1
|
Liu W, Jiang H, Liu X, Zheng Y, Liu Y, Pan F, Yu F, Li Z, Gu M, Du Q, Li X, Zhang H, Han D. Altered intestinal microbiota enhances adenoid hypertrophy by disrupting the immune balance. Front Immunol 2023; 14:1277351. [PMID: 38090578 PMCID: PMC10715246 DOI: 10.3389/fimmu.2023.1277351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/06/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction Adenoid hypertrophy (AH) is a common upper respiratory disorder in children. Disturbances of gut microbiota have been implicated in AH. However, the interplay of alteration of gut microbiome and enlarged adenoids remains elusive. Methods 119 AH children and 100 healthy controls were recruited, and microbiome profiling of fecal samples in participants was performed using 16S rRNA gene sequencing. Fecal microbiome transplantation (FMT) was conducted to verify the effects of gut microbiota on immune response in mice. Results In AH individuals, only a slight decrease of diversity in bacterial community was found, while significant changes of microbial composition were observed between these two groups. Compared with HCs, decreased abundances of Akkermansia, Oscillospiraceae and Eubacterium coprostanoligenes genera and increased abundances of Bacteroides, Faecalibacterium, Ruminococcus gnavus genera were revealed in AH patients. The abundance of Bacteroides remained stable with age in AH children. Notably, a microbial marker panel of 8 OTUs were identified, which discriminated AH from HC individuals with an area under the curve (AUC) of 0.9851 in the discovery set, and verified in the geographically different validation set, achieving an AUC of 0.9782. Furthermore, transfer of mice with fecal microbiota from AH patients dramatically reduced the proportion of Treg subsets within peripheral blood and nasal-associated lymphoid tissue (NALT) and promoted the expansion of Th2 cells in NALT. Conclusion These findings highlight the effect of the altered gut microbiota in the AH pathogenesis.
Collapse
Affiliation(s)
- Wenxin Liu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Huier Jiang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiling Liu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai, China
| | - Yue Zheng
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yanan Liu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fen Pan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangyuan Yu
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Zhi Li
- Department of Pathology, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Meizhen Gu
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qingqing Du
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaoyan Li
- Department of Otolaryngology-Head and Neck Surgery, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dingding Han
- Department of Clinical Laboratory, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Institute of Pediatric Infection, Immunity, and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
- Medical School, Guangxi University, Nanning, China
| |
Collapse
|
2
|
Ding Q, Ye C. Microbial engineering for shikimate biosynthesis. Enzyme Microb Technol 2023; 170:110306. [PMID: 37598506 DOI: 10.1016/j.enzmictec.2023.110306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/22/2023]
Abstract
Shikimate, a precursor to the antiviral drug oseltamivir (Tamiflu®), can influence aromatic metabolites and finds extensive use in antimicrobial, antitumor, and cardiovascular applications. Consequently, various strategies have been developed for chemical synthesis and plant extraction to enhance shikimate biosynthesis, potentially impacting environmental conditions, economic sustainability, and separation and purification processes. Microbial engineering has been developed as an environmentally friendly approach for shikimate biosynthesis. In this review, we provide a comprehensive summary of microbial strategies for shikimate biosynthesis. These strategies primarily include chassis construction, biochemical optimization, pathway remodelling, and global regulation. Furthermore, we discuss future perspectives on shikimate biosynthesis and emphasize the importance of utilizing advanced metabolic engineering tools to regulate microbial networks for constructing robust microbial cell factories.
Collapse
Affiliation(s)
- Qiang Ding
- School of Life Sciences, Anhui University, Hefei 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China; Anhui Key Laboratory of Modern Biomanufacturing, Hefei 230601, Anhui, China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| |
Collapse
|
3
|
Bo T, Wu C, Wang Z, Jiang H, Wang F, Chen N, Li Y. Multiple Metabolic Engineering Strategies to Improve Shikimate Titer in Escherichia coli. Metabolites 2023; 13:747. [PMID: 37367905 DOI: 10.3390/metabo13060747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/28/2023] Open
Abstract
Shikimate is a valuable chiral precursor for synthesizing oseltamivir (Tamiflu®) and other chemicals. High production of shikimate via microbial fermentation has attracted increasing attention to overcome the unstable and expensive supply of shikimate extracted from plant resources. The current cost of microbial production of shikimate via engineered strains is still unsatisfactory, and thus more metabolic strategies need to be investigated to further increase the production efficiency. In this study, we first constructed a shikimate E. coli producer through the application of the non-phosphoenolpyruvate: carbohydrate phosphotransferase system (non-PTS) glucose uptake pathway, the attenuation of the shikimate degradation metabolism, and the introduction of a mutant of feedback-resistant 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase. Inspired by the natural presence of bifunctional 3-dehydroquinate dehydratase (DHD)-shikimate dehydrogenase (SDH) enzyme in plants, we then designed an artificial fusion protein of DHD-SDH to decrease the accumulation of the byproduct 3-dehydroshikimate (DHS). Subsequently, a repressed shikimate kinase (SK) mutant was selected to promote shikimate accumulation without the supplementation of expensive aromatic substances. Furthermore, EsaR-based quorum sensing (QS) circuits were employed to regulate the metabolic flux distribution between cell growth and product synthesis. The final engineered strain dSA10 produced 60.31 g/L shikimate with a yield of 0.30 g/g glucose in a 5 L bioreactor.
Collapse
Affiliation(s)
- Taidong Bo
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Chen Wu
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Zeting Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Hao Jiang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Feiao Wang
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Ning Chen
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| | - Yanjun Li
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China
- Key Laboratory of Industrial Fermentation Microbiology, Ministry of Education, Tianjin University of Science and Technology, Tianjin 300457, China
- National and Local United Engineering Lab of Metabolic Control Fermentation Technology, Tianjin University of Science and Technology, Tianjin 300457, China
| |
Collapse
|
4
|
Sheng Q, Yi L, Zhong B, Wu X, Liu L, Zhang B. Shikimic acid biosynthesis in microorganisms: Current status and future direction. Biotechnol Adv 2023; 62:108073. [PMID: 36464143 DOI: 10.1016/j.biotechadv.2022.108073] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/03/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
Shikimic acid (SA), a hydroaromatic natural product, is used as a chiral precursor for organic synthesis of oseltamivir (Tamiflu®, an antiviral drug). The process of microbial production of SA has recently undergone vigorous development. Particularly, the sustainable construction of recombinant Corynebacterium glutamicum (141.2 g/L) and Escherichia coli (87 g/L) laid a solid foundation for the microbial fermentation production of SA. However, its industrial application is restricted by limitations such as the lack of fermentation tests for industrial-scale and the requirement of growth-limiting factors, antibiotics, and inducers. Therefore, the development of SA biosensors and dynamic molecular switches, as well as genetic modification strategies and optimization of the fermentation process based on omics technology could improve the performance of SA-producing strains. In this review, recent advances in the development of SA-producing strains, including genetic modification strategies, metabolic pathway construction, and biosensor-assisted evolution, are discussed and critically reviewed. Finally, future challenges and perspectives for further reinforcing the development of robust SA-producing strains are predicted, providing theoretical guidance for the industrial production of SA.
Collapse
Affiliation(s)
- Qi Sheng
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Lingxin Yi
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bin Zhong
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xiaoyu Wu
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China.
| | - Bin Zhang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Nanchang 330045, China; Jiangxi Engineering Laboratory for the Development and Utilization of Agricultural Microbial Resources, Jiangxi Agricultural University, Nanchang 330045, China.
| |
Collapse
|
5
|
Volk MJ, Tran VG, Tan SI, Mishra S, Fatma Z, Boob A, Li H, Xue P, Martin TA, Zhao H. Metabolic Engineering: Methodologies and Applications. Chem Rev 2022; 123:5521-5570. [PMID: 36584306 DOI: 10.1021/acs.chemrev.2c00403] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Metabolic engineering aims to improve the production of economically valuable molecules through the genetic manipulation of microbial metabolism. While the discipline is a little over 30 years old, advancements in metabolic engineering have given way to industrial-level molecule production benefitting multiple industries such as chemical, agriculture, food, pharmaceutical, and energy industries. This review describes the design, build, test, and learn steps necessary for leading a successful metabolic engineering campaign. Moreover, we highlight major applications of metabolic engineering, including synthesizing chemicals and fuels, broadening substrate utilization, and improving host robustness with a focus on specific case studies. Finally, we conclude with a discussion on perspectives and future challenges related to metabolic engineering.
Collapse
Affiliation(s)
- Michael J Volk
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Vinh G Tran
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Shih-I Tan
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Shekhar Mishra
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zia Fatma
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aashutosh Boob
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Hongxiang Li
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Teresa A Martin
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
6
|
Metabolic Engineering of Shikimic Acid Biosynthesis Pathway for the Production of Shikimic Acid and Its Branched Products in Microorganisms: Advances and Prospects. Molecules 2022; 27:molecules27154779. [PMID: 35897952 PMCID: PMC9332510 DOI: 10.3390/molecules27154779] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/10/2022] [Accepted: 07/12/2022] [Indexed: 02/06/2023] Open
Abstract
The shikimate pathway is a necessary pathway for the synthesis of aromatic compounds. The intermediate products of the shikimate pathway and its branching pathway have promising properties in many fields, especially in the pharmaceutical industry. Many important compounds, such as shikimic acid, quinic acid, chlorogenic acid, gallic acid, pyrogallol, catechol and so on, can be synthesized by the shikimate pathway. Among them, shikimic acid is the key raw material for the synthesis of GS4104 (Tamiflu®), an inhibitor of neuraminidase against avian influenza virus. Quininic acid is an important intermediate for synthesis of a variety of raw chemical materials and drugs. Gallic acid and catechol receive widespread attention as pharmaceutical intermediates. It is one of the hotspots to accumulate many kinds of target products by rationally modifying the shikimate pathway and its branches in recombinant strains by means of metabolic engineering. This review considers the effects of classical metabolic engineering methods, such as central carbon metabolism (CCM) pathway modification, key enzyme gene modification, blocking the downstream pathway on the shikimate pathway, as well as several expansion pathways and metabolic engineering strategies of the shikimate pathway, and expounds the synthetic biology in recent years in the application of the shikimate pathway and the future development direction.
Collapse
|
7
|
Slagman S, Fessner WD. Biocatalytic routes to anti-viral agents and their synthetic intermediates. Chem Soc Rev 2021; 50:1968-2009. [DOI: 10.1039/d0cs00763c] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
An assessment of biocatalytic strategies for the synthesis of anti-viral agents, offering guidelines for the development of sustainable production methods for a future COVID-19 remedy.
Collapse
Affiliation(s)
- Sjoerd Slagman
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| | - Wolf-Dieter Fessner
- Institut für Organische Chemie und Biochemie
- Technische Universität Darmstadt
- Germany
| |
Collapse
|
8
|
Evolution of an Escherichia coli PTS - strain: a study of reproducibility and dynamics of an adaptive evolutive process. Appl Microbiol Biotechnol 2020; 104:9309-9325. [PMID: 32954454 DOI: 10.1007/s00253-020-10885-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 08/12/2020] [Accepted: 09/04/2020] [Indexed: 10/23/2022]
Abstract
Adaptive laboratory evolution (ALE) has been used to study and solve pressing questions about evolution, especially for the study of the development of mutations that confer increased fitness during evolutionary processes. In this contribution, we investigated how the evolutionary process conducted with the PTS- mutant of Escherichia coli PB11 in three parallel batch cultures allowed the restoration of rapid growth with glucose as the carbon source. The significant findings showed that genomic sequence analysis of a set of newly evolved mutants isolated from ALE experiments 2-3 developed some essential mutations, which efficiently improved the fast-growing phenotypes throughout different fitness landscapes. Regulator galR was the target of several mutations such as SNPs, partial and total deletions, and insertion of an IS1 element and thus indicated the relevance of a null mutation of this gene in the adaptation of the evolving population of PB11 during the parallel ALE experiments. These mutations resulted in the selection of MglB and GalP as the primary glucose transporters by the evolving population, but further selection of at least a second adaptive mutation was also necessary. We found that mutations in the yfeO, rppH, and rng genes improved the fitness advantage of evolving PTS- mutants and resulted in amplification of leaky activity in Glk for glucose phosphorylation and upregulation of glycolytic and other growth-related genes. Notably, we determined that these mutations appeared and were fixed in the evolving populations between 48 and 72 h of cultivation, which resulted in the selection of fast-growing mutants during one ALE experiments in batch cultures of 80 h duration.Key points• ALE experiments selected evolved mutants through different fitness landscapes in which galR was the target of different mutations: SNPs, deletions, and insertion of IS.• Key mutations in evolving mutants appeared and fixed at 48-72 h of cultivation.• ALE experiments led to increased understanding of the genetics of cellular adaptation to carbon source limitation.
Collapse
|
9
|
Braga A, Faria N. Bioprocess Optimization for the Production of Aromatic Compounds With Metabolically Engineered Hosts: Recent Developments and Future Challenges. Front Bioeng Biotechnol 2020; 8:96. [PMID: 32154231 PMCID: PMC7044121 DOI: 10.3389/fbioe.2020.00096] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/03/2020] [Indexed: 12/18/2022] Open
Abstract
The most common route to produce aromatic chemicals - organic compounds containing at least one benzene ring in their structure - is chemical synthesis. These processes, usually starting from an extracted fossil oil molecule such as benzene, toluene, or xylene, are highly environmentally unfriendly due to the use of non-renewable raw materials, high energy consumption and the usual production of toxic by-products. An alternative way to produce aromatic compounds is extraction from plants. These extractions typically have a low yield and a high purification cost. This motivates the search for alternative platforms to produce aromatic compounds through low-cost and environmentally friendly processes. Microorganisms are able to synthesize aromatic amino acids through the shikimate pathway. The construction of microbial cell factories able to produce the desired molecule from renewable feedstock becomes a promising alternative. This review article focuses on the recent advances in microbial production of aromatic products, with a special emphasis on metabolic engineering strategies, as well as bioprocess optimization. The recent combination of these two techniques has resulted in the development of several alternative processes to produce phenylpropanoids, aromatic alcohols, phenolic aldehydes, and others. Chemical species that were unavailable for human consumption due to the high cost and/or high environmental impact of their production, have now become accessible.
Collapse
Affiliation(s)
- Adelaide Braga
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | | |
Collapse
|
10
|
Zhu L, Fang Y, Ding Z, Zhang S, Wang X. Developing an l-threonine-producing strain from wild-type Escherichia coli by modifying the glucose uptake, glyoxylate shunt, and l-threonine biosynthetic pathway. Biotechnol Appl Biochem 2019; 66:962-976. [PMID: 31486127 DOI: 10.1002/bab.1813] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022]
Abstract
Wild-type Escherichia coli MG1655 usually does not accumulate l-threonine. In this study, the effects of 13 genes related to the glucose uptake, glycolysis, TCA cycle, l-threonine biosynthesis, or their regulation on l-threonine accumulation in E. coli MG1655 were investigated. Sixteen E. coli mutant strains were constructed by chromosomal deletion or overexpression of one or more genes of rsd, ptsG, ptsH, ptsI, crr, galP, glk, iclR, and gltA; the plasmid pFW01-thrA*BC-rhtC harboring the key genes for l-threonine biosynthesis and secretion was introduced into these mutants. The analyses on cell growth, glucose consumption, and l-threonine production of these recombinant strains showed that most of these strains could accumulate l-threonine, and the highest yield was obtained in WMZ016/pFW01-thrA*BC-rhtC. WMZ016 was derived from MG1655 by deleting crr and iclR and enhancing the expression of gltA. WMZ016/pFW01-thrA*BC-rhtC could produce 17.98 g/L l-threonine with a yield of 0.346 g/g glucose, whereas the control strain MG1655/pFW01-thrA*BC-rhtC could only produce 0.68 g/L l-threonine. In addition, WMZ016/pFW01-thrA*BC-rhtC could tolerate the high concentration of glucose and produced no detectable by-products; therefore, it should be an ideal platform strain for further development. The results indicate that manipulating the glucose uptake and TCA cycle could efficiently increase l-threonine production in E. coli.
Collapse
Affiliation(s)
- Lifei Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Yu Fang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhixiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Shuyan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| |
Collapse
|
11
|
Wu F, Cai D, Li L, Li Y, Yang H, Li J, Ma X, Chen S. Modular metabolic engineering of lysine supply for enhanced production of bacitracin in Bacillus licheniformis. Appl Microbiol Biotechnol 2019; 103:8799-8812. [DOI: 10.1007/s00253-019-10110-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/12/2019] [Accepted: 08/28/2019] [Indexed: 02/06/2023]
|
12
|
Unraveling the specific regulation of the shikimate pathway for tyrosine accumulation in Bacillus licheniformis. ACTA ACUST UNITED AC 2019; 46:1047-1059. [DOI: 10.1007/s10295-019-02213-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 07/04/2019] [Indexed: 12/24/2022]
Abstract
Abstract
l-Tyrosine serves as a common precursor for multiple valuable secondary metabolites. Synthesis of this aromatic amino acid in Bacillus licheniformis occurs via the shikimate pathway, but the underlying mechanisms involving metabolic regulation remain unclear. In this work, improved l-tyrosine accumulation was achieved in B. licheniformis via co-overexpression of aroGfbr and tyrAfbr from Escherichia coli to yield strain 45A12, and the l-tyrosine titer increased to 1005 mg/L with controlled glucose feeding. Quantitative RT-PCR results indicated that aroA, encoding DAHP synthase, and aroK, encoding shikimate kinase, were feedback-repressed by the end product l-tyrosine in the modified strain. Therefore, the native aroK was first expressed with multiple copies to yield strain 45A13, which could accumulate 1201 mg/L l-tyrosine. Compared with strain 45A12, the expression of aroB and aroF in strain 45A13 was upregulated by 21% and 27%, respectively, which may also have resulted in the improvement of l-tyrosine production. Furthermore, supplementation with 5 g/L shikimate enhanced the l-tyrosine titers of 45A12 and 45A13 by 29.1% and 24.0%, respectively. However, the yield of l-tyrosine per unit of shikimate decreased from 0.365 to 0.198 mol/mol after aroK overexpression in strain 45A12, which suggested that the gene product was also involved in uncharacterized pathways. This study provides a good starting point for further modification to achieve industrial-scale production of l-tyrosine using B. licheniformis, a generally recognized as safe workhorse.
Collapse
|
13
|
|
14
|
Fordjour E, Adipah FK, Zhou S, Du G, Zhou J. Metabolic engineering of Escherichia coli BL21 (DE3) for de novo production of L-DOPA from D-glucose. Microb Cell Fact 2019; 18:74. [PMID: 31023316 PMCID: PMC6482505 DOI: 10.1186/s12934-019-1122-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 04/16/2019] [Indexed: 12/31/2022] Open
Abstract
Background Production of l-tyrosine is gaining grounds as the market size of 3,4-dihydroxyphenyl-l-alanine (l-DOPA) is expected to increase due to increasing cases of Parkinson’s disease a neurodegenerative disease. Attempts to overproduce l-tyrosine for conversion to l-DOPA has stemmed on the overexpressing of critical pathway enzymes, an introduction of feedback-resistant enzymes, and deregulation of transcriptional regulators. Results An E. coli BL21 (DE3) was engineered by deleting tyrR, ptsG, crr, pheA and pykF while directing carbon flow through the overexpressing of galP and glk. TktA and PpsA were also overexpressed to enhance the accumulation of E4P and PEP. Directed evolution was then applied on HpaB to optimize its activity. Three mutants, G883R, G883A, L1231M, were identified to have improved activity as compared to the wild-type hpaB showing a 3.03-, 2.9- and 2.56-fold increase in l-DOPA production respectively. The use of strain LP-8 resulted in the production of 691.24 mg/L and 25.53 g/L of l-DOPA in shake flask and 5 L bioreactor, respectively. Conclusion Deletion of key enzymes to channel flux towards the shikimate pathway coupled with the overexpression of pathway enzymes enhanced the availability of l-tyrosine for L-DOPA production. Enhancing the activity of HpaB increased l-DOPA production from glucose and glycerol. This work demonstrates that increasing the availability of l-tyrosine and enhancing enzyme activity ensures maximum l-DOPA productivity. Electronic supplementary material The online version of this article (10.1186/s12934-019-1122-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Eric Fordjour
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Frederick Komla Adipah
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Shenghu Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China
| | - Guocheng Du
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, China.
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China. .,Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, Jiangsu, China.
| |
Collapse
|
15
|
Liu X, Niu H, Li Q, Gu P. Metabolic engineering for the production of l-phenylalanine in Escherichia coli. 3 Biotech 2019; 9:85. [PMID: 30800596 DOI: 10.1007/s13205-019-1619-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Accepted: 02/08/2019] [Indexed: 10/27/2022] Open
Abstract
As one of the three proteinogenic aromatic amino acids, l-phenylalanine is widely applied in the food, chemical and pharmaceutical industries, especially in production of the low-calorie sweetener aspartame. Microbial production of l-phenylalanine has become attractive as it possesses the advantages of environmental friendliness, low cost, and feedstock renewability. With the progress of metabolic engineering, systems biology and synthetic biology, production of l-phenylalanine from glucose in Escherichia coli with relatively high titer has been achieved by improving the intracellular levels of precursors, alleviating transcriptional repression and feedback inhibition of key enzymes, increasing the export of l-phenylalanine, engineering of global regulators, and overexpression of rate-limiting enzymes. In this review, successful metabolic engineering strategies for increasing l-phenylalanine accumulation from glucose in E. coli are described. In addition, perspectives for further improvement of production of l-phenylalanine are discussed.
Collapse
|
16
|
Metabolic engineering for improving l-tryptophan production in Escherichia coli. ACTA ACUST UNITED AC 2019; 46:55-65. [DOI: 10.1007/s10295-018-2106-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 11/03/2018] [Indexed: 11/26/2022]
Abstract
Abstract
l-Tryptophan is an important aromatic amino acid that is used widely in the food, chemical, and pharmaceutical industries. Compared with the traditional synthetic methods, production of l-tryptophan by microbes is environmentally friendly and has low production costs, and feed stocks are renewable. With the development of metabolic engineering, highly efficient production of l-tryptophan in Escherichia coli has been achieved by eliminating negative regulation factors, improving the intracellular level of precursors, engineering of transport systems and overexpression of rate-limiting enzymes. However, challenges remain for l-tryptophan biosynthesis to be cost-competitive. In this review, successful and applicable strategies derived from metabolic engineering for increasing l-tryptophan accumulation in E. coli are summarized. In addition, perspectives for further efficient production of l-tryptophan are discussed.
Collapse
|
17
|
Kshirsagr PR, Pai SR, Hegde HV. Comparison of Shikimic Acid Content: A Precursor for Drug Against H5N1 from Various Plant Species of Western Ghats, India. NATIONAL ACADEMY SCIENCE LETTERS 2018. [DOI: 10.1007/s40009-018-0687-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
18
|
Candeias NR, Assoah B, Simeonov SP. Production and Synthetic Modifications of Shikimic Acid. Chem Rev 2018; 118:10458-10550. [PMID: 30350584 DOI: 10.1021/acs.chemrev.8b00350] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Shikimic acid is a natural product of industrial importance utilized as a precursor of the antiviral Tamiflu. It is nowadays produced in multihundred ton amounts from the extraction of star anise ( Illicium verum) or by fermentation processes. Apart from the production of Tamiflu, shikimic acid has gathered particular notoriety as its useful carbon backbone and inherent chirality provide extensive use as a versatile chiral precursor in organic synthesis. This review provides an overview of the main synthetic and microbial methods for production of shikimic acid and highlights selected methods for isolation from available plant sources. Furthermore, we have attempted to demonstrate the synthetic utility of shikimic acid by covering the most important synthetic modifications and related applications, namely, synthesis of Tamiflu and derivatives, synthetic manipulations of the main functional groups, and its use as biorenewable material and in total synthesis. Given its rich chemistry and availability, shikimic acid is undoubtedly a promising platform molecule for further exploration. Therefore, in the end, we outline some challenges and promising future directions.
Collapse
Affiliation(s)
- Nuno R Candeias
- Laboratory of Chemistry and Bioengineering , Tampere University of Technology , Korkeakoulunkatu 8 , 33101 Tampere , Finland
| | - Benedicta Assoah
- Laboratory of Chemistry and Bioengineering , Tampere University of Technology , Korkeakoulunkatu 8 , 33101 Tampere , Finland
| | - Svilen P Simeonov
- Laboratory Organic Synthesis and Stereochemistry, Institute of Organic Chemistry with Centre of Phytochemistry , Bulgarian Academy of Sciences , Acad. G. Bontchev str. Bl. 9 , 1113 Sofia , Bulgaria
| |
Collapse
|
19
|
Bilal M, Wang S, Iqbal HMN, Zhao Y, Hu H, Wang W, Zhang X. Metabolic engineering strategies for enhanced shikimate biosynthesis: current scenario and future developments. Appl Microbiol Biotechnol 2018; 102:7759-7773. [PMID: 30014168 DOI: 10.1007/s00253-018-9222-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 07/03/2018] [Accepted: 07/04/2018] [Indexed: 02/08/2023]
Abstract
Shikimic acid is an important intermediate for the manufacture of the antiviral drug oseltamivir (Tamiflu®) and many other pharmaceutical compounds. Much of its existing supply is obtained from the seeds of Chinese star anise (Illicium verum). Nevertheless, plants cannot supply a stable source of affordable shikimate along with laborious and cost-expensive extraction and purification process. Microbial biosynthesis of shikimate through metabolic engineering and synthetic biology approaches represents a sustainable, cost-efficient, and environmentally friendly route than plant-based methods. Metabolic engineering allows elevated shikimate production titer by inactivating the competing pathways, increasing intracellular level of key precursors, and overexpressing rate-limiting enzymes. The development of synthetic and systems biology-based novel technologies have revealed a new roadmap for the construction of high shikimate-producing strains. This review elaborates the enhanced biosynthesis of shikimate by utilizing an array of traditional metabolic engineering along with novel advanced technologies. The first part of the review is focused on the mechanistic pathway for shikimate production, use of recombinant and engineered strains, improving metabolic flux through the shikimate pathway, chemically inducible chromosomal evolution, and bioprocess engineering strategies. The second part discusses a variety of industrially pertinent compounds derived from shikimate with special reference to aromatic amino acids and phenazine compound, and main engineering strategies for their production in diverse bacterial strains. Towards the end, the work is wrapped up with concluding remarks and future considerations.
Collapse
Affiliation(s)
- Muhammad Bilal
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Songwei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, CP 64849, Monterrey, NL, Mexico
| | - Yuping Zhao
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
- National Experimental Teaching Center for Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
20
|
Recent advances in metabolic engineering of Corynebacterium glutamicum for bioproduction of value-added aromatic chemicals and natural products. Appl Microbiol Biotechnol 2018; 102:8685-8705. [DOI: 10.1007/s00253-018-9289-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/06/2023]
|
21
|
Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System. Metab Eng 2018; 48:233-242. [DOI: 10.1016/j.ymben.2018.06.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 11/20/2022]
|
22
|
Zuo S, Xiao J, Zhang Y, Zhang X, Nomura CT, Chen S, Wang Q. Rational design and medium optimization for shikimate production in recombinant Bacillus licheniformis strains. Process Biochem 2018. [DOI: 10.1016/j.procbio.2017.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
23
|
Liu C, Zhang B, Liu YM, Yang KQ, Liu SJ. New Intracellular Shikimic Acid Biosensor for Monitoring Shikimate Synthesis in Corynebacterium glutamicum. ACS Synth Biol 2018; 7:591-601. [PMID: 29087704 DOI: 10.1021/acssynbio.7b00339] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The quantitative monitoring of intracellular metabolites with in vivo biosensors provides an efficient means of identifying high-yield strains and observing product accumulation in real time. In this study, a shikimic acid (SA) biosensor was constructed from a LysR-type transcriptional regulator (ShiR) of Corynebacterium glutamicum. The SA biosensor specifically responded to the increase of intracellular SA concentration over a linear range of 19.5 ± 3.6 to 120.9 ± 1.2 fmole at the single-cell level. This new SA biosensor was successfully used to (1) monitor the SA production of different C. glutamicum strains; (2) develop a novel result-oriented high-throughput ribosome binding site screening and sorting strategy that was used for engineering high-yield shikimate-producing strains; and (3) engineer a whole-cell biosensor through the coexpression of the SA sensor and a shikimate transporter shiA gene in C. glutamicum RES167. This work demonstrated that a new intracellular SA biosensor is a valuable tool facilitating the fast development of microbial SA producer.
Collapse
Affiliation(s)
- Chang Liu
- State Key Laboratory
of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, West Beichen Road No.1, 100101 Beijing, PR China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049 Beijing, PR China
| | - Bo Zhang
- State Key Laboratory
of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, West Beichen Road No.1, 100101 Beijing, PR China
- Zhejiang University of Technology, 310014 Hangzhou, PR China
| | - Yi-Ming Liu
- State Key Laboratory
of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, West Beichen Road No.1, 100101 Beijing, PR China
| | - Ke-Qian Yang
- State Key Laboratory
of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, West Beichen Road No.1, 100101 Beijing, PR China
| | - Shuang-Jiang Liu
- State Key Laboratory
of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, West Beichen Road No.1, 100101 Beijing, PR China
| |
Collapse
|
24
|
Liu Y, Xu Y, Ding D, Wen J, Zhu B, Zhang D. Genetic engineering of Escherichia coli to improve L-phenylalanine production. BMC Biotechnol 2018; 18:5. [PMID: 29382315 PMCID: PMC5791370 DOI: 10.1186/s12896-018-0418-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 01/18/2018] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND L-phenylalanine (L-Phe) is an essential amino acid for mammals and applications expand into human health and nutritional products. In this study, a system level engineering was conducted to enhance L-Phe biosynthesis in Escherichia coli. RESULTS We inactivated the PTS system and recruited glucose uptake via combinatorial modulation of galP and glk to increase PEP supply in the Xllp01 strain. In addition, the HTH domain of the transcription factor TyrR was engineered to decrease the repression on the transcriptional levels of L-Phe pathway enzymes. Finally, proteomics analysis demonstrated the third step of the SHIK pathway (catalyzed via AroD) as the rate-limiting step for L-Phe production. After optimization of the aroD promoter strength, the titer of L-Phe increased by 13.3%. Analysis of the transcriptional level of genes involved in the central metabolic pathways and L-Phe biosynthesis via RT-PCR showed that the recombinant L-Phe producer exhibited a great capability in the glucose utilization and precursor (PEP and E4P) generation. Via systems level engineering, the L-Phe titer of Xllp21 strain reached 72.9 g/L in a 5 L fermenter under the non-optimized fermentation conditions, which was 1.62-times that of the original strain Xllp01. CONCLUSION The metabolic engineering strategy reported here can be broadly employed for developing genetically defined organisms for the efficient production of other aromatic amino acids and derived compounds.
Collapse
Affiliation(s)
- Yongfei Liu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Yiran Xu
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China.,Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Dongqin Ding
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China
| | - Jianping Wen
- Department of Biological Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Beiwei Zhu
- School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, People's Republic of China
| | - Dawei Zhang
- Tianjin Institutes of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, People's Republic of China. .,School of Food Science and Technology, National Engineering Research Center of Seafood, Dalian Polytechnic University, Dalian, 116034, People's Republic of China.
| |
Collapse
|
25
|
Novel technologies combined with traditional metabolic engineering strategies facilitate the construction of shikimate-producing Escherichia coli. Microb Cell Fact 2017; 16:167. [PMID: 28962609 PMCID: PMC5622527 DOI: 10.1186/s12934-017-0773-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/14/2017] [Indexed: 11/10/2022] Open
Abstract
Shikimate is an important intermediate in the aromatic amino acid pathway, which can be used as a promising building block for the synthesis of biological compounds, such as neuraminidase inhibitor Oseltamivir (Tamiflu®). Compared with traditional methods, microbial production of shikimate has the advantages of environmental friendliness, low cost, feed stock renewability, and product selectivity and diversity, thus receiving more and more attentions. The development of metabolic engineering allows for high-efficiency production of shikimate of Escherichia coli by improving the intracellular level of precursors, blocking downstream pathway, releasing negative regulation factors, and overexpressing rate-limiting enzymes. In addition, novel technologies derived from systems and synthetic biology have opened a new avenue towards construction of shikimate-producing strains. This review summarized successful and applicable strategies derived from traditional metabolic engineering and novel technologies for increasing accumulation of shikimate in E. coli.
Collapse
|
26
|
Liu L, Chen S, Wu J. Phosphoenolpyruvate:glucose phosphotransferase system modification increases the conversion rate during L-tryptophan production in Escherichia coli. J Ind Microbiol Biotechnol 2017; 44:1385-1395. [PMID: 28726163 DOI: 10.1007/s10295-017-1959-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/09/2017] [Indexed: 11/27/2022]
Abstract
Escherichia coli FB-04(pta1), a recombinant L-tryptophan production strain, was constructed in our laboratory. However, the conversion rate (L-tryptophan yield per glucose) of this strain is somewhat low. In this study, additional genes have been deleted in an effort to increase the conversion rate of E. coli FB-04(pta1). Initially, the pykF gene, which encodes pyruvate kinase I (PYKI), was inactivated to increase the accumulation of phosphoenolpyruvate, a key L-tryptophan precursor. The resulting strain, E. coli FB-04(pta1)ΔpykF, showed a slightly higher L-tryptophan yield and a higher conversion rate in fermentation processes. To further improve the conversion rate, the phosphoenolpyruvate:glucose phosphotransferase system (PTS) was disrupted by deleting the ptsH gene, which encodes the phosphocarrier protein (HPr). The levels of biomass, L-tryptophan yield, and conversion rate of this strain, E. coli FB-04(pta1)ΔpykF/ptsH, were especially low during fed-batch fermentation process, even though it achieved a significant increase in conversion rate during shake-flask fermentation. To resolve this issue, four HPr mutations (N12S, N12A, S46A, and S46N) were introduced into the genomic background of E. coli FB-04(pta1)ΔpykF/ptsH, respectively. Among them, the strain harboring the N12S mutation (E. coli FB-04(pta1)ΔpykF-ptsHN12S) showed a prominently increased conversion rate of 0.178 g g-1 during fed-batch fermentation; an increase of 38.0% compared with parent strain E. coli FB-04(pta1). Thus, mutation of the genomic of ptsH gene provided an alternative method to weaken the PTS and improve the efficiency of carbon source utilization.
Collapse
Affiliation(s)
- Lina Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Sheng Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.,School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China
| | - Jing Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China. .,School of Biotechnology and Key Laboratory of Industrial Biotechnology Ministry of Education, Jiangnan University, 1800 Lihu Avenue, Wuxi, 214122, China.
| |
Collapse
|
27
|
Zhang X, Lai L, Xu G, Zhang X, Shi J, Xu Z. Effects of pyruvate kinase on the growth of Corynebacterium glutamicum and L-serine accumulation. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.01.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
28
|
Rodriguez A, Martínez JA, Millard P, Gosset G, Portais JC, Létisse F, Bolivar F. Plasmid-encoded biosynthetic genes alleviate metabolic disadvantages while increasing glucose conversion to shikimate in an engineeredEscherichia colistrain. Biotechnol Bioeng 2017; 114:1319-1330. [DOI: 10.1002/bit.26264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 01/17/2017] [Accepted: 02/08/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Alberto Rodriguez
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | - Juan A. Martínez
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | - Pierre Millard
- LISBP, Université de Toulouse, CNRS, INRA; INSA; Toulouse France
| | - Guillermo Gosset
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| | | | - Fabien Létisse
- LISBP, Université de Toulouse, CNRS, INRA; INSA; Toulouse France
| | - Francisco Bolivar
- Instituto de Biotecnología; Universidad Nacional Autónoma de México (UNAM); Cuernavaca Morelos Mexico
| |
Collapse
|
29
|
Improvement of shikimic acid production in Escherichia coli with growth phase-dependent regulation in the biosynthetic pathway from glycerol. World J Microbiol Biotechnol 2017; 33:25. [DOI: 10.1007/s11274-016-2192-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 12/19/2016] [Indexed: 10/20/2022]
|
30
|
García S, Flores N, De Anda R, Hernández G, Gosset G, Bolívar F, Escalante A. The Role of the ydiB Gene, Which Encodes Quinate/Shikimate Dehydrogenase, in the Production of Quinic, Dehydroshikimic and Shikimic Acids in a PTS - Strain of Escherichia coli. J Mol Microbiol Biotechnol 2016; 27:11-21. [DOI: 10.1159/000450611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 09/06/2016] [Indexed: 11/19/2022] Open
Abstract
The culture of engineered <i>Escherichia coli</i> for shikimic acid (SA) production results in the synthesis of quinic acid (QA) and dehydroshikimic acid (DHS), reducing SA yield and impairing downstream processes. The synthesis of QA by quinate/shikimate dehydrogenase (YdiB, <i>ydiB</i>) has been previously proposed; however, the precise role for this enzyme in the production of QA in engineered strains of <i>E. coli</i> for SA production remains unclear. We report the effect of the inactivation or the overexpression of <i>ydiB</i> in <i>E. coli</i> strain PB12.SA22 on SA, QA, and DHS production in batch fermentor cultures. The results showed that the inactivation of <i>ydiB </i>resulted in a 75% decrease in the molar yield of QA and a 6.17% reduction in the yield of QA (mol/mol) relative to SA with respect to the parental strain. The overexpression of <i>ydiB</i> caused a 500% increase in the molar yield of QA and resulted in a 152% increase in QA (mol/mol) relative to SA, with a sharp decrease in SA production. Production of SA, QA, and DHS in parental and derivative <i>ydiB </i>strains suggests that the synthesis of QA results from the reduction of 3-dehydroquinate by YdiB before its conversion to DHS.
Collapse
|
31
|
Kogure T, Kubota T, Suda M, Hiraga K, Inui M. Metabolic engineering of Corynebacterium glutamicum for shikimate overproduction by growth-arrested cell reaction. Metab Eng 2016; 38:204-216. [DOI: 10.1016/j.ymben.2016.08.005] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/30/2022]
|
32
|
Kubota T, Watanabe A, Suda M, Kogure T, Hiraga K, Inui M. Production of para-aminobenzoate by genetically engineered Corynebacterium glutamicum and non-biological formation of an N-glucosyl byproduct. Metab Eng 2016; 38:322-330. [DOI: 10.1016/j.ymben.2016.07.010] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/23/2016] [Accepted: 07/25/2016] [Indexed: 11/26/2022]
|
33
|
Application of CRISPRi in Corynebacterium glutamicum for shikimic acid production. Biotechnol Lett 2016; 38:2153-2161. [PMID: 27623797 DOI: 10.1007/s10529-016-2207-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
OBJECTIVES To construct, test and exploit the CRISPRi system for enhancement of shikimic acid production with Corynebacterium glutamicum. RESULTS The CRISPRi system was used to regulate C. glutamicum gene expression at the transcriptional level. Hfq protein-mediated small regulatory RNAs system was compared with CRISPRi system. The more efficient CRISPRi system was used to adjust the metabolic flux involving the shikimic acid (SA) synthetic pathway. In 11 candidate genes, including transcription regulator, three targets were effective for increasing SA production. Through over-expression of ncgl1512 and down-regulating the expression of ncgl2008, ncgl2809, ncgl1856, the titers of SA increased 115 % to 7.76 g/l in 250 ml flasks and 23.8 g/l in 5 l fermentor, which is the highest shikimic acid yield reported for C. glutamicum. CONCLUSIONS CRISPRi system was constructed and is a high-performance and time-saving method to manipulate multiple genes in C. glutamicum for shikimic acid production. Moreover, CRISPRi-system was also effective in regulating the expression of a transcription regulator.
Collapse
|
34
|
Liu K, Hu H, Wang W, Zhang X. Genetic engineering of Pseudomonas chlororaphis GP72 for the enhanced production of 2-Hydroxyphenazine. Microb Cell Fact 2016; 15:131. [PMID: 27470070 PMCID: PMC4965901 DOI: 10.1186/s12934-016-0529-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 07/21/2016] [Indexed: 12/01/2022] Open
Abstract
Background The biocontrol strain Pseudomonas chlororaphis GP72 isolated from the green pepper rhizosphere synthesizes three antifungal phenazine compounds, 2-Hydroxyphenazine (2-OH-PHZ), 2-hydroxy-phenazine-1-carboxylic acid (2-OH-PCA) and phenazine-1-carboxylic acid (PCA). PCA has been a commercialized antifungal pesticide registered as “Shenqinmycin” in China since 2011. It is found that 2-OH-PHZ shows stronger fungistatic and bacteriostatic activity to some pathogens than PCA. 2-OH-PHZ could be developed as a potential antifungal pesticide. But the yield of 2-OH-PHZ generally is quite low, such as P. chlororaphis GP72, the production of 2-OH-PHZ by the wide-type strain is only 4.5 mg/L, it is necessary to enhance the yield of 2-OH-PHZ for its application in agriculture. Results Different strategies were used to improve the yield of 2-OH-PHZ: knocking out the negative regulatory genes, enhancing the shikimate pathway, deleting the competing pathways of 2-OH-PHZ synthesis based on chorismate, and improving the activity of PhzO which catalyzes the conversion of PCA to 2-OH-PHZ, although the last two strategies did not give us satisfactory results. In this study, four negative regulatory genes (pykF, rpeA, rsmE and lon) were firstly knocked out of the strain GP72 genome stepwise. The yield of 2-OH-PHZ improved more than 60 folds and increased from 4.5 to about 300 mg/L. Then six key genes (ppsA, tktA, phzC, aroB, aroD and aroE) selected from the gluconeogenesis, pentose phosphate and shikimate pathways which used to enhance the shikimate pathway were overexpressed to improve the production of 2-OH-PHZ. At last a genetically engineered strain that increased the 2-OH-PHZ production by 99-fold to 450.4 mg/L was obtained. Conclusions The 2-OH-PHZ production of P. chlororaphis GP72 was greatly improved through disruption of four negative regulatory genes and overexpression of six key genes, and it is shown that P. chlororaphis GP72 could be modified as a potential cell factory to produce 2-OH-PHZ and other phenazine biopesticides by genetic and metabolic engineering. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0529-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Kaiquan Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hongbo Hu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xuehong Zhang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
35
|
Gu P, Su T, Wang Q, Liang Q, Qi Q. Tunable switch mediated shikimate biosynthesis in an engineered non-auxotrophic Escherichia coli. Sci Rep 2016; 6:29745. [PMID: 27406890 PMCID: PMC4942831 DOI: 10.1038/srep29745] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/23/2016] [Indexed: 12/28/2022] Open
Abstract
Shikimate is a key intermediate in the synthesis of neuraminidase inhibitors. Compared with traditional methods, microbial production of shikimate has the advantages of environmental friendliness, low cost, feed stock renewability, and product selectivity and diversity. Despite these advantages, shikimate kinase I and II respectively encoded by aroK and aroL are inactivated in most shikimate microbial producers, thus requiring the addition of aromatic compounds during the fermentation process. To overcome this problem, we constructed a non-auxotrophic, shikimate-synthesising strain of Escherichia coli. By inactivation of repressor proteins, blocking of competitive pathways and overexpression of key enzymes, we increased the shikimate production of wild-type E. coli BW25113 to 1.73 g/L. We then designed a tunable switch that can conditionally decrease gene expression and substituted it for the original aroK promoters. Expression of aroK in the resulting P-9 strain was maintained at a high level during the growth phase and then reduced at a suitable time by addition of an optimal concentration of inducer. In 5-L fed-batch fermentation, strain P-9 produced 13.15 g/L shikimate without the addition of any aromatic compounds. The tunable switch developed in this study is an efficient tool for regulating indispensable genes involved in critical metabolic pathways.
Collapse
Affiliation(s)
- Pengfei Gu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Tianyuan Su
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Qian Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Quanfeng Liang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, People's Republic of China
| |
Collapse
|
36
|
Ghosh S, Mohan U, Banerjee UC. Studies on the production of shikimic acid using the aroK knockout strain of Bacillus megaterium. World J Microbiol Biotechnol 2016; 32:127. [DOI: 10.1007/s11274-016-2092-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 05/24/2016] [Indexed: 11/29/2022]
|
37
|
LIU XL, LIN J, HU HF, ZHOU B, ZHU BQ. Enhanced production of shikimic acid using a multi-gene co-expression system in Escherichia coli. Chin J Nat Med 2016; 14:286-293. [DOI: 10.1016/s1875-5364(16)30029-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Indexed: 11/26/2022]
|
38
|
Liu X, Lin J, Hu H, Zhou B, Zhu B. Site-specific integration and constitutive expression of key genes into Escherichia coli chromosome increases shikimic acid yields. Enzyme Microb Technol 2016; 82:96-104. [DOI: 10.1016/j.enzmictec.2015.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 08/30/2015] [Accepted: 08/31/2015] [Indexed: 01/05/2023]
|
39
|
Aguilar C, Flores N, Riveros-McKay F, Sahonero-Canavesi D, Carmona SB, Geiger O, Escalante A, Bolívar F. Deletion of the 2-acyl-glycerophosphoethanolamine cycle improve glucose metabolism in Escherichia coli strains employed for overproduction of aromatic compounds. Microb Cell Fact 2015; 14:194. [PMID: 26627477 PMCID: PMC4666226 DOI: 10.1186/s12934-015-0382-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/11/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND As a metabolic engineering tool, an adaptive laboratory evolution (ALE) experiment was performed to increase the specific growth rate (µ) in an Escherichia coli strain lacking PTS, originally engineered to increase the availability of intracellular phosphoenolpyruvate and redirect to the aromatic biosynthesis pathway. As result, several evolved strains increased their growth fitness on glucose as the only carbon source. Two of these clones isolated at 120 and 200 h during the experiment, increased their μ by 338 and 373 %, respectively, compared to the predecessor PB11 strain. The genome sequence and analysis of the genetic changes of these two strains (PB12 and PB13) allowed for the identification of a novel strategy to enhance carbon utilization to overcome the absence of the major glucose transport system. RESULTS Genome sequencing data of evolved strains revealed the deletion of chromosomal region of 10,328 pb and two punctual non-synonymous mutations in the dhaM and glpT genes, which occurred prior to their divergence during the early stages of the evolutionary process. Deleted genes related to increased fitness in the evolved strains are rppH, aas, lplT and galR. Furthermore, the loss of mutH, which was also lost during the deletion event, caused a 200-fold increase in the mutation rate. CONCLUSIONS During the ALE experiment, both PB12 and PB13 strains lost the galR and rppH genes, allowing the utilization of an alternative glucose transport system and allowed enhanced mRNA half-life of many genes involved in the glycolytic pathway resulting in an increment in the μ of these derivatives. Finally, we demonstrated the deletion of the aas-lplT operon, which codes for the main components of the phosphatidylethanolamine turnover metabolism increased the further fitness and glucose uptake in these evolved strains by stimulating the phospholipid degradation pathway. This is an alternative mechanism to its regeneration from 2-acyl-glycerophosphoethanolamine, whose utilization improved carbon metabolism likely by the elimination of a futile cycle under certain metabolic conditions. The origin and widespread occurrence of a mutated population during the ALE indicates a strong stress condition present in strains lacking PTS and the plasticity of this bacterium that allows it to overcome hostile conditions.
Collapse
Affiliation(s)
- César Aguilar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico.
| | - Noemí Flores
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico.
| | - Fernando Riveros-McKay
- Winter Genomics, Manizales 906, Colonia Lindavista, Delegación Gustavo A. Madero, 07300, México D.F., México.
| | | | - Susy Beatriz Carmona
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico.
| | - Otto Geiger
- Centro de Ciencias Genómicas, UNAM, Apdo. Postal 565-A, 62210, Cuernavaca, Morelos, Mexico.
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico.
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México (UNAM), 62210, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
40
|
Martínez JA, Bolívar F, Escalante A. Shikimic Acid Production in Escherichia coli: From Classical Metabolic Engineering Strategies to Omics Applied to Improve Its Production. Front Bioeng Biotechnol 2015; 3:145. [PMID: 26442259 PMCID: PMC4585142 DOI: 10.3389/fbioe.2015.00145] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/07/2015] [Indexed: 12/02/2022] Open
Abstract
Shikimic acid (SA) is an intermediate of the SA pathway that is present in bacteria and plants. SA has gained great interest because it is a precursor in the synthesis of the drug oseltamivir phosphate (OSF), an efficient inhibitor of the neuraminidase enzyme of diverse seasonal influenza viruses, the avian influenza virus H5N1, and the human influenza virus H1N1. For the purposes of OSF production, SA is extracted from the pods of Chinese star anise plants (Illicium spp.), yielding up to 17% of SA (dry basis content). The high demand for OSF necessary to manage a major influenza outbreak is not adequately met by industrial production using SA from plants sources. As the SA pathway is present in the model bacteria Escherichia coli, several "intuitive" metabolically engineered strains have been applied for its successful overproduction by biotechnological processes, resulting in strains producing up to 71 g/L of SA, with high conversion yields of up to 0.42 (mol SA/mol Glc), in both batch and fed-batch cultures using complex fermentation broths, including glucose as a carbon source and yeast extract. Global transcriptomic analyses have been performed in SA-producing strains, resulting in the identification of possible key target genes for the design of a rational strain improvement strategy. Because possible target genes are involved in the transport, catabolism, and interconversion of different carbon sources and metabolic intermediates outside the central carbon metabolism and SA pathways, as genes involved in diverse cellular stress responses, the development of rational cellular strain improvement strategies based on omics data constitutes a challenging task to improve SA production in currently overproducing engineered strains. In this review, we discuss the main metabolic engineering strategies that have been applied for the development of efficient SA-producing strains, as the perspective of omics analysis has focused on further strain improvement for the production of this valuable aromatic intermediate.
Collapse
Affiliation(s)
- Juan Andrés Martínez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Adelfo Escalante
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| |
Collapse
|
41
|
Metabolic engineering of Escherichia coli using CRISPR–Cas9 meditated genome editing. Metab Eng 2015; 31:13-21. [DOI: 10.1016/j.ymben.2015.06.006] [Citation(s) in RCA: 267] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 12/17/2022]
|
42
|
Ribosome binding site libraries and pathway modules for shikimic acid synthesis with Corynebacterium glutamicum. Microb Cell Fact 2015; 14:71. [PMID: 25981633 PMCID: PMC4453273 DOI: 10.1186/s12934-015-0254-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 05/06/2015] [Indexed: 11/15/2022] Open
Abstract
Background The shikimic acid (SA) pathway is a fundamental route to synthesize aromatic building blocks for cell growth and metabolic processes, as well as for fermentative production of various aromatic compounds. Genes encoding enzymes of SA pathway are not continuous on genome and they are differently regulated. Results In this study, efforts were made to construct continuous genetic modules of SA pathway that are regulated by a same Ptac promoter. Firstly, aro genes [aroG (NCgl2098), aroB (NCgl1559), aroD (NCgl0408) and aroE (NCgl1567)] from Corynebacterium glutamicum and ribosome binding site (RBS) libraries that were tailored for the above genes were obtained, and the strength of each RBS in the 4 libraries was quantified. Secondly, 9 genetic modules were built up from the RBS libraries, a previously characterized ribozyme insulator (RiboJ) and transcriptional promoter (Ptac) and terminator, and aroG, aroB, aroD and aroE. The functionality and efficiency of the constructed genetic modules were evaluated in C. glutamicum by determination of SA synthesis. Results showed that C. glutamicum RES167ΔaroK carrying a genetic module produced 4.3 g/L of SA, which was 54 folds higher compared to that of strain RES167ΔaroK (80 mg/L, without the genetic module) during fermentation in 250-mL flasks. The same strain produced 7.4, and 11.3 g/L of SA during 5-L batch and fed-batch fermentations, respectively, which corresponding to SA molar yields of 0.39 and 0.24 per mole sucrose consumption. Conclusion These results demonstrated that the constructed SA pathway modules are effective in increasing SA synthesis in C. glutamicum, and they might be useful for fermentative production of aromatic compounds derived from SA pathway.
Collapse
|
43
|
Zhang B, Jiang CY, Liu YM, Liu C, Liu SJ. Engineering of a hybrid route to enhance shikimic acid production in Corynebacterium glutamicum. Biotechnol Lett 2015; 37:1861-8. [DOI: 10.1007/s10529-015-1852-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 05/01/2015] [Indexed: 11/28/2022]
|
44
|
Tripathi P, Rawat G, Yadav S, Saxena RK. Shikimic acid, a base compound for the formulation of swine/avian flu drug: statistical optimization, fed-batch and scale up studies along with its application as an antibacterial agent. Antonie van Leeuwenhoek 2014; 107:419-31. [PMID: 25563634 DOI: 10.1007/s10482-014-0340-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2014] [Accepted: 11/17/2014] [Indexed: 11/25/2022]
Abstract
The sudden outbreak of swine flu has increased the global demand of shikimic acid which is an industrially interesting compound, as it is used as a key starting material for the synthesis of a neuraminidase inhibitor Tamiflu(®), for the treatment of antiviral infections such as swine flu. Statistical optimization and evaluation of medium components for the production of shikimic acid by Citrobacter freundii is addressed in the present investigation. Plackett-Burman design was applied for the screening of the most significant variables affecting shikimic acid production, where glucose, asparagine, KH2PO4, CaCO3 and agitation rate were the most significant factors. Response surface methodology was also employed to study the interaction among the most significant variables through which shikimic acid production increased to 12.76 g/L. Further, fed-batch studies resulted in the production of 22.32 g/L of shikimic acid. The scalability of the process was also confirmed by running 14 L bioreactor (7.5 L production medium) where 20.12 g/L of shikimic acid was produced. In addition the antibacterial activity of the shikimic acid produced was analysed against four Gram positive and four Gram negative bacteria and it was found to have a greater inhibition effect against the Gram negative bacteria.
Collapse
Affiliation(s)
- P Tripathi
- Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021, India
| | | | | | | |
Collapse
|
45
|
Bloch SE, Schmidt-Dannert C. Construction of a chimeric biosynthetic pathway for the de novo biosynthesis of rosmarinic acid in Escherichia coli. Chembiochem 2014; 15:2393-401. [PMID: 25205019 PMCID: PMC4264569 DOI: 10.1002/cbic.201402275] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Indexed: 11/10/2022]
Abstract
Hydroxycinnamic acid esters (HCEs) are widely-distributed phenylpropanoid-derived plant natural products. Rosmarinic acid (RA), the most well-known HCE, shows promise as a treatment for cancer and neurological disorders. In contrast to extraction from plant material or plant cell culture, microbial production of HCEs could be a sustainable, controlled means of production. Through the overexpression of a six-enzyme chimeric bacterial and plant pathway, we show the de novo biosynthesis of RA, and the related HCE isorinic acid (IA), in Escherichia coli. Probing the pathway through precursor supplementation showed several potential pathway bottlenecks. We demonstrated HCE biosynthesis using three plant rosmarinic acid synthase (RAS) orthologues, which exhibited different levels of HCE biosynthesis but produced the same ratio of IA to RA. This work serves as a proof-of-concept for a microbial production platform for HCEs by using a modular biosynthetic approach to access diverse natural and non-natural HCEs.
Collapse
Affiliation(s)
- Sarah E. Bloch
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, St. Paul, MN 55108, USA
| |
Collapse
|
46
|
Rodriguez A, Martínez JA, Flores N, Escalante A, Gosset G, Bolivar F. Engineering Escherichia coli to overproduce aromatic amino acids and derived compounds. Microb Cell Fact 2014; 13:126. [PMID: 25200799 PMCID: PMC4174253 DOI: 10.1186/s12934-014-0126-z] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/17/2014] [Indexed: 11/10/2022] Open
Abstract
The production of aromatic amino acids using fermentation processes with recombinant microorganisms can be an advantageous approach to reach their global demands. In addition, a large array of compounds with alimentary and pharmaceutical applications can potentially be synthesized from intermediates of this metabolic pathway. However, contrary to other amino acids and primary metabolites, the artificial channelling of building blocks from central metabolism towards the aromatic amino acid pathway is complicated to achieve in an efficient manner. The length and complex regulation of this pathway have progressively called for the employment of more integral approaches, promoting the merge of complementary tools and techniques in order to surpass metabolic and regulatory bottlenecks. As a result, relevant insights on the subject have been obtained during the last years, especially with genetically modified strains of Escherichia coli. By combining metabolic engineering strategies with developments in synthetic biology, systems biology and bioprocess engineering, notable advances were achieved regarding the generation, characterization and optimization of E. coli strains for the overproduction of aromatic amino acids, some of their precursors and related compounds. In this paper we review and compare recent successful reports dealing with the modification of metabolic traits to attain these objectives.
Collapse
|
47
|
Chen X, Li M, Zhou L, Shen W, Algasan G, Fan Y, Wang Z. Metabolic engineering of Escherichia coli for improving shikimate synthesis from glucose. BIORESOURCE TECHNOLOGY 2014; 166:64-71. [PMID: 24905044 DOI: 10.1016/j.biortech.2014.05.035] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Revised: 05/10/2014] [Accepted: 05/12/2014] [Indexed: 06/03/2023]
Abstract
Shikimate is a key intermediate for the synthesis of the neuraminidase inhibitors. Microbial production of shikimate and related derivatives has the benefit of cost reduction when compared to traditional methods. In this study, an overproducing shikimate Escherichia coli strain was developed by rationally engineering certain metabolic pathways. To achieve this, the shikimate pathway was blocked by deletion of shikimate kinases and quinic acid/shikimate dehydrogenase. EIICB(glc) protein involved in the phosphotransferase system, and acetic acid pathway were also removed to increase the amount of available phosphoenolpyruvate and decrease byproduct formation, respectively. Thereafter, three critical enzymes of mutated 3-deoxy-D-arabinoheptulosonate-7-phosphate (DAHP) synthase (encoded by aroG(fbr)), PEP synthase (encoded by ppsA), and transketolase A (encoded by tktA) were modularly overexpressed and the resulting recombinant strain produced 1207 mg/L shikimate in shake flask cultures. Using the fed-batch process, 14.6g/L shikimate with a yield of 0.29 g/g glucose was generated in a 7-L bioreactor.
Collapse
Affiliation(s)
- Xianzhong Chen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China.
| | - Mingming Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Wei Shen
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Govender Algasan
- Department of Biotechnology & Food Technology, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4001, South Africa
| | - You Fan
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Avenue, Wuxi 214122, China
| | - Zhengxiang Wang
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin University of Science & Technology, Tianjin 300457, China
| |
Collapse
|
48
|
Ghosh S, Pawar H, Pai O, Banerjee UC. Microbial transformation of quinic acid to shikimic acid by Bacillus megaterium. BIORESOUR BIOPROCESS 2014. [DOI: 10.1186/s40643-014-0007-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Biotransformation of quinic acid to shikimic acid was attempted using whole cells of Bacillus megaterium as a biocatalyst.
Results
Physico-chemical parameters such as temperature (37°C), pH (7.0), agitation (200 rpm), substrate (5 mM) and cell mass concentrations (200 kg/m 3) and reaction time (3 h) were found optimum to enhance the bioconversion. Maximum conversion (89%) of quinic acid to shikimic acid was achieved using the above optimized parameters. Shikimic acid was extracted from the reaction mixture by a pH-dependent method and maximum recovery (76%) was obtained with petroleum ether.
Conclusions
Biotransformation of quinic acid to shikimic acid seems to be a better alternative over its fermentative production.
Collapse
|
49
|
Liu X, Lin J, Hu H, Zhou B, Zhu B. Metabolic engineering of Escherichia coli to enhance shikimic acid production from sorbitol. World J Microbiol Biotechnol 2014; 30:2543-50. [DOI: 10.1007/s11274-014-1679-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 05/27/2014] [Indexed: 12/28/2022]
|
50
|
Abstract
Shikimic acid is a very important precursor for industrial synthesis of oseltamivir (Tamiflu®) which is used for the antiviral treatment. In this study, callus culture of Ginkgo biloba for shikimic acid production was reported. Callus induced from either leaves or nodal stems of sterilized ginkgo was grown on MS medium supplemented with a combination of plant growth regulators as followed: MS+KD, MS+BD, MS+KN and MS+BN for 90 days. Morphological changes, fresh weight and shikimic acid content of callus in each medium were monitored every 30 days. The result showed that callus cultures from each treatment were morphologically different. It is likely due to explant used for callus induction and type of plant growth regulators added into the medium. Browning effect was noticeably detected from 60 days to 90 days. Moreover, fresh weight and shikimic acid content of callus culture depended on cultivation time, cultivation medium and type of explants used for callus induction. Callus induced from nodal stem grown on MS+BN for 30 days offered the highest fresh weight. For shikimic acid production, the most satisfied quantity of shikimic acid was achieved from callus cultured on MS+KN for 30 days by exploiting nodal stem as explant.
Collapse
|