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Ni M, Pan Y, Li D, Huang Y, Chen Z, Li L, Bi Z, Wu R, Song Z. Metagenomics, metatranscriptomics, and proteomics reveal the metabolic mechanism of biofilm sequencing batch reactor with higher phosphate enrichment capacity under low phosphorus load. ENVIRONMENTAL RESEARCH 2023; 238:117237. [PMID: 37793587 DOI: 10.1016/j.envres.2023.117237] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/21/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023]
Abstract
The biofilm sequencing batch reactor (BSBR) process has higher phosphate recovery efficiency and enrichment multiple when the phosphorus load is lower, but the mechanism of phosphate enrichment at low phosphorus load remains unclear. In this study, we operated two BSBR operating under low and high phosphorus load (0.012 and 0.032 kg/(m3·d)) respectively, and used metagenomic, metatranscriptomic, and proteomics methods to analyze the community structure of the phosphorus accumulating organisms (PAOs) in the biofilm, the transcription and protein expression of key functional genes and enzymes, and the metabolism of intracellular polymers. Compared with at high phosphorus load, the BSBR at low phosphorus load have different PAOs and fewer types of PAOs, but in both cases the PAOs must have the PHA, PPX, Pst, and acs genes to become dominant. Some key differences in the metabolism of PAOs from the BSBR with different phosphorus load can be identified as follows. When the phosphorus load is low, the adenosine triphosphoric acid (ATP) and NAD(P)H in the anaerobic stage come from the TCA cycle and the second half of the EMP pathway. The key genes that are upregulated include GAPDH, PGK, ENO, ppdk in the EMP pathway, actP in acetate metabolism, phnB in polyhydroxybutyrate (PHB) synthesis, and aceA, mdh, sdhA, and IDH1 in the TCA cycle. In the meantime, the ccr gene in the PHV pathway is inhibited. As a result, the metabolism of the PAOs features low glycogen with high PHB, Pupt, Prel, and low PHV. That is, more ATP and NAD(P)H flow to phosphorus enrichment metabolism, thus allowing the highly efficient enrichment of phosphorus from low concentration phosphate thanks to the higher abundance of PAOs. The current results provide theoretical support and a new technical option for the enrichment and recovery of low concentrations of phosphate from wastewater by the BSBR process.
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Affiliation(s)
- Min Ni
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; Jiangsu Key Laboratory of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yang Pan
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China.
| | - Dapeng Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Yong Huang
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Zhiqiang Chen
- Harbin Institute of Technology, Harbin, 150006, China
| | - Lu Li
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Zhen Bi
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China; National and Local Joint Engineering Laboratory of Municipal Sewage Resource Utilization Technology, Suzhou University of Science and Technology, Suzhou, 215009, China
| | - Ruijing Wu
- School of Environmental Science and Engineering, Suzhou University of Science and Technology, Suzhou, 215009, China
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Cortada-Garcia J, Daly R, Arnold SA, Burgess K. Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Sci Rep 2023; 13:12990. [PMID: 37563133 PMCID: PMC10415327 DOI: 10.1038/s41598-023-39661-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowing a more unbiased approach, but data interpretation using multivariate analysis is usually not straightforward and requires time and effort. Here we show, for the first time, the application of metabolic pathway enrichment analysis using untargeted and targeted metabolomics data to identify genetic targets for bioprocess improvement in a more streamlined way. The analysis of an Escherichia coli succinate production bioprocess with this methodology revealed three significantly modulated pathways during the product formation phase: the pentose phosphate pathway, pantothenate and CoA biosynthesis and ascorbate and aldarate metabolism. From these, the two former pathways are consistent with previous efforts to improve succinate production in Escherichia coli. Furthermore, to the best of our knowledge, ascorbate and aldarate metabolism is a newly identified target that has so far never been explored for improving succinate production in this microorganism. This methodology therefore represents a powerful tool for the streamlined identification of strain engineering targets that can accelerate bioprocess optimisation.
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Affiliation(s)
- Joan Cortada-Garcia
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, UK
| | - S Alison Arnold
- Ingenza Ltd., Roslin Innovation Centre, Roslin, EH25 9RG, UK
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK.
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3
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Ma Y, Han L, Raza SHA, Gui L, Zhang X, Hou S, Sun S, Yuan Z, Wang Z, Yang B, Hassan MM, Alghsham RS, Al Abdulmonem W, Alkhalil SS. Exploring the effects of palm kernel meal feeding on the meat quality and rumen microorganisms of Qinghai Tibetan sheep. Food Sci Nutr 2023; 11:3516-3534. [PMID: 37324863 PMCID: PMC10261763 DOI: 10.1002/fsn3.3340] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 10/03/2023] Open
Abstract
Palm kernel meal (PKM) has been shown to be a high-quality protein source in ruminant feeds. This study focused on the effects of feed, supplemented with different amounts of PKM (ZL-0 as blank group, and ZL-15, ZL-18, and ZL-21 as treatment group), on the quality and flavor profile of Tibetan sheep meat. Furthermore, the deposition of beneficial metabolites in Tibetan sheep and the composition of rumen microorganisms on underlying regulatory mechanisms of meat quality were studied based on ultra-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry as well as 16S rDNA sequencing. The results of the study showed that Tibetan sheep in the ZL-18 group exhibited superior eating quality and flavor profile while depositing more protein and fat relative to the other groups. The ZL-18 group also changed significantly in terms of the concentration and metabolic pathways of meat metabolites, as revealed by metabolomics. Metabolomics and correlation analyses finally showed that PKM feed mainly affected carbohydrate metabolism in muscle, which in turn affects meat pH, tenderness, and flavor. In addition, 18% of PKM increased the abundance of Christensenellaceae R-7 group, Ruminococcaceae UCG-013, Lachnospiraceae UCG-002, and Family XIII AD3011 group in the rumen but decreased the abundance of Prevotella 1; the above bacteria groups regulate meat quality by regulating rumen metabolites (succinic acid, DL-glutamic acid, etc.). Overall, the addition of PKM may improve the quality and flavor of the meat by affecting muscle metabolism and microorganisms in the rumen.
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Affiliation(s)
- Ying Ma
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Lijuan Han
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Sayed Haidar Abbas Raza
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation‐Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry ProductsSouth China Agricultural UniversityGuangzhou510642China
- College of Animal Science and Technology, Northwest A&F UniversityYangling712100ShaanxiPeople's Republic of China
| | - Linsheng Gui
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Xue Zhang
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Shengzhen Hou
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Shengnan Sun
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Zhenzhen Yuan
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Zhiyou Wang
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Baochun Yang
- College of Agriculture and Animal Husbandry, Qinghai University XiningXining810016People's Republic of China
| | - Mohamed M. Hassan
- Department of BiologyCollege of Science, Taif UniversityP.O. Box 11099Taif21944Saudi Arabia
| | - Ruqaih S. Alghsham
- Department of PathologyCollege of Medicine, Qassim UniversityQassimSaudi Arabia
| | - Waleed Al Abdulmonem
- Department of PathologyCollege of Medicine, Qassim UniversityP.O. Box 6655Buraidah51452Kingdom of Saudi Arabia
| | - Samia S. Alkhalil
- Department of Clinical Laboratory SciencesCollege of Applied Medical Sciences, Shaqra UniversityAlquwayiyahRiyadhSaudi Arabia
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4
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Yan W, Cao Z, Ding M, Yuan Y. Design and construction of microbial cell factories based on systems biology. Synth Syst Biotechnol 2023; 8:176-185. [PMID: 36874510 PMCID: PMC9979088 DOI: 10.1016/j.synbio.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 10/25/2022] [Accepted: 11/03/2022] [Indexed: 11/19/2022] Open
Abstract
Environmental sustainability is an increasingly important issue in industry. As an environmentally friendly and sustainable way, constructing microbial cell factories to produce all kinds of valuable products has attracted more and more attention. In the process of constructing microbial cell factories, systems biology plays a crucial role. This review summarizes the recent applications of systems biology in the design and construction of microbial cell factories from four perspectives, including functional genes/enzymes discovery, bottleneck pathways identification, strains tolerance improvement and design and construction of synthetic microbial consortia. Systems biology tools can be employed to identify functional genes/enzymes involved in the biosynthetic pathways of products. These discovered genes are introduced into appropriate chassis strains to build engineering microorganisms capable of producing products. Subsequently, systems biology tools are used to identify bottleneck pathways, improve strains tolerance and guide design and construction of synthetic microbial consortia, resulting in increasing the yield of engineered strains and constructing microbial cell factories successfully.
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Affiliation(s)
- Wenlong Yan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
| | - Zhibei Cao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
| | - Mingzhu Ding
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072, China
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5
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Metabolic Engineering of Microorganisms to Produce Pyruvate and Derived Compounds. Molecules 2023; 28:molecules28031418. [PMID: 36771084 PMCID: PMC9919917 DOI: 10.3390/molecules28031418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Pyruvate is a hub of various endogenous metabolic pathways, including glycolysis, TCA cycle, amino acid, and fatty acid biosynthesis. It has also been used as a precursor for pyruvate-derived compounds such as acetoin, 2,3-butanediol (2,3-BD), butanol, butyrate, and L-alanine biosynthesis. Pyruvate and derivatives are widely utilized in food, pharmaceuticals, pesticides, feed additives, and bioenergy industries. However, compounds such as pyruvate, acetoin, and butanol are often chemically synthesized from fossil feedstocks, resulting in declining fossil fuels and increasing environmental pollution. Metabolic engineering is a powerful tool for producing eco-friendly chemicals from renewable biomass resources through microbial fermentation. Here, we review and systematically summarize recent advances in the biosynthesis pathways, regulatory mechanisms, and metabolic engineering strategies for pyruvate and derivatives. Furthermore, the establishment of sustainable industrial synthesis platforms based on alternative substrates and new tools to produce these compounds is elaborated. Finally, we discuss the potential difficulties in the current metabolic engineering of pyruvate and derivatives and promising strategies for constructing efficient producers.
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Yang P, Liu W, Chen Y, Gong AD. Engineering the glyoxylate cycle for chemical bioproduction. Front Bioeng Biotechnol 2022; 10:1066651. [PMID: 36532595 PMCID: PMC9755347 DOI: 10.3389/fbioe.2022.1066651] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/17/2022] [Indexed: 07/24/2023] Open
Abstract
With growing concerns about environmental issues and sustainable economy, bioproduction of chemicals utilizing microbial cell factories provides an eco-friendly alternative to current petro-based processes. Creating high-performance strains (with high titer, yield, and productivity) through metabolic engineering strategies is critical for cost-competitive production. Commonly, it is inevitable to fine-tuning or rewire the endogenous or heterologous pathways in such processes. As an important pathway involved in the synthesis of many kinds of chemicals, the potential of the glyoxylate cycle in metabolic engineering has been studied extensively these years. Here, we review the metabolic regulation of the glyoxylate cycle and summarize recent achievements in microbial production of chemicals through tuning of the glyoxylate cycle, with a focus on studies implemented in model microorganisms. Also, future prospects for bioproduction of glyoxylate cycle-related chemicals are discussed.
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Iman MN, Herawati E, Fukusaki E, Putri SP. Metabolomics-driven strain improvement: A mini review. Front Mol Biosci 2022; 9:1057709. [PMID: 36438656 PMCID: PMC9681786 DOI: 10.3389/fmolb.2022.1057709] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 10/28/2022] [Indexed: 07/22/2023] Open
Abstract
In recent years, mass spectrometry-based metabolomics has been established as a powerful and versatile technique for studying cellular metabolism by comprehensive analysis of metabolites in the cell. Although there are many scientific reports on the use of metabolomics for the elucidation of mechanism and physiological changes occurring in the cell, there are surprisingly very few reports on its use for the identification of rate-limiting steps in a synthetic biological system that can lead to the actual improvement of the host organism. In this mini review, we discuss different strategies for improving strain performance using metabolomics data and compare the application of metabolomics-driven strain improvement techniques in different host microorganisms. Finally, we highlight several success stories on the use of metabolomics-driven strain improvement strategies, which led to significant bioproductivity improvements.
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Affiliation(s)
- Marvin Nathanael Iman
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Elisa Herawati
- Department of Biology, Faculty of Mathematics and Natural Sciences, Universitas Sebelas Maret, Surakarta, Indonesia
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
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8
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Shimizu H, Toya Y. Recent advances in metabolic engineering-integration of in silico design and experimental analysis of metabolic pathways. J Biosci Bioeng 2021; 132:429-436. [PMID: 34509367 DOI: 10.1016/j.jbiosc.2021.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/07/2021] [Indexed: 11/29/2022]
Abstract
Microorganisms are widely used to produce valuable compounds. Because thousands of metabolic reactions occur simultaneously and many metabolic reactions are related to target production and cell growth, the development of a rational design method for metabolic pathway modification to optimize target production is needed. In this paper, recent advances in metabolic engineering are reviewed, specifically considering computational pathway modification design and experimental evaluation of metabolic fluxes by 13C-metabolic flux analysis. Computational tools for seeking effective gene deletion targets and recruiting heterologous genes are described in flux balance analysis approaches. A kinetic model and adaptive laboratory evolution were applied to identify and eliminate the rate-limiting step in metabolic pathways. Data science-based approaches for process monitoring and control are described to maximize the performance of engineered cells in bioreactors.
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Affiliation(s)
- Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871, Japan
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Bai SK, Hong Y, Wu YR. Emerging technologies for genetic modification of solventogenic clostridia: From tool to strategy development. BIORESOURCE TECHNOLOGY 2021; 334:125222. [PMID: 33951568 DOI: 10.1016/j.biortech.2021.125222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Solventogenic clostridia has been considered as one of the most potential microbial cell factories for biofuel production in the biorefinery industry. However, the inherent shortcomings of clostridia strains such as low productivity, by-products formation and toxic tolerance still strongly restrict the large-scale application. Therefore, concerns regarding the genetic modification of solventogenic clostridia have spurred interests into the development of modern gene-editing tools. In this review, we summarize the latest advances of genetic tools involved in modifying solventogenic clostridia. Following a systematic comparison on their respective characteristics, we then review the corresponding strategies for overcoming the obstacles to the enhanced production. Discussing the progress of other microbial cell factories for solventogenesis, we finally describe the key challenges and trends with valuable recommendations for future large-scale biosolvent industrial application.
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Affiliation(s)
- Sheng-Kai Bai
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Ying Hong
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China
| | - Yi-Rui Wu
- Department of Biology, Shantou University, Shantou, Guangdong 515063, China; Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, Guangdong 515063, China; Institute of Marine Sciences, Shantou University, Shantou, Guangdong 515063, China.
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10
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Nitta K, Breitling R, Takano E, Putri SP, Fukusaki E. Investigation of the effects of actinorhodin biosynthetic gene cluster expression and a rpoB point mutation on the metabolome of Streptomyces coelicolor M1146. J Biosci Bioeng 2021; 131:525-536. [PMID: 33549493 DOI: 10.1016/j.jbiosc.2021.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 02/07/2023]
Abstract
The previously reported Streptomyces coelicolor M1146 is commonly used as a host strain for engineering of secondary metabolite production. In this study, absolute quantification of intracellular and extracellular metabolites of M1146 was performed in mid-log phase and stationary phase to observe major metabolites and the changes that occurred during growth. Decreased levels of central carbon metabolites (glycolysis, TCA cycle, and pentose phosphate pathway) and increased levels of amino acids were observed in stationary phase compared to mid-log phase. Furthermore, comparative metabolome analyses of M1146 upon expression of the actinorhodin biosynthetic gene cluster (M1146+ACT), a point mutation on the rpoB gene encoding RNA polymerase beta-subunit (M1152), and both expression of actinorhodin biosynthetic gene cluster and a rpoB point mutation (M1152+ACT) were performed. M1146+ACT showed higher levels of important cofactors, such as ATP, NADPH, and FMN while M1152 led to higher levels of intracellular S-adenosyl-methionine, acyl-CoAs, and extracellular nucleosides compared to M1146. M1152+ACT exhibited the highest levels of actinorhodin with elevated bases, nucleosides, and nucleotides, such as intracellular PRPP (phosphoribosyl phosphate), ATP, along with extracellular inosine, uridine, and guanine compared to the other three strains, which were considered to be combined effects of actinorhodin gene cluster expression and a rpoB point mutation. Metabolites analysis by means of absolute quantification demonstrated changes in precursors of secondary metabolites before and after phosphate depletion in M1146. Comparative metabolome analysis provided further insights into the effects of actinorhodin gene cluster expression along with a rpoB point mutation on the metabolome of S. coelicolor.
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Affiliation(s)
- Katsuaki Nitta
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Rainer Breitling
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Eriko Takano
- Manchester Institute of Biotechnology, Manchester Synthetic Biology Research Centre SYNBIOCHEM, Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Sastia P Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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11
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Liang L, Liu R, Freed EF, Eckert CA. Synthetic Biology and Metabolic Engineering Employing Escherichia coli for C2-C6 Bioalcohol Production. Front Bioeng Biotechnol 2020; 8:710. [PMID: 32719784 PMCID: PMC7347752 DOI: 10.3389/fbioe.2020.00710] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/08/2020] [Indexed: 12/18/2022] Open
Abstract
Biofuel production from renewable and sustainable resources is playing an increasingly important role within the fuel industry. Among biofuels, bioethanol has been most widely used as an additive for gasoline. Higher alcohols can be blended at a higher volume compared to ethanol and generate lower greenhouse gas (GHG) emissions without a need to change current fuel infrastructures. Thus, these fuels have the potential to replace fossil fuels in support of more environmentally friendly processes. This review summarizes the efforts to enhance bioalcohol production in engineered Escherichia coli over the last 5 years and analyzes the current challenges for increasing productivities for industrial applications.
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Affiliation(s)
- Liya Liang
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Rongming Liu
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Emily F. Freed
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
| | - Carrie A. Eckert
- Renewable and Sustainable Energy Institute, University of Colorado Boulder, Boulder, CO, United States
- National Renewable Energy Laboratory, Golden, CO, United States
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12
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Laviña WA, Sakurai SSM, Pontrelli S, Putri SP, Fukusaki E. Metabolomics Analysis Reveals Global Metabolic Changes in the Evolved E. coli Strain with Improved Growth and 1-Butanol Production in Minimal Medium. Metabolites 2020; 10:metabo10050192. [PMID: 32414016 PMCID: PMC7281505 DOI: 10.3390/metabo10050192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 04/29/2020] [Accepted: 05/07/2020] [Indexed: 11/30/2022] Open
Abstract
Production of 1-butanol from microorganisms has garnered significant interest due to its prospect as a drop-in biofuel and precursor for a variety of commercially relevant chemicals. Previously, high 1-butanol titer has been reported in Escherichia coli strain JCL166, which contains a modified clostridial 1-butanol pathway. Although conventional and metabolomics-based strain improvement strategies of E. coli strain JCL166 have been successful in improving production in rich medium, 1-butanol titer was severely limited in minimal medium. To further improve growth and consequently 1-butanol production in minimal medium, adaptive laboratory evolution (ALE) using mutD5 mutator plasmid was done on JCL166. Comparative metabolomics analysis of JCL166 and BP1 revealed global perturbations in the evolved strain BP1 compared to JCL166 (44 out of 64 metabolites), encompassing major metabolic pathways such as glycolysis, nucleotide biosynthesis, and CoA-related processes. Collectively, these metabolic changes in BP1 result in improved growth and, consequently, 1-butanol production in minimal medium. Furthermore, we found that the mutation in ihfB caused by ALE had a significant effect on the metabolome profile of the evolved strain. This study demonstrates how metabolomics was utilized for characterization of ALE-developed strains to understand the overall effect of mutations acquired through evolution.
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Affiliation(s)
- Walter A. Laviña
- Microbiology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Laguna 4031, Philippines;
| | - Sana Subhan Memon Sakurai
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.S.M.S.); (S.P.P.)
| | - Sammy Pontrelli
- Institute of Molecular Systems Biology, D-BIOL, ETH Zurich, 8092 Zurich, Switzerland;
| | - Sastia Prama Putri
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.S.M.S.); (S.P.P.)
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan; (S.S.M.S.); (S.P.P.)
- Correspondence: ; Tel.: +81-6-6879-7416
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