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Pham NN, Wu YH, Dai TA, Tu J, Liang RM, Hsieh HY, Chang CW, Hu YC. Auto-inducible synthetic pathway in E. coli enhanced sustainable indigo production from glucose. Metab Eng 2024; 85:14-25. [PMID: 38971492 DOI: 10.1016/j.ymben.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/10/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Indigo is widely used in textile industries for denim garments dyeing and is mainly produced by chemical synthesis which, however, raises environmental sustainability issues. Bio-indigo may be produced by fermentation of metabolically engineering bacteria, but current methods are economically incompetent due to low titer and the need for an inducer. To address these problems, we first characterized several synthetic promoters in E. coli and demonstrated the feasibility of inducer-free indigo production from tryptophan using the inducer-free promoter. We next coupled the tryptophan-to-indigo and glucose-to-tryptophan pathways to generate a de novo glucose-to-indigo pathway. By rational design and combinatorial screening, we identified the optimal promoter-gene combinations, which underscored the importance of promoter choice and expression levels of pathway genes. We thus created a new E. coli strain that exploited an indole pathway to enhance the indigo titer to 123 mg/L. We further assessed a panel of heterologous tryptophan synthase homologs and identified a plant indole lyase (TaIGL), which along with modified pathway design, improved the indigo titer to 235 mg/L while reducing the tryptophan byproduct accumulation. The optimal E. coli strain expressed 8 genes essential for rewiring carbon flux from glucose to indole and then to indigo: mFMO, ppsA, tktA, trpD, trpC, TaIGL and feedback-resistant aroG and trpE. Fed-batch fermentation in a 3-L bioreactor with glucose feeding further increased the indigo titer (≈965 mg/L) and total quantity (≈2183 mg) at 72 h. This new synthetic glucose-to-indigo pathway enables high-titer indigo production without the need of inducer and holds promise for bio-indigo production.
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Affiliation(s)
- Nam Ngoc Pham
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yi-Hsiu Wu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Ting-An Dai
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Jui Tu
- Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan
| | - Ruei-Ming Liang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Hsin-Yun Hsieh
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Chin-Wei Chang
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan
| | - Yu-Chen Hu
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan; Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan.
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2
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Kim HJ, Ham S, Shin N, Hwang JH, Oh SJ, Choi TR, Joo JC, Bhatia SK, Yang YH. Tryptophan-Based Hyperproduction of Bioindigo by Combinatorial Overexpression of Two Different Tryptophan Transporters. J Microbiol Biotechnol 2024; 34:969-977. [PMID: 38213292 PMCID: PMC11091664 DOI: 10.4014/jmb.2308.08039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/18/2023] [Accepted: 11/22/2023] [Indexed: 01/13/2024]
Abstract
Indigo is a valuable, natural blue dye that has been used for centuries in the textile industry. The large-scale commercial production of indigo relies on its extraction from plants and chemical synthesis. Studies are being conducted to develop methods for environment-friendly and sustainable production of indigo using genetically engineered microbes. Here, to enhance the yield of bioindigo from an E. coli whole-cell system containing tryptophanase (TnaA) and flavin-containing monooxygenase (FMO), we evaluated tryptophan transporters to improve the transport of aromatic compounds, such as indole and tryptophan, which are not easily soluble and passable through cell walls. Among the three transporters, Mtr, AroP, and TnaB, AroP enhanced indigo production the most. The combination of each transporter with AroP was also evaluated, and the combination of AroP and TnaB showed the best performance compared to the single transporters and two transporters. Bioindigo production was then optimized by examining the culture medium, temperature, isopropyl β-D-1-thiogalactopyranoside concentration, shaking speed (rpm), and pH. The novel strain containing aroP and tnaB plasmid with tnaA and FMO produced 8.77 mM (2.3 g/l) of bioindigo after 66 h of culture. The produced bioindigo was further recovered using a simple method and used as a watercolor dye, showing good mixing with other colors and color retention for a relatively long time. This study presents an effective strategy for enhancing indigo production using a combination of transporters.
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Affiliation(s)
- Hyun Jin Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Sion Ham
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Nara Shin
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong Hyeon Hwang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Suk Jin Oh
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Tae-Rim Choi
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
| | - Jeong Chan Joo
- Department of Chemical Engineering, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
- Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea
- Institute for Ubiquitous Information Technology and Application, Konkuk University, Seoul 05029, Republic of Korea
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Sharma K, Ghiffary MR, Lee G, Kim HU. Efficient production of an antitumor precursor actinocin and other medicinal molecules from kynurenine pathway in Escherichia coli. Metab Eng 2024; 81:144-156. [PMID: 38043641 DOI: 10.1016/j.ymben.2023.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/05/2023]
Abstract
Kynurenine pathway has a potential to convert L-tryptophan into multiple medicinal molecules. This study aims to explore the biosynthetic potential of kynurenine pathway for the efficient production of actinocin, an antitumor precursor selected as a proof-of-concept target molecule. Kynurenine pathway is first constructed in Escherichia coli by testing various combinations of biosynthetic genes from four different organisms. Metabolic engineering strategies are next performed to improve the production by inhibiting a competing pathway, and enhancing intracellular supply of a cofactor S-adenosyl-L-methionine, and ultimately to produce actinocin from glucose. Metabolome analysis further suggests additional gene overexpression targets, which finally leads to the actinocin titer of 719 mg/L. E. coli strain engineered to produce actinocin is further successfully utilized to produce 350 mg/L of kynurenic acid, a neuroprotectant, and 1401 mg/L of 3-hydroxyanthranilic acid, an antioxidant, also from glucose. These competitive production titers demonstrate the biosynthetic potential of kynurenine pathway as a source of multiple medicinal molecules. The approach undertaken in this study can be useful for the sustainable production of molecules derived from kynurenine pathway, which are otherwise chemically synthesized.
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Affiliation(s)
- Komal Sharma
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Mohammad Rifqi Ghiffary
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - GaRyoung Lee
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Systems Biology and Medicine Laboratory, Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; Graduate School of Engineering Biology, KAIST, Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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Ren X, Wei Y, Zhao H, Shao J, Zeng F, Wang Z, Li L. A comprehensive review and comparison of L-tryptophan biosynthesis in Saccharomyces cerevisiae and Escherichia coli. Front Bioeng Biotechnol 2023; 11:1261832. [PMID: 38116200 PMCID: PMC10729320 DOI: 10.3389/fbioe.2023.1261832] [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: 07/20/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
L-tryptophan and its derivatives are widely used in the chemical, pharmaceutical, food, and feed industries. Microbial fermentation is the most commonly used method to produce L-tryptophan, which calls for an effective cell factory. The mechanism of L-tryptophan biosynthesis in Escherichia coli, the widely used producer of L-tryptophan, is well understood. Saccharomyces cerevisiae also plays a significant role in the industrial production of biochemicals. Because of its robustness and safety, S. cerevisiae is favored for producing pharmaceuticals and food-grade biochemicals. However, the biosynthesis of L-tryptophan in S. cerevisiae has been rarely summarized. The synthetic pathways and engineering strategies of L-tryptophan in E. coli and S. cerevisiae have been reviewed and compared in this review. Furthermore, the information presented in this review pertains to the existing understanding of how L-tryptophan affects S. cerevisiae's stress fitness, which could aid in developing a novel plan to produce more resilient industrial yeast and E. coli cell factories.
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Affiliation(s)
- Xinru Ren
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Yue Wei
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Honglu Zhao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Juanjuan Shao
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
| | - Fanli Zeng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China
| | - Zhen Wang
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
- Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China
| | - Li Li
- College of Science and Technology, Hebei Agricultural University, Cangzhou, China
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Bitzenhofer NL, Classen T, Jaeger KE, Loeschcke A. Biotransformation Of l-Tryptophan To Produce Arcyriaflavin A With Pseudomonas putida KT2440. Chembiochem 2023; 24:e202300576. [PMID: 37743253 DOI: 10.1002/cbic.202300576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 09/26/2023]
Abstract
Natural products such as indolocarbazoles are a valuable source of highly bioactive compounds with numerous potential applications in the pharmaceutical industry. Arcyriaflavin A, isolated from marine invertebrates and slime molds, is one representative of this group and acts as a cyclin D1-cyclin-dependent kinase 4 inhibitor. To date, access to this compound has mostly relied on multi-step total synthesis. In this study, biosynthetic access to arcyriaflavin A was explored using recombinant Pseudomonas putida KT2440 based on a previously generated producer strain. We used a Design of Experiment approach to analyze four key parameters, which led to the optimization of the bioprocess. By engineering the formation of outer membrane vesicles and using an adsorbent in the culture broth, we succeeded to increase the yield of arcyriaflavin A in the cell-free supernatant, resulting in a nearly eight-fold increase in the overall production titers. Finally, we managed to scale up the bioprocess leading to a final yield of 4.7 mg arcyriaflavin A product isolated from 1 L of bacterial culture. Thus, this study showcases an integrative approach to improve biotransformation and moreover also provides starting points for further optimization of indolocarbazole production in P. putida.
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Affiliation(s)
- Nora Lisa Bitzenhofer
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
| | - Thomas Classen
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
- Institute of Bio- and Geosciences (IBG-1): Biotechnology, Forschungszentrum Jülich GmbH, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology (IMET), Heinrich Heine University Düsseldorf located at Forschungszentrum Jülich, Stetternicher Forst, Building 15.8, 52426, Jülich, Germany
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6
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Jeong SH, Kim HJ, Lee SJ. New Target Gene Screening Using Shortened and Random sgRNA Libraries in Microbial CRISPR Interference. ACS Synth Biol 2023; 12:800-808. [PMID: 36787424 PMCID: PMC10028695 DOI: 10.1021/acssynbio.2c00595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
CRISPR interference (CRISPRi) screening has been used for identification of target genes related to specific phenotypes using single-molecular guide RNA (sgRNA) libraries. In CRISPRi screening, the sizes of random sgRNA libraries contained with the original target recognition sequences are large (∼1012). Here, we demonstrated that the length of the target recognition sequence (TRS) can be shortened in sgRNAs from the original 20 nucleotides (N20) to 9 nucleotides (N9) that is still sufficient for dCas9 to repress target genes in the xylose operon of Escherichia coli, regardless of binding to a promoter or open reading frame region. Based on the results, we constructed random sgRNA plasmid libraries with 5'-shortened TRS lengths, and identified xylose metabolic target genes by Sanger sequencing of sgRNA plasmids purified from Xyl- phenotypic cells. Next, the random sgRNA libraries were harnessed to screen for target genes to enhance violacein pigment production in synthetic E. coli cells. Seventeen target genes were selected by analyzing the redundancy of the TRS in sgRNA plasmids in dark purple colonies. Among them, seven genes (tyrR, pykF, cra, ptsG, pykA, sdaA, and tnaA) have been known to increase the intracellular l-tryptophan pool, the precursor of a violacein. Seventeen cells with a single deletion of each target gene exhibited a significant increase in violacein production. These results indicate that using shortened random TRS libraries for CRISPRi can be simple and cost-effective for phenotype-based target gene screening.
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Affiliation(s)
- Song Hee Jeong
- Department of Systems Biotechnology, and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, and Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea
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Castillo-Alfonso F, Quintana-Menéndez A, Vigueras-Ramírez G, Sales-Cruz AM, Rosales-Colunga LM, Olivares-Hernández R. Analysis of the Propionate Metabolism in Bacillus subtilis during 3-Indolacetic Production. Microorganisms 2022; 10:microorganisms10122352. [PMID: 36557605 PMCID: PMC9782769 DOI: 10.3390/microorganisms10122352] [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: 10/31/2022] [Revised: 11/23/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022] Open
Abstract
The genera Bacillus belongs to the group of microorganisms that are known as plant growth-promoting bacteria, their metabolism has evolved to produce molecules that benefit the growth of the plant, and the production of 3-indole acetic acid (IAA) is part of its secondary metabolism. In this work, Bacillus subtilis was cultivated in a bioreactor to produce IAA using propionate and glucose as carbon sources in an M9-modified media; in both cases, tryptophan was added as a co-substrate. The yield of IAA using propionate is 17% higher compared to glucose. After 48 h of cultivation, the final concentration was 310 mg IAA/L using propionate and 230 mg IAA/L using glucose, with a concentration of 500 mg Trp/L. To gain more insight into propionate metabolism and its advantages, the genome-scale metabolic model of B. subtilis (iBSU 1147) and computational analysis were used to calculate flux distribution and evaluate the metabolic capabilities to produce IAA using propionate. The metabolic fluxes demonstrate that propionate uptake favors the production of precursors needed for the synthesis of the hormone, and the sensitivity analysis shows that the control of a specific growth rate has a positive impact on the production of IAA.
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Affiliation(s)
- Freddy Castillo-Alfonso
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Ciudad de México 05370, Mexico
| | - Alejandro Quintana-Menéndez
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana Unidad Cuajimalpa, Ciudad de México 05370, Mexico
| | - Gabriel Vigueras-Ramírez
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Cuajimalpa de Morelos, Ciudad de México 05348, Mexico
| | - Alfonso Mauricio Sales-Cruz
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Cuajimalpa de Morelos, Ciudad de México 05348, Mexico
| | - Luis Manuel Rosales-Colunga
- Facultad de Ingeniería, Universidad Autónoma de San Luis Potosí, Av. Dr Manuel Nava 8, Zona Universitaria, San Luis Potosí 78290, Mexico
| | - Roberto Olivares-Hernández
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Cuajimalpa de Morelos, Ciudad de México 05348, Mexico
- Correspondence:
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8
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Jiao P, Zhang X, Wei Y, Wang P. Simulation of Adsorption Process of l-Tryptophan on Mixed-Mode Resin HD-1 with Combined Physical Adsorption and Ion Exchange. ACS OMEGA 2022; 7:35331-35338. [PMID: 36211030 PMCID: PMC9535704 DOI: 10.1021/acsomega.2c05194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/19/2022] [Indexed: 06/16/2023]
Abstract
The mass-transfer process of l-tryptophan (l-Trp) in the hydrophobic interaction/ion-exchange mixed-mode resin HD-1 particles and fixed bed was studied experimentally and theoretically. The adsorption kinetics of l-Trp in single-component and multicomponent adsorption systems was investigated under different pH conditions. The co-adsorption of sodium ions (Na+) and l-Trp anions was found to be negligible. A modified liquid-film linear driving force model considering the physical adsorption of l-Trp zwitterions and anions as well as ion exchange of l-Trp cations was proposed. The dissociation equilibria of l-Trp molecules and functional groups on the resin were introduced in the model. The model could well fit the kinetic adsorption curves of l-Trp at different pH values. The presence of Na+ and the impurity amino acid l-glutamic acid (l-Glu) did not significantly affect the mass-transfer rate of l-Trp. The dynamic adsorption processes of l-Trp under different pH and concentration conditions were studied. A modified transport-dispersive model considering axial diffusion, liquid-film mass transfer, and a combined physical adsorption and ion-exchange equilibrium was established, which could predict the adsorption breakthrough curves of l-Trp well. During the dynamic adsorption process, the pH of mobile phase in the fixed bed changed with changing the l-Trp concentration in the mobile phase. l-Trp was well separated from Na+ and l-Glu with the purity of l-Trp higher than 99%, the recovery rate higher than 95%, and a concentration of 4.69 × 10-3 mol/L. The elution chromatographic peaks of l-Trp, l-Glu, and Na+ and the pH of the outlet solution were predicted satisfactorily.
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Affiliation(s)
- Pengfei Jiao
- . Phone +86-0377-63513605. Fax: +86-0377-63512517
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9
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Schoppel K, Trachtmann N, Korzin EJ, Tzanavari A, Sprenger GA, Weuster-Botz D. Metabolic control analysis enables rational improvement of E. coli L-tryptophan producers but methylglyoxal formation limits glycerol-based production. Microb Cell Fact 2022; 21:201. [PMID: 36195869 PMCID: PMC9531422 DOI: 10.1186/s12934-022-01930-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/24/2022] [Indexed: 11/24/2022] Open
Abstract
Background Although efficient l-tryptophan production using engineered Escherichia coli is established from glucose, the use of alternative carbon sources is still very limited. Through the application of glycerol as an alternate, a more sustainable substrate (by-product of biodiesel preparation), the well-studied intracellular glycolytic pathways are rerouted, resulting in the activity of different intracellular control sites and regulations, which are not fully understood in detail. Metabolic analysis was applied to well-known engineered E. coli cells with 10 genetic modifications. Cells were withdrawn from a fed-batch production process with glycerol as a carbon source, followed by metabolic control analysis (MCA). This resulted in the identification of several additional enzymes controlling the carbon flux to l-tryptophan. Results These controlling enzyme activities were addressed stepwise by the targeted overexpression of 4 additional enzymes (trpC, trpB, serB, aroB). Their efficacy regarding l-tryptophan productivity was evaluated under consistent fed-batch cultivation conditions. Although process comparability was impeded by process variances related to a temporal, unpredictable break-off in l-tryptophan production, process improvements of up to 28% with respect to the l-tryptophan produced were observed using the new producer strains. The intracellular effects of these targeted genetic modifications were revealed by metabolic analysis in combination with MCA and expression analysis. Furthermore, it was discovered that the E. coli cells produced the highly toxic metabolite methylglyoxal (MGO) during the fed-batch process. A closer look at the MGO production and detoxification on the metabolome, fluxome, and transcriptome level of the engineered E. coli indicated that the highly toxic metabolite plays a critical role in the production of aromatic amino acids with glycerol as a carbon source. Conclusions A detailed process analysis of a new l-tryptophan producer strain revealed that several of the 4 targeted genetic modifications of the E. colil-tryptophan producer strain proved to be effective, and, for others, new engineering approaches could be derived from the results. As a starting point for further strain and process optimization, the up-regulation of MGO detoxifying enzymes and a lowering of the feeding rate during the last third of the cultivation seems reasonable. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01930-1.
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Affiliation(s)
- Kristin Schoppel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Emil J Korzin
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Angelina Tzanavari
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstrasse 15, 85748, Garching, Germany.
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10
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Ferreira Dos Santos A, Amancio Frutuoso FK, de Amorim de Carvalho C, Sousa Aguiar Lira VN, Mendes Barros AR, Bezerra Dos Santos A. Carbon source affects the resource recovery in aerobic granular sludge systems treating wastewater. BIORESOURCE TECHNOLOGY 2022; 357:127355. [PMID: 35609753 DOI: 10.1016/j.biortech.2022.127355] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/17/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
This study evaluated the influence of carbon sources on alginate-like exopolymers (ALE) and tryptophan (Trp) biosynthesis in the aerobic granular sludge (AGS). With acetate, the highest biopolymers levels, per gram of volatile suspended solids (VSS) (418.7 mgALE∙g-1 and 4.1 mgTrp∙gVSS-1), were found likely due to biomass loss throughout the operation, which resulted in lower sludge age (4-7 days) and shorter famine period. During granulation, encouraging results on ALE production were obtained with propionate (>250 mgALE∙gVSS-1), significantly higher than those found with glycerol, glucose, and sucrose. Regarding tryptophan production, propionate and glycerol proved to be good substrates, although the content was still lower than acetate (1.6 mgTrp∙gVSS-1). Granules fed with glucose showed the worst results compared to the other substrates (38.5 mgALE∙VSS-1 and 0.6 mgTrp∙gVSS-1) due to the filamentous microorganisms' abundance found. Therefore, this study provides insights to value the production of compounds of industrial interest in AGS systems.
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Affiliation(s)
- Amanda Ferreira Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | - Clara de Amorim de Carvalho
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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11
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Ferrer L, Mindt M, Suarez-Diez M, Jilg T, Zagorščak M, Lee JH, Gruden K, Wendisch VF, Cankar K. Fermentative Indole Production via Bacterial Tryptophan Synthase Alpha Subunit and Plant Indole-3-Glycerol Phosphate Lyase Enzymes. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:5634-5645. [PMID: 35500281 PMCID: PMC9100643 DOI: 10.1021/acs.jafc.2c01042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/14/2022] [Accepted: 04/18/2022] [Indexed: 06/14/2023]
Abstract
Indole is produced in nature by diverse organisms and exhibits a characteristic odor described as animal, fecal, and floral. In addition, it contributes to the flavor in foods, and it is applied in the fragrance and flavor industry. In nature, indole is synthesized either from tryptophan by bacterial tryptophanases (TNAs) or from indole-3-glycerol phosphate (IGP) by plant indole-3-glycerol phosphate lyases (IGLs). While it is widely accepted that the tryptophan synthase α-subunit (TSA) has intrinsically low IGL activity in the absence of the tryptophan synthase β-subunit, in this study, we show that Corynebacterium glutamicum TSA functions as a bona fide IGL and can support fermentative indole production in strains providing IGP. By bioprospecting additional bacterial TSAs and plant IGLs that function as bona fide IGLs were identified. Capturing indole in an overlay enabled indole production to titers of about 0.7 g L-1 in fermentations using C. glutamicum strains expressing either the endogenous TSA gene or the IGL gene from wheat.
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Affiliation(s)
- Lenny Ferrer
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Melanie Mindt
- Wageningen
Plant Research, Wageningen University &
Research, 6708PB Wageningen, The Netherlands
- Axxence
Aromatic GmbH, 46446 Emmerich am Rhein, Germany
| | - Maria Suarez-Diez
- Laboratory
of Systems and Synthetic Biology, Wageningen
University & Research, 6708WE Wageningen, The Netherlands
| | - Tatjana Jilg
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Maja Zagorščak
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Jin-Ho Lee
- Department
of Food Science & Biotechnology, Kyungsung
University, 608-736 Busan, Republic of Korea
| | - Kristina Gruden
- Department
of Biotechnology and Systems Biology, National
Institute of Biology, 1000 Ljubljana, Slovenia
| | - Volker F. Wendisch
- Genetics
of Prokaryotes, Faculty of Biology & CeBiTec, Bielefeld University, 33615 Bielefeld, Germany
| | - Katarina Cankar
- Wageningen
Plant Research, Wageningen University &
Research, 6708PB Wageningen, The Netherlands
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12
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Jiao P, Zhang X, Wei Y, Meng Y. Adsorption Equilibria, Kinetics, and Column Dynamics of L-Tryptophan on Mixed-Mode Resin HD-1. ACS OMEGA 2022; 7:9614-9621. [PMID: 35350352 PMCID: PMC8945088 DOI: 10.1021/acsomega.1c06960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The adsorption amount and selectivity of L-tryptophan (l-Trp) on the hydrophobic interaction and ion exchange mixed-mode chromatography medium HD-1 were studied as well as the salt resistance of the resin via adsorption equilibrium experiments. The adsorption mechanisms of l-Trp were illuminated by combining adsorption equilibria and a kinetics analysis. The separation effect was studied by dynamic separation experiments in a fixed-bed. The results indicate that an increase of the concentration proportion of l-Trp zwitterion benefits the adsorption of l-Trp. The resin shows a high adsorption selectivity for l-Trp at different pH values. The adsorption amount of l-Trp is not affected significantly by NaCl. Various groups play a role in the adsorption of l-Trp. An adsorption energy lower than 8 kJ/mol indicates that the adsorption of l-Trp is mainly based on non-electrostatic interactions, with an electrostatic interaction as a supplement. The adsorption equilibrium model considering the dissociation equilibrium of the resin and l-Trp proposed in this work can simulate the adsorption equilibrium data of l-Trp at different pH values as well. The mass transfer rate of l-Trp is controlled by intraparticle and liquid film diffusion simultaneously. The fixed-bed packed with resin HD-1 can separate l-Trp with the purity of l-Trp higher than 99%, recovery rate higher than 95%, and concentration of 4.69 × 10-3 mol/L.
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Affiliation(s)
- Pengfei Jiao
- E-mail: . Phone +86-0377-63513605. Fax: +86-0377-63512517
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13
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G6P-capturing molecules in the periplasm of Escherichia coli accelerate the shikimate pathway. Metab Eng 2022; 72:68-81. [DOI: 10.1016/j.ymben.2022.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/17/2022] [Accepted: 03/02/2022] [Indexed: 11/21/2022]
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14
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Menon N, Richmond D, Rahman MR, Menon BRK. Versatile and Facile One-Pot Biosynthesis for Amides and Carboxylic Acids in E. coli by Engineering Auxin Pathways of Plant Microbiomes. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Navya Menon
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
- Collaborative Teaching Laboratory, The University of Birmingham, Birmingham B15 2TT, U.K
| | - Daniel Richmond
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
| | - Mohammad Rejaur Rahman
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
| | - Binuraj R. K. Menon
- The Warwick Integrative Synthetic Biology Centre, The University of Warwick, Coventry CV4 7AL, U.K
- School of Biological Sciences, The University of Portsmouth, Portsmouth PO1 2DY, U.K
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15
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Liu S, Xu JZ, Zhang WG. Advances and prospects in metabolic engineering of Escherichia coli for L-tryptophan production. World J Microbiol Biotechnol 2022; 38:22. [PMID: 34989926 DOI: 10.1007/s11274-021-03212-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
As an important raw material for pharmaceutical, food and feed industry, highly efficient production of L-tryptophan by Escherichia coli has attracted a considerable attention. However, there are complicated and multiple layers of regulation networks in L-tryptophan biosynthetic pathway and thus have difficulty to rewrite the biosynthetic pathway for producing L-tryptophan with high efficiency in E. coli. This review summarizes the biosynthetic pathway of L-tryptophan and highlights the main regulatory mechanisms in E. coli. In addition, we discussed the latest metabolic engineering strategies achieved in E. coli to reconstruct the L-tryptophan biosynthetic pathway. Moreover, we also review a few strategies that can be used in E. coli to improve robustness and streamline of L-tryptophan high-producing strains. Lastly, we also propose the potential strategies to further increase L-tryptophan production by systematic metabolic engineering and synthetic biology techniques.
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Affiliation(s)
- Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China
| | - Jian-Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
| | - Wei-Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800# Lihu Road, WuXi, 214122, People's Republic of China.
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16
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Advances in microbial production of feed amino acid. ADVANCES IN APPLIED MICROBIOLOGY 2022; 119:1-33. [DOI: 10.1016/bs.aambs.2022.05.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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17
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Guo L, Ding S, Liu Y, Gao C, Hu G, Song W, Liu J, Chen X, Liu L. Enhancing tryptophan production by balancing precursors in Escherichia coli. Biotechnol Bioeng 2021; 119:983-993. [PMID: 34936092 DOI: 10.1002/bit.28019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/20/2021] [Accepted: 11/27/2021] [Indexed: 11/11/2022]
Abstract
Tryptophan, an essential aromatic amino acid, is widely used in animal feed, food additives, and pharmaceuticals. Although sustainable and environmentally friendly, microbial tryptophan production from renewable feedstocks is limited by low biosynthesis and transport rates. Here, an Escherichia coli strain capable of efficient tryptophan production was generated by improving and balancing the supply of precursors and by engineering membrane transporters. Tryptophan biosynthesis was increased by eliminating negative regulatory factors, blocking competing pathways, and preventing tryptophan degradation. Promoter engineering balanced the supply of the precursors erythrose-4-phosphate and phosphoenolpyruvate, as well as the availability of serine. Finally, the engineering of tryptophan transporters prevented feedback inhibition and growth toxicity. Fed-batch fermentation of the final strain (TRP12) in a 5 L bioreactor produced 52.1 g·L-1 of tryptophan, with a yield of 0.171 g·g-1 glucose and productivity of 1.45 g·L-1 ·h-1 . The metabolic engineering strategy described here paves the way for high-performance microbial cell factories aimed at the production of tryptophan as well as other valuable chemicals.
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Affiliation(s)
- Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Shuang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Yadi Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Guipeng Hu
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi, China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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18
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Shimizu K, Matsuoka Y. Feedback regulation and coordination of the main metabolism for bacterial growth and metabolic engineering for amino acid fermentation. Biotechnol Adv 2021; 55:107887. [PMID: 34921951 DOI: 10.1016/j.biotechadv.2021.107887] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 12/05/2021] [Accepted: 12/09/2021] [Indexed: 12/28/2022]
Abstract
Living organisms such as bacteria are often exposed to continuous changes in the nutrient availability in nature. Therefore, bacteria must constantly monitor the environmental condition, and adjust the metabolism quickly adapting to the change in the growth condition. For this, bacteria must orchestrate (coordinate and integrate) the complex and dynamically changing information on the environmental condition. In particular, the central carbon metabolism (CCM), monomer synthesis, and macromolecular synthesis must be coordinately regulated for the efficient growth. It is a grand challenge in bioscience, biotechnology, and synthetic biology to understand how living organisms coordinate the metabolic regulation systems. Here, we consider the integrated sensing of carbon sources by the phosphotransferase system (PTS), and the feed-forward/feedback regulation systems incorporated in the CCM in relation to the pool sizes of flux-sensing metabolites and αketoacids. We also consider the metabolic regulation of amino acid biosynthesis (as well as purine and pyrimidine biosyntheses) paying attention to the feedback control systems consisting of (fast) enzyme level regulation with (slow) transcriptional regulation. The metabolic engineering for the efficient amino acid production by bacteria such as Escherichia coli and Corynebacterium glutamicum is also discussed (in relation to the regulation mechanisms). The amino acid synthesis is important for determining the rate of ribosome biosynthesis. Thus, the growth rate control (growth law) is further discussed on the relationship between (p)ppGpp level and the ribosomal protein synthesis.
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Affiliation(s)
- Kazuyuki Shimizu
- Kyushu institute of Technology, Iizuka, Fukuoka 820-8502, Japan; Institute of Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
| | - Yu Matsuoka
- Department of Fisheries Distribution and Management, National Fisheries University, Shimonoseki, Yamaguchi 759-6595, Japan
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19
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Tryptophan Production Maximization in a Fed-Batch Bioreactor with Modified E. coli Cells, by Optimizing Its Operating Policy Based on an Extended Structured Cell Kinetic Model. Bioengineering (Basel) 2021; 8:bioengineering8120210. [PMID: 34940363 PMCID: PMC8698263 DOI: 10.3390/bioengineering8120210] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/17/2022] Open
Abstract
Hybrid kinetic models, linking structured cell metabolic processes to the dynamics of macroscopic variables of the bioreactor, are more and more used in engineering evaluations to derive more precise predictions of the process dynamics under variable operating conditions. Depending on the cell model complexity, such a math tool can be used to evaluate the metabolic fluxes in relation to the bioreactor operating conditions, thus suggesting ways to genetically modify the microorganism for certain purposes. Even if development of such an extended dynamic model requires more experimental and computational efforts, its use is advantageous. The approached probative example refers to a model simulating the dynamics of nanoscale variables from several pathways of the central carbon metabolism (CCM) of Escherichia coli cells, linked to the macroscopic state variables of a fed-batch bioreactor (FBR) used for the tryptophan (TRP) production. The used E. coli strain was modified to replace the PTS system for glucose (GLC) uptake with a more efficient one. The study presents multiple elements of novelty: (i) the experimentally validated modular model itself, and (ii) its efficiency in computationally deriving an optimal operation policy of the FBR.
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20
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Ma X, Ma L, Huo YX. Reconstructing the transcription regulatory network to optimize resource allocation for robust biosynthesis. Trends Biotechnol 2021; 40:735-751. [PMID: 34895933 DOI: 10.1016/j.tibtech.2021.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/07/2021] [Accepted: 11/08/2021] [Indexed: 11/16/2022]
Abstract
An ideal microbial cell factory (MCF) should deliver maximal resources to production, which conflicts with the microbe's native growth-oriented resource allocation strategy and can therefore lead to early termination of the high-yield period. Reallocating resources from growth to production has become a critical factor in constructing robust MCFs. Instead of strengthening specific biosynthetic pathways, emerging endeavors are focused on rearranging the gene regulatory network to fundamentally reprogram the resource allocation pattern. Combining this idea with transcriptional regulation within the hierarchical regulatory network, this review discusses recent engineering strategies targeting the transcription machinery, module networks, regulatory edges, and bottom network layer. This global view will help to construct a production-oriented phenotype that fully harnesses the potential of MCFs.
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Affiliation(s)
- Xiaoyan Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Lianjie Ma
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China
| | - Yi-Xin Huo
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Haidian District, Beijing 100081, People's Republic of China; Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, People's Republic of China.
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21
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Kayastha S, Sagwan-Barkdoll L, Anterola A, Jayakody LN. Developing synthetic microbes to produce indirubin-derivatives. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2021. [DOI: 10.1016/j.bcab.2021.102162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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22
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MARIA G. A CCM-based modular and hybrid kinetic model to simulate the tryptophan synthesis in a fed-batch bioreactor using modified E. coli cells. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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23
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Cao Y, Tian R, Lv X, Li J, Liu L, Du G, Chen J, Liu Y. Inducible Population Quality Control of Engineered Bacillus subtilis for Improved N-Acetylneuraminic Acid Biosynthesis. ACS Synth Biol 2021; 10:2197-2209. [PMID: 34404207 DOI: 10.1021/acssynbio.1c00086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Biosynthesis by microorganisms using renewable feedstocks is an important approach for realizing sustainable chemical manufacturing. However, cell-to-cell variation in biosynthesis capability during fermentation restricts the robustness and efficiency of bioproduction, hampering the industrialization of biosynthesis. Herein, we developed an inducible population quality control system (iPopQC) for dynamically modulating the producing and nonproducing subpopulations of engineered Bacillus subtilis, which was constructed via inducible promoter- and metabolite-responsive biosensor-based genetic circuit for regulating essential genes. Moreover, iPopQC achieved a 1.97-fold increase in N-acetylneuraminic acid (NeuAc) titer by enriching producing cell subpopulation during cultivation, representing 52% higher than that of previous PopQC. Strains with double-output iPopQC cocoupling the expression of double essential genes with NeuAc production improved production robustness further, retaining NeuAc production throughout 96 h of fermentation, upon which the strains cocoupling one essential gene expression with NeuAc production abolished the production ability.
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Affiliation(s)
- Yanting Cao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Rongzhen Tian
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jian Chen
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
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24
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Schoppel K, Trachtmann N, Mittermeier F, Sprenger GA, Weuster-Botz D. Metabolic control analysis of L-tryptophan producing Escherichia coli applying targeted perturbation with shikimate. Bioprocess Biosyst Eng 2021; 44:2591-2613. [PMID: 34519841 PMCID: PMC8536597 DOI: 10.1007/s00449-021-02630-7] [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: 06/07/2021] [Accepted: 08/27/2021] [Indexed: 12/26/2022]
Abstract
L-tryptophan production from glycerol with Escherichia coli was analysed by perturbation studies and metabolic control analysis. The insertion of a non-natural shikimate transporter into the genome of an Escherichia coli L-tryptophan production strain enabled targeted perturbation within the product pathway with shikimate during parallelised short-term perturbation experiments with cells withdrawn from a 15 L fed-batch production process. Expression of the shikimate/H+-symporter gene (shiA) from Corynebacterium glutamicum did not alter process performance within the estimation error. Metabolic analyses and subsequent extensive data evaluation were performed based on the data of the parallel analysis reactors and the production process. Extracellular rates and intracellular metabolite concentrations displayed evident deflections in cell metabolism and particularly in chorismate biosynthesis due to the perturbations with shikimate. Intracellular flux distributions were estimated using a thermodynamics-based flux analysis method, which integrates thermodynamic constraints and intracellular metabolite concentrations to restrain the solution space. Feasible flux distributions, Gibbs reaction energies and concentration ranges were computed simultaneously for the genome-wide metabolic model, with minimum bias in relation to the direction of metabolic reactions. Metabolic control analysis was applied to estimate elasticities and flux control coefficients, predicting controlling sites for L-tryptophan biosynthesis. The addition of shikimate led to enhanced deviations in chorismate biosynthesis, revealing a so far not observed control of 3-dehydroquinate synthase on L-tryptophan formation. The relative expression of the identified target genes was analysed with RT-qPCR. Transcriptome analysis revealed disparities in gene expression and the localisation of target genes to further improve the microbial L-tryptophan producer by metabolic engineering.
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Affiliation(s)
- Kristin Schoppel
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Fabian Mittermeier
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany
| | - Georg A Sprenger
- Institute of Microbiology, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Institute of Biochemical Engineering, Technical University of Munich, Boltzmannstraße 15, 85748, Garching, Germany.
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25
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Tavares Ferreira TJ, Luiz de Sousa Rollemberg S, Nascimento de Barros A, Machado de Lima JP, Bezerra Dos Santos A. Integrated review of resource recovery on aerobic granular sludge systems: Possibilities and challenges for the application of the biorefinery concept. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2021; 291:112718. [PMID: 33962280 DOI: 10.1016/j.jenvman.2021.112718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 04/15/2021] [Accepted: 04/25/2021] [Indexed: 06/12/2023]
Abstract
Aerobic Granular Sludge (AGS) is a biological treatment technology that has been extensively studied in the last decade. The possibility of resource recovery has always been highlighted in these systems, but real-scale applications are still scarce. Therefore, this paper aimed to present a systematic review of resources recovery such as water, energy, chemicals, raw materials, and nutrients from AGS systems, also analyzing aspects of engineering and economic viability. In the solid phase, sludge application in agriculture is an interesting possibility. However, the biosolids' metal concentration (the granules have high adsorption capacity due to the high concentration of extracellular polymeric substances, EPS) may be an issue. Another possibility is the recovery of Polyhydroxyalkanoates (PHAs) and Alginate-like exopolymers (bio-ALE) in the solid phase, emphasizing the last one, which has already been made in some Wastewater Treatment Plants (WWTPs), named and patented as Kaumera® process. The Operational Expenditure (OPEX) can be reduced by 50% in the WWTP when recovery of ALE is made. The ALE recovery reduced sludge yield by up to 35%, less CO2 emissions, and energy saving. Finally, the discharged sludge can also be evaluated to be used for energetic purposes via anaerobic digestion (AD) or combustion. However, the AD route has faced difficulties due to the low biodegradability of aerobic granules.
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Affiliation(s)
| | | | - Amanda Nascimento de Barros
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - João Pedro Machado de Lima
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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26
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Amorim de Carvalho CD, Ferreira Dos Santos A, Tavares Ferreira TJ, Sousa Aguiar Lira VN, Mendes Barros AR, Bezerra Dos Santos A. Resource recovery in aerobic granular sludge systems: is it feasible or still a long way to go? CHEMOSPHERE 2021; 274:129881. [PMID: 33582539 DOI: 10.1016/j.chemosphere.2021.129881] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
Lately, wastewater treatment plants are much often being designed as wastewater-resource factories inserted in circular cities. Among biological treatment technologies, aerobic granular sludge (AGS), considered an evolution of activated sludge (AS), has received great attention regarding its resource recovery potential. This review presents the state-of-the-art concerning the influence of operational parameters on the recovery of alginate-like exopolysaccharides (ALE), tryptophan, phosphorus, and polyhydroxyalkanoates (PHA) from AGS systems. The carbon to nitrogen ratio was identified as a parameter that plays an important role for the optimal production of ALE, tryptophan, and PHA. The sludge retention time effect is more pronounced for the production of ALE and tryptophan. Additionally, salinity levels in the bioreactors can potentially be manipulated to increase ALE and phosphorus yields simultaneously. Some existing knowledge gaps in the scientific literature concerning the recovery of these resources from AGS were also identified. Regarding industrial applications, tryptophan has the longest way to go. On the other hand, ALE production/recovery could be considered the most mature process if we take into account that existing alternatives for phosphorus and PHA production/recovery are optimized for activated sludge rather than granular sludge. Consequently, to maintain the same effectiveness, these processes likely could not be applied to AGS without undergoing some modification. Therefore, investigating to what extent these adaptations are necessary and designing alternatives is essential.
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Affiliation(s)
- Clara de Amorim de Carvalho
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Amanda Ferreira Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | | | | | | | - André Bezerra Dos Santos
- Department of Hydraulic and Environmental Engineering, Federal University of Ceará, Fortaleza, Ceará, Brazil.
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27
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Liu L, Bilal M, Luo H, Iqbal HMN. Impact of Transcriptional Regulation by Crp, FruR, FlhD, and TyrR on L-tryptophan Biosynthesis in Escherichia coli. APPL BIOCHEM MICRO+ 2021. [DOI: 10.1134/s0003683821030091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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28
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Park H, Park S, Yang YH, Choi KY. Microbial synthesis of violacein pigment and its potential applications. Crit Rev Biotechnol 2021; 41:879-901. [PMID: 33730942 DOI: 10.1080/07388551.2021.1892579] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Violacein is a pigment synthesized by Gram-negative bacteria such as Chromobacterium violaceum. It has garnered significant interest owing to its unique physiological and biological activities along with its synergistic effects with various antibiotics. In addition to C. violaceum, several microorganisms, including: Duganella sp., Pseudoalteromonas sp., Iodobacter sp., and Massilia sp., are known to produce violacein. Along with the identification of violacein-producing strains, the genetic regulation, quorum sensing mechanism, and sequence of the vio-operon involved in the biosynthesis of violacein have been elucidated. From an engineering perspective, the heterologous production of violacein using the genetically engineered Escherichia coli or Citrobacter freundii host has also been attempted. Genetic engineering of host cells involves the heterologous expression of genes involved in the vio operon and the optimization of metabolic pathways and gene regulation. Further, the crystallography of VioD and VioE was revealed, and mass production by enzyme engineering has been accelerated. In this review, we highlight the biologically assisted end-use applications of violacein (such as functional fabric development, nanoparticles, functional polymer composites, and sunscreen ingredients) and violacein activation mechanisms, production strains, and the results of mass production with engineered methods. The prospects for violacein research and engineering applications have also been discussed.
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Affiliation(s)
- HyunA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - SeoA Park
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea
| | - Yung-Hun Yang
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, South Korea
| | - Kwon-Young Choi
- Department of Environmental Engineering, College of Engineering, Ajou University, Suwon, South Korea.,Department of Environmental and Safety Engineering, College of Engineering, Ajou University, Suwon, South Korea
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29
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Fan X, Zhang T, Ji Y, Li J, Long K, Yuan Y, Li Y, Xu Q, Chen N, Xie X. Pathway engineering of Escherichia coli for one-step fermentative production of L-theanine from sugars and ethylamine. Metab Eng Commun 2020; 11:e00151. [PMID: 33251110 PMCID: PMC7677707 DOI: 10.1016/j.mec.2020.e00151] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 10/26/2020] [Accepted: 11/03/2020] [Indexed: 01/08/2023] Open
Abstract
L-theanine is the most abundant free amino acid in tea that offers various favorable physiological and pharmacological effects. Bacterial enzyme of γ-glutamylmethylamide synthetase (GMAS) can catalyze the synthesis of theanine from glutamate, ethylamine and ATP, but the manufacturing cost is uncompetitive due to the expensive substrates and complex processes. In this study, we described pathway engineering of wild-type Escherichia coli for one-step fermentative production of theanine from sugars and ethylamine. First, the synthetic pathway of theanine was conducted by heterologous introduction of a novel GMAS from Paracoccus aminovorans. A xylose-induced T7 RNA polymerase-PT7 promoter system was used to enhance and control gmas gene expression. Next, the precursor glutamate pool was increased by overexpression of native citrate synthase and introduction of glutamate dehydrogenase from Corynebacterium glutamicum. Then, in order to push more carbon flux towards theanine synthesis, the tricarboxylic acid cycle was interrupted and pyruvate carboxylase from C. glutamicum was introduced as a bypath supplying oxaloacetate from pyruvate. Finally, an energy-conserving phosphoenolpyruvate carboxykinase from Mannheimia succiniciproducens was introduced to increase ATP yield for theanine synthesis. After optimizing the addition time and concentration of ethylamine hydrochloride in the fed-batch fermentation, the recombinant strain TH11 produced 70.6 g/L theanine in a 5-L bioreactor with a yield and productivity of 0.42 g/g glucose and 2.72 g/L/h, respectively. To our knowledge, this is the first report regarding the pathway engineering of E. coli for fermentative production of theanine. The high production capacity of recombinant strain, combined with the easy processes, will hold attractive industrial application potential for the future. γ-Glutamylmethylamide synthetase from P. aminovorans showed high ligation activity. Xylose-induced T7 RNA polymerase-PT7 promoter system was used to control gene expression. TCA cycle was rewired to push more carbon flux toward theanine synthesis. Ethylamine feeding strategy was optimized to balance cell growth and theanine production.
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Affiliation(s)
- Xiaoguang Fan
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Tong Zhang
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yuanqing Ji
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Jie Li
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Keyi Long
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yue Yuan
- College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Yanjun Li
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Qingyang Xu
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Ning Chen
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
| | - Xixian Xie
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science & Technology, Tianjin, 300457, PR China.,College of Biotechnology, Tianjin University of Science & Technology, Tianjin, 300457, PR China
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30
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Chen Y, Tang J, Wang L, Tian Z, Cardenas A, Fang X, Chatterjee A, Xiao H. Creation of Bacterial cells with 5-Hydroxytryptophan as a 21 st Amino Acid Building Block. Chem 2020; 6:2717-2727. [PMID: 33102928 DOI: 10.1016/j.chempr.2020.07.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
While most organisms utilize 20 canonical amino acid building blocks for protein synthesis, adding additional candidates to the amino acid repertoire can greatly facilitate the investigation and manipulation of protein structures and functions. In this study, we report the generation of completely autonomous organisms with a 21st ncAA, 5-hydroxytryptophan (5HTP). Like 20 canonical amino acids, 5-hydroxytryptophan can be biosynthesized in vivo from simple carbon sources and is subsequently incorporated into proteins in response to the amber stop codon. Using this unnatural organism, we have prepared a single-chain immunoglobulin variable fragment conjugated with a fluorophore and demonstrated the utility of these autonomous cells to monitor oxidative stress. Creation of this and other cells containing the 21st amino acid will provide an opportunity to generate proteins and organisms with novel activities, as well as to determine the evolutionary consequences of using additional amino acid buildings.
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Affiliation(s)
- Yuda Chen
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Juan Tang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Lushun Wang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Zeru Tian
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Adam Cardenas
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Xinlei Fang
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A
| | - Abhishek Chatterjee
- Department of Chemistry, Boston College, 2609 Beacon Street, 246B Merkert Chemistry Center, Chestnut Hill, MA, 02467, U.S.A
| | - Han Xiao
- Department of Chemistry, Rice University, 6100 Main Street, Houston, Texas, 77005. U.S.A.,Department of Biosciences, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A.,Department of Bioengineering, Rice University, 6100 Main Street, Houston, Texas, 77005, U.S.A.,Lead Contact
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31
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Li Z, Ding D, Wang H, Liu L, Fang H, Chen T, Zhang D. Engineering Escherichia coli to improve tryptophan production via genetic manipulation of precursor and cofactor pathways. Synth Syst Biotechnol 2020; 5:200-205. [PMID: 32671235 PMCID: PMC7334480 DOI: 10.1016/j.synbio.2020.06.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 01/01/2023] Open
Abstract
Optimizing the supply of biosynthetic precursors and cofactors is usually an effective metabolic strategy to improve the production of target compounds. Here, the combination of optimizing precursor synthesis and balancing cofactor metabolism was adopted to improve tryptophan production in Escherichia coli. First, glutamine synthesis was improved by expressing heterologous glutamine synthetase from Bacillus subtilis and Bacillus megaterium in the engineered Escherichia coli strain KW001, resulting in the best candidate strain TS-1. Then icd and gdhA were overexpressed in TS-1, which led to the accumulation of 1.060 g/L tryptophan. Subsequently, one more copy of prs was introduced on the chromosome to increase the flux of 5-phospho-α-d-ribose 1-diphosphate followed by the expression of mutated serA and thrA to increase the precursor supply of serine, resulting in the accumulation of 1.380 g/L tryptophan. Finally, to maintain cofactor balance, sthA and pntAB, encoding transhydrogenase, were overexpressed. With sufficient amounts of precursors and balanced cofactors, the engineered strain could produce 1.710 g/L tryptophan after 48 h of shake-flask fermentation, which was 2.76-times higher than the titer of the parent strain. Taken together, our results demonstrate that the combination of optimizing precursor supply and regulating cofactor metabolism is an effective approach for high-level production of tryptophan. Similar strategies could be applied to the production of other amino acids or related derivatives.
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Affiliation(s)
- Zhu Li
- Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072, China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Dongqin Ding
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huiying Wang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Linxia Liu
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Huan Fang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Tao Chen
- Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering, Tianjin University, Tianjin, 300072, China
| | - Dawei Zhang
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
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32
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Common problems associated with the microbial productions of aromatic compounds and corresponding metabolic engineering strategies. Biotechnol Adv 2020; 41:107548. [DOI: 10.1016/j.biotechadv.2020.107548] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 04/06/2020] [Accepted: 04/08/2020] [Indexed: 01/06/2023]
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33
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Xu D, Zhang L. Pathway Engineering for Phenethylamine Production in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:5917-5926. [PMID: 32367713 DOI: 10.1021/acs.jafc.0c01706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, the metabolic pathway of phenethylamine synthesis was reconstructed by chromosomal integration and overexpression of the Enterococcus faecium pdc gene encoding phenylalanine decarboxylase in Escherichia coli. The genes encoding 3-deoxy-d-arabinoheptulosonate-7-phosphate synthase (aroG), shikimate kinase II (aroL), chorismate mutase/prephenate dehydratase (pheA), and tyrosine aminotransferase (tyrB) in the phenethylamine synthetic pathway were sequentially chromosomally overexpressed. The phosphotransferase system was replaced by deleting the ptsH-ptsI-crr genes and chromosomally overexpressing the genes encoding galactose permease (galP) and glucokinase (glk). In addition, the zwf gene encoding glucose-6-phosphate dehydrogenase in the pentose phosphate pathway was chromosomally overexpressed, generating the final engineered E. coli strain AUD9. The AUD9 strain produced 2.65 g L-1 phenethylamine with a yield of 0.27 g of phenethylamine g-1 glucose in batch fermentation; fed-batch fermentation of AUD9 produced 38.82 g L-1 phenethylamine with a productivity of 1.08 g L-1 h-1 phenethylamine, demonstrating its potential for industrial fermentative production of phenethylamine.
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Affiliation(s)
- Daqing Xu
- College of Life Sciences, Hebei Agricultural University, Baoding 071000, China
| | - Lirong Zhang
- College of Plant Protection, Hebei Agricultural University, Baoding 071000, China
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34
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De novo biosynthesis of indole-3-ethanol and indole-3-ethanol acetate in engineered Escherichia coli. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2019.107432] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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35
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Zhao C, Fang H, Wang J, Zhang S, Zhao X, Li Z, Lin C, Shen Z, Cheng L. Application of fermentation process control to increase l-tryptophan production in Escherichia coli. Biotechnol Prog 2019; 36:e2944. [PMID: 31804750 DOI: 10.1002/btpr.2944] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 11/04/2019] [Accepted: 11/26/2019] [Indexed: 11/11/2022]
Abstract
In this study, process engineering and process control were applied to increase the production of l-tryptophan using Escherichia coli Dmtr/pta-Y. Different dissolved oxygen (DO) and pH control strategies were applied in l-tryptophan production. DO and pH were maintained at [20% (0-20 hr); 30% (20-40 hr)] and [7.0 (0-20 hr), 6.5 (20-40 hr)], respectively, which increased l-tryptophan production, glucose conversion percentage [g (l-tryptophan)/g (glucose)], and transcription levels of key genes for tryptophan biosynthesis and tryptophan biosynthesis flux, and decreased the accumulation of acetate and transcription levels of genes related to acetate synthesis and acetate synthesis flux. Using E. coli Dmtr/pta-Y with optimized DO [20% (0-20 hr); 30% (20-40 hr)] and pH [7.0 (0-20 hr), 6.5 (20-40 hr)] values, the highest l-tryptophan production (52.57 g/L) and glucose conversion percentage (20.15%) were obtained. The l-tryptophan production was increased by 26.58%, the glucose conversion percentage was increased by 22.64%, and the flux of tryptophan biosynthesis was increased to 21.5% compared with different conditions for DO [50% (0-20 hr), 20% (20-40 hr)] and pH [7.0].
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Affiliation(s)
- Chunguang Zhao
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,School of Agriculture, Ningxia University, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China
| | - Haitian Fang
- School of Agriculture, Ningxia University, Ningxia Eppen Biotech Co., Ltd, Yinchuan, China
| | - Jing Wang
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Department of Critical Care Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - Shasha Zhang
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Xiubao Zhao
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Zengliang Li
- Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
| | - Chuwen Lin
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
| | - Zhiqiang Shen
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
| | - Likun Cheng
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Shandong Research Center of High Cell Density Fermentation and Efficient Expression Technology, Shandong Lvdu Bio-science and Technology Co., Ltd, Binzhou, China
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36
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Tröndle J, Schoppel K, Bleidt A, Trachtmann N, Sprenger GA, Weuster-Botz D. Metabolic control analysis of L-tryptophan production with Escherichia coli based on data from short-term perturbation experiments. J Biotechnol 2019; 307:15-28. [PMID: 31639341 DOI: 10.1016/j.jbiotec.2019.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 10/10/2019] [Indexed: 12/21/2022]
Abstract
E. coli strain NT1259 /pF112aroFBLkan was able to produce 14.3 g L-1 L-tryptophan within 68 h in a fed-batch process from glycerol on a 15 L scale. To gain detailed insight into metabolism of this E. coli strain in the fed-batch process, a sample of L-tryptophan producing cells was withdrawn after 47 h, was separated rapidly and then resuspended in four parallel stirred-tank bioreactors with fresh media. Four different carbon sources (glucose, glycerol, succinate, pyruvate) were supplied individually with varying feeding rates within 19 min and the metabolic reactions of the cells in the four parallel reactors were analyzed by quantification of extracellular and intracellular substrate, product and metabolite concentrations. Data analysis allowed the estimation of intracellular carbon fluxes and of thermodynamic limitations concerning intracellular concentrations and reaction energies. Carbon fluxes and intracellular metabolite concentrations enabled the estimation of elasticities and flux control coefficients by applying metabolic control analysis making use of a metabolic model considering 48 enzymatic reactions and 56 metabolites. As the flux control coefficients describe connections between enzyme activities and metabolic fluxes, they reveal genetic targets for strain improvement. Metabolic control analysis of the recombinant E. coli cells withdrawn from the fed-batch production process clearly indicated that (i) the supply of two precursors for L-tryptophan biosynthesis, L-serine and phosphoribosyl-pyrophosphate, as well as (ii) the formation of aromatic byproducts and (iii) the enzymatic steps of igps and trps2 within the L-tryptophan biosynthesis pathway have major impact on fed-batch production of L-tryptophan from glycerol and should be the targets for further strain improvements.
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Affiliation(s)
- Julia Tröndle
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
| | - Kristin Schoppel
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
| | - Arne Bleidt
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany
| | - Natalia Trachtmann
- University of Stuttgart, Institute of Microbiology, Allmandring 31, 70569, Stuttgart, Germany
| | - Georg A Sprenger
- University of Stuttgart, Institute of Microbiology, Allmandring 31, 70569, Stuttgart, Germany
| | - Dirk Weuster-Botz
- Technical University of Munich, Institute of Biochemical Engineering, Boltzmannstr. 15, 85748, Garching, Germany.
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37
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Metabolic Engineering and Fermentation Process Strategies for L-Tryptophan Production by Escherichia coli. Processes (Basel) 2019. [DOI: 10.3390/pr7040213] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
L-tryptophan is an essential aromatic amino acid that has been widely used in medicine, food, and animal feed. Microbial biosynthesis of L-tryptophan through metabolic engineering approaches represents a sustainable, cost-effective, and environmentally friendly route compared to chemical synthesis. In particular, metabolic pathway engineering allows enhanced product titers by inactivating/blocking the competing pathways, increasing the intracellular level of essential precursors, and overexpressing rate-limiting enzymatic steps. Based on the route of the l-tryptophan biosynthesis pathway, this review presents a systematic and detailed summary of the contemporary metabolic engineering approaches employed for l-tryptophan production. In addition to the engineering of the l-tryptophan biosynthesis pathway, the metabolic engineering modification of carbon source uptake, by-product formation, key regulatory factors, and the polyhydroxybutyrate biosynthesis pathway in l-tryptophan biosynthesis are discussed. Moreover, fermentation bioprocess optimization strategies used for l-tryptophan overproduction are also delineated. Towards the end, the review is wrapped up with the concluding remarks, and future strategies are outlined for the development of a high l-tryptophan production strain.
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38
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Indole-3-Propionic Acid, a Tryptophan-Derived Bacterial Metabolite, Reduces Weight Gain in Rats. Nutrients 2019; 11:nu11030591. [PMID: 30862081 PMCID: PMC6471155 DOI: 10.3390/nu11030591] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 03/05/2019] [Accepted: 03/10/2019] [Indexed: 12/20/2022] Open
Abstract
Recent evidence suggests that tryptophan, an essential amino acid, may exert biological effects by means of tryptophan-derived gut bacteria products. We evaluated the potential contribution of tryptophan-derived bacterial metabolites to body weight gain. The study comprised three experimental series performed on separate groups of male, Sprague-Dawley rats: (i) rats on standard laboratory diet treated with water solution of neomycin, an antibiotic, or tap water (controls-1); (ii) rats on standard diet (controls-2) or tryptophan-high (TH) or tryptophan-free (TF) diet; and (iii) rats treated with indole-3-propionic acid (I3P), a bacterial metabolite of tryptophan, or a vehicle (controls-3). (i) Rats treated with neomycin showed a significantly higher weight gain but lower stool and blood concentration of I3P than controls-1. (ii) The TH group showed significantly smaller increases in body weight but higher stool and plasma concentration of I3P than controls-2. In contrast, the TF group showed a decrease in body weight, decreased total serum protein and a significant increase in urine output. (iii) Rats treated with I3P showed significantly smaller weight gain than controls-3. Our study suggests that I3P, a gut bacteria metabolite of tryptophan, contributes to changes in body weight gain produced by antibiotics and tryptophan-rich diet.
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