51
|
Satheeshkumar PK, Anu PV, Junaida MI, Madanan MG, Jebasingh T, Nair AJ, Nair GA, Nair GPM, Sudhakaran PR. Expression of Leptospira membrane proteins Signal Peptidase (SP) and Leptospira Endostatin like A (Len A) in BL-21(DE3) is toxic to the host cells. J Genet Eng Biotechnol 2018; 16:393-398. [PMID: 30733752 PMCID: PMC6353657 DOI: 10.1016/j.jgeb.2018.01.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 01/18/2018] [Accepted: 01/24/2018] [Indexed: 02/06/2023]
Abstract
Heterologous expression of Integral Membrane Proteins (IMPs) is reported to be toxic to the host system in many studies. Even though there are reports on various concerns like transformation efficiency, growth properties, protein toxicity, inefficient expression and protein degradation in IMP overexpression, no studies so far addressed these issues in a comprehensive way. In the present study, two transmembrane proteins of the pathogen Leptospira interrogans, namely Signal peptidase (SP), and Leptospira Endostatin like A (Len-A) were taken along with a cytosolic protein Hydrolase (HYD) to assess the differences in transformation efficiency, protein toxicity, and protein stability when over expressed in Escherichia coli (E. coli). Bioinformatics analysis to predict the transmembrane localization indicated that both SP and Len are targeted to the membrane. The three proteins were expressed in full length in the E. coli expression strain, BL 21 (DE3). Significant changes were observed for the strains transformed with IMP genes under the parameters analysed such as, the transformation efficiency, survival of colonies on IPTG-plate, culture growth kinetics and protein expression compared to the strain harbouring the cytosolic protein gene.
Collapse
Affiliation(s)
- Padikara K Satheeshkumar
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Prasannan V Anu
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Mohmed I Junaida
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | | | | | - Ananthakrishnan J Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Gangaprasad A Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Govinda Pillai M Nair
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| | - Perumana R Sudhakaran
- Interuniversity Centre for Genomics and Gene Technology, Department of Biotechnology, University of Kerala, Trivandrum, Kerala, India
| |
Collapse
|
52
|
Efficient production of lycopene by engineered E. coli strains harboring different types of plasmids. Bioprocess Biosyst Eng 2018; 41:489-499. [DOI: 10.1007/s00449-017-1883-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/14/2017] [Indexed: 02/02/2023]
|
53
|
Wu W, Liu F, Davis RW. Engineering Escherichia coli for the production of terpene mixture enriched in caryophyllene and caryophyllene alcohol as potential aviation fuel compounds. Metab Eng Commun 2018; 6:13-21. [PMID: 29349039 PMCID: PMC5767561 DOI: 10.1016/j.meteno.2018.01.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 12/23/2017] [Accepted: 01/02/2018] [Indexed: 11/26/2022] Open
Abstract
Recent studies have revealed that caryophyllene and its stereoisomers not only exhibit multiple biological activities but also have desired properties as renewable candidates for ground transportation and jet fuel applications. This study presents the first significant production of caryophyllene and caryolan-1-ol by an engineered E. coli with heterologous expression of mevalonate pathway genes with a caryophyllene synthase and a caryolan-1-ol synthase. By optimizing metabolic flux and fermentation parameters, the engineered strains yielded 449 mg/L of total terpene, including 406 mg/L sesquiterpene with 100 mg/L caryophyllene and 10 mg/L caryolan-1-ol. Furthermore, a marine microalgae hydrolysate was used as the sole carbon source for the production of caryophyllene and other terpene compounds. Under the optimal fermentation conditions, 360 mg/L of total terpene, 322 mg/L of sesquiterpene, and 75 mg/L caryophyllene were obtained from the pretreated algae hydrolysates. The highest yields achieved on the biomass basis were 48 mg total terpene/g algae and 10 mg caryophyllene/g algae and the caryophyllene yield is approximately ten times higher than that from plant tissues by solvent extraction. The study provides a sustainable alternative for production of caryophyllene and its alcohol from microalgae biomass as potential candidates for next generation aviation fuels. E. coli was engineered to yield terpene enriched in caryophyllene and caryolan-1-ol. Yields were improved through metabolic flux and culture parameters optimization. Algae hydrolysate was converted to terpene at high yields using engineered strains.
Collapse
Affiliation(s)
- Weihua Wu
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| | - Fang Liu
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| | - Ryan W Davis
- Department of Biomass Science & Conversion Technologies, Sandia National Laboratories, 7011 East Avenue, Livermore, CA, USA
| |
Collapse
|
54
|
Wang X, Wang X, Hui K, Wei W, Zhang W, Miao A, Xiao L, Yang L. Highly Effective Polyphosphate Synthesis, Phosphate Removal, and Concentration Using Engineered Environmental Bacteria Based on a Simple Solo Medium-Copy Plasmid Strategy. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:214-222. [PMID: 29190088 DOI: 10.1021/acs.est.7b04532] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Microbial polyphosphate (polyP) production is vital to the removal of phosphate from wastewater. However, to date, engineered polyP synthesis using genetically accessible environmental bacteria remains a challenge. This study develops a simple solo medium-copy plasmid-based polyphosphate kinase (PPK1) overexpression strategy for achieving maximum intracellular polyphosphate accumulation by environmental bacteria. The polyP content of the subsequently engineered Citrobacter freundii (CPP) could reach as high as 12.7% of its dry weight. The biomass yield of CPP was also guaranteed because of negligible metabolic burden effects resulting from the medium plasmid copy number. Consequently, substantial removal of phosphate (Pi) from the ambient environment was achieved simultaneously. Because of the need for exogenous Pi for in vivo ATP regeneration, CPP could thoroughly remove Pi from synthetic municipal wastewater when it was applied for the "one-step" removal of Pi with a bench-scale sequence batch membrane reactor. Almost all the phosphorus except for that assimilated by CPP for cellular growth could be recovered in the form of more concentrated Pi. Overall, engineering environmental bacteria to overexpress PPK1 via a solo medium-copy plasmid strategy may represent a valuable general option for not only biotechnological research based on sufficient intracellular polyP production but also removal of Pi from wastewater and Pi enrichment.
Collapse
Affiliation(s)
- Xin Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210046, P. R. China
| | - Xiaomeng Wang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210046, P. R. China
| | - Kaimin Hui
- Jiangsu Key Laboratory for Biodiversity & Biotechnology and Jiangsu Key Laboratory for Aquatic Crustacean Diseases, College of Life Sciences, Nanjing Normal University , Nanjing 210046, P. R. China
| | - Wei Wei
- Institute of Chemistry and BioMedical Science, State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University , Nanjing 210046, P. R. China
| | - Wen Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210046, P. R. China
| | - Aijun Miao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210046, P. R. China
| | - Lin Xiao
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210046, P. R. China
| | - Liuyan Yang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University , Nanjing 210046, P. R. China
| |
Collapse
|
55
|
Park SY, Yang D, Ha SH, Lee SY. Metabolic Engineering of Microorganisms for the Production of Natural Compounds. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/adbi.201700190] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Seon Young Park
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Dongsoo Yang
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Shin Hee Ha
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory; Department of Chemical and Biomolecular Engineering (BK21 Plus Program); Institute for the BioCentury; Korea Advanced Institute of Science and Technology (KAIST); Daejeon 34141 Republic of Korea
- BioProcess Engineering Research Center; KAIST; Daejeon 34141 Republic of Korea
- BioInformatics Research Center; KAIST; Daejeon 34141 Republic of Korea
| |
Collapse
|
56
|
Choi JW, Yim SS, Jeong KJ. Development of a high-copy-number plasmid via adaptive laboratory evolution of Corynebacterium glutamicum. Appl Microbiol Biotechnol 2017; 102:873-883. [DOI: 10.1007/s00253-017-8653-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 11/08/2017] [Accepted: 11/13/2017] [Indexed: 01/29/2023]
|
57
|
Lehouritis P, Hogan G, Tangney M. Designer bacteria as intratumoural enzyme biofactories. Adv Drug Deliv Rev 2017; 118:8-23. [PMID: 28916496 DOI: 10.1016/j.addr.2017.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 08/18/2017] [Accepted: 09/07/2017] [Indexed: 02/07/2023]
Abstract
Bacterial-directed enzyme prodrug therapy (BDEPT) is an emerging form of treatment for cancer. It is a biphasic variant of gene therapy in which a bacterium, armed with an enzyme that can convert an inert prodrug into a cytotoxic compound, induces tumour cell death following tumour-specific prodrug activation. BDEPT combines the innate ability of bacteria to selectively proliferate in tumours, with the capacity of prodrugs to undergo contained, compartmentalised conversion into active metabolites in vivo. Although BDEPT has undergone clinical testing, it has received limited clinical exposure, and has yet to achieve regulatory approval. In this article, we review BDEPT from the system designer's perspective, and provide detailed commentary on how the designer should strategize its development de novo. We report on contemporary advancements in this field which aim to enhance BDEPT in terms of safety and efficacy. Finally, we discuss clinical and regulatory barriers facing BDEPT, and propose promising approaches through which these hurdles may best be tackled.
Collapse
|
58
|
Qian Y, Huang HH, Jiménez JI, Del Vecchio D. Resource Competition Shapes the Response of Genetic Circuits. ACS Synth Biol 2017; 6:1263-1272. [PMID: 28350160 DOI: 10.1021/acssynbio.6b00361] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
A common approach to design genetic circuits is to compose gene expression cassettes together. While appealing, this modular approach is challenged by the fact that expression of each gene depends on the availability of transcriptional/translational resources, which is in turn determined by the presence of other genes in the circuit. This raises the question of how competition for resources by different genes affects a circuit's behavior. Here, we create a library of genetic activation cascades in E. coli bacteria, where we explicitly tune the resource demand by each gene. We develop a general Hill-function-based model that incorporates resource competition effects through resource demand coefficients. These coefficients lead to nonregulatory interactions among genes that reshape the circuit's behavior. For the activation cascade, such interactions result in surprising biphasic or monotonically decreasing responses. Finally, we use resource demand coefficients to guide the choice of ribosome binding site and DNA copy number to restore the cascade's intended monotonically increasing response. Our results demonstrate how unintended circuit's behavior arises from resource competition and provide a model-guided methodology to minimize the resulting effects.
Collapse
Affiliation(s)
- Yili Qian
- Department
of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Hsin-Ho Huang
- Department
of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - José I. Jiménez
- Department
of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Faculty
of Health of Medical Sciences, University of Surrey, Guildford, Surrey GU2 7XH, U.K
| | - Domitilla Del Vecchio
- Department
of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Synthetic
Biology Center, Massachusetts Institute of Technology, 500 Technology
Square, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
59
|
Sanders S, Vierling RJ, Bartee D, DeColli AA, Harrison MJ, Aklinski JL, Koppisch AT, Freel Meyers CL. Challenges and Hallmarks of Establishing Alkylacetylphosphonates as Probes of Bacterial 1-Deoxy-d-xylulose 5-Phosphate Synthase. ACS Infect Dis 2017. [PMID: 28636325 DOI: 10.1021/acsinfecdis.6b00168] [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] [Indexed: 02/02/2023]
Abstract
1-Deoxy-d-xylulose 5-phosphate (DXP) synthase catalyzes the thiamin diphosphate (ThDP)-dependent formation of DXP from pyruvate and d-glyceraldehyde 3-phosphate. DXP is at a metabolic branch point in bacteria, feeding into the methylerythritol phosphate pathway to indispensable isoprenoids and acting as a precursor for biosynthesis of essential cofactors in central metabolism, pyridoxal phosphate and ThDP, the latter of which is also required for DXP synthase catalysis. DXP synthase follows a unique random sequential mechanism and possesses an unusually large active site. These features have guided the design of sterically demanding alkylacetylphosphonates (alkylAPs) toward the development of selective DXP synthase inhibitors. alkylAPs studied here display selective, low μM inhibitory activity against DXP synthase. They are weak inhibitors of bacterial growth in standard nutrient rich conditions. However, bacteria are significantly sensitized to most alkylAPs in defined minimal growth medium, with minimal inhibitory concentrations (MICs) ranging from low μM to low mM and influenced by alkyl-chain length. The longest analog (C8) displays the weakest antimicrobial activity and is a substrate for efflux via AcrAB-TolC. The dependence of inhibitor potency on growth environment emphasizes the need for antimicrobial screening conditions that are relevant to the in vivo microbial microenvironment during infection. DXP synthase expression and thiamin supplementation studies offer support for DXP synthase as an intracellular target for some alkylAPs and reveal both the challenges and intriguing aspects of these approaches to study target engagement.
Collapse
Affiliation(s)
- Sara Sanders
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Ryan J. Vierling
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - David Bartee
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Alicia A. DeColli
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Mackenzie J. Harrison
- Department
of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Joseph L. Aklinski
- Department
of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Andrew T. Koppisch
- Department
of Chemistry, Northern Arizona University, Flagstaff, Arizona 86011, United States
| | - Caren L. Freel Meyers
- Department of Pharmacology
and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| |
Collapse
|
60
|
Gomes L, Mergulhão F. Heterologous protein production in Escherichia coli biofilms: A non-conventional form of high cell density cultivation. Process Biochem 2017. [DOI: 10.1016/j.procbio.2017.03.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
61
|
Huang D, Yang K, Liu J, Xu Y, Wang Y, Wang R, Liu B, Feng L. Metabolic engineering of Escherichia coli for the production of 2′-fucosyllactose and 3-fucosyllactose through modular pathway enhancement. Metab Eng 2017; 41:23-38. [DOI: 10.1016/j.ymben.2017.03.001] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 02/14/2017] [Accepted: 03/08/2017] [Indexed: 01/20/2023]
|
62
|
He X, Chen Y, Liang Q, Qi Q. Autoinduced AND Gate Controls Metabolic Pathway Dynamically in Response to Microbial Communities and Cell Physiological State. ACS Synth Biol 2017; 6:463-470. [PMID: 27997131 DOI: 10.1021/acssynbio.6b00177] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Quorum sensing (QS) systems have been widely applied in biotechnology and synthetic biology that require coordinated, community-level behaviors. Meanwhile, the cell physiological state is another key parameter that affects metabolic pathway regulation. Here, we designed an autoinduced AND gate that responds to both microbial communities and the cell physiological state. A series of tunable QS systems in response to different cell densities were obtained through random mutagenesis of LuxR and optimization of the luxRI promoter; the corresponding suitable stationary phase sensing system was selected after monitoring the fluorescence process during cell growth. The application of the final synthetic device was demonstrated using the polyhydroxybutyrate (PHB) production system. The AND gate system increased PHB production by 1-2-fold in Escherichia coli. This synthetic logic gate is a tool for developing a general dynamic regulation system in metabolic engineering in response to complex signals, without using a specific sensor.
Collapse
Affiliation(s)
- Xinyuan He
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| | - Yan Chen
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| | - Quanfeng Liang
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| | - Qingsheng Qi
- State Key Laboratory of Microbial
Technology, Shandong University, Jinan 250100, P. R. China
| |
Collapse
|
63
|
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
|
64
|
Chen H, Huang R, Zhang YHP. Systematic comparison of co-expression of multiple recombinant thermophilic enzymes in Escherichia coli BL21(DE3). Appl Microbiol Biotechnol 2017; 101:4481-4493. [PMID: 28251267 DOI: 10.1007/s00253-017-8206-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/14/2017] [Accepted: 02/17/2017] [Indexed: 01/08/2023]
Abstract
The precise control of multiple heterologous enzyme expression levels in one Escherichia coli strain is important for cascade biocatalysis, metabolic engineering, synthetic biology, natural product synthesis, and studies of complexed proteins. We systematically investigated the co-expression of up to four thermophilic enzymes (i.e., α-glucan phosphorylase (αGP), phosphoglucomutase (PGM), glucose 6-phosphate dehydrogenase (G6PDH), and 6-phosphogluconate dehydrogenase (6PGDH)) in E. coli BL21(DE3) by adding T7 promoter or T7 terminator of each gene for multiple genes in tandem, changing gene alignment, and comparing one or two plasmid systems. It was found that the addition of T7 terminator after each gene was useful to decrease the influence of the upstream gene. The co-expression of the four enzymes in E. coli BL21(DE3) was demonstrated to generate two NADPH molecules from one glucose unit of maltodextrin, where NADPH was oxidized to convert xylose to xylitol. The best four-gene co-expression system was based on two plasmids (pET and pACYC) which harbored two genes. As a result, apparent enzymatic activities of the four enzymes were regulated to be at similar levels and the overall four-enzyme activity was the highest based on the formation of xylitol. This study provides useful information for the precise control of multi-enzyme-coordinated expression in E. coli BL21(DE3).
Collapse
Affiliation(s)
- Hui Chen
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
| | - Rui Huang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA
| | - Y-H Percival Zhang
- Biological Systems Engineering Department, Virginia Tech, 304 Seitz Hall, Blacksburg, VA, 24061, USA. .,Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 West 7th Avenue, Tianjin Airport Economic Area, Tianjin, 300308, China.
| |
Collapse
|
65
|
Abstract
Combinatorial engineering approaches are becoming increasingly popular, yet they are hindered by the lack of specialized techniques for both efficient introduction of sequence variability and assembly of numerous DNA parts, required for the construction of lengthy multigene pathways. In this contribution, we introduce a new combinatorial multigene pathway assembly scheme based on Single Strand Assembly (SSA) methods and Golden Gate Assembly, exploiting the strengths of both assembly techniques. With a minimum of intermediary steps and an accompanying set of well-characterized and ready-to-use genetic parts, the developed workflow allows effective introduction of various libraries and efficient assembly of multigene pathways. It was put to the test by optimizing the lycopene pathway as proof-of-principle. The here constructed libraries yield ample variation in lycopene production. In addition, good-performing transformants with a significantly higher lycopene production were obtained as compared to previously published reference strains. The best selected producer yielded 3-fold improvement in lycopene titers up to 448 mg lycopene/g CDW. The proposed workflow in combination with the accompanying sets of ready-to-use expression and carrier plasmids, will allow the combinatorial assembly of increasingly lengthy product pathways with minimal effort.
Collapse
Affiliation(s)
- Pieter Coussement
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - David Bauwens
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Jo Maertens
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| | - Marjan De Mey
- Department
of Biochemical
and Microbial Technology, Ghent University, Coupure Links 653, 9000 Gent, Belgium
| |
Collapse
|
66
|
Liang M, Frank S, Lünsdorf H, Warren MJ, Prentice MB. Bacterial microcompartment-directed polyphosphate kinase promotes stable polyphosphate accumulation inE. coli. Biotechnol J 2017; 12. [DOI: 10.1002/biot.201600415] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Mingzhi Liang
- Department of Microbiology; University College Cork; Cork Ireland
- School of Biosciences; University of Kent; Canterbury Kent UK
| | - Stefanie Frank
- Department of Biochemical Engineering; University College London; London UK
| | - Heinrich Lünsdorf
- Central Facility for Microscopy; Helmholtz Center of Infection Research; Braunschweig Germany
| | | | - Michael B. Prentice
- Department of Microbiology; University College Cork; Cork Ireland
- Department of Pathology; University College Cork; Cork Ireland
- APC Microbiome Institute; University College Cork; Cork Ireland
| |
Collapse
|
67
|
Guo W, Sheng J, Feng X. Synergizing 13C Metabolic Flux Analysis and Metabolic Engineering for Biochemical Production. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2017; 162:265-299. [PMID: 28424826 DOI: 10.1007/10_2017_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Metabolic engineering of industrial microorganisms to produce chemicals, fuels, and drugs has attracted increasing interest as it provides an environment-friendly and renewable route that does not depend on depleting petroleum sources. However, the microbial metabolism is so complex that metabolic engineering efforts often have difficulty in achieving a satisfactory yield, titer, or productivity of the target chemical. To overcome this challenge, 13C Metabolic Flux Analysis (13C-MFA) has been developed to investigate rigorously the cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, 13C-MFA has been widely used in academic labs and the biotechnology industry to pinpoint the key issues related to microbial-based chemical production and to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this chapter we introduce the basics of 13C-MFA and illustrate how 13C-MFA has been applied to synergize with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production.
Collapse
Affiliation(s)
- Weihua Guo
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Jiayuan Sheng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA
| | - Xueyang Feng
- Department of Biological Systems Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA, 24061, USA.
| |
Collapse
|
68
|
Jahn M, Vorpahl C, Hübschmann T, Harms H, Müller S. Copy number variability of expression plasmids determined by cell sorting and Droplet Digital PCR. Microb Cell Fact 2016; 15:211. [PMID: 27993152 PMCID: PMC5168713 DOI: 10.1186/s12934-016-0610-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Accepted: 12/02/2016] [Indexed: 12/31/2022] Open
Abstract
Background Plasmids are widely used for molecular cloning or production of proteins in laboratory and industrial settings. Constant modification has brought forth countless plasmid vectors whose characteristics in terms of average plasmid copy number (PCN) and stability are rarely known. The crucial factor determining the PCN is the replication system; most replication systems in use today belong to a small number of different classes and are available through repositories like the Standard European Vector Architecture (SEVA). Results In this study, the PCN was determined in a set of seven SEVA-based expression plasmids only differing in the replication system. The average PCN for all constructs was determined by Droplet Digital PCR and ranged between 2 and 40 per chromosome in the host organism Escherichia coli. Furthermore, a plasmid-encoded EGFP reporter protein served as a means to assess variability in reporter gene expression on the single cell level. Only cells with one type of plasmid (RSF1010 replication system) showed a high degree of heterogeneity with a clear bimodal distribution of EGFP intensity while the others showed a normal distribution. The heterogeneous RSF1010-carrying cell population and one normally distributed population (ColE1 replication system) were further analyzed by sorting cells of sub-populations selected according to EGFP intensity. For both plasmids, low and highly fluorescent sub-populations showed a remarkable difference in PCN, ranging from 9.2 to 123.4 for ColE1 and from 0.5 to 11.8 for RSF1010, respectively. Conclusions The average PCN determined here for a set of standardized plasmids was generally at the lower end of previously reported ranges and not related to the degree of heterogeneity. Further characterization of a heterogeneous and a homogeneous population demonstrated considerable differences in the PCN of sub-populations. We therefore present direct molecular evidence that the average PCN does not represent the true number of plasmid molecules in individual cells. Electronic supplementary material The online version of this article (doi:10.1186/s12934-016-0610-8) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Michael Jahn
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.,School of Biotechnology, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Carsten Vorpahl
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Thomas Hübschmann
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Hauke Harms
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany
| | - Susann Müller
- Helmholtz-Centre for Environmental Research-UFZ, Permoserstraße 15, 04318, Leipzig, Germany.
| |
Collapse
|
69
|
Sun J, Alper H. Synthetic Biology: An Emerging Approach for Strain Engineering. Ind Biotechnol (New Rochelle N Y) 2016. [DOI: 10.1002/9783527807796.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Jie Sun
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| | - Hal Alper
- Department of Chemical Engineering; The University of Texas at Austin; 200 E Dean Keeton Street Stop C0400, Austin TX 78712 USA
| |
Collapse
|
70
|
Lechner A, Brunk E, Keasling JD. The Need for Integrated Approaches in Metabolic Engineering. Cold Spring Harb Perspect Biol 2016; 8:cshperspect.a023903. [PMID: 27527588 DOI: 10.1101/cshperspect.a023903] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must be considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.
Collapse
Affiliation(s)
- Anna Lechner
- Joint Bioenergy Institute (JBEI), Emeryville, California 94608.,Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720
| | - Elizabeth Brunk
- Department of Bioengineering, University of California, San Diego, California 92093
| | - Jay D Keasling
- Joint Bioenergy Institute (JBEI), Emeryville, California 94608.,Department of Chemical & Biomolecular Engineering, Department of Bioengineering, University of California, Berkeley, California 94720.,Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| |
Collapse
|
71
|
Phosphoenolpyruvate-supply module in Escherichia coli improves N-acetyl-d-neuraminic acid biocatalysis. Biotechnol Lett 2016; 39:227-234. [DOI: 10.1007/s10529-016-2235-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/03/2016] [Indexed: 01/21/2023]
|
72
|
Optimization of phage λ promoter strength for synthetic small regulatory RNA-based metabolic engineering. BIOTECHNOL BIOPROC E 2016. [DOI: 10.1007/s12257-016-0245-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
73
|
Production of glucaric acid from myo-inositol in engineered Pichia pastoris. Enzyme Microb Technol 2016; 91:8-16. [DOI: 10.1016/j.enzmictec.2016.05.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/11/2016] [Accepted: 05/22/2016] [Indexed: 02/02/2023]
|
74
|
Chen S, Jia N, Ding MZ, Yuan YJ. Comparative analysis of L-sorbose dehydrogenase by docking strategy for 2-keto-L-gulonic acid production in Ketogulonicigenium vulgare and Bacillus endophyticus consortium. J Ind Microbiol Biotechnol 2016; 43:1507-1516. [PMID: 27565673 DOI: 10.1007/s10295-016-1829-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 07/28/2016] [Indexed: 12/11/2022]
Abstract
Improving the yield of 2-keto-L-gulonic acid (2-KGA), the direct precursor of vitamin C, draws more and more attention in industrial production. In this study, we try to increase the 2-KGA productivity by computer-aided selection of genes encoding L-sorbose dehydrogenases (SDH) of Ketogulonicigenium vulgare. First, six SDHs were modeled by docking strategy to predict the binding mode with co-factor PQQ. The binding energy between SSDA1-H/SSDA1-L and PQQ was the highest, followed by SSDA3/SSDA2. The binding energy between SSDA1-P/SSDB and PQQ was the lowest. Then, these genes were overexpressed, respectively, in an industrial strain K. vulgare HKv604. Overexpression of ssda1-l and ssda1-h enhanced the 2-KGA production by 7.89 and 12.56 % in mono-cultured K. vulgare, and by 13.21 and 16.86 % when K. vulgare was co-cultured with Bacillus endophyticus. When the engineered K. vulgare SyBE_Kv000116013 (overexpression of ssda1-p) or SyBE_Kv000116016 (overexpression of ssdb) was co-cultured with B. endophyticus, the 2-KGA production decreased significantly. The docking results were in accordance with the experimental data, which indicated that computer-aided modeling is an efficient strategy for screening more efficient enzymes.
Collapse
Affiliation(s)
- Si Chen
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Nan Jia
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| | - Ming-Zhu Ding
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China. .,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China.
| | - Ying-Jin Yuan
- Key Laboratory of Systems Bioengineering (Ministry of Education) School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin, 300072, People's Republic of China
| |
Collapse
|
75
|
Kushwaha M, Rostain W, Prakash S, Duncan JN, Jaramillo A. Using RNA as Molecular Code for Programming Cellular Function. ACS Synth Biol 2016; 5:795-809. [PMID: 26999422 DOI: 10.1021/acssynbio.5b00297] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
RNA is involved in a wide-range of important molecular processes in the cell, serving diverse functions: regulatory, enzymatic, and structural. Together with its ease and predictability of design, these properties can lead RNA to become a useful handle for biological engineers with which to control the cellular machinery. By modifying the many RNA links in cellular processes, it is possible to reprogram cells toward specific design goals. We propose that RNA can be viewed as a molecular programming language that, together with protein-based execution platforms, can be used to rewrite wide ranging aspects of cellular function. In this review, we catalogue developments in the use of RNA parts, methods, and associated computational models that have contributed to the programmability of biology. We discuss how RNA part repertoires have been combined to build complex genetic circuits, and review recent applications of RNA-based parts and circuitry. We explore the future potential of RNA engineering and posit that RNA programmability is an important resource for firmly establishing an era of rationally designed synthetic biology.
Collapse
Affiliation(s)
- Manish Kushwaha
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - William Rostain
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| | - Satya Prakash
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - John N. Duncan
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- Warwick
Integrative Synthetic Biology Centre (WISB) and School of Life Sciences, University of Warwick, Coventry, CV4 7AL, U.K
- iSSB, Genopole,
CNRS, UEVE, Université Paris-Saclay, Évry, France
| |
Collapse
|
76
|
Diner RE, Bielinski VA, Dupont CL, Allen AE, Weyman PD. Refinement of the Diatom Episome Maintenance Sequence and Improvement of Conjugation-Based DNA Delivery Methods. Front Bioeng Biotechnol 2016; 4:65. [PMID: 27551676 PMCID: PMC4976089 DOI: 10.3389/fbioe.2016.00065] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 07/21/2016] [Indexed: 11/13/2022] Open
Abstract
Conjugation of episomal plasmids from bacteria to diatoms advances diatom genetic manipulation by simplifying transgene delivery and providing a stable and consistent gene expression platform. To reach its full potential, this nascent technology requires new optimized expression vectors and a deeper understanding of episome maintenance. Here, we present the development of an additional diatom vector (pPtPBR1), based on the parent plasmid pBR322, to add a plasmid maintained at medium copy number in Escherichia coli to the diatom genetic toolkit. Using this new vector, we evaluated the contribution of individual yeast DNA elements comprising the 1.4-kb tripartite CEN6-ARSH4-HIS3 sequence that enables episome maintenance in Phaeodactylum tricornutum. While various combinations of these individual elements enable efficient conjugation and high exconjugant yield in P. tricornutum, individual elements alone do not. Conjugation of episomes containing CEN6-ARSH4 and a small sequence from the low GC content 3' end of HIS3 produced the highest number of diatom exconjugant colonies, resulting in a smaller and more efficient vector design. Our findings suggest that the CEN6 and ARSH4 sequences function differently in yeast and diatoms, and that low GC content regions of greater than ~500 bp are a potential indicator of a functional diatom episome maintenance sequence. Additionally, we have developed improvements to the conjugation protocol including a high-throughput option utilizing 12-well plates and plating methods that improve exconjugant yield and reduce time and materials required for the conjugation protocol. The data presented offer additional information regarding the mechanism by which the yeast-derived sequence enables diatom episome maintenance and demonstrate options for flexible vector design.
Collapse
Affiliation(s)
- Rachel E Diner
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA; Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Vincent A Bielinski
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute , La Jolla, CA , USA
| | - Christopher L Dupont
- Microbial and Environmental Genomics Group, J. Craig Venter Institute , La Jolla, CA , USA
| | - Andrew E Allen
- Microbial and Environmental Genomics Group, J. Craig Venter Institute, La Jolla, CA, USA; Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Philip D Weyman
- Synthetic Biology and Bioenergy Group, J. Craig Venter Institute , La Jolla, CA , USA
| |
Collapse
|
77
|
Mi J, Sydow A, Schempp F, Becher D, Schewe H, Schrader J, Buchhaupt M. Investigation of plasmid-induced growth defect in Pseudomonas putida. J Biotechnol 2016; 231:167-173. [DOI: 10.1016/j.jbiotec.2016.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 02/03/2016] [Accepted: 06/06/2016] [Indexed: 02/07/2023]
|
78
|
Song Y, Nikoloff JM, Fu G, Chen J, Li Q, Xie N, Zheng P, Sun J, Zhang D. Promoter Screening from Bacillus subtilis in Various Conditions Hunting for Synthetic Biology and Industrial Applications. PLoS One 2016; 11:e0158447. [PMID: 27380260 PMCID: PMC4933340 DOI: 10.1371/journal.pone.0158447] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2016] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
The use of Bacillus subtilis in synthetic biology and metabolic engineering is highly desirable to take advantage of the unique metabolic pathways present in this organism. To do this, an evaluation of B. subtilis’ intrinsic biological parts is required to determine the best strategies to accurately regulate metabolic circuits and expression of target proteins. The strengths of promoter candidates were evaluated by measuring relative fluorescence units of a green fluorescent protein reporter, integrated into B. subtilis’ chromosome. A total of 84 predicted promoter sequences located upstream of different classes of proteins including heat shock proteins, cell-envelope proteins, and proteins resistant against toxic metals (based on similarity) and other kinds of genes were tested. The expression levels measured ranged from 0.0023 to 4.53-fold of the activity of the well-characterized strong promoter P43. No significant shifts were observed when strains, carrying different promoter candidates, were cultured at high temperature or in media with ethanol, but some strains showed increased activity when cultured under high osmotic pressure. Randomly selected promoter candidates were tested and found to activate transcription of thermostable β-galactosidase (bgaB) at a similar level, implying the ability of these sequences to function as promoter elements in multiple genetic contexts. In addition, selected promoters elevated the final production of both cytoplasmic bgaB and secreted protein α-amylase to about fourfold and twofold, respectively. The generated data allows a deeper understanding of B. subtilis’ metabolism and will facilitate future work to develop this organism for synthetic biology.
Collapse
Affiliation(s)
- Yafeng Song
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jonas M Nikoloff
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Gang Fu
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jingqi Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Qinggang Li
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Nengzhong Xie
- National Engineering Research Center for Non-food Biorefinery, State Key Laboratory of Non-food Biomass Energy and Enzyme Technology, Nanning 5300074, P. R. China
- Guangxi Biomass Industrialization Engineering Institute, Guangxi Academy of Sciences, Nanning 530007, P. R. China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| | - Dawei Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, P. R. China
| |
Collapse
|
79
|
A novel process for obtaining phenylpropanoic acid precursor using Escherichia coli with a constitutive expression system. Food Sci Biotechnol 2016; 25:795-801. [PMID: 30263338 DOI: 10.1007/s10068-016-0134-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 03/28/2016] [Accepted: 03/28/2016] [Indexed: 10/21/2022] Open
Abstract
Phenylpropanoids are widely used in food supplements, pharmaceuticals, and cosmetics with diverse benefits to human health. Trans-cinnamic acid or p-coumaric acid is usually used as the starting precursor to produce phenylpropanoids. Synthetic bioengineering of microbial cell factories offers a sustainable and flexible alternative method for obtaining these compounds. In this study, a constitutive expression system consisting of Rhodotorula glutinis phenylalanine/tyrosine ammonia lyase was developed to produce a phenylpropanoic acid precursor in Escherichia coli. To improve trans-cinnamic acid and p-coumaric acid production, BioBrick optimization was investigated, causing a 7.2- and 14.2-fold increase in the yield of these compounds, respectively. The optimum strain was capable of de novo producing 78.81 mg/L of trans-cinnamic acid and 34.67 mg/L of p-coumaric acid in a shake flask culture. The work presented here paves the way for the development of a sustainable and economical process for microbial production of a phenylpropanoic acid precursor.
Collapse
|
80
|
Su B, Zhang Z, Wu M, Lin J, Yang L. Construction of plasmid-free Escherichia coli for the production of arabitol-free xylitol from corncob hemicellulosic hydrolysate. Sci Rep 2016; 6:26567. [PMID: 27225023 PMCID: PMC4880924 DOI: 10.1038/srep26567] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 05/04/2016] [Indexed: 11/22/2022] Open
Abstract
High costs and low production efficiency are a serious constraint to bio-based xylitol production. For industrial-scale production of xylitol, a plasmid-free Escherichia coli for arabitol-free xylitol production from corncob hemicellulosic hydrolysate has been constructed. Instead of being plasmid and inducer dependent, this strain relied on multiple-copy integration of xylose reductase (XR) genes into the chromosome, where their expression was controlled by the constitutive promoter P43. In addition, to minimize the flux from L-arabinose to arabitol, two strategies including low XR total activity and high selectivity of XR has been adopted. Arabitol was significantly decreased using plasmid-free strain which had lower XR total activity and an eight point-mutations of XR with a 27-fold lower enzyme activity toward L-arabinose was achieved. The plasmid-free strain in conjunction with this mutant XR can completely eliminate arabitol formation in xylitol production. In fed-batch fermentation, this plasmid-free strain produced 143.8 g L(-1) xylitol at 1.84 g L(-1) h(-1) from corncob hemicellulosic hydrolysate. From these results, we conclude that this route by plasmid-free E. coli has potential to become a commercially viable process for xylitol production.
Collapse
Affiliation(s)
- Buli Su
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhe Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Mianbin Wu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jianping Lin
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Lirong Yang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| |
Collapse
|
81
|
Liang JL, Guo LQ, Lin JF, He ZQ, Cai FJ, Chen JF. A novel process for obtaining pinosylvin using combinatorial bioengineering in Escherichia coli. World J Microbiol Biotechnol 2016; 32:102. [PMID: 27116968 DOI: 10.1007/s11274-016-2062-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/29/2016] [Indexed: 12/22/2022]
Abstract
Pinosylvin as a bioactive stilbene is of great interest for food supplements and pharmaceuticals development. In comparison to conventional extraction of pinosylvin from plant sources, biosynthesis engineering of microbial cell factories is a sustainable and flexible alternative method. Current synthetic strategies often require expensive phenylpropanoic precursor and inducer, which are not available for large-scale fermentation process. In this study, three bioengineering strategies were described to the development of a simple and economical process for pinosylvin biosynthesis in Escherichia coli. Firstly, we evaluated different construct environments to give a highly efficient constitutive system for enzymes of pinosylvin pathway expression: 4-coumarate: coenzyme A ligase (4CL) and stilbene synthase (STS). Secondly, malonyl coenzyme A (malonyl-CoA) is a key precursor of pinosylvin bioproduction and at low level in E. coli cell. Thus clustered regularly interspaced short palindromic repeats interference (CRISPRi) was explored to inactivate malonyl-CoA consumption pathway to increase its availability. The resulting pinosylvin content in engineered E. coli was obtained a 1.9-fold increase depending on the repression of fabD (encoding malonyl-CoA-ACP transacylase) gene. Eventually, a phenylalanine over-producing E. coli consisting phenylalanine ammonia lyase was introduced to produce the precursor of pinosylvin, trans-cinnamic acid, the crude extraction of cultural medium was used as supplementation for pinosylvin bioproduction. Using these combinatorial processes, 47.49 mg/L pinosylvin was produced from glycerol.
Collapse
Affiliation(s)
- Jing-Long Liang
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, 483 Wushan Road, Tianhe District, Guangzhou, 510640, China.,Joint Research and Development Center for Natural Products of Alchemy Biotechnology Co. Ltd. and South China Agricultural University, Guangzhou, 510640, China
| | - Li-Qiong Guo
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, 483 Wushan Road, Tianhe District, Guangzhou, 510640, China.,Joint Research and Development Center for Natural Products of Alchemy Biotechnology Co. Ltd. and South China Agricultural University, Guangzhou, 510640, China
| | - Jun-Fang Lin
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, 483 Wushan Road, Tianhe District, Guangzhou, 510640, China. .,Joint Research and Development Center for Natural Products of Alchemy Biotechnology Co. Ltd. and South China Agricultural University, Guangzhou, 510640, China.
| | - Ze-Qi He
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Fa-Ji Cai
- Department of Bioengineering, College of Food Science and Institute of Food Biotechnology, South China Agricultural University, 483 Wushan Road, Tianhe District, Guangzhou, 510640, China
| | - Jun-Fei Chen
- The School of Chemistry and Pharmaceutical Engineering, Qi-Lu University of Technology, Jinan, 250353, China
| |
Collapse
|
82
|
Jones JA, Koffas MAG. Optimizing Metabolic Pathways for the Improved Production of Natural Products. Methods Enzymol 2016; 575:179-93. [PMID: 27417929 DOI: 10.1016/bs.mie.2016.02.010] [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] [Indexed: 12/25/2022]
Abstract
Metabolic engineering strives to develop microbial strains that are capable of high-titer production of a variety of industrially significant pharmaceuticals, nutraceuticals, commodity, and high-value compounds. Despite extensive success with many proof-of-concept systems there is still the need for optimization to achieve industrially relevant titers, yields, and productivities. The field of metabolic pathway optimization and balancing has formed to address this need using a scientific and systematic approach. In this chapter, we aim to outline various pathway optimization and system balancing strategies while giving insights and tips into the systems and procedures that have demonstrated recent success in the peer-reviewed literature.
Collapse
Affiliation(s)
- J A Jones
- Rensselaer Polytechnic Institute, Troy, NY, United States; Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States
| | - M A G Koffas
- Rensselaer Polytechnic Institute, Troy, NY, United States; Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States.
| |
Collapse
|
83
|
Anindyajati, Artarini AA, Riani C, Retnoningrum DS. Plasmid Copy Number Determination by Quantitative Polymerase Chain Reaction. Sci Pharm 2016; 84:89-101. [PMID: 27110501 PMCID: PMC4839616 DOI: 10.3797/scipharm.isp.2015.02] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Accepted: 12/15/2015] [Indexed: 01/24/2023] Open
Abstract
Recombinant therapeutic proteins are biopharmaceutical products that develop rapidly for years. Recombinant protein production in certain hosts requires vector expression harboring the gene encoding the corresponding protein. Escherichia coli is the prokaryote organism mostly used in recombinant protein production, commonly using a plasmid as the expression vector. Recombinant protein production is affected by plasmid copy number harboring the encoded gene, hence the determination of plasmid copy number also plays an important role in establishing a recombinant protein production system. On the industrial scale, a low copy number of plasmids are more suitable due to their better stability. In the previous study we constructed pCAD, a plasmid derived from the low copy number pBR322 plasmid. This study was aimed to confirm pCAD’s copy number by quantitative polymerase chain reaction (qPCR). Plasmid copy number was determined by comparing the quantification signal from the plasmid to those from the chromosome. Copy number was then calculated by using a known copy number plasmid as a standard. Two pairs of primers, called tdk and ori, were designed for targeting a single gene tdk in the chromosome and a conserved domain in the plasmid’s ori, respectively. Primer quality was analyzed in silico using PrimerSelect DNASTAR and PraTo software prior to in vitro evaluation on primer specificity and efficiency as well as optimization of qPCR conditions. Plasmid copy number determination was conducted on E. coli lysates harboring each plasmid, with the number of cells ranging from 102–105 cells/μL. Cells were lysed by incubation at 95ºC for 10 minutes, followed by immediate freezing at −4°C. pBR322 plasmid with the copy number of ~19 copies/cell was used as the standard, while pJExpress414-sod plasmid possessing the high copy number pUC ori was also determined to test the method being used. In silico analysis based on primer-primer and primer-template interactions showed that both primer pairs were acceptable and were predicted to have good performance. Those predictions were in agreement with the in vitro test that gave a single band in the PCR product’s electropherogram and a single peak in DNA amplicon’s melting curve with a Tm value of 79.01 ± 0.11°C for the tdk primer and 81.53 ± 0.29°C for the ori primer. The efficiency of each primer was 1.95 and 1.97, respectively. The calculation result of pCAD’s copy number was 13.1 ± 0.3 copies/cell, showing that pCAD’s low copy number has been determined and confirmed. Meanwhile, it was 576.3 ± 91.9 copies/cell for pJExpress414-sod, in accordance with the hypothesis that pUC ori regulates the high copy number plasmid. In conclusion, the designed primers and qPCR conditions used in this study can be used to determine plasmid copy number for plasmids with pBR322 and pUC ori. The method should be tested further on plasmids harboring other type of ori.
Collapse
Affiliation(s)
- Anindyajati
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - A Anita Artarini
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Catur Riani
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| | - Debbie S Retnoningrum
- Laboratory of Pharmaceutical Biotechnology, School of Pharmacy, Institut Teknologi Bandung, Jalan Ganesha 10, 40132, Bandung, Indonesia
| |
Collapse
|
84
|
Gan R, Jewett MC. Evolution of translation initiation sequences using in vitro yeast ribosome display. Biotechnol Bioeng 2016; 113:1777-86. [PMID: 26757179 DOI: 10.1002/bit.25933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Revised: 12/13/2015] [Accepted: 01/07/2016] [Indexed: 11/08/2022]
Abstract
We report a novel in vitro yeast ribosome display method based on cell-free protein synthesis (CFPS) using linear DNA templates. We demonstrate that our platform can enrich a target gene from a model library by 100-fold per round of selection. We demonstrate the utility of our approach by evolving cap-independent translation initiation (CITI) sequences, which result in a 13-fold increase in CFPS yields after four rounds of selection, and a threefold further increase by placing the beneficial short sequences in tandem. We also show that 12 of the selected CITI sequences permit precise control of gene expression in vitro over a range of up to 80-fold by enhancing translation (and not as cryptic promoters). These 12 sequences are then shown to tune protein expression in vivo, though likely due to a different mechanism. Looking forward, yeast ribosome display holds promise for evolving libraries of proteins and DNA regulatory parts for protein engineering and synthetic biology. Biotechnol. Bioeng. 2016;113: 1777-1786. © 2016 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Rui Gan
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois, 60208. .,Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois. .,Member, Robert H. Lurie Comprehensive Cancer Center, Northwestern University, Evanston, Illinois. .,Simpson Querrey Institute, Northwestern University, Evanston, Illinois.
| |
Collapse
|
85
|
Merrick C, Wardrope C, Paget J, Colloms S, Rosser S. Rapid Optimization of Engineered Metabolic Pathways with Serine Integrase Recombinational Assembly (SIRA). Methods Enzymol 2016; 575:285-317. [DOI: 10.1016/bs.mie.2016.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
|
86
|
Tan Z, Chen J, Zhang X. Systematic engineering of pentose phosphate pathway improves Escherichia coli succinate production. BIOTECHNOLOGY FOR BIOFUELS 2016; 9:262. [PMID: 27980672 PMCID: PMC5134279 DOI: 10.1186/s13068-016-0675-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Accepted: 11/24/2016] [Indexed: 05/04/2023]
Abstract
BACKGROUND Succinate biosynthesis of Escherichia coli is reducing equivalent-dependent and the EMP pathway serves as the primary reducing equivalent source under anaerobic condition. Compared with EMP, pentose phosphate pathway (PPP) is reducing equivalent-conserving but suffers from low efficacy. In this study, the ribosome binding site library and modified multivariate modular metabolic engineering (MMME) approaches are employed to overcome the low efficacy of PPP and thus increase succinate production. RESULTS Altering expression levels of different PPP enzymes have distinct effects on succinate production. Specifically, increased expression of five enzymes, i.e., Zwf, Pgl, Gnd, Tkt, and Tal, contributes to increased succinate production, while the increased expression of two enzymes, i.e., Rpe and Rpi, significantly decreases succinate production. Modular engineering strategy is employed to decompose PPP into three modules according to position and function. Engineering of Zwf/Pgl/Gnd and Tkt/Tal modules effectively increases succinate yield and production, while engineering of Rpe/Rpi module decreases. Imbalance of enzymatic reactions in PPP is alleviated using MMME approach. Finally, combinational utilization of engineered PPP and SthA transhydrogenase enables succinate yield up to 1.61 mol/mol glucose, which is 94% of theoretical maximum yield (1.71 mol/mol) and also the highest succinate yield in minimal medium to our knowledge. CONCLUSIONS In summary, we systematically engineered the PPP for improving the supply of reducing equivalents and thus succinate production. Besides succinate, these PPP engineering strategies and conclusions can also be applicable to the production of other reducing equivalent-dependent biorenewables.
Collapse
Affiliation(s)
- Zaigao Tan
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Park, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Jing Chen
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Park, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| | - Xueli Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 XiQiDao, Tianjin Airport Economic Park, Tianjin, 300308 China
- Key Laboratory of Systems Microbial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308 China
| |
Collapse
|
87
|
Ma T, Deng Z, Liu T. Microbial production strategies and applications of lycopene and other terpenoids. World J Microbiol Biotechnol 2015; 32:15. [PMID: 26715120 DOI: 10.1007/s11274-015-1975-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 10/14/2015] [Indexed: 12/14/2022]
Abstract
Terpenoids are a large class of compounds that have far-reaching applications and economic value, particularly those most commonly found in plants; however, the extraction and synthesis of these compounds is often expensive and technically challenging. Recent advances in microbial metabolic engineering comprise a breakthrough that may enable the efficient, cost-effective production of these limited natural resources. Via the engineering of safe, industrial microorganisms that encode product-specific enzymes, and even entire metabolic pathways of interest, microbial-derived semisynthetic terpenoids may soon replace plant-derived terpenoids as the primary source of these valuable compounds. Indeed, the recent metabolic engineering of an Escherichia coli strain that produces the precursor to lycopene, a commercially and medically important compound, with higher yields than those in tomato plants serves as a successful example. Here, we review the recent developments in the metabolic engineering of microbes for the production of certain terpenoid compounds, particularly lycopene, which has been increasingly used in pharmaceuticals, nutritional supplements, and cosmetics. Furthermore, we summarize the metabolic engineering strategies used to achieve successful microbial production of some similar compounds. Based on this overview, there is a reason to believe that metabolic engineering comprises an optimal approach for increasing the production of lycopene and other terpenoids.
Collapse
Affiliation(s)
- Tian Ma
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Donghu Road, Wuhan, 430071, People's Republic of China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Donghu Road, Wuhan, 430071, People's Republic of China
- Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, People's Republic of China
| | - Tiangang Liu
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, Donghu Road, Wuhan, 430071, People's Republic of China.
- Hubei Engineering Laboratory for Synthetic Microbiology, Wuhan Institute of Biotechnology, Wuhan, People's Republic of China.
- Hubei Provincial Cooperative Innovation Center of Industrial Fermentation, Wuhan, People's Republic of China.
| |
Collapse
|
88
|
13C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production. Bioengineering (Basel) 2015; 3:bioengineering3010003. [PMID: 28952565 PMCID: PMC5597161 DOI: 10.3390/bioengineering3010003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 12/10/2015] [Accepted: 12/18/2015] [Indexed: 12/15/2022] Open
Abstract
Metabolic engineering of various industrial microorganisms to produce chemicals, fuels, and drugs has raised interest since it is environmentally friendly, sustainable, and independent of nonrenewable resources. However, microbial metabolism is so complex that only a few metabolic engineering efforts have been able to achieve a satisfactory yield, titer or productivity of the target chemicals for industrial commercialization. In order to overcome this challenge, 13C Metabolic Flux Analysis (13C-MFA) has been continuously developed and widely applied to rigorously investigate cell metabolism and quantify the carbon flux distribution in central metabolic pathways. In the past decade, many 13C-MFA studies have been performed in academic labs and biotechnology industries to pinpoint key issues related to microbe-based chemical production. Insightful information about the metabolic rewiring has been provided to guide the development of the appropriate metabolic engineering strategies for improving the biochemical production. In this review, we will introduce the basics of 13C-MFA and illustrate how 13C-MFA has been applied via integration with metabolic engineering to identify and tackle the rate-limiting steps in biochemical production for various host microorganisms
Collapse
|
89
|
Dvorak P, Chrast L, Nikel PI, Fedr R, Soucek K, Sedlackova M, Chaloupkova R, de Lorenzo V, Prokop Z, Damborsky J. Exacerbation of substrate toxicity by IPTG in Escherichia coli BL21(DE3) carrying a synthetic metabolic pathway. Microb Cell Fact 2015; 14:201. [PMID: 26691337 PMCID: PMC4687329 DOI: 10.1186/s12934-015-0393-3] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 12/05/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Heterologous expression systems based on promoters inducible with isopropyl-β-D-1-thiogalactopyranoside (IPTG), e.g., Escherichia coli BL21(DE3) and cognate LacI(Q)/P(lacUV5)-T7 vectors, are commonly used for production of recombinant proteins and metabolic pathways. The applicability of such cell factories is limited by the complex physiological burden imposed by overexpression of the exogenous genes during a bioprocess. This burden originates from a combination of stresses that may include competition for the expression machinery, side-reactions due to the activity of the recombinant proteins, or the toxicity of their substrates, products and intermediates. However, the physiological impact of IPTG-induced conditional expression on the recombinant host under such harsh conditions is often overlooked. RESULTS The physiological responses to IPTG of the E. coli BL21(DE3) strain and three different recombinants carrying a synthetic metabolic pathway for biodegradation of the toxic anthropogenic pollutant 1,2,3-trichloropropane (TCP) were investigated using plating, flow cytometry, and electron microscopy. Collected data revealed unexpected negative synergistic effect of inducer of the expression system and toxic substrate resulting in pronounced physiological stress. Replacing IPTG with the natural sugar effector lactose greatly reduced such stress, demonstrating that the effect was due to the original inducer's chemical properties. CONCLUSIONS IPTG is not an innocuous inducer; instead, it exacerbates the toxicity of haloalkane substrate and causes appreciable damage to the E. coli BL21(DE3) host, which is already bearing a metabolic burden due to its content of plasmids carrying the genes of the synthetic metabolic pathway. The concentration of IPTG can be effectively tuned to mitigate this negative effect. Importantly, we show that induction with lactose, the natural inducer of P lac , dramatically lightens the burden without reducing the efficiency of the synthetic TCP degradation pathway. This suggests that lactose may be a better inducer than IPTG for the expression of heterologous pathways in E. coli BL21(DE3).
Collapse
Affiliation(s)
- Pavel Dvorak
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Lukas Chrast
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Pablo I Nikel
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, 28049, Madrid, Spain.
| | - Radek Fedr
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65, Brno, Czech Republic.
| | - Karel Soucek
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612 65, Brno, Czech Republic.
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00, Brno, Czech Republic.
| | - Miroslava Sedlackova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, 625 00, Brno, Czech Republic.
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program, Centro Nacional de Biotecnología CNB-CSIC, Cantoblanco, 28049, Madrid, Spain.
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.
- International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic.
| |
Collapse
|
90
|
Ehrenworth AM, Sarria S, Peralta-Yahya P. Pterin-Dependent Mono-oxidation for the Microbial Synthesis of a Modified Monoterpene Indole Alkaloid. ACS Synth Biol 2015. [PMID: 26214239 DOI: 10.1021/acssynbio.5b00025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Monoterpene indole alkaloids (MIAs) have important therapeutic value, including as anticancer and antimalarial agents. Because of their chemical complexity, therapeutic MIAs, or advanced intermediates thereof, are often isolated from the native plants. The microbial synthesis of MIAs would allow for the rapid and scalable production of complex MIAs and MIA analogues for therapeutic use. Here, we produce the modified MIA hydroxystrictosidine from glucose and the monoterpene secologanin via a pterin-dependent mono-oxidation strategy. Specifically, we engineered the yeast Saccharomyces cerevisiae for the high-level synthesis of tetrahydrobiopterin to mono-oxidize tryptophan to 5-hydroxytryptophan, which, after decarboxylation to serotonin, is coupled to exogenously fed secologanin to produce 10-hydroxystrictosidine in an eight-enzyme pathway. We selected hydroxystrictosidine as our synthetic target because hydroxylation at the 10' position of the alkaloid core strictosidine provides a chemical handle for the future chemical semisynthesis of therapeutics. We show the generality of the pterin-dependent mono-oxidation strategy for alkaloid synthesis by hydroxylating tyrosine to L-DOPA-a key intermediate in benzylisoquinoline alkaloid (BIA) biosynthesis-and, thereafter, further converting it to dopamine. Together, these results present the first microbial synthesis of a modified alkaloid, the first production of tetrahydrobiopterin in yeast, and the first use of a pterin-dependent mono-oxidation strategy for the synthesis of L-DOPA. This work opens the door to the scalable production of MIAs as well as the production of modified MIAs to serve as late intermediates in the semisynthesis of known and novel therapeutics. Further, the microbial strains in this work can be used as plant pathway discovery tools to elucidate known MIA biosynthetic pathways or to identify pathways leading to novel MIAs.
Collapse
Affiliation(s)
- A. M. Ehrenworth
- School of Chemistry and Biochemistry, and ‡School of Chemical
and Biomolecular
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - S. Sarria
- School of Chemistry and Biochemistry, and ‡School of Chemical
and Biomolecular
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - P. Peralta-Yahya
- School of Chemistry and Biochemistry, and ‡School of Chemical
and Biomolecular
Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| |
Collapse
|
91
|
Jakočiūnas T, Jensen MK, Keasling JD. CRISPR/Cas9 advances engineering of microbial cell factories. Metab Eng 2015; 34:44-59. [PMID: 26707540 DOI: 10.1016/j.ymben.2015.12.003] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Revised: 11/29/2015] [Accepted: 12/10/2015] [Indexed: 12/19/2022]
Abstract
One of the key drivers for successful metabolic engineering in microbes is the efficacy by which genomes can be edited. As such there are many methods to choose from when aiming to modify genomes, especially those of model organisms like yeast and bacteria. In recent years, clustered regularly interspaced palindromic repeats (CRISPR) and its associated proteins (Cas) have become the method of choice for precision genome engineering in many organisms due to their orthogonality, versatility and efficacy. Here we review the strategies adopted for implementation of RNA-guided CRISPR/Cas9 genome editing with special emphasis on their application for metabolic engineering of yeast and bacteria. Also, examples of how nuclease-deficient Cas9 has been applied for RNA-guided transcriptional regulation of target genes will be reviewed, as well as tools available for computer-aided design of guide-RNAs will be highlighted. Finally, this review will provide a perspective on the immediate challenges and opportunities foreseen by the use of CRISPR/Cas9 genome engineering and regulation in the context of metabolic engineering.
Collapse
Affiliation(s)
- Tadas Jakočiūnas
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Michael K Jensen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark.
| | - Jay D Keasling
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark; Joint BioEnergy Institute, Emeryville, CA, USA; Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Department of Chemical and Biomolecular Engineering & Department of Bioengineering University of California, Berkeley, CA, USA
| |
Collapse
|
92
|
Liu M, Feng X, Ding Y, Zhao G, Liu H, Xian M. Metabolic engineering of Escherichia coli to improve recombinant protein production. Appl Microbiol Biotechnol 2015; 99:10367-77. [DOI: 10.1007/s00253-015-6955-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 08/18/2015] [Accepted: 08/22/2015] [Indexed: 01/13/2023]
|
93
|
Unique plasmids generated via pUC replicon mutagenesis in an error-prone thermophile derived from Geobacillus kaustophilus HTA426. Appl Environ Microbiol 2015; 81:7625-32. [PMID: 26319877 DOI: 10.1128/aem.01574-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/17/2015] [Indexed: 01/10/2023] Open
Abstract
The plasmid pGKE75-catA138T, which comprises pUC18 and the catA138T gene encoding thermostable chloramphenicol acetyltransferase with an A138T amino acid replacement (CATA138T), serves as an Escherichia coli-Geobacillus kaustophilus shuttle plasmid that confers moderate chloramphenicol resistance on G. kaustophilus HTA426. The present study examined the thermoadaptation-directed mutagenesis of pGKE75-catA138T in an error-prone thermophile, generating the mutant plasmid pGKE75(αβ)-catA138T responsible for substantial chloramphenicol resistance at 65°C. pGKE75(αβ)-catA138T contained no mutation in the catA138T gene but had two mutations in the pUC replicon, even though the replicon has no apparent role in G. kaustophilus. Biochemical characterization suggested that the efficient chloramphenicol resistance conferred by pGKE75(αβ)-catA138T is attributable to increases in intracellular CATA138T and acetyl-coenzyme A following a decrease in incomplete forms of pGKE75(αβ)-catA138T. The decrease in incomplete plasmids may be due to optimization of plasmid replication by RNA species transcribed from the mutant pUC replicon, which were actually produced in G. kaustophilus. It is noteworthy that G. kaustophilus was transformed with pGKE75(αβ)-catA138T using chloramphenicol selection at 60°C. In addition, a pUC18 derivative with the two mutations propagated in E. coli at a high copy number independently of the culture temperature and high plasmid stability. Since these properties have not been observed in known plasmids, the outcomes extend the genetic toolboxes for G. kaustophilus and E. coli.
Collapse
|
94
|
Winkler JD, Erickson K, Choudhury A, Halweg-Edwards AL, Gill RT. Complex systems in metabolic engineering. Curr Opin Biotechnol 2015; 36:107-14. [PMID: 26319897 DOI: 10.1016/j.copbio.2015.08.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 01/11/2023]
Abstract
Metabolic engineers manipulate intricate biological networks to build efficient biological machines. The inherent complexity of this task, derived from the extensive and often unknown interconnectivity between and within these networks, often prevents researchers from achieving desired performance. Other fields have developed methods to tackle the issue of complexity for their unique subset of engineering problems, but to date, there has not been extensive and comprehensive examination of how metabolic engineers use existing tools to ameliorate this effect on their own research projects. In this review, we examine how complexity affects engineering at the protein, pathway, and genome levels within an organism, and the tools for handling these issues to achieve high-performing strain designs. Quantitative complexity metrics and their applications to metabolic engineering versus traditional engineering fields are also discussed. We conclude by predicting how metabolic engineering practices may advance in light of an explicit consideration of design complexity.
Collapse
Affiliation(s)
- James D Winkler
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USA
| | - Keesha Erickson
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USA
| | - Alaksh Choudhury
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USA
| | - Andrea L Halweg-Edwards
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USA
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Jennie Smoly Caruthers Biotechnology Building, Research Park, Boulder, CO 80303, USA.
| |
Collapse
|
95
|
Luo Y, Li BZ, Liu D, Zhang L, Chen Y, Jia B, Zeng BX, Zhao H, Yuan YJ. Engineered biosynthesis of natural products in heterologous hosts. Chem Soc Rev 2015; 44:5265-90. [PMID: 25960127 PMCID: PMC4510016 DOI: 10.1039/c5cs00025d] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Natural products produced by microorganisms and plants are a major resource of antibacterial and anticancer drugs as well as industrially useful compounds. However, the native producers often suffer from low productivity and titers. Here we summarize the recent applications of heterologous biosynthesis for the production of several important classes of natural products such as terpenoids, flavonoids, alkaloids, and polyketides. In addition, we will discuss the new tools and strategies at multi-scale levels including gene, pathway, genome and community levels for highly efficient heterologous biosynthesis of natural products.
Collapse
Affiliation(s)
- Yunzi Luo
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300072, P. R. China.
| | | | | | | | | | | | | | | | | |
Collapse
|
96
|
Leavitt JM, Alper HS. Advances and current limitations in transcript-level control of gene expression. Curr Opin Biotechnol 2015; 34:98-104. [DOI: 10.1016/j.copbio.2014.12.015] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 12/14/2014] [Accepted: 12/15/2014] [Indexed: 11/25/2022]
|
97
|
Volmer J, Schmid A, Bühler B. Guiding bioprocess design by microbial ecology. Curr Opin Microbiol 2015; 25:25-32. [DOI: 10.1016/j.mib.2015.02.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Revised: 02/26/2015] [Accepted: 02/26/2015] [Indexed: 12/20/2022]
|
98
|
Bayer T, Milker S, Wiesinger T, Rudroff F, Mihovilovic MD. Designer Microorganisms for Optimized Redox Cascade Reactions - Challenges and Future Perspectives. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500202] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
|
99
|
Jeong J, Seo HN, Jung YK, Lee J, Ryu G, Lee W, Kwon E, Ryoo K, Kim J, Cho HY, Cho KM, Park JH, Bang D. Repetitive genomic insertion of gene-sized dsDNAs by targeting the promoter region of a counter-selectable marker. Sci Rep 2015; 5:8712. [PMID: 25736821 PMCID: PMC4348660 DOI: 10.1038/srep08712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 01/30/2015] [Indexed: 11/18/2022] Open
Abstract
Genome engineering can be used to produce bacterial strains with a wide range of desired phenotypes. However, the incorporation of gene-sized DNA fragments is often challenging due to the intricacy of the procedure, off-target effects, and low insertion efficiency. Here we report a genome engineering method enabling the continuous incorporation of gene-sized double-stranded DNAs (dsDNAs) into the Escherichia coli genome. DNA substrates are inserted without introducing additional marker genes, by synchronously turning an endogenous counter-selectable marker gene ON and OFF. To accomplish this, we utilized λ Red protein-mediated recombination to insert dsDNAs within the promoter region of a counter-selectable marker gene, tolC. By repeatedly switching the marker gene ON and OFF, a number of desired gene-sized dsDNAs can be inserted consecutively. With this method, we successfully inserted approximately 13 kb gene clusters to generate engineered E. coli strains producing 1,4-butanediol (1,4-BDO).
Collapse
Affiliation(s)
- Jaehwan Jeong
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Han Na Seo
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Yu Kyung Jung
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Jeewon Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Gyuri Ryu
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Wookjae Lee
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Euijin Kwon
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Keunsoo Ryoo
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| | - Jungyeon Kim
- Department of Chemistry, University College London, 20 Gordon Street, London, WC1H 0AJ, U.K
| | - Hwa-Young Cho
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Kwang Myung Cho
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Jin Hwan Park
- Samsung Advanced Institute of Technology, 130 Samsung-ro, Yeongtong-gu, Suwon-si, Gyeonggi-do, 443-803, Korea
| | - Duhee Bang
- Department of Chemistry, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 120-749, Korea
| |
Collapse
|
100
|
Zhang C, Zou R, Chen X, Stephanopoulos G, Too HP. Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production. Appl Microbiol Biotechnol 2015; 99:3825-37. [DOI: 10.1007/s00253-015-6463-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 01/29/2015] [Accepted: 02/05/2015] [Indexed: 12/26/2022]
|