Jiang H, Liu T. Systematic Mining and Evaluation of the Sesquiterpene Skeletons as High Energy Aviation Fuel Molecules. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2300889. [PMID: 37271925 PMCID: PMC10427387 DOI: 10.1002/advs.202300889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/26/2023] [Indexed: 06/06/2023]
Abstract
Sesquiterpenes have been identified as promising ingredients for aviation fuels due to their high energy density and combustion heat properties. Despite the characterization of numerous sesquiterpene structures, studies testing their performance properties and feasibility as fuels are scarce. In this study, 122 sesquiterpenoid skeleton compounds, obtained from existing literature reports, are tested using group contribution and gaussian quantum chemistry methods to assess their potential as high-energy aviation fuels. Seventeen sesquiterpene compounds exhibit good predictive performance and nine compounds are further selected for overproduction in yeast. Through fed-batch fermentation, all compounds achieve the highest reported titers to date. Subsequently, three representative products, pentalenene, presilphiperfol-1-ene, and α-farnesene, are selected, produced, purified in large quantities, and tested for use as potential fuels. The performance of pentalenene, presilphiperfol-1-ene, and their derivatives reveals favorable prospects as high-energy aviation fuels.
Collapse
Affiliation(s)
- Yanglei Huang
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Ziling Ye
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Xiukun Wan
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Ge Yao
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Jingyu Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Jiajia Liu
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education)School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China
- Frontier Technology Research InstituteTianjin UniversityTianjin301700China
| | - Xiang Sun
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- State Key Laboratory of Microbial MetabolismSchool of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai200030China
| | - Kun Shen
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
| | - Hui Jiang
- State Key Laboratory of NBC Protection for CivilianBeijing102205China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug DiscoveryMinistry of Education and School of Pharmaceutical SciencesWuhan UniversityWuhan430071China
- Hubei Engineering Laboratory for Synthetic MicrobiologyWuhan Institute of BiotechnologyWuhan430075China
| |
Collapse
|
2
|
Gomes Souza F, Pal K, Ampah JD, Dantas MC, Araújo A, Maranhão F, Domingues P. Biofuels and Nanocatalysts: Python Boosting Visualization of Similarities. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1175. [PMID: 36770184 PMCID: PMC9921263 DOI: 10.3390/ma16031175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/11/2023] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
Among the most relevant themes of modernity, using renewable resources to produce biofuels attracts several countries' attention, constituting a vital part of the global geopolitical chessboard since humanity's energy needs will grow faster and faster. Fortunately, advances in personal computing associated with free and open-source software production facilitate this work of prospecting and understanding complex scenarios. Thus, for the development of this work, the keywords "biofuel" and "nanocatalyst" were delivered to the Scopus database, which returned 1071 scientific articles. The titles and abstracts of these papers were saved in Research Information Systems (RIS) format and submitted to automatic analysis via the Visualization of Similarities Method implemented in VOSviewer 1.6.18 software. Then, the data extracted from the VOSviewer were processed by software written in Python, which allowed the use of the network data generated by the Visualization of Similarities Method. Thus, it was possible to establish the relationships for the pair between the nodes of all clusters classified by Link Strength Between Items or Terms (LSBI) or by year. Indeed, other associations should arouse particular interest in the readers. However, here, the option was for a numerical criterion. However, all data are freely available, and stakeholders can infer other specific connections directly. Therefore, this innovative approach allowed inferring that the most recent pairs of terms associate the need to produce biofuels from microorganisms' oils besides cerium oxide nanoparticles to improve the performance of fuel mixtures by reducing the emission of hydrocarbons (HC) and oxides of nitrogen (NOx).
Collapse
Affiliation(s)
- Fernando Gomes Souza
- Biopolymers & Sensors Lab, Instituto de Macromoléculas Professora Eloisa Mano, Centro de Tecnologia-Cidade Universitária, Universidade Federal de Rio de Janeiro, Rio de Janeiro 21941-914, RJ, Brazil
- Biopolymers & Sensors Lab, Programa de Engenharia da Nanotecnologia, COPPE, Centro de Tecnologia-Cidade Universitária, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-914, RJ, Brazil
| | - Kaushik Pal
- University Center for Research and Development (UCRD), Department of Physics, Chandigarh University, Ludhiana–Chandigarh State Hwy, Mohali 140413, Punjab, India
| | | | - Maria Clara Dantas
- Biopolymers & Sensors Lab, Programa de Engenharia da Nanotecnologia, COPPE, Centro de Tecnologia-Cidade Universitária, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-914, RJ, Brazil
| | - Aruzza Araújo
- LABPROBIO, Institute of Chemistry, Universidade Federal do Rio Grande do Norte, Natal 59078-970, RN, Brazil
| | - Fabíola Maranhão
- Biopolymers & Sensors Lab, Instituto de Macromoléculas Professora Eloisa Mano, Centro de Tecnologia-Cidade Universitária, Universidade Federal de Rio de Janeiro, Rio de Janeiro 21941-914, RJ, Brazil
| | - Priscila Domingues
- Biopolymers & Sensors Lab, Programa de Engenharia da Nanotecnologia, COPPE, Centro de Tecnologia-Cidade Universitária, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-914, RJ, Brazil
| |
Collapse
|
3
|
Foster-Nyarko E, Pallen MJ. OUP accepted manuscript. FEMS Microbiol Rev 2022; 46:6522174. [PMID: 35134909 PMCID: PMC9075585 DOI: 10.1093/femsre/fuac008] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 11/13/2022] Open
Abstract
Escherichia coli has a rich history as biology's ‘rock star’, driving advances across many fields. In the wild, E. coli resides innocuously in the gut of humans and animals but is also a versatile pathogen commonly associated with intestinal and extraintestinal infections and antimicrobial resistance—including large foodborne outbreaks such as the one that swept across Europe in 2011, killing 54 individuals and causing approximately 4000 infections and 900 cases of haemolytic uraemic syndrome. Given that most E. coli are harmless gut colonizers, an important ecological question plaguing microbiologists is what makes E. coli an occasionally devastating pathogen? To address this question requires an enhanced understanding of the ecology of the organism as a commensal. Here, we review how our knowledge of the ecology and within-host diversity of this organism in the vertebrate gut has progressed in the 137 years since E. coli was first described. We also review current approaches to the study of within-host bacterial diversity. In closing, we discuss some of the outstanding questions yet to be addressed and prospects for future research.
Collapse
Affiliation(s)
- Ebenezer Foster-Nyarko
- Corresponding author: Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom. E-mail:
| | - Mark J Pallen
- Quadram Institute Bioscience, Norwich Research Park, Norwich, NR4 7UQ, United Kingdom
- School of Veterinary Medicine, University of Surrey, Guildford, Surrey, GU2 7AL, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TU, United Kingdom
| |
Collapse
|
4
|
Jin Z, Zou G, Mao X, Guan S, Guan W. Rapid Determination of Free Fatty Acids in the Extracellular Medium of Cyanobacteria by Stir Bar Sorptive Extraction (SBSE) Coupled to Ultra-High-Performance Liquid Chromatography – Triple Quadrupole Tandem Mass Spectrometry (UHPLC-MS/MS). ANAL LETT 2021. [DOI: 10.1080/00032719.2021.1891547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Zhao Jin
- School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao, China
| | - Guanyu Zou
- Public Laboratory of Bioenergy and Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Xintao Mao
- Public Laboratory of Bioenergy and Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Shanshan Guan
- Public Laboratory of Bioenergy and Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wenna Guan
- Public Laboratory of Bioenergy and Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| |
Collapse
|
5
|
Characterization and genome sequence of the genetically unique Escherichia bacteriophage vB_EcoM_IME392. Arch Virol 2021; 166:2505-2520. [PMID: 34236511 DOI: 10.1007/s00705-021-05160-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 05/17/2021] [Indexed: 10/20/2022]
Abstract
In this study, a novel Escherichia coli-specific bacteriophage, vB_EcoM_IME392, was isolated from chicken farm sewage in Qingdao, China. The genome of IME392 was found by next-generation sequencing to be 116,460 base pairs in length with a G+C content of 45.4% (GenBank accession number MH719082). BLASTn results revealed that only 2% of the genome sequence of IME392 shows sequence similarity to known phage sequences in the GenBank database, which indicates that IME392 is a novel bacteriophage. Transmission electron microscopy showed that IME392 belongs to the family Myoviridae. The host range, the multiplicity of infection, and a one-step growth curve were also determined.
Collapse
|
6
|
Shanmugam KT, Ingram LO. Principles and practice of designing microbial biocatalysts for fuel and chemical production. J Ind Microbiol Biotechnol 2021; 49:6158391. [PMID: 33686428 PMCID: PMC9118985 DOI: 10.1093/jimb/kuab016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 03/03/2021] [Indexed: 11/14/2022]
Abstract
The finite nature of fossil fuels and the environmental impact of its use have raised interest in alternate renewable energy sources. Specifically, non-food carbohydrates, such as lignocellulosic biomass, can be used to produce next generation biofuels, including cellulosic ethanol and other non-ethanol fuels like butanol. However, currently there is no native microorganism that can ferment all lignocellulosic sugars to fuel molecules. Thus, research is focused on engineering improved microbial biocatalysts for production of liquid fuels at high productivity, titer and yield. A clear understanding and application of the basic principles of microbial physiology and biochemistry are crucial to achieve this goal. In this review, we present and discuss the construction of microbial biocatalysts that integrate these principles with ethanol-producing Escherichia coli as an example of metabolic engineering. These principles also apply to fermentation of lignocellulosic sugars to other chemicals that are currently produced from petroleum.
Collapse
Affiliation(s)
- K T Shanmugam
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Lonnie O Ingram
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| |
Collapse
|
7
|
Liu Y, Cruz-Morales P, Zargar A, Belcher MS, Pang B, Englund E, Dan Q, Yin K, Keasling JD. Biofuels for a sustainable future. Cell 2021; 184:1636-1647. [PMID: 33639085 DOI: 10.1016/j.cell.2021.01.052] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/16/2021] [Accepted: 01/27/2021] [Indexed: 12/26/2022]
Abstract
Rapid increases of energy consumption and human dependency on fossil fuels have led to the accumulation of greenhouse gases and consequently, climate change. As such, major efforts have been taken to develop, test, and adopt clean renewable fuel alternatives. Production of bioethanol and biodiesel from crops is well developed, while other feedstock resources and processes have also shown high potential to provide efficient and cost-effective alternatives, such as landfill and plastic waste conversion, algal photosynthesis, as well as electrochemical carbon fixation. In addition, the downstream microbial fermentation can be further engineered to not only increase the product yield but also expand the chemical space of biofuels through the rational design and fine-tuning of biosynthetic pathways toward the realization of "designer fuels" and diverse future applications.
Collapse
Affiliation(s)
- Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Pablo Cruz-Morales
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Amin Zargar
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Michael S Belcher
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Bo Pang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Elias Englund
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Qingyun Dan
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
| | - Kevin Yin
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, USA; Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Departments of Chemical and Biomolecular Engineering and of Bioengineering, University of California, Berkeley, Berkeley, CA, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, Horsholm, Denmark; Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China.
| |
Collapse
|
8
|
Schalck T, den Bergh BV, Michiels J. Increasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics. Microorganisms 2021; 9:249. [PMID: 33530454 PMCID: PMC7912173 DOI: 10.3390/microorganisms9020249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/14/2021] [Accepted: 01/20/2021] [Indexed: 12/16/2022] Open
Abstract
Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.
Collapse
Affiliation(s)
- Thomas Schalck
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Bram Van den Bergh
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| | - Jan Michiels
- VIB Center for Microbiology, Flanders Institute for Biotechnology, B-3001 Leuven, Belgium; (T.S.); (B.V.d.B.)
- Centre of Microbial and Plant Genetics, KU Leuven, Kasteelpark Arenberg 20, B-3001 Leuven, Belgium
| |
Collapse
|
9
|
Abstract
Biological wax esters offer a sustainable, renewable and biodegradable alternative to many fossil fuel derived chemicals including plastics and paraffins. Many species of bacteria accumulate waxes with similar structure and properties to highly desirable animal and plant waxes such as Spermaceti and Jojoba oils, the use of which is limited by resource requirements, high cost and ethical concerns. While bacterial fermentations overcome these issues, a commercially viable bacterial wax production process would require high yields and renewable, affordable feedstock to make it economically competitive and environmentally beneficial. This review describes recent progress in wax ester generation in both wild type and genetically engineered bacteria, with a focus on comparing substrates and quantifying obtained waxes. The full breadth of wax accumulating species is discussed, with emphasis on species generating high yields and utilising renewable substrates. Key areas of the field that have, thus far, received limited attention are highlighted, such as waste stream valorisation, mixed microbial cultures and efficient wax extraction, as, until effectively addressed, these will slow progress in creating commercially viable wax production methods.
Collapse
|
10
|
|
11
|
Distributed flux balance analysis simulations of serial biomass fermentation by two organisms. PLoS One 2020; 15:e0227363. [PMID: 31945096 PMCID: PMC6964848 DOI: 10.1371/journal.pone.0227363] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 12/17/2019] [Indexed: 12/16/2022] Open
Abstract
Intelligent biorefinery design that addresses both the composition of the biomass feedstock as well as fermentation microorganisms could benefit from dedicated tools for computational simulation and computer-assisted optimization. Here we present the BioLego Vn2.0 framework, based on Microsoft Azure Cloud, which supports large-scale simulations of biomass serial fermentation processes by two different organisms. BioLego enables the simultaneous analysis of multiple fermentation scenarios and the comparison of fermentation potential of multiple feedstock compositions. Thanks to the effective use of cloud computing it further allows resource intensive analysis and exploration of media and organism modifications. We use BioLego to obtain biological and validation results, including (1) exploratory search for the optimal utilization of corn biomasses-corn cobs, corn fiber and corn stover-in fermentation biorefineries; (2) analysis of the possible effects of changes in the composition of K. alvarezi biomass on the ethanol production yield in an anaerobic two-step process (S. cerevisiae followed by E. coli); (3) analysis of the impact, on the estimated ethanol production yield, of knocking out single organism reactions either in one or in both organisms in an anaerobic two-step fermentation process of Ulva sp. into ethanol (S. cerevisiae followed by E. coli); and (4) comparison of several experimentally measured ethanol fermentation rates with the predictions of BioLego.
Collapse
|
12
|
Zhang J, Nanjaraj Urs AN, Lin L, Zhou Y, Hu Y, Hua G, Gao Q, Yuchi Z, Zhang Y. Structure of glycerol dehydrogenase (GldA) from Escherichia coli. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2019; 75:176-183. [PMID: 30839292 DOI: 10.1107/s2053230x19000037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 01/02/2019] [Indexed: 11/10/2022]
Abstract
Escherichia coli (strain K-12, substrain MG1655) glycerol dehydrogenase (GldA) is required to catalyze the first step in fermentative glycerol metabolism. The protein was expressed and purified to homogeneity using a simple combination of heat-shock and chromatographic methods. The high yield of the protein (∼250 mg per litre of culture) allows large-scale production for potential industrial applications. Purified GldA exhibited a homogeneous tetrameric state (∼161 kDa) in solution and relatively high thermostability (Tm = 65.6°C). Sitting-drop sparse-matrix screens were used for protein crystallization. An optimized condition with ammonium sulfate (2 M) provided crystals suitable for diffraction, and a binary structure containing glycerol in the active site was solved at 2.8 Å resolution. Each GldA monomer consists of nine β-strands, thirteen α-helices, two 310-helices and several loops organized into two domains, the N- and C-terminal domains; the active site is located in a deep cleft between the two domains. The N-terminal domain contains a classic Rossmann fold for NAD+ binding. The O1 and O2 atoms of glycerol serve as ligands for the tetrahedrally coordinated Zn2+ ion. The orientation of the glycerol within the active site is mainly stabilized by van der Waals and electrostatic interactions with the benzyl ring of Phe245. Computer modeling suggests that the glycerol molecule is sandwiched by the Zn2+ and NAD+ ions. Based on this, the mechanism for the relaxed substrate specificity of this enzyme is also discussed.
Collapse
Affiliation(s)
- Jun Zhang
- The Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Ankanahalli N Nanjaraj Urs
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yan Zhou
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yiling Hu
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Gaoqun Hua
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Qiang Gao
- The Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, State Key Laboratory of Food Nutrition and Safety, Tianjin Engineering Research Center of Microbial Metabolism and Fermentation Process Control, College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, People's Republic of China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| | - Yan Zhang
- Tianjin Key Laboratory for Modern Drug Delivery and High Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, People's Republic of China
| |
Collapse
|
13
|
Herrou J, Czyż DM, Fiebig A, Willett JW, Kim Y, Wu R, Babnigg G, Crosson S. Molecular control of gene expression by Brucella BaaR, an IclR-type transcriptional repressor. J Biol Chem 2018; 293:7437-7456. [PMID: 29567835 PMCID: PMC5949995 DOI: 10.1074/jbc.ra118.002045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/19/2018] [Indexed: 01/06/2023] Open
Abstract
The general stress response sigma factor σE1 directly and indirectly regulates the transcription of dozens of genes that influence stress survival and host infection in the zoonotic pathogen Brucella abortus Characterizing the functions of σE1-regulated genes therefore would contribute to our understanding of B. abortus physiology and infection biology. σE1 indirectly activates transcription of the IclR family regulator Bab2_0215, but the function of this regulator remains undefined. Here, we present a structural and functional characterization of Bab2_0215, which we have named B rucella adipic acid-activated regulator (BaaR). We found that BaaR adopts a classic IclR-family fold and directly represses the transcription of two operons with predicted roles in carboxylic acid oxidation. BaaR binds two sites on chromosome II between baaR and a divergently transcribed hydratase/dehydrogenase (acaD2), and it represses transcription of both genes. We identified three carboxylic acids (adipic acid, tetradecanedioic acid, and ϵ-aminocaproic acid) and a lactone (ϵ-caprolactone) that enhance transcription from the baaR and acaD2 promoters. However, neither the activating acids nor caprolactone enhanced transcription by binding directly to BaaR. Induction of baaR transcription by adipic acid required the gene bab2_0213, which encodes a major facilitator superfamily transporter, suggesting that Bab2_0213 transports adipic acid across the inner membrane. We conclude that a suite of structurally related organic molecules activate transcription of genes repressed by BaaR. Our study provides molecular-level understanding of a gene expression program in B. abortus that is downstream of σE1.
Collapse
Affiliation(s)
- Julien Herrou
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | - Daniel M Czyż
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | - Aretha Fiebig
- Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | - Jonathan W Willett
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439
| | | | - Ruiying Wu
- Argonne National Laboratory, Argonne, Illinois 60439
| | | | - Sean Crosson
- Departments of Biochemistry and Molecular Biology, Chicago, Illinois 60637; Howard Taylor Ricketts Laboratory, University of Chicago, Argonne, Illinois 60439; Microbiology, University of Chicago, Chicago, Illinois 60637.
| |
Collapse
|
14
|
Thuan NH, Chaudhary AK, Van Cuong D, Cuong NX. Engineering co-culture system for production of apigetrin in Escherichia coli. J Ind Microbiol Biotechnol 2018; 45:175-185. [PMID: 29362971 DOI: 10.1007/s10295-018-2012-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/13/2018] [Indexed: 12/17/2022]
Abstract
Microbial cells have extensively been utilized to produce value-added bioactive compounds. Based on advancement in protein engineering, DNA recombinant technology, genome engineering, and metabolic remodeling, the microbes can be re-engineered to produce industrially and medicinally important platform chemicals. The emergence of co-culture system which reduces the metabolic burden and allows parallel optimization of the engineered pathway in a modular fashion restricting the formation of undesired byproducts has become an alternative way to synthesize and produce bioactive compounds. In this study, we present genetically engineered E. coli-based co-culture system to the de novo synthesis of apigetrin (APG), an apigenin-7-O-β-D-glucopyranoside of apigenin. The culture system consists of an upstream module including 4-coumarate: CoA ligase (4CL), chalcone synthase, chalcone flavanone isomerase (CHS, CHI), and flavone synthase I (FNSI) to synthesize apigenin (API) from p-coumaric acid (PCA). Whereas, the downstream system contains a metabolizing module to enhance the production of UDP-glucose and expression of glycosyltransferase (PaGT3) to convert API into APG. To accomplish this improvement in titer, the initial inoculum ratio of strains for making the co-culture system, temperature, and media component was optimized. Following large-scale production, a yield of 38.5 µM (16.6 mg/L) of APG was achieved. In overall, this study provided an efficient tool to synthesize bioactive compounds in microbial cells.
Collapse
Affiliation(s)
- Nguyen Huy Thuan
- Center for Molecular Biology, Duy Tan University, 03 Quang Trung Street, Haichau District, Danang, Vietnam.
| | - Amit Kumar Chaudhary
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, NE, 68198, USA
| | - Duong Van Cuong
- Faculty of Biotechnology and Food Technology, Thainguyen University of Agriculture and Forestry, Thainguyen, Vietnam
| | - Nguyen Xuan Cuong
- Lab of Marine Medicinal Materials, Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Hanoi, Vietnam
| |
Collapse
|
15
|
Shchemelinina TN, Matistov NV, Kovaleva VA, Markarova MY, Gruzdev IV, Volodin VV, Anchugova EM. Microfungal strains—potential lipid producers for biodiesel. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817040135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
16
|
Chen X, Gao C, Guo L, Hu G, Luo Q, Liu J, Nielsen J, Chen J, Liu L. DCEO Biotechnology: Tools To Design, Construct, Evaluate, and Optimize the Metabolic Pathway for Biosynthesis of Chemicals. Chem Rev 2017; 118:4-72. [DOI: 10.1021/acs.chemrev.6b00804] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Xiulai Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Cong Gao
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liang Guo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Guipeng Hu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Qiuling Luo
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jia Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Jens Nielsen
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800 Lyngby, Denmark
| | - Jian Chen
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Liming Liu
- State
Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- Department
of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg SE-412 96, Sweden
- Key
Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
17
|
Yu P, Chen X, Li P. Enhancing microbial production of biofuels by expanding microbial metabolic pathways. Biotechnol Appl Biochem 2017; 64:606-619. [PMID: 27507087 DOI: 10.1002/bab.1529] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 07/31/2016] [Indexed: 12/29/2022]
Abstract
Fatty acid, isoprenoid, and alcohol pathways have been successfully engineered to produce biofuels. By introducing three genes, atfA, adhE, and pdc, into Escherichia coli to expand fatty acid pathway, up to 1.28 g/L of fatty acid ethyl esters can be achieved. The isoprenoid pathway can be expanded to produce bisabolene with a high titer of 900 mg/L in Saccharomyces cerevisiae. Short- and long-chain alcohols can also be effectively biosynthesized by extending the carbon chain of ketoacids with an engineered "+1" alcohol pathway. Thus, it can be concluded that expanding microbial metabolic pathways has enormous potential for enhancing microbial production of biofuels for future industrial applications. However, some major challenges for microbial production of biofuels should be overcome to compete with traditional fossil fuels: lowering production costs, reducing the time required to construct genetic elements and to increase their predictability and reliability, and creating reusable parts with useful and predictable behavior. To address these challenges, several aspects should be further considered in future: mining and transformation of genetic elements related to metabolic pathways, assembling biofuel elements and coordinating their functions, enhancing the tolerance of host cells to biofuels, and creating modular subpathways that can be easily interconnected.
Collapse
Affiliation(s)
- Ping Yu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Xingge Chen
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| | - Peng Li
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang Province, People's Republic of China
| |
Collapse
|
18
|
Jeon JM, Kim HJ, Bhatia SK, Sung C, Seo HM, Kim JH, Park HY, Lee D, Brigham CJ, Yang YH. Application of acetyl-CoA acetyltransferase (AtoAD) in Escherichia coli to increase 3-hydroxyvalerate fraction in poly(3-hydroxybutyrate-co-3-hydroxyvalerate). Bioprocess Biosyst Eng 2017; 40:781-789. [DOI: 10.1007/s00449-017-1743-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/22/2017] [Indexed: 12/21/2022]
|
19
|
Motwalli O, Essack M, Jankovic BR, Ji B, Liu X, Ansari HR, Hoehndorf R, Gao X, Arold ST, Mineta K, Archer JAC, Gojobori T, Mijakovic I, Bajic VB. In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria. BMC Genomics 2017; 18:33. [PMID: 28056772 PMCID: PMC5217662 DOI: 10.1186/s12864-016-3389-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Finding a source from which high-energy-density biofuels can be derived at an industrial scale has become an urgent challenge for renewable energy production. Some microorganisms can produce free fatty acids (FFA) as precursors towards such high-energy-density biofuels. In particular, photosynthetic cyanobacteria are capable of directly converting carbon dioxide into FFA. However, current engineered strains need several rounds of engineering to reach the level of production of FFA to be commercially viable; thus new chassis strains that require less engineering are needed. Although more than 120 cyanobacterial genomes are sequenced, the natural potential of these strains for FFA production and excretion has not been systematically estimated. RESULTS Here we present the FFA SC (FFASC), an in silico screening method that evaluates the potential for FFA production and excretion of cyanobacterial strains based on their proteomes. A literature search allowed for the compilation of 64 proteins, most of which influence FFA production and a few of which affect FFA excretion. The proteins are classified into 49 orthologous groups (OGs) that helped create rules used in the scoring/ranking of algorithms developed to estimate the potential for FFA production and excretion of an organism. Among 125 cyanobacterial strains, FFASC identified 20 candidate chassis strains that rank in their FFA producing and excreting potential above the specifically engineered reference strain, Synechococcus sp. PCC 7002. We further show that the top ranked cyanobacterial strains are unicellular and primarily include Prochlorococcus (order Prochlorales) and marine Synechococcus (order Chroococcales) that cluster phylogenetically. Moreover, two principal categories of enzymes were shown to influence FFA production the most: those ensuring precursor availability for the biosynthesis of lipids, and those involved in handling the oxidative stress associated to FFA synthesis. CONCLUSION To our knowledge FFASC is the first in silico method to screen cyanobacteria proteomes for their potential to produce and excrete FFA, as well as the first attempt to parameterize the criteria derived from genetic characteristics that are favorable/non-favorable for this purpose. Thus, FFASC helps focus experimental evaluation only on the most promising cyanobacteria.
Collapse
Affiliation(s)
- Olaa Motwalli
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Boris R. Jankovic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Boyang Ji
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Xinyao Liu
- SABIC Corporate Research and Development (CRD), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Hifzur Rahman Ansari
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Robert Hoehndorf
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Stefan T. Arold
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - John A. C. Archer
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| | - Ivan Mijakovic
- Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Kemivägen 10, 41296 Gothenburg, Sweden
| | - Vladimir B. Bajic
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900 Kingdom of Saudi Arabia
| |
Collapse
|
20
|
Wood TK. Metabolic manipulation of methanogens for methane machinations. Microb Biotechnol 2017; 10:9-10. [PMID: 27748569 PMCID: PMC5270729 DOI: 10.1111/1751-7915.12425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 09/18/2016] [Indexed: 11/26/2022] Open
Affiliation(s)
- Thomas K. Wood
- Department of Chemical EngineeringPennsylvania State UniversityUniversity ParkPA16802‐4400USA
- Department of Biochemistry and Molecular BiologyPennsylvania State UniversityUniversity ParkPA16802‐4400USA
| |
Collapse
|
21
|
Wise CE, Grant JL, Amaya JA, Ratigan SC, Hsieh CH, Manley OM, Makris TM. Divergent mechanisms of iron-containing enzymes for hydrocarbon biosynthesis. J Biol Inorg Chem 2016; 22:221-235. [DOI: 10.1007/s00775-016-1425-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
|
22
|
Chen CY, Lee CC, Chen HS, Yang CH, Wang SP, Wu JH, Meng M. Modification of lignin in sugarcane bagasse by a monocopper hydrogen peroxide-generating oxidase from Thermobifida fusca. Process Biochem 2016. [DOI: 10.1016/j.procbio.2016.07.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
23
|
Herman NA, Zhang W. Enzymes for fatty acid-based hydrocarbon biosynthesis. Curr Opin Chem Biol 2016; 35:22-28. [PMID: 27573483 DOI: 10.1016/j.cbpa.2016.08.009] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/10/2016] [Accepted: 08/12/2016] [Indexed: 01/08/2023]
Abstract
Surging energy consumption and environmental concerns have stimulated interest in the production of chemicals and fuels through sustainable and renewable approaches. Fatty acid-based hydrocarbons, such as alkanes and alkenes, are of particular interest to directly replace fossil fuels. Towards this effort, understanding of hydrocarbon-producing enzymes is the first indispensable step to bio-production of hydrocarbons. Here, we review recent advances in the discovery and mechanistic study of enzymes capable of converting fatty acid precursors into hydrocarbons, and provide perspectives on the future of this rapidly growing field.
Collapse
Affiliation(s)
- Nicolaus A Herman
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States
| | - Wenjun Zhang
- Department of Chemical and Biomolecular Engineering, University of California Berkeley, Berkeley, CA 94720, United States.
| |
Collapse
|
24
|
Rajaraman E, Agarwal A, Crigler J, Seipelt-Thiemann R, Altman E, Eiteman MA. Transcriptional analysis and adaptive evolution of Escherichia coli strains growing on acetate. Appl Microbiol Biotechnol 2016; 100:7777-85. [DOI: 10.1007/s00253-016-7724-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 06/25/2016] [Accepted: 07/02/2016] [Indexed: 10/21/2022]
|
25
|
Koppolu V, Vasigala VK. Role of Escherichia coli in Biofuel Production. Microbiol Insights 2016; 9:29-35. [PMID: 27441002 PMCID: PMC4946582 DOI: 10.4137/mbi.s10878] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 06/26/2016] [Accepted: 06/28/2016] [Indexed: 12/19/2022] Open
Abstract
Increased energy consumption coupled with depleting petroleum reserves and increased greenhouse gas emissions have renewed our interest in generating fuels from renewable energy sources via microbial fermentation. Central to this problem is the choice of microorganism that catalyzes the production of fuels at high volumetric productivity and yield from cheap and abundantly available renewable energy sources. Microorganisms that are metabolically engineered to redirect renewable carbon sources into desired fuel products are contemplated as best choices to obtain high volumetric productivity and yield. Considering the availability of vast knowledge in genomic and metabolic fronts, Escherichia coli is regarded as a primary choice for the production of biofuels. Here, we reviewed the microbial production of liquid biofuels that have the potential to be used either alone or in combination with the present-day fuels. We specifically highlighted the metabolic engineering and synthetic biology approaches used to improve the production of biofuels from E. coli over the past few years. We also discussed the challenges that still exist for the biofuel production from E. coli and their possible solutions.
Collapse
Affiliation(s)
- Veerendra Koppolu
- Scientist, Department of Analytical Biotechnology, MedImmune/AstraZeneca, Gaithersburg, MD, USA.; Former affiliation: Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Veneela Kr Vasigala
- Rangaraya Medical College, NTR University of Health Sciences, Kakinada, AP, India
| |
Collapse
|
26
|
Rahman Z, Rashid N, Nawab J, Ilyas M, Sung BH, Kim SC. Escherichia coli as a fatty acid and biodiesel factory: current challenges and future directions. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:12007-12018. [PMID: 26961532 DOI: 10.1007/s11356-016-6367-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 02/29/2016] [Indexed: 06/05/2023]
Abstract
Biodiesel has received widespread attention as a sustainable, environment-friendly, and alternative source of energy. It can be derived from plant, animal, and microbial organisms in the form of vegetable oil, fats, and lipids, respectively. However, biodiesel production from such sources is not economically feasible due to extensive downstream processes, such as trans-esterification and purification. To obtain cost-effective biodiesel, these bottlenecks need to be overcome. Escherichia coli, a model microorganism, has the potential to produce biodiesel directly from ligno-cellulosic sugars, bypassing trans-esterification. In this process, E. coli is engineered to produce biodiesel using metabolic engineering technology. The entire process of biodiesel production is carried out in a single microbial cell, bypassing the expensive downstream processing steps. This review focuses mainly on production of fatty acid and biodiesel in E. coli using metabolic engineering approaches. In the first part, we describe fatty acid biosynthesis in E. coli. In the second half, we discuss bottlenecks and strategies to enhance the production yield. A complete understanding of current developments in E. coli-based biodiesel production and pathway optimization strategies would reduce production costs for biofuels and plant-derived chemicals.
Collapse
Affiliation(s)
- Ziaur Rahman
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
- Department of Environmental and Conservation Sciences, University of Swat, Swat, 19130, Pakistan.
- Center for Biotechnology and Microbiology, University of Swat, Swat, Pakistan.
- Department of Microbiology, AWKUM, Mardan, Pakistan.
| | - Naim Rashid
- Department of Chemical Engineering, COMSATS, Lahore, Pakistan
| | - Javed Nawab
- Department of Environmental and Conservation Sciences, University of Swat, Swat, 19130, Pakistan
| | | | - Bong Hyun Sung
- Bioenergy and Biochemical Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 34141, Republic of Korea
| | - Sun Chang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
| |
Collapse
|
27
|
Production of FAME biodiesel in E. coli by direct methylation with an insect enzyme. Sci Rep 2016; 6:24239. [PMID: 27053100 PMCID: PMC4823748 DOI: 10.1038/srep24239] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [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.
Collapse
|
28
|
In vitro reconstitution guide for targeted synthetic metabolism of chemicals, nutraceuticals and drug precursors. Synth Syst Biotechnol 2016; 1:25-33. [PMID: 29062924 PMCID: PMC5640587 DOI: 10.1016/j.synbio.2016.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 01/27/2016] [Accepted: 02/12/2016] [Indexed: 11/24/2022] Open
Abstract
With the developments in metabolic engineering and the emergence of synthetic biology, many breakthroughs in medicinal, biological and chemical products as well as biofuels have been achieved in recent decades. As an important barrier to traditional metabolic engineering, however, the identification of rate-limiting step(s) for the improvement of specific cellular functions is often difficult. Meanwhile, in the case of synthetic biology, more and more BioBricks could be constructed for targeted purposes, but the optimized assembly or engineering of these components for high-efficiency cell factories is still a challenge. Owing to the lack of steady-state kinetic data for overall flux, balancing many multistep biosynthetic pathways is time-consuming and needs vast resources of labor and materials. A strategy called targeted engineering is proposed in an effort to solve this problem. Briefly, a targeted biosynthetic pathway is to be reconstituted in vitro and then the contribution of cofactors, substrates and each enzyme will be analyzed systematically. Next is in vivo engineering or de novo pathway assembly with the guidance of information gained from in vitro assays. To demonstrate its practical application, biosynthesis pathways for the production of important products, e.g. chemicals, nutraceuticals and drug precursors, have been engineered in Escherichia coli and Saccharomyces cerevisiae. These cases can be regarded as concept proofs indicating targeted engineering might help to create high-efficiency cell factories based upon constructed biological components.
Collapse
|
29
|
Menendez-Bravo S, Roulet J, Sabatini M, Comba S, Dunn R, Gramajo H, Arabolaza A. High cell density production of multimethyl-branched long-chain esters in Escherichia coli and determination of their physicochemical properties. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:215. [PMID: 27757170 PMCID: PMC5064953 DOI: 10.1186/s13068-016-0631-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 09/28/2016] [Indexed: 05/09/2023]
Abstract
BACKGROUND Microbial synthesis of oleochemicals derived from native fatty acid (FA) metabolism has presented significant advances in recent years. Even so, native FA biosynthetic pathways often provide a narrow variety of usually linear hydrocarbons, thus yielding end products with limited structural diversity. To overcome this limitation, we took advantage of a polyketide synthase-based system from Mycobacterium tuberculosis and developed an Escherichia coli platform with the capacity to synthesize multimethyl-branched long-chain esters (MBE) with novel chemical structures. RESULTS With the aim to initiate the characterization of these novel waxy compounds, here, we describe the chassis optimization of the MBE producer E. coli strain for an up-scaled oil production. By carrying out systematic metabolic engineering, we improved the final titer to 138.1 ± 5.3 mg MBE L-1 in batch cultures. Fed-batch microbial fermentation process was also optimized achieving a maximum yield of 790.2 ± 6.9 mg MBE L-1 with a volumetric productivity of 15.8 ± 1.1 mg MBE (L h)-1. Purified MBE oil was subjected to various physicochemical analyses, including differential scanning calorimetry (DSC) and pressurized-differential scanning calorimetry (P-DSC) studies. CONCLUSIONS The analysis of the pour point, DSC, and P-DSC data obtained showed that bacterial MBE possess improved cold flow properties than several plant oils and some chemically modified derivatives, while exhibiting high oxidation stability at elevated temperatures. These encouraging data indicate that the presence of multiple methyl branches in these novel esters, indeed, conferred favorable properties which are superior to those of linear esters.
Collapse
Affiliation(s)
- Simón Menendez-Bravo
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Julia Roulet
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Martín Sabatini
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Santiago Comba
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Robert Dunn
- US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University St, Peoria, IL 61604 USA
| | - Hugo Gramajo
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| | - Ana Arabolaza
- Microbiology Division, IBR (Instituto de Biología Molecular y Celular de Rosario), Consejo Nacional de Investigaciones Científicas y Técnicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Ocampo y Esmeralda (2000), Rosario, Argentina
| |
Collapse
|
30
|
Hinks J, Wang Y, Matysik A, Kraut R, Kjelleberg S, Mu Y, Bazan GC, Wuertz S, Seviour T. Increased Microbial Butanol Tolerance by Exogenous Membrane Insertion Molecules. CHEMSUSCHEM 2015; 8:3718-3726. [PMID: 26404512 DOI: 10.1002/cssc.201500194] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 07/13/2015] [Indexed: 06/05/2023]
Abstract
Butanol is an ideal biofuel, although poor titers lead to high recovery costs by distillation. Fluidization of microbial membranes by butanol is one of the major factors limiting titers in butanol-producing bioprocesses. Starting with the hypothesis that certain membrane insertion molecules would stabilize the lipid bilayer in the presence of butanol, we applied a combination of in vivo and in vitro techniques within an in silico framework to describe a new approach to achieve solvent tolerance in bacteria. Single-molecule tracking of a model supported bilayer showed that COE1-5C, a five-ringed oligo-polyphenylenevinylene conjugated oligoelectrolyte (COE), reduced the diffusion rate of phospholipids in a microbially derived lipid bilayer to a greater extent than three-ringed and four-ringed COEs. Furthermore, COE1-5C treatment increased the specific growth rate of E. coli K12 relative to a control at inhibitory butanol concentrations. Consequently, to confer butanol tolerance to microbes by exogenous means is complementary to genetic modification of strains in industrial bioprocesses, extends the physiological range of microbes to match favorable bioprocess conditions, and is amenable with complex and undefined microbial consortia for biobutanol production. Molecular dynamics simulations indicated that the π-conjugated aromatic backbone of COE1-5C likely acts as a hydrophobic tether for glycerophospholipid acyl chains by enhancing bilayer integrity in the presence of high butanol concentrations, which thereby counters membrane fluidization. COE1-5C-mitigated E. coli K12 membrane depolarization by butanol is consistent with the hypothesis that improved growth rates in the presence of butanol are a consequence of improved bilayer stability.
Collapse
Affiliation(s)
- Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore.
| | - Yaofeng Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Artur Matysik
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Rachel Kraut
- Division of Molecular Genetics and Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
- Centre for Marine BioInnovation and School of Biotechnology and Bimolecular Sciences, University of New South Wales, Sydney, 2052, Australia
| | - Yuguang Mu
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore
| | - Guillermo C Bazan
- Department of Chemistry & Biochemistry and Materials, Center for Polymers and Organic Solids, University of California, Santa Barbara, California, 93106, USA
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore
- Department of Civil and Environmental Engineering, University of California, Davis, California, 95616, USA
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore, 637551, Singapore.
| |
Collapse
|
31
|
Jiang W, Jiang Y, Bentley GJ, Liu D, Xiao Y, Zhang F. Enhanced production of branched-chain fatty acids by replacing β-ketoacyl-(acyl-carrier-protein) synthase III (FabH). Biotechnol Bioeng 2015; 112:1613-22. [DOI: 10.1002/bit.25583] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/09/2015] [Accepted: 02/23/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Wen Jiang
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
| | - Yanfang Jiang
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
| | - Gayle J. Bentley
- Division of Biological & Biomedical Sciences; Washington University in St. Louis; Saint Louis Missouri
| | - Di Liu
- Division of Biological & Biomedical Sciences; Washington University in St. Louis; Saint Louis Missouri
| | - Yi Xiao
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
| | - Fuzhong Zhang
- Department of Energy, Environmental, and Chemical Engineering; Washington University in St. Louis; 1 Brookings Drive, Saint Louis Missouri 63130
- Division of Biological & Biomedical Sciences; Washington University in St. Louis; Saint Louis Missouri
| |
Collapse
|
32
|
Abstract
E. coli's hardiness, versatility, broad palate and ease of handling have made it the most intensively studied and best understood organism on the planet. However, research on E.coli has primarily examined it as a model organism, one that is abstracted from any natural history. But E. coli is far more than just a microbial lab rat. Rather, it is a highly diverse organism with a complex, multi-faceted niche in the wild. Recent studies of 'wild' E. coli have, for example, revealed a great deal about its presence in the environment, its diversity and genomic evolution, as well as its role in the human microbiome and disease. These findings have shed light on aspects of its biology and ecology that pose far-reaching questions and illustrate how an appreciation of E. coli's natural history can expand its value as a model organism.
Collapse
Affiliation(s)
- Zachary D Blount
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, United States; BEACON Center for the Study of Evolution in Action, East Lansing, United States
| |
Collapse
|
33
|
In silico analysis of bioethanol overproduction by genetically modified microorganisms in coculture fermentation. BIOTECHNOLOGY RESEARCH INTERNATIONAL 2015; 2015:238082. [PMID: 25785200 PMCID: PMC4345248 DOI: 10.1155/2015/238082] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/28/2015] [Indexed: 11/18/2022]
Abstract
Lignocellulosic biomass is an attractive sustainable carbon source for fermentative production of bioethanol. In this context, use of microbial consortia consisting of substrate-selective microbes is advantageous as it eliminates the negative impacts of glucose catabolite repression. In this study, a detailed in silico analysis of bioethanol production from glucose-xylose mixtures of various compositions by coculture fermentation of xylose-selective Escherichia coli strain ZSC113 and glucose-selective wild-type Saccharomyces cerevisiae is presented. Dynamic flux balance models based on available genome-scale metabolic networks of the microorganisms have been used to analyze bioethanol production and the maximization of ethanol productivity is addressed by computing optimal aerobic-anaerobic switching times. A set of genetic engineering strategies for ethanol overproduction by E. coli strain ZSC113 have been evaluated for their efficiency in the context of batch coculture process. Finally, simulations are carried out to determine the pairs of genetically modified E. coli strain ZSC113 and S. cerevisiae that significantly enhance ethanol productivity in batch coculture fermentation.
Collapse
|
34
|
Modification of emodin and aloe-emodin by glycosylation in engineered Escherihia coli. World J Microbiol Biotechnol 2015; 31:611-9. [PMID: 25663173 DOI: 10.1007/s11274-015-1815-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 01/30/2015] [Indexed: 12/11/2022]
Abstract
Glycosyltransferase from Bacillus licheniformis DSM13 (YjiC) was used for enzymatic modification of emodin and aloe-emodin in vitro and in vivo. In order to increase the availability of UDP-glucose, three genes involved in the production of precursors of NDP-sugar in Escherichia coli BL21 (DE3) viz. D-glucose phosphate isomerase (pgi), D-glucose-6-phosphate dehydrogenase (zwf), and UDP-sugar hydrolase (ushA) were deleted and glucose-1-phosphate urididyltransferase (galU) gene was over expressed. To improve the yield of the products; substrate, time and media parameters were optimized, and the production was scaled up using a 3 L fermentor. The maximum yield of glycosylated products of emodin (emodin-O-β-D-glucoside) and aloe-emodin (aloe-emodin-O-β-D-glucoside) were approximately 144 µM (38 mg/L) and 168 µM (45 mg/L) respectively, representing almost 72 % and 84 % bioconversion of emodin and aloe-emodin when 200 µM of emodin and aloe-emodin were supplemented in the culture. Additionally, the emodin and aloe emodin major glycosylated products exhibited the highest stability at pH 8.0 and the stability of products was up to 70 °C and 60 °C respectively. Furthermore, the biological activities of emodin and its major glucoside (P1) were compared and their anti-cancer activities were assayed in several cancer cell lines. The results demonstrate that YjiC has the capacity to catalyze the glycosylation of these aromatic compounds and that glycosylation of anthraquinones enhances their aqueous solubility while retaining their biological activities.
Collapse
|
35
|
Jung Y, Kim S, Lee S, Ha KS, Lee J. Effect of heterologous expression of genes involved in the elongation cycle of fatty acid synthesis on fatty acid production in Saccharomyces cerevisiae. BIOTECHNOL BIOPROC E 2015. [DOI: 10.1007/s12257-014-0484-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
36
|
Choi G, Hassett DJ, Choi S. A paper-based microbial fuel cell array for rapid and high-throughput screening of electricity-producing bacteria. Analyst 2015; 140:4277-83. [DOI: 10.1039/c5an00492f] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a 48-well, paper-based sensing platform was developed for the high-throughput and rapid characterization of the electricity-producing capability of microbes.
Collapse
Affiliation(s)
- Gihoon Choi
- Bioelectronics & Microsystems Laboratory
- Department of Electrical & Computer Engineering
- State University of New York-Binghamton
- Binghamton
- USA
| | - Daniel J. Hassett
- Department of Molecular Genetics
- Biochemistry and Microbiology
- University of Cincinnati College of Medicine
- Cincinnati
- USA
| | - Seokheun Choi
- Bioelectronics & Microsystems Laboratory
- Department of Electrical & Computer Engineering
- State University of New York-Binghamton
- Binghamton
- USA
| |
Collapse
|
37
|
Liu Q, Wu K, Cheng Y, Lu L, Xiao E, Zhang Y, Deng Z, Liu T. Engineering an iterative polyketide pathway in Escherichia coli results in single-form alkene and alkane overproduction. Metab Eng 2014; 28:82-90. [PMID: 25536488 DOI: 10.1016/j.ymben.2014.12.004] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/07/2014] [Accepted: 12/12/2014] [Indexed: 11/28/2022]
Abstract
Alkanes and alkenes are ideal biofuels, due to their high energy content and ability to be safely transported. To date, fatty acid-derived pathways for alkane and alkene bioproduction have been thoroughly explored. In this study, we engineered the pathway of the iterative Type I polyketide synthase (PKS) SgcE with the cognate thioesterase (TE) SgcE10 in Escherichia coli, with the goal of overproducing pentadecaheptaene (PDH) followed by its hydrogenation to pentadecane (PD). Based on initial in vitro titration assays, we learned that PDH production is strongly dependent on the SgcE10:SgcE ratio. Thus, we engineered a high-yield E. coli strain by fine-tuning SgcE10 expression via synthetic promoters. We analyzed engineered E. coli strains using a modified multiple reactions monitoring mass spectrometry (MRM-MS)-based targeted proteomic approach, using a chimeric SgcE10 and SgcE fusion construct to gain insight into expression levels of the two proteins. Lastly, through fed-batch fermentation followed by flow chemical hydrogenation, we obtained a PD yield of nearly 140mg/L in single-alkane form. Thus, we not only employed a metabolic engineering approach to the iterative polyketide pathway, we highlighted the potential of PKS shunt products to play a role in the production of single-form and high-value chemicals.
Collapse
Affiliation(s)
- Qian Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Kaiyue Wu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; J1 Biotech, Co. Ltd., Wuhan 430075, China
| | - Yongbo Cheng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Lei Lu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Erting Xiao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Yuchen Zhang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, and Wuhan University School of Pharmaceutical Sciences, Wuhan 430071, China; Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan 430075, China.
| |
Collapse
|
38
|
Messerschmidt SJ, Kemter FS, Schindler D, Waldminghaus T. Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae. Biotechnol J 2014; 10:302-14. [PMID: 25359671 DOI: 10.1002/biot.201400031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 10/02/2014] [Accepted: 10/30/2014] [Indexed: 01/25/2023]
Abstract
Recent developments in DNA-assembly methods make the synthesis of synthetic chromosomes a reachable goal. However, the redesign of primary chromosomes bears high risks and still requires enormous resources. An alternative approach is the addition of synthetic chromosomes to the cell. The natural secondary chromosome of Vibrio cholerae could potentially serve as template for a synthetic secondary chromosome in Escherichia coli. To test this assumption we constructed a replicon named synVicII based on the replication module of V. cholerae chromosome II (oriII). A new assay for the assessment of replicon stability was developed based on flow-cytometric analysis of unstable GFP variants. Application of this assay to cells carrying synVicII revealed an improved stability compared to a secondary replicon based on E. coli oriC. Cell cycle analysis and determination of cellular copy numbers of synVicII indicate that replication timing of the synthetic replicon in E. coli is comparable to the natural chromosome II (ChrII) in V. cholerae. The presented synthetic biology work provides the basis to use secondary chromosomes in E. coli to answer basic research questions as well as for several biotechnological applications.
Collapse
Affiliation(s)
- Sonja J Messerschmidt
- LOEWE Center for Synthetic Microbiology, SYNMIKRO, Philipps-Universität Marburg, Germany
| | | | | | | |
Collapse
|
39
|
Lisha KP, Sarkar D. In silico analysis of bioethanol production from glucose/xylose mixtures during fed-batch fermentation of co-culture and mono-culture systems. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0320-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
40
|
Wang H, Wang F, Wang W, Yao X, Wei D, Cheng H, Deng Z. Improving the expression of recombinant proteins in E. coli BL21 (DE3) under acetate stress: an alkaline pH shift approach. PLoS One 2014; 9:e112777. [PMID: 25402470 PMCID: PMC4234529 DOI: 10.1371/journal.pone.0112777] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 10/20/2014] [Indexed: 11/23/2022] Open
Abstract
Excess acetate has long been an issue for the production of recombinant proteins in E. coli cells. Recently, improvements in acetate tolerance have been achieved through the use of genetic strategies and medium supplementation with certain amino acids and pyrimidines. The aim of our study was to evaluate an alternative to improve the acetate tolerance of E. coli BL21 (DE3), a popular strain used to express recombinant proteins. In this work we reported the cultivation of BL21 (DE3) in complex media containing acetate at high concentrations. In the presence of 300 mM acetate, compared with pH 6.5, pH 7.5 improved cell growth by approximately 71%, reduced intracellular acetate by approximately 50%, and restored the expression of glutathione S-transferase (GST), green fluorescent protein (GFP) and cytochrome P450 monooxygenase (CYP). Further experiments showed that alkaline pHs up to 8.5 had little inhibition in the expression of GST, GFP and CYP. In addition, the detrimental effect of acetate on the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) by the cell membrane, an index of cellular metabolic capacity, was substantially alleviated by a shift to alkaline pH values of 7.5–8.0. Thus, we suggest an approach of cultivating E. coli BL21 (DE3) at pH 8.0±0.5 to minimize the effects caused by acetate stress. The proposed strategy of an alkaline pH shift is a simple approach to solving similar bioprocessing problems in the production of biofuels and biochemicals from sugars.
Collapse
Affiliation(s)
- Hengwei Wang
- Innovation & Application Institute (IAI), Zhejiang Ocean University, Zhoushan, China
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Fengqing Wang
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Wei Wang
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Xueling Yao
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Dongzhi Wei
- New World Institute of Biotechnology, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Hairong Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail:
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
41
|
Yuzbasheva EY, Yuzbashev TV, Mostova EB, Perkovskaya NI, Sineokii SP. Microbial synthesis of biodiesel and its prospects. APPL BIOCHEM MICRO+ 2014. [DOI: 10.1134/s0003683814090075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
42
|
Luska KL, Julis J, Stavitski E, Zakharov DN, Adams A, Leitner W. Bifunctional nanoparticle–SILP catalysts (NPs@SILP) for the selective deoxygenation of biomass substrates. Chem Sci 2014. [DOI: 10.1039/c4sc02033b] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
43
|
Glycosylation and subsequent malonylation of isoflavonoids in E. coli: strain development, production and insights into future metabolic perspectives. J Ind Microbiol Biotechnol 2014; 41:1647-58. [PMID: 25189810 DOI: 10.1007/s10295-014-1504-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/22/2014] [Indexed: 01/25/2023]
Abstract
Genistin and daidzein exhibit a protective effect on DNA damage and inhibit cell proliferation. Glycosylation and malonylation of the compounds increase water solubility and stability. Constructed pET15b-GmIF7GT and pET28a-GmIF7MAT were used for the transformation of Escherichia coli and bioconversion of genistein and daidzein. To increase the availability of malonyl-CoA, a critical precursor of GmIF7MAT, genes for the acyl-CoA carboxylase α and β subunits (nfa9890 and nfa9940), biotin ligase (nfa9950), and acetyl-CoA synthetase (nfa3550) from Nocardia farcinia were also introduced. Thus, the isoflavonoids were glycosylated at position 7 by 7-O-glycosyltranferase and were further malonylated at position 6(″) of glucose by malonyl-CoA: isoflavone 7-O-glucoside-6(″)-O-malonyltransferase both from Glycine max. Engineered E. coli produced 175.7 µM (75.90 mg/L) of genistin and 14.2 µM (7.37 mg/L) genistin 6''-O-malonate. Similar conditions produced 162.2 µM (67.65 mg/L) daidzin and 12.4 µM (6.23 mg/L) daidzin 6''-O-malonate when 200 µM of each substrate was supplemented in the culture. Based on our findings, we speculate that isoflavonoids and their glycosides may prove useful as anticancer drugs with added advantage of increased solubility, stability and bioavailability.
Collapse
|
44
|
Sherkhanov S, Korman TP, Bowie JU. Improving the tolerance of Escherichia coli to medium-chain fatty acid production. Metab Eng 2014; 25:1-7. [DOI: 10.1016/j.ymben.2014.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 05/22/2014] [Accepted: 06/04/2014] [Indexed: 12/17/2022]
|
45
|
Menendez-Bravo S, Comba S, Sabatini M, Arabolaza A, Gramajo H. Expanding the chemical diversity of natural esters by engineering a polyketide-derived pathway into Escherichia coli. Metab Eng 2014; 24:97-106. [DOI: 10.1016/j.ymben.2014.05.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 04/29/2014] [Accepted: 05/05/2014] [Indexed: 01/25/2023]
|
46
|
Ruegg TL, Kim EM, Simmons BA, Keasling JD, Singer SW, Lee TS, Thelen MP. An auto-inducible mechanism for ionic liquid resistance in microbial biofuel production. Nat Commun 2014; 5:3490. [PMID: 24667370 DOI: 10.1038/ncomms4490] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2013] [Accepted: 02/21/2014] [Indexed: 01/16/2023] Open
Abstract
Ionic liquids (ILs) are emerging as superior solvents for numerous industrial applications, including the pretreatment of biomass for the microbial production of biofuels. However, some of the most effective ILs used to solubilize cellulose inhibit microbial growth, decreasing efficiency in the overall process. Here we identify an IL-resistance mechanism consisting of two adjacent genes from Enterobacter lignolyticus, a rain forest soil bacterium that is tolerant to an imidazolium-based IL. These genes retain their full functionality when transferred to an Escherichia coli biofuel host, with IL resistance established by an inner membrane transporter, regulated by an IL-inducible repressor. Expression of the transporter is dynamically adjusted in direct response to IL, enabling growth and biofuel production at levels of IL that are toxic to native strains. This natural auto-regulatory system provides the basis for engineering IL-tolerant microbes, which should accelerate progress towards effective conversion of lignocellulosic biomass to fuels and renewable chemicals.
Collapse
Affiliation(s)
- Thomas L Ruegg
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Institute of Botany, University of Basel, Basel 4056, Switzerland [3] Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| | - Eun-Mi Kim
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Blake A Simmons
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Biological and Materials Science Center, Sandia National Laboratories, Livermore, California 94550, USA
| | - Jay D Keasling
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA [3] Department of Chemical and Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Steven W Singer
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Taek Soon Lee
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Michael P Thelen
- 1] Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, USA [2] Biology and Biotechnology Division, Lawrence Livermore National Laboratory, Livermore, California 94550, USA
| |
Collapse
|
47
|
Tee TW, Chowdhury A, Maranas CD, Shanks JV. Systems metabolic engineering design: fatty acid production as an emerging case study. Biotechnol Bioeng 2014; 111:849-57. [PMID: 24481660 PMCID: PMC4241050 DOI: 10.1002/bit.25205] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/21/2014] [Accepted: 01/28/2014] [Indexed: 12/20/2022]
Abstract
Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities.
Collapse
Affiliation(s)
- Ting Wei Tee
- Department of Chemical and Biological Engineering, Iowa State University, Ames, Iowa
| | | | | | | |
Collapse
|
48
|
Bhutto AW, Qureshi K, Harijan K, Zahedi G, Bahadori A. Strategies for the consolidation of biologically mediated events in the conversion of pre-treated lignocellulose into ethanol. RSC Adv 2014. [DOI: 10.1039/c3ra44020f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
49
|
Badra J, Elwardany AE, Farooq A. Reaction rate constants of H-abstraction by OH from large ketones: measurements and site-specific rate rules. Phys Chem Chem Phys 2014; 16:12183-93. [DOI: 10.1039/c4cp01253d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reaction rate constants of the reaction of four large ketones with hydroxyl (OH) are investigated behind reflected shock waves using OH laser absorption.
Collapse
Affiliation(s)
- Jihad Badra
- Clean Combustion Research Center
- Division of Physical Sciences and Engineering
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955, Saudi Arabia
- Saudi Aramco Research and Development Center
| | - Ahmed E. Elwardany
- Clean Combustion Research Center
- Division of Physical Sciences and Engineering
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955, Saudi Arabia
| | - Aamir Farooq
- Clean Combustion Research Center
- Division of Physical Sciences and Engineering
- King Abdullah University of Science and Technology (KAUST)
- Thuwal 23955, Saudi Arabia
| |
Collapse
|
50
|
Expression of dehydratase domains from a polyunsaturated fatty acid synthase increases the production of fatty acids in Escherichia coli. Enzyme Microb Technol 2013; 55:133-9. [PMID: 24411456 DOI: 10.1016/j.enzmictec.2013.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Revised: 10/24/2013] [Accepted: 10/25/2013] [Indexed: 12/26/2022]
Abstract
Increasing the production of fatty acids by microbial fermentation remains an important step toward the generation of biodiesel and other portable liquid fuels. In this work, we report an Escherichia coli strain engineered to overexpress a fragment consisting of four dehydratase domains from the polyunsaturated fatty acid (PUFA) synthase enzyme complex from the deep-sea bacterium, Photobacterium profundum. The DH1-DH2-UMA enzyme fragment was excised from its natural context within a multi-enzyme PKS and expressed as a stand-alone protein. Fatty acids were extracted from the cell pellet, esterified with methanol and quantified by GC-MS analysis. Results show that the E. coli strain expressing the DH tetradomain fragment was capable of producing up to a 5-fold increase (80.31 mg total FA/L culture) in total fatty acids over the negative control strain lacking the recombinant enzyme. The enhancement in production was observed across the board for all the fatty acids that are typically made by E. coli. The overexpression of the DH tetradomain did not affect E. coli cell growth, thus showing that the observed enhancement in fatty acid production was not a result of effects associated with cell density. The observed enhancement was more pronounced at lower temperatures (3.8-fold at 16 °C, 3.5-fold at 22 °C and 1.5-fold at 30 °C) and supplementation of the media with 0.4% glycerol did not result in an increase in fatty acid production. All these results taken together suggest that either the dehydration of fatty acid intermediates are a limiting step in the E. coli fatty acid biosynthesis machinery, or that the recombinant dehydratase domains used in this study are also capable of catalyzing thioester hydrolysis of the final products. The enzyme in this report is a new tool which could be incorporated into other existing strategies aimed at improving fatty acid production in bacterial fermentations toward accessible biodiesel precursors.
Collapse
|