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Fang S, Cao W, Wu Q, Cheng S, Jin H, Pang H, Zhou A, Feng L, Cao J, Luo J. Dynamic microbiome disassembly and evolution induced by antimicrobial methylisothiazolinone in sludge anaerobic fermentation for volatile fatty acids generation. WATER RESEARCH 2024; 251:121139. [PMID: 38237458 DOI: 10.1016/j.watres.2024.121139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 01/11/2024] [Accepted: 01/14/2024] [Indexed: 02/12/2024]
Abstract
In the post-COVID-19 pandemic era, various antimicrobials have emerged and concentrated in waste-activated sludge (WAS), affecting the biological treatment of WAS. However, there is still a knowledge gap in the dynamic response and adaptive mechanism of anaerobic microbiome under exogenous antimicrobial stress. This study found that methylisothiazolinone (MIT, as a typic antimicrobial) caused an interesting lag effect on the volatile fatty acids (VFAs) promotion in the WAS anaerobic fermentation process. MIT was effective to disintegrate the extracellular polymeric substances (EPS), and those functional anaerobic microorganisms were easily exposed and negatively impacted by the MIT interference after the loss of protective barriers. Correspondingly, the ecological interactions and microbial metabolic functions related to VFA biosynthesis (e.g., pyruvate metabolism) were downregulated at the initial stage. The syntrophic consortia gradually adapted to the interference and attenuated the MIT stress by activating chemotaxis and resistance genes (e.g., excreting, binding, and inactivating). Due to the increased bioavailable substrates in the fermentation systems, the dominant microorganisms (i.e., Clostridium and Caloramator) with both VFAs production and MIT-tolerance functions have been domesticated. Moreover, MIT disrupted the syntrophic interaction between acetogens and methanogens and totally suppressed methanogens' metabolic activities. The VFA production derived from WAS anaerobic fermentation was therefore enhanced due to the interference of antimicrobial MIT stress. This work deciphered dynamic changes and adaptive evolution of anaerobic syntrophic consortia in response to antimicrobial stress and provided guidance on the evaluation and control of the ecological risks of exogenous pollutants in WAS treatment.
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Affiliation(s)
- Shiyu Fang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Wangbei Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Qian Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Song Cheng
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Hongqi Jin
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Heliang Pang
- School of Environmental and Municipal Engineering, Xi 'an University of Architecture and Technology, Xi 'an 710055, China
| | - Aijuan Zhou
- College of Environmental Science and Engineering, Taiyuan University of Technology, Taiyuan 030024, China
| | - Leiyu Feng
- State Key Laboratory of Pollution Control and Resource Reuse, School of Environmental Science and Engineering, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Jiashun Cao
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China
| | - Jingyang Luo
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, Hohai University, Nanjing 210098, China; College of Environment, Hohai University, Nanjing 210098, China.
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2
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Hosmer J, McEwan AG, Kappler U. Bacterial acetate metabolism and its influence on human epithelia. Emerg Top Life Sci 2024; 8:1-13. [PMID: 36945843 PMCID: PMC10903459 DOI: 10.1042/etls20220092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/16/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Short-chain fatty acids are known modulators of host-microbe interactions and can affect human health, inflammation, and outcomes of microbial infections. Acetate is the most abundant but least well-studied of these modulators, with most studies focusing on propionate and butyrate, which are considered to be more potent. In this mini-review, we summarize current knowledge of acetate as an important anti-inflammatory modulator of interactions between hosts and microorganisms. This includes a summary of the pathways by which acetate is metabolized by bacteria and human cells, the functions of acetate in bacterial cells, and the impact that microbially derived acetate has on human immune function.
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Affiliation(s)
- Jennifer Hosmer
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Alastair G. McEwan
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
| | - Ulrike Kappler
- School of Chemistry and Molecular Biosciences, Australian Infectious Diseases Research Centre, The University of Queensland, St. Lucia, Australia
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3
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Lozano-Terol G, Chiozzi RZ, Gallego-Jara J, Sola-Martínez RA, Vivancos AM, Ortega Á, Heck AJ, Díaz MC, de Diego Puente T. Relative impact of three growth conditions on the Escherichia coli protein acetylome. iScience 2024; 27:109017. [PMID: 38333705 PMCID: PMC10850759 DOI: 10.1016/j.isci.2024.109017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/04/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
Nε-lysine acetylation is a common posttranslational modification observed in Escherichia coli. In the present study, integrative analysis of the proteome and acetylome was performed using label-free quantitative mass spectrometry to analyze the relative influence of three factors affecting growth. The results revealed differences in the proteome, mainly owing to the type of culture medium used (defined or complex). In the acetylome, 7482 unique acetylation sites were identified. Acetylation is directly related to the abundance of proteins, and the level of acetylation in each type of culture is associated with extracellular acetate concentration. Furthermore, most acetylated lysines in the exponential phase remained in the stationary phase without dynamic turnover. Interestingly, unique acetylation sites were detected in proteins whose presence or abundance was linked to the type of culture medium. Finally, the biological function of the acetylation changes was demonstrated for three central metabolic proteins (GapA, Mdh, and AceA).
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Affiliation(s)
- Gema Lozano-Terol
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Riccardo Zenezini Chiozzi
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Rosa Alba Sola-Martínez
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Adrián Martínez Vivancos
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Álvaro Ortega
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Albert J.R. Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padulaan 8, Utrecht 3584 CH, the Netherlands
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology and Immunology (B), Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence “Campus Mare Nostrum”, 30100 Murcia, Spain
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4
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Yuan D, Liu B, Yuan X, Feng L, Xu X, Zhu J, Chen Z, Xu R, Chen J, Xu G, Lin J, Yang L, Li M, Lian J, Wu M. Multisite Mutation of the Escherichia coli cAMP Receptor Protein: Enhancing Xylitol Biosynthesis by Activating Xylose Catabolism and Improving Strain Tolerance. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37921650 DOI: 10.1021/acs.jafc.3c05445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The bioproduction of xylitol from hemicellulose hydrolysate has good potential for industrial development. However, xylitol productivity has always been limited due to corncob hydrolysate toxicity and glucose catabolic repression. To address these challenges, this work selected the S83 and S128 amino acid residues of the cyclic AMP receptor protein (CRP) as the modification target. By introducing multisite mutation in CRP, this approach successfully enhanced xylose catabolism and improved the strain's tolerance to corncob hydrolysate. The resulting mutant strain, designated as CPH (CRP S83H-S128P), underwent fermentation in a 20 L bioreactor with semicontinuous feeding of corncob hydrolysate. Remarkably, xylitol yield and xylitol productivity for 41 h fermentation were 175 and 4.32 g/L/h, respectively. Therefore, multisite CRP mutation was demonstrated as an efficient global regulatory strategy to effectively improve xylitol productivity from lime-pretreated corncob hydrolysates.
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Affiliation(s)
- Dongxu Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Bingbing Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Xinsong Yuan
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
- School of Chemistry and Chemical Engineering, Hefei Normal University, Hefei 230601, PR China
| | - Leilei Feng
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Xudong Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Jialin Zhu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Zhengjie Chen
- Shandong Weiyan Biotechnology Co., Ltd, Binzhou 256660, PR China
| | - Renhao Xu
- Hangzhou No. 14 Middle School, Hangzhou 310006, PR China
| | - Jiao Chen
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou 318000, PR China
- Haizheng Pharmaceutical Co., Ltd, Taizhou 318000, PR China
| | - Gang Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd, Quzhou 324302, PR China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310030, PR China
- Ningbo Research Institute, Zhejiang University, Ningbo 315100, PR China
- Zhejiang Key Laboratory of Antifungal Drugs, Taizhou 318000, PR China
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5
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Sanmarco LM, Rone JM, Polonio CM, Fernandez Lahore G, Giovannoni F, Ferrara K, Gutierrez-Vazquez C, Li N, Sokolovska A, Plasencia A, Faust Akl C, Nanda P, Heck ES, Li Z, Lee HG, Chao CC, Rejano-Gordillo CM, Fonseca-Castro PH, Illouz T, Linnerbauer M, Kenison JE, Barilla RM, Farrenkopf D, Stevens NA, Piester G, Chung EN, Dailey L, Kuchroo VK, Hava D, Wheeler MA, Clish C, Nowarski R, Balsa E, Lora JM, Quintana FJ. Lactate limits CNS autoimmunity by stabilizing HIF-1α in dendritic cells. Nature 2023; 620:881-889. [PMID: 37558878 PMCID: PMC10725186 DOI: 10.1038/s41586-023-06409-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Dendritic cells (DCs) have a role in the development and activation of self-reactive pathogenic T cells1,2. Genetic variants that are associated with the function of DCs have been linked to autoimmune disorders3,4, and DCs are therefore attractive therapeutic targets for such diseases. However, developing DC-targeted therapies for autoimmunity requires identification of the mechanisms that regulate DC function. Here, using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies, we identify a regulatory loop of negative feedback that operates in DCs to limit immunopathology. Specifically, we find that lactate, produced by activated DCs and other immune cells, boosts the expression of NDUFA4L2 through a mechanism mediated by hypoxia-inducible factor 1α (HIF-1α). NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs that are involved in the control of pathogenic autoimmune T cells. We also engineer a probiotic that produces lactate and suppresses T cell autoimmunity through the activation of HIF-1α-NDUFA4L2 signalling in DCs. In summary, we identify an immunometabolic pathway that regulates DC function, and develop a synthetic probiotic for its therapeutic activation.
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Affiliation(s)
- Liliana M Sanmarco
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Joseph M Rone
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Carolina M Polonio
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Gonzalo Fernandez Lahore
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Federico Giovannoni
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Kylynne Ferrara
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Cristina Gutierrez-Vazquez
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Ning Li
- Synlogic Therapeutics, Cambridge, MA, USA
| | | | - Agustin Plasencia
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Camilo Faust Akl
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Payal Nanda
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Evelin S Heck
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Hong-Gyun Lee
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Chun-Cheih Chao
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Claudia M Rejano-Gordillo
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Pedro H Fonseca-Castro
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Tomer Illouz
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Mathias Linnerbauer
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Jessica E Kenison
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Rocky M Barilla
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Farrenkopf
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Nikolas A Stevens
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Gavin Piester
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth N Chung
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Lucas Dailey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Vijay K Kuchroo
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - David Hava
- Synlogic Therapeutics, Cambridge, MA, USA
| | - Michael A Wheeler
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Clary Clish
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Roni Nowarski
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
- Evergrande Center for Immunologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA
| | - Eduardo Balsa
- Centro de Biología Molecular Severo Ochoa UAM-CSIC, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Harvard Medical School, Brigham and Women's Hospital, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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Cao L, Lu M, Zhao M, Zhang Y, Nong Y, Hu M, Wang Y, Li T, Chen F, Wang M, Liu J, Li E, Sun H. Physiological and transcriptional studies reveal Cr(VI) reduction mechanisms in the exoelectrogen Cellulomonas fimi Clb-11. Front Microbiol 2023; 14:1161303. [PMID: 37303804 PMCID: PMC10251745 DOI: 10.3389/fmicb.2023.1161303] [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: 02/08/2023] [Accepted: 04/24/2023] [Indexed: 06/13/2023] Open
Abstract
A facultative exoelectrogen, Cellulomonas fimi strain Clb-11, was isolated from polluted river water. This strain could generate electricity in microbial fuel cells (MFCs) with carboxymethyl cellulose (CMC) as the carbon source, and the maximum output power density was 12.17 ± 2.74 mW·m-2. In addition, Clb-11 could secrete extracellular chromate reductase or extracellular electron mediator to reduce Cr(VI) to Cr(III). When the Cr(VI) concentration was less than 0.5 mM in Luria-Bertani (LB) medium, Cr(VI) could be completely reduced by Clb-11. However, the Clb-11 cells swelled significantly in the presence of Cr(VI). We employed transcriptome sequencing analysis to identify genes involved in different Cr(VI) stress responses in Clb-11. The results indicate that 99 genes were continuously upregulated while 78 genes were continuously downregulated as the Cr(VI) concentration increased in the growth medium. These genes were mostly associated with DNA replication and repair, biosynthesis of secondary metabolites, ABC transporters, amino sugar and nucleotide sugar metabolism, and carbon metabolism. The swelling of Clb-11 cells might have been related to the upregulation of the genes atoB, INO1, dhaM, dhal, dhak, and bccA, which encode acetyl-CoA C-acetyltransferase, myo-inositol-1-phosphate synthase, phosphoenolpyruvate-glycerone phosphotransferase, and acetyl-CoA/propionyl-CoA carboxylase, respectively. Interestingly, the genes cydA and cydB related to electron transport were continuously downregulated as the Cr(VI) concentration increased. Our results provide clues to the molecular mechanism of Cr(VI) reduction by microorganisms in MFCs systems.
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Tan W, Tian Y, Zhang Q, Miao S, Wu W, Miao X, Kuang H, Yang W. Antioxidant and antibacterial activity of Apis laboriosa honey against Salmonella enterica serovar Typhimurium. Front Nutr 2023; 10:1181492. [PMID: 37252242 PMCID: PMC10211265 DOI: 10.3389/fnut.2023.1181492] [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: 03/07/2023] [Accepted: 04/18/2023] [Indexed: 05/31/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common food-borne pathogen that commonly causes gastroenteritis in humans and animals. Apis laboriosa honey (ALH) harvested in China has significant antibacterial activity against Staphylococcus aureus, Escherichia coli, and Bacillus subtilis. We hypothesize that ALH has antibacterial activity against S. Typhimurium. The physicochemical parameters, minimum inhibitory and bactericidal concentrations (MIC and MBC) and the possible mechanism were determined. The results showed that there were significantly different physicochemical parameters, including 73 phenolic compounds, among ALH samples harvested at different times and from different regions. Their antioxidant activity was affected by their components, especially total phenol and flavonoid contents (TPC, TFC), which had a high correlation with antioxidant activities except for the O2- assay. The MIC and MBC of ALH against S. Typhimurium were 20-30% and 25-40%, respectively, which were close to those of UMF5+ manuka honey. The proteomic experiment revealed the possible antibacterial mechanism of ALH1 at IC50 (2.97%, w/v), whose antioxidant activity reduced the bacterial reduction reaction and energy supply, mainly by inhibiting the citrate cycle (TCA cycle), amino acid metabolism pathways and enhancing the glycolysis pathway. The results provide a theoretical basis for the development of bacteriostatic agents and application of ALH.
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Affiliation(s)
- Weihua Tan
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Bee Product Processing and Application Research Center of the Ministry of Education, Fuzhou, Fujian, China
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Yuanyuan Tian
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Bee Product Processing and Application Research Center of the Ministry of Education, Fuzhou, Fujian, China
| | - Qingya Zhang
- Bee Product Processing and Application Research Center of the Ministry of Education, Fuzhou, Fujian, China
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Siwei Miao
- M.X.’s Expert Workstation, Pu’er, Yunnan, China
| | - Wenrong Wu
- Bee Product Processing and Application Research Center of the Ministry of Education, Fuzhou, Fujian, China
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaoqing Miao
- Bee Product Processing and Application Research Center of the Ministry of Education, Fuzhou, Fujian, China
- M.X.’s Expert Workstation, Pu’er, Yunnan, China
| | - Haiou Kuang
- M.X.’s Expert Workstation, Pu’er, Yunnan, China
- Research Institute of Eastern Honeybee, Yunnan Agricultural University, Kunming, Yunnan, China
| | - Wenchao Yang
- College of Animal Science (College of Bee Science), Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Bee Product Processing and Application Research Center of the Ministry of Education, Fuzhou, Fujian, China
- College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- M.X.’s Expert Workstation, Pu’er, Yunnan, China
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8
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Sanmarco LM, Rone JM, Polonio CM, Giovannoni F, Lahore GF, Ferrara K, Gutierrez-Vazquez C, Li N, Sokolovska A, Plasencia A, Akl CF, Nanda P, Heck ES, Li Z, Lee HG, Chao CC, Rejano-Gordillo CM, Fonseca-Castro PH, Illouz T, Linnerbauer M, Kenison JE, Barilla RM, Farrenkopf D, Piester G, Dailey L, Kuchroo VK, Hava D, Wheeler MA, Clish C, Nowarski R, Balsa E, Lora JM, Quintana FJ. Engineered probiotics limit CNS autoimmunity by stabilizing HIF-1α in dendritic cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.17.532101. [PMID: 36993446 PMCID: PMC10055137 DOI: 10.1101/2023.03.17.532101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Dendritic cells (DCs) control the generation of self-reactive pathogenic T cells. Thus, DCs are considered attractive therapeutic targets for autoimmune diseases. Using single-cell and bulk transcriptional and metabolic analyses in combination with cell-specific gene perturbation studies we identified a negative feedback regulatory pathway that operates in DCs to limit immunopathology. Specifically, we found that lactate, produced by activated DCs and other immune cells, boosts NDUFA4L2 expression through a mechanism mediated by HIF-1α. NDUFA4L2 limits the production of mitochondrial reactive oxygen species that activate XBP1-driven transcriptional modules in DCs involved in the control of pathogenic autoimmune T cells. Moreover, we engineered a probiotic that produces lactate and suppresses T-cell autoimmunity in the central nervous system via the activation of HIF-1α/NDUFA4L2 signaling in DCs. In summary, we identified an immunometabolic pathway that regulates DC function, and developed a synthetic probiotic for its therapeutic activation.
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9
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El-Mansi M. Control of central metabolism’s architecture in Escherichia coli: An overview. Microbiol Res 2023; 266:127224. [DOI: 10.1016/j.micres.2022.127224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 10/05/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
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10
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Mutyala S, Kim JR. Recent advances and challenges in the bioconversion of acetate to value-added chemicals. BIORESOURCE TECHNOLOGY 2022; 364:128064. [PMID: 36195215 DOI: 10.1016/j.biortech.2022.128064] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Acetate is a major byproduct of the bioconversion of the greenhouse gas carbon dioxide, pretreatment of lignocellulose biomass, and microbial fermentation. The utilization and valorization of acetate have been emphasized in transforming waste to clean energy and value-added platform chemicals, contributing to the development of a closed carbon loop toward a low-carbon circular bio-economy. Acetate has been used to produce several platform chemicals, including succinate, 3-hydroxypropionate, and itaconic acid, highlighting the potential of acetate to synthesize many biochemicals and biofuels. On the other hand, the yields and titers have not reached the theoretical maximum. Recently, recombinant strain development and pathway regulation have been suggested to overcome this limitation. This review provides insights into the important constraints limiting the yields and titers of the biochemical and metabolic pathways of bacteria capable of metabolizing acetate for acetate bioconversion. The current developments in recombinant strain engineering are also discussed.
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Affiliation(s)
- Sakuntala Mutyala
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea
| | - Jung Rae Kim
- School of Chemical Engineering, Pusan National University, 63 Busandeahak-ro, Geumjeong-Gu, Busan 46241, Republic of Korea.
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11
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Chen X, Sheng Y, Wang G, Guo L, Zhang H, Zhang F, Yang T, Huang D, Han X, Zhou L. Microbial compositional and functional traits of BTEX and salinity co-contaminated shallow groundwater by produced water. WATER RESEARCH 2022; 215:118277. [PMID: 35305487 DOI: 10.1016/j.watres.2022.118277] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/03/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Intrusion of salinity and petroleum hydrocarbons (e.g., benzene, toluene, ethylbenzene, and xylenes, BTEX) into shallow groundwater by so-called 'produced water' (the water associated with oil and gas production) has recently drawn much attention. However, how this co-contamination affects the groundwater microbial community remains unknown. Herein, geochemical methods (e.g., ion ratios) and high-throughput sequencing (amplicon and shotgun metagenomic) were used to study the contaminant source, hydrogeochemical conditions, microbial community and function in salinity and BTEX co-contaminated shallow groundwater in an oil field, northwest China. The desulfurization coefficient (100rSO42-/rCl-), coefficient of sodium and chloride (rNa+/rCl-), and coefficient of magnesium and chloride (rMg2+/rCl-) revealed an intrusion of produced water into groundwater, resulting in elevated levels of salinity and BTEX. The consumption of terminal electron acceptors (e.g., NO3-, Fe3+, and SO42-) was likely coupled with BTEX degradation. Relative to the bacteria, decreased archaeal diversity and enriched community in produced water-contaminated groundwater suggested that archaea were more susceptible to elevated BTEX and salinity. Relative to the nitrate and sulfate reduction genes, the abundance of marker genes encoding fermentation (acetate and hydrogen production) and methanogenesis (aceticlastic and methylotrophic) was more proportional to BTEX concentration. The produced water intrusion significantly enriched the salt-tolerant anaerobic fermentative heterotroph Woesearchaeia in shallow groundwater, and its co-occurrence with BTEX-degrading bacteria and methanogen Methanomicrobia suggested mutualistic interactions among the archaeal and bacterial communities to couple BTEX degradation with fermentation and methanogenesis. This study offers a first insight into the microbial community and function in groundwater contaminated by produced water.
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Affiliation(s)
- Xianglong Chen
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Yizhi Sheng
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China; Department of Geology and Environmental Earth Science, Miami University, OH 45056, USA.
| | - Guangcai Wang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China.
| | - Liang Guo
- College of Geology and Environment, Xi'an University of Science and Technology, Xi'an 710054, PR China
| | - Hongyu Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Fan Zhang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Tao Yang
- State Key Laboratory of Biogeology and Environmental Geology & MOE Key Laboratory of Groundwater Circulation and Environment Evolution, China University of Geosciences, No.29, Xueyuan Road, Haidian District, Beijing 100083, PR China; School of Water Resources and Environment, China University of Geosciences, Beijing 100083, PR China
| | - Dandan Huang
- School of Water Resources and Environmental Engineering, East China University of Technology, Nanchang 330013, PR China
| | - Xu Han
- Geology Institute of China Chemical Geology and Mine Bureau, Beijing, PR China
| | - Ling Zhou
- Beijing Key Laboratory of Urban Hydrological Cycle and Sponge City Technology, College of Water Sciences, Beijing Normal University, Beijing 100875, PR China
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12
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Okoye CO, Dong K, Wang Y, Gao L, Li X, Wu Y, Jiang J. Comparative genomics reveals the organic acid biosynthesis metabolic pathways among five lactic acid bacterial species isolated from fermented vegetables. N Biotechnol 2022; 70:73-83. [PMID: 35525431 DOI: 10.1016/j.nbt.2022.05.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 02/28/2022] [Accepted: 05/02/2022] [Indexed: 10/18/2022]
Abstract
Lactic acid bacteria (LAB) comprise a widespread bacterial group, inhabiting the niches of fermented vegetables and capable of producing beneficial organic acids. In the present study, several bioinformatics approaches were used to perform whole-genome sequencing and comparative genomics of five LAB species, Lactobacillus plantarum PC1-1, Pediococcus pentosaceus PC2-1(F2), Weissella hellenica PC1A, Lactobacillus buchneri PC-C1, and Enterococcus sp. YC2-6, to enhance understanding of their different genetic functionalities and organic acid biosynthesis. The results revealed major carbohydrate-active enzymes, putative operons and unique mobile genetic elements, including plasmids, resistance genes, insertion sequences and composite transposons involved in organic acid biosynthesis. The metabolic pathways of organic acid biosynthesis emphasize the key genes encoding specific enzymes required for organic acid metabolism. The five genomes were found to contain various regions of secondary metabolite biosynthetic gene clusters, including the type III polyketide synthases (T3PKS) enriched with unique genes encoding a hydroxymethylglutaryl-CoA synthase, capable of exhibiting specific antimicrobial activity with biopreservative potential, and a cyclic AMP receptor protein (CPR) transcription factor acting as a glucose sensor in organic acid biosynthesis. This could enable the organisms to prevail in the fermentation process, suggesting potential industrial applications.
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Affiliation(s)
- Charles Obinwanne Okoye
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China; Department of Zoology & Environmental Biology, University of Nigeria, Nsukka 410001, Nigeria
| | - Ke Dong
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongli Wang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lu Gao
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xia Li
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yanfang Wu
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Jianxiong Jiang
- Biofuels Institute, Jiangsu University, Zhenjiang 212013, China; School of Environment & Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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13
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Shi LL, Zheng Y, Tan BW, Li ZJ. Establishment of a carbon-efficient xylulose cleavage pathway in Escherichia coli to metabolize xylose. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108331] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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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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15
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Enhancement of Ethanol Production Using a Hybrid of Firefly Algorithm and Dynamic Flux Balance Analysis. INTERNATIONAL JOURNAL OF SWARM INTELLIGENCE RESEARCH 2022. [DOI: 10.4018/ijsir.299845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Many high-demand industrial products are generated by microorganisms, including fuels, food, vitamins, and other chemicals. Metabolic engineering is the method of circumventing cellular control to manufacture a desirable product or to create a new product that the host cells do not normally need to produce. One of the objectives of microorganism metabolic engineering is to maximise the production of a desired product. However, owing to the structure of the regulatory cellular and metabolic network, identifying specific genes to be knocked out is difficult. The development of optimization algorithms often confronts issues such as easily trapping in local maxima and handling multivariate and multimodal functions inefficiently. To predict the gene knockout list that can generate high yields of desired product, a hybrid of Firefly Algorithm and Dynamic Flux Balance Analysis (FADFBA) is proposed. This paper focuses on the ethanol production of Escherichia coli (E. coli). The findings of the experiments include gene lists, ethanol production, growth rate, and the performance of FADFBA.
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Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. THE ISME JOURNAL 2022; 16:307-320. [PMID: 34331018 PMCID: PMC8692467 DOI: 10.1038/s41396-021-01057-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023]
Abstract
Deltaproteobacteria, now proposed to be the phyla Desulfobacterota, Myxococcota, and SAR324, are ubiquitous in marine environments and play essential roles in global carbon, sulfur, and nutrient cycling. Despite their importance, our understanding of these bacteria is biased towards cultured organisms. Here we address this gap by compiling a genomic catalog of 1 792 genomes, including 402 newly reconstructed and characterized metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments. Phylogenomic analyses reveal that many of these novel MAGs are uncultured representatives of Myxococcota and Desulfobacterota that are understudied. To better characterize Deltaproteobacteria diversity, metabolism, and ecology, we clustered ~1 500 genomes based on the presence/absence patterns of their protein families. Protein content analysis coupled with large-scale metabolic reconstructions separates eight genomic clusters of Deltaproteobacteria with unique metabolic profiles. While these eight clusters largely correspond to phylogeny, there are exceptions where more distantly related organisms appear to have similar ecological roles and closely related organisms have distinct protein content. Our analyses have identified previously unrecognized roles in the cycling of methylamines and denitrification among uncultured Deltaproteobacteria. This new view of Deltaproteobacteria diversity expands our understanding of these dominant bacteria and highlights metabolic abilities across diverse taxa.
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17
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Man MY, Mohamad MS, Choon YW, Ismail MA. In silico gene knockout prediction using a hybrid of Bat algorithm and minimization of metabolic adjustment. J Integr Bioinform 2021; 18:jib-2020-0037. [PMID: 34348418 PMCID: PMC8573224 DOI: 10.1515/jib-2020-0037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 06/21/2021] [Indexed: 11/17/2022] Open
Abstract
Microorganisms commonly produce many high-demand industrial products like fuels, food, vitamins, and other chemicals. Microbial strains are the strains of microorganisms, which can be optimized to improve their technological properties through metabolic engineering. Metabolic engineering is the process of overcoming cellular regulation in order to achieve a desired product or to generate a new product that the host cells do not usually need to produce. The prediction of genetic manipulations such as gene knockout is part of metabolic engineering. Gene knockout can be used to optimize the microbial strains, such as to maximize the production rate of chemicals of interest. Metabolic and genetic engineering is important in producing the chemicals of interest as, without them, the product yields of many microorganisms are normally low. As a result, the aim of this paper is to propose a combination of the Bat algorithm and the minimization of metabolic adjustment (BATMOMA) to predict which genes to knock out in order to increase the succinate and lactate production rates in Escherichia coli (E. coli).
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Affiliation(s)
- Mei Yen Man
- School of Computing, Faculty of Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia
| | - Mohd Saberi Mohamad
- Department of Genetics and Genomics, College of Medical and Health Sciences, United Arab Emirates University, Al Ain17666, Abu Dhabi, United Arab Emirates
| | - Yee Wen Choon
- Institute for Artificial Intelligence and Big Data, Universiti Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia; and Department of Data Science, Universiti Malaysia Kelantan, Kota Bharu 16100, Kelantan, Malaysia
| | - Mohd Arfian Ismail
- Faculty of Computing (FKOM), College of Computing and Applied Sciences, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300 Gambang, Kuantan, Pahang, Malaysia
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18
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2,3-Butanediol synthesis from glucose supplies NADH for elimination of toxic acetate produced during overflow metabolism. Cell Discov 2021; 7:43. [PMID: 34103474 PMCID: PMC8187413 DOI: 10.1038/s41421-021-00273-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 04/09/2021] [Indexed: 12/19/2022] Open
Abstract
Overflow metabolism-caused acetate accumulation is a major problem that restricts industrial applications of various bacteria. 2,3-Butanediol (2,3-BD) synthesis in microorganisms is an ancient metabolic process with unidentified functions. We demonstrate here that acetate increases and then decreases during the growth of a bacterium Enterobacter cloacae subsp. dissolvens SDM. Both bifunctional acetaldehyde/ethanol dehydrogenase AdhE-catalyzed ethanol production and acetate-induced 2,3-BD biosynthesis are indispensable for the elimination of acetate generated during overflow metabolism. 2,3-BD biosynthesis from glucose supplies NADH required for acetate elimination via AdhE-catalyzed ethanol production. The coupling strategy involving 2,3-BD biosynthesis and ethanol production is widely distributed in bacteria and is important for toxic acetate elimination. Finally, we realized the co-production of ethanol and acetoin from chitin, the second most abundant natural biopolymer whose catabolism involves inevitable acetate production through the coupling acetate elimination strategy. The synthesis of a non-toxic chemical such as 2,3-BD may be viewed as a unique overflow metabolism with desirable metabolic functions.
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19
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He Z, Liu Z, Gong L. Biomarker identification and pathway analysis of rheumatoid arthritis based on metabolomics in combination with ingenuity pathway analysis. Proteomics 2021; 21:e2100037. [PMID: 33969925 DOI: 10.1002/pmic.202100037] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/19/2022]
Abstract
Rheumatoid arthritis (RA) is a common autoimmune and inflammatory disease worldwide, but understanding its pathogenesis is still limited. In this study, plasma untargeted metabolomics of a discovery cohort and targeted analysis of a verification cohort were performed by gas chromatograph mass spectrometry (GC/MS). Univariate and multivariate statistical analysis were utilized to reveal differential metabolites, followed by the construction of biomarker panel through random forest (RF) algorithm. The pathways involved in RA were enriched by differential metabolites using Ingenuity Pathway Analysis (IPA) suite. Untargeted metabolomics revealed eighteen significantly altered metabolites in RA. Among these metabolites, a three-metabolite marker panel consisting of L-cysteine, citric acid and L-glutamine was constructed, using random forest algorithm that could predict RA with high accuracy, sensitivity and specificity based on a multivariate exploratory receiver operator characteristic (ROC) curve analysis. The panel was further validated by support vector machine (SVM) and partial least squares discriminant analysis (PLS-DA) algorithms, and also verified with targeted metabolomics using a verification cohort. Additionally, the dysregulated taurine biosynthesis pathway in RA was revealed by an integrated analysis of metabolomics and transcriptomics. Our findings in this study not only provided a mechanism underlying RA pathogenesis, but also offered alternative therapeutic targets for RA.
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Affiliation(s)
- Zhuoru He
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China
| | - Lingzhi Gong
- International Institute for Translational Chinese Medicine, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, PR China
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20
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Application of a dissolved oxygen control strategy to increase the expression of Streptococcus suis glutamate dehydrogenase in Escherichia coli. World J Microbiol Biotechnol 2021; 37:60. [PMID: 33709221 DOI: 10.1007/s11274-021-03025-2] [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] [Received: 09/08/2020] [Accepted: 02/25/2021] [Indexed: 12/11/2022]
Abstract
The accumulation of acetate in Escherichia coli inhibits cell growth and desired protein synthesis, and cell density and protein expression are increased by reduction of acetate excretion. Dissolved oxygen (DO) is an important parameter for acetate synthesis, and the accumulation of acetate is inversely correlated to DO level. In this study, the effect of DO levels on glutamate dehydrogenase (GDH) expression was investigated, and then different DO control strategies were tested for effects on GDH expression. DO control strategy IV (50% 0-9 h, 30% 9-18 h) provided the highest cell density (15.43 g/L) and GDH concentration (3.42 g/L), values 1.59- and 1.99-times higher than those achieved at 10% DO. The accumulation of acetate was 2.24 g/L with DO control strategy IV, a decrease of 40.74% relative to that achieved for growth at 10% DO. Additionally, under DO control strategy IV, there was lower expression of PoxB, a key enzyme for acetate synthesis, at both the transcriptional and translational level. At the same time, higher transcription and protein expression levels were observed for a glyoxylate shunt gene (aceA), an acetate uptake gene (acs), gluconeogensis and anaplerotic pathways genes (pckA, ppsA, ppc, and sfcA), and a TCA cycle gene (gltA). The flux of acetate with DO strategy IV was 8.4%, a decrease of 62.33% compared with the flux at 10% DO. This decrease represents both lower flux for acetate synthesis and increased flux of reused acetate.
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21
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Kutscha R, Pflügl S. Microbial Upgrading of Acetate into Value-Added Products-Examining Microbial Diversity, Bioenergetic Constraints and Metabolic Engineering Approaches. Int J Mol Sci 2020; 21:ijms21228777. [PMID: 33233586 PMCID: PMC7699770 DOI: 10.3390/ijms21228777] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/18/2020] [Indexed: 01/20/2023] Open
Abstract
Ecological concerns have recently led to the increasing trend to upgrade carbon contained in waste streams into valuable chemicals. One of these components is acetate. Its microbial upgrading is possible in various species, with Escherichia coli being the best-studied. Several chemicals derived from acetate have already been successfully produced in E. coli on a laboratory scale, including acetone, itaconic acid, mevalonate, and tyrosine. As acetate is a carbon source with a low energy content compared to glucose or glycerol, energy- and redox-balancing plays an important role in acetate-based growth and production. In addition to the energetic challenges, acetate has an inhibitory effect on microorganisms, reducing growth rates, and limiting product concentrations. Moreover, extensive metabolic engineering is necessary to obtain a broad range of acetate-based products. In this review, we illustrate some of the necessary energetic considerations to establish robust production processes by presenting calculations of maximum theoretical product and carbon yields. Moreover, different strategies to deal with energetic and metabolic challenges are presented. Finally, we summarize ways to alleviate acetate toxicity and give an overview of process engineering measures that enable sustainable acetate-based production of value-added chemicals.
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22
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Liu EJ, Tseng IT, Chen YL, Pang JJ, Shen ZX, Li SY. The Physiological Responses of Escherichia coli Triggered by Phosphoribulokinase (PrkA) and Ribulose-1,5-Bisphosphate Carboxylase/Oxygenase (Rubisco). Microorganisms 2020; 8:microorganisms8081187. [PMID: 32759862 PMCID: PMC7463662 DOI: 10.3390/microorganisms8081187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/24/2020] [Accepted: 07/24/2020] [Indexed: 11/20/2022] Open
Abstract
Phosphoribulokinase (PrkA) and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) have been proposed to create a heterologous Rubisco-based engineered pathway in Escherichia coli for in situ CO2 recycling. While the feasibility of a Rubisco-based engineered pathway has been shown, heterologous expressions of PrkA and Rubisco also induced physiological responses in E. coli that may compete with CO2 recycling. In this study, the metabolic shifts caused by PrkA and Rubisco were investigated in recombinant strains where ppc and pta genes (encodes phosphoenolpyruvate carboxylase and phosphate acetyltransferase, respectively) were deleted from E. coli MZLF (E. coli BL21(DE3) Δzwf, ΔldhA, Δfrd). It has been shown that the demand for ATP created by the expression of PrkA significantly enhanced the glucose consumptions of E. coli CC (MZLF Δppc) and E. coli CA (MZLF Δppc, Δpta). The accompanying metabolic shift is suggested to be the mgsA route (the methylglyoxal pathway) which results in the lactate production for reaching the redox balance. The overexpression of Rubisco not only enhanced glucose consumption but also bacterial growth. Instead of the mgsA route, the overproduction of the reducing power was balanced by the ethanol production. It is suggested that Rubisco induces a high demand for acetyl-CoA which is subsequently used by the glyoxylate shunt. Therefore, Rubisco can enhance bacterial growth. This study suggests that responses induced by the expression of PrkA and Rubisco will reach a new energy balance profile inside the cell. The new profile results in a new distribution of the carbon flow and thus carbons cannot be majorly directed to the Rubisco-based engineered pathway.
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Affiliation(s)
- En-Jung Liu
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - I-Ting Tseng
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Yi-Ling Chen
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Ju-Jiun Pang
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Zhi-Xuan Shen
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
| | - Si-Yu Li
- Department of Chemical Engineering, National Chung Hsing University, Taichung City 40227, Taiwan.; (E.-J.L.); (I.-T.T.); (Y.-L.C.); (J.-J.P.); (Z.-X.S.)
- Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung City 40227, Taiwan
- Correspondence: ; Tel.: +886-4-2284-0510 (ext. #509)
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23
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Yu Y, Shao M, Li D, Fan F, Xu H, Lu F, Bi C, Zhu X, Zhang X. Construction of a carbon-conserving pathway for glycolate production by synergetic utilization of acetate and glucose in Escherichia coli. Metab Eng 2020; 61:152-159. [PMID: 32531344 DOI: 10.1016/j.ymben.2020.06.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/05/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
Abstract
Glycolate is a bulk chemical which has been widely used in textile, food processing, and pharmaceutical industries. Glycolate can be produced from sugars by microbial fermentation. However, when using glucose as the sole carbon source, the theoretical maximum carbon molar yield of glycolate is 0.67 mol/mol due to the loss of carbon as CO2. In this study, a synergetic system for simultaneous utilization of acetate and glucose was designed to increase the carbon yield. The main function of glucose is to provide NADPH while acetate to provide the main carbon backbone for glycolate production. Theoretically, 1 glucose and 5 acetate can produce 6 glycolate, and the carbon molar yield can be increased to 0.75 mol/mol. The whole synthetic pathway was divided into two modules, one for converting acetate to glycolate and another to utilize glucose to provide NADPH. After engineering module I through activation of acs, gltA, aceA and ycdW, glycolate titer increased from 0.07 to 2.16 g/L while glycolate yields increased from 0.04 to 0.35 mol/mol-acetate and from 0.03 to 1.04 mol/mol-glucose. Module II was then engineered to increase NADPH supply. Through deletion of pfkA, pfkB, ptsI and sthA genes as well as upregulating zwf, pgl and tktA, glycolate titer increased from 2.16 to 4.86 g/L while glycolate yields increased from 0.35 to 0.82 mol/mol-acetate and from 1.04 to 6.03 mol/mol-glucose. The activities of AceA and YcdW were further increased to pull the carbon flux to glycolate, which increased glycolate yield from 0.82 to 0.92 mol/mol-acetate. Fed-batch fermentation of the final strain NZ-Gly303 produced 73.3 g/L glycolate with a productivity of 1.04 g/(L·h). The acetate to glycolate yield was 0.85 mol/mol (1.08 g/g), while glucose to glycolate yield was 6.1 mol/mol (2.58 g/g). The total carbon molar yield was 0.60 mol/mol, which reached 80% of the theoretical value.
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Affiliation(s)
- Yong Yu
- University of Chinese Academy of Sciences, Beijing, 100049, China; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Mengyao Shao
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Di Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Feiyu Fan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Hongtao Xu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Fuping Lu
- College of Biotechnology, Tianjin University of Sciences and Technology, Tianjin, 300457, China
| | - Changhao Bi
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China
| | - Xinna Zhu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China; Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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Guo W, Huang Q, Feng Y, Tan T, Niu S, Hou S, Chen Z, Du Z, Shen Y, Fang X. Rewiring central carbon metabolism for tyrosol and salidroside production in
Saccharomyces cerevisiae. Biotechnol Bioeng 2020; 117:2410-2419. [DOI: 10.1002/bit.27370] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 01/23/2023]
Affiliation(s)
- Wei Guo
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Qiulan Huang
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Yuhui Feng
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Taicong Tan
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Suhao Niu
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Shaoli Hou
- Yantai Huakangrongzan Biotechnology Co., Ltd.Yantai China
| | - Zhigang Chen
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Zhi‐Qiang Du
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Yu Shen
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
| | - Xu Fang
- State Key Laboratory of Microbial TechnologyShandong University Qingdao China
- National Glycoengineering Research CenterShandong University Qingdao China
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25
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Bueno E, Pinedo V, Cava F. Adaptation of Vibrio cholerae to Hypoxic Environments. Front Microbiol 2020; 11:739. [PMID: 32425907 PMCID: PMC7212424 DOI: 10.3389/fmicb.2020.00739] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/30/2020] [Indexed: 01/02/2023] Open
Abstract
Bacteria can colonize virtually any environment on Earth due to their remarkable capacity to detect and respond quickly and adequately to environmental stressors. Vibrio cholerae is a cosmopolitan bacterium that inhabits a vast range of environments. The V. cholerae life cycle comprises diverse environmental and infective stages. The bacterium is found in aquatic ecosystems both under free-living conditions or associated with a wide range of aquatic organisms, and some strains are also capable of causing epidemics in humans. In order to adapt between environments, V. cholerae possesses a versatile metabolism characterized by the rapid cross-regulation of energy-producing pathways. Low oxygen concentration is a key environmental factor that governs V. cholerae physiology. This article reviews the metabolic plasticity that enables V. cholerae to thrive on low oxygen concentrations and its role in environmental and host adaptation.
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Affiliation(s)
- Emilio Bueno
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
| | | | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden, Department of Molecular Biology, Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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26
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Schütze A, Benndorf D, Püttker S, Kohrs F, Bettenbrock K. The Impact of ackA, pta, and ackA-pta Mutations on Growth, Gene Expression and Protein Acetylation in Escherichia coli K-12. Front Microbiol 2020; 11:233. [PMID: 32153530 PMCID: PMC7047895 DOI: 10.3389/fmicb.2020.00233] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 01/31/2020] [Indexed: 01/06/2023] Open
Abstract
Acetate is a characteristic by-product of Escherichia coli K-12 growing in batch cultures with glucose, both under aerobic as well as anaerobic conditions. While the reason underlying aerobic acetate production is still under discussion, during anaerobic growth acetate production is important for ATP generation by substrate level phosphorylation. Under both conditions, acetate is produced by a pathway consisting of the enzyme phosphate acetyltransferase (Pta) producing acetyl-phosphate from acetyl-coenzyme A, and of the enzyme acetate kinase (AckA) producing acetate from acetyl-phosphate, a reaction that is coupled to the production of ATP. Mutants in the AckA-Pta pathway differ from each other in the potential to produce and accumulate acetyl-phosphate. In the publication at hand, we investigated different mutants in the acetate pathway, both under aerobic as well as anaerobic conditions. While under aerobic conditions only small changes in growth rate were observed, all acetate mutants showed severe reduction in growth rate and changes in the by-product pattern during anaerobic growth. The AckA– mutant showed the most severe growth defect. The glucose uptake rate and the ATP concentration were strongly reduced in this strain. This mutant exhibited also changes in gene expression. In this strain, the atoDAEB operon was significantly upregulated under anaerobic conditions hinting to the production of acetoacetate. During anaerobic growth, protein acetylation increased significantly in the ackA mutant. Acetylation of several enzymes of glycolysis and central metabolism, of aspartate carbamoyl transferase, methionine synthase, catalase and of proteins involved in translation was increased. Supplementation of methionine and uracil eliminated the additional growth defect of the ackA mutant. The data show that anaerobic, fermentative growth of mutants in the AckA-Pta pathway is reduced but still possible. Growth reduction can be explained by the lack of an important ATP generating pathway of mixed acid fermentation. An ackA deletion mutant is more severely impaired than pta or ackA-pta deletion mutants. This is most probably due to the production of acetyl-P in the ackA mutant, leading to increased protein acetylation.
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Affiliation(s)
- Andrea Schütze
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Dirk Benndorf
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
| | - Sebastian Püttker
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
| | - Fabian Kohrs
- Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany
| | - Katja Bettenbrock
- Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
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Wang J, Shang Q, Zhao C, Zhang S, Li Z, Lin C, Shen Z, Cheng L. Improvement of Streptococcus suis glutamate dehydrogenase expression in Escherichia coli through genetic modification of acetate synthesis pathway. Lett Appl Microbiol 2019; 70:64-70. [PMID: 31665809 DOI: 10.1111/lam.13244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/26/2022]
Abstract
Escherichia coli generates acetate as an undesirable by-product that has several negative effects on protein expression, and the reduction of acetate accumulation by modifying genes of acetate synthesis pathway can improve the expression of recombinant proteins. In the present study, the effect of phosphotransacetylase (pta) or/and acetate kinase (ackA) deletion on glutamate dehydrogenase (GDH) expression was investigated. The results indicated that the disruptions of pta or/and ackA decreased the acetate accumulation and synthesis of per gram cell, and increased cell density, and GDH expression and synthesis of per gram cell. The pta gene was more important for acetate formation than the ackA gene. Using the strain with deletions of pta-ackA (SSGPA) for GDH expression, acetate accumulation (2·61 g l-1 ) and acetate synthesis of per gram cell (0·229 g g-1 ) were lowest, decreasing by 28·29 and 41·43% compared with those of the parental strain (SSG) respectively. The flux of acetate synthesis (6·6%) was decreased by 72·15% compared with that of SSG, and the highest cell density (11·38 g l-1 ), GDH expression (2·78 mg ml-1 ), and GDH formation of per gram cell (0·2442 mg mg-1 ) were obtained, which were 1·22-, 1·43- and 1·17-times higher than the parental strain respectively. SIGNIFICANCE AND IMPACT OF THE STUDY: Significance and Impact of the Study: Acetate is the key undesirable by-product in Escherichia coli cultivation, and both biomass and production of desired products are increased by the reduction of acetate accumulation. In the present study, the strains with deletions of pta or/and ackA were constructed to reduce the acetate accumulation and improve the GDH expression, and the highest expression level of GDH was obtained using the strain with lesion in pta-ackA that was 1·17-times higher than that of the parental strain. The construction strategy of recombinant E. coli for decreasing the acetate excretion can be used for high expression level of other desired products.
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Affiliation(s)
- J Wang
- Department of Critical Care Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, China.,Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Q Shang
- Department of Critical Care Medicine, Affiliated Hospital of Binzhou Medical University, Binzhou, China
| | - C Zhao
- Research and Development Center, Ningxia Eppen Biotech Co. Ltd, Yinchuan, China
| | - S Zhang
- 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
| | - Z Li
- Research and Development Center, Ningxia Eppen Biotech Co. Ltd, Yinchuan, China
| | - C Lin
- Key Laboratory of Fermentation Engineering, Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China.,Research and Development Center, Ningxia Eppen Biotech Co. Ltd, Yinchuan, China
| | - Z 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
| | - L 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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Gutiérrez-García AK, Alvarez-Guzmán CL, De Leon-Rodriguez A. Autodisplay of alpha amylase from Bacillus megaterium in E. coli for the bioconversion of starch into hydrogen, ethanol and succinic acid. Enzyme Microb Technol 2019; 134:109477. [PMID: 32044024 DOI: 10.1016/j.enzmictec.2019.109477] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/29/2019] [Accepted: 11/16/2019] [Indexed: 11/16/2022]
Abstract
In this work, the expression of an α-amylase from Bacillus megaterium on the cell surface of Escherichia coli strains WDHA (Δ hycA and Δ ldhA) and WDHFP (Δ hycA, Δ frdD and Δ pta) by the autodisplay adhesin involved in diffuse adherence (AIDA) system was carried out with the purpose to confer the ability to E. coli strains to degrade starch and thus produce hydrogen, ethanol and succinic acid. For the characterization of the biocatalyst, the effect of temperature (30-70 °C), pH (3-6) and CaCl2 concentration (0-25 mM), as well as the thermostability of the biocatalyst (55-80 °C) at several time intervals (15-60 min) were evaluated. The results showed that the biocatalyst had a maximum activity at 55 °C and pH 4.5. Calcium was required for the activity as well for the thermal stability of the biocatalyst. The calculated Vmax and Km values were 0.24 U/cm3 and 5.8 mg/cm3, respectively. Furthermore, a set of anaerobic batch fermentations was carried out using 10 g/dm3 of starch and 1 g/dm3 of glucose as carbon sources in 120 cm3 serological bottles, using WDHA and WDHFP strains harboring the pAIDA-amyA plasmid. The hydrogen production for WDHA was 1056.06 cm3/dm3 and the succinic acid yield was 0.68 g/gstarch, whereas WDHFP strain produced 1689.68 cm3/dm3 of hydrogen and an ethanol yield of 0.28 g/gstarch. This work represents a promising strategy to improve the exploitation of starchy biomass for the production of biofuels (hydrogen and ethanol) or succinate without the need of a pre-saccharification process.
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Affiliation(s)
- Ana K Gutiérrez-García
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa San José 2055, Col. Lomas 4ª Sección, C.P. 78216, San Luis Potosí, México
| | - Cecilia Lizeth Alvarez-Guzmán
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa San José 2055, Col. Lomas 4ª Sección, C.P. 78216, San Luis Potosí, México
| | - Antonio De Leon-Rodriguez
- División de Biología Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C. Camino a la Presa San José 2055, Col. Lomas 4ª Sección, C.P. 78216, San Luis Potosí, México.
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29
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Lozano Terol G, Gallego-Jara J, Sola Martínez RA, Cánovas Díaz M, de Diego Puente T. Engineering protein production by rationally choosing a carbon and nitrogen source using E. coli BL21 acetate metabolism knockout strains. Microb Cell Fact 2019; 18:151. [PMID: 31484572 PMCID: PMC6724240 DOI: 10.1186/s12934-019-1202-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/29/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is a bacteria that is widely employed in many industries for the production of high interest bio-products such as recombinant proteins. Nevertheless, the use of E. coli for recombinant protein production may entail some disadvantages such as acetate overflow. Acetate is accumulated under some culture conditions, involves a decrease in biomass and recombinant protein production, and its metabolism is related to protein lysine acetylation. Thereby, the carbon and nitrogen sources employed are relevant factors in cell host metabolism, and the study of the central metabolism of E. coli and its regulation is essential for optimizing the production of biomass and recombinant proteins. In this study, our aim was to find the most favourable conditions for carrying out recombinant protein production in E. coli BL21 using two different approaches, namely, manipulation of the culture media composition and the deletion of genes involved in acetate metabolism and Nε-lysine acetylation. RESULTS We evaluated protein overexpression in E. coli BL21 wt and five mutant strains involved in acetate metabolism (Δacs, ΔackA and Δpta) and lysine acetylation (ΔpatZ and ΔcobB) grown in minimal medium M9 (inorganic ammonium nitrogen source) and in complex TB7 medium (peptide-based nitrogen source) supplemented with glucose (PTS carbon source) or glycerol (non-PTS carbon source). We observed a dependence of recombinant protein production on acetate metabolism and the carbon and nitrogen source employed. The use of complex medium supplemented with glycerol as a carbon source entails an increase in protein production and an efficient use of resources, since is a sub-product of biodiesel synthesis. Furthermore, the deletion of the ackA gene results in a fivefold increase in protein production with respect to the wt strain and a reduction in acetate accumulation. CONCLUSION The results showed that the use of diverse carbon and nitrogen sources and acetate metabolism knockout strains can redirect E. coli carbon fluxes to different pathways and affect the final yield of the recombinant protein bioprocess. Thereby, we obtained a fivefold increase in protein production and an efficient use of the resources employing the most suitable strain and culture conditions.
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Affiliation(s)
- Gema Lozano Terol
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain
| | - Julia Gallego-Jara
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain.
| | - Rosa Alba Sola Martínez
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain
| | - Manuel Cánovas Díaz
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain
| | - Teresa de Diego Puente
- Department of Biochemistry and Molecular Biology (B) and Immunology, Faculty of Chemistry, University of Murcia, Campus of Espinardo, Regional Campus of International Excellence ''Campus Mare Nostrum'', P.O. Box 4021, 30100, Murcia, Spain.
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Zhou J, Lu X, Tian B, Wang C, Shi H, Luo C, Zhu X, Yuan X, Li X. Knockout of acetoacetate degradation pathway gene atoDA enhances the toxicity tolerance of Escherichia coli to isopropanol and acetone. 3 Biotech 2019; 9:343. [PMID: 31497461 DOI: 10.1007/s13205-019-1867-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/12/2019] [Indexed: 01/13/2023] Open
Abstract
Isopropanol and acetone are important chemical products and potential high-quality new fuels. Both of them are metabolites of isopropanol synthesis pathway, but they are toxic to most bacteria. In this study, toxicity tolerance of Escherichia coli strains was evaluated by detecting their growth rates under different concentrations of isopropanol and acetone. It was showed that isopropanol was more toxic to E. coli than acetone, and the native strain MG1655 had better tolerance over DH5α to either acetone or isopropanol of 300 mM. Key genes of ethanol synthesis pathway, acetic acid metabolism pathway, and acetoacetic acid degradation pathway, including adhE, ackA-pta, and atoDA, were knocked out in MG1655 to form mutants MGΔadhE, MGΔackA-pta, and MGΔatoDA. The tolerance performances of the mutants to isopropanol and acetone were determined under various concentrations including 300 mM, 500 mM, and 700 mM, respectively. The mutant MGΔatoDA exhibited excellent tolerance to both acetone and isopropanol of 500 mM, and MGΔackA-pta could tolerate acetone at 500 mM rather than isopropanol, while the deletion of adhE in MGΔadhE resulted in a severe cell growth defection. Although isopropanol and acetone at 700 mM caused severe growth inhibition on each strain, cell growth could be restored to varying degrees with the prolongation of culture time. This phenomenon was suggested to be related to the volatilization of isopropanol and acetone based on volatilization tests. It was envisioned that MG1655 was a suitable host strain for isopropanol metabolic engineering research, and the acetoacetic acid degradation pathway gene atoDA, was probably the key optimizing point for isopropanol production.
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Affiliation(s)
- Jia Zhou
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Xiaoqing Lu
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Baoxia Tian
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Chonglong Wang
- 3School of Biology and Basic Medical Sciences, Soochow University, 199 Renai Road, Suzhou, 215123 People's Republic of China
| | - Hao Shi
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Chuping Luo
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Xiaoyan Zhu
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
| | - Xiaoqing Yuan
- Suzhou Xuhui Analysis Co., Ltd, 168 Yuan Feng Road, Kunshan High Tech Zone, Suzhou, 215300 People's Republic of China
| | - Xiangqian Li
- 1Faculty of Life Science and Food Engineering, HuaiYin Institute of Technology, Huaian, 223003 People's Republic of China
- 2Jiangsu Provincial Engineering Laboratory for Biomass Conversion and Process Integration, Huaiyin Institute of Technology, Huaian, 223003 People's Republic of China
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Sigala JC, Quiroz L, Arteaga E, Olivares R, Lara AR, Martinez A. Physiological and transcriptional comparison of acetate catabolism between Acinetobacter schindleri ACE and Escherichia coli JM101. FEMS Microbiol Lett 2019; 366:5529389. [DOI: 10.1093/femsle/fnz151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 07/04/2019] [Indexed: 01/12/2023] Open
Abstract
ABSTRACTAcinetobacter bacteria preferentially use gluconeogenic substrates instead of hexoses or pentoses. Accordingly, Acinetobacter schindleri ACE reaches a high growth rate on acetate but is unable to grow on glucose, xylose or arabinose. In this work, we compared the physiology of A. schindleri ACE and Escherichia coli JM101 growing on acetate as the carbon source. In contrast to JM101, ACE grew on acetate threefold faster, had a twofold higher biomass yield, and a 45% higher specific acetate consumption rate. Transcriptional analysis revealed that genes like ackA, pta, aceA, glcB, fumA, tktA and talA were overexpressed while acsA, sfcA, ppc and rpiA were underexpressed in ACE relative to JM101. This transcriptional profile together with carbon flux balance analysis indicated that ACE forms acetyl-CoA preferentially by the AckA-Pta (acetate kinase-phosphotransacetylase) pathway instead of Acs (acetyl-CoA synthetase) and that the glyoxylate shunt and tricarboxylic acid cycle are more active in ACE than in JM101. Moreover, in ACE, ribose 5-phosphate and erythrose 4-phosphate are formed from trioses, and NADPH is mainly produced by isocitrate dehydrogenase. This knowledge will contribute to an understanding of the carbon metabolism of Acinetobacter species of medical, biotechnological and microbiological relevance.
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Affiliation(s)
- Juan-Carlos Sigala
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Lucy Quiroz
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México 05348, México
| | - Eduardo Arteaga
- Posgrado en Ciencias Naturales e Ingeniería, Universidad Autónoma Metropolitana, Unidad Cuajimalpa, Ciudad de México 05348, México
| | - Roberto Olivares
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Alvaro R Lara
- Departamento de Procesos y Tecnología, Universidad Autónoma Metropolitana, Unidad Cuajimalpa. Av. Vasco de Quiroga 4871, Col. Santa Fe Cuajimalpa, Delegación Cuajimalpa, Ciudad de México 05348, México
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. Av. Universidad 2001, Col. Chamilpa, Cuernavaca, Mor. 62210, México
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Pinhal S, Ropers D, Geiselmann J, de Jong H. Acetate Metabolism and the Inhibition of Bacterial Growth by Acetate. J Bacteriol 2019; 201:e00147-19. [PMID: 30988035 PMCID: PMC6560135 DOI: 10.1128/jb.00147-19] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/26/2019] [Indexed: 11/24/2022] Open
Abstract
During aerobic growth on glucose, Escherichia coli excretes acetate, a mechanism called "overflow metabolism." At high concentrations, the secreted acetate inhibits growth. Several mechanisms have been proposed for explaining this phenomenon, but a thorough analysis is hampered by the diversity of experimental conditions and strains used in these studies. Here, we describe the construction of a set of isogenic strains that remove different parts of the metabolic network involved in acetate metabolism. Analysis of these strains reveals that (i) high concentrations of acetate in the medium inhibit growth without significantly perturbing central metabolism; (ii) growth inhibition persists even when acetate assimilation is completely blocked; and (iii) regulatory interactions mediated by acetyl-phosphate play a small but significant role in growth inhibition by acetate. The major contribution to growth inhibition by acetate may originate in systemic effects like the uncoupling effect of organic acids or the perturbation of the anion composition of the cell, as previously proposed. Our data suggest, however, that under the conditions considered here, the uncoupling effect plays only a limited role.IMPORTANCE High concentrations of organic acids such as acetate inhibit growth of Escherichia coli and other bacteria. This phenomenon is of interest for understanding bacterial physiology but is also of practical relevance. Growth inhibition by organic acids underlies food preservation and causes problems during high-density fermentation in biotechnology. What causes this phenomenon? Classical explanations invoke the uncoupling effect of acetate and the establishment of an anion imbalance. Here, we propose and investigate an alternative hypothesis: the perturbation of acetate metabolism due to the inflow of excess acetate. We find that this perturbation accounts for 20% of the growth-inhibitory effect through a modification of the acetyl phosphate concentration. Moreover, we argue that our observations are not expected based on uncoupling alone.
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Affiliation(s)
- Stéphane Pinhal
- Univ. Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, Grenoble, France
| | | | - Johannes Geiselmann
- Univ. Grenoble Alpes, CNRS, Laboratoire Interdisciplinaire de Physique, Grenoble, France
- Univ. Grenoble Alpes, Inria, Grenoble, France
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Chacón MG, Marriott A, Kendrick EG, Styles MQ, Leak DJ. Esterification of geraniol as a strategy for increasing product titre and specificity in engineered Escherichia coli. Microb Cell Fact 2019; 18:105. [PMID: 31176369 PMCID: PMC6556219 DOI: 10.1186/s12934-019-1130-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/30/2019] [Indexed: 12/27/2022] Open
Abstract
Background Geraniol, an acyclic monoterpene alcohol, is found as a primary constituent in the essential oils of plants such as geranium, lemongrass and rose. The floral-like scent of geraniol has made it a popular constituent of flavour and fragrance products. Over recent decades biotechnology has made significant progress towards the development of industrial platforms for the production of commercially valuable monoterpenoids, such as geraniol, through expression of recombinant terpene biosynthetic pathways in microbial hosts. Titres, however, have been hindered due to the inherent toxicity of these compounds—which are often utilised for anti-microbial and anti-fungal functions in their host plant. Results In this study we modified an Escherichia coli strain, engineered to express a heterologous mevalonate pathway, by replacement of the terpene synthase with a geraniol synthase from Ocimum basilicum for the production of geraniol, and co-expressed an alcohol acyltransferase (AAT) from Rosa hybrida for the specific acetylation of geraniol. The low water solubility of geranyl acetate facilitated its partition into the organic phase of a two-phase system, relieving the cellular toxicity attributed to the build-up of geraniol in the aqueous phase. In a partially optimised system this strain produced 4.8 g/L geranyl acetate (based on the aqueous volume) which, on a molar equivalent basis, represents the highest monoterpene titre achieved from microbial culture to date. It was also found that esterification of geraniol prevented bioconversion into other monoterpenoids, leading to a significant improvement in product specificity, with geranyl acetate being the sole product observed. Conclusion In this study we have shown that it is possible to both overcome the toxicity limit impeding the production of the monoterpene alcohol geraniol and mitigate product loss in culture through endogenous metabolism by using an in vivo esterification strategy. This strategy has resulted in the highest geraniol (equivalent) titres achieved from a microbial host, and presents esterification as a viable approach to increasing the titres obtained in microbial monoterpenoid production. Electronic supplementary material The online version of this article (10.1186/s12934-019-1130-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Micaela G Chacón
- Department of Biology and Biochemistry, University of Bath, Bath, England, BA2 7AY, UK
| | - Alice Marriott
- Department of Biology and Biochemistry, University of Bath, Bath, England, BA2 7AY, UK
| | - Emanuele G Kendrick
- Department of Biology and Biochemistry, University of Bath, Bath, England, BA2 7AY, UK
| | - Matthew Q Styles
- Department of Biology and Biochemistry, University of Bath, Bath, England, BA2 7AY, UK
| | - David J Leak
- Department of Biology and Biochemistry, University of Bath, Bath, England, BA2 7AY, UK.
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Kitamura S, Toya Y, Shimizu H. 13C-Metabolic Flux Analysis Reveals Effect of Phenol on Central Carbon Metabolism in Escherichia coli. Front Microbiol 2019; 10:1010. [PMID: 31134035 PMCID: PMC6514248 DOI: 10.3389/fmicb.2019.01010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/23/2019] [Indexed: 11/13/2022] Open
Abstract
Phenol is an important chemical product that can be used in a wide variety of applications, and it is currently produced from fossil resources. Fermentation production of phenol from renewable biomass resources by microorganisms is highly desirable for sustainable development. However, phenol toxicity hampers phenol production in industrial microorganisms such as Escherichia coli. In the present study, it was revealed that culturing E. coli in the presence of phenol not only decreased growth rate, but also biomass yield. This suggests that phenol affects the carbon flow of the metabolism, but the mechanism is unknown. To investigate the effect of phenol on the flux distribution of central carbon metabolism, 13C-metabolic flux analysis (13C-MFA) was performed on cells grown under different phenol concentrations (0, 0.1, and 0.15%). 13C-MFA revealed that the TCA cycle flux reduced by 25% increased acetate production from acetyl-CoA by 30% in the presence of 0.1% phenol. This trend of flux changes was emphasized at a phenol concentration of 0.15%. Although the expression level of citrate synthase, which catalyzes the first reaction of the TCA cycle, does not change regardless of phenol concentrations, the in vitro enzyme activity assay shows that the reaction was inhibited by phenol. These results suggest that the TCA cycle flux decreased due to phenol inhibition of citrate synthase; therefore, ATP could not be sufficiently produced by respiration, and growth rate decreased. Furthermore, since carbon was lost as acetate due to overflow metabolism, the biomass yield became low in the presence of phenol.
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Affiliation(s)
- Sayaka Kitamura
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Yoshihiro Toya
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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Mori M, Marinari E, De Martino A. A yield-cost tradeoff governs Escherichia coli's decision between fermentation and respiration in carbon-limited growth. NPJ Syst Biol Appl 2019; 5:16. [PMID: 31069113 PMCID: PMC6494807 DOI: 10.1038/s41540-019-0093-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/12/2019] [Indexed: 12/21/2022] Open
Abstract
Living cells react to changes in growth conditions by re-shaping their proteome. This accounts for different stress-response strategies, both specific (i.e., aimed at increasing the availability of stress-mitigating proteins) and systemic (such as large-scale changes in the use of metabolic pathways aimed at a more efficient exploitation of resources). Proteome re-allocation can, however, imply significant biosynthetic costs. Whether and how such costs impact the growth performance are largely open problems. Focusing on carbon-limited E. coli growth, we integrate genome-scale modeling and proteomic data to address these questions at quantitative level. After deriving a simple formula linking growth rate, carbon intake, and biosynthetic costs, we show that optimal growth results from the tradeoff between yield maximization and protein burden minimization. Empirical data confirm that E. coli growth is indeed close to Pareto-optimal over a broad range of growth rates. Moreover, we establish that, while most of the intaken carbon is diverted into biomass precursors, the efficiency of ATP synthesis is the key driver of the yield-cost tradeoff. These findings provide a quantitative perspective on carbon overflow, the origin of growth laws and the multidimensional optimality of E. coli metabolism.
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Affiliation(s)
- Matteo Mori
- Department of Physics, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Enzo Marinari
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, Rome, 00185 Italy
- INFN, Sezione di Roma 1, Piazzale Aldo Moro 2, Rome, 00185 Italy
| | - Andrea De Martino
- Soft & Living Matter Lab, Institute of Nanotechnology (CNR-NANOTEC), c/o Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, Rome, 00185 Italy
- Italian Institute for Genomic Medicine, via Nizza 52, Turin, 10126 Italy
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36
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Liu X. Hydrolysing the soluble protein secreted by Escherichia coli in trans-4-hydroxy-L-proline fermentation increased dissolve oxygen to promote high-level trans-4-hydroxy-L-proline production. Bioengineered 2019; 10:52-58. [PMID: 30955438 PMCID: PMC6527073 DOI: 10.1080/21655979.2019.1600966] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Trans-4-hydroxy-L-proline (Hyp) production by Escherichia coli (E. coli) in fermentation is a high-oxygen-demand process. E. coli secretes large amounts of soluble protein, especially in the anaphase of fermentation, which is an important factor leading to inadequate oxygen supply. And acetic acid that is the major by-product of Hyp production accumulates under low dissolved oxygen (DO). To increase DO and achieve high-level Hyp production, soluble protein was hydrolysed by adding protease in Hyp fermentation. The optimal protease, concentration, and addition time were trypsin, 0.2 g/L, and 18 h, respectively. With the addition of trypsin, the soluble protein in Hyp fermentation decreased by 43.5%. The DO could be maintained at 20–30% throughout fermentation. Hyp production and glucose conversion rate were 45.3 g/L and 18.1%, which were increases of 24.1% and 8.4%, respectively. The accumulation of acetic acid was decreased by 52.1%. The metabolic flux of Hyp was increased by 44.2% and the flux of acetate was decreased by 51.0%.
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Affiliation(s)
- Xiaocui Liu
- a School of Life Sciences of Shanxi Datong University , Datong Shanxi , China
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37
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Nitta K, Laviña WA, Pontrelli S, Liao JC, Putri SP, Fukusaki E. Metabolome analysis revealed the knockout of glyoxylate shunt as an effective strategy for improvement of 1-butanol production in transgenic Escherichia coli. J Biosci Bioeng 2019; 127:301-308. [DOI: 10.1016/j.jbiosc.2018.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 08/27/2018] [Accepted: 08/28/2018] [Indexed: 10/28/2022]
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Woolston BM, Emerson DF, Currie DH, Stephanopoulos G. Rediverting carbon flux in Clostridium ljungdahlii using CRISPR interference (CRISPRi). Metab Eng 2018; 48:243-253. [PMID: 29906505 DOI: 10.1016/j.ymben.2018.06.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 06/10/2018] [Indexed: 12/28/2022]
Abstract
Clostridium ljungdahlii has emerged as an attractive candidate for the bioconversion of synthesis gas (CO, CO2, H2) to a variety of fuels and chemicals through the Wood-Ljungdahl pathway. However, metabolic engineering and pathway elucidation in this microbe is limited by the lack of genetic tools to downregulate target genes. To overcome this obstacle, here we developed an inducible CRISPR interference (CRISPRi) system for C. ljungdahlii that enables efficient (> 94%) transcriptional repression of several target genes, both individually and in tandem. We then applied CRISPRi in a strain engineered for 3-hydroxybutyrate (3HB) production to examine targets for increasing carbon flux toward the desired product. Downregulating phosphotransacetylase (pta) with a single sgRNA led to a 97% decrease in enzyme activity and a 2.3-fold increase in titer during heterotrophic growth. However, acetate production still accounted for 40% of the carbon flux. Repression of aldehyde:ferredoxin oxidoreductase (aor2), another potential route for acetate production, led to a 5% reduction in acetate flux, whereas using an additional sgRNA targeted to pta reduced the enzyme activity to 0.7% of the wild-type level, and further reduced acetate production to 25% of the carbon flux with an accompanying increase in 3HB titer and yield. These results demonstrate the utility of CRISPRi for elucidating and controlling carbon flow in C. ljungdahlii.
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Affiliation(s)
- Benjamin M Woolston
- Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames Street, MIT 56-469 C, Cambridge, MA 02139, United States
| | - David F Emerson
- Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames Street, MIT 56-469 C, Cambridge, MA 02139, United States
| | - Devin H Currie
- Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames Street, MIT 56-469 C, Cambridge, MA 02139, United States
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, 25 Ames Street, MIT 56-469 C, Cambridge, MA 02139, United States.
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Sriram R, Sun J, Villanueva-Meyer J, Mutch C, De Los Santos J, Peters J, Korenchan DE, Neumann K, Van Criekinge M, Kurhanewicz J, Rosenberg O, Wilson D, Ohliger MA. Detection of Bacteria-Specific Metabolism Using Hyperpolarized [2- 13C]Pyruvate. ACS Infect Dis 2018; 4:797-805. [PMID: 29405697 DOI: 10.1021/acsinfecdis.7b00234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The differentiation of bacterial infection from other causes of inflammation is difficult in clinical practice and is critical where patient outcomes rely heavily on early interventions. In addition to physical exam and laboratory markers, several imaging modalities are frequently employed, but these techniques generally target the host immune response, rather than the living microorganisms themselves. Here, we describe a method to detect bacteria-specific metabolism using hyperpolarized (HP) 13C magnetic resonance spectroscopy. This technology allows visualization of the real-time conversion of enriched 13C substrates to their metabolic products, identified by their distinct chemical shifts. We have identified the rapid metabolism of HP [2-13C]pyruvate to [1-13C]acetate as a metabolic signature of common bacterial pathogens. We demonstrate this conversion in representative Gram-negative and Gram-positive bacteria, namely, Escherichia coli and Staphylococcus aureus, and its absence in key mammalian cell types. Furthermore, this conversion was successfully modulated in three mutant strains, corresponding to deletions of relevant enzymes.
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Affiliation(s)
- Renuka Sriram
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Jinny Sun
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Javier Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Christopher Mutch
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Justin De Los Santos
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Jason Peters
- Microbiology and Immunology, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, United States
| | - David E. Korenchan
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Kiel Neumann
- Department of Radiology, University of Virginia, 480 Ray C. Hunt Drive, Charlottesville, Virginia 22903, United States
| | - Mark Van Criekinge
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - John Kurhanewicz
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Oren Rosenberg
- Division of Infectious Diseases, School of Medicine, University of California, San Francisco, 505 Parnassus Avenue, San Francisco, California 94143, United States
| | - David Wilson
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
| | - Michael A. Ohliger
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, 1600 Fourth Street, Box 2520, San Francisco, California 94158, United States
- Zuckerberg San Francisco General Hospital, 1001 Potrero Avenue, San Francisco, California 94110, United States
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40
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Lim HG, Lee JH, Noh MH, Jung GY. Rediscovering Acetate Metabolism: Its Potential Sources and Utilization for Biobased Transformation into Value-Added Chemicals. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:3998-4006. [PMID: 29637770 DOI: 10.1021/acs.jafc.8b00458] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
One of the great advantages of microbial fermentation is the capacity to convert various carbon compounds into value-added chemicals. In this regard, there have been many efforts to engineer microorganisms to facilitate utilization of abundant carbon sources. Recently, the potential of acetate as a feedstock has been discovered; efforts have been made to produce various biochemicals from acetate based on understanding of its metabolism. In this review, we discuss the potential sources of acetate and summarized the recent progress to improve acetate utilization with microorganisms. Furthermore, we also describe representative studies that engineered microorganisms for the production of biochemicals from acetate.
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41
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Lu Q, Chen P, Addy M, Zhang R, Deng X, Ma Y, Cheng Y, Hussain F, Chen C, Liu Y, Ruan R. Carbon-dependent alleviation of ammonia toxicity for algae cultivation and associated mechanisms exploration. BIORESOURCE TECHNOLOGY 2018; 249:99-107. [PMID: 29040866 DOI: 10.1016/j.biortech.2017.09.175] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 09/24/2017] [Accepted: 09/25/2017] [Indexed: 06/07/2023]
Abstract
Ammonia toxicity in wastewater is one of the factors that limit the application of algae technology in wastewater treatment. This work explored the correlation between carbon sources and ammonia assimilation and applied a glucose-assisted nitrogen starvation method to alleviate ammonia toxicity. In this study, ammonia toxicity to Chlorella sp. was observed when NH3-N concentration reached 28.03mM in artificial wastewater. Addition of alpha-ketoglutarate in wastewater promoted ammonia assimilation, but low utilization efficiency and high cost of alpha-ketoglutarate limits its application in wastewater treatment. Comparison of three common carbon sources, glucose, citric acid, and sodium bicarbonate, indicates that in terms of ammonia assimilation, glucose is the best carbon source. Experimental results suggest that organic carbon with good ability of generating energy and hydride donor may be critical to ammonia assimilation. Nitrogen starvation treatment assisted by glucose increased ammonia removal efficiencies and algal viabilities.
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Affiliation(s)
- Qian Lu
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Paul Chen
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Min Addy
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Renchuan Zhang
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Xiangyuan Deng
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yiwei Ma
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yanling Cheng
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Fida Hussain
- Faculty of Science and Technology, Qurtuba University of Science and Technology, Peshawar, KP, Pakistan
| | - Chi Chen
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yuhuan Liu
- MOE Biomass Energy Research Center and State Key Laboratory of Food Science, Nanchang University, Nanchang 330000, China
| | - Roger Ruan
- Center for Biorefining, and Department of Bioproducts and Biosystems Engineering, University of Minnesota, Saint Paul, MN 55108, USA; Department of Food Science and Nutrition, University of Minnesota, Saint Paul, MN 55108, USA; MOE Biomass Energy Research Center and State Key Laboratory of Food Science, Nanchang University, Nanchang 330000, China.
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42
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Veeravalli K, Schindler T, Dong E, Yamada M, Hamilton R, Laird MW. Strain engineering to reduce acetate accumulation during microaerobic growth conditions inEscherichia coli. Biotechnol Prog 2017; 34:303-314. [DOI: 10.1002/btpr.2592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/16/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Karthik Veeravalli
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Tony Schindler
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Emily Dong
- Early Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Masaki Yamada
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Ryan Hamilton
- Late Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
| | - Michael W. Laird
- Early Stage Cell Culture, Genentech, Inc., 1 DNA Way; South San Francisco California 94080
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43
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Kim SK, Seong W, Han GH, Lee DH, Lee SG. CRISPR interference-guided multiplex repression of endogenous competing pathway genes for redirecting metabolic flux in Escherichia coli. Microb Cell Fact 2017; 16:188. [PMID: 29100516 PMCID: PMC5670510 DOI: 10.1186/s12934-017-0802-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/30/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Multiplex control of metabolic pathway genes is essential for maximizing product titers and conversion yields of fuels, chemicals, and pharmaceuticals in metabolic engineering. To achieve this goal, artificial transcriptional regulators, such as clustered regularly interspaced short palindromic repeats (CRISPR) interference (CRISPRi), have been developed to specifically repress genes of interest. RESULTS In this study, we deployed a tunable CRISPRi system for multiplex repression of competing pathway genes and, thus, directed carbon flux toward production of molecules of interest in Escherichia coli. The tunable CRISPRi system with an array of sgRNAs successfully repressed four endogenous genes (pta, frdA, ldhA, and adhE) individually and in double, triple, or quadruple combination that are involved in the formation of byproducts (acetate, succinate, lactate, and ethanol) and the consumption of NADH in E. coli. Single-target CRISPRi effectively reduced the amount of each byproduct and, interestingly, pta repression also decreased ethanol production (41%), whereas ldhA repression increased ethanol production (197%). CRISPRi-mediated multiplex repression of competing pathway genes also resulted in simultaneous reductions of acetate, succinate, lactate, and ethanol production in E. coli. Among 15 conditions repressing byproduct-formation genes, we chose the quadruple-target CRISPRi condition to produce n-butanol in E. coli as a case study. When heterologous n-butanol-pathway enzymes were introduced into E. coli simultaneously repressing the expression of the pta, frdA, ldhA, and adhE genes via CRISPRi, n-butanol yield and productivity increased up to 5.4- and 3.2-fold, respectively. CONCLUSIONS We demonstrated the tunable CRISPRi system to be a robust platform for multiplex modulation of endogenous gene expression that can be used to enhance biosynthetic pathway productivity, with n-butanol as the test case. CRISPRi applications potentially enable the development of microbial "smart cell" factories capable of producing other industrially valuable products.
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Affiliation(s)
- Seong Keun Kim
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Wonjae Seong
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Gui Hwan Han
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
| | - Dae-Hee Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Seung-Goo Lee
- Synthetic Biology and Bioengineering Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, 34141 Republic of Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
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44
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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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Gene modification of Escherichia coli and incorporation of process control to decrease acetate accumulation and increase ʟ-tryptophan production. ANN MICROBIOL 2017. [DOI: 10.1007/s13213-017-1289-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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46
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Thapa LP, Lee SJ, Park C, Kim SW. Production of L-lactic acid from metabolically engineered strain of Enterobacter aerogenes ATCC 29007. Enzyme Microb Technol 2017; 102:1-8. [DOI: 10.1016/j.enzmictec.2017.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 10/20/2022]
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Gene modification of the acetate biosynthesis pathway in Escherichia coli and implementation of the cell recycling technology to increase L-tryptophan production. PLoS One 2017. [PMID: 28622378 PMCID: PMC5473561 DOI: 10.1371/journal.pone.0179240] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The implementation of a novel cell recycling technology based on a special disk centrifuge during microbial fermentation process can continuously separate the product and harmful intermediates, while maintaining the cell viability owing to the installed cooling system. Acetate accumulation is an often encountered problem in L-tryptophan fermentation by Escherichia coli. To extend our previous studies, the current study deleted the key genes underlying acetate biosynthesis to improve l-tryptophan production. The deletion of the phosphotransacetylase (pta)-acetate kinase (ackA) pathway in a gltB (encoding glutamate synthase) mutant of E. coli TRTHB, led to the highest production of l-tryptophan (47.18 g/L) and glucose conversion rate (17.83%), with a marked reduction in acetate accumulation (1.22 g/L). This strain, TRTHBPA, was then used to investigate the effects of the cell recycling process on L-tryptophan fermentation. Four different strategies were developed concerning two issues, the volume ratio of the concentrated cell solution and clear solution and the cell recycling period. With strategy I (concentrated cell solution: clear solution, 1: 1; cell recycling within 24-30 h), L-tryptophan production and the glucose conversion rate increased to 55.12 g/L and 19.75%, respectively, 17.55% and 10.77% higher than those without the cell recycling. In addition, the biomass increased by 13.52% and the fermentation period was shortened from 40 h to 32 h. These results indicated that the cell recycling technology significantly improved L-tryptophan production by E. coli.
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Yaman S, Çalık P. Beet molasses-based feeding strategy enhances recombinant thermostable glucose isomerase production byEscherichia coliBL21 (DE3). Biotechnol Appl Biochem 2017; 64:944-954. [DOI: 10.1002/bab.1549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 12/02/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Sena Yaman
- Industrial Biotechnology and Metabolic Engineering Laboratory; Department of Chemical Engineering; Middle East Technical University; Ankara Turkey
- Department of Biotechnology; Graduate School of Natural and Applied Sciences; Middle East Technical University; Ankara Turkey
| | - Pınar Çalık
- Industrial Biotechnology and Metabolic Engineering Laboratory; Department of Chemical Engineering; Middle East Technical University; Ankara Turkey
- Department of Biotechnology; Graduate School of Natural and Applied Sciences; Middle East Technical University; Ankara Turkey
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Förster AH, Beblawy S, Golitsch F, Gescher J. Electrode-assisted acetoin production in a metabolically engineered Escherichia coli strain. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:65. [PMID: 28293295 PMCID: PMC5348906 DOI: 10.1186/s13068-017-0745-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Accepted: 02/28/2017] [Indexed: 05/31/2023]
Abstract
BACKGROUND This paper describes the metabolic engineering of Escherichia coli for the anaerobic fermentation of glucose to acetoin. Acetoin has well-established applications in industrial food production and was suggested to be a platform chemical for a bio-based economy. However, the biotechnological production is often hampered by the simultaneous formation of several end products in the absence of an electron acceptor. Moreover, typical production strains are often potentially pathogenic. The goal of this study was to overcome these limitations by establishing an electrode-assisted fermentation process in E. coli. Here, the surplus of electrons released in the production process is transferred to an electrode as anoxic and non-depletable electron acceptor. RESULTS In a first step, the central metabolism was steered towards the production of pyruvate from glucose by deletion of genes encoding for enzymes of central reactions of the anaerobic carbon metabolism (ΔfrdA-D ΔadhE ΔldhA Δpta-ack). Thereafter, the genes for the acetolactate synthase (alsS) and the acetolactate decarboxylase (alsD) were expressed in this strain from a plasmid. Addition of nitrate as electron acceptor led to an anaerobic acetoin production with a yield of up to 0.9 mol acetoin per mol of glucose consumed (90% of the theoretical maximum). In a second step, the electron acceptor nitrate was replaced by a carbon electrode. This interaction necessitated the further expression of c-type cytochromes from Shewanella oneidensis and the addition of the soluble redox shuttle methylene blue. The interaction with the non-depletable electron acceptor led to an acetoin formation with a yield of 79% of the theoretical maximum (0.79 mol acetoin per mol glucose). CONCLUSION Electrode-assisted fermentations are a new strategy to produce substances of biotechnological value that are more oxidized than the substrates. Here, we show for the first time a process in which the commonly used chassis strain E. coli was tailored for an electrode-assisted fermentation approach branching off from the central metabolite pyruvate. At this early stage, we see promising results regarding carbon and electron recovery and will use further strain development to increase the anaerobic metabolic turnover rate.
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Affiliation(s)
- Andreas H. Förster
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sebastian Beblawy
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Frederik Golitsch
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Johannes Gescher
- Department of Applied Biology, Institute for Applied Biosciences, Karlsruhe Institute of Technology, Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
- Department of Microbiology of Natural and Technical Interfaces, Institute of Functional Interfaces, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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50
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Enjalbert B, Millard P, Dinclaux M, Portais JC, Létisse F. Acetate fluxes in Escherichia coli are determined by the thermodynamic control of the Pta-AckA pathway. Sci Rep 2017; 7:42135. [PMID: 28186174 PMCID: PMC5301487 DOI: 10.1038/srep42135] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 12/28/2016] [Indexed: 12/30/2022] Open
Abstract
Escherichia coli excretes acetate upon growth on fermentable sugars, but the regulation of this production remains elusive. Acetate excretion on excess glucose is thought to be an irreversible process. However, dynamic 13C-metabolic flux analysis revealed a strong bidirectional exchange of acetate between E. coli and its environment. The Pta-AckA pathway was found to be central for both flux directions, while alternative routes (Acs or PoxB) play virtually no role in glucose consumption. Kinetic modelling of the Pta-AckA pathway predicted that its flux is thermodynamically controlled by the extracellular acetate concentration in vivo. Experimental validations confirmed that acetate production can be reduced and even reversed depending solely on its extracellular concentration. Consistently, the Pta-AckA pathway can rapidly switch from acetate production to consumption. Contrary to current knowledge, E. coli is thus able to co-consume glucose and acetate under glucose excess. These metabolic capabilities were confirmed on other glycolytic substrates which support the growth of E. coli in the gut. These findings highlight the dual role of the Pta-AckA pathway in acetate production and consumption during growth on glycolytic substrates, uncover a novel regulatory mechanism that controls its flux in vivo, and significantly expand the metabolic capabilities of E. coli.
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Affiliation(s)
- Brice Enjalbert
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Mickael Dinclaux
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | | | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
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