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Guo F, Wu M, Zhang S, Feng Y, Jiang Y, Jiang W, Xin F, Zhang W, Jiang M. Improved succinic acid production through the reconstruction of methanol dissimilation in Escherichia coli. BIORESOUR BIOPROCESS 2022; 9:62. [PMID: 38647636 PMCID: PMC10991533 DOI: 10.1186/s40643-022-00547-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Synthetic biology has boosted the rapid development on using non-methylotrophy as chassis for value added chemicals production from one-carbon feedstocks, such as methanol and formic acid. The one-carbon dissimilation pathway can provide more NADH than monosaccharides including glucose, which is conducive for reductive chemicals production, such as succinic acid. In this study, the one-carbon dissimilation pathway was introduced in E. coli Suc260 to enhance the succinic acid production capability. Through the rational construction of methanol dissimilation pathway, the succinic acid yield was increased from 0.91 to 0.95 g/g with methanol and sodium formate as auxiliary substrates in anaerobic fed-batch fermentation. Furthermore, the metabolic flux of by-product pyruvate was redirected to succinic acid together with the CO2 fixation. Finally, through the immobilization on a specially designed glycosylated membrane, E. coli cells are more resistant to adverse environments, and the final yield of succinic acid was improved to 0.98 g/g. This study proved the feasibility of endowing producers with methanol dissimilation pathway to enhance the production of reductive metabolites.
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Affiliation(s)
- Feng Guo
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Min Wu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Shangjie Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yifan Feng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China.
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Puzhu South Road 30#, Nanjing, 211800, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University, Nanjing, 211800, People's Republic of China
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DsrA Modulates Central Carbon Metabolism and Redox Balance by Directly Repressing pflB Expression in Salmonella Typhimurium. Microbiol Spectr 2022; 10:e0152221. [PMID: 35107349 PMCID: PMC8809350 DOI: 10.1128/spectrum.01522-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacterial small RNAs (sRNAs) function as vital regulators in response to various environmental stresses by base pairing with target mRNAs. The sRNA DsrA, an important posttranscriptional regulator, has been reported to play a crucial role in defense against oxidative stress in Salmonella enterica serovar Typhimurium, but its regulatory mechanism remains unclear. The transcriptome sequencing (RNA-seq) results in this study showed that the genes involved in glycolysis, pyruvate metabolism, the tricarboxylic acid (TCA) cycle, and NADH-dependent respiration exhibited significantly different expression patterns between S. Typhimurium wild type (WT) and the dsrA deletion mutant (ΔdsrA strain) before and after H2O2 treatment. This indicated the importance of DsrA in regulating central carbon metabolism (CCM) and NAD(H) homeostasis of S. Typhimurium. To reveal the direct target of DsrA action, fusion proteins of six candidate genes (acnA, srlE, tdcB, nuoH, katG, and pflB) with green fluorescent protein (GFP) were constructed, and the fluorescence analysis showed that the expression of pflB encoding pyruvate-formate lyase was repressed by DsrA. Furthermore, site-directed mutagenesis and RNase E-dependent experiments showed that the direct base pairing of DsrA with pflB mRNA could recruit RNase E to degrade pflB mRNA and reduce the stability of pflB mRNA. In addition, the NAD+/NADH ratio in WT-ppflB-pdsrA was significantly lower than that in WT-ppflB, suggesting that the repression of pflB by DsrA could contribute greatly to the redox balance in S. Typhimurium. Taken together, a novel target of DsrA was identified, and its regulatory role was clarified, which demonstrated that DsrA could modulate CCM and redox balance by directly repressing pflB expression in S. Typhimurium. IMPORTANCE Small RNA DsrA plays an important role in defending against oxidative stress in bacteria. In this study, we identified a novel target (pflB, encoding pyruvate-formate lyase) of DsrA and demonstrated its potential regulatory mechanism in S. Typhimurium by transcriptome analysis. In silico prediction revealed a direct base pairing between DsrA and pflB mRNA, which was confirmed in site-directed mutagenesis experiments. The interaction of DsrA-pflB mRNA could greatly contribute to the regulation of central carbon metabolism and intracellular redox balance in S. Typhimurium. These findings provided a better understanding of the critical roles of small RNA in central metabolism and stress responses in foodborne pathogens.
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Insights on the Advancements of In Silico Metabolic Studies of Succinic Acid Producing Microorganisms: A Review with Emphasis on Actinobacillus succinogenes. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Succinic acid (SA) is one of the top candidate value-added chemicals that can be produced from biomass via microbial fermentation. A considerable number of cell factories have been proposed in the past two decades as native as well as non-native SA producers. Actinobacillus succinogenes is among the best and earliest known natural SA producers. However, its industrial application has not yet been realized due to various underlying challenges. Previous studies revealed that the optimization of environmental conditions alone could not entirely resolve these critical problems. On the other hand, microbial in silico metabolic modeling approaches have lately been the center of attention and have been applied for the efficient production of valuable commodities including SA. Then again, literature survey results indicated the absence of up-to-date reviews assessing this issue, specifically concerning SA production. Hence, this review was designed to discuss accomplishments and future perspectives of in silico studies on the metabolic capabilities of SA producers. Herein, research progress on SA and A. succinogenes, pathways involved in SA production, metabolic models of SA-producing microorganisms, and status, limitations and prospects on in silico studies of A. succinogenes were elaborated. All in all, this review is believed to provide insights to understand the current scenario and to develop efficient mathematical models for designing robust SA-producing microbial strains.
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Li Q, Huang B, He Q, Lu J, Li X, Li Z, Wu H, Ye Q. Production of succinate from simply purified crude glycerol by engineered Escherichia coli using two-stage fermentation. BIORESOUR BIOPROCESS 2018. [DOI: 10.1186/s40643-018-0227-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Tejero Rioseras A, Singh KD, Nowak N, Gaugg MT, Bruderer T, Zenobi R, Sinues PML. Real-Time Monitoring of Tricarboxylic Acid Metabolites in Exhaled Breath. Anal Chem 2018; 90:6453-6460. [DOI: 10.1021/acs.analchem.7b04600] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Alberto Tejero Rioseras
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
- SEADM, S.L., 28036 Madrid, Spain
- Department of Analytical Chemistry, University of Cordoba, 14005 Cordoba, Spain
| | - Kapil Dev Singh
- University Children’s Hospital Basel, University of Basel, 4056 Basel, Switzerland
- Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
| | - Nora Nowak
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Martin T. Gaugg
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Tobias Bruderer
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Pablo M.-L. Sinues
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
- University Children’s Hospital Basel, University of Basel, 4056 Basel, Switzerland
- Department of Biomedical Engineering, University of Basel, 4123 Allschwil, Switzerland
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Wei S, Jian X, Chen J, Zhang C, Hua Q. Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol. BIORESOUR BIOPROCESS 2017. [DOI: 10.1186/s40643-017-0180-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Li W, Wu H, Li M, San KY. Effect of NADPH availability on free fatty acid production in Escherichia coli. Biotechnol Bioeng 2017; 115:444-452. [PMID: 28976546 DOI: 10.1002/bit.26464] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Revised: 09/17/2017] [Accepted: 09/25/2017] [Indexed: 11/06/2022]
Abstract
Microbial conversion of renewable carbon sources to free fatty acids has attracted significant attention in recent years. Accumulation of free fatty acids in Escherichia coli by overexpression of an acyl-ACP thioesterase which can break the fatty acid elongation has been well established. Various efforts have been made to increase fatty acid production in E. coli by enhancing the enzymes involved in the fatty acid synthesis cycle or host strain manipulations. The current study focused on the effect of NADPH availability on free fatty acids (FFAs) productivity. There are two reduction steps in the fatty acid elongation cycle which are catalyzed by beta keto-ACP reductase (FabG) and enoyl-ACP reductase (FabI), respectively. It is reported that FabI can use either NADH or NADPH as cofactor, while FabG only uses NADPH in E. coli. Fatty acid production dropped dramatically in the glucose-6-phosphate dehydrogenase (encoded by the zwf gene) deficient strain. Similarly, the pntB (which encodes one of the subunit of proton-translocating membrane bounded transhydrogenase PntAB) and udhA (which encodes the energy dependent cytoplasmic transhydrogenase UdhA) double mutant strain also showed an 88.8% decrease in free fatty acid production. Overexpression of PntAB and NadK restored the fatty acid production capability of these two mutant strains. These results indicated that the availability of NADPH played a very important role in fatty acid production.
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Affiliation(s)
- Wei Li
- Department of Bioengineering, Rice University, Houston, Texas
| | - Hui Wu
- Department of Bioengineering, Rice University, Houston, Texas.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Mai Li
- Department of Bioengineering, Rice University, Houston, Texas
| | - Ka-Yiu San
- Department of Bioengineering, Rice University, Houston, Texas.,Department of Chemical & Biomolecular Engineering, Rice University, Houston, Texas
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Jian X, Li N, Chen Q, Hua Q. Model-guided identification of novel gene amplification targets for improving succinate production in Escherichia coli NZN111. Integr Biol (Camb) 2017; 9:830-835. [PMID: 28884171 DOI: 10.1039/c7ib00077d] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Reconstruction and application of genome-scale metabolic models (GEMs) have facilitated metabolic engineering by providing a platform on which systematic computational analysis of metabolic networks can be performed. In this study, a GEM of Escherichia coli NZN111 was employed by the analysis of production and growth coupling (APGC) algorithm to identify genetic strategies for the overproduction of succinate. Through in silico simulation and reaction expression analysis, glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), triosephosphate isomerase (TPI), and phosphoenolpyruvate carboxylase (PPC), encoded by gapA, pgk, tpiA, and ppc, respectively, were selected for experimental overexpression. The results showed that overexpressing any of these could improve both growth and succinate production. Specifically, overexpression of GAPDH or PGK showed a significant effect with up to 24% increase in succinate production. These results indicate that the APGC algorithm can be effectively used to guide genetic manipulation for strain design by identifying genome-wide gene amplification targets.
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Affiliation(s)
- Xingxing Jian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
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Jung HM, Kim YH, Oh MK. Formate and Nitrate Utilization in Enterobacter aerogenes for Semi-Anaerobic Production of Isobutanol. Biotechnol J 2017; 12. [PMID: 28731532 DOI: 10.1002/biot.201700121] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 07/07/2017] [Indexed: 11/07/2022]
Abstract
Anaerobic bioprocessing is preferred because of its economic advantages. However, low productivity and decreased growth of the host strain have limited the use of the anaerobic process. Anaerobic respiration can be applied to anoxic processing using formate and nitrate metabolism to improve the productivity of value-added metabolites. A isobutanol-producing strains is constructed using Enterobacter aerogenes as a host strain by metabolic engineering approaches. The byproduct pathway (ldhA, budA, and pflB) is knocked out, and heterologous keto-acid decarboxylase (kivD) and alcohol dehydrogenase (adhA) are expressed along with the L-valine synthesis pathway (ilvCD and budB). The pyruvate formate-lyase mutant shows decreased growth rates when cultivated in semi-anaerobic conditions, which results in a decline in productivity. When formate and nitrate are supplied in the culture medium, the growth rates and amount of isobutanol production is restored (4.4 g L-1 , 0.23 g g-1 glucose, 0.18 g L-1 h-1 ). To determine the function of the formate and nitrate coupling reaction system, the mutant strains that could not utilize formate or nitrate is contructed. Decreased growth and productivity are observed in the nitrate reductase (narG) mutant strain. This is the first report of engineering isobutanol-producing E. aerogenes to increase strain fitness via augmentation of formate and nitrate metabolism during anaerobic cultivation.
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Affiliation(s)
- Hwi-Min Jung
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
| | - Yong Hwan Kim
- School of Energy and Chemical Engineering, UNIST, Ulsan, Korea
| | - Min-Kyu Oh
- Department of Chemical and Biological Engineering, Korea University, Seoul, Korea
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